# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 14:33:48 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 2-(1H-pyrazol-4-yloxy)-3H-pyrido[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=Nc2cnccc12)Oc3c[nH]nc3
#
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
 HA6  HA6  2-(1H-pyrazol-4-yloxy)-3H-pyrido[3,4-d]pyrimidin-4-one  ligand  24  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HA6
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
 HA6  C1    C  CR66  0  -0.103  -2.2422  -0.2435  -0.0067
 HA6  N1    N  N     0  -0.437  -2.8238   2.3522   0.7591
 HA6  O1    O  O2    0  -0.455   1.6195  -1.2720  -0.5036
 HA6  C01   C  CR6   0   0.566  -1.8994  -1.6081  -0.4090
 HA6  N01   N  NR16  0  -0.698  -0.5403  -1.8044  -0.5347
 HA6  O01   O  O     0  -0.401  -2.6920  -2.5004  -0.6207
 HA6  C02   C  CR6   0   0.777   0.3803  -0.8289  -0.3118
 HA6  N02   N  NR15  0  -0.383   4.3714   0.6772   0.3812
 HA6  C03   C  CR5   0   0.153   2.6561  -0.3860  -0.3628
 HA6  N03   N  N     0  -0.211   4.1896   1.1581  -0.8413
 HA6  C04   C  CR15  0  -0.139   3.4753  -0.2584   0.7304
 HA6  N04   N  N     0  -0.615   0.1153   0.3686   0.0393
 HA6  C05   C  CR15  0  -0.185   3.1381   0.5179  -1.3172
 HA6  C06   C  CR66  0   0.334  -1.2114   0.6761   0.1980
 HA6  C07   C  CR16  0  -0.127  -1.5771   1.9761   0.5859
 HA6  C08   C  CR16  0  -0.103  -3.8020   1.4609   0.5584
 HA6  C09   C  CR16  0  -0.340  -3.5631   0.1591   0.1770
 HA6  HN01  H  HNR6  0   0.447  -0.2261  -2.7283  -0.8102
 HA6  H04   H  HCR5  0   0.304   3.4828  -0.7520   1.6879
 HA6  H05   H  HCR5  0   0.347   2.7625   0.7170  -2.3091
 HA6  H07   H  HCR6  0   0.283  -0.7976   2.7120   0.7537
 HA6  H08   H  HCR6  0   0.288  -4.8150   1.8112   0.7119
 HA6  H09   H  HCR6  0   0.263  -4.3817  -0.5309   0.0253
 HA6  HN02  H  HNR5  0   0.437   5.1326   1.0195   0.9457

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
 HA6  C1   C01   single    1.463  0.020  1.463
 HA6  C1   C06   aromatic  1.396  0.020  1.396
 HA6  C1   C09   aromatic  1.393  0.020  1.393
 HA6  N1   C07   aromatic  1.314  0.020  1.314
 HA6  N1   C08   aromatic  1.338  0.020  1.338
 HA6  O1   C02   single    1.330  0.020  1.330
 HA6  O1   C03   single    1.371  0.020  1.371
 HA6  C01  N01   single    1.379  0.020  1.379
 HA6  C01  O01   double    1.212  0.020  1.212
 HA6  N01  C02   single    1.360  0.020  1.360
 HA6  C02  N04   double    1.276  0.020  1.276
 HA6  N02  N03   aromatic  1.326  0.020  1.326
 HA6  N02  C04   aromatic  1.342  0.020  1.342
 HA6  C03  C04   aromatic  1.372  0.020  1.372
 HA6  C03  C05   aromatic  1.400  0.020  1.400
 HA6  N03  C05   aromatic  1.320  0.020  1.320
 HA6  N04  C06   single    1.371  0.020  1.371
 HA6  C06  C07   aromatic  1.405  0.020  1.405
 HA6  C08  C09   aromatic  1.377  0.020  1.377
 HA6  N01  HN01  single    0.860  0.020  1.020
 HA6  N02  HN02  single    0.860  0.020  1.020
 HA6  C04  H04   single    0.930  0.020  1.080
 HA6  C05  H05   single    0.930  0.020  1.080
 HA6  C07  H07   single    0.930  0.020  1.080
 HA6  C08  H08   single    0.930  0.020  1.080
 HA6  C09  H09   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
 HA6  C09   C1   C06  119.36  3.000
 HA6  C09   C1   C01  121.86  3.000
 HA6  C06   C1   C01  118.78  3.000
 HA6  C08   N1   C07  118.89  3.000
 HA6  C03   O1   C02  118.32  3.000
 HA6  O01   C01  N01  121.58  3.000
 HA6  O01   C01  C1   125.54  3.000
 HA6  N01   C01  C1   112.87  3.000
 HA6  HN01  N01  C02  119.24  3.000
 HA6  HN01  N01  C01  117.38  3.000
 HA6  C02   N01  C01  123.38  3.000
 HA6  N04   C02  N01  125.31  3.000
 HA6  N04   C02  O1   123.09  3.000
 HA6  N01   C02  O1   111.61  3.000
 HA6  HN02  N02  C04  126.55  3.000
 HA6  HN02  N02  N03  119.79  3.000
 HA6  C04   N02  N03  113.66  3.000
 HA6  C05   C03  C04  106.11  3.000
 HA6  C05   C03  O1   127.41  3.000
 HA6  C04   C03  O1   126.40  3.000
 HA6  C05   N03  N02  105.41  3.000
 HA6  H04   C04  C03  132.05  3.000
 HA6  H04   C04  N02  123.11  3.000
 HA6  C03   C04  N02  104.84  3.000
 HA6  C06   N04  C02  116.32  3.000
 HA6  H05   C05  N03  121.28  3.000
 HA6  H05   C05  C03  128.74  3.000
 HA6  N03   C05  C03  109.97  3.000
 HA6  C07   C06  N04  119.43  3.000
 HA6  C07   C06  C1   117.23  3.000
 HA6  N04   C06  C1   123.34  3.000
 HA6  H07   C07  C06  118.90  3.000
 HA6  H07   C07  N1   117.85  3.000
 HA6  C06   C07  N1   123.25  3.000
 HA6  H08   C08  C09  120.48  3.000
 HA6  H08   C08  N1   116.55  3.000
 HA6  C09   C08  N1   122.97  3.000
 HA6  H09   C09  C08  120.70  3.000
 HA6  H09   C09  C1   121.00  3.000
 HA6  C08   C09  C1   118.30  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
 HA6  CONST_01  N1    C07  C06  C1     0.00   0.0  0
 HA6  CONST_02  N1    C08  C09  C1     0.00   0.0  0
 HA6  CONST_03  C03   C05  N03  N02    0.00   0.0  0
 HA6  CONST_04  C05   C03  C04  N02    0.00   0.0  0
 HA6  CONST_05  N03   N02  C04  C03    0.00   0.0  0
 HA6  CONST_06  C04   C03  C05  N03    0.00   0.0  0
 HA6  CONST_07  C05   N03  N02  C04    0.00   0.0  0
 HA6  CONST_08  C08   C09  C1   C06    0.00   0.0  0
 HA6  CONST_09  C08   N1   C07  C06    0.00   0.0  0
 HA6  CONST_10  C09   C08  N1   C07    0.00   0.0  0
 HA6  CONST_11  C09   C1   C06  C07    0.00   0.0  0
 HA6  CONST_12  C02   N01  C01  C1     0.00   0.0  0
 HA6  CONST_13  N04   C02  N01  C01    0.00   0.0  0
 HA6  CONST_14  C06   N04  C02  N01    0.00   0.0  0
 HA6  CONST_15  N02   C04  C03  O1   180.00   0.0  0
 HA6  CONST_16  N03   C05  C03  O1   180.00   0.0  0
 HA6  CONST_17  C01   N01  C02  O1   180.00   0.0  0
 HA6  CONST_18  C06   N04  C02  O1   180.00   0.0  0
 HA6  CONST_19  C02   N01  C01  O01  180.00   0.0  0
 HA6  CONST_20  H07   C07  C06  C1   180.00   0.0  0
 HA6  CONST_21  H08   C08  C09  C1   180.00   0.0  0
 HA6  CONST_22  H09   C09  C08  N1   180.00   0.0  0
 HA6  CONST_23  H05   C05  N03  N02  180.00   0.0  0
 HA6  CONST_24  HN02  N02  C04  C03  180.00   0.0  0
 HA6  CONST_25  H04   C04  N02  N03  180.00   0.0  0
 HA6  CONST_26  HN01  N01  C01  C1   180.00   0.0  0
 HA6  Var_01    C04   C03  O1   C02  100.48  30.0  2
 HA6  Var_02    N04   C02  O1   C03   -2.38  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
 HA6  plan-1  O1    0.020
 HA6  plan-1  N02   0.020
 HA6  plan-1  C03   0.020
 HA6  plan-1  N03   0.020
 HA6  plan-1  C04   0.020
 HA6  plan-1  C05   0.020
 HA6  plan-1  H04   0.020
 HA6  plan-1  H05   0.020
 HA6  plan-1  HN02  0.020
 HA6  plan-2  C1    0.020
 HA6  plan-2  N1    0.020
 HA6  plan-2  O1    0.020
 HA6  plan-2  C01   0.020
 HA6  plan-2  N01   0.020
 HA6  plan-2  O01   0.020
 HA6  plan-2  C02   0.020
 HA6  plan-2  N04   0.020
 HA6  plan-2  C06   0.020
 HA6  plan-2  C07   0.020
 HA6  plan-2  C08   0.020
 HA6  plan-2  C09   0.020
 HA6  plan-2  HN01  0.020
 HA6  plan-2  H07   0.020
 HA6  plan-2  H08   0.020
 HA6  plan-2  H09   0.020

