# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 10:48:31 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-[(4-aminophenyl)amino]pyrido[2,3-d]pyrimidin-5(6H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(Nc2ncnc3N=CCC(=O)c23)cc1
#
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
 3WK  3WK  4-[(4-aminophenyl)amino]pyrido[2,3-d]pyrimidin-5(6H)-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_3WK
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
 3WK  C1   C  C     0  -0.664   3.8525   1.6213  -0.0489
 3WK  C2   C  CR16  0  -0.003   4.6628   0.3929   0.1245
 3WK  C8   C  CR16  0   0.073   1.1661  -2.4869   0.3684
 3WK  C10  C  CR6   0   0.555   0.5349  -0.3269   0.1127
 3WK  C13  C  CR6   0   0.295  -1.8227   0.3582  -0.0301
 3WK  C14  C  CR16  0  -0.264  -2.4180  -0.6241  -0.8158
 3WK  C15  C  CR16  0  -0.328  -3.7934  -0.7729  -0.8309
 3WK  C16  C  CR6   0   0.301  -4.6233   0.0663  -0.0765
 3WK  N3   N  N     0  -0.394   4.2194  -0.7915   0.2566
 3WK  C4   C  CR6   0   0.453   2.3652   1.4208  -0.0201
 3WK  C5   C  CR66  0  -0.289   1.9110   0.0505   0.1093
 3WK  C6   C  CR66  0   0.396   2.8402  -0.9897   0.2434
 3WK  N7   N  N     0  -0.440   2.4733  -2.2580   0.3716
 3WK  N9   N  N     0  -0.450   0.1921  -1.6144   0.2478
 3WK  O11  O  O     0  -0.439   1.6094   2.3788  -0.1084
 3WK  N12  N  NH1   0  -0.758  -0.4301   0.5860  -0.0142
 3WK  C17  C  CR16  0  -0.323  -4.0153   1.0598   0.6991
 3WK  C18  C  CR16  0  -0.304  -2.6385   1.1960   0.7234
 3WK  N19  N  NH2   0  -0.859  -5.9951  -0.0427  -0.1434
 3WK  H1   H  H     0   0.327   4.1442   2.3528   0.7126
 3WK  H2   H  H     0   0.330   4.1356   2.0884  -1.0000
 3WK  H3   H  HCR6  0   0.291   5.7417   0.5228   0.1345
 3WK  H4   H  HCR6  0   0.268   0.8645  -3.5231   0.4814
 3WK  H5   H  HCR6  0   0.262  -1.8107  -1.2783  -1.4248
 3WK  H6   H  HCR6  0   0.259  -4.2343  -1.5476  -1.4474
 3WK  H7   H  HNH1  0   0.424  -0.1107   1.5479  -0.0456
 3WK  H8   H  HCR6  0   0.260  -4.6277   1.7281   1.2926
 3WK  H9   H  HCR6  0   0.264  -2.1924   1.9679   1.3392
 3WK  H10  H  HNH2  0   0.379  -6.3510  -0.9381  -0.4364
 3WK  H11  H  HNH2  0   0.380  -6.5033   0.3200   0.6470

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
 3WK  N7   C8   aromatic  1.327  0.020  1.327
 3WK  N7   C6   aromatic  1.326  0.020  1.326
 3WK  C8   N9   aromatic  1.313  0.020  1.313
 3WK  N3   C6   single    1.393  0.020  1.393
 3WK  N3   C2   double    1.271  0.020  1.271
 3WK  C6   C5   aromatic  1.401  0.020  1.401
 3WK  C2   C1   single    1.482  0.020  1.482
 3WK  N9   C10  aromatic  1.339  0.020  1.339
 3WK  C5   C10  aromatic  1.427  0.020  1.427
 3WK  C5   C4   single    1.449  0.020  1.449
 3WK  C10  N12  single    1.334  0.020  1.334
 3WK  C1   C4   single    1.501  0.020  1.501
 3WK  C4   O11  double    1.223  0.020  1.223
 3WK  N12  C13  single    1.411  0.020  1.411
 3WK  C13  C18  aromatic  1.391  0.020  1.391
 3WK  C13  C14  aromatic  1.392  0.020  1.392
 3WK  C18  C17  aromatic  1.384  0.020  1.384
 3WK  C14  C15  aromatic  1.384  0.020  1.384
 3WK  C17  C16  aromatic  1.399  0.020  1.399
 3WK  C15  C16  aromatic  1.401  0.020  1.401
 3WK  C16  N19  single    1.378  0.020  1.378
 3WK  C1   H1   single    0.970  0.020  1.090
 3WK  C1   H2   single    0.970  0.020  1.090
 3WK  C2   H3   single    0.930  0.020  1.080
 3WK  C8   H4   single    0.930  0.020  1.080
 3WK  C14  H5   single    0.930  0.020  1.080
 3WK  C15  H6   single    0.930  0.020  1.080
 3WK  N12  H7   single    0.860  0.020  1.020
 3WK  C17  H8   single    0.930  0.020  1.080
 3WK  C18  H9   single    0.930  0.020  1.080
 3WK  N19  H10  single    0.890  0.020  1.040
 3WK  N19  H11  single    0.890  0.020  1.040

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
 3WK  H2   C1   H1   104.47  3.000
 3WK  H2   C1   C4   109.22  3.000
 3WK  H1   C1   C4   109.86  3.000
 3WK  H2   C1   C2   108.27  3.000
 3WK  H1   C1   C2   109.06  3.000
 3WK  C4   C1   C2   115.39  3.000
 3WK  H3   C2   N3   117.17  3.000
 3WK  H3   C2   C1   116.41  3.000
 3WK  N3   C2   C1   126.42  3.000
 3WK  H4   C8   N9   115.97  3.000
 3WK  H4   C8   N7   115.99  3.000
 3WK  N9   C8   N7   128.04  3.000
 3WK  N12  C10  N9   118.83  3.000
 3WK  N12  C10  C5   121.08  3.000
 3WK  N9   C10  C5   120.09  3.000
 3WK  C18  C13  N12  118.38  3.000
 3WK  C18  C13  C14  118.69  3.000
 3WK  N12  C13  C14  122.85  3.000
 3WK  H5   C14  C15  119.17  3.000
 3WK  H5   C14  C13  120.34  3.000
 3WK  C15  C14  C13  120.49  3.000
 3WK  H6   C15  C16  119.58  3.000
 3WK  H6   C15  C14  119.17  3.000
 3WK  C16  C15  C14  121.24  3.000
 3WK  N19  C16  C17  121.04  3.000
 3WK  N19  C16  C15  121.09  3.000
 3WK  C17  C16  C15  117.80  3.000
 3WK  C6   N3   C2   118.47  3.000
 3WK  O11  C4   C5   123.59  3.000
 3WK  O11  C4   C1   120.40  3.000
 3WK  C5   C4   C1   116.01  3.000
 3WK  C6   C5   C4   120.18  3.000
 3WK  C4   C5   C10  123.53  3.000
 3WK  C6   C5   C10  116.29  3.000
 3WK  N7   C6   C5   122.39  3.000
 3WK  C5   C6   N3   123.48  3.000
 3WK  N7   C6   N3   114.13  3.000
 3WK  C6   N7   C8   115.92  3.000
 3WK  C10  N9   C8   117.27  3.000
 3WK  H7   N12  C13  117.62  3.000
 3WK  H7   N12  C10  115.10  3.000
 3WK  C13  N12  C10  127.18  3.000
 3WK  H8   C17  C18  119.47  3.000
 3WK  H8   C17  C16  119.74  3.000
 3WK  C18  C17  C16  120.79  3.000
 3WK  H9   C18  C17  119.32  3.000
 3WK  H9   C18  C13  119.70  3.000
 3WK  C17  C18  C13  120.98  3.000
 3WK  H11  N19  H10  111.72  3.000
 3WK  H11  N19  C16  115.83  3.000
 3WK  H10  N19  C16  115.87  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
 3WK  CONST_01  C5   C6   N7   C8     0.00   0.0  0
 3WK  CONST_02  C5   C10  N9   C8     0.00   0.0  0
 3WK  CONST_03  N7   C8   N9   C10    0.00   0.0  0
 3WK  CONST_04  N7   C6   C5   C10    0.00   0.0  0
 3WK  CONST_05  C16  C17  C18  C13    0.00   0.0  0
 3WK  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 3WK  CONST_07  C17  C18  C13  C14    0.00   0.0  0
 3WK  CONST_08  C17  C16  C15  C14    0.00   0.0  0
 3WK  CONST_09  C18  C13  C14  C15    0.00   0.0  0
 3WK  CONST_10  C18  C17  C16  C15    0.00   0.0  0
 3WK  CONST_11  N9   C8   N7   C6     0.00   0.0  0
 3WK  CONST_12  N9   C10  C5   C6     0.00   0.0  0
 3WK  CONST_13  N12  C10  N9   C8   180.00   0.0  0
 3WK  CONST_14  N19  C16  C15  C14  180.00   0.0  0
 3WK  CONST_15  N12  C13  C14  C15  180.00   0.0  0
 3WK  CONST_16  N12  C10  C5   C4     0.00   0.0  0
 3WK  CONST_17  N12  C10  C5   C6   180.00   0.0  0
 3WK  CONST_18  C17  C18  C13  N12  180.00   0.0  0
 3WK  CONST_19  N19  C16  C17  C18  180.00   0.0  0
 3WK  CONST_20  H4   C8   N9   C10  180.00   0.0  0
 3WK  CONST_21  H8   C17  C18  C13  180.00   0.0  0
 3WK  CONST_22  H6   C15  C14  C13  180.00   0.0  0
 3WK  CONST_23  H9   C18  C13  C14  180.00   0.0  0
 3WK  CONST_24  H5   C14  C15  C16  180.00   0.0  0
 3WK  Var_01    C6   C5   C4   C1     2.11  30.0  1
 3WK  Var_02    N7   C6   N3   C2   179.24  30.0  1
 3WK  Var_03    C5   C4   C1   C2    -2.81  30.0  1
 3WK  Var_04    C4   C1   C2   N3     1.96  30.0  1
 3WK  Var_05    C18  C13  N12  C10  135.19  30.0  2
 3WK  Var_06    N9   C10  N12  C13   -0.28  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
 3WK  plan-1  C13  0.020
 3WK  plan-1  C14  0.020
 3WK  plan-1  C15  0.020
 3WK  plan-1  C16  0.020
 3WK  plan-1  N12  0.020
 3WK  plan-1  C17  0.020
 3WK  plan-1  C18  0.020
 3WK  plan-1  N19  0.020
 3WK  plan-1  H5   0.020
 3WK  plan-1  H6   0.020
 3WK  plan-1  H8   0.020
 3WK  plan-1  H9   0.020
 3WK  plan-2  C8   0.020
 3WK  plan-2  C10  0.020
 3WK  plan-2  N3   0.020
 3WK  plan-2  C4   0.020
 3WK  plan-2  C5   0.020
 3WK  plan-2  C6   0.020
 3WK  plan-2  N7   0.020
 3WK  plan-2  N9   0.020
 3WK  plan-2  N12  0.020
 3WK  plan-2  H4   0.020
 3WK  plan-3  C16  0.020
 3WK  plan-3  N19  0.020
 3WK  plan-3  H10  0.020
 3WK  plan-3  H11  0.020
 3WK  plan-4  C1   0.020
 3WK  plan-4  C4   0.020
 3WK  plan-4  C5   0.020
 3WK  plan-4  O11  0.020

