# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 03:58:41 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: (7~{R},8~{R},9~{S})-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2n(ccc3[C@@H](O)[C@H](O)[C@@H](Nc23)c4ccccc4)c1C
#
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
 J3C  J3C  "(7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol"
  ligand  42  23  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J3C
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
 J3C  C10  C  CH3   0  -0.749  -51.4976  10.9967   -7.5167
 J3C  C11  C  CH1   0  -0.021  -50.4770  18.2914   -8.9457
 J3C  C12  C  CH1   0  -0.101  -50.3247  18.1964   -7.4166
 J3C  C13  C  CR6   0   0.072  -49.2157  19.1000   -6.9415
 J3C  C14  C  CR16  0  -0.295  -49.5001  20.4385   -6.6774
 J3C  C15  C  CR16  0  -0.239  -48.4956  21.3178   -6.3029
 J3C  C16  C  CR16  0  -0.263  -47.1864  20.8678   -6.1823
 J3C  C17  C  CR16  0  -0.236  -46.8939  19.5365   -6.4405
 J3C  C18  C  CR16  0  -0.317  -47.9005  18.6577   -6.8230
 J3C  C1   C  CR16  0  -0.016  -51.9397  13.6333   -9.0021
 J3C  C2   C  CR16  0  -0.447  -52.0381  14.8857   -9.5092
 J3C  C3   C  CR6   0   0.108  -51.4384  16.0023   -8.8732
 J3C  C4   C  CR6   0   0.257  -50.7204  15.8171   -7.7123
 J3C  C5   C  CR56  0   0.438  -50.6230  14.5012   -7.1828
 J3C  C6   C  CH1   0  -0.034  -51.6177  17.3862   -9.4157
 J3C  C7   C  CR5   0   0.081  -50.2333  12.7502   -6.0321
 J3C  C8   C  CR5   0   0.243  -50.9879  12.3266   -7.1040
 J3C  C9   C  CH3   0  -0.746  -49.6937  11.9253   -4.9156
 J3C  N1   N  N     0  -0.546  -51.2336  13.4630   -7.8372
 J3C  N2   N  N     0  -0.491  -50.0125  14.0911   -6.0895
 J3C  N3   N  NH1   0  -0.714  -50.0818  16.8235   -7.0570
 J3C  O1   O  OH1   0  -0.660  -52.8681  17.8660   -8.9641
 J3C  O2   O  OH1   0  -0.660  -49.3234  17.8752   -9.6250
 J3C  H1   H  HCH3  0   0.249  -51.1113  10.6962   -8.4934
 J3C  H2   H  HCH3  0   0.263  -51.1965  10.2370   -6.7985
 J3C  H3   H  HCH3  0   0.249  -52.5885  10.9764   -7.5773
 J3C  H4   H  HCH1  0   0.243  -50.7319  19.3337   -9.1852
 J3C  H5   H  HCH1  0   0.254  -51.2698  18.5580   -6.9874
 J3C  H6   H  HCR6  0   0.250  -50.5209  20.7940   -6.7632
 J3C  H7   H  HCR6  0   0.255  -48.7353  22.3534   -6.0989
 J3C  H8   H  HCR6  0   0.255  -46.4010  21.5505   -5.8848
 J3C  H9   H  HCR6  0   0.255  -45.8772  19.1766   -6.3474
 J3C  H10  H  HCR6  0   0.255  -47.6585  17.6202   -7.0154
 J3C  H11  H  HCR6  0   0.294  -52.3786  12.7560   -9.4515
 J3C  H12  H  HCR6  0   0.262  -52.5930  15.0325  -10.4266
 J3C  H13  H  HCH1  0   0.238  -51.5904  17.3542  -10.5139
 J3C  H14  H  HCH3  0   0.243  -50.0696  12.2739   -3.9525
 J3C  H15  H  HCH3  0   0.241  -49.9686  10.8770   -5.0182
 J3C  H16  H  HCH3  0   0.242  -48.6047  11.9804   -4.8765
 J3C  H17  H  HNH1  0   0.385  -49.7924  16.6311   -6.1106
 J3C  H18  H  HOH1  0   0.449  -53.0517  18.7009   -9.4097
 J3C  H19  H  HOH1  0   0.456  -48.6060  18.4877   -9.4306

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
 J3C  O1   C6   single    1.413  0.020  1.413
 J3C  O2   C11  single    1.402  0.020  1.402
 J3C  C6   C3   single    1.497  0.020  1.497
 J3C  C6   C11  single    1.530  0.020  1.530
 J3C  C2   C3   aromatic  1.418  0.020  1.418
 J3C  C2   C1   aromatic  1.355  0.020  1.355
 J3C  C3   C4   aromatic  1.378  0.020  1.378
 J3C  C11  C12  single    1.540  0.020  1.540
 J3C  C1   N1   aromatic  1.373  0.020  1.373
 J3C  C4   N3   single    1.360  0.020  1.360
 J3C  C4   C5   aromatic  1.422  0.020  1.422
 J3C  N1   C5   aromatic  1.371  0.020  1.371
 J3C  N1   C8   aromatic  1.374  0.020  1.374
 J3C  C18  C17  aromatic  1.390  0.020  1.390
 J3C  C18  C13  aromatic  1.393  0.020  1.393
 J3C  C12  N3   single    1.440  0.020  1.440
 J3C  C12  C13  single    1.507  0.020  1.507
 J3C  C5   N2   aromatic  1.318  0.020  1.318
 J3C  C17  C16  aromatic  1.387  0.020  1.387
 J3C  C13  C14  aromatic  1.394  0.020  1.394
 J3C  C10  C8   single    1.483  0.020  1.483
 J3C  C8   C7   aromatic  1.378  0.020  1.378
 J3C  N2   C7   aromatic  1.360  0.020  1.360
 J3C  C7   C9   single    1.489  0.020  1.489
 J3C  C16  C15  aromatic  1.390  0.020  1.390
 J3C  C14  C15  aromatic  1.387  0.020  1.387
 J3C  C10  H1   single    0.970  0.020  1.090
 J3C  C10  H2   single    0.970  0.020  1.090
 J3C  C10  H3   single    0.970  0.020  1.090
 J3C  C11  H4   single    0.970  0.020  1.090
 J3C  C12  H5   single    0.970  0.020  1.090
 J3C  C14  H6   single    0.930  0.020  1.080
 J3C  C15  H7   single    0.930  0.020  1.080
 J3C  C16  H8   single    0.930  0.020  1.080
 J3C  C17  H9   single    0.930  0.020  1.080
 J3C  C18  H10  single    0.930  0.020  1.080
 J3C  C1   H11  single    0.930  0.020  1.080
 J3C  C2   H12  single    0.930  0.020  1.080
 J3C  C6   H13  single    0.970  0.020  1.090
 J3C  C9   H14  single    0.970  0.020  1.090
 J3C  C9   H15  single    0.970  0.020  1.090
 J3C  C9   H16  single    0.970  0.020  1.090
 J3C  N3   H17  single    0.890  0.020  1.040
 J3C  O1   H18  single    0.850  0.020  0.980
 J3C  O2   H19  single    0.850  0.020  0.980

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
 J3C  H3   C10  H2   107.45  3.000
 J3C  H3   C10  H1   107.35  3.000
 J3C  H2   C10  H1   107.47  3.000
 J3C  H3   C10  C8   112.04  3.000
 J3C  H2   C10  C8   110.33  3.000
 J3C  H1   C10  C8   111.96  3.000
 J3C  H4   C11  O2   111.52  3.000
 J3C  H4   C11  C6   108.73  3.000
 J3C  O2   C11  C6   106.79  3.000
 J3C  H4   C11  C12  107.33  3.000
 J3C  C6   C11  C12  110.02  3.000
 J3C  O2   C11  C12  112.43  3.000
 J3C  H5   C12  N3   111.17  3.000
 J3C  H5   C12  C13  108.20  3.000
 J3C  N3   C12  C13  111.64  3.000
 J3C  H5   C12  C11  106.40  3.000
 J3C  C13  C12  C11  110.41  3.000
 J3C  N3   C12  C11  108.88  3.000
 J3C  C18  C13  C14  118.79  3.000
 J3C  C14  C13  C12  119.03  3.000
 J3C  C18  C13  C12  122.09  3.000
 J3C  H6   C14  C15  119.70  3.000
 J3C  H6   C14  C13  119.48  3.000
 J3C  C15  C14  C13  120.82  3.000
 J3C  H7   C15  C16  120.13  3.000
 J3C  H7   C15  C14  119.82  3.000
 J3C  C16  C15  C14  120.05  3.000
 J3C  H8   C16  C17  120.23  3.000
 J3C  H8   C16  C15  120.22  3.000
 J3C  C17  C16  C15  119.55  3.000
 J3C  H9   C17  C18  119.58  3.000
 J3C  H9   C17  C16  120.07  3.000
 J3C  C18  C17  C16  120.35  3.000
 J3C  H10  C18  C17  119.54  3.000
 J3C  H10  C18  C13  120.02  3.000
 J3C  C17  C18  C13  120.43  3.000
 J3C  H11  C1   N1   117.50  3.000
 J3C  H11  C1   C2   124.48  3.000
 J3C  N1   C1   C2   118.02  3.000
 J3C  H12  C2   C3   119.36  3.000
 J3C  H12  C2   C1   118.69  3.000
 J3C  C3   C2   C1   121.96  3.000
 J3C  C6   C3   C4   119.48  3.000
 J3C  C4   C3   C2   119.51  3.000
 J3C  C6   C3   C2   120.97  3.000
 J3C  N3   C4   C5   118.25  3.000
 J3C  C5   C4   C3   118.30  3.000
 J3C  N3   C4   C3   123.45  3.000
 J3C  N2   C5   N1   111.52  3.000
 J3C  N2   C5   C4   128.96  3.000
 J3C  N1   C5   C4   119.52  3.000
 J3C  H13  C6   O1   110.56  3.000
 J3C  H13  C6   C3   109.40  3.000
 J3C  O1   C6   C3   107.69  3.000
 J3C  H13  C6   C11  107.80  3.000
 J3C  C3   C6   C11  110.25  3.000
 J3C  O1   C6   C11  111.14  3.000
 J3C  N2   C7   C9   121.26  3.000
 J3C  C9   C7   C8   127.70  3.000
 J3C  N2   C7   C8   111.05  3.000
 J3C  N1   C8   C7   105.00  3.000
 J3C  C7   C8   C10  132.89  3.000
 J3C  N1   C8   C10  122.11  3.000
 J3C  H16  C9   H15  107.70  3.000
 J3C  H16  C9   H14  107.22  3.000
 J3C  H15  C9   H14  107.68  3.000
 J3C  H16  C9   C7   111.14  3.000
 J3C  H15  C9   C7   111.79  3.000
 J3C  H14  C9   C7   111.10  3.000
 J3C  C8   N1   C5   106.97  3.000
 J3C  C8   N1   C1   130.33  3.000
 J3C  C5   N1   C1   122.70  3.000
 J3C  C7   N2   C5   105.47  3.000
 J3C  H17  N3   C4   116.47  3.000
 J3C  H17  N3   C12  117.70  3.000
 J3C  C4   N3   C12  120.40  3.000
 J3C  H18  O1   C6   108.35  3.000
 J3C  H19  O2   C11  109.04  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
 J3C  CONST_01  C16  C17  C18  C13     0.00   0.0  0
 J3C  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 J3C  CONST_03  C17  C18  C13  C14     0.00   0.0  0
 J3C  CONST_04  C17  C16  C15  C14     0.00   0.0  0
 J3C  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 J3C  CONST_06  C18  C13  C14  C15     0.00   0.0  0
 J3C  CONST_07  C4   C3   C2   C1      0.00   0.0  0
 J3C  CONST_08  C4   C5   N1   C1      0.00   0.0  0
 J3C  CONST_09  N2   C5   N1   C1    180.00   0.0  0
 J3C  CONST_10  C7   C8   N1   C1    180.00   0.0  0
 J3C  CONST_11  C5   C4   C3   C2      0.00   0.0  0
 J3C  CONST_12  C5   N1   C1   C2      0.00   0.0  0
 J3C  CONST_13  C8   N1   C1   C2    180.00   0.0  0
 J3C  CONST_14  N1   C1   C2   C3      0.00   0.0  0
 J3C  CONST_15  N1   C5   C4   C3      0.00   0.0  0
 J3C  CONST_16  N2   C5   C4   C3    180.00   0.0  0
 J3C  CONST_17  C8   N1   C5   C4    180.00   0.0  0
 J3C  CONST_18  C7   N2   C5   C4    180.00   0.0  0
 J3C  CONST_19  C7   C8   N1   C5      0.00   0.0  0
 J3C  CONST_20  C8   C7   N2   C5      0.00   0.0  0
 J3C  CONST_21  N1   C5   N2   C7      0.00   0.0  0
 J3C  CONST_22  N2   C5   N1   C8      0.00   0.0  0
 J3C  CONST_23  N2   C7   C8   N1      0.00   0.0  0
 J3C  CONST_24  C17  C18  C13  C12   180.00   0.0  0
 J3C  CONST_25  C15  C14  C13  C12   180.00   0.0  0
 J3C  CONST_26  C1   N1   C8   C10     0.00   0.0  0
 J3C  CONST_27  C5   N1   C8   C10   180.00   0.0  0
 J3C  CONST_28  N2   C7   C8   C10   180.00   0.0  0
 J3C  CONST_29  C9   C7   N2   C5    180.00   0.0  0
 J3C  CONST_30  N1   C8   C7   C9    180.00   0.0  0
 J3C  CONST_31  H10  C18  C13  C12     0.00   0.0  0
 J3C  CONST_32  H6   C14  C13  C12     0.00   0.0  0
 J3C  CONST_33  H9   C17  C18  C13   180.00   0.0  0
 J3C  CONST_34  H7   C15  C14  C13   180.00   0.0  0
 J3C  CONST_35  H10  C18  C13  C14   180.00   0.0  0
 J3C  CONST_36  H8   C16  C15  C14   180.00   0.0  0
 J3C  CONST_37  H9   C17  C16  C15   180.00   0.0  0
 J3C  CONST_38  H10  C18  C17  C16   180.00   0.0  0
 J3C  CONST_39  H6   C14  C15  C16   180.00   0.0  0
 J3C  CONST_40  H7   C15  C16  C17   180.00   0.0  0
 J3C  CONST_41  H8   C16  C17  C18   180.00   0.0  0
 J3C  CONST_42  H6   C14  C13  C18   180.00   0.0  0
 J3C  CONST_43  H11  C1   C2   C3    180.00   0.0  0
 J3C  CONST_44  H12  C2   C3   C4    180.00   0.0  0
 J3C  CONST_45  H11  C1   N1   C5    180.00   0.0  0
 J3C  CONST_46  H12  C2   C3   C6      0.00   0.0  0
 J3C  CONST_47  H11  C1   N1   C8      0.00   0.0  0
 J3C  CONST_48  H12  C2   C1   N1    180.00   0.0  0
 J3C  Var_01    C3   C4   N3   C12    11.37  30.0  1
 J3C  Var_02    C5   C4   N3   C12  -169.71  30.0  1
 J3C  Var_03    C6   C3   C2   C1   -176.94  30.0  1
 J3C  Var_04    N3   C4   C3   C2    178.10  30.0  1
 J3C  Var_05    C6   C3   C4   C5    176.86  30.0  1
 J3C  Var_06    N3   C4   C3   C6     -4.21  30.0  1
 J3C  Var_07    N3   C4   C5   N1   -178.68  30.0  1
 J3C  Var_08    N3   C4   C5   N2      2.02  30.0  1
 J3C  Var_09    H17  N3   C4   C3    164.78  30.0  1
 J3C  Var_10    H17  N3   C4   C5    -16.30  30.0  1
 J3C  Var_11    H1   C10  C8   C7   -119.25  30.0  2
 J3C  Var_12    H2   C10  C8   C7      0.40  30.0  2
 J3C  Var_13    H3   C10  C8   C7    120.08  30.0  2
 J3C  Var_14    H14  C9   C7   C8   -120.64  30.0  2
 J3C  Var_15    H15  C9   C7   C8     -0.31  30.0  2
 J3C  Var_16    H16  C9   C7   C8    120.06  30.0  2
 J3C  Var_17    H1   C10  C8   N1     60.64  30.0  2
 J3C  Var_18    H2   C10  C8   N1   -179.71  30.0  2
 J3C  Var_19    H3   C10  C8   N1    -60.03  30.0  2
 J3C  Var_20    H14  C9   C7   N2     59.19  30.0  2
 J3C  Var_21    H15  C9   C7   N2    179.52  30.0  2
 J3C  Var_22    H16  C9   C7   N2    -60.11  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
 J3C  chir_01  C11  O2  C6   C12  negativ
 J3C  chir_02  C12  N3  C11  C13  positiv
 J3C  chir_03  C6   O1  C11  C3   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
 J3C  plan-1  C12  0.020
 J3C  plan-1  C13  0.020
 J3C  plan-1  C14  0.020
 J3C  plan-1  C15  0.020
 J3C  plan-1  C16  0.020
 J3C  plan-1  C17  0.020
 J3C  plan-1  C18  0.020
 J3C  plan-1  H6   0.020
 J3C  plan-1  H7   0.020
 J3C  plan-1  H8   0.020
 J3C  plan-1  H9   0.020
 J3C  plan-1  H10  0.020
 J3C  plan-2  C10  0.020
 J3C  plan-2  C1   0.020
 J3C  plan-2  C4   0.020
 J3C  plan-2  C5   0.020
 J3C  plan-2  C7   0.020
 J3C  plan-2  C8   0.020
 J3C  plan-2  C9   0.020
 J3C  plan-2  N1   0.020
 J3C  plan-2  N2   0.020

