# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 05:06:35 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2R,3R)-7-(methylsulfonyl)-3-(2,4,5-trifluorophenyl)-1,2,3,4-tetrahydropyrido[1,2-a]benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1ccc2n3C[C@H](N)[C@H](Cc3nc2c1)c4cc(F)c(F)cc4F
#
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
 677  677  (2R,3R)-7-(methylsulfonyl)-3-(2,4,5-trifluorophenyl)-1,2,3,4-tetrahydropyrido[1,2-a]benzimidazol-2-amine  ligand  43  27  .  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_677
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
 677  F27   F  F     0  -0.298  -7.5510   0.8839  -0.2647
 677  C6    C  CR6   0   0.405  -6.2596   0.5538  -0.2800
 677  C1    C  CR16  0  -0.557  -5.7762  -0.3117  -1.2354
 677  C2    C  CR6   0   0.523  -4.4279  -0.6241  -1.2146
 677  F22   F  F     0  -0.301  -3.9781  -1.4709  -2.1504
 677  C5    C  CR6   0   0.410  -5.4091   1.0900   0.6721
 677  F21   F  F     0  -0.304  -5.9019   1.9268   1.5900
 677  C4    C  CR16  0  -0.443  -4.0715   0.7663   0.6701
 677  C3    C  CR6   0  -0.050  -3.5436  -0.1050  -0.2828
 677  C9    C  CH1   0  -0.357  -2.0796  -0.4610  -0.2764
 677  C10   C  CH2   0  -0.520  -1.2191   0.7816  -0.5280
 677  C14   C  CH1   0  -0.089  -1.6571  -1.1249   1.0430
 677  N23   N  NH2   0  -0.795  -2.5003  -2.2681   1.3298
 677  C13   C  CH2   0  -0.280  -0.2262  -1.6298   0.9020
 677  N12   N  NR5   0  -0.559   0.6343  -0.5945   0.3689
 677  C11   C  CR5   0   0.488   0.2279   0.4980  -0.3367
 677  N18   N  N     0  -0.487   1.2187   1.2325  -0.7628
 677  C29   C  CR56  0   0.374   1.9983  -0.5705   0.3882
 677  C23   C  CR16  0  -0.298   2.9391  -1.4282   0.9443
 677  C22   C  CR16  0  -0.254   4.2678  -1.0874   0.7813
 677  C19   C  CR56  0   0.145   2.3489   0.5920  -0.3231
 677  C20   C  CR16  0  -0.317   3.6869   0.9312  -0.4795
 677  C21   C  CR6   0  -0.229   4.6213   0.0745   0.0806
 677  S24   S  S     0   1.214   6.3402   0.4571  -0.0990
 677  O26   O  OS    0  -0.672   6.4779   1.8973  -0.3130
 677  O25   O  OS    0  -0.672   7.0666  -0.1551   1.0131
 677  C27   C  CH3   0  -0.788   6.8208  -0.3733  -1.5969
 677  H1    H  HCR6  0   0.316  -6.4350  -0.7368  -1.9814
 677  H4    H  HCR6  0   0.298  -3.4339   1.2014   1.4304
 677  H9    H  HCH1  0   0.282  -1.8880  -1.1843  -1.0729
 677  H10   H  HCH2  0   0.295  -1.3790   1.1644  -1.5363
 677  H10A  H  HCH2  0   0.282  -1.5024   1.5875   0.1563
 677  H14   H  HCH1  0   0.233  -1.6737  -0.3618   1.8378
 677  HN23  H  HNH2  0   0.357  -2.2076  -2.6947   2.2011
 677  HN2A  H  HNH2  0   0.359  -3.4505  -1.9586   1.4930
 677  H13   H  HCH2  0   0.279   0.1623  -1.9427   1.8724
 677  H13A  H  HCH2  0   0.267  -0.2146  -2.4958   0.2352
 677  H23   H  HCR6  0   0.284   2.6602  -2.3226   1.4850
 677  H22   H  HCR6  0   0.282   5.0334  -1.7229   1.2042
 677  H20   H  HCR6  0   0.282   3.9761   1.8272  -1.0129
 677  H27   H  HCH3  0   0.294   6.2564   0.0330  -2.4329
 677  H27A  H  HCH3  0   0.309   7.8854  -0.1915  -1.7395
 677  H27B  H  HCH3  0   0.294   6.6339  -1.4398  -1.4966

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
 677  C6   F27   single    1.333  0.020  1.333
 677  C1   C6    aromatic  1.377  0.020  1.377
 677  C6   C5    aromatic  1.385  0.020  1.385
 677  C2   C1    aromatic  1.384  0.020  1.384
 677  C1   H1    single    0.930  0.020  1.080
 677  F22  C2    single    1.340  0.020  1.340
 677  C2   C3    aromatic  1.386  0.020  1.386
 677  C4   C5    aromatic  1.376  0.020  1.376
 677  C5   F21   single    1.336  0.020  1.336
 677  C3   C4    aromatic  1.395  0.020  1.395
 677  C4   H4    single    0.930  0.020  1.080
 677  C9   C3    single    1.507  0.020  1.507
 677  C14  C9    single    1.536  0.020  1.536
 677  C9   C10   single    1.532  0.020  1.532
 677  C9   H9    single    0.970  0.020  1.090
 677  C11  C10   single    1.487  0.020  1.487
 677  C10  H10   single    0.970  0.020  1.090
 677  C10  H10A  single    0.970  0.020  1.090
 677  C13  C14   single    1.524  0.020  1.524
 677  N23  C14   single    1.449  0.020  1.449
 677  C14  H14   single    0.970  0.020  1.090
 677  N23  HN23  single    0.890  0.020  1.040
 677  N23  HN2A  single    0.890  0.020  1.040
 677  C13  N12   single    1.448  0.020  1.448
 677  C13  H13   single    0.970  0.020  1.090
 677  C13  H13A  single    0.970  0.020  1.090
 677  C29  N12   aromatic  1.364  0.020  1.364
 677  N12  C11   aromatic  1.363  0.020  1.363
 677  C11  N18   aromatic  1.305  0.020  1.305
 677  C19  N18   aromatic  1.372  0.020  1.372
 677  C23  C29   aromatic  1.389  0.020  1.389
 677  C29  C19   aromatic  1.407  0.020  1.407
 677  C22  C23   aromatic  1.381  0.020  1.381
 677  C23  H23   single    0.930  0.020  1.080
 677  C22  C21   aromatic  1.402  0.020  1.402
 677  C22  H22   single    0.930  0.020  1.080
 677  C20  C19   aromatic  1.389  0.020  1.389
 677  C21  C20   aromatic  1.386  0.020  1.386
 677  C20  H20   single    0.930  0.020  1.080
 677  S24  C21   single    1.770  0.020  1.770
 677  O25  S24   double    1.463  0.020  1.463
 677  O26  S24   double    1.463  0.020  1.463
 677  S24  C27   single    1.779  0.020  1.779
 677  C27  H27   single    0.970  0.020  1.090
 677  C27  H27A  single    0.970  0.020  1.090
 677  C27  H27B  single    0.970  0.020  1.090

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
 677  C5    C6   C1    120.33  3.000
 677  C5    C6   F27   119.42  3.000
 677  C1    C6   F27   120.25  3.000
 677  H1    C1   C2    120.98  3.000
 677  H1    C1   C6    120.76  3.000
 677  C2    C1   C6    118.26  3.000
 677  C3    C2   F22   119.48  3.000
 677  C3    C2   C1    123.18  3.000
 677  F22   C2   C1    117.34  3.000
 677  C4    C5   F21   120.45  3.000
 677  F21   C5   C6    119.23  3.000
 677  C4    C5   C6    120.33  3.000
 677  H4    C4   C3    120.49  3.000
 677  H4    C4   C5    118.46  3.000
 677  C3    C4   C5    121.04  3.000
 677  C9    C3   C4    120.82  3.000
 677  C9    C3   C2    122.31  3.000
 677  C4    C3   C2    116.87  3.000
 677  H9    C9   C14   106.97  3.000
 677  H9    C9   C10   108.58  3.000
 677  C14   C9   C10   109.70  3.000
 677  H9    C9   C3    108.88  3.000
 677  C10   C9   C3    110.69  3.000
 677  C14   C9   C3    111.90  3.000
 677  H10A  C10  H10   106.36  3.000
 677  H10A  C10  C11   108.17  3.000
 677  H10   C10  C11   109.18  3.000
 677  H10A  C10  C9    110.44  3.000
 677  H10   C10  C9    110.75  3.000
 677  C11   C10  C9    111.76  3.000
 677  H14   C14  C13   108.08  3.000
 677  H14   C14  N23   113.25  3.000
 677  C13   C14  N23   107.66  3.000
 677  H14   C14  C9    108.43  3.000
 677  N23   C14  C9    110.54  3.000
 677  C13   C14  C9    108.78  3.000
 677  HN2A  N23  HN23  105.13  3.000
 677  HN2A  N23  C14   109.69  3.000
 677  HN23  N23  C14   109.52  3.000
 677  H13A  C13  H13   108.16  3.000
 677  H13A  C13  N12   109.61  3.000
 677  H13   C13  N12   108.72  3.000
 677  H13A  C13  C14   109.20  3.000
 677  H13   C13  C14   110.31  3.000
 677  N12   C13  C14   110.81  3.000
 677  C29   N12  C11   106.95  3.000
 677  C11   N12  C13   125.92  3.000
 677  C29   N12  C13   126.98  3.000
 677  N18   C11  N12   113.20  3.000
 677  N18   C11  C10   126.12  3.000
 677  N12   C11  C10   120.65  3.000
 677  C19   N18  C11   104.96  3.000
 677  C19   C29  C23   122.93  3.000
 677  C19   C29  N12   104.86  3.000
 677  C23   C29  N12   132.21  3.000
 677  H23   C23  C22   120.73  3.000
 677  H23   C23  C29   122.41  3.000
 677  C22   C23  C29   116.86  3.000
 677  H22   C22  C21   120.27  3.000
 677  H22   C22  C23   119.34  3.000
 677  C21   C22  C23   120.39  3.000
 677  C20   C19  C29   119.90  3.000
 677  C20   C19  N18   130.06  3.000
 677  C29   C19  N18   110.03  3.000
 677  H20   C20  C21   122.07  3.000
 677  H20   C20  C19   121.00  3.000
 677  C21   C20  C19   116.93  3.000
 677  S24   C21  C20   118.69  3.000
 677  S24   C21  C22   118.33  3.000
 677  C20   C21  C22   122.98  3.000
 677  C27   S24  O25   108.10  3.000
 677  C27   S24  O26   108.12  3.000
 677  O25   S24  O26   118.47  3.000
 677  C27   S24  C21   104.29  3.000
 677  O26   S24  C21   108.61  3.000
 677  O25   S24  C21   108.34  3.000
 677  H27B  C27  H27A  110.10  3.000
 677  H27B  C27  H27   110.37  3.000
 677  H27A  C27  H27   110.14  3.000
 677  H27B  C27  S24   109.50  3.000
 677  H27A  C27  S24   107.24  3.000
 677  H27   C27  S24   109.44  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
 677  CONST_01  C3   C2   C1   C6     0.00   0.0  0
 677  CONST_02  C3   C4   C5   C6     0.00   0.0  0
 677  CONST_03  C4   C5   C6   C1     0.00   0.0  0
 677  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 677  CONST_05  C5   C6   C1   C2     0.00   0.0  0
 677  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 677  CONST_07  C22  C23  C29  N12  180.00   0.0  0
 677  CONST_08  N18  C19  C29  N12    0.00   0.0  0
 677  CONST_09  C20  C19  C29  N12  180.00   0.0  0
 677  CONST_10  C19  N18  C11  N12    0.00   0.0  0
 677  CONST_11  C23  C29  N12  C11  180.00   0.0  0
 677  CONST_12  C19  C29  N12  C11    0.00   0.0  0
 677  CONST_13  C29  C19  N18  C11    0.00   0.0  0
 677  CONST_14  C20  C19  N18  C11  180.00   0.0  0
 677  CONST_15  C29  N12  C11  N18    0.00   0.0  0
 677  CONST_16  C23  C29  C19  N18  180.00   0.0  0
 677  CONST_17  C21  C20  C19  N18  180.00   0.0  0
 677  CONST_18  C21  C22  C23  C29    0.00   0.0  0
 677  CONST_19  C21  C20  C19  C29    0.00   0.0  0
 677  CONST_20  C20  C19  C29  C23    0.00   0.0  0
 677  CONST_21  C20  C21  C22  C23    0.00   0.0  0
 677  CONST_22  C19  C29  C23  C22    0.00   0.0  0
 677  CONST_23  C19  C20  C21  C22    0.00   0.0  0
 677  CONST_24  C9   C3   C2   C1   180.00   0.0  0
 677  CONST_25  C9   C3   C4   C5   180.00   0.0  0
 677  CONST_26  C2   C1   C6   F27  180.00   0.0  0
 677  CONST_27  C4   C5   C6   F27  180.00   0.0  0
 677  CONST_28  F22  C2   C1   C6   180.00   0.0  0
 677  CONST_29  F21  C5   C6   C1   180.00   0.0  0
 677  CONST_30  C4   C3   C2   F22  180.00   0.0  0
 677  CONST_31  C9   C3   C2   F22    0.00   0.0  0
 677  CONST_32  C3   C4   C5   F21  180.00   0.0  0
 677  CONST_33  S24  C21  C22  C23  180.00   0.0  0
 677  CONST_34  S24  C21  C20  C19  180.00   0.0  0
 677  CONST_35  H4   C4   C5   C6   180.00   0.0  0
 677  CONST_36  H1   C1   C6   C5   180.00   0.0  0
 677  CONST_37  H23  C23  C29  N12    0.00   0.0  0
 677  CONST_38  H20  C20  C19  N18    0.00   0.0  0
 677  CONST_39  H22  C22  C23  C29  180.00   0.0  0
 677  Var_01    N12  C11  C10  C9   -18.71  30.0  1
 677  Var_02    C29  N12  C13  C14  164.02  30.0  1
 677  Var_03    O25  S24  C21  C22  -25.99  30.0  1
 677  Var_04    H27  C27  S24  C21   62.11  30.0  3

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
 677  chir_01  C9   C3   C14  C10  positiv
 677  chir_02  C14  N23  C9   C13  positiv

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
 677  plan-1  F27  0.020
 677  plan-1  C6   0.020
 677  plan-1  C1   0.020
 677  plan-1  C2   0.020
 677  plan-1  F22  0.020
 677  plan-1  C5   0.020
 677  plan-1  F21  0.020
 677  plan-1  C4   0.020
 677  plan-1  C3   0.020
 677  plan-1  C9   0.020
 677  plan-1  H1   0.020
 677  plan-1  H4   0.020
 677  plan-2  C10  0.020
 677  plan-2  C13  0.020
 677  plan-2  N12  0.020
 677  plan-2  C11  0.020
 677  plan-2  N18  0.020
 677  plan-2  C29  0.020
 677  plan-2  C23  0.020
 677  plan-2  C22  0.020
 677  plan-2  C19  0.020
 677  plan-2  C20  0.020
 677  plan-2  C21  0.020
 677  plan-2  S24  0.020
 677  plan-2  H23  0.020
 677  plan-2  H22  0.020
 677  plan-2  H20  0.020

