# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 03:42:01 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 4-(cyclohexylamino)pyrido[3,4-d]pyrimidin-8(7H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=Cc2c(NC3CCCCC3)ncnc12
#
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
 1Q4  1Q4  4-(cyclohexylamino)pyrido[3,4-d]pyrimidin-8(7H)-one  ligand  34  18  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1Q4
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
 1Q4  C1   C  CR16  0  -0.449   1.6363   1.7715  -0.1716
 1Q4  C2   C  CR16  0   0.043   2.9098   2.1880  -0.3067
 1Q4  N3   N  NR16  0  -0.670   3.9486   1.3074  -0.2607
 1Q4  C5   C  CR6   0   0.515   3.8373  -0.0440  -0.0750
 1Q4  O6   O  O     0  -0.469   4.8165  -0.7704  -0.0382
 1Q4  C7   C  CR66  0   0.017   2.4504  -0.5203   0.0716
 1Q4  C8   C  CR66  0   0.082   1.3921   0.3772   0.0198
 1Q4  C9   C  CR6   0   0.548   0.0847  -0.2038   0.1718
 1Q4  N10  N  N     0  -0.469  -0.0474  -1.5115   0.3468
 1Q4  C11  C  CR16  0   0.039   1.0581  -2.2514   0.3816
 1Q4  N12  N  N     0  -0.440   2.2951  -1.8441   0.2535
 1Q4  N13  N  NH1   0  -0.675  -1.0114   0.5584   0.1544
 1Q4  C14  C  CH1   0  -0.052  -2.3700   0.0533   0.2462
 1Q4  C15  C  CH2   0  -0.451  -3.2731   1.1350   0.8306
 1Q4  C16  C  CH2   0  -0.437  -4.7121   0.6412   0.9427
 1Q4  C17  C  CH2   0  -0.432  -5.2413   0.1544  -0.4024
 1Q4  C18  C  CH2   0  -0.441  -4.3331  -0.9192  -0.9929
 1Q4  C19  C  CH2   0  -0.429  -2.8941  -0.4250  -1.1087
 1Q4  H1   H  HCR6  0   0.271   0.8461   2.5053  -0.2112
 1Q4  H3   H  HCR6  0   0.315   3.1794   3.2222  -0.4564
 1Q4  H4   H  HCR6  0   0.252   0.9051  -3.3157   0.5300
 1Q4  H5   H  HNH1  0   0.406  -0.9104   1.5389  -0.0491
 1Q4  H6   H  HCH1  0   0.241  -2.3581  -0.7973   0.9328
 1Q4  H7   H  HCH2  0   0.244  -2.8962   1.4419   1.8091
 1Q4  H8   H  HCH2  0   0.221  -3.2462   2.0198   0.1827
 1Q4  H9   H  HCH2  0   0.216  -4.7585  -0.1773   1.6689
 1Q4  H10  H  HCH2  0   0.234  -5.3444   1.4402   1.3361
 1Q4  H11  H  HCH2  0   0.231  -6.2589  -0.2277  -0.2921
 1Q4  H12  H  HCH2  0   0.212  -5.2982   1.0003  -1.0961
 1Q4  H13  H  HCH2  0   0.214  -4.3590  -1.8087  -0.3536
 1Q4  H14  H  HCH2  0   0.233  -4.6990  -1.2315  -1.9734
 1Q4  H15  H  HCH2  0   0.215  -2.8437   0.4060  -1.8208
 1Q4  H16  H  HCH2  0   0.238  -2.2485  -1.2168  -1.4954
 1Q4  H2   H  HNR6  0   0.426   4.8860   1.6706  -0.3692

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
 1Q4  O6   C5   double    1.220  0.020  1.220
 1Q4  N12  C11  aromatic  1.309  0.020  1.309
 1Q4  N12  C7   aromatic  1.345  0.020  1.345
 1Q4  C11  N10  aromatic  1.331  0.020  1.331
 1Q4  C5   C7   single    1.474  0.020  1.474
 1Q4  C5   N3   single    1.369  0.020  1.369
 1Q4  C7   C8   aromatic  1.389  0.020  1.389
 1Q4  N10  C9   aromatic  1.326  0.020  1.326
 1Q4  N3   C2   single    1.363  0.020  1.363
 1Q4  C8   C9   aromatic  1.439  0.020  1.439
 1Q4  C8   C1   single    1.428  0.020  1.428
 1Q4  C9   N13  single    1.335  0.020  1.335
 1Q4  C19  C18  single    1.526  0.020  1.526
 1Q4  C19  C14  single    1.529  0.020  1.529
 1Q4  C2   C1   double    1.347  0.020  1.347
 1Q4  C18  C17  single    1.525  0.020  1.525
 1Q4  C14  N13  single    1.452  0.020  1.452
 1Q4  C14  C15  single    1.525  0.020  1.525
 1Q4  C15  C16  single    1.526  0.020  1.526
 1Q4  C17  C16  single    1.525  0.020  1.525
 1Q4  C1   H1   single    0.930  0.020  1.080
 1Q4  C2   H3   single    0.930  0.020  1.080
 1Q4  C11  H4   single    0.930  0.020  1.080
 1Q4  N13  H5   single    0.860  0.020  1.020
 1Q4  C14  H6   single    0.970  0.020  1.090
 1Q4  C15  H7   single    0.970  0.020  1.090
 1Q4  C15  H8   single    0.970  0.020  1.090
 1Q4  C16  H9   single    0.970  0.020  1.090
 1Q4  C16  H10  single    0.970  0.020  1.090
 1Q4  C17  H11  single    0.970  0.020  1.090
 1Q4  C17  H12  single    0.970  0.020  1.090
 1Q4  C18  H13  single    0.970  0.020  1.090
 1Q4  C18  H14  single    0.970  0.020  1.090
 1Q4  C19  H15  single    0.970  0.020  1.090
 1Q4  C19  H16  single    0.970  0.020  1.090
 1Q4  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
 1Q4  H1   C1   C8   122.93  3.000
 1Q4  H1   C1   C2   118.58  3.000
 1Q4  C8   C1   C2   118.49  3.000
 1Q4  H3   C2   N3   115.69  3.000
 1Q4  H3   C2   C1   123.13  3.000
 1Q4  N3   C2   C1   121.17  3.000
 1Q4  H2   N3   C5   116.39  3.000
 1Q4  H2   N3   C2   118.10  3.000
 1Q4  C5   N3   C2   125.50  3.000
 1Q4  C7   C5   O6   124.06  3.000
 1Q4  C7   C5   N3   114.15  3.000
 1Q4  O6   C5   N3   121.79  3.000
 1Q4  N12  C7   C8   123.58  3.000
 1Q4  C8   C7   C5   120.31  3.000
 1Q4  N12  C7   C5   116.11  3.000
 1Q4  C9   C8   C7   115.31  3.000
 1Q4  C9   C8   C1   124.31  3.000
 1Q4  C7   C8   C1   120.37  3.000
 1Q4  N13  C9   N10  118.88  3.000
 1Q4  N13  C9   C8   120.94  3.000
 1Q4  N10  C9   C8   120.18  3.000
 1Q4  C11  N10  C9   117.97  3.000
 1Q4  H4   C11  N12  116.87  3.000
 1Q4  H4   C11  N10  115.57  3.000
 1Q4  N12  C11  N10  127.56  3.000
 1Q4  C11  N12  C7   115.38  3.000
 1Q4  H5   N13  C14  116.45  3.000
 1Q4  H5   N13  C9   118.45  3.000
 1Q4  C14  N13  C9   124.65  3.000
 1Q4  H6   C14  C19  108.47  3.000
 1Q4  H6   C14  C15  108.52  3.000
 1Q4  C19  C14  C15  111.00  3.000
 1Q4  H6   C14  N13  107.46  3.000
 1Q4  C15  C14  N13  109.35  3.000
 1Q4  C19  C14  N13  111.92  3.000
 1Q4  H8   C15  H7   107.09  3.000
 1Q4  H8   C15  C16  109.12  3.000
 1Q4  H7   C15  C16  110.52  3.000
 1Q4  H8   C15  C14  109.34  3.000
 1Q4  H7   C15  C14  109.76  3.000
 1Q4  C16  C15  C14  110.92  3.000
 1Q4  H10  C16  H9   106.46  3.000
 1Q4  H10  C16  C17  110.51  3.000
 1Q4  H9   C16  C17  109.37  3.000
 1Q4  H10  C16  C15  109.61  3.000
 1Q4  H9   C16  C15  109.30  3.000
 1Q4  C17  C16  C15  111.46  3.000
 1Q4  H12  C17  H11  106.60  3.000
 1Q4  H12  C17  C18  109.23  3.000
 1Q4  H11  C17  C18  110.34  3.000
 1Q4  H12  C17  C16  109.27  3.000
 1Q4  H11  C17  C16  110.22  3.000
 1Q4  C18  C17  C16  111.07  3.000
 1Q4  H14  C18  H13  106.49  3.000
 1Q4  H14  C18  C19  109.90  3.000
 1Q4  H13  C18  C19  109.24  3.000
 1Q4  H14  C18  C17  110.45  3.000
 1Q4  H13  C18  C17  109.36  3.000
 1Q4  C19  C18  C17  111.28  3.000
 1Q4  H16  C19  H15  107.01  3.000
 1Q4  H16  C19  C18  110.45  3.000
 1Q4  H15  C19  C18  109.78  3.000
 1Q4  H16  C19  C14  109.74  3.000
 1Q4  H15  C19  C14  108.83  3.000
 1Q4  C18  C19  C14  110.93  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
 1Q4  CONST_01  N10  C11  N12  C7     0.00   0.0  0
 1Q4  CONST_02  N10  C9   C8   C7     0.00   0.0  0
 1Q4  CONST_03  C11  N12  C7   C8     0.00   0.0  0
 1Q4  CONST_04  C11  N10  C9   C8     0.00   0.0  0
 1Q4  CONST_05  N12  C11  N10  C9     0.00   0.0  0
 1Q4  CONST_06  N12  C7   C8   C9     0.00   0.0  0
 1Q4  CONST_07  C7   C5   N3   C2     0.00   0.0  0
 1Q4  CONST_08  N13  C9   C8   C1     0.00   0.0  0
 1Q4  CONST_09  N13  C9   C8   C7   180.00   0.0  0
 1Q4  CONST_10  N13  C9   N10  C11  180.00   0.0  0
 1Q4  CONST_11  C14  N13  C9   C8   180.00   0.0  0
 1Q4  CONST_12  C14  N13  C9   N10    0.00   0.0  0
 1Q4  CONST_13  O6   C5   N3   C2   180.00   0.0  0
 1Q4  CONST_14  H4   C11  N12  C7   180.00   0.0  0
 1Q4  CONST_15  H2   N3   C5   C7   180.00   0.0  0
 1Q4  CONST_16  H5   N13  C9   C8     0.00   0.0  0
 1Q4  Var_01    C17  C18  C19  C14   55.84  30.0  1
 1Q4  Var_02    C17  C16  C15  C14  -55.74  30.0  1
 1Q4  Var_03    C18  C17  C16  C15   55.35  30.0  1
 1Q4  Var_04    C19  C18  C17  C16  -55.37  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 1Q4  chir_01  C14  C19  N13  C15  negativ

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
 1Q4  plan-1  C1   0.020
 1Q4  plan-1  C2   0.020
 1Q4  plan-1  N3   0.020
 1Q4  plan-1  C5   0.020
 1Q4  plan-1  O6   0.020
 1Q4  plan-1  C7   0.020
 1Q4  plan-1  C8   0.020
 1Q4  plan-1  C9   0.020
 1Q4  plan-1  N10  0.020
 1Q4  plan-1  C11  0.020
 1Q4  plan-1  N12  0.020
 1Q4  plan-1  N13  0.020
 1Q4  plan-1  H1   0.020
 1Q4  plan-1  H3   0.020
 1Q4  plan-1  H4   0.020
 1Q4  plan-1  H2   0.020
 1Q4  plan-2  C9   0.020
 1Q4  plan-2  N13  0.020
 1Q4  plan-2  C14  0.020
 1Q4  plan-2  H5   0.020

