# # file: oplsaa.define # author: Pieter J. in 't Veld # date: November 16, 25, 2012, March 17, 24, 2013, December 30, 2014, # January 15, 2016, February 3, 2017, November 9, 2020 # purpose: OPLS-AA typing rules # version: 0.3beta # # rule keys: # ~ any bond # - single bond # : partial bond # = double bond # # triple bond # * wildcard, specified number of bonds # # template keys: # . skipped index # # Empty lines are skipped # Specified types represent numerical OPLS assignments # # notes: # 20121116 - Creation date, v0.1beta # 20121125 - Addition of keywords DEFINE, REFERENCES, EXTRA, PRECEDENCES # 20130317 - Addition of keywords EQUIVALENCE, BOND, ANGLE, TORSION, # IMPROPER # 20130324 - Redefinition of EXTRA to include management of double # torsions # - Addition of REDEFINE # 20141230 - Switch to v0.2beta # - Refinement of mass comments # - Refinement of existing rules to phase out ? as connectivity # - Additional rules for halogenides and acids # - Testing with simple compounds: alkanes, benzenes (see # examples) # 20160115 - Corrected typing of acid side groups # - Corrected typing of alpha hydrogen for acid side groups # 20170203 - Switch to 0.3beta # - Corrected typing of alkenes # - Corrected dicarboxylic acid entries # - Added isocyanate entries # 20201109 - Added sulfone and ionic liquid entries # 20230814 - Added carbonate entries (DLV, Vigil/Sandia) # # Definitions ITEM DEFINE FFNAME OPLS FFTYPE ATOMISTIC FFCHARGE ALL FFDEPTH 4 ITEM END # Literature references ITEM REFERENCES # year volume page journal 1984 106 6638 J. Am. Chem. Soc. 1996 118 11225 J. Am. Chem. Soc. 1999 121 4827 J. Am. Chem. Soc. 1983 79 926 J. Chem. Phys. 2006 2 1499 J. Chem. Theory Comput. 2009 5 1038 J. Chem. Theory Comput. 1990 11 958 J. Comput. Chem. 1997 18 1955 J. Comput. Chem. 1986 90 1276 J. Phys. Chem. 1986 90 2174 J. Phys. Chem. 1986 90 6379 J. Phys. Chem. 1990 94 1683 J. Phys. Chem. 1991 95 3315 J. Phys. Chem. 2001 105 4118 J. Phys. Chem. A 1998 102 8049 J. Phys. Chem. B 2004 18 16264 J. Phys. Chem. B 1972 24 1013 Mol. Phys. 1988 63 547 Mol. Phys. 1998 424 145 Theochem. 1954 ?? ?? Wiley (Hirschfelder) 2007 806 23 J. Mol. Struct. THEOCHEM ITEM END # Masses ITEM MASSES # type mass element ncons charge comment ar 39.948 Ar 0 0 Argon ba+2 137.327 Ba 0 2 Ba2+ cation br- 79.904 Br 0 -1 Br- ion c 12.011 C 3 0 C(=O) in ketones c_1 12.011 C 3 0 C(=O) in amides c_2 12.011 C 3 -0.5 C(:O) in deprotonated acids c_3 12.011 C 3 0 C(=O) in protonated acids c_4 12.011 C 3 0 C(=O) in benzoic esters c_5 12.011 C 3 0 C(=O) in dicarboxylic acids c= 12.011 C 3 0 C in dialkenes ca 12.011 C 3 0 C in aromatic rings car 12.011 C 3 0 C in aromatic rings caw 12.011 C 3 0 C in aromatic rings ca+2 40.078 C 3 2 Ca2+ cation ca1 12.011 C 3 0 C in guanidinium C+ cb 12.011 C 3 0 C in tryptophan beta carbon cg 12.011 C 3 0 C in tryptophan gamma carbon ch 12.011 C 3 0 C in chloroform cl 34.453 Cl 1 0 Cl in CCl4 cl- 34.453 Cl 1 -1 Cl- ion cl1 34.453 Cl 1 0 Cl in halogens cm 12.011 C 3 0 SP2 carbon cm1 12.011 C 3 0 C in trifluorothymine cn 12.011 C 3 0 C in tryptophan epsilon carbon co 12.011 C 3 0 C in diesters cs+ 132.905 Cs 0 1 Cs+ ion ct 12.011 C 3 0 SP3 carbon ct1 12.011 C 3 0 C in trifluoromethane ct2 12.011 C 3 0 C in cytosine carbon C-N1 ct3 12.011 C 3 0 C in methyl substituents ct4 12.011 C 3 0 COH in trifluoroethanol ct5 12.011 C 4 0.35 C in TFSI anion (CF3) ctm 12.011 C 3 0 SP3 carbon in RMIM+ cz 12.011 C 2 0 C in methyl cyanide f 18.998 F 1 0 F in fluoroalkanes f_1 18.998 F 1 0 F in fluorobenzenes f_2 18.998 F 1 0 F in perfluoroalkanes f_3 18.998 F 1 0 F in trifluoroanisoles f_4 18.998 F 1 -0.16 F in TFSI anion f- 18.998 F 0 -1 F- ion h 1.0079 H 1 0 H in neutral nitrogen compounds h3 1.0079 H 1 0 H in charged nitrogen compounds ha 1.0079 H 1 0 Aromatic hydrogen har 1.0079 H 1 0 Aromatic hydrogen haw 1.0079 H 1 0 Aromatic hydrogen hc 1.0079 H 1 0 SP3 hydrogen hc1 1.0079 H 1 0 SP2 hydrogen hc2 1.0079 H 1 0 Formimide hydrogen hc3 1.0079 H 1 0 H in ketones, aldehydes, and acyl halides hc4 1.0079 H 1 0 H in cytosine H-C-N1 he 4.0026 He 0 0 Helium ho 1.0079 H 1 0 H in acid and alcohol -OH hs 1.0079 H 1 0 H in thiol -SH hw 1.0079 H 1 0 H n water i- 126.904 I 0 -1 I- ion k+ 39.098 K 0 1 K+ cation kr 83.80 Kr 0 0 Krypton li+ 6.941 Li 0 1 Li+ ion lp 1.0000 LP 1 0 Lone pair lp1 1.0000 LP 1 0 Lone pair TIP5P n 14.0067 N 3 0 N in imides and ureas n_1 14.0067 N 3 0 N in amides n2 14.0067 N 3 0 N in guanidinium n3 14.0067 N 4 0 N in charged nitrogen compounds n_4 14.0067 N 2 -0.66 N in TFSI anion n= 14.0067 N 2 0 N in cyanates na 14.0067 N 3 0 N in aromatic rings nam 14.0067 N 3 0 N in aromatic rings in RMIM+ na+ 22.990 Na 0 1 Sodium ion ne 20.180 Ne 0 0 Neon nh4+ 18.0383 N 0 1 Ammonium ion nt 14.0067 N 3 0 N in ammonia nz 14.0067 N 3 0 N in nitriles o 15.9994 O 1 0 SP2 oxygen in acids, ketones, esters o2 15.9994 O 1 0 O in acid ion o3 15.9994 O 1 -0.53 O in TFSI anion oh 15.9994 O 1 0 O in alcohols oh1 15.9994 O 1 0 O in diols and triols oh2 15.9994 O 1 0 O in acids oh3 15.9994 O 1 0 O in hydroxide os 15.9994 O 1 0 O in ethers os1 15.9994 O 1 0 O in esters o1s 15.9994 O 1 0 O in sulfonate ow 13.9994 O 4 0 O in TIP5P water (2 g/mol to 2 lp1) ow1 15.9994 OW3P 2 0 O in TIP3P water ow2 14.9994 O 3 0 O in TIP4P water (1 g/mol to lp) ow3 15.9994 OW3F 2 0 O in TIP3F water ow4 15.9994 O 2 0 O in SPC/E water oy 15.9994 O 1 0 O in sulfoxides oy1 15.9994 O 1 0 O in sulfoxides p 30.974 P 1 0 phosphorus rb+ 85.468 Rb 0 1 Rb+ cation s 32.066 S 4 0 S attached to C, O, or S s2 32.066 S 4 1.02 S in TFSI anion sh 32.066 S 2 0 S in hydrogen sulfide sh1 32.066 S 2 0 S in -SH sr+2 87.62 Sr 0 2 Sr2+ cation sy 32.066 S 4 0 S in sulfone sz 32.066 S 3 0 S in sulfoxide xe 131.29 Xe 0 0 Xenon ITEM END # Type redefinitions ITEM REDEFINE # old new C* CG N* NG ITEM END # Type repairs ITEM REPAIR # index number element type (first three entries in oplsaa.par nonbond) 99 99 lp lp1 405 7 N nh4+ 1100 9 F f- 1101 17 Cl cl- 1102 35 Br br- 1103 53 I i- 1106 3 Li li+ 1107 11 Na na+ 1108 19 K k+ 1109 37 Rb rb+ 1110 55 Cs cs+ 1111 12 Mg mg+2 1112 20 Ca ca+2 1113 38 Sr sr+2 1114 56 Ba ba+2 ITEM END # Precedences ITEM PRECEDENCE (? (ba+2) (br-) (ca+2) (cs+) (c) (c_5) (c_1) (c_3) (c_4) (c_2) (cg) (c=) (ca) (car) (caw) (ca1) (cb) (ch) (cm) (cm1) (cn) (co) (ct) (ct5) (ct1) (ct2) (ct3) (ct4) (ctm) (cz) (o3) (os1) (n_4) (n) (n_1) (n2) (n3) (na) (nam) (h) (h3) (ha) (har) (haw) (hcm) (hc) (hc1) (hc2) (hc3) (hc4) (ho) (hs) (hw) (cl-) (f_4) (f) (f_1) (f_2) (f_3) (f-) (i-) (k+) (li+) (mg+2) (na+) (rb+) (sr+2) (s2) ) ITEM END # Extra types (needed for rules in addition to standard OPLS rules) ITEM EXTRA # index basis type charge torsions ... (index[:occurence]) # Torsion corrections 160 ct ct4 - 134:2 135 136:2 235 c c_1 - 60 62 68 69 70 71 271 c c_2 - 70 93 94 95 96 267 c c_3 - 70 94 95 96 465.1 c c_4 - 70 210.1 267.1 c c_5 - 101 104 105 106 138 139 140:1 271.1 c c_5 - 237 n n_1 - 63 65 238 n n_1 - 239 n n_1 - # TFSI anion (Lopez & Padua parameters) # index.serial basis type charge # basis chosen so sigma/eps in oplsaa.par match TFSI targets exactly: # 135: CT sigma=3.500 eps=0.066 -> ct5 target 3.500/0.066 EXACT # 965: F sigma=2.950 eps=0.053 -> f_4 target 2.950/0.053 EXACT # 251: N sigma=3.250 eps=0.170 -> n_4 target 3.250/0.170 EXACT # 474: SY sigma=3.550 eps=0.250 -> s2 target 3.550/0.250 EXACT # 278: O sigma=2.960 eps=0.210 -> o3 target 2.960/0.210 EXACT 135.2 ct ct5 0.35 965.1 f f_4 -0.16 1021.1 n n_4 -0.66 474.2 sy s2 1.02 278.1 o o3 -0.53 # Alkanes 140.1 hc hc 0.06 140.2 hc hc 0.06 140.3 hc hc 0.06 244.1 ct ct 0.15 # Imides 251.1 n n -0.37 # based on parallels to other force fields 259.1 ct ct 0.07 # ditto 259.2 ct ct 0.13 # ditto 259.3 ct ct 0.19 # ditto 259.4 ct ct 0.25 # ditto 997.1 ct ct 0.195 # Isocyanates 150.1 c= c= 0.785 # RCNCO through similarities; PJV 20170203 251.2 n= n= -0.724 # ditto 253.1 o o -0.45 # ditto 256.1 ct ct 0.209 # OCN-CH3 257.1 ct ct 0.269 # OCN-CH2-R 258.1 ct ct 0.329 # OCN-CH-R 259.5 ct ct 0.389 # OCN-C-R # Sulfonates 202.1 s s 1.18 # sulfur in sulfonate 311.1 o1s o1s -0.68 # oxygen in sulfonate 145.1 ca ca -0.14 # aromatic carbon in sulfonate # Carbonates (2023.08.14 J. Mol. Struct. 2007, 806, 23) 771 o o -0.512 # originally -0.5 772 c c 0.85 # originally 0.86 773 os1 os1 -0.429 # originally -0.45 775 ct ct 0.235 # originally 0.16 776 ct ct 0.185 # originally -0.1 777 hc hc 0.025 # originally 0.03 # Sulfones 135.1 ct ct -0.18 # CH3-sulfone 136.1 ct ct -0.12 # CH2-sulfone 137.1 ct ct -0.06 # CH-sulfone 139.1 ct ct 0.00 # C-sulfone 147.1 ca ca 0.00 # aromatic C-sulfone # RMIM+ (2020.11.09, J. Chem. Theory Comput. 2009, 5, 1038) 139.2 ct ctm -0.17 # C bound to aromatic N in imidazole ring 139.3 ct ctm -0.1125 # C bound to aromatic N in imidazole ring 140.4 hc hcm 0.18 # H bound to previous C 145.2 ca caw -0.24 # aromatic C in imidazole ring 145.3 ca car -0.09 # aromatic C in imidazole ring 146.1 ha haw 0.27 # H bound to aromatic C in imidazole ring 146.2 ha har 0.21 # H bound to aromatic C in imidazole ring 657.1 na nam 0.22 # aromatic N in imidazole ring ITEM END # Equivalences ITEM EQUIVALENCE # type pair incr bond angle torsion improper car ca ca ca ca ca ca caw ca ca ca ca ca ca ctm ct ct ct ct ct ct har ha ha ha ha ha ha haw ha ha ha ha ha ha hcm hc hc hc hc hc hc nam na na na na na na lp1 lp1 lp1 lp1 lp1 lp lp n= n= n= n= n= n= n= o1s o1s o1s o1s o1s o1s o1s os1 os1 os os os os os ow1 ow1 ow1 ow ow ow ow ow2 ow2 ow2 ow ow ow ow ow3 ow3 ow3 ow ow ow ow ow4 ow4 ow4 ow4 ow4 ow4 ow4 f_4 f_4 f_4 f_4 f_4 f_4 f_4 n_4 n_4 n_4 n_4 n_4 n_4 n_4 s2 s2 s2 s2 s2 s2 s2 o3 o3 o3 o3 o3 o3 o3 ct5 ct5 ct5 ct5 ct5 ct5 ct5 ITEM END # Pair parameters ITEM NONBOND # type1 type2 sigma epsilon h h 1.01 0 h3 h3 1.01 0 ho ho 0.945 0 hs hs 1.336 0 hw hw 0.9572 0 lp lp 0.2476 0 lp1 lp1 1.1431 0 n= n= 3.35 0.109 # through similarities PJV 20170203 o1s o1s 3.15 0.2 # O in sulfonate PJV 20180724 ow4 ow4 3.16556 0.155394 # SPC/E water PJV 20210401 ct5 ct5 3.500 0.06600 # C in TFSI CF3 f_4 f_4 2.950 0.05300 # F in TFSI CF3 n_4 n_4 3.250 0.17000 # N in TFSI s2 s2 3.550 0.25000 # S in TFSI SO2 o3 o3 2.960 0.21000 # O in TFSI SO2 ITEM END # Bond parameters ITEM BOND # type1 type2 k l0 lp1 ow 900 0.70 c= o 795 1.16 # through similarities; PJV 20170203 c= n= 685 1.2 # ditto ct n= 337 1.47 # ditto s ca 250 1.76 # sulfonate to benzyl s o1s 637.1 1.455 # sulfonate hw ow4 600 1.0 # SPC/E water PJV 20210401 ct5 f_4 441.802 1.323 # CF3-F TFSI ct5 s2 235.420 1.818 # CF3-S TFSI s2 o3 637.069 1.442 # S-O TFSI n_4 s2 372.012 1.570 # N-S TFSI ITEM END # Angle parameters ITEM ANGLE # type1 type2 type3 k theta0 cm c os 81 111.4 hw ow lp1 50 110.695 lp1 ow lp1 0 109.47 ct ct n= 55.2 117.3 # through similarities PJV 20170203 n= c= o 45 174 # ditto ct n= c= 50 143 # ditto hc ct n= 62.7 107.5 # ditto o1s s o1s 115.8 114 # sulfonate PJV 20180724 o1s s ca 62 104.2 # ditto s ca ca 70 120 # ditto ca os ca 75 110 # ca-os-cm PJV 20201110 ca s ca 78.7 104.4 # diphenyl sulfone ca sy ca 78.7 104.4 # diphenyl sulfone ct ct na 80 111.2 # ct-ct-n3 PJV 20201110 ct na ca 70 125.2 # c-na-ca na ca na 70 109.8 # imidazole hw ow4 hw 75 109.47 # SPC/E water PJV 20210401 os c os 69.9 118.18 # carbonate DLV 20230814 f_4 ct5 f_4 93.3317 107.1 # F-C-F TFSI s2 ct5 f_4 82.9349 111.8 # S-C-F TFSI ct5 s2 o3 103.9674 102.6 # C-S-O TFSI o3 s2 o3 115.7982 118.5 # O-S-O TFSI o3 s2 n_4 94.2877 113.6 # O-S-N TFSI ct5 s2 n_4 97.5143 100.2 # C-S-N TFSI s2 n_4 s2 80.1864 125.6 # S-N-S TFSI ITEM END # Torsion parameters ITEM TORSION # type1 type2 type3 type4 [k n delta [...]] [index] # override automated pruning interpretation ct ct nt ct 199 c ct ct hc 115 # based on equivalents cm c os ct 4 1 0 5 2 0 - # 211.1 cm cm c os 0 1 0 2.1 2 0 - # 207.2 ca ct ct ct 1.3 1 0 -0.05 2 0 0.2 3 0 - # 3.1 os co co os -0.55 1 0 - # 16 * c n * 0 1 0 7 2 0 # isocyanate additions; PJV 20170203 * ct n= c= -0.02 3 0 - # analogy ct n= c= o 0.3 2 0 - # analogy hc ct ct n= -0.1 3 0 - # 70 ct ct ct n= 0.845 1 0 -0.962 2 0 0.713 3 0 - # 35 # in analogy to ca cm ct ct ct 1.3 1 0 -0.05 2 0 0.2 3 0 - # 3.1 c* c= c= c* 0 1 0 0.3 3 0 - # 1.3 c* c= cm c* 0 1 0 0.3 3 0 - # 1.3 # taken care of by improper c n c * 0 1 0 - # improper c cm ct hc 0 1 0 - # improper ct ct cm hc 0 1 0 - # improper # sulfonate; PJV 20180724 o1s s ca ca 2.6 2 0 - # polysulfone; PJV 20201110 ca ca ct ca 0 1 0 - ca ca os ca 0 1 0 1.5 2 180 - ca ca s ca 0 1 0 -0.45 2 180 - ca ca sy ca 0 1 0 -0.45 2 180 - ca ct os ca 0 1 0 1.5 2 180 - # sulfoxide; PJV 20231024 ct sz ct hc 0 1 0 0.275 3 0 - # from ct:c:ct:hc hc ct sz oy 0 1 0 - # from hc:ct:c:o # RMIM+; PJV 20201110 ca ca na ca 0 1 0 3 2 0 - ca na ca ha 0 1 0 4.651 2 0 - ca na ca na 0 1 0 4.651 2 - - ct ct ct na -0.788 1 0 -0.8 2 0 0.4 3 0 - hc ct ct na 0 1 0 0.3 3 0 - ct na ca ca 0 1 0 - ct na ca ha 0 1 0 4.651 2 0 - ct na ca na 0 1 0 4.651 2 0 - # carbonate; DLV 20230814 ct os c os 4.669 1 0 5.124 2 0 - s2 n_4 s2 ct5 7.8329 1 0 # S-N-S-C TFSI s2 n_4 s2 ct5 -2.4904 2 0 # S-N-S-C TFSI s2 n_4 s2 ct5 -0.7636 3 0 # S-N-S-C TFSI f_4 ct5 s2 n_4 0.3159 3 0 # F-C-S-N TFSI f_4 ct5 s2 o3 0.3468 3 0 # F-C-S-O TFSI s2 n_4 s2 o3 -0.0036 3 0 # S-N-S-O TFSI ITEM END # Improper parameters ITEM IMPROPER # type1 type2 type3 type4 k psi0 ca * * * 2.2 0 n * * * 2.0 0 c o * * 21.0 0 cm * * * 30.0 0 ITEM END # Typing rules ITEM RULES # type rule(s) # Generic connectivity #1 H(*) H #2 [He] #3 [Li] #4 [Be] #5 B #6 C(*)(*)(*)(*) C(*)(*)(*) C #7 N(*)(*)(*)(*) N(*)(*)(*) N #8 O(*)(*) O(*) O #9 F(*) F #10 [Ne] #11 [Na] #12 [Mg] #13 [Al](*)(*)(*)(*)(*)(*) [Al](*)(*)(*)(*) [Al] #14 [Si](*)(*)(*)(*) [Si](*)(*)* [Si] #15 P #16 S(*)(*)(*)(*) S(*)(*)(*) S(*)(*) S #17 [Cl](*) [Cl] #18 [Ar] #35 [Br](*) [Br] #53 I(*) I # United-atom force field connectivity 94 N(#C)(C) 95 C(#N)(C) 100 [DM] 101 [He] 102 [Ne] 103 [Ar] 104 [Kr] 105 [Xe] 120 C([Cl])([Cl])([Cl]) 123 [Cl](C([Cl])([Cl])([Cl])) 127 N(H)(H)(H) 128 H(N(H)(H)) # Water models # TIP5P 97 [O](H)(H)([LP])([LP]) 98 H([O](H)([LP])([LP])) 99 [LP][O](H)(H)([LP]) # TIP3P 111 [OW3P](H)(H) 112 H([OW3P](H)) # TIP4P 113 [O](H)(H)([LP]) 114 H([O](H)([LP])) 115 [LP][O](H)(H) # TIP3F 116 [OW3F](H)(H) 117 H([OW3F](H)) # SPC/E 133 [O](H)(H) 134 H(O(H)) # All-atom force field connectivity # Alkanes 135 C(C)(H)(H)(H) 136 C(C)(C)(H)(H) 137 C(C)(C)(C)(H) 138 C(H)(H)(H)(H) 139 C(C)(C)(C)(C) 140 H(C(H)(H)(H)) H(C(C)(H)(H)) H(C(C)(C)(H)) H(C(C)(C)(C)) 140.1 H(C(N)(H)(H)) H(C(N)(C)(H)) H(C(N)(C)(C)) 140.2 H(C(c)(H)(H)) H(C(c)(C)(H)) H(C(c)(C)(C)) 140.3 H(C(S)(H)(H)) H(C(S)(C)(H)) H(C(S)(C)(C)) #TFSI anion typing rules # index.serial must match EXTRA section exactly 135.2 C(F)(F)(F)(S) 965.1 F(C(F)(F)(S)) 1021.1 [N-](S)(S) 474.2 S(~O)(~O)(C)[N-] 278.1 O(~S(~O)(C)[N-]) # Alkenes 141 C(=C)(*)(*) 142 C(=C)(H)(*) 143 C(=C)(H)(H) 144 H(C(=C)(C)) # Aromatics 145 c(:c)(:c)(H) c(:c)(:c)(C) 1004 c(:c)(:c)(C(c)(H)(H)) c(:c)(:c)(C(c)(C)(H)) c(:c)(:c)(C(c)(C)(C)) c(:c)(:c)(C(n)(H)(H)) c(:c)(:c)(C(n)(C)(H)) c(:c)(:c)(C(n)(C)(C)) 146 H(c(:c)(:c)) 147 c(:c)(:c)(:c) c(:c)(:c)(c) 148 C(c(:c)(:c))(H)(H)(H) 149 C(c(:c)(:c))(C)(H)(H) C(c(:c)(:c))(c(:c)(:c))(H)(H) 515 C(c(:c)(:c))(C)(C)(H) C(c(:c)(:c))(c(:c)(:c))(C)(H) 516 C(c(:c)(:c))(C)(C)(C) C(c(:c)(:c))(c(:c)(:c))(C)(C) 150 C(=C)(C(=C)(*))(H) # Halogens (see 970-972) #151 [Cl](C(*)(*)(*)) #152 C([Cl])(H)(H)(*) #153 H(C([Cl])(H)(*)) # Alcohols 154 O(C(*)(*)*)(H) 155 H(O(C(*)(*)(*))) 156 H(C(O(H))(H)(H)) 157 C(O(H))(H)(H)(*) 158 C(O(H))(H)(*)(*) 159 C(O(H))(*)(*)(*) 160 C(O(H))(C(F)(F)(F))(H)(H) 161 C(C(O(H))(H)(H))(F)(F)(F) 162 O(C(C(F)(F)(F))(H)(H))(H) 163 H(O(C(C(F)(F)(F))(H)(H))) 164 F(C(C(O(H))(H)(H))(F)(F)) 165 H(C(C(F)(F)(F))(O(H))(H)) 166 c(:c)(:c)(O(H)) 167 O(c(:c)(:c))(H) 168 H(O(c(:c)(:c))) 169 O(C(C(O(H))(*)(*))(*)(*))(H) 170 H(O(C(C(O(H))(*)(*))(*)(*))) 171 O(C(C(O(H))(C(O(H))(*))(*)(*)))(H) O(C(C(O(H))(*)(*))(C(C(O(H))(*)(*))(*)))(H) 172 H(O(C(C(O(H))(C(O(H))(*))(*)(*)))) 173 C(C)(O(H))(H)(H) 174 C(C)(C)(O(H))(H) 175 C(C)(C)(C)(O(H)) 176 H(C(O(H))(*)(*)) # Ethers 177 O(c(:c)(:c))(c(:c)(:c)) 178 C(=C)(=C) C(=C)(C(=C)(*))C 179 O(c(:c)(:c))(C) 180 O(C)(C) 181 C(O(*))(H)(H)(H) 182 C(O(*))(H)(H)(*) 183 C(O(*))(H)(*)(*) 184 C(O(*))(*)(*)(*) 997 C(O(*))(c(:c)(:c))(H)(*) 997.1 C(O(*))(c(:c)(:c))(H)(H) 998 C(O(*))(c(:c)(:c))(*)(*) 185 H(C(O(*))(*)(*)) # Acetals and hemiacetals 186 O(C(O(*))(*)(*))(C) 187 O(C(O(C(*)(*)(*)))(*)(*))(H) 188 H(O(C(O(C(*)(*)(*)))(*)(*))) 189 C(O(C(*)(*)(*)))(O(C(*)(*)(*)))(H)(H) 190 H(C(O(C(*)(*)(*)))(O(C(*)(*)(*)))(H)) 191 C(O(C(*)(*)(*)))(O(H))(H)(H) 192 H(C(O(C(*)(*)(*)))(O(H))(H)) 193 C(O(C(*)(*)(*)))(O(C(*)(*)(*)))(H)(*) 194 H(C(O(C(*)(*)(*)))(O(C(*)(*)(*)))(*)) 195 C(O(C(*)(*)(*)))(O(H))(H)(*) 196 H(C(O(C(*)(*)(*)))(O(H))(*)) 197 C(O(C(*)(*)(*)))(O(C(*)(*)(*)))(*)(*) 198 C(O(C(*)(*)(*)))(O(H))(*)(*) 199 c(:c)(:c)(O(C)) # Thiols, sulfides and disulfides 200 S(H)(*) 201 S(H)(H) 202 S(*)(*) 203 S(S)(*) 204 H(S(*)) 205 H(S(H)) 206 C(S(H))(H)(H)(*) 207 C(S(H))(H)(*)(*) 208 C(S(H))(*)(*)(*) 209 C(S(*))(H)(H)(H) 210 C(S(*))(H)(H)(*) 211 C(S(*))(H)(*)(*) 212 C(S(*))(*)(*)(*) 213 C(S(S))(H)(H)(H) 214 C(S(S))(H)(H)(*) 215 C(S(S))(H)(*)(*) 216 C(S(S))(*)(*)(*) 217 C(S(H))(H)(H)(H) # Sulfonate 202.1 S(c(:c)(:c))(=O)(:O)(:O) S(c(:c)(:c))(=O)(=O)([O-]) 311.1 O(=S(:O)(:O)(c(:c)(:c))) O(:S(=O)(:O)(c(:c)(:c))) O(=S(=O)([O-])(c(:c)(:c))) [O-](S(=O)(=O)(c(:c)(:c))) 145.1 c(:c)(:c)(S(=O)(:O)(:O)) c(:c)(:c)(S(=O)(=O)([O-])) # Benzyl alcohols 218 C(c(:c)(:c))(OH)(H)(H) 219 C(c(:c)(:c))(OH)(H)(*) 220 C(c(:c)(:c))(OH)(*)(*) 221 c(:c)(:c)(C(O(H))(*)(*)) 221.1 c(:c)(:c)(C(O(C))(*)(*)) 221.2 c(:c)(:c)(C(O(N))(*)(*)) # Thiolanisole 222 S(c(:c)(:c))(C) 228 c(:c)(:c)(S(C)) # Amines 223 C(N(H)(H))(C)(H)(H) 224 C(N(H)(H))(C)(*)(H) 225 C(N(H)(H))(C)(*)(*) 989 C(N(H)(H))(c(:c)(:c))(H)(H) # Halogens 226 [Cl](C(=C)(H)(*)) 227 C(=C)([Cl])(H)(*) # Ketones and phenyl rings 231 C(c(:c)(:c))(c(:c)(:c))(=O) 232 C(c(:c)(:c))(=O)(H) 233 C(c(:c)(:c))(C)(=O) # Amides 229 C(N(C(=O)(*))(H))(H)(*)(*) 230 C(N(C(=O)(*))(H))(*)(*)(*) 234 C(c(:c)(:c))(=O)(N(H)(H)) 235 C(=O)(N(H)(*))(*) 236 O(=C(N(H)(*))(*)) 237 N(C(=O)(*))(H)(H) 238 N(C(=O)(*))(H)(*) 239 N(C(=O)(*))(*)(*) 240 H(N(C(=O)(*))(H)) 241 H(N(C(=O)(*))(*)) 242 C(N(C(=O)(*))(H))(H)(H)(H) 243 C(N(C(=O)(*))(*))(H)(H)(H) 244 C(N(C(=O)(*))H)(H)(H)(*) 244.1 C(N(C(=O)(O))H)(H)(H)(*) 245 C(N(C(=O)(*))(*))(H)(H)(*) 246 C(N(C(=O)(*))(*))(H)(*)(*) 987 N(c(:c)(:c))(C(=O)(*))(C) 988 c(:c)(:c)(N(C(=O)(*))(C)) # Urea 247 C(=O)(N(H)(H))(N(H)(H)) 248 O(=C(N(H)(H))(N(H)(H))) 249 N(C(=O)(N(H)(H)))(H)(H) 250 H(N(C(=O)(N(H)(H)))(H)) # Imides 251 N(C(=O)(*))(C(=O)(*))(H) 251.1 N(C(=O)(*))(C(=O)(*))(C) 252 C(N(C(=O)(*)))(=O)(*) 253 O(=C(N(C(=O)(*)))(*)) 254 H(N(C(=O)(*))(C(=O)(*))) 255 H(C(N(C(=O)(*))(C(=O)(*)))(*)(*)(*)) 256 C(C(=O)N(*))(H)(H)(H) 257 C(C(=O)N(*))(H)(H)(C) 258 C(C(=O)N(*))(H)(C)(C) 259 C(C(=O)N(*))(C)(C)(C) 259.1 C(N(C(=O)(*))(C(=O)(*)))(H)(H)(H) 259.2 C(N(C(=O)(*))(C(=O)(*)))(H)(H)(C) 259.3 C(N(C(=O)(*))(C(=O)(*)))(H)(C)(C) 259.4 C(N(C(=O)(*))(C(=O)(*)))(C)(C)(C) # Isocyanates 150.1 C(=N(C))(=O) 251.2 N(=C(=O))(C) 253.1 O(=C(=N(C))) 256.1 C(N(=C(=O)))(H)(H)(H) 257.1 C(N(=C(=O)))(H)(H)(C) 258.1 C(N(=C(=O)))(H)(C)(C) 259.5 C(N(=C(=O)))(C)(C)(C) # Aromatics (nitrile, amide, chloride) 260 c(:c)(:c)(C(#N)) 261 C(c(:c)(:c))(#N) 262 N(#C(c(:c)(:c))) 263 c(:c)(:c)([Cl]) 264 [Cl](c(:c)(:c)) 265 N(c(:c)(:c))(C(=O)(*))(H) 266 c(:c)(:c)(N(C(=O)(*))(H)) # Acids # Generic acids and ions 267 C(C)(=O)(O(H)) 268 O(C(C)(=O))(H) 269 O(=C(C)O(H)) 270 H(O(C(C)(=O))) 271 C(C)(:O)(:O) 272 O(:C(C)(:O)) 273 C(C(:O)(:O))(H)(H)(H) 274 C(C(:O)(:O))(H)(H)(*) 275 C(C(:O)(:O))(H)(*)(*) 276 C(C(:O)(:O))(*)(*)(*) # Hydroxamic acids (2014.12.30) 990 C(=O)(N(O(H))(*))(*) 991 C(=O)(N(O(H))(*))(c(:c)(:c)) 992 O(=C(N(O(H))(*))(*)) 993 N(O(H))(C(=O)(*))(*) 994 H(N(O(H))(C(=O)(*))) 995 O(H)(N(C(=O)(*))(*)) 996 H(O(N(C(=O)(*))(*))) # Dicarboxylic acids (2017.02.06) 267.1 C(C(C(C(=O)(OH))))(=O)(OH) C(C(C(C(:O)(:O))))(=O)(OH) 271.1 C(C(C(C(=O)(OH))))(:O)(:O) C(C(C(C(:O)(:O))))(:O)(:O) # Aldehydes and ketones 277 C(C)(=O)(H) 278 O(=C(C)(H)) 279 H(C(C)(=O)) 280 C(=O)(C)(H) C(=O)(C)(C) C(=O)(C)(c) C(=O)(c)(c) 281 O(=C(C)(H)) O(=C(C)(C)) O(=C(C)(c)) O(=C(c)(c)) 282 H(C(C(=O)(*))(*)(*)) H(C(C(:O)(:O))(*)(*)) 283 C(C(=O)(O(H)))(N(H)(H))(C)(H) 284 C(C(=O)(O(H)))(N(H)(H))(H)(H) 285 C1(C(=O)(O(H)))N(H)C(H)(H)C(H)(H)C1(H)(H) # Ammonium 286 [N+](H)(H)(H)(H) 287 [N+](C)(H)(H)(H) 309 [N+](C)(C)(H)(H) 940 [N+](C)(C)(C)(H) 288 [N+](C)(C)(C)(C) 1125 [N+](c(:c)(:c))(C)(C)(C) 1127 [N+](c(:c)(:c))(C)(C)(H) 289 H([N+](H)(H)(H)) 290 H([N+](C)(H)(H)) 310 H([N+](C)(C)(H)) 941 H([N+](C)(C)(C)) 1124 H(C([N+](C)(C)(C))(H)(H)) 291 C([N+](H)(H)(H))(H)(H)(H) 292 C([N+](H)(H)(H))(C)(H)(H) 293 C([N+](H)(H)(H))(C)(C)(H) 294 C([N+](H)(H)(H))(C)(C)(C) 297 C([N+](C)(H)(H))(H)(H)(H) 942 C([N+](C)(C)(H))(H)(H)(H) 943 C([N+](C)(C)(H))(C)(H)(H) 944 C([N+](C)(C)(H))(C)(C)(H) 945 C([N+](C)(C)(H))(C)(C)(C) 1120 C([N+](C)(C)(C))(H)(H)(H) 1121 C([N+](C)(C)(C))(C)(H)(H) 1122 C([N+](C)(C)(C))(C)(C)(H) 1123 C([N+](C)(C)(C))(C)(C)(C) 1126 c([N+](C)(C)(C))(:c)(:c) 1128 c([N+](C)(C)(H))(:c)(:c) # Nitrogen compounds (charged) => Use N instead of [N+]! 295 C1(C(=O)(O(H)))(H)C(H)(H)C(H)(H)C(H)(H)N1(C) 296 C1N(C)C(C(=O)OH)(H)C(H)(H)C(H)(H)C1(H)(H) #297 C(H)(H)(H)[N+](H)(H)C 298 C(C(:O):O)(H)(H)[N+](H)(H)(H) 299 C([N+](H)(H)(H))(C(H)(H)(H))(H)C(=O)OH 300 N(H)(H)[C+](N(*)(*))N(*)(*) 301 HN(H)[C+](N(*)(*))N(*)(*) 302 [C+](N(*)(*))(N(*)(*))N(*)(*) 303 N(C)(H)[C+](N(*)(*))N(*)(*) 304 HN(C)[C+](N(*)(*))N(*)(*) 305 C(H)(H)(H)N(H)[C+](N(*)(*))N(*)(*) 306 C(H)(H)(H)C(H)(H)N(H)[C+](N(*)(*))N(*)(*) 307 C(C(*)(H)(H))(H)(H)N(H)[C+](N(*)(*))N(*)(*) 308 C(C(H)(H)C)(H)(H)C(H)(H)N(H)[C+](N(*)(*))N(*)(*) # Nucleobases (see templates) 371 C(H)(*)(*)n1c(H)nc(*)c1* 372 HC(*)(*)n1c(H)nc(*)c1* 373 C(H)(*)(*)n1c(=O)n(H)c(=O)c(*)c1(H) 374 HC(*)(*)n1c(=O)n(H)c(=O)c(*)c1(H) 375 C(H)(*)(*)c1c(=O)nc(N(H)H)c(H)c1(H) 376 HC(*)(*)c1c(=O)nc(N(H)H)c(H)c1(H) 391 C(H)(*)(*)c1c(=O)n(H)c(N(H)H)c(H)c1(H) 392 HC(*)(*)c1c(=O)n(H)c(N(H)H)c(H)c1(H) 393 P(OC(*)(*)*)(OC(*)(*)*)(=O)=O 394 O=P(*)(*)* 395 OP(*)(*)* 396 C(*)(*)(*)OP(OC(*)(*)*)(=O)=O 397 C(c1c(=O)n(H)c(=O)n(*)c1(H))(F)(F)(F) 398 [Cl]C([Cl])=C(*)(*)* 399 C([Cl])([Cl])=C(*)(*)* # Ions 1100 [F-] 1101 [Cl-] 1102 [Br-] 1103 [I-] 405 [NH4+] 1106 [Li+] 1107 [Na+] 1108 [K+] 1109 [Rb+] 1110 [Cs+] 1111 [Mg++] 1112 [Ca++] 1113 [Sr++] 1114 [Ba++] 434 [O-](H) 435 H([O-]) # Organic ions 439 O(P(~O)(~O)(~O))(P(~O)(~O)(~O)) 457 c(:c)(:c)(OP(~O)(~O)(~O)) 458 C(O(P(~O)(~O)(O(c(:c)(:c)))))(H)(H)(H) 459 H(C(H)(H)(O(P(~O)(~O)(O(c(:c)(:c)))))) 460 c(:c)(:c)(P(~O)(~O)(~O)) 461 C(O(P(~O)(~O)(c(:c)(:c))))(H)(H)(H) 462 H(C(O(P(~O)(~O)(c(:c)(:c))))(H)(H)) 464 C1(C)(C)C(=O)N(H)C(=O)N(H)C1=O # Carbonates; DLV 20230814 771 O=C(OC)(OC) 772 C(=O)(OC)(OC) 774 C(OC(=O)O)(H)(H)(*) 775 C(OC(=O)O)(H)(*)(*) 776 C(OC(=O)O)(H)(H)(H) 773 O(C(=O)(O(C(*)(*)(*))))(C(*)(*)(*)) 777 H(C(OC(=O)O)(H)(*)) 779 H(C(OC(=O)O)(H)(H)) # Esters 465 C(=O)(O(C))(*) 465.1 C(=O)(O(C))(c(:c)(:c)) 466 O(=C(O(C))(*)) 467 O(C)(C(=O)(*)) 468 C(O(C(=O)(*)))(H)(H)(H) 469 H(C(O(C(=O)(*))(H)(H)(H))) # Benzyl acids and esters 470 C(c(:c)(:c))(=O)(O(H)) C(c(:c)(:c))(:O)(:O) 471 C(O(c(:c)(:c)))(=O)(*) 472 c(:c)(:c)(O(C(=O)(*))) 473 O(c(:c)(:c))(C(=O)(*)) # Sulfonamides 474 S(C)(=O)(=O)(N) 475 O(=S(C)(=O)(N)) 476 C(S(=O)(=O)(N))(H)(H)(H) 477 H(C(S(=O)(=O)(N))(H)(H)) 478 N(S(=O)(=O)(C))(H)(H) 479 H(N(S(=O)(=O)(C))(H)) 480 N(S(=O)(=O)(C))(H)(*) 481 H(N(S(=O)(=O)(C))(*)) 482 C(N(S(=O)(=O)(C))(H))(H)(H)(H) 483 H(C(N(S(=O)(=O)(C))(H))(H)(H)) 484 C(N(S(=O)(=O)(C))(H))(C)(H)(H) 485 H(C(N(S(=O)(=O)(C))(H))(C)(H)) 486 C(C(N(S(=O)(=O)(C))(H))(H)(H))(H)(H)(H) 487 H(C(C(N(S(=O)(=O)(C))(H))(H)(H))(H)(H)) 488 c(:c)(:c)(S(=O)(=O)(N)) c(:c)(:c)(S(=O)(=O)(C)) c(:c)(:c)(S(=O)(=O)(c)) # Thioesters (2020.11.09) 490 C(O(S(=O)(*)))(C)(H)(H) 491 C(O(S(=O)(*)))(C)(C)(H) 492 C(O(S(=O)(*)))(C)(C)(C) # Sulfones (2020.11.09) 135.1 C(H)(H)(H)(S(=O)(=O)(*)) 136.1 C(C)(H)(H)(S(=O)(=O)(*)) 137.1 C(C)(C)(H)(S(=O)(=O)(*)) 139.1 C(C)(C)(C)(S(=O)(=O)(*)) 147.1 c(:c)(:c)(S(=O)(=O)(*)) 493 S(C)(C)(=O)(=O) S(C)(c)(=O)(=O) S(c)(c)(=O)(=O) 494 O(=S(C)(C)(=O)) O(=S(C)(c)(=O)) O(=S(c)(c)(=O)) # Sulfoxides (2020.11.09) 489 c(:c)(:c)(S(=O)(C)) 495 S(=O)(C)(c) 496 S(=O)(C)(C) S(=O)(c)(c) 497 O(=S(C)(C)) O(=S(C)(c)) O(=S(c)(c)) 498 C(S(=O)(C))(H)(H)(H) C(S(=O)(c))(H)(H)(H) 499 C(S(=O)(C))(C)(H)(H) C(S(=O)(C))(c)(H)(H) # Amino acids # c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O)N 500 c(c(:c)(:c))(c(n)(H))(C(C)(H)(H)) 501 c(c(c)(C))(n(c)(H))(H) 502 c(:c(:c)(c))(:c(:c)(H))(n(c)(H)) 503 n(c(c)(H))(c(:c)(:c))(H) 504 H(n(c(c)(H))(c(:c)(:c))) # Halogenides # 2014.12.30: added 718-732, 956-998 # Fluorides 718 c(:c)(:c)(F) 719 F(c(:c)(:c)) 720 c1(F):c(F):c(F):c(F):c(F):c1(F) 721 F(c1c(F)c(F)c(F)c(F)c1(F)) 724 c(:c)(:c)(C(F)(F)(F)) 725 C(c(:c)(:c))(F)(F)(F) 726 F(C(c(:c)(:c))(F)(F)) 727 c1(F):c(F):c(*):c(*):c(*):c1(*) c1(F):c(*)c(F):c(*):c(*):c1(*) c1(F):c(*):c(*):c(F):c(*):c1(*) 728 F(c1:c(F):c(*):c(*):c(*):c1(*)) F(c1:c(*):c(F):c(*):c(*):c1(*)) F(c1:c(*):c(*):c(F):c(*):c1(*)) 956 F(C(C)(C)(C)) F(C(C)(C)(H)) F(C(C)(H)(H)) 957 C(F)(C)(H)(H) 958 H(C(F)(C)(C)) H(C(F)(C)(H)) 959 C(F)(C)(C)(H) 960 C(F)(C)(C)(C) 961 C(F)(F)(F)(C) 962 C(F)(F)(C)(C) 963 C(F)(C)(C)(C) 964 C(F)(F)(F)(F) 965 F(C) 966 C(c(:c)(:c))(F)(F)(H) 967 H(C(c(:c)(:c))(F)(F)) 968 C(C(:O)(:O))(F)(H)(H) 980 F(C(=O)(*)) 983 c(:c)(:c)(O(C(F)(F)(F))) 984 O(c(:c)(:c))(C(F)(F)(F)) 985 C(O(c(:c)(:c)))(F)(F)(F) 986 F(C(O(c(:c)(:c)))(F)(F)) # Chlorides 969 C(C(:O)(:O))([Cl])(H)(H) 970 [Cl](C) 971 C([Cl])(H)(H)(*) 972 H(C([Cl])(*)(*)) 973 C([Cl])(H)(*)(*) 974 C([Cl])(*)(*)(*) 981 [Cl](C(=O)(*)) # Bromides 729 c(:c)(:c)([Br]) 730 [Br](c(:c)(:c)) 975 [Br](C) 976 C([Br])(H)(H)(*) 977 H(C([Br])(*)(*)) 978 C([Br])(H)(*)(*) 979 C([Br])(*)(*)(*) 982 [Br](C(=O)(*)) # Iodines 731 c(:c)(:c)(I) 732 I(c(:c)(:c)) # Ionic liquids # RMIM+ (2020.11.09, J. Chem. Theory Comput. 2009, 5, 1038) 657.1 n(:c(:c)(H))(:c(:n)(H))(C(C)(H)(H)) n(:c(:c)(H))(:c(:n)(H))(C(c)(H)(H)) 145.2 c(:n(:c(:n)(H))(C))(:c(:n(:c)(C))(H))(H) 145.3 c(:n(:c)(C))(:n(:c)(C))(H) 146.1 H(c(:n(:c(:n)(H))(C))(:c(:n(:c)(C))(H))) 146.2 H(c(:n(:c)(C))(:n(:c)(C))) 139.2 C(n(:c(:n(:c)(C))(H))(:c(:c)(H)))(C)(H)(H) 139.3 C(n(:c(:n(:c)(C))(H))(:c(:c)(H)))(c)(H)(H) 140.4 H(C(n(:c(:c)(H))(:c(:n)(H)))(C)(H)) H(C(n(:c(:c)(H))(:c(:n)(H)))(c)(H)) ITEM END # Typing templates ITEM COMPLEX_RULES # name[,..] template[,..] indices # [,..] indicate alternative notations # fragment indicates a generic name # non implemented yet # Nucleobases uracil n1(*)c(=O)n(H)c(=O)c(H)c1(H) 938 . 320 326 321 327 322 328 323 329 324 330 uracil n1(H)c(=O)n(H)c(=O)c(H)c1(H) 319 325 320 326 321 327 322 328 323 329 324 330 thymine n1(*)c(=O)n(H)c(=O)c(C(H)(H)H)c1(H) 938 . 320 326 321 327 322 328 331 332 332 332 329 324 330 thymine n1(H)c(=O)n(H)c(=O)c(C(H)(H)H)c1(H) 319 325 320 326 321 327 322 328 331 332 332 332 329 324 330 cytosine c1(*)c(=O)nc(N(H)H)c(H)c1(H) 937 . 334 340 335 336 341 342 343 337 344 338 345 cytosine c1(H)c(=O)nc(N(H)H)c(H)c1(H) 333 339 334 340 335 336 341 342 343 337 344 338 345 cytosine+ c1(*)c(=O)n(H)c(N(H)H)c(H)c1(H) 377 383 378 384 379 385 380 386 387 388 381 389 382 390 cytosine+ c1(H)c(=O)n(H)c(N(H)H)c(H)c1(H) 937 . 378 384 379 385 380 386 387 388 381 389 382 390 adenine n1c(H)nc2c(nc(H)n2(*))c1N(H)(H) 346 347 355 348 349 350 352 353 359 936 . 351 356 357 358 adenine n1c(H)nc2c(nc(H)n2(H))c1N(H)(H) 346 347 355 348 349 350 352 353 359 354 360 351 356 357 358 Guanine n1c(N(H)(H))nc2c(nc(H)n2(*))c1=O 361 362 368 369 369 363 364 365 352 353 359 936 . 366 370 Guanine n1c(N(H)(H))nc2c(nc(H)n2(H))c1=O 361 362 368 369 369 363 364 365 352 353 359 354 360 366 370 # Organic ions methanethiolate C(H)(H)(H)[S-],C(H)(H)(H)S 415 416 416 416 417 methoxide C(H)(H)(H)[O-],C(H)(H)(H)O 418 419 419 419 420 acetonitrile,methylcyanide C(H)(H)CN 421 422 422 423 424 methylamine C(H)(H)(H)NH 425 426 426 426 427 428 fragment C(H)(H)(H)[C-](H)(H)([DM]) 429 430 430 431 432 433 hydroxide [O-]H 434 435 urianiumoxide O[U++]O 437 436 437 dimethylphospate P(OC(H)(H)H)(OC(H)(H)H)(=O)[O-] 440 439 438 444 444 444 442 438 444 444 444 441 442 methylphosphate P(OC(H)(H)H)(=O)([O-])[O-] 445 439 448 449 449 449 446 447 447 methylphosphonate P(OC(H)(H)H)(C(H)(H)H)(=O)[O-] 450 439 453 454 454 454 455 456 456 456 446 447 benzylphosphate c1(H)c(H)c(H)c(H)c(H)c1OP(=O)([O-])[O-] . . . . . . . . . . 463 439 445 446 447 447 triptophane c1(H)c(H)c(H)c2c(c1)c(H)(cn2(H))C(H)(H)C(C(=O)*)N(H)* ITEM END