# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 11:11:59 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-[(3-aminophenyl)amino]pyrido[2,3-d]pyrimidin-5(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(Nc2ncnc3NC=CC(=O)c23)c1
#
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
 3WN  3WN  4-[(3-aminophenyl)amino]pyrido[2,3-d]pyrimidin-5(8H)-one  ligand  30  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3WN
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
 3WN  C1   C  CR16  0  -0.457   3.6882   1.5992   0.1729
 3WN  C2   C  CR16  0   0.076   4.5236   0.5408   0.0903
 3WN  C8   C  CR16  0   0.111   1.1116  -2.5255  -0.2591
 3WN  C10  C  CR6   0   0.584   0.4470  -0.3624  -0.0843
 3WN  C13  C  CR6   0   0.390  -1.8928   0.5172  -0.0450
 3WN  C14  C  CR16  0  -0.395  -2.6289  -0.6577  -0.1643
 3WN  C15  C  CR16  0  -0.327  -4.6818   0.6140  -0.0520
 3WN  C16  C  CR16  0  -0.214  -3.9371   1.7757   0.0647
 3WN  N3   N  NR16  0  -0.662   4.0644  -0.7231  -0.0394
 3WN  C4   C  CR6   0   0.490   2.2597   1.4217   0.1228
 3WN  C5   C  CR66  0  -0.355   1.8177   0.0404  -0.0164
 3WN  C6   C  CR66  0   0.544   2.7397  -1.0043  -0.0922
 3WN  N7   N  N     0  -0.459   2.4039  -2.2926  -0.2141
 3WN  N9   N  N     0  -0.482   0.1223  -1.6476  -0.2032
 3WN  O11  O  O     0  -0.503   1.4693   2.3747   0.1926
 3WN  N12  N  NH1   0  -0.794  -0.4993   0.5859  -0.0259
 3WN  C17  C  CR6   0   0.357  -4.0273  -0.6145  -0.1680
 3WN  C18  C  CR16  0  -0.380  -2.5554   1.7448   0.0684
 3WN  N19  N  NH2   0  -0.838  -4.7473  -1.7788  -0.3408
 3WN  H1   H  HCR6  0   0.260   4.0949   2.5943   0.2760
 3WN  H3   H  HCR6  0   0.297   5.5973   0.6444   0.1209
 3WN  H4   H  HCR6  0   0.243   0.8148  -3.5641  -0.3531
 3WN  H5   H  HCR6  0   0.279  -2.1185  -1.6035  -0.2575
 3WN  H6   H  HCR6  0   0.228  -5.7636   0.6611  -0.0516
 3WN  H7   H  HCR6  0   0.236  -4.4460   2.7259   0.1583
 3WN  H8   H  HNH1  0   0.432  -0.0999   1.5219   0.0665
 3WN  H9   H  HCR6  0   0.235  -1.9914   2.6640   0.1663
 3WN  H10  H  HNH2  0   0.352  -4.2766  -2.6306  -0.0885
 3WN  H11  H  HNH2  0   0.351  -5.6987  -1.7580  -0.0171
 3WN  H2   H  HNR6  0   0.402   4.7144  -1.4903  -0.0988

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
 3WN  N7   C8   aromatic  1.314  0.020  1.314
 3WN  N7   C6   aromatic  1.337  0.020  1.337
 3WN  C8   N9   aromatic  1.324  0.020  1.324
 3WN  N3   C6   single    1.355  0.020  1.355
 3WN  N3   C2   single    1.351  0.020  1.351
 3WN  C6   C5   aromatic  1.395  0.020  1.395
 3WN  N9   C10  aromatic  1.331  0.020  1.331
 3WN  C2   C1   double    1.351  0.020  1.351
 3WN  C5   C10  aromatic  1.430  0.020  1.430
 3WN  C5   C4   single    1.457  0.020  1.457
 3WN  C10  N12  single    1.341  0.020  1.341
 3WN  C1   C4   single    1.440  0.020  1.440
 3WN  C18  C16  aromatic  1.382  0.020  1.382
 3WN  C18  C13  aromatic  1.400  0.020  1.400
 3WN  C4   O11  double    1.240  0.020  1.240
 3WN  C16  C15  aromatic  1.385  0.020  1.385
 3WN  N12  C13  single    1.395  0.020  1.395
 3WN  C13  C14  aromatic  1.392  0.020  1.392
 3WN  C15  C17  aromatic  1.397  0.020  1.397
 3WN  C14  C17  aromatic  1.399  0.020  1.399
 3WN  C17  N19  single    1.380  0.020  1.380
 3WN  C1   H1   single    0.930  0.020  1.080
 3WN  C2   H3   single    0.930  0.020  1.080
 3WN  C8   H4   single    0.930  0.020  1.080
 3WN  C14  H5   single    0.930  0.020  1.080
 3WN  C15  H6   single    0.930  0.020  1.080
 3WN  C16  H7   single    0.930  0.020  1.080
 3WN  N12  H8   single    0.860  0.020  1.020
 3WN  C18  H9   single    0.930  0.020  1.080
 3WN  N19  H10  single    0.890  0.020  1.040
 3WN  N19  H11  single    0.890  0.020  1.040
 3WN  N3   H2   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
 3WN  H1   C1   C4   119.37  3.000
 3WN  H1   C1   C2   119.66  3.000
 3WN  C4   C1   C2   120.97  3.000
 3WN  H3   C2   N3   115.51  3.000
 3WN  H3   C2   C1   122.57  3.000
 3WN  N3   C2   C1   121.92  3.000
 3WN  H4   C8   N9   115.74  3.000
 3WN  H4   C8   N7   116.23  3.000
 3WN  N9   C8   N7   128.03  3.000
 3WN  N12  C10  N9   120.97  3.000
 3WN  N12  C10  C5   118.36  3.000
 3WN  N9   C10  C5   120.66  3.000
 3WN  C18  C13  N12  115.37  3.000
 3WN  N12  C13  C14  124.83  3.000
 3WN  C18  C13  C14  119.81  3.000
 3WN  H5   C14  C17  119.98  3.000
 3WN  H5   C14  C13  119.82  3.000
 3WN  C17  C14  C13  120.19  3.000
 3WN  H6   C15  C17  120.43  3.000
 3WN  H6   C15  C16  120.05  3.000
 3WN  C17  C15  C16  119.52  3.000
 3WN  H7   C16  C18  119.32  3.000
 3WN  H7   C16  C15  119.41  3.000
 3WN  C18  C16  C15  121.27  3.000
 3WN  H2   N3   C6   118.06  3.000
 3WN  H2   N3   C2   119.93  3.000
 3WN  C6   N3   C2   122.01  3.000
 3WN  O11  C4   C5   122.72  3.000
 3WN  O11  C4   C1   122.37  3.000
 3WN  C5   C4   C1   114.90  3.000
 3WN  C6   C5   C4   120.96  3.000
 3WN  C4   C5   C10  124.22  3.000
 3WN  C6   C5   C10  114.82  3.000
 3WN  N7   C6   C5   124.09  3.000
 3WN  C5   C6   N3   119.23  3.000
 3WN  N7   C6   N3   116.68  3.000
 3WN  C6   N7   C8   114.89  3.000
 3WN  C10  N9   C8   117.51  3.000
 3WN  H8   N12  C13  115.90  3.000
 3WN  H8   N12  C10  112.08  3.000
 3WN  C13  N12  C10  132.01  3.000
 3WN  N19  C17  C15  120.53  3.000
 3WN  N19  C17  C14  119.73  3.000
 3WN  C15  C17  C14  119.69  3.000
 3WN  H9   C18  C16  120.13  3.000
 3WN  H9   C18  C13  120.35  3.000
 3WN  C16  C18  C13  119.52  3.000
 3WN  H11  N19  H10  112.33  3.000
 3WN  H11  N19  C17  115.86  3.000
 3WN  H10  N19  C17  116.05  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
 3WN  CONST_01  C5   C6   N7   C8     0.00   0.0  0
 3WN  CONST_02  C5   C10  N9   C8     0.00   0.0  0
 3WN  CONST_03  N7   C8   N9   C10    0.00   0.0  0
 3WN  CONST_04  N7   C6   C5   C10    0.00   0.0  0
 3WN  CONST_05  C15  C16  C18  C13    0.00   0.0  0
 3WN  CONST_06  C15  C17  C14  C13    0.00   0.0  0
 3WN  CONST_07  C16  C18  C13  C14    0.00   0.0  0
 3WN  CONST_08  C16  C15  C17  C14    0.00   0.0  0
 3WN  CONST_09  N9   C8   N7   C6     0.00   0.0  0
 3WN  CONST_10  N9   C10  C5   C6     0.00   0.0  0
 3WN  CONST_11  C18  C16  C15  C17    0.00   0.0  0
 3WN  CONST_12  C18  C13  C14  C17    0.00   0.0  0
 3WN  CONST_13  N12  C10  N9   C8   180.00   0.0  0
 3WN  CONST_14  N19  C17  C14  C13  180.00   0.0  0
 3WN  CONST_15  N12  C13  C18  C16  180.00   0.0  0
 3WN  CONST_16  N19  C17  C15  C16  180.00   0.0  0
 3WN  CONST_17  N12  C10  C5   C4     0.00   0.0  0
 3WN  CONST_18  N12  C10  C5   C6   180.00   0.0  0
 3WN  CONST_19  C17  C14  C13  N12  180.00   0.0  0
 3WN  CONST_20  H4   C8   N9   C10  180.00   0.0  0
 3WN  CONST_21  H7   C16  C18  C13  180.00   0.0  0
 3WN  CONST_22  H9   C18  C13  C14  180.00   0.0  0
 3WN  CONST_23  H6   C15  C17  C14  180.00   0.0  0
 3WN  CONST_24  H5   C14  C17  C15  180.00   0.0  0
 3WN  Var_01    C18  C13  N12  C10  178.55  30.0  2
 3WN  Var_02    N9   C10  N12  C13    1.18  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
 3WN  plan-1  C13  0.020
 3WN  plan-1  C14  0.020
 3WN  plan-1  C15  0.020
 3WN  plan-1  C16  0.020
 3WN  plan-1  N12  0.020
 3WN  plan-1  C17  0.020
 3WN  plan-1  C18  0.020
 3WN  plan-1  N19  0.020
 3WN  plan-1  H5   0.020
 3WN  plan-1  H6   0.020
 3WN  plan-1  H7   0.020
 3WN  plan-1  H9   0.020
 3WN  plan-2  C1   0.020
 3WN  plan-2  C2   0.020
 3WN  plan-2  C8   0.020
 3WN  plan-2  C10  0.020
 3WN  plan-2  N3   0.020
 3WN  plan-2  C4   0.020
 3WN  plan-2  C5   0.020
 3WN  plan-2  C6   0.020
 3WN  plan-2  N7   0.020
 3WN  plan-2  N9   0.020
 3WN  plan-2  O11  0.020
 3WN  plan-2  N12  0.020
 3WN  plan-2  H1   0.020
 3WN  plan-2  H3   0.020
 3WN  plan-2  H4   0.020
 3WN  plan-2  H2   0.020
 3WN  plan-3  C17  0.020
 3WN  plan-3  N19  0.020
 3WN  plan-3  H10  0.020
 3WN  plan-3  H11  0.020

