# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 16:32:10 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-{[(1H-1,2,4-triazol-5-ylsulfanyl)acetyl]amino}thiophene-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccsc1NC(=O)CSc2[nH]ncn2
#
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
 1RV  1RV  2-{[(1H-1,2,4-triazol-5-ylsulfanyl)acetyl]amino}thiophene-3-carboxamide  ligand  27  18  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1RV
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
 1RV  N01  N  NH2   0  -0.885   4.5934  -2.5682  -0.0157
 1RV  C01  C  C     0   0.492   3.4284  -1.9137  -0.0051
 1RV  O01  O  O     0  -0.277   2.3461  -2.5081  -0.0085
 1RV  C02  C  CR5   0  -0.171   3.4886  -0.4395   0.0077
 1RV  C05  C  CR5   0   0.104   2.3468   0.3348   0.0143
 1RV  N02  N  NH1   0  -0.658   1.0629  -0.1542   0.0144
 1RV  C06  C  C     0   0.629  -0.0496   0.6102   0.0135
 1RV  O02  O  O     0  -0.522  -0.0164   1.8263   0.0107
 1RV  C07  C  CH2   0  -0.744  -1.3401  -0.1702   0.0160
 1RV  S01  S  S2    0   0.149  -2.6846   1.0396  -0.0109
 1RV  C08  C  CR5   0   0.311  -4.0181  -0.0772  -0.0012
 1RV  N03  N  NR15  0  -0.492  -5.2931   0.3271  -0.0374
 1RV  N04  N  N     0  -0.286  -6.1147  -0.7305  -0.0153
 1RV  C09  C  CR15  0   0.015  -5.2807  -1.7358   0.0331
 1RV  N05  N  N     0  -0.415  -3.9732  -1.3893   0.0461
 1RV  S02  S  S2    0   0.193   2.7031   2.0191   0.0252
 1RV  C04  C  CR15  0  -0.488   4.3944   1.6963   0.0227
 1RV  C03  C  CR15  0  -0.154   4.6645   0.3712   0.0115
 1RV  H1   H  HNH2  0   0.393   4.5999  -3.5753  -0.0272
 1RV  H2   H  HNH2  0   0.410   5.4852  -2.1063  -0.0168
 1RV  H3   H  HNH1  0   0.444   1.0189  -1.1744   0.0135
 1RV  H4   H  HCH2  0   0.367  -1.3968  -0.8247  -0.8550
 1RV  H5   H  HCH2  0   0.343  -1.4068  -0.7952   0.9078
 1RV  H6   H  HNR5  0   0.414  -5.6662   1.2623  -0.0780
 1RV  H7   H  HCR5  0   0.296  -5.6175  -2.7603   0.0635
 1RV  H8   H  HCR5  0   0.280   5.0970   2.5141   0.0280
 1RV  H9   H  HCR5  0   0.252   5.6765  -0.0079   0.0072

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
 1RV  C09  N05  aromatic  1.353  0.020  1.353
 1RV  C09  N04  aromatic  1.307  0.020  1.307
 1RV  N05  C08  aromatic  1.314  0.020  1.314
 1RV  N04  N03  aromatic  1.339  0.020  1.339
 1RV  C04  S02  aromatic  1.722  0.020  1.722
 1RV  C04  C03  aromatic  1.352  0.020  1.352
 1RV  S02  C05  aromatic  1.722  0.020  1.722
 1RV  C03  C02  aromatic  1.428  0.020  1.428
 1RV  N03  C08  aromatic  1.338  0.020  1.338
 1RV  C08  S01  single    1.739  0.020  1.739
 1RV  O02  C06  double    1.217  0.020  1.217
 1RV  C05  C02  aromatic  1.380  0.020  1.380
 1RV  C05  N02  single    1.374  0.020  1.374
 1RV  C02  C01  single    1.475  0.020  1.475
 1RV  S01  C07  single    1.809  0.020  1.809
 1RV  C06  N02  single    1.350  0.020  1.350
 1RV  C06  C07  single    1.508  0.020  1.508
 1RV  C01  O01  double    1.235  0.020  1.235
 1RV  C01  N01  single    1.336  0.020  1.336
 1RV  N01  H1   single    0.860  0.020  1.020
 1RV  N01  H2   single    0.860  0.020  1.020
 1RV  N02  H3   single    0.860  0.020  1.020
 1RV  C07  H4   single    0.970  0.020  1.090
 1RV  C07  H5   single    0.970  0.020  1.090
 1RV  N03  H6   single    0.860  0.020  1.020
 1RV  C09  H7   single    0.930  0.020  1.080
 1RV  C04  H8   single    0.930  0.020  1.080
 1RV  C03  H9   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
 1RV  H2   N01  H1   117.01  3.000
 1RV  H2   N01  C01  123.28  3.000
 1RV  H1   N01  C01  119.71  3.000
 1RV  C02  C01  O01  121.11  3.000
 1RV  O01  C01  N01  121.89  3.000
 1RV  C02  C01  N01  117.00  3.000
 1RV  C03  C02  C05  111.27  3.000
 1RV  C05  C02  C01  121.81  3.000
 1RV  C03  C02  C01  126.92  3.000
 1RV  S02  C05  N02  122.79  3.000
 1RV  N02  C05  C02  125.00  3.000
 1RV  S02  C05  C02  112.20  3.000
 1RV  H3   N02  C06  122.02  3.000
 1RV  H3   N02  C05  113.32  3.000
 1RV  C06  N02  C05  124.65  3.000
 1RV  C07  C06  O02  122.73  3.000
 1RV  C07  C06  N02  114.34  3.000
 1RV  O02  C06  N02  122.93  3.000
 1RV  H5   C07  H4   107.80  3.000
 1RV  H5   C07  S01  110.48  3.000
 1RV  H4   C07  S01  110.53  3.000
 1RV  H5   C07  C06  110.50  3.000
 1RV  H4   C07  C06  110.71  3.000
 1RV  S01  C07  C06  106.85  3.000
 1RV  C08  S01  C07   98.06  3.000
 1RV  N05  C08  N03  109.59  3.000
 1RV  N03  C08  S01  122.44  3.000
 1RV  N05  C08  S01  127.97  3.000
 1RV  H6   N03  N04  120.42  3.000
 1RV  H6   N03  C08  129.37  3.000
 1RV  N04  N03  C08  110.21  3.000
 1RV  C09  N04  N03  102.51  3.000
 1RV  H7   C09  N05  123.01  3.000
 1RV  H7   C09  N04  122.16  3.000
 1RV  N05  C09  N04  114.84  3.000
 1RV  C09  N05  C08  102.86  3.000
 1RV  C04  S02  C05   91.14  3.000
 1RV  H8   C04  C03  127.82  3.000
 1RV  H8   C04  S02  119.86  3.000
 1RV  C03  C04  S02  112.33  3.000
 1RV  H9   C03  C04  122.06  3.000
 1RV  H9   C03  C02  124.88  3.000
 1RV  C04  C03  C02  113.06  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
 1RV  CONST_01  S02  C04  C03  C02     0.00   0.0  0
 1RV  CONST_02  C04  S02  C05  C02     0.00   0.0  0
 1RV  CONST_03  C03  C04  S02  C05     0.00   0.0  0
 1RV  CONST_04  C04  C03  C02  C05     0.00   0.0  0
 1RV  CONST_05  N04  C09  N05  C08     0.00   0.0  0
 1RV  CONST_06  C09  N04  N03  C08     0.00   0.0  0
 1RV  CONST_07  N05  C09  N04  N03     0.00   0.0  0
 1RV  CONST_08  C09  N05  C08  N03     0.00   0.0  0
 1RV  CONST_09  N05  C08  N03  N04     0.00   0.0  0
 1RV  CONST_10  C03  C02  C05  S02     0.00   0.0  0
 1RV  CONST_11  C04  C03  C02  C01   180.00   0.0  0
 1RV  CONST_12  S02  C05  C02  C01   180.00   0.0  0
 1RV  CONST_13  C04  S02  C05  N02   180.00   0.0  0
 1RV  CONST_14  C03  C02  C05  N02   180.00   0.0  0
 1RV  CONST_15  C09  N05  C08  S01   180.00   0.0  0
 1RV  CONST_16  N04  N03  C08  S01   180.00   0.0  0
 1RV  CONST_17  H8   C04  C03  C02   180.00   0.0  0
 1RV  CONST_18  H9   C03  C02  C05   180.00   0.0  0
 1RV  CONST_19  H7   C09  N05  C08   180.00   0.0  0
 1RV  CONST_20  H6   N03  N04  C09   180.00   0.0  0
 1RV  CONST_21  C06  N02  C05  C02   180.00   0.0  0
 1RV  CONST_22  S02  C05  N02  C06     0.00   0.0  0
 1RV  CONST_23  H3   N02  C05  C02     0.00   0.0  0
 1RV  CONST_24  O02  C06  N02  C05     0.00   0.0  0
 1RV  CONST_25  C07  C06  N02  C05   180.00   0.0  0
 1RV  CONST_26  H1   N01  C01  C02   180.00   0.0  0
 1RV  CONST_27  H2   N01  C01  C02     0.00   0.0  0
 1RV  Var_01    C03  C02  C01  N01    -0.08  30.0  2
 1RV  Var_02    N05  C08  S01  C07     1.46  30.0  2
 1RV  Var_03    H4   C07  S01  C08    59.56  30.0  3
 1RV  Var_04    S01  C07  C06  N02  -179.17  30.0  3

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
 1RV  plan-1  S01  0.020
 1RV  plan-1  C08  0.020
 1RV  plan-1  N03  0.020
 1RV  plan-1  N04  0.020
 1RV  plan-1  C09  0.020
 1RV  plan-1  N05  0.020
 1RV  plan-1  H6   0.020
 1RV  plan-1  H7   0.020
 1RV  plan-2  C01  0.020
 1RV  plan-2  C02  0.020
 1RV  plan-2  C05  0.020
 1RV  plan-2  N02  0.020
 1RV  plan-2  S02  0.020
 1RV  plan-2  C04  0.020
 1RV  plan-2  C03  0.020
 1RV  plan-2  H8   0.020
 1RV  plan-2  H9   0.020
 1RV  plan-3  N01  0.020
 1RV  plan-3  C01  0.020
 1RV  plan-3  O01  0.020
 1RV  plan-3  C02  0.020
 1RV  plan-3  H1   0.020
 1RV  plan-3  H2   0.020
 1RV  plan-4  C05  0.020
 1RV  plan-4  N02  0.020
 1RV  plan-4  C06  0.020
 1RV  plan-4  O02  0.020
 1RV  plan-4  C07  0.020
 1RV  plan-4  H3   0.020

