| no. | SYBYL atom type | description |
| 1. | C.3 | carbon sp3 |
| 2. | C.2 | carbon sp2 |
| 4. | C.1 | carbon sp1 |
| 3. | C.ar | carbon aromatic |
| 33. | C.cat | carbocation (C+) used in guadinium |
| 5. | N.3 | nitrogen sp3 |
| 6. | N.2 | nitrogen sp2 |
| 7. | N.1 | nitrogen sp1 |
| 11. | N.ar | nitrogen aromatic |
| 28. | N.am | nitrogen amide |
| 19. | N.pl3 | nitrogen trigonal planar |
| 31. | N.4 | nitrogen sp3 positively charged |
| 8. | O.3 | oxygen sp3 |
| 9. | O.2 | oxygen sp2 |
| 32. | O.co2 | oxygen in carboxylate and phosphate groups |
| 8. | O.t3p | oxygen in Transferable Intermolecular Potential (TIP3P) water model |
| - | - | etc. |
| - | - | etc. |
| no. | SYBYL bond type | description |
| 1 | 1 | single bond |
| 2 | 2 | double bond |
| 3 | 3 | triple bond |
| 4 | am | amide bond |
| 5 | ar | aromatic bond |
| 8 | du | dummy bond |
| 9 | un | unknown bond (displayed) |
| 10 | nc | not connected (not displayed) |
(atom1 | atom2 | bond-type | equilibrium distance | k | reference)
C.1 C.1 3 1.204 1400 JL_EST C.1 C.1 1 1.38 700 MC_88 Br C.2 1 1.89 500 EXP C.1 C.2 1 1.44 1340 * C.1 C.2 2 1.44 1340 * C.2 C.2 2 1.335 1340 WHITE_77 C.2 C.2 1 1.47 700 MC_88 C.1 C.3 1 1.458 640 * C.2 C.3 1 1.501 639 WHITE_75 C.3 C.3 1 1.54 633.6 * Br C.ar 1 1.85 500 * C.1 C.ar 1 1.44 1340 * C.2 C.ar 1 1.51 1340 * C.3 C.ar 1 1.525 640 * C.ar C.ar ar 1.395 1400 * C.ar C.ar 1 1.48 1000 * C.2 Cl 1 1.75 520 * C.3 Cl 1 1.767 600 * C.ar Cl 1 1.75 513.36 * C.2 F 1 1.33 1200 * C.3 F 1 1.36 600 * C.ar F 1 1.33 500 * * H 1 1.008 700 * C.1 H 1 1.056 700 JL_EST C.2 H 1 1.089 692 * C.3 H 1 1.1 662.4 WHITE_77 C.ar H 1 1.084 692 * C.ar I 1 2.05 490 * C.1 N.1 3 1.158 1600 * C.1 N.2 1 1.33 1300 * C.1 N.2 2 1.33 1300 * C.2 N.2 2 1.27 1305.94 * C.2 N.2 1 1.444 1300 MC_88 C.3 N.2 1 1.44 760.2 * C.ar N.2 1 1.346 1305.94 * N.2 N.2 2 1.346 1305.94 * N.2 N.2 1 1.418 1300 MC_88 C.2 N.3 1 1.33 1300 EXP C.3 N.3 1 1.47 760 * C.ar N.3 1 1.41 720 EXP H N.3 1 1.08 692 * C.2 N.4 1 1.33 1300 * C.3 N.4 1 1.47 760 * C.ar N.4 1 1.41 720 * C.2 N.am am 1.345 870.1 * C.2 N.am 1 1.345 870.1 * C.3 N.am 1 1.45 677.6 * C.ar N.am 1 1.416 1090.08 * H N.am 1 1 700 * N.2 N.am 1 1.44 667.6 * N.am N.am 1 1.45 744.48 * C.ar N.ar ar 1.346 1305.94 * N.ar N.ar ar 1.33 1400 * C.2 N.pl3 1 1.3 1200 * C.cat N.pl3 ar 1.3 1200 MAC91 C.3 N.pl3 1 1.45 676 * C.ar N.pl3 1 1.35 1306 * H N.pl3 1 1.03 692 * N.2 N.pl3 1 1.35 1305.94 EXP C.2 O.2 2 1.22 1555.2 * C.2 O.co2 ar 1.26 699.84 MAC91 N.am O.2 1 1.24 1120 * N.pl3 O.2 2 1.21 680 EXP C.2 O.3 1 1.33 699.84 * C.3 O.3 1 1.43 618.9 * C.ar O.3 1 1.39 700 * H O.3 1 .95 1007.5 * N.2 O.3 1 1.405 1200 * N.pl3 O.3 1 1.4 620 EXP O.3 O.3 1 1.48 1172.16 * C.3 P.3 1 1.83 407.6 * O.2 P.3 1 1.49 1400 * O.2 P.3 2 1.49 1400 * O.co2 P.3 ar 1.49 1400 MAC91 O.3 P.3 1 1.6 800 * C.2 S.2 2 1.71 400 * C.3 S.2 1 1.8 381.6 * C.ar S.2 1 1.74 700 * C.2 S.3 1 1.78 360 * C.3 S.3 1 1.817 381.6 * C.ar S.3 1 1.77 360 * N.3 S.3 1 1.625 360 * N.4 S.3 1 1.625 360 * O.2 S.3 2 1.45 600 * S.3 S.3 1 2.03 600 EXP C.2 S.o 1 1.71 360 TRIPOS_86 C.3 S.o 1 1.8 381.6 TRIPOS_86 O.2 S.o 2 1.45 600 * O.3 S.o 1 1.5 600 * C.3 S.o2 1 1.8 381.6 TRIPOS_86 O.2 S.o2 2 1.45 600 TRIPOS_86 O.3 S.o2 1 1.5 600 * H.spc H.spc 1 1.633 6000 * H.spc O.spc 1 1 6000 * H.t3p H.t3p 1 1.514 6000 * H.t3p O.t3p 1 0.9572 6000 * . . ANY ANY 1 1.5 600 * ANY ANY 2 1.5 600 * ANY ANY 3 1.5 600 * ANY ANY am 1.5 600 * ANY ANY ar 1.5 600 * ANY ANY du 1.5 600 * ANY ANY nc 1.5 600 * ANY ANY un 1.5 600 * . . .
(atom1 | atom2 | atom 3 | equilibrium angle | k | reference)
* C.1 * 180 0.04 * C.1 C.1 C.2 180 0.04 JL_EST C.2 C.1 N.1 180 0.04 * C.3 C.1 N.1 180 0.04 * C.ar C.1 N.1 180 0.04 * N.1 C.1 O.3 180 0.04 * * C.2 * 120 0.024 WHITE_77 * C.2 O.co2 120 0.024 MAC91 * C.cat * 120 0.024 WHITE_77 Br C.2 Br 120 0.02 EXP Br C.2 C.2 120 0.036 EXP C.2 C.2 C.2 121.7 0.018 * C.1 C.2 C.3 120 0.024 JL_EST C.2 C.2 C.3 121 0.024 WHITE_77 C.3 C.2 C.3 116.4 0.046 WHITE_77 C.1 C.2 C.ar 120 0.024 * C.2 C.2 C.ar 120 0.026 * C.3 C.2 C.ar 120 0.024 EXP C.ar C.2 C.ar 120 0.024 * C.2 C.2 Cl 120 0.036 * C.ar C.2 Cl 120 0.036 * Cl C.2 Cl 122 0.03 * * C.2 H 120 0.012 JL_EST C.1 C.2 N.2 123 0.07 * C.2 C.2 N.2 120 0.024 * C.3 C.2 N.2 118 0.02 * C.ar C.2 N.2 120 0.04 * C.2 C.2 N.3 120 0.024 * C.3 C.2 N.3 118 0.04 EXP N.2 C.2 N.3 121.8 0.03 EXP N.3 C.2 N.3 116.4 0.03 EXP C.2 C.2 N.am 120 0.024 * C.3 C.2 N.am 117 0.02 WHITE_75 C.ar C.2 N.am 120 0.04 * N.2 C.2 N.am 123 0.07 * N.am C.2 N.am 120 0.03 * C.2 C.2 N.pl3 120 0.024 * C.3 C.2 N.pl3 117 0.02 EXP N.2 C.2 N.pl3 123 0.07 EXP C.1 C.2 O.2 120 0.06 JL_EST C.1 C.2 O.co2 120 0.06 MAC91 C.2 C.2 O.2 120 0.026 * C.2 C.2 O.co2 120 0.026 MAC91 C.3 C.2 O.2 120 0.026 * C.3 C.2 O.co2 118 0.026 MAC91 C.ar C.2 O.2 120 0.026 * C.ar C.2 O.co2 120 0.026 MAC91 N.3 C.2 O.2 120 0.026 EXP N.3 C.2 O.co2 120 0.026 MAC91 N.am C.2 O.2 123 0.03 WHITE_75 N.am C.2 O.co2 123 0.03 MAC91 N.pl3 C.2 O.2 123 0.03 EXP N.pl3 C.2 O.co2 123 0.03 MAC91 C.2 C.2 O.3 120 0.072 * C.3 C.2 O.3 114 0.03 * C.ar C.2 O.3 120 0.03 * N.am C.2 O.3 110.5 0.014 * O.2 C.2 O.3 120 0.03 * O.co2 C.2 O.co2 124 0.03 MAC91 N.2 C.2 S.3 125.6 0.028 * N.am C.2 S.3 111.5 0.03 * O.2 C.2 S.3 125 0.016 * O.co2 C.2 S.3 125 0.016 MAC91 * C.3 * 109.5 0.02 WHITE_77 C.2 C.3 C.2 109.5 0.018 * C.1 C.3 C.3 109.5 0.024 * C.2 C.3 C.3 109.5 0.018 WHITE_75 C.3 C.3 C.3 109.5 0.024 * C.2 C.3 C.ar 109.47 0.018 * C.3 C.3 C.ar 109.5 0.024 * C.ar C.3 C.ar 109.5 0.018 * C.3 C.3 Cl 109.5 0.02 * Cl C.3 Cl 109.5 0.02 * C.ar C.3 F 110 0.024 JL_EST F C.3 F 109.5 0.04 * * C.3 H 109.5 0.016 WHITE_77 C.2 C.3 H 110 0.016 WHITE_75 H C.3 H 109.5 0.024 WHITE_75 C.3 C.3 N.2 109.5 0.018 * C.2 C.3 N.3 109.5 0.018 * C.3 C.3 N.3 109.5 0.024 * C.ar C.3 N.3 109.5 0.018 * C.2 C.3 N.am 109.5 0.022 * C.3 C.3 N.am 109.5 0.018 * C.ar C.3 N.am 109.5 0.02 EXP H C.3 N.am 110 0.02 WHITE_75 N.2 C.3 N.am 109.5 0.02 EXP N.am C.3 N.am 109.5 0.04 * F C.3 N.ar 109.5 0.04 * C.2 C.3 N.pl3 109.5 0.018 * C.3 C.3 N.pl3 109.5 0.02 * C.ar C.3 N.pl3 109.5 0.02 * C.2 C.3 O.3 109.5 0.022 * C.3 C.3 O.3 109.5 0.022 * C.ar C.3 O.3 109.5 0.018 * N.am C.3 O.3 109.5 0.02 * O.3 C.3 O.3 109.5 0.02 * C.3 C.3 P.3 112 0.014 * C.2 C.3 S.2 109.5 0.018 * C.3 C.3 S.2 109.5 0.018 * N.am C.3 S.2 109.5 0.04 * C.2 C.3 S.3 107.8 0.018 * C.3 C.3 S.3 107.8 0.018 * C.ar C.3 S.3 107.8 0.018 * N.am C.3 S.3 109.5 0.024 JL_EST O.3 C.3 S.3 107.8 0.02 * * C.ar * 120 0.024 * Br C.ar C.ar 120 0.036 * C.2 C.ar C.ar 120 0.024 * C.3 C.ar C.ar 120 0.024 * C.ar C.ar C.ar 120 0.024 * C.ar C.ar Cl 120 0.036 * C.ar C.ar F 120 0.036 * C.ar C.ar I 120 0.036 * C.3 C.ar N.2 120 0.04 * C.ar C.ar N.2 120 0.04 * N.2 C.ar N.2 120 0.04 * C.ar C.ar N.3 120 0.062 EXP C.ar C.ar N.am 120 0.062 * N.2 C.ar N.am 118 0.04 * N.am C.ar N.am 120 0.03 * C.2 C.ar N.ar 120 0.04 EXP C.3 C.ar N.ar 120 0.04 EXP C.ar C.ar N.ar 120 0.024 EXP N.am C.ar N.ar 118 0.04 EXP C.3 C.ar N.pl3 120 0.04 * C.ar C.ar N.pl3 120 0.04 * N.2 C.ar N.pl3 120 0.04 * N.am C.ar N.pl3 120 0.04 * N.pl3 C.ar N.pl3 120 0.04 * C.3 C.ar O.3 120 0.04 * C.ar C.ar O.3 120 0.062 * C.ar C.ar S.2 120 0.062 * C.ar C.ar S.3 120 0.062 * * N.1 * 180 0.08 * * N.2 * 120 0.04 * C.1 N.2 C.2 120 0.04 * C.2 N.2 C.2 123 0.08 EXP C.2 N.2 C.3 110 0.082 * C.2 N.2 C.ar 123 0.08 * C.3 N.2 C.ar 110 0.082 * C.ar N.2 C.ar 120 0.04 * C.2 N.2 N.2 112 0.044 * C.3 N.2 N.2 118 0.04 * C.ar N.2 N.2 118 0.04 * C.2 N.2 N.am 120 0.044 EXP C.2 N.2 N.pl3 120 0.044 EXP C.2 N.2 O.3 105 0.044 EXP * N.3 * 109.5 0.04 * C.2 N.3 C.3 110 0.04 EXP C.3 N.3 C.3 109.5 0.018 * C.3 N.3 C.ar 118 0.04 EXP C.ar N.3 C.ar 118 0.04 EXP C.3 N.3 S.2 109.5 0.04 * * N.4 * 109.5 0.01 TRIPOS_86 C.3 N.4 C.3 109.5 0.018 * * N.am * 120 0.02 * C.2 N.am C.2 120 0.018 * C.2 N.am C.3 118 0.044 * C.3 N.am C.3 122 0.04 * C.2 N.am C.ar 120 0.052 * C.3 N.am C.ar 118 0.044 * C.ar N.am C.ar 120 0.044 * C.2 N.am H 119 0.016 WHITE_75 C.3 N.am H 117 0.02 WHITE_75 C.2 N.am N.2 120 0.018 EXP C.3 N.am N.2 120 0.024 * C.ar N.am N.2 109.5 0.044 * C.2 N.am N.am 120 0.018 * C.3 N.am N.am 120 0.024 * C.ar N.am N.am 120 0.052 * C.2 N.am O.2 120 0.024 * C.3 N.am O.2 120 0.02 * C.ar N.am O.2 120 0.024 * O.2 N.am O.2 120 0.02 * * N.ar * 120 0.02 * C.ar N.ar C.ar 120 0.04 EXP * N.pl3 * 120 0.04 * C.2 N.pl3 C.2 120 0.04 EXP C.2 N.pl3 C.ar 120 0.04 EXP C.3 N.pl3 C.ar 120 0.04 * C.ar N.pl3 C.ar 120 0.04 * C.2 N.pl3 N.2 120 0.018 EXP C.ar N.pl3 N.2 120 0.018 EXP C.2 N.pl3 O.2 112 0.04 EXP O.2 N.pl3 O.2 127 0.06 EXP * O.3 * 109.5 0.02 * C.2 O.3 C.2 110 0.02 * C.2 O.3 C.3 109.5 0.044 * C.3 O.3 C.3 109.5 0.044 * C.2 O.3 C.ar 110 0.02 * C.3 O.3 C.ar 110 0.02 * C.ar O.3 C.ar 110 0.02 * C.2 O.3 N.2 108.5 0.044 EXP C.3 O.3 O.3 103.9 0.094 * C.3 O.3 P.3 120 0.01 * H O.3 H 104.5 0.02 MC90 * P.3 * 109.5 0.02 * O.2 P.3 O.2 109.5 0.02 * Du P.3 O.3 109.5 0.014 * O.2 P.3 O.3 109.5 0.02 * O.3 P.3 O.3 109.5 0.02 * * S.2 * 110 0.04 * C.3 S.2 N.3 111 0.04 * C.ar S.2 N.3 111 0.04 * * S.3 * 97 0.02 * C.2 S.3 C.3 94.3 0.022 * C.3 S.3 C.3 98 0.02 * C.ar S.3 C.ar 97.5 0.062 * C.3 S.3 S.3 102.9 0.06 EXP * S.o O.2 107 0.04 TRIPOS_86 * S.o2 O.2 107 0.04 TRIPOS_86 O.2 S.o2 O.2 118 0.04 TRIPOS_86 H.spc H.spc O.spc 35.265 1.0 * H.spc O.spc H.spc 109.47 1.0 * H.t3p H.t3p O.t3p 37.74 1.0 * H.t3p O.t3p H.t3p 104.52 1.0 *
(atom1 | atom2 | atom 3 | atom 4 | bond type | k | periodicity | reference)
* C.1 C.1 * 3 0 1 JL_EST * C.1 C.1 * 1 0 1 * * C.1 C.2 * 1 0 1 * * C.1 C.2 * 2 0 1 * * C.2 C.2 * 2 12.5 -2 WHITE_77 * C.2 C.2 * 1 1.424 -2 * * C.2 C.cat * 1 1.424 -2 * * C.1 C.3 * 1 0 1 * * C.2 C.3 * 1 .12 -3 * * C.2 C.3 C.2 1 .126 3 WHITE_77 * C.2 C.3 C.3 1 .126 3 WHITE_77 * C.2 C.3 H 1 .274 3 WHITE_77 O.2 C.2 C.3 C.3 1 .7 -3 JL_EST O.co2 C.2 C.3 C.3 1 .7 -3 MAC91 * C.3 C.3 * 1 .2 3 * C.2 C.3 C.3 C.2 1 0.04 3 WHITE_77 C.2 C.3 C.3 C.3 1 .126 3 WHITE_77 C.3 C.3 C.3 C.3 1 .5 3 MC_88 * C.3 C.3 H 1 .32 3 MC_88 * C.1 C.ar * 1 0 1 * * C.2 C.ar * 1 1.6 -2 * * C.3 C.ar * 1 .12 -3 * * C.ar C.ar C.ar ar 2.35 -2 MCAROM * C.ar C.ar * ar 2 -2 * * C.ar C.ar * 1 .6 -2 * * C.1 N.2 * 1 0 1 * * C.1 N.2 * 2 0 1 * * C.2 N.2 * 2 12 -2 * * C.2 N.2 * 1 12 -2 * * C.3 N.2 * 1 .4 -3 * * C.ar N.2 * 1 1.6 -2 * * N.2 N.2 * 2 1.6 -2 * * N.2 N.2 * 1 1.6 -2 * * C.2 N.3 * 1 .12 -3 * * C.3 N.3 * 1 .2 3 * * C.ar N.3 * 1 .12 -3 * * N.3 N.3 * 1 .2 3 * * C.2 N.am * am 6.46 -2 * * C.2 N.am * 1 6.46 -2 * * C.3 N.am * 1 .2 3 * * C.ar N.am * 1 1.6 -2 * * N.2 N.am * 1 1.6 -2 * * N.3 N.am * 1 .12 -3 * * N.am N.am * 1 1.6 -2 * * C.ar N.ar * ar 1.6 -2 EXP * C.2 N.pl3 * 1 12 -2 * * C.cat N.pl3 * ar 12 -2 MAC91 * C.3 N.pl3 * 1 .4 -3 * * C.ar N.pl3 * 1 1.6 -2 * * N.2 N.pl3 * 1 1.6 -2 * * N.pl3 N.pl3 * 1 1.6 -2 * * C.2 O.3 * 1 5.8 -2 * * C.3 O.3 * 1 1.2 3 * * C.ar O.3 * 1 1.2 -2 * * N.2 O.3 * 1 1 2 EXP * N.3 O.3 * 1 .2 3 * * C.2 P.3 * 1 1 -2 * * C.3 P.3 * 1 .4 3 * * C.ar P.3 * 1 1 3 * * O.3 P.3 * 1 .4 3 * * C.2 S.2 * 2 1 -2 * * C.3 S.2 * 1 .4 3 * * C.ar S.2 * 1 1 3 * * N.3 S.2 * 1 .4 3 * * C.2 S.3 * 1 1 -2 * * C.3 S.3 * 1 .4 3 * * C.ar S.3 * 1 1 3 * * S.3 S.3 * 1 6.75 2 EXP C.2 C.2 C.3 C.2 1 .126 -3 WHITE_77 C.2 C.2 C.3 H 1 .273 -3 WHITE_77 C.3 C.2 C.3 C.2 1 .126 3 WHITE_77 C.3 C.2 C.3 C.3 1 .126 3 WHITE_77 C.3 C.2 C.3 H 1 .274 3 WHITE_77 H C.2 C.3 C.2 1 .274 3 WHITE_77 H C.2 C.3 C.3 1 .274 3 WHITE_77 H C.2 C.3 H 1 .274 3 WHITE_77 C.2 C.2 C.3 * 1 .126 -3 WHITE_77 C.3 C.2 C.3 * 1 .126 3 WHITE_77 H C.2 C.3 * 1 .274 3 WHITE_77 C.2 C.2 C.3 C.3 1 .126 -3 WHITE_77