# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 06:15:16 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-(1H-imidazol-1-yl)-9-methoxy-8-(2-methoxyethoxy)benzo[c][2,7]naphthyridin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOc1cc2ncc3c(N)nc(cc3c2cc1OC)n4ccnc4
#
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
 9BD  9BD  2-(1H-imidazol-1-yl)-9-methoxy-8-(2-methoxyethoxy)benzo[c][2,7]naphthyridin-4-amine  ligand  46  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9BD
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
 9BD  C1    C  CH3   0  -0.396   8.0247  -1.0283  -0.8456
 9BD  C2    C  CH2   0  -0.158   6.4616   0.2226   0.3558
 9BD  C6    C  CR66  0   0.188   0.9188   1.5211   0.1170
 9BD  C9    C  CR6   0   0.358   1.9591  -1.0783   0.1808
 9BD  C12   C  CR16  0  -0.544  -2.3278  -0.3513  -0.0208
 9BD  C15   C  CR66  0  -0.205  -1.7784   2.0068   0.0104
 9BD  C18   C  CR15  0  -0.219  -6.6105  -1.8948  -0.2897
 9BD  O1    O  O2    0  -0.483   6.7320  -0.4784  -0.8282
 9BD  C3    C  CH2   0  -0.225   5.0778   0.8111   0.2890
 9BD  O2    O  O2    0  -0.455   4.1380  -0.2516   0.2671
 9BD  C4    C  CR6   0   0.330   2.8370   0.0478   0.2093
 9BD  C5    C  CR16  0  -0.452   2.3123   1.3140   0.1772
 9BD  C7    C  CR66  0   0.075   0.0524   0.4159   0.0876
 9BD  C8    C  CR16  0  -0.521   0.6032  -0.8829   0.1213
 9BD  C10   C  CH3   0  -0.443   1.7681  -3.4341   0.1738
 9BD  C11   C  CR66  0   0.379  -1.3598   0.6655   0.0280
 9BD  C13   C  CR6   0   0.578  -3.6459   0.0338  -0.0575
 9BD  N1    N  N     0  -0.505  -4.0729   1.2916  -0.0737
 9BD  C14   C  CR6   0   0.456  -3.1849   2.2712  -0.0516
 9BD  C16   C  CR16  0  -0.110  -0.7953   3.0291   0.0417
 9BD  N2    N  N     0  -0.446   0.4808   2.8138   0.0912
 9BD  N3    N  NH2   0  -0.833  -3.6697   3.5208  -0.1094
 9BD  N4    N  NR5   0  -0.530  -4.6735  -0.9250  -0.0814
 9BD  C17   C  CR15  0  -0.092  -5.9902  -0.6907  -0.4038
 9BD  N5    N  N     0  -0.442  -5.7175  -2.8593   0.1015
 9BD  C19   C  CR15  0   0.108  -4.5738  -2.2511   0.2163
 9BD  H1    H  HCH3  0   0.205   8.8001  -0.2596  -0.7448
 9BD  H1A   H  HCH3  0   0.206   8.1726  -1.7613  -0.0436
 9BD  H1B   H  HCH3  0   0.235   8.1620  -1.5331  -1.8010
 9BD  H2    H  HCH2  0   0.212   6.5502  -0.4292   1.2368
 9BD  H2A   H  HCH2  0   0.216   7.1691   1.0511   0.5007
 9BD  H12   H  HCR6  0   0.269  -2.0470  -1.3919  -0.0487
 9BD  H18   H  HCR5  0   0.259  -7.6505  -2.1196  -0.4663
 9BD  H3    H  HCH2  0   0.240   4.9222   1.4489   1.1655
 9BD  H3A   H  HCH2  0   0.238   4.9716   1.4374  -0.6037
 9BD  H5    H  HCR6  0   0.289   2.9441   2.1912   0.1969
 9BD  H8    H  HCR6  0   0.287  -0.0575  -1.7378   0.1032
 9BD  H10   H  HCH3  0   0.266   2.4504  -4.2795   0.1995
 9BD  H10A  H  HCH3  0   0.233   1.0959  -3.4963   1.0334
 9BD  H10B  H  HCH3  0   0.232   1.1768  -3.4839  -0.7438
 9BD  H16   H  HCR6  0   0.252  -1.0929   4.0724   0.0220
 9BD  HN3   H  HNH2  0   0.415  -3.1031   4.3302   0.0679
 9BD  HN3A  H  HNH2  0   0.405  -4.6657   3.6484  -0.0471
 9BD  H17   H  HCR5  0   0.298  -6.3480   0.2838  -0.6831
 9BD  H19   H  HCR5  0   0.289  -3.6493  -2.7113   0.5276
 9BD  O3    O  O2    0  -0.459   2.5700  -2.2695   0.2171

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
 9BD  C1   O1    single    1.405  0.020  1.405
 9BD  C2   O1    single    1.402  0.020  1.402
 9BD  C2   C3    single    1.505  0.020  1.505
 9BD  C6   C5    aromatic  1.410  0.020  1.410
 9BD  C6   C7    aromatic  1.405  0.020  1.405
 9BD  C6   N2    aromatic  1.365  0.020  1.365
 9BD  C9   C4    aromatic  1.428  0.020  1.428
 9BD  C9   C8    aromatic  1.371  0.020  1.371
 9BD  C9   O3    single    1.339  0.020  1.339
 9BD  C12  C11   aromatic  1.405  0.020  1.405
 9BD  C12  C13   aromatic  1.374  0.020  1.374
 9BD  C15  C11   aromatic  1.405  0.020  1.405
 9BD  C15  C14   aromatic  1.432  0.020  1.432
 9BD  C15  C16   aromatic  1.419  0.020  1.419
 9BD  C18  C17   aromatic  1.359  0.020  1.359
 9BD  C18  N5    aromatic  1.371  0.020  1.371
 9BD  C3   O2    single    1.419  0.020  1.419
 9BD  O2   C4    single    1.336  0.020  1.336
 9BD  C4   C5    aromatic  1.371  0.020  1.371
 9BD  C7   C8    aromatic  1.411  0.020  1.411
 9BD  C7   C11   aromatic  1.435  0.020  1.435
 9BD  O3   C10   single    1.415  0.020  1.415
 9BD  C13  N1    aromatic  1.328  0.020  1.328
 9BD  C13  N4    single    1.406  0.020  1.406
 9BD  N1   C14   aromatic  1.322  0.020  1.322
 9BD  C14  N3    single    1.342  0.020  1.342
 9BD  C16  N2    aromatic  1.295  0.020  1.295
 9BD  N4   C17   aromatic  1.376  0.020  1.376
 9BD  N4   C19   aromatic  1.363  0.020  1.363
 9BD  N5   C19   aromatic  1.300  0.020  1.300
 9BD  C1   H1    single    0.970  0.020  1.090
 9BD  C1   H1A   single    0.970  0.020  1.090
 9BD  C1   H1B   single    0.970  0.020  1.090
 9BD  C2   H2    single    0.970  0.020  1.090
 9BD  C2   H2A   single    0.970  0.020  1.090
 9BD  C12  H12   single    0.930  0.020  1.080
 9BD  C18  H18   single    0.930  0.020  1.080
 9BD  C3   H3    single    0.970  0.020  1.090
 9BD  C3   H3A   single    0.970  0.020  1.090
 9BD  C5   H5    single    0.930  0.020  1.080
 9BD  C8   H8    single    0.930  0.020  1.080
 9BD  C10  H10   single    0.970  0.020  1.090
 9BD  C10  H10A  single    0.970  0.020  1.090
 9BD  C10  H10B  single    0.970  0.020  1.090
 9BD  C16  H16   single    0.930  0.020  1.080
 9BD  N3   HN3   single    0.860  0.020  1.020
 9BD  N3   HN3A  single    0.860  0.020  1.020
 9BD  C17  H17   single    0.930  0.020  1.080
 9BD  C19  H19   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
 9BD  H1B   C1   H1A   108.34  3.000
 9BD  H1B   C1   H1    108.44  3.000
 9BD  H1A   C1   H1    107.82  3.000
 9BD  H1B   C1   O1    107.95  3.000
 9BD  H1A   C1   O1    112.13  3.000
 9BD  H1    C1   O1    112.03  3.000
 9BD  H2A   C2   H2    106.82  3.000
 9BD  H2A   C2   C3    107.63  3.000
 9BD  H2    C2   C3    109.97  3.000
 9BD  H2A   C2   O1    111.35  3.000
 9BD  H2    C2   O1    111.39  3.000
 9BD  C3    C2   O1    109.59  3.000
 9BD  N2    C6   C7    123.15  3.000
 9BD  N2    C6   C5    117.19  3.000
 9BD  C7    C6   C5    119.66  3.000
 9BD  O3    C9   C8    125.38  3.000
 9BD  O3    C9   C4    114.86  3.000
 9BD  C8    C9   C4    119.76  3.000
 9BD  H12   C12  C13   121.31  3.000
 9BD  H12   C12  C11   121.33  3.000
 9BD  C13   C12  C11   117.34  3.000
 9BD  C16   C15  C14   123.25  3.000
 9BD  C16   C15  C11   118.76  3.000
 9BD  C14   C15  C11   117.98  3.000
 9BD  H18   C18  N5    121.87  3.000
 9BD  H18   C18  C17   127.65  3.000
 9BD  N5    C18  C17   110.48  3.000
 9BD  C2    O1   C1    112.55  3.000
 9BD  H3A   C3   H3    107.79  3.000
 9BD  H3A   C3   O2    110.57  3.000
 9BD  H3    C3   O2    110.76  3.000
 9BD  H3A   C3   C2    110.41  3.000
 9BD  H3    C3   C2    108.84  3.000
 9BD  O2    C3   C2    108.47  3.000
 9BD  C4    O2   C3    118.54  3.000
 9BD  C5    C4   O2    125.49  3.000
 9BD  C5    C4   C9    119.51  3.000
 9BD  O2    C4   C9    115.01  3.000
 9BD  H5    C5   C4    121.69  3.000
 9BD  H5    C5   C6    117.33  3.000
 9BD  C4    C5   C6    120.99  3.000
 9BD  C11   C7   C8    123.03  3.000
 9BD  C11   C7   C6    118.09  3.000
 9BD  C8    C7   C6    118.87  3.000
 9BD  H8    C8   C7    119.28  3.000
 9BD  H8    C8   C9    119.51  3.000
 9BD  C7    C8   C9    121.21  3.000
 9BD  H10B  C10  H10A  108.97  3.000
 9BD  H10B  C10  H10   108.91  3.000
 9BD  H10A  C10  H10   108.86  3.000
 9BD  H10B  C10  O3    111.71  3.000
 9BD  H10A  C10  O3    111.80  3.000
 9BD  H10   C10  O3    106.49  3.000
 9BD  C7    C11  C15   117.36  3.000
 9BD  C7    C11  C12   123.61  3.000
 9BD  C15   C11  C12   119.02  3.000
 9BD  N4    C13  N1    114.25  3.000
 9BD  N4    C13  C12   120.71  3.000
 9BD  N1    C13  C12   125.04  3.000
 9BD  C14   N1   C13   119.04  3.000
 9BD  N3    C14  N1    116.53  3.000
 9BD  N3    C14  C15   121.91  3.000
 9BD  N1    C14  C15   121.55  3.000
 9BD  H16   C16  N2    115.52  3.000
 9BD  H16   C16  C15   120.16  3.000
 9BD  N2    C16  C15   124.32  3.000
 9BD  C16   N2   C6    118.31  3.000
 9BD  HN3A  N3   HN3   116.46  3.000
 9BD  HN3A  N3   C14   118.24  3.000
 9BD  HN3   N3   C14   122.65  3.000
 9BD  C19   N4   C17   106.68  3.000
 9BD  C19   N4   C13   127.34  3.000
 9BD  C17   N4   C13   125.98  3.000
 9BD  H17   C17  N4    122.26  3.000
 9BD  H17   C17  C18   132.30  3.000
 9BD  N4    C17  C18   105.44  3.000
 9BD  C19   N5   C18   105.60  3.000
 9BD  H19   C19  N5    125.44  3.000
 9BD  H19   C19  N4    122.74  3.000
 9BD  N5    C19  N4    111.81  3.000
 9BD  C10   O3   C9    118.22  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
 9BD  CONST_01  C9    C4   C5   C6     0.00   0.0  0
 9BD  CONST_02  C9    C8   C7   C6     0.00   0.0  0
 9BD  CONST_03  C12   C11  C7   C6   180.00   0.0  0
 9BD  CONST_04  C15   C11  C7   C6     0.00   0.0  0
 9BD  CONST_05  C15   C16  N2   C6     0.00   0.0  0
 9BD  CONST_06  C11   C7   C8   C9   180.00   0.0  0
 9BD  CONST_07  C14   C15  C11  C12    0.00   0.0  0
 9BD  CONST_08  C16   C15  C11  C12  180.00   0.0  0
 9BD  CONST_09  C8    C7   C11  C12    0.00   0.0  0
 9BD  CONST_10  C14   N1   C13  C12    0.00   0.0  0
 9BD  CONST_11  C17   N4   C13  C12  180.00   0.0  0
 9BD  CONST_13  C13   C12  C11  C15    0.00   0.0  0
 9BD  CONST_14  C8    C7   C11  C15  180.00   0.0  0
 9BD  CONST_15  C13   N1   C14  C15    0.00   0.0  0
 9BD  CONST_16  C13   N4   C17  C18  180.00   0.0  0
 9BD  CONST_17  C19   N4   C17  C18    0.00   0.0  0
 9BD  CONST_18  N4    C19  N5   C18    0.00   0.0  0
 9BD  CONST_19  C7    C8   C9   C4     0.00   0.0  0
 9BD  CONST_20  C7    C6   C5   C4     0.00   0.0  0
 9BD  CONST_21  N2    C6   C5   C4   180.00   0.0  0
 9BD  CONST_22  C8    C7   C6   C5     0.00   0.0  0
 9BD  CONST_23  C11   C7   C6   C5   180.00   0.0  0
 9BD  CONST_24  C16   N2   C6   C5   180.00   0.0  0
 9BD  CONST_25  C8    C9   C4   C5     0.00   0.0  0
 9BD  CONST_26  C16   N2   C6   C7     0.00   0.0  0
 9BD  CONST_27  C13   C12  C11  C7   180.00   0.0  0
 9BD  CONST_28  C14   C15  C11  C7   180.00   0.0  0
 9BD  CONST_29  C16   C15  C11  C7     0.00   0.0  0
 9BD  CONST_30  N2    C6   C7   C8   180.00   0.0  0
 9BD  CONST_31  N1    C13  C12  C11    0.00   0.0  0
 9BD  CONST_32  N4    C13  C12  C11  180.00   0.0  0
 9BD  CONST_33  N1    C14  C15  C11    0.00   0.0  0
 9BD  CONST_34  N2    C16  C15  C11    0.00   0.0  0
 9BD  CONST_35  N2    C6   C7   C11    0.00   0.0  0
 9BD  CONST_36  N5    C19  N4   C13  180.00   0.0  0
 9BD  CONST_37  C17   N4   C13  N1     0.00   0.0  0
 9BD  CONST_39  C16   C15  C14  N1   180.00   0.0  0
 9BD  CONST_40  N2    C16  C15  C14  180.00   0.0  0
 9BD  CONST_41  N4    C13  N1   C14  180.00   0.0  0
 9BD  CONST_42  N5    C18  C17  N4     0.00   0.0  0
 9BD  CONST_43  C19   N5   C18  C17    0.00   0.0  0
 9BD  CONST_44  N5    C19  N4   C17    0.00   0.0  0
 9BD  CONST_45  O2    C4   C5   C6   180.00   0.0  0
 9BD  CONST_46  C8    C9   C4   O2   180.00   0.0  0
 9BD  CONST_47  O3    C9   C4   C5   180.00   0.0  0
 9BD  CONST_48  O3    C9   C8   C7   180.00   0.0  0
 9BD  CONST_49  N3    C14  C15  C11  180.00   0.0  0
 9BD  CONST_50  N3    C14  N1   C13  180.00   0.0  0
 9BD  CONST_51  N3    C14  C15  C16    0.00   0.0  0
 9BD  CONST_52  H8    C8   C7   C6   180.00   0.0  0
 9BD  CONST_53  H16   C16  N2   C6   180.00   0.0  0
 9BD  CONST_54  H5    C5   C4   C9   180.00   0.0  0
 9BD  CONST_55  H12   C12  C11  C15  180.00   0.0  0
 9BD  CONST_56  H19   C19  N5   C18  180.00   0.0  0
 9BD  CONST_57  H17   C17  N4   C13    0.00   0.0  0
 9BD  CONST_58  H18   C18  C17  N4   180.00   0.0  0
 9BD  CONST_59  HN3   N3   C14  C15    0.00   0.0  0
 9BD  CONST_60  HN3A  N3   C14  C15  180.00   0.0  0
 9BD  Var_01    C5    C4   O2   C3    -0.46  30.0  2
 9BD  Var_02    H10   C10  O3   C9   179.23  30.0  3
 9BD  Var_03    H3    C3   O2   C4    60.58  30.0  1
 9BD  Var_04    C3    C2   O1   C1   178.56  30.0  1
 9BD  Var_05    O2    C3   C2   O1    65.83  30.0  3
 9BD  Var_06    H1    C1   O1   C2   -59.41  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
 9BD  plan-1  C18   0.020
 9BD  plan-1  C13   0.020
 9BD  plan-1  N4    0.020
 9BD  plan-1  C17   0.020
 9BD  plan-1  N5    0.020
 9BD  plan-1  C19   0.020
 9BD  plan-1  H18   0.020
 9BD  plan-1  H17   0.020
 9BD  plan-1  H19   0.020
 9BD  plan-2  C6    0.020
 9BD  plan-2  C9    0.020
 9BD  plan-2  C12   0.020
 9BD  plan-2  C15   0.020
 9BD  plan-2  O2    0.020
 9BD  plan-2  C4    0.020
 9BD  plan-2  C5    0.020
 9BD  plan-2  C7    0.020
 9BD  plan-2  C8    0.020
 9BD  plan-2  C11   0.020
 9BD  plan-2  C13   0.020
 9BD  plan-2  N1    0.020
 9BD  plan-2  C14   0.020
 9BD  plan-2  C16   0.020
 9BD  plan-2  N2    0.020
 9BD  plan-2  N3    0.020
 9BD  plan-2  N4    0.020
 9BD  plan-2  H12   0.020
 9BD  plan-2  H5    0.020
 9BD  plan-2  H8    0.020
 9BD  plan-2  H16   0.020
 9BD  plan-2  O3    0.020
 9BD  plan-3  C14   0.020
 9BD  plan-3  N3    0.020
 9BD  plan-3  HN3   0.020
 9BD  plan-3  HN3A  0.020

