# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 05:33:34 2021
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-[2-[2,4-bis(fluoranyl)phenoxy]-5-(methylsulfonylmethyl)pyridin-3-yl]-8-methyl-2~{H}-pyrrolo[1,2-a]pyrazin-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(n2C=CNC(=O)c12)c3cc(C[S](C)(=O)=O)cnc3Oc4ccc(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
 D7U  D7U  6-[2-[2,4-bis(fluoranyl)phenoxy]-5-(methylsulfonylmethyl)pyridin-3-yl]-8-methyl-2~{H}-pyrrolo[1,2-a]pyrazin-1-one  ligand  48  31  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D7U
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
 D7U  C10   C  CH3   0  -0.734  -12.4288   -3.6432  -2.2468
 D7U  C13   C  CR16  0  -0.180   -7.7153   -6.9295  -1.7755
 D7U  C15   C  CR16  0  -0.062   -6.0895   -7.6140  -0.1880
 D7U  C17   C  CR6   0   0.489   -8.0707   -6.8137   0.5601
 D7U  C22   C  CH3   0  -0.794   -4.7555   -9.9113  -4.3683
 D7U  C26   C  CR16  0  -0.423   -8.7018   -7.8979   4.9346
 D7U  C28   C  CR16  0  -0.569   -7.1718   -6.0254   4.7825
 D7U  N1    N  NR16  0  -0.670  -13.5586   -7.4244   0.0788
 D7U  C2    C  CR16  0  -0.061  -12.4767   -8.2102   0.4031
 D7U  C3    C  CR16  0  -0.091  -11.2295   -7.8382   0.1032
 D7U  N4    N  N     0  -0.558  -11.0456   -6.6281  -0.5499
 D7U  C5    C  CR56  0   0.140  -12.1209   -5.8485  -0.9380
 D7U  C6    C  CR6   0   0.501  -13.4711   -6.2386  -0.6015
 D7U  C7    C  CR5   0   0.368   -9.8968   -6.0478  -0.9809
 D7U  C8    C  CR15  0  -0.437  -10.2419   -4.8942  -1.6632
 D7U  C09   C  CR5   0   0.042  -11.6396   -4.7543  -1.6392
 D7U  O11   O  O     0  -0.479  -14.4634   -5.5824  -0.8892
 D7U  C12   C  CR6   0  -0.118   -8.5701   -6.6104  -0.7348
 D7U  C14   C  CR6   0   0.019   -6.4427   -7.4336  -1.5146
 D7U  N16   N  N     0  -0.433   -6.8882   -7.3037   0.8270
 D7U  C19   C  CR6   0   0.203   -8.4802   -6.6910   2.8651
 D7U  S21   S  S     0   1.200   -5.9217   -9.5346  -3.0826
 D7U  O23   O  OS    0  -0.678   -5.6554  -10.3919  -1.9286
 D7U  O24   O  OS    0  -0.677   -7.2720   -9.5445  -3.6448
 D7U  C25   C  CR16  0  -0.290   -9.0520   -7.7093   3.6048
 D7U  C27   C  CR6   0   0.544   -7.7657   -7.0523   5.4943
 D7U  C29   C  CR6   0   0.528   -7.5467   -5.8600   3.4660
 D7U  F30   F  F     0  -0.295   -7.0048   -4.8757   2.7480
 D7U  F31   F  F     0  -0.308   -7.4147   -7.2225   6.7747
 D7U  H101  H  HCH3  0   0.243  -13.1586   -4.0129  -2.9667
 D7U  H102  H  HCH3  0   0.243  -12.9811   -3.0788  -1.4953
 D7U  H103  H  HCH3  0   0.239  -11.7683   -2.9503  -2.7657
 D7U  H131  H  HCR6  0   0.274   -8.0472   -6.7797  -2.7948
 D7U  H151  H  HCR6  0   0.278   -5.1157   -8.0120   0.0734
 D7U  H202  H  HCH2  0   0.329   -4.4755   -7.8251  -2.3068
 D7U  H201  H  HCH2  0   0.331   -5.6333   -7.2167  -3.5054
 D7U  H222  H  HCH3  0   0.297   -3.7461   -9.8496  -3.9687
 D7U  H221  H  HCH3  0   0.315   -4.9619  -10.9260  -4.7063
 D7U  H223  H  HCH3  0   0.297   -4.8855   -9.2116  -5.1908
 D7U  H261  H  HCR6  0   0.293   -9.1515   -8.6892   5.5178
 D7U  H281  H  HCR6  0   0.311   -6.4415   -5.3703   5.2394
 D7U  H021  H  HCR6  0   0.314  -12.6888   -9.1417   0.9023
 D7U  H031  H  HCR6  0   0.307  -10.3685   -8.4491   0.3160
 D7U  H081  H  HCR5  0   0.259   -9.5393   -4.2108  -2.1161
 D7U  H251  H  HCR6  0   0.289   -9.7857   -8.3559   3.1413
 D7U  H2    H  HNR6  0   0.420  -14.4818   -7.7501   0.3247
 D7U  O18   O  O2    0  -0.504   -8.8882   -6.4677   1.5769
 D7U  C20   C  CH2   0  -0.713   -5.5216   -7.8363  -2.6151

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
 D7U  C22  S21   single    1.776  0.020  1.776
 D7U  O24  S21   double    1.463  0.020  1.463
 D7U  S21  O23   double    1.462  0.020  1.462
 D7U  S21  C20   single    1.806  0.020  1.806
 D7U  C20  C14   single    1.491  0.020  1.491
 D7U  C10  C09   single    1.492  0.020  1.492
 D7U  C13  C14   aromatic  1.393  0.020  1.393
 D7U  C13  C12   aromatic  1.384  0.020  1.384
 D7U  C8   C09   aromatic  1.405  0.020  1.405
 D7U  C8   C7    aromatic  1.384  0.020  1.384
 D7U  C09  C5    aromatic  1.386  0.020  1.386
 D7U  C14  C15   aromatic  1.385  0.020  1.385
 D7U  O11  C6    double    1.224  0.020  1.224
 D7U  C7   C12   single    1.462  0.020  1.462
 D7U  C7   N4    aromatic  1.357  0.020  1.357
 D7U  C5   C6    single    1.445  0.020  1.445
 D7U  C5   N4    aromatic  1.384  0.020  1.384
 D7U  C12  C17   aromatic  1.403  0.020  1.403
 D7U  C6   N1    single    1.370  0.020  1.370
 D7U  N4   C3    single    1.387  0.020  1.387
 D7U  C15  N16   aromatic  1.328  0.020  1.328
 D7U  N1   C2    single    1.376  0.020  1.376
 D7U  C3   C2    double    1.336  0.020  1.336
 D7U  C17  N16   aromatic  1.308  0.020  1.308
 D7U  C17  O18   single    1.350  0.020  1.350
 D7U  O18  C19   single    1.370  0.020  1.370
 D7U  F30  C29   single    1.333  0.020  1.333
 D7U  C19  C29   aromatic  1.387  0.020  1.387
 D7U  C19  C25   aromatic  1.382  0.020  1.382
 D7U  C29  C28   aromatic  1.379  0.020  1.379
 D7U  C25  C26   aromatic  1.388  0.020  1.388
 D7U  C28  C27   aromatic  1.383  0.020  1.383
 D7U  C27  C26   aromatic  1.380  0.020  1.380
 D7U  C27  F31   single    1.339  0.020  1.339
 D7U  C10  H101  single    0.970  0.020  1.090
 D7U  C10  H102  single    0.970  0.020  1.090
 D7U  C10  H103  single    0.970  0.020  1.090
 D7U  C13  H131  single    0.930  0.020  1.080
 D7U  C15  H151  single    0.930  0.020  1.080
 D7U  C20  H202  single    0.970  0.020  1.090
 D7U  C20  H201  single    0.970  0.020  1.090
 D7U  C22  H222  single    0.970  0.020  1.090
 D7U  C22  H221  single    0.970  0.020  1.090
 D7U  C22  H223  single    0.970  0.020  1.090
 D7U  C26  H261  single    0.930  0.020  1.080
 D7U  C28  H281  single    0.930  0.020  1.080
 D7U  C2   H021  single    0.930  0.020  1.080
 D7U  C3   H031  single    0.930  0.020  1.080
 D7U  C8   H081  single    0.930  0.020  1.080
 D7U  C25  H251  single    0.930  0.020  1.080
 D7U  N1   H2    single    0.860  0.020  1.020

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
 D7U  H103  C10  H102  107.84  3.000
 D7U  H103  C10  H101  107.89  3.000
 D7U  H102  C10  H101  106.97  3.000
 D7U  H103  C10  C09   110.30  3.000
 D7U  H102  C10  C09   111.89  3.000
 D7U  H101  C10  C09   111.75  3.000
 D7U  H131  C13  C14   120.43  3.000
 D7U  H131  C13  C12   119.13  3.000
 D7U  C14   C13  C12   120.44  3.000
 D7U  H151  C15  N16   116.21  3.000
 D7U  H151  C15  C14   120.54  3.000
 D7U  N16   C15  C14   123.24  3.000
 D7U  O18   C17  N16   119.34  3.000
 D7U  O18   C17  C12   116.27  3.000
 D7U  N16   C17  C12   124.38  3.000
 D7U  H223  C22  H221  110.00  3.000
 D7U  H223  C22  H222  110.63  3.000
 D7U  H221  C22  H222  110.05  3.000
 D7U  H223  C22  S21   109.42  3.000
 D7U  H221  C22  S21   107.32  3.000
 D7U  H222  C22  S21   109.35  3.000
 D7U  H261  C26  C27   120.79  3.000
 D7U  H261  C26  C25   120.76  3.000
 D7U  C27   C26  C25   118.45  3.000
 D7U  H281  C28  C29   120.93  3.000
 D7U  H281  C28  C27   121.45  3.000
 D7U  C29   C28  C27   117.62  3.000
 D7U  H2    N1   C6    117.30  3.000
 D7U  H2    N1   C2    118.52  3.000
 D7U  C6    N1   C2    124.14  3.000
 D7U  H021  C2   C3    121.90  3.000
 D7U  H021  C2   N1    116.61  3.000
 D7U  C3    C2   N1    121.48  3.000
 D7U  H031  C3   N4    118.80  3.000
 D7U  H031  C3   C2    122.97  3.000
 D7U  N4    C3   C2    118.20  3.000
 D7U  C7    N4   C5    109.13  3.000
 D7U  C5    N4   C3    121.36  3.000
 D7U  C7    N4   C3    129.39  3.000
 D7U  C09   C5   C6    130.95  3.000
 D7U  C6    C5   N4    120.57  3.000
 D7U  C09   C5   N4    108.47  3.000
 D7U  O11   C6   C5    123.92  3.000
 D7U  C5    C6   N1    114.14  3.000
 D7U  O11   C6   N1    121.94  3.000
 D7U  C12   C7   C8    129.06  3.000
 D7U  C12   C7   N4    123.38  3.000
 D7U  C8    C7   N4    107.57  3.000
 D7U  H081  C8   C09   126.27  3.000
 D7U  H081  C8   C7    124.90  3.000
 D7U  C09   C8   C7    108.83  3.000
 D7U  C8    C09  C5    106.00  3.000
 D7U  C5    C09  C10   127.60  3.000
 D7U  C8    C09  C10   126.40  3.000
 D7U  C7    C12  C17   122.29  3.000
 D7U  C17   C12  C13   116.16  3.000
 D7U  C7    C12  C13   121.51  3.000
 D7U  C20   C14  C15   120.96  3.000
 D7U  C15   C14  C13   117.36  3.000
 D7U  C20   C14  C13   121.59  3.000
 D7U  C17   N16  C15   118.39  3.000
 D7U  C29   C19  C25   119.21  3.000
 D7U  C25   C19  O18   120.01  3.000
 D7U  C29   C19  O18   120.69  3.000
 D7U  O24   S21  O23   117.88  3.000
 D7U  O23   S21  C22   109.11  3.000
 D7U  O24   S21  C22   109.05  3.000
 D7U  O23   S21  C20   107.86  3.000
 D7U  O24   S21  C20   108.08  3.000
 D7U  C22   S21  C20   103.96  3.000
 D7U  H251  C25  C19   119.43  3.000
 D7U  H251  C25  C26   120.01  3.000
 D7U  C19   C25  C26   120.55  3.000
 D7U  F31   C27  C28   118.29  3.000
 D7U  F31   C27  C26   119.20  3.000
 D7U  C28   C27  C26   122.50  3.000
 D7U  F30   C29  C19   118.85  3.000
 D7U  C19   C29  C28   121.66  3.000
 D7U  F30   C29  C28   119.48  3.000
 D7U  C19   O18  C17   119.10  3.000
 D7U  H201  C20  H202  108.86  3.000
 D7U  H201  C20  S21   107.47  3.000
 D7U  H202  C20  S21   107.18  3.000
 D7U  H201  C20  C14   112.70  3.000
 D7U  H202  C20  C14   112.41  3.000
 D7U  S21   C20  C14   107.95  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
 D7U  CONST_01  N16   C15  C14  C13     0.00   0.0  0
 D7U  CONST_04  N16   C17  C12  C13     0.00   0.0  0
 D7U  CONST_05  C12   C13  C14  C15     0.00   0.0  0
 D7U  CONST_06  C12   C17  N16  C15     0.00   0.0  0
 D7U  CONST_07  C14   C13  C12  C17     0.00   0.0  0
 D7U  CONST_10  C14   C15  N16  C17     0.00   0.0  0
 D7U  CONST_11  C29   C19  C25  C26     0.00   0.0  0
 D7U  CONST_12  C29   C28  C27  C26     0.00   0.0  0
 D7U  CONST_13  C25   C19  C29  C28     0.00   0.0  0
 D7U  CONST_14  C25   C26  C27  C28     0.00   0.0  0
 D7U  CONST_15  C09   C8   C7   N4      0.00   0.0  0
 D7U  CONST_16  C8    C09  C5   N4      0.00   0.0  0
 D7U  CONST_17  C7    C8   C09  C5      0.00   0.0  0
 D7U  CONST_18  C8    C7   N4   C5      0.00   0.0  0
 D7U  CONST_19  C12   C7   N4   C5    180.00   0.0  0
 D7U  CONST_20  C14   C13  C12  C7    180.00   0.0  0
 D7U  CONST_21  N16   C17  C12  C7    180.00   0.0  0
 D7U  CONST_22  C09   C5   N4   C7      0.00   0.0  0
 D7U  CONST_23  C12   C7   C8   C09   180.00   0.0  0
 D7U  CONST_24  C27   C28  C29  C19     0.00   0.0  0
 D7U  CONST_25  C27   C26  C25  C19     0.00   0.0  0
 D7U  CONST_26  C12   C7   N4   C3      0.00   0.0  0
 D7U  CONST_27  C5    C6   N1   C2      0.00   0.0  0
 D7U  CONST_28  C7    C8   C09  C10   180.00   0.0  0
 D7U  CONST_29  C6    C5   C09  C10     0.00   0.0  0
 D7U  CONST_30  N4    C5   C09  C10   180.00   0.0  0
 D7U  CONST_31  O18   C17  C12  C13   180.00   0.0  0
 D7U  CONST_32  O18   C17  N16  C15   180.00   0.0  0
 D7U  CONST_33  C12   C13  C14  C20   180.00   0.0  0
 D7U  CONST_34  N16   C15  C14  C20   180.00   0.0  0
 D7U  CONST_35  O18   C19  C25  C26   180.00   0.0  0
 D7U  CONST_36  O18   C19  C29  C28   180.00   0.0  0
 D7U  CONST_37  O18   C17  C12  C7      0.00   0.0  0
 D7U  CONST_38  F30   C29  C19  C25   180.00   0.0  0
 D7U  CONST_39  F31   C27  C26  C25   180.00   0.0  0
 D7U  CONST_40  F30   C29  C28  C27   180.00   0.0  0
 D7U  CONST_41  F31   C27  C28  C29   180.00   0.0  0
 D7U  CONST_42  O11   C6   N1   C2    180.00   0.0  0
 D7U  CONST_43  H151  C15  C14  C13   180.00   0.0  0
 D7U  CONST_44  H131  C13  C14  C15   180.00   0.0  0
 D7U  CONST_45  H281  C28  C27  C26   180.00   0.0  0
 D7U  CONST_46  H261  C26  C27  C28   180.00   0.0  0
 D7U  CONST_47  H081  C8   C7   N4    180.00   0.0  0
 D7U  CONST_48  H251  C25  C26  C27   180.00   0.0  0
 D7U  CONST_49  H2    N1   C6   C5    180.00   0.0  0
 D7U  Var_01    C29   C19  O18  C17    76.46  30.0  2
 D7U  Var_02    S21   C20  C14  C13   -84.89  30.0  2
 D7U  Var_03    H101  C10  C09  C5    -57.79  30.0  2
 D7U  Var_04    C14   C20  S21  C22  -179.10  30.0  3
 D7U  Var_05    H222  C22  S21  C20    61.70  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
 D7U  plan-1  C13   0.020
 D7U  plan-1  C15   0.020
 D7U  plan-1  C17   0.020
 D7U  plan-1  C7    0.020
 D7U  plan-1  C12   0.020
 D7U  plan-1  C14   0.020
 D7U  plan-1  N16   0.020
 D7U  plan-1  H131  0.020
 D7U  plan-1  H151  0.020
 D7U  plan-1  O18   0.020
 D7U  plan-1  C20   0.020
 D7U  plan-2  C26   0.020
 D7U  plan-2  C28   0.020
 D7U  plan-2  C19   0.020
 D7U  plan-2  C25   0.020
 D7U  plan-2  C27   0.020
 D7U  plan-2  C29   0.020
 D7U  plan-2  F30   0.020
 D7U  plan-2  F31   0.020
 D7U  plan-2  H261  0.020
 D7U  plan-2  H281  0.020
 D7U  plan-2  H251  0.020
 D7U  plan-2  O18   0.020
 D7U  plan-3  C10   0.020
 D7U  plan-3  N1    0.020
 D7U  plan-3  C2    0.020
 D7U  plan-3  C3    0.020
 D7U  plan-3  N4    0.020
 D7U  plan-3  C5    0.020
 D7U  plan-3  C6    0.020
 D7U  plan-3  C7    0.020
 D7U  plan-3  C8    0.020
 D7U  plan-3  C09   0.020
 D7U  plan-3  O11   0.020
 D7U  plan-3  C12   0.020
 D7U  plan-3  H021  0.020
 D7U  plan-3  H031  0.020
 D7U  plan-3  H081  0.020
 D7U  plan-3  H2    0.020

