# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 20:53:36 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2c(c1)nc(Nc3cccc(Cl)c3)c4ccncc24
#
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
 3NG  3NG  '5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid'  ligand  37  25  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3NG
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
 3NG  C1    C   CR66  0   0.235  -1.7114   0.3258  -0.0299
 3NG  C2    C   CR66  0   0.049  -2.5636  -0.7848   0.1047
 3NG  C3    C   CR16  0  -0.351  -3.9469  -0.5718   0.1939
 3NG  C4    C   CR16  0  -0.256  -4.4737   0.6971   0.1533
 3NG  C5    C   CR6   0  -0.097  -3.6233   1.8065   0.0196
 3NG  C6    C   CR16  0  -0.309  -2.2605   1.6143  -0.0715
 3NG  C7    C   CR66  0   0.036  -0.5421  -2.1819   0.0374
 3NG  C8    C   CR66  0   0.134  -1.9377  -2.0850   0.1376
 3NG  N9    N   N     0  -0.519  -0.3535   0.2193  -0.1202
 3NG  C10   C   CR6   0   0.512   0.2182  -0.9388  -0.0876
 3NG  C11   C   CR16  0  -0.061  -0.7861  -4.5583   0.1814
 3NG  N12   N   N     0  -0.389  -2.1165  -4.4753   0.2842
 3NG  C13   C   CR16  0  -0.110  -2.6640  -3.2827   0.2611
 3NG  C14   C   CR16  0  -0.385   0.0302  -3.4591   0.0580
 3NG  N15   N   NH1   0  -0.803   1.5725  -1.0403  -0.1698
 3NG  C16   C   CR6   0   0.385   2.5478  -0.0607  -0.3246
 3NG  C17   C   CR16  0  -0.334   3.8723  -0.5051  -0.2272
 3NG  C18   C   CR6   0  -0.023   4.9121   0.3878  -0.3906
 3NG  C19   C   CR16  0  -0.240   4.6883   1.7319  -0.6481
 3NG  C20   C   CR16  0  -0.251   3.3738   2.1595  -0.7399
 3NG  C21   C   CR16  0  -0.304   2.3033   1.2901  -0.5830
 3NG  CL22  CL  CL    0  -0.126   6.5404  -0.1960  -0.2687
 3NG  C23   C   C     0   0.540  -4.1376   3.1991  -0.0303
 3NG  O24   O   O     0  -0.434  -3.4329   4.1704  -0.1645
 3NG  O25   O   OH1   0  -0.592  -5.4552   3.2674   0.0881
 3NG  H3    H   HCR6  0   0.266  -4.6259  -1.4066   0.2935
 3NG  H4    H   HCR6  0   0.271  -5.5445   0.8226   0.2238
 3NG  H6    H   HCR6  0   0.271  -1.5867   2.4546  -0.1738
 3NG  H11   H   HCR6  0   0.282  -0.3590  -5.5534   0.1983
 3NG  H13   H   HCR6  0   0.275  -3.7442  -3.2561   0.3437
 3NG  H14   H   HCR6  0   0.273   1.0945  -3.6303  -0.0233
 3NG  HN15  H   HNH1  0   0.430   1.9530  -1.9653  -0.0657
 3NG  H17   H   HCR6  0   0.292   4.0814  -1.5486  -0.0252
 3NG  H19   H   HCR6  0   0.278   5.5114   2.4212  -0.7729
 3NG  H20   H   HCR6  0   0.269   3.1714   3.2035  -0.9400
 3NG  H21   H   HCR6  0   0.296   1.2948   1.6581  -0.6598
 3NG  HO25  H   HOH1  0   0.489  -5.7430   4.1918   0.0487

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
 3NG  C1   C2    aromatic  1.406  0.020  1.406
 3NG  C1   N9    aromatic  1.365  0.020  1.365
 3NG  C1   C6    aromatic  1.401  0.020  1.401
 3NG  C2   C3    aromatic  1.402  0.020  1.402
 3NG  C8   C2    aromatic  1.443  0.020  1.443
 3NG  C3   C4    aromatic  1.375  0.020  1.375
 3NG  C3   H3    single    0.930  0.020  1.080
 3NG  C4   C5    aromatic  1.404  0.020  1.404
 3NG  C4   H4    single    0.930  0.020  1.080
 3NG  C5   C6    aromatic  1.379  0.020  1.379
 3NG  C5   C23   single    1.485  0.020  1.485
 3NG  C6   H6    single    0.930  0.020  1.080
 3NG  C14  C7    aromatic  1.400  0.020  1.400
 3NG  C10  C7    aromatic  1.462  0.020  1.462
 3NG  C7   C8    aromatic  1.403  0.020  1.403
 3NG  C8   C13   aromatic  1.406  0.020  1.406
 3NG  C10  N9    aromatic  1.292  0.020  1.292
 3NG  N15  C10   single    1.361  0.020  1.361
 3NG  C14  C11   aromatic  1.375  0.020  1.375
 3NG  C11  N12   aromatic  1.337  0.020  1.337
 3NG  C11  H11   single    0.930  0.020  1.080
 3NG  N12  C13   aromatic  1.312  0.020  1.312
 3NG  C13  H13   single    0.930  0.020  1.080
 3NG  C14  H14   single    0.930  0.020  1.080
 3NG  C16  N15   single    1.391  0.020  1.391
 3NG  N15  HN15  single    0.860  0.020  1.020
 3NG  C21  C16   aromatic  1.397  0.020  1.397
 3NG  C16  C17   aromatic  1.400  0.020  1.400
 3NG  C18  C17   aromatic  1.380  0.020  1.380
 3NG  C17  H17   single    0.930  0.020  1.080
 3NG  C19  C18   aromatic  1.387  0.020  1.387
 3NG  C18  CL22  single    1.734  0.020  1.734
 3NG  C20  C19   aromatic  1.385  0.020  1.385
 3NG  C19  H19   single    0.930  0.020  1.080
 3NG  C20  C21   aromatic  1.388  0.020  1.388
 3NG  C20  H20   single    0.930  0.020  1.080
 3NG  C21  H21   single    0.930  0.020  1.080
 3NG  O24  C23   double    1.207  0.020  1.207
 3NG  C23  O25   single    1.325  0.020  1.325
 3NG  O25  HO25  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
 3NG  N9    C1   C6   117.37  3.000
 3NG  C6    C1   C2   119.44  3.000
 3NG  N9    C1   C2   123.20  3.000
 3NG  C8    C2   C3   124.27  3.000
 3NG  C8    C2   C1   116.79  3.000
 3NG  C3    C2   C1   118.94  3.000
 3NG  H3    C3   C4   118.36  3.000
 3NG  H3    C3   C2   120.55  3.000
 3NG  C4    C3   C2   121.09  3.000
 3NG  H4    C4   C5   120.98  3.000
 3NG  H4    C4   C3   119.02  3.000
 3NG  C5    C4   C3   120.00  3.000
 3NG  C23   C5   C6   118.07  3.000
 3NG  C23   C5   C4   122.29  3.000
 3NG  C6    C5   C4   119.64  3.000
 3NG  H6    C6   C5   120.89  3.000
 3NG  H6    C6   C1   118.22  3.000
 3NG  C5    C6   C1   120.89  3.000
 3NG  C14   C7   C10  124.35  3.000
 3NG  C10   C7   C8   117.69  3.000
 3NG  C14   C7   C8   117.96  3.000
 3NG  C13   C8   C7   117.47  3.000
 3NG  C13   C8   C2   123.05  3.000
 3NG  C7    C8   C2   119.48  3.000
 3NG  C10   N9   C1   120.56  3.000
 3NG  N15   C10  N9   120.38  3.000
 3NG  N15   C10  C7   117.34  3.000
 3NG  N9    C10  C7   122.28  3.000
 3NG  H11   C11  C14  120.12  3.000
 3NG  H11   C11  N12  116.64  3.000
 3NG  C14   C11  N12  123.24  3.000
 3NG  C13   N12  C11  118.05  3.000
 3NG  H13   C13  N12  115.90  3.000
 3NG  H13   C13  C8   120.04  3.000
 3NG  N12   C13  C8   124.06  3.000
 3NG  H14   C14  C11  117.69  3.000
 3NG  H14   C14  C7   123.09  3.000
 3NG  C11   C14  C7   119.22  3.000
 3NG  HN15  N15  C16  113.20  3.000
 3NG  HN15  N15  C10  116.04  3.000
 3NG  C16   N15  C10  130.71  3.000
 3NG  C21   C16  C17  119.03  3.000
 3NG  C17   C16  N15  115.59  3.000
 3NG  C21   C16  N15  125.37  3.000
 3NG  H17   C17  C18  119.99  3.000
 3NG  H17   C17  C16  120.08  3.000
 3NG  C18   C17  C16  119.93  3.000
 3NG  CL22  C18  C19  119.40  3.000
 3NG  CL22  C18  C17  118.76  3.000
 3NG  C19   C18  C17  121.84  3.000
 3NG  H19   C19  C20  121.21  3.000
 3NG  H19   C19  C18  121.11  3.000
 3NG  C20   C19  C18  117.68  3.000
 3NG  H20   C20  C21  118.75  3.000
 3NG  H20   C20  C19  119.17  3.000
 3NG  C21   C20  C19  122.07  3.000
 3NG  H21   C21  C20  120.03  3.000
 3NG  H21   C21  C16  120.52  3.000
 3NG  C20   C21  C16  119.45  3.000
 3NG  O25   C23  O24  123.29  3.000
 3NG  O25   C23  C5   112.94  3.000
 3NG  O24   C23  C5   123.77  3.000
 3NG  HO25  O25  C23  109.94  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
 3NG  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 3NG  CONST_02  C7    C8   C2   C1      0.00   0.0  0
 3NG  CONST_03  C13   C8   C2   C1    180.00   0.0  0
 3NG  CONST_04  C7    C10  N9   C1      0.00   0.0  0
 3NG  CONST_05  C4    C5   C6   C1      0.00   0.0  0
 3NG  CONST_06  C10   N9   C1   C2      0.00   0.0  0
 3NG  CONST_07  C5    C6   C1   C2      0.00   0.0  0
 3NG  CONST_08  C5    C4   C3   C2      0.00   0.0  0
 3NG  CONST_09  C14   C7   C8   C2    180.00   0.0  0
 3NG  CONST_10  C10   C7   C8   C2      0.00   0.0  0
 3NG  CONST_11  N12   C13  C8   C2    180.00   0.0  0
 3NG  CONST_12  N9    C1   C2   C3    180.00   0.0  0
 3NG  CONST_13  C6    C1   C2   C3      0.00   0.0  0
 3NG  CONST_14  C7    C8   C2   C3    180.00   0.0  0
 3NG  CONST_15  C13   C8   C2   C3      0.00   0.0  0
 3NG  CONST_16  C6    C5   C4   C3      0.00   0.0  0
 3NG  CONST_17  C8    C2   C3   C4    180.00   0.0  0
 3NG  CONST_18  N9    C1   C6   C5    180.00   0.0  0
 3NG  CONST_19  C8    C2   C1   C6    180.00   0.0  0
 3NG  CONST_20  C10   N9   C1   C6    180.00   0.0  0
 3NG  CONST_21  N12   C11  C14  C7      0.00   0.0  0
 3NG  CONST_22  N12   C13  C8   C7      0.00   0.0  0
 3NG  CONST_23  N9    C1   C2   C8      0.00   0.0  0
 3NG  CONST_24  C11   C14  C7   C8      0.00   0.0  0
 3NG  CONST_25  N9    C10  C7   C8      0.00   0.0  0
 3NG  CONST_26  C11   N12  C13  C8      0.00   0.0  0
 3NG  CONST_27  C14   C7   C10  N9    180.00   0.0  0
 3NG  CONST_28  C11   C14  C7   C10   180.00   0.0  0
 3NG  CONST_29  C13   C8   C7   C10   180.00   0.0  0
 3NG  CONST_30  C14   C7   C8   C13     0.00   0.0  0
 3NG  CONST_31  C14   C11  N12  C13     0.00   0.0  0
 3NG  CONST_32  C19   C20  C21  C16     0.00   0.0  0
 3NG  CONST_33  C19   C18  C17  C16     0.00   0.0  0
 3NG  CONST_34  C20   C21  C16  C17     0.00   0.0  0
 3NG  CONST_35  C20   C19  C18  C17     0.00   0.0  0
 3NG  CONST_36  C21   C16  C17  C18     0.00   0.0  0
 3NG  CONST_37  C21   C20  C19  C18     0.00   0.0  0
 3NG  CONST_38  N15   C10  N9   C1    180.00   0.0  0
 3NG  CONST_39  C23   C5   C6   C1    180.00   0.0  0
 3NG  CONST_40  C23   C5   C4   C3    180.00   0.0  0
 3NG  CONST_41  N15   C10  C7   C8    180.00   0.0  0
 3NG  CONST_42  N15   C10  C7   C14     0.00   0.0  0
 3NG  CONST_43  C20   C21  C16  N15   180.00   0.0  0
 3NG  CONST_44  C18   C17  C16  N15   180.00   0.0  0
 3NG  CONST_45  CL22  C18  C17  C16   180.00   0.0  0
 3NG  CONST_46  CL22  C18  C19  C20   180.00   0.0  0
 3NG  CONST_47  H3    C3   C2   C1    180.00   0.0  0
 3NG  CONST_48  H6    C6   C1   C2    180.00   0.0  0
 3NG  CONST_49  H4    C4   C3   C2    180.00   0.0  0
 3NG  CONST_50  H13   C13  C8   C2      0.00   0.0  0
 3NG  CONST_51  H11   C11  C14  C7    180.00   0.0  0
 3NG  CONST_52  H14   C14  C7   C8    180.00   0.0  0
 3NG  CONST_53  H20   C20  C21  C16   180.00   0.0  0
 3NG  CONST_54  H21   C21  C16  C17   180.00   0.0  0
 3NG  CONST_55  H19   C19  C18  C17   180.00   0.0  0
 3NG  CONST_56  H17   C17  C18  C19   180.00   0.0  0
 3NG  CONST_57  HO25  O25  C23  C5    180.00   0.0  0
 3NG  Var_01    C16   N15  C10  C7    178.28  30.0  2
 3NG  Var_02    C21   C16  N15  C10    -7.63  30.0  2
 3NG  Var_03    O24   C23  C5   C4   -178.86  30.0  2

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
 3NG  plan-1  N15   0.020
 3NG  plan-1  C16   0.020
 3NG  plan-1  C17   0.020
 3NG  plan-1  C18   0.020
 3NG  plan-1  C19   0.020
 3NG  plan-1  C20   0.020
 3NG  plan-1  C21   0.020
 3NG  plan-1  CL22  0.020
 3NG  plan-1  H17   0.020
 3NG  plan-1  H19   0.020
 3NG  plan-1  H20   0.020
 3NG  plan-1  H21   0.020
 3NG  plan-2  C1    0.020
 3NG  plan-2  C2    0.020
 3NG  plan-2  C3    0.020
 3NG  plan-2  C4    0.020
 3NG  plan-2  C5    0.020
 3NG  plan-2  C6    0.020
 3NG  plan-2  C7    0.020
 3NG  plan-2  C8    0.020
 3NG  plan-2  N9    0.020
 3NG  plan-2  C10   0.020
 3NG  plan-2  C11   0.020
 3NG  plan-2  N12   0.020
 3NG  plan-2  C13   0.020
 3NG  plan-2  C14   0.020
 3NG  plan-2  N15   0.020
 3NG  plan-2  C23   0.020
 3NG  plan-2  H3    0.020
 3NG  plan-2  H4    0.020
 3NG  plan-2  H6    0.020
 3NG  plan-2  H11   0.020
 3NG  plan-2  H13   0.020
 3NG  plan-2  H14   0.020
 3NG  plan-3  C5    0.020
 3NG  plan-3  C23   0.020
 3NG  plan-3  O24   0.020
 3NG  plan-3  O25   0.020
 3NG  plan-3  HO25  0.020

