# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 11:10:32 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 3-{[(4-methylphenyl)methyl]sulfanyl}-1-phenyl-1H-1,2,4-triazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CSc2ncn(n2)c3ccccc3)cc1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 XRP  XRP  "3-{[(4-methylphenyl)methyl]sulfanyl}-1-phenyl-1H-1,2,4-triazole"
  ligand  35  20  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XRP
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 XRP  C13   C  CR16  0  -0.247  -37.6306  5.1203  520.9489
 XRP  C15   C  CR16  0  -0.249  -39.6292  3.8621  520.5186
 XRP  C17   C  CR15  0   0.104  -37.6963  6.0407  516.6706
 XRP  C20   C  CR16  0  -0.285  -43.2005  3.6983  513.9980
 XRP  C02   C  CR6   0   0.086  -43.6592  3.4339  515.2888
 XRP  C03   C  CR16  0  -0.288  -42.7720  2.8520  516.1886
 XRP  C04   C  CR16  0  -0.277  -41.4671  2.5524  515.8178
 XRP  C05   C  CR6   0   0.141  -41.0130  2.8242  514.5332
 XRP  C06   C  CH2   0  -0.674  -39.6136  2.4781  514.1229
 XRP  C08   C  CR5   0   0.186  -38.3266  4.6353  515.2709
 XRP  C11   C  CR6   0   0.365  -38.3723  4.7758  518.6967
 XRP  C12   C  CR16  0  -0.300  -37.4455  5.3037  519.5866
 XRP  C14   C  CR16  0  -0.252  -38.7179  4.3974  521.4196
 XRP  C16   C  CR16  0  -0.286  -39.4657  4.0518  519.1551
 XRP  C19   C  CR16  0  -0.269  -41.9000  3.4002  513.6261
 XRP  N09   N  N     0  -0.261  -38.6143  4.0655  516.4143
 XRP  N10   N  NR5   0  -0.389  -38.2048  4.9792  517.3112
 XRP  N18   N  N     0  -0.457  -37.7566  5.8579  515.3745
 XRP  H131  H  HCR6  0   0.267  -36.9097  5.5328  521.6420
 XRP  H151  H  HCR6  0   0.266  -40.4802  3.2982  520.8765
 XRP  H171  H  HCR5  0   0.314  -37.3184  6.9163  517.1760
 XRP  H201  H  HCR6  0   0.245  -43.8736  4.1397  513.2723
 XRP  H012  H  HCH3  0   0.246  -45.1187  4.8320  516.0177
 XRP  H013  H  HCH3  0   0.242  -45.7599  3.6674  514.8714
 XRP  H011  H  HCH3  0   0.243  -45.4024  3.1751  516.5281
 XRP  H031  H  HCR6  0   0.244  -43.1024  2.6269  517.1961
 XRP  H041  H  HCR6  0   0.247  -40.7974  2.0981  516.5372
 XRP  H062  H  HCH2  0   0.311  -39.6077  1.8920  513.2020
 XRP  H061  H  HCH2  0   0.304  -39.1019  1.8912  514.8849
 XRP  H121  H  HCR6  0   0.282  -36.5766  5.8405  519.2282
 XRP  H141  H  HCR6  0   0.264  -38.8529  4.2492  522.4826
 XRP  H161  H  HCR6  0   0.286  -40.1848  3.6471  518.4560
 XRP  H191  H  HCR6  0   0.248  -41.5707  3.6172  512.6162
 XRP  S07   S  S2    0   0.062  -38.5913  3.9263  513.7025
 XRP  C01   C  CH3   0  -0.720  -45.0587  3.7897  515.6967

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 XRP  C06  S07   single    1.822  0.020  1.822
 XRP  C06  C05   single    1.499  0.020  1.499
 XRP  S07  C08   single    1.741  0.020  1.741
 XRP  C05  C04   aromatic  1.389  0.020  1.389
 XRP  C05  C19   aromatic  1.393  0.020  1.393
 XRP  C04  C03   aromatic  1.389  0.020  1.389
 XRP  C19  C20   aromatic  1.385  0.020  1.385
 XRP  C03  C02   aromatic  1.391  0.020  1.391
 XRP  C20  C02   aromatic  1.395  0.020  1.395
 XRP  C02  C01   single    1.501  0.020  1.501
 XRP  C08  N18   aromatic  1.353  0.020  1.353
 XRP  C08  N09   aromatic  1.309  0.020  1.309
 XRP  N18  C17   aromatic  1.310  0.020  1.310
 XRP  N09  N10   aromatic  1.344  0.020  1.344
 XRP  C17  N10   aromatic  1.340  0.020  1.340
 XRP  N10  C11   single    1.410  0.020  1.410
 XRP  C11  C16   aromatic  1.389  0.020  1.389
 XRP  C11  C12   aromatic  1.389  0.020  1.389
 XRP  C16  C15   aromatic  1.386  0.020  1.386
 XRP  C12  C13   aromatic  1.387  0.020  1.387
 XRP  C15  C14   aromatic  1.389  0.020  1.389
 XRP  C13  C14   aromatic  1.388  0.020  1.388
 XRP  C13  H131  single    0.930  0.020  1.080
 XRP  C15  H151  single    0.930  0.020  1.080
 XRP  C17  H171  single    0.930  0.020  1.080
 XRP  C20  H201  single    0.930  0.020  1.080
 XRP  C01  H012  single    0.970  0.020  1.090
 XRP  C01  H013  single    0.970  0.020  1.090
 XRP  C01  H011  single    0.970  0.020  1.090
 XRP  C03  H031  single    0.930  0.020  1.080
 XRP  C04  H041  single    0.930  0.020  1.080
 XRP  C06  H062  single    0.970  0.020  1.090
 XRP  C06  H061  single    0.970  0.020  1.090
 XRP  C12  H121  single    0.930  0.020  1.080
 XRP  C14  H141  single    0.930  0.020  1.080
 XRP  C16  H161  single    0.930  0.020  1.080
 XRP  C19  H191  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 XRP  H131  C13  C14   120.22  3.000
 XRP  H131  C13  C12   119.33  3.000
 XRP  C14   C13  C12   120.44  3.000
 XRP  H151  C15  C16   119.31  3.000
 XRP  H151  C15  C14   120.16  3.000
 XRP  C16   C15  C14   120.53  3.000
 XRP  H171  C17  N18   126.34  3.000
 XRP  H171  C17  N10   123.48  3.000
 XRP  N18   C17  N10   110.17  3.000
 XRP  H201  C20  C19   119.41  3.000
 XRP  H201  C20  C02   119.50  3.000
 XRP  C19   C20  C02   121.09  3.000
 XRP  C03   C02  C01   121.21  3.000
 XRP  C01   C02  C20   120.88  3.000
 XRP  C03   C02  C20   117.90  3.000
 XRP  H031  C03  C04   119.32  3.000
 XRP  H031  C03  C02   119.58  3.000
 XRP  C04   C03  C02   121.11  3.000
 XRP  H041  C04  C05   119.62  3.000
 XRP  H041  C04  C03   119.61  3.000
 XRP  C05   C04  C03   120.77  3.000
 XRP  C19   C05  C06   120.77  3.000
 XRP  C19   C05  C04   118.34  3.000
 XRP  C06   C05  C04   120.87  3.000
 XRP  H061  C06  H062  107.35  3.000
 XRP  H061  C06  S07   109.03  3.000
 XRP  H062  C06  S07   103.25  3.000
 XRP  H061  C06  C05   111.80  3.000
 XRP  H062  C06  C05   111.10  3.000
 XRP  S07   C06  C05   113.80  3.000
 XRP  S07   C08  N18   120.06  3.000
 XRP  N18   C08  N09   114.77  3.000
 XRP  S07   C08  N09   125.16  3.000
 XRP  N10   C11  C16   119.53  3.000
 XRP  C16   C11  C12   120.78  3.000
 XRP  N10   C11  C12   119.69  3.000
 XRP  H121  C12  C11   120.79  3.000
 XRP  H121  C12  C13   119.87  3.000
 XRP  C11   C12  C13   119.33  3.000
 XRP  H141  C14  C15   120.19  3.000
 XRP  H141  C14  C13   120.16  3.000
 XRP  C15   C14  C13   119.65  3.000
 XRP  H161  C16  C11   120.33  3.000
 XRP  H161  C16  C15   120.41  3.000
 XRP  C11   C16  C15   119.26  3.000
 XRP  H191  C19  C05   119.72  3.000
 XRP  H191  C19  C20   119.49  3.000
 XRP  C05   C19  C20   120.79  3.000
 XRP  N10   N09  C08   102.70  3.000
 XRP  N09   N10  C11   121.42  3.000
 XRP  C11   N10  C17   128.97  3.000
 XRP  N09   N10  C17   109.58  3.000
 XRP  C08   N18  C17   102.78  3.000
 XRP  C08   S07  C06   101.60  3.000
 XRP  H011  C01  H013  108.16  3.000
 XRP  H011  C01  H012  107.27  3.000
 XRP  H013  C01  H012  107.12  3.000
 XRP  H011  C01  C02   111.58  3.000
 XRP  H013  C01  C02   111.56  3.000
 XRP  H012  C01  C02   110.94  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 XRP  CONST_01  N10   C11  C12  C13   180.00   0.0  0
 XRP  CONST_02  C16   C11  C12  C13     0.00   0.0  0
 XRP  CONST_03  C16   C15  C14  C13     0.00   0.0  0
 XRP  CONST_04  N10   C11  C16  C15   180.00   0.0  0
 XRP  CONST_05  C12   C11  C16  C15     0.00   0.0  0
 XRP  CONST_06  C12   C13  C14  C15     0.00   0.0  0
 XRP  CONST_07  N09   C08  N18  C17     0.00   0.0  0
 XRP  CONST_08  C08   N09  N10  C17     0.00   0.0  0
 XRP  CONST_11  C04   C05  C19  C20     0.00   0.0  0
 XRP  CONST_12  C04   C03  C02  C20     0.00   0.0  0
 XRP  CONST_13  C05   C04  C03  C02     0.00   0.0  0
 XRP  CONST_14  C05   C19  C20  C02     0.00   0.0  0
 XRP  CONST_15  C19   C05  C04  C03     0.00   0.0  0
 XRP  CONST_16  C19   C20  C02  C03     0.00   0.0  0
 XRP  CONST_17  N10   C17  N18  C08     0.00   0.0  0
 XRP  CONST_18  C11   N10  N09  C08   180.00   0.0  0
 XRP  CONST_19  N18   C17  N10  C11   180.00   0.0  0
 XRP  CONST_20  C14   C15  C16  C11     0.00   0.0  0
 XRP  CONST_21  C14   C13  C12  C11     0.00   0.0  0
 XRP  CONST_24  N18   C17  N10  N09     0.00   0.0  0
 XRP  CONST_25  N18   C08  N09  N10     0.00   0.0  0
 XRP  CONST_26  S07   C08  N18  C17   180.00   0.0  0
 XRP  CONST_27  C06   C05  C19  C20   180.00   0.0  0
 XRP  CONST_28  C04   C03  C02  C01   180.00   0.0  0
 XRP  CONST_29  C19   C20  C02  C01   180.00   0.0  0
 XRP  CONST_30  C06   C05  C04  C03   180.00   0.0  0
 XRP  CONST_31  S07   C08  N09  N10   180.00   0.0  0
 XRP  CONST_32  H151  C15  C14  C13   180.00   0.0  0
 XRP  CONST_33  H131  C13  C14  C15   180.00   0.0  0
 XRP  CONST_34  H031  C03  C02  C20   180.00   0.0  0
 XRP  CONST_35  H041  C04  C03  C02   180.00   0.0  0
 XRP  CONST_36  H191  C19  C20  C02   180.00   0.0  0
 XRP  CONST_37  H201  C20  C02  C03   180.00   0.0  0
 XRP  CONST_38  H191  C19  C05  C04   180.00   0.0  0
 XRP  CONST_39  H031  C03  C04  C05   180.00   0.0  0
 XRP  CONST_40  H201  C20  C19  C05   180.00   0.0  0
 XRP  CONST_41  H171  C17  N18  C08   180.00   0.0  0
 XRP  CONST_42  H171  C17  N10  C11     0.00   0.0  0
 XRP  CONST_43  H151  C15  C16  C11   180.00   0.0  0
 XRP  CONST_44  H131  C13  C12  C11   180.00   0.0  0
 XRP  CONST_45  H161  C16  C11  C12   180.00   0.0  0
 XRP  CONST_46  H141  C14  C13  C12   180.00   0.0  0
 XRP  CONST_47  H161  C16  C15  C14   180.00   0.0  0
 XRP  CONST_48  H121  C12  C13  C14   180.00   0.0  0
 XRP  CONST_49  H121  C12  C11  C16   180.00   0.0  0
 XRP  CONST_50  H141  C14  C15  C16   180.00   0.0  0
 XRP  CONST_51  H041  C04  C05  C19   180.00   0.0  0
 XRP  CONST_52  H171  C17  N10  N09   180.00   0.0  0
 XRP  CONST_53  H161  C16  C11  N10     0.00   0.0  0
 XRP  CONST_54  H121  C12  C11  N10     0.00   0.0  0
 XRP  Var_01    S07   C06  C05  C04  -116.08  30.0  2
 XRP  Var_02    C08   S07  C06  C05    71.81  30.0  3
 XRP  Var_03    N18   C08  S07  C06  -170.57  30.0  2
 XRP  Var_04    N09   C08  S07  C06    10.89  30.0  2
 XRP  Var_05    S07   C06  C05  C19    65.34  30.0  2
 XRP  Var_06    H012  C01  C02  C20   -84.68  30.0  2
 XRP  Var_07    H013  C01  C02  C20    34.67  30.0  2
 XRP  Var_08    H011  C01  C02  C20   155.78  30.0  2
 XRP  Var_09    H012  C01  C02  C03    94.23  30.0  2
 XRP  Var_10    H013  C01  C02  C03  -146.43  30.0  2
 XRP  Var_11    H011  C01  C02  C03   -25.32  30.0  2
 XRP  Var_12    H062  C06  C05  C04   127.91  30.0  2
 XRP  Var_13    H061  C06  C05  C04     7.99  30.0  2
 XRP  Var_14    H062  C06  C05  C19   -50.68  30.0  2
 XRP  Var_15    H061  C06  C05  C19  -170.59  30.0  2
 XRP  Var_16    H062  C06  S07  C08  -167.66  30.0  2
 XRP  Var_17    H061  C06  S07  C08   -53.75  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 XRP  plan-1  C17   0.020
 XRP  plan-1  C08   0.020
 XRP  plan-1  C11   0.020
 XRP  plan-1  N09   0.020
 XRP  plan-1  N10   0.020
 XRP  plan-1  N18   0.020
 XRP  plan-1  H171  0.020
 XRP  plan-1  S07   0.020
 XRP  plan-2  C20   0.020
 XRP  plan-2  C02   0.020
 XRP  plan-2  C03   0.020
 XRP  plan-2  C04   0.020
 XRP  plan-2  C05   0.020
 XRP  plan-2  C06   0.020
 XRP  plan-2  C19   0.020
 XRP  plan-2  H201  0.020
 XRP  plan-2  H031  0.020
 XRP  plan-2  H041  0.020
 XRP  plan-2  H191  0.020
 XRP  plan-2  C01   0.020
 XRP  plan-3  C13   0.020
 XRP  plan-3  C15   0.020
 XRP  plan-3  C11   0.020
 XRP  plan-3  C12   0.020
 XRP  plan-3  C14   0.020
 XRP  plan-3  C16   0.020
 XRP  plan-3  N10   0.020
 XRP  plan-3  H131  0.020
 XRP  plan-3  H151  0.020
 XRP  plan-3  H121  0.020
 XRP  plan-3  H141  0.020
 XRP  plan-3  H161  0.020

