# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:05:16 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 5-(1H-benzimidazol-1-yl)-3-{(1R)-1-[2-(trifluoromethyl)phenyl]ethoxy}thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Oc1cc(sc1C(N)=O)n2cnc3ccccc23)c4ccccc4C(F)(F)F
#
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
 430  430  5-(1H-benzimidazol-1-yl)-3-{(1R)-1-[2-(trifluoromethyl)phenyl]ethoxy}thiophene-2-carboxamide  ligand  46  30  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_430
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
 430  C01   C  CH3   0  -0.680  -1.6557  -0.0167  -1.9110
 430  C02   C  CH1   0  -0.095  -2.0346  -0.1647  -0.4449
 430  O03   O  O2    0  -0.467  -1.3906   0.8254   0.3654
 430  C04   C  CR5   0   0.464  -0.0552   0.8886   0.3472
 430  C05   C  CR15  0  -0.272   0.8117  -0.2398   0.4034
 430  C06   C  CR5   0   0.062   2.1172   0.1337   0.4515
 430  N07   N  NR5   0  -0.611   3.2156  -0.7086   0.5600
 430  C08   C  CR15  0   0.117   3.3551  -1.7212   1.4747
 430  N09   N  N     0  -0.448   4.4816  -2.3487   1.3791
 430  C10   C  CR56  0   0.130   5.1553  -1.7313   0.3463
 430  C11   C  CR16  0  -0.316   6.4144  -2.0010  -0.1850
 430  C12   C  CR16  0  -0.267   6.8511  -1.2205  -1.2400
 430  C13   C  CR16  0  -0.270   6.0551  -0.1937  -1.7674
 430  C14   C  CR16  0  -0.293   4.8013   0.0900  -1.2534
 430  C15   C  CR56  0   0.326   4.3786  -0.6930  -0.1872
 430  S16   S  S2    0   0.271   2.3223   1.8409   0.4457
 430  C17   C  CR5   0  -0.426   0.6148   2.0862   0.3346
 430  C18   C  C     0   0.514   0.0353   3.4378   0.1754
 430  N19   N  NH2   0  -0.816   0.7916   4.4451   0.6536
 430  O20   O  O     0  -0.457  -1.0331   3.6170  -0.3873
 430  C21   C  CR6   0   0.133  -3.5192   0.0608  -0.2473
 430  C22   C  CR16  0  -0.297  -3.9860   1.3692  -0.3487
 430  C23   C  CR16  0  -0.230  -5.3343   1.6644  -0.2298
 430  C24   C  CR16  0  -0.248  -6.2482   0.6469  -0.0093
 430  C25   C  CR16  0  -0.285  -5.8042  -0.6606   0.0932
 430  C26   C  CR6   0  -0.258  -4.4497  -0.9610  -0.0236
 430  C27   C  CT    0   1.055  -4.0188  -2.3928   0.1128
 430  F28   F  F     0  -0.296  -5.0482  -3.2272   0.2691
 430  F29   F  F     0  -0.317  -3.3403  -2.8224  -0.9635
 430  F30   F  F     0  -0.316  -3.2153  -2.5757   1.1731
 430  H011  H  HCH3  0   0.252  -0.5981  -0.2252  -2.0754
 430  H012  H  HCH3  0   0.257  -2.2254  -0.7223  -2.5139
 430  H013  H  HCH3  0   0.247  -1.8708   0.9903  -2.2697
 430  H02   H  HCH1  0   0.253  -1.7268  -1.1503  -0.0926
 430  H05   H  HCR5  0   0.307   0.4900  -1.2716   0.4025
 430  H08   H  HCR5  0   0.304   2.5741  -1.9256   2.1927
 430  H11   H  HCR6  0   0.263   7.0267  -2.7966   0.2189
 430  H12   H  HCR6  0   0.259   7.8262  -1.4046  -1.6711
 430  H13   H  HCR6  0   0.263   6.4285   0.3908  -2.5977
 430  H14   H  HCR6  0   0.275   4.1914   0.8792  -1.6724
 430  H191  H  HNH2  0   0.410   1.5314   4.2949   1.3190
 430  H192  H  HNH2  0   0.409   0.4409   5.3873   0.5882
 430  H22   H  HCR6  0   0.284  -3.2823   2.1732  -0.5188
 430  H23   H  HCR6  0   0.268  -5.6677   2.6905  -0.3113
 430  H24   H  HCR6  0   0.269  -7.3037   0.8632   0.0839
 430  H25   H  HCR6  0   0.274  -6.5287  -1.4432   0.2665

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
 430  C01  C02   single    1.521  0.020  1.521
 430  C02  O03   single    1.432  0.020  1.432
 430  C02  C21   single    1.515  0.020  1.515
 430  O03  C04   single    1.337  0.020  1.337
 430  C04  C05   aromatic  1.424  0.020  1.424
 430  C04  C17   aromatic  1.372  0.020  1.372
 430  C05  C06   aromatic  1.359  0.020  1.359
 430  C06  N07   single    1.388  0.020  1.388
 430  C06  S16   aromatic  1.719  0.020  1.719
 430  N07  C08   aromatic  1.372  0.020  1.372
 430  N07  C15   aromatic  1.383  0.020  1.383
 430  C08  N09   aromatic  1.293  0.020  1.293
 430  N09  C10   aromatic  1.379  0.020  1.379
 430  C10  C11   aromatic  1.393  0.020  1.393
 430  C10  C15   aromatic  1.402  0.020  1.402
 430  C11  C12   aromatic  1.383  0.020  1.383
 430  C12  C13   aromatic  1.402  0.020  1.402
 430  C13  C14   aromatic  1.385  0.020  1.385
 430  C14  C15   aromatic  1.389  0.020  1.389
 430  S16  C17   aromatic  1.729  0.020  1.729
 430  C17  C18   single    1.479  0.020  1.479
 430  C18  N19   single    1.347  0.020  1.347
 430  C18  O20   double    1.221  0.020  1.221
 430  C21  C22   aromatic  1.393  0.020  1.393
 430  C21  C26   aromatic  1.400  0.020  1.400
 430  C22  C23   aromatic  1.385  0.020  1.385
 430  C23  C24   aromatic  1.385  0.020  1.385
 430  C24  C25   aromatic  1.385  0.020  1.385
 430  C25  C26   aromatic  1.392  0.020  1.392
 430  C26  C27   single    1.501  0.020  1.501
 430  C27  F28   single    1.334  0.020  1.334
 430  C27  F29   single    1.343  0.020  1.343
 430  C27  F30   single    1.343  0.020  1.343
 430  C01  H011  single    0.970  0.020  1.090
 430  C01  H012  single    0.970  0.020  1.090
 430  C01  H013  single    0.970  0.020  1.090
 430  C02  H02   single    0.970  0.020  1.090
 430  C05  H05   single    0.930  0.020  1.080
 430  C08  H08   single    0.930  0.020  1.080
 430  C11  H11   single    0.930  0.020  1.080
 430  C12  H12   single    0.930  0.020  1.080
 430  C13  H13   single    0.930  0.020  1.080
 430  C14  H14   single    0.930  0.020  1.080
 430  N19  H191  single    0.890  0.020  1.040
 430  N19  H192  single    0.890  0.020  1.040
 430  C22  H22   single    0.930  0.020  1.080
 430  C23  H23   single    0.930  0.020  1.080
 430  C24  H24   single    0.930  0.020  1.080
 430  C25  H25   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
 430  H013  C01  H012  108.24  3.000
 430  H013  C01  H011  108.57  3.000
 430  H012  C01  H011  107.46  3.000
 430  H013  C01  C02   110.96  3.000
 430  H012  C01  C02   109.89  3.000
 430  H011  C01  C02   111.60  3.000
 430  H02   C02  C21   111.65  3.000
 430  H02   C02  O03   108.36  3.000
 430  C21   C02  O03   105.31  3.000
 430  H02   C02  C01   109.20  3.000
 430  C21   C02  C01   110.82  3.000
 430  O03   C02  C01   111.46  3.000
 430  C04   O03  C02   118.30  3.000
 430  C17   C04  C05   113.25  3.000
 430  C17   C04  O03   121.94  3.000
 430  C05   C04  O03   124.75  3.000
 430  H05   C05  C06   123.26  3.000
 430  H05   C05  C04   125.12  3.000
 430  C06   C05  C04   111.62  3.000
 430  S16   C06  N07   120.54  3.000
 430  S16   C06  C05   112.80  3.000
 430  N07   C06  C05   126.59  3.000
 430  C15   N07  C08   106.45  3.000
 430  C15   N07  C06   128.06  3.000
 430  C08   N07  C06   125.48  3.000
 430  H08   C08  N09   125.95  3.000
 430  H08   C08  N07   120.61  3.000
 430  N09   C08  N07   113.43  3.000
 430  C10   N09  C08   105.29  3.000
 430  C15   C10  C11   119.93  3.000
 430  C15   C10  N09   110.24  3.000
 430  C11   C10  N09   129.83  3.000
 430  H11   C11  C12   121.40  3.000
 430  H11   C11  C10   120.76  3.000
 430  C12   C11  C10   117.84  3.000
 430  H12   C12  C13   119.10  3.000
 430  H12   C12  C11   119.50  3.000
 430  C13   C12  C11   121.39  3.000
 430  H13   C13  C14   119.12  3.000
 430  H13   C13  C12   119.24  3.000
 430  C14   C13  C12   121.64  3.000
 430  H14   C14  C15   122.49  3.000
 430  H14   C14  C13   121.08  3.000
 430  C15   C14  C13   116.43  3.000
 430  C14   C15  C10   122.76  3.000
 430  C14   C15  N07   132.63  3.000
 430  C10   C15  N07   104.60  3.000
 430  C17   S16  C06    91.33  3.000
 430  C18   C17  S16   121.58  3.000
 430  C18   C17  C04   127.38  3.000
 430  S16   C17  C04   110.96  3.000
 430  O20   C18  N19   123.03  3.000
 430  O20   C18  C17   121.78  3.000
 430  N19   C18  C17   115.15  3.000
 430  H192  N19  H191  116.00  3.000
 430  H192  N19  C18   118.73  3.000
 430  H191  N19  C18   122.40  3.000
 430  C26   C21  C22   118.33  3.000
 430  C26   C21  C02   124.31  3.000
 430  C22   C21  C02   117.31  3.000
 430  H22   C22  C23   119.22  3.000
 430  H22   C22  C21   119.45  3.000
 430  C23   C22  C21   121.34  3.000
 430  H23   C23  C24   120.34  3.000
 430  H23   C23  C22   119.71  3.000
 430  C24   C23  C22   119.95  3.000
 430  H24   C24  C25   119.70  3.000
 430  H24   C24  C23   120.71  3.000
 430  C25   C24  C23   119.59  3.000
 430  H25   C25  C26   120.63  3.000
 430  H25   C25  C24   118.74  3.000
 430  C26   C25  C24   120.63  3.000
 430  C27   C26  C25   118.51  3.000
 430  C27   C26  C21   121.32  3.000
 430  C25   C26  C21   120.16  3.000
 430  F30   C27  F29   106.67  3.000
 430  F30   C27  F28   106.49  3.000
 430  F29   C27  F28   106.48  3.000
 430  F30   C27  C26   111.92  3.000
 430  F29   C27  C26   112.16  3.000
 430  F28   C27  C26   112.68  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
 430  CONST_01  N07   C06  C05  C04   180.00   0.0  0
 430  CONST_02  S16   C06  C05  C04     0.00   0.0  0
 430  CONST_03  C06   S16  C17  C04     0.00   0.0  0
 430  CONST_04  S16   C17  C04  C05     0.00   0.0  0
 430  CONST_07  C17   S16  C06  C05     0.00   0.0  0
 430  CONST_08  C17   C04  C05  C06     0.00   0.0  0
 430  CONST_09  N09   C08  N07  C06   180.00   0.0  0
 430  CONST_10  C10   C15  N07  C06   180.00   0.0  0
 430  CONST_11  C14   C15  N07  C06     0.00   0.0  0
 430  CONST_12  C17   S16  C06  N07   180.00   0.0  0
 430  CONST_13  C10   N09  C08  N07     0.00   0.0  0
 430  CONST_14  N09   C10  C15  N07     0.00   0.0  0
 430  CONST_15  C11   C10  C15  N07   180.00   0.0  0
 430  CONST_16  C13   C14  C15  N07   180.00   0.0  0
 430  CONST_18  C10   C15  N07  C08     0.00   0.0  0
 430  CONST_19  C14   C15  N07  C08   180.00   0.0  0
 430  CONST_20  C11   C10  N09  C08   180.00   0.0  0
 430  CONST_21  C15   C10  N09  C08     0.00   0.0  0
 430  CONST_22  C15   N07  C08  N09     0.00   0.0  0
 430  CONST_23  C12   C11  C10  N09   180.00   0.0  0
 430  CONST_24  C14   C15  C10  N09   180.00   0.0  0
 430  CONST_25  C13   C12  C11  C10     0.00   0.0  0
 430  CONST_26  C13   C14  C15  C10     0.00   0.0  0
 430  CONST_27  C14   C15  C10  C11     0.00   0.0  0
 430  CONST_28  C14   C13  C12  C11     0.00   0.0  0
 430  CONST_29  C15   C10  C11  C12     0.00   0.0  0
 430  CONST_30  C15   C14  C13  C12     0.00   0.0  0
 430  CONST_32  C24   C23  C22  C21     0.00   0.0  0
 430  CONST_33  C24   C25  C26  C21     0.00   0.0  0
 430  CONST_34  C25   C26  C21  C22     0.00   0.0  0
 430  CONST_35  C25   C24  C23  C22     0.00   0.0  0
 430  CONST_36  C26   C21  C22  C23     0.00   0.0  0
 430  CONST_37  C26   C25  C24  C23     0.00   0.0  0
 430  CONST_38  C23   C22  C21  C02   180.00   0.0  0
 430  CONST_39  C25   C26  C21  C02   180.00   0.0  0
 430  CONST_40  C06   C05  C04  O03   180.00   0.0  0
 430  CONST_41  S16   C17  C04  O03   180.00   0.0  0
 430  CONST_42  C18   C17  C04  C05   180.00   0.0  0
 430  CONST_43  C18   C17  S16  C06   180.00   0.0  0
 430  CONST_44  C27   C26  C21  C22   180.00   0.0  0
 430  CONST_45  C27   C26  C25  C24   180.00   0.0  0
 430  CONST_46  H08   C08  N07  C06     0.00   0.0  0
 430  CONST_47  H05   C05  C06  N07     0.00   0.0  0
 430  CONST_48  H14   C14  C15  N07     0.00   0.0  0
 430  CONST_49  H11   C11  C10  N09     0.00   0.0  0
 430  CONST_50  H12   C12  C11  C10   180.00   0.0  0
 430  CONST_51  H13   C13  C12  C11   180.00   0.0  0
 430  CONST_52  H23   C23  C22  C21   180.00   0.0  0
 430  CONST_53  H25   C25  C26  C21   180.00   0.0  0
 430  CONST_54  H24   C24  C23  C22   180.00   0.0  0
 430  CONST_55  H22   C22  C23  C24   180.00   0.0  0
 430  CONST_57  H192  N19  C18  C17   180.00   0.0  0
 430  Var_01    C05   C04  O03  C02   -43.83  30.0  2
 430  Var_02    N19   C18  C17  C04   157.64  30.0  2
 430  Var_03    F28   C27  C26  C21  -177.53  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 430  chir_01  C02  C01  O03  C21  negativ

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
 430  plan-1  O03   0.020
 430  plan-1  C04   0.020
 430  plan-1  C05   0.020
 430  plan-1  C06   0.020
 430  plan-1  N07   0.020
 430  plan-1  S16   0.020
 430  plan-1  C17   0.020
 430  plan-1  C18   0.020
 430  plan-1  H05   0.020
 430  plan-2  C02   0.020
 430  plan-2  C21   0.020
 430  plan-2  C22   0.020
 430  plan-2  C23   0.020
 430  plan-2  C24   0.020
 430  plan-2  C25   0.020
 430  plan-2  C26   0.020
 430  plan-2  C27   0.020
 430  plan-2  H22   0.020
 430  plan-2  H23   0.020
 430  plan-2  H24   0.020
 430  plan-2  H25   0.020
 430  plan-3  C06   0.020
 430  plan-3  N07   0.020
 430  plan-3  C08   0.020
 430  plan-3  N09   0.020
 430  plan-3  C10   0.020
 430  plan-3  C11   0.020
 430  plan-3  C12   0.020
 430  plan-3  C13   0.020
 430  plan-3  C14   0.020
 430  plan-3  C15   0.020
 430  plan-3  H08   0.020
 430  plan-3  H11   0.020
 430  plan-3  H12   0.020
 430  plan-3  H13   0.020
 430  plan-3  H14   0.020
 430  plan-4  C17   0.020
 430  plan-4  C18   0.020
 430  plan-4  N19   0.020
 430  plan-4  O20   0.020
 430  plan-4  H191  0.020
 430  plan-4  H192  0.020

