# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 16:09:16 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (4S)-4-(2-fluorophenyl)-2,4,6,7,8,9-hexahydro-5H-pyrazolo[3,4-b][1,7]naphthyridin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccccc1[C@H]2c3c[nH]nc3NC4=C2C(=O)CNC4
#
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
 JVE  JVE  (4S)-4-(2-fluorophenyl)-2,4,6,7,8,9-hexahydro-5H-pyrazolo[3,4-b][1,7]naphthyridin-5-one  ligand  34  21  .  2022-07-25  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_JVE
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
 JVE  C8    C  CH2   0  -0.392  -3.2200  -0.9531  -0.9032
 JVE  N9    N  NH1   0  -0.572  -3.3820  -2.1867  -0.1775
 JVE  C10   C  CH2   0  -0.431  -2.1242  -2.8878  -0.0359
 JVE  C11   C  C     0   0.345  -0.9717  -2.0456   0.4834
 JVE  C12   C  C     0   0.326  -2.1138  -0.0799  -0.3693
 JVE  C13   C  C     0  -0.139  -1.0398  -0.6166   0.2881
 JVE  C14   C  CH1   0  -0.401   0.1515   0.1976   0.7605
 JVE  O15   O  O     0  -0.451  -0.0102  -2.5819   1.0210
 JVE  C16   C  CR6   0   0.000   1.3930  -0.1544  -0.0416
 JVE  C17   C  CR6   0   0.496   2.5937  -0.5029   0.5524
 JVE  C18   C  CR16  0  -0.278   1.3704  -0.1140  -1.4333
 JVE  C19   C  CR16  0  -0.408   3.7338  -0.8053  -0.1701
 JVE  F20   F  F     0  -0.316   2.6708  -0.5510   1.8958
 JVE  C21   C  CR16  0  -0.259   2.4941  -0.4113  -2.1889
 JVE  C22   C  CR16  0  -0.257   3.6804  -0.7597  -1.5552
 JVE  C24   C  CR5   0  -0.104  -0.1753   1.6502   0.6055
 JVE  N25   N  N     0  -0.310  -1.3792   3.4212  -0.1425
 JVE  N26   N  NH1   0  -0.738  -2.2397   1.2432  -0.6070
 JVE  C27   C  CR15  0  -0.013   0.4628   2.8122   0.9758
 JVE  N28   N  NR15  0  -0.432  -0.2866   3.8244   0.5115
 JVE  H81C  H  HCH2  0   0.271  -2.9970  -1.1772  -1.9528
 JVE  H82C  H  HCH2  0   0.272  -4.1626  -0.4015  -0.8963
 JVE  H9    H  HNH1  0   0.358  -3.7613  -1.9853   0.7395
 JVE  H101  H  HCH2  0   0.267  -2.2573  -3.7496   0.6196
 JVE  H102  H  HCH2  0   0.259  -1.8250  -3.2835  -1.0150
 JVE  H26   H  HNH1  0   0.411  -3.0784   1.6079  -1.0307
 JVE  H14   H  HCH1  0   0.277   0.3394  -0.0294   1.8121
 JVE  H18   H  HCR6  0   0.258   0.4462   0.1515  -1.9335
 JVE  H19   H  HCR6  0   0.274   4.6462  -1.0769   0.3457
 JVE  H21   H  HCR6  0   0.257   2.4439  -0.3741  -3.2690
 JVE  H22   H  HCR6  0   0.263   4.5629  -0.9987  -2.1335
 JVE  H27   H  HCR5  0   0.290   1.3780   2.9855   1.5184
 JVE  H28   H  HNR5  0   0.424  -0.1013   4.8090   0.6097
 JVE  C23   C  CR5   0   0.454  -1.3044   2.1094  -0.0824

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
 JVE  C8   N9    single    1.440  0.020  1.440
 JVE  C8   C12   single    1.507  0.020  1.507
 JVE  N9   C10   single    1.447  0.020  1.447
 JVE  C10  C11   single    1.519  0.020  1.519
 JVE  C11  C13   single    1.444  0.020  1.444
 JVE  C11  O15   double    1.225  0.020  1.225
 JVE  C12  C13   double    1.369  0.020  1.369
 JVE  C12  N26   single    1.350  0.020  1.350
 JVE  C13  C14   single    1.518  0.020  1.518
 JVE  C14  C16   single    1.519  0.020  1.519
 JVE  C14  C24   single    1.497  0.020  1.497
 JVE  C16  C17   aromatic  1.384  0.020  1.384
 JVE  C16  C18   aromatic  1.393  0.020  1.393
 JVE  C17  C19   aromatic  1.383  0.020  1.383
 JVE  C17  F20   single    1.346  0.020  1.346
 JVE  C18  C21   aromatic  1.386  0.020  1.386
 JVE  C19  C22   aromatic  1.387  0.020  1.387
 JVE  C21  C22   aromatic  1.389  0.020  1.389
 JVE  C23  C24   aromatic  1.400  0.020  1.400
 JVE  C23  N25   aromatic  1.315  0.020  1.315
 JVE  C23  N26   single    1.379  0.020  1.379
 JVE  C24  C27   aromatic  1.376  0.020  1.376
 JVE  N25  N28   aromatic  1.336  0.020  1.336
 JVE  C27  N28   aromatic  1.342  0.020  1.342
 JVE  C8   H81C  single    0.970  0.020  1.090
 JVE  C8   H82C  single    0.970  0.020  1.090
 JVE  N9   H9    single    0.890  0.020  1.040
 JVE  C10  H101  single    0.970  0.020  1.090
 JVE  C10  H102  single    0.970  0.020  1.090
 JVE  N26  H26   single    0.860  0.020  1.020
 JVE  C14  H14   single    0.970  0.020  1.090
 JVE  C18  H18   single    0.930  0.020  1.080
 JVE  C19  H19   single    0.930  0.020  1.080
 JVE  C21  H21   single    0.930  0.020  1.080
 JVE  C22  H22   single    0.930  0.020  1.080
 JVE  C27  H27   single    0.930  0.020  1.080
 JVE  N28  H28   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
 JVE  H82C  C8   H81C  106.55  3.000
 JVE  H82C  C8   C12   109.79  3.000
 JVE  H81C  C8   C12   107.96  3.000
 JVE  H82C  C8   N9    109.40  3.000
 JVE  H81C  C8   N9    109.28  3.000
 JVE  C12   C8   N9    113.60  3.000
 JVE  H9    N9   C10   109.47  3.000
 JVE  H9    N9   C8    109.15  3.000
 JVE  C10   N9   C8    111.50  3.000
 JVE  H102  C10  H101  106.53  3.000
 JVE  H102  C10  C11   107.34  3.000
 JVE  H101  C10  C11   108.97  3.000
 JVE  H102  C10  N9    108.93  3.000
 JVE  H101  C10  N9    109.61  3.000
 JVE  C11   C10  N9    115.11  3.000
 JVE  O15   C11  C13   121.97  3.000
 JVE  O15   C11  C10   120.19  3.000
 JVE  C13   C11  C10   117.82  3.000
 JVE  N26   C12  C13   122.82  3.000
 JVE  N26   C12  C8    115.91  3.000
 JVE  C13   C12  C8    121.26  3.000
 JVE  C14   C13  C12   123.69  3.000
 JVE  C14   C13  C11   116.85  3.000
 JVE  C12   C13  C11   119.34  3.000
 JVE  H14   C14  C24   109.81  3.000
 JVE  H14   C14  C16   108.64  3.000
 JVE  C24   C14  C16   110.40  3.000
 JVE  H14   C14  C13   108.85  3.000
 JVE  C24   C14  C13   108.47  3.000
 JVE  C16   C14  C13   110.65  3.000
 JVE  C18   C16  C17   116.76  3.000
 JVE  C18   C16  C14   120.50  3.000
 JVE  C17   C16  C14   122.72  3.000
 JVE  F20   C17  C19   117.78  3.000
 JVE  F20   C17  C16   119.13  3.000
 JVE  C19   C17  C16   123.08  3.000
 JVE  H18   C18  C21   119.48  3.000
 JVE  H18   C18  C16   118.83  3.000
 JVE  C21   C18  C16   121.69  3.000
 JVE  H19   C19  C22   121.10  3.000
 JVE  H19   C19  C17   120.03  3.000
 JVE  C22   C19  C17   118.87  3.000
 JVE  H21   C21  C22   120.24  3.000
 JVE  H21   C21  C18   119.95  3.000
 JVE  C22   C21  C18   119.82  3.000
 JVE  H22   C22  C21   120.53  3.000
 JVE  H22   C22  C19   119.69  3.000
 JVE  C21   C22  C19   119.78  3.000
 JVE  C27   C24  C23   103.25  3.000
 JVE  C27   C24  C14   133.64  3.000
 JVE  C23   C24  C14   123.05  3.000
 JVE  N28   N25  C23   103.43  3.000
 JVE  H26   N26  C23   119.81  3.000
 JVE  H26   N26  C12   120.41  3.000
 JVE  C23   N26  C12   119.05  3.000
 JVE  H27   C27  N28   121.80  3.000
 JVE  H27   C27  C24   131.66  3.000
 JVE  N28   C27  C24   106.54  3.000
 JVE  H28   N28  C27   126.94  3.000
 JVE  H28   N28  N25   119.58  3.000
 JVE  C27   N28  N25   113.48  3.000
 JVE  N26   C23  N25   124.80  3.000
 JVE  N26   C23  C24   121.88  3.000
 JVE  N25   C23  C24   113.30  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
 JVE  CONST_01  C22  C19  C17  C16    0.00   0.0  0
 JVE  CONST_02  C22  C21  C18  C16    0.00   0.0  0
 JVE  CONST_03  C21  C18  C16  C17    0.00   0.0  0
 JVE  CONST_04  C21  C22  C19  C17    0.00   0.0  0
 JVE  CONST_05  C19  C17  C16  C18    0.00   0.0  0
 JVE  CONST_06  C19  C22  C21  C18    0.00   0.0  0
 JVE  CONST_07  N28  C27  C24  C23    0.00   0.0  0
 JVE  CONST_08  C27  N28  N25  C23    0.00   0.0  0
 JVE  CONST_09  N28  N25  C23  C24    0.00   0.0  0
 JVE  CONST_10  N25  N28  C27  C24    0.00   0.0  0
 JVE  CONST_11  C27  C24  C23  N25    0.00   0.0  0
 JVE  CONST_12  C19  C17  C16  C14  180.00   0.0  0
 JVE  CONST_13  C21  C18  C16  C14  180.00   0.0  0
 JVE  CONST_14  F20  C17  C16  C14    0.00   0.0  0
 JVE  CONST_15  F20  C17  C16  C18  180.00   0.0  0
 JVE  CONST_16  C22  C19  C17  F20  180.00   0.0  0
 JVE  CONST_17  H18  C18  C16  C14    0.00   0.0  0
 JVE  CONST_18  H27  C27  C24  C14    0.00   0.0  0
 JVE  CONST_19  H19  C19  C17  C16  180.00   0.0  0
 JVE  CONST_20  H21  C21  C18  C16  180.00   0.0  0
 JVE  CONST_21  H22  C22  C19  C17  180.00   0.0  0
 JVE  CONST_22  H28  N28  N25  C23  180.00   0.0  0
 JVE  Var_01    C11  C10  N9   C8    49.83  30.0  1
 JVE  Var_02    C11  C13  C12  C8    -0.53  30.0  1
 JVE  Var_03    C23  N26  C12  C8   176.35  30.0  1
 JVE  Var_04    C13  C12  C8   N9    27.12  30.0  1
 JVE  Var_05    C13  C11  C10  N9   -23.96  30.0  1
 JVE  Var_06    C12  C8   N9   C10  -50.82  30.0  1
 JVE  Var_07    C12  C13  C11  C10   -1.11  30.0  1
 JVE  Var_08    C24  C23  N26  C12    4.80  30.0  1

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
 JVE  chir_01  C14  C13  C16  C24  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
 JVE  plan-1  C14  0.020
 JVE  plan-1  C16  0.020
 JVE  plan-1  C17  0.020
 JVE  plan-1  C18  0.020
 JVE  plan-1  C19  0.020
 JVE  plan-1  F20  0.020
 JVE  plan-1  C21  0.020
 JVE  plan-1  C22  0.020
 JVE  plan-1  H18  0.020
 JVE  plan-1  H19  0.020
 JVE  plan-1  H21  0.020
 JVE  plan-1  H22  0.020
 JVE  plan-2  C14  0.020
 JVE  plan-2  C24  0.020
 JVE  plan-2  N25  0.020
 JVE  plan-2  N26  0.020
 JVE  plan-2  C27  0.020
 JVE  plan-2  N28  0.020
 JVE  plan-2  H27  0.020
 JVE  plan-2  H28  0.020
 JVE  plan-2  C23  0.020
 JVE  plan-3  C10  0.020
 JVE  plan-3  C11  0.020
 JVE  plan-3  C13  0.020
 JVE  plan-3  O15  0.020
 JVE  plan-4  C12  0.020
 JVE  plan-4  N26  0.020
 JVE  plan-4  H26  0.020
 JVE  plan-4  C23  0.020

