# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:39:55 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 10,11-dimethoxy-4-methyldibenzo[c,f][2,7]naphthyridine-3,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2ncc3c(N)nc4c(C)c(N)ccc4c3c2cc1OC
#
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
 253  253  10,11-dimethoxy-4-methyldibenzo[c,f][2,7]naphthyridine-3,6-diamine  ligand  43  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_253
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
 253  C1    C  CH3   0  -0.441   6.0443   0.4286  -0.1635
 253  O2    O  O2    0  -0.454   5.0525  -0.5740  -0.0361
 253  C3    C  CR6   0   0.323   3.7704  -0.1966  -0.0424
 253  C23   C  CR6   0   0.350   2.8269  -1.2443   0.1797
 253  O24   O  O2    0  -0.459   3.3678  -2.4488   0.4091
 253  C25   C  CH3   0  -0.444   2.5000  -3.5409   0.6392
 253  C22   C  CR16  0  -0.540   1.4849  -0.9701   0.1675
 253  C21   C  CR66  0   0.066   0.9901   0.3372  -0.0637
 253  C11   C  CR66  0   0.318  -0.4041   0.6830  -0.1080
 253  C12   C  CR66  0   0.006  -1.4982  -0.2421  -0.2199
 253  C19   C  CR66  0   0.183  -2.8049   0.2484   0.0520
 253  N20   N  N     0  -0.510  -3.0479   1.5664   0.2871
 253  C17   C  CR6   0  -0.036  -3.9161  -0.6236   0.0576
 253  C18   C  CH3   0  -0.746  -5.2914  -0.1355   0.4053
 253  C15   C  CR6   0   0.267  -3.7396  -1.9599  -0.2975
 253  N16   N  NH2   0  -0.854  -4.8027  -2.8247  -0.3457
 253  C14   C  CR16  0  -0.328  -2.4659  -2.4096  -0.7056
 253  C13   C  CR16  0  -0.382  -1.3847  -1.5742  -0.6628
 253  C8    C  CR66  0  -0.197  -0.7076   2.0475  -0.0115
 253  C9    C  CR6   0   0.400  -2.0853   2.4360   0.1937
 253  N1    N  NH2   0  -0.841  -2.4076   3.7392   0.3823
 253  C7    C  CR16  0  -0.113   0.3384   2.9951  -0.0970
 253  N6    N  N     0  -0.444   1.5933   2.6930  -0.2297
 253  C5    C  CR66  0   0.195   1.9355   1.3792  -0.1764
 253  C4    C  CR16  0  -0.450   3.3166   1.0850  -0.1985
 253  H11   H  HCH3  0   0.234   5.9792   0.9444  -1.1246
 253  H12   H  HCH3  0   0.234   5.9774   1.1656   0.6401
 253  H13A  H  HCH3  0   0.265   7.0034  -0.0785  -0.1010
 253  H251  H  HCH3  0   0.267   3.1324  -4.4132   0.7821
 253  H252  H  HCH3  0   0.233   1.8911  -3.3955   1.5353
 253  H253  H  HCH3  0   0.230   1.8395  -3.7205  -0.2135
 253  H22   H  HCR6  0   0.296   0.7920  -1.7591   0.4081
 253  H181  H  HCH3  0   0.238  -5.9955  -0.2990  -0.4149
 253  H182  H  HCH3  0   0.235  -5.6937  -0.6602   1.2768
 253  H183  H  HCH3  0   0.263  -5.2867   0.9252   0.6357
 253  H161  H  HNH2  0   0.388  -5.5958  -2.6157   0.2381
 253  H162  H  HNH2  0   0.385  -4.5791  -3.8063  -0.3531
 253  H14   H  HCR6  0   0.259  -2.3486  -3.4243  -1.0666
 253  H13   H  HCR6  0   0.270  -0.4455  -1.9497  -1.0387
 253  HN11  H  HNH2  0   0.392  -3.3894   3.9610   0.3619
 253  HN12  H  HNH2  0   0.403  -1.8044   4.4745   0.0612
 253  H7    H  HCR6  0   0.249   0.1184   4.0570  -0.0781
 253  H4    H  HCR6  0   0.287   3.9952   1.9188  -0.3144

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
 253  N1   C9    single    1.356  0.020  1.356
 253  C18  C17   single    1.500  0.020  1.500
 253  N20  C9    aromatic  1.301  0.020  1.301
 253  N20  C19   aromatic  1.361  0.020  1.361
 253  C9   C8    aromatic  1.446  0.020  1.446
 253  C17  C19   aromatic  1.413  0.020  1.413
 253  C17  C15   aromatic  1.394  0.020  1.394
 253  C19  C12   aromatic  1.422  0.020  1.422
 253  C8   C7    aromatic  1.414  0.020  1.414
 253  C8   C11   aromatic  1.401  0.020  1.401
 253  C7   N6    aromatic  1.298  0.020  1.298
 253  N16  C15   single    1.371  0.020  1.371
 253  C15  C14   aromatic  1.411  0.020  1.411
 253  N6   C5    aromatic  1.359  0.020  1.359
 253  C12  C11   aromatic  1.437  0.020  1.437
 253  C12  C13   aromatic  1.408  0.020  1.408
 253  C11  C21   aromatic  1.437  0.020  1.437
 253  C5   C21   aromatic  1.412  0.020  1.412
 253  C5   C4    aromatic  1.412  0.020  1.412
 253  C14  C13   aromatic  1.367  0.020  1.367
 253  C21  C22   aromatic  1.417  0.020  1.417
 253  C4   C3    aromatic  1.369  0.020  1.369
 253  C22  C23   aromatic  1.370  0.020  1.370
 253  C25  O24   single    1.414  0.020  1.414
 253  C3   C23   aromatic  1.427  0.020  1.427
 253  C3   O2    single    1.336  0.020  1.336
 253  C23  O24   single    1.340  0.020  1.340
 253  O2   C1    single    1.416  0.020  1.416
 253  C1   H11   single    0.970  0.020  1.090
 253  C1   H12   single    0.970  0.020  1.090
 253  C1   H13A  single    0.970  0.020  1.090
 253  C25  H251  single    0.970  0.020  1.090
 253  C25  H252  single    0.970  0.020  1.090
 253  C25  H253  single    0.970  0.020  1.090
 253  C22  H22   single    0.930  0.020  1.080
 253  C18  H181  single    0.970  0.020  1.090
 253  C18  H182  single    0.970  0.020  1.090
 253  C18  H183  single    0.970  0.020  1.090
 253  N16  H161  single    0.890  0.020  1.040
 253  N16  H162  single    0.890  0.020  1.040
 253  C14  H14   single    0.930  0.020  1.080
 253  C13  H13   single    0.930  0.020  1.080
 253  N1   HN11  single    0.890  0.020  1.040
 253  N1   HN12  single    0.890  0.020  1.040
 253  C7   H7    single    0.930  0.020  1.080
 253  C4   H4    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
 253  H13A  C1   H12   109.06  3.000
 253  H13A  C1   H11   108.87  3.000
 253  H12   C1   H11   108.95  3.000
 253  H13A  C1   O2    106.42  3.000
 253  H12   C1   O2    111.63  3.000
 253  H11   C1   O2    111.81  3.000
 253  C3    O2   C1    118.14  3.000
 253  C4    C3   C23   119.07  3.000
 253  C23   C3   O2    115.23  3.000
 253  C4    C3   O2    125.67  3.000
 253  C22   C23  O24   125.23  3.000
 253  O24   C23  C3    114.80  3.000
 253  C22   C23  C3    119.96  3.000
 253  C25   O24  C23   118.32  3.000
 253  H253  C25  H252  108.94  3.000
 253  H253  C25  H251  108.80  3.000
 253  H252  C25  H251  108.85  3.000
 253  H253  C25  O24   111.76  3.000
 253  H252  C25  O24   111.87  3.000
 253  H251  C25  O24   106.51  3.000
 253  H22   C22  C21   119.18  3.000
 253  H22   C22  C23   118.79  3.000
 253  C21   C22  C23   121.89  3.000
 253  C5    C21  C11   118.01  3.000
 253  C5    C21  C22   117.40  3.000
 253  C11   C21  C22   124.47  3.000
 253  C8    C11  C12   117.86  3.000
 253  C12   C11  C21   125.87  3.000
 253  C8    C11  C21   116.26  3.000
 253  C13   C12  C19   117.42  3.000
 253  C13   C12  C11   124.89  3.000
 253  C19   C12  C11   117.55  3.000
 253  C17   C19  N20   117.18  3.000
 253  C17   C19  C12   120.71  3.000
 253  N20   C19  C12   122.09  3.000
 253  C9    N20  C19   120.20  3.000
 253  C15   C17  C18   119.15  3.000
 253  C15   C17  C19   119.42  3.000
 253  C18   C17  C19   121.41  3.000
 253  H183  C18  H182  107.53  3.000
 253  H183  C18  H181  107.95  3.000
 253  H182  C18  H181  106.80  3.000
 253  H183  C18  C17   111.30  3.000
 253  H182  C18  C17   111.45  3.000
 253  H181  C18  C17   111.59  3.000
 253  C14   C15  N16   119.25  3.000
 253  C14   C15  C17   119.57  3.000
 253  N16   C15  C17   121.02  3.000
 253  H162  N16  H161  112.43  3.000
 253  H162  N16  C15   116.29  3.000
 253  H161  N16  C15   117.35  3.000
 253  H14   C14  C13   119.81  3.000
 253  H14   C14  C15   119.51  3.000
 253  C13   C14  C15   120.67  3.000
 253  H13   C13  C14   117.70  3.000
 253  H13   C13  C12   120.58  3.000
 253  C14   C13  C12   121.61  3.000
 253  C7    C8   C9    122.23  3.000
 253  C7    C8   C11   119.22  3.000
 253  C9    C8   C11   118.54  3.000
 253  N1    C9   C8    120.30  3.000
 253  C8    C9   N20   122.39  3.000
 253  N1    C9   N20   117.18  3.000
 253  HN12  N1   HN11  114.72  3.000
 253  HN12  N1   C9    121.11  3.000
 253  HN11  N1   C9    116.15  3.000
 253  H7    C7   N6    115.20  3.000
 253  H7    C7   C8    120.34  3.000
 253  N6    C7   C8    124.44  3.000
 253  C5    N6   C7    117.69  3.000
 253  C4    C5   N6    116.56  3.000
 253  C4    C5   C21   120.16  3.000
 253  N6    C5   C21   123.25  3.000
 253  H4    C4   C5    117.05  3.000
 253  H4    C4   C3    121.75  3.000
 253  C5    C4   C3    121.18  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
 253  CONST_01  N6    C5   C4   C3   180.00   0.0  0
 253  CONST_02  C21   C5   C4   C3     0.00   0.0  0
 253  CONST_03  C21   C22  C23  C3     0.00   0.0  0
 253  CONST_04  C11   C21  C22  C23  180.00   0.0  0
 253  CONST_05  C5    C21  C22  C23    0.00   0.0  0
 253  CONST_06  C5    C4   C3   C23    0.00   0.0  0
 253  CONST_08  C12   C11  C21  C22    0.00   0.0  0
 253  CONST_09  N6    C5   C21  C22  180.00   0.0  0
 253  CONST_10  C4    C5   C21  C22    0.00   0.0  0
 253  CONST_11  C4    C3   C23  C22    0.00   0.0  0
 253  CONST_12  C9    C8   C11  C21  180.00   0.0  0
 253  CONST_13  C7    C8   C11  C21    0.00   0.0  0
 253  CONST_14  C19   C12  C11  C21  180.00   0.0  0
 253  CONST_16  C7    N6   C5   C21    0.00   0.0  0
 253  CONST_17  N20   C9   C8   C11    0.00   0.0  0
 253  CONST_18  N6    C7   C8   C11    0.00   0.0  0
 253  CONST_19  N20   C19  C12  C11    0.00   0.0  0
 253  CONST_20  C17   C19  C12  C11  180.00   0.0  0
 253  CONST_21  C14   C13  C12  C11  180.00   0.0  0
 253  CONST_22  N6    C5   C21  C11    0.00   0.0  0
 253  CONST_23  C4    C5   C21  C11  180.00   0.0  0
 253  CONST_24  C9    N20  C19  C12    0.00   0.0  0
 253  CONST_25  C15   C17  C19  C12    0.00   0.0  0
 253  CONST_26  C9    C8   C11  C12    0.00   0.0  0
 253  CONST_27  C7    C8   C11  C12  180.00   0.0  0
 253  CONST_28  C5    C21  C11  C12  180.00   0.0  0
 253  CONST_29  C15   C14  C13  C12    0.00   0.0  0
 253  CONST_30  C8    C9   N20  C19    0.00   0.0  0
 253  CONST_31  C14   C15  C17  C19    0.00   0.0  0
 253  CONST_32  C8    C11  C12  C19    0.00   0.0  0
 253  CONST_33  C14   C13  C12  C19    0.00   0.0  0
 253  CONST_34  C7    C8   C9   N20  180.00   0.0  0
 253  CONST_35  C15   C17  C19  N20  180.00   0.0  0
 253  CONST_36  C13   C12  C19  N20  180.00   0.0  0
 253  CONST_37  C9    N20  C19  C17  180.00   0.0  0
 253  CONST_38  C13   C12  C19  C17    0.00   0.0  0
 253  CONST_39  C13   C14  C15  C17    0.00   0.0  0
 253  CONST_41  C5    N6   C7   C8     0.00   0.0  0
 253  CONST_42  C5    C21  C11  C8     0.00   0.0  0
 253  CONST_43  N6    C7   C8   C9   180.00   0.0  0
 253  CONST_44  C4    C5   N6   C7   180.00   0.0  0
 253  CONST_45  C5    C4   C3   O2   180.00   0.0  0
 253  CONST_46  C22   C23  C3   O2   180.00   0.0  0
 253  CONST_47  C21   C22  C23  O24  180.00   0.0  0
 253  CONST_48  C4    C3   C23  O24  180.00   0.0  0
 253  CONST_49  N1    C9   C8   C11  180.00   0.0  0
 253  CONST_50  C18   C17  C19  C12  180.00   0.0  0
 253  CONST_51  N1    C9   N20  C19  180.00   0.0  0
 253  CONST_52  N16   C15  C17  C19  180.00   0.0  0
 253  CONST_53  C18   C17  C19  N20    0.00   0.0  0
 253  CONST_54  C14   C15  C17  C18  180.00   0.0  0
 253  CONST_55  C13   C14  C15  N16  180.00   0.0  0
 253  CONST_56  C7    C8   C9   N1     0.00   0.0  0
 253  CONST_57  H22   C22  C23  C3   180.00   0.0  0
 253  CONST_58  H4    C4   C3   C23  180.00   0.0  0
 253  CONST_59  H7    C7   C8   C11  180.00   0.0  0
 253  CONST_60  H13   C13  C12  C11    0.00   0.0  0
 253  CONST_61  H14   C14  C13  C12  180.00   0.0  0
 253  CONST_62  HN11  N1   C9   N20    0.00   0.0  0
 253  Var_01    C4    C3   O2   C1     1.88  30.0  2
 253  Var_02    C22   C23  O24  C25    1.02  30.0  3
 253  Var_03    H181  C18  C17  C19  120.63  30.0  2
 253  Var_04    H11   C1   O2   C3   -63.14  30.0  3
 253  Var_05    H251  C25  O24  C23  178.96  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
 253  plan-1  O2    0.020
 253  plan-1  C3    0.020
 253  plan-1  C23   0.020
 253  plan-1  O24   0.020
 253  plan-1  C22   0.020
 253  plan-1  C21   0.020
 253  plan-1  C11   0.020
 253  plan-1  C12   0.020
 253  plan-1  C19   0.020
 253  plan-1  N20   0.020
 253  plan-1  C17   0.020
 253  plan-1  C18   0.020
 253  plan-1  C15   0.020
 253  plan-1  N16   0.020
 253  plan-1  C14   0.020
 253  plan-1  C13   0.020
 253  plan-1  C8    0.020
 253  plan-1  C9    0.020
 253  plan-1  N1    0.020
 253  plan-1  C7    0.020
 253  plan-1  N6    0.020
 253  plan-1  C5    0.020
 253  plan-1  C4    0.020
 253  plan-1  H22   0.020
 253  plan-1  H14   0.020
 253  plan-1  H13   0.020
 253  plan-1  H7    0.020
 253  plan-1  H4    0.020
 253  plan-2  C15   0.020
 253  plan-2  N16   0.020
 253  plan-2  H161  0.020
 253  plan-2  H162  0.020
 253  plan-3  C9    0.020
 253  plan-3  N1    0.020
 253  plan-3  HN11  0.020
 253  plan-3  HN12  0.020

