# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:57:09 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2-[(1-benzyl-1H-pyrazol-4-yl)oxy]pyrido[3,4-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=Nc2cnccc12)Oc3cnn(Cc4ccccc4)c3
#
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
 GZA  GZA  2-[(1-benzyl-1H-pyrazol-4-yl)oxy]pyrido[3,4-d]pyrimidin-4(3H)-one  ligand  37  24  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GZA
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
 GZA  C01   C  CH2   0  -0.415  -3.4266  -0.0457  -1.4302
 GZA  C02   C  CR6   0   0.131  -4.6600  -0.1223  -0.5698
 GZA  C03   C  CR16  0  -0.284  -5.3347   1.0392  -0.2025
 GZA  C04   C  CR16  0  -0.242  -6.4586   0.9723   0.6082
 GZA  C05   C  CR16  0  -0.262  -6.9196  -0.2581   1.0611
 GZA  C06   C  CR16  0  -0.242  -6.2526  -1.4198   0.6980
 GZA  C07   C  CR16  0  -0.300  -5.1272  -1.3502  -0.1136
 GZA  N08   N  NR5   0  -0.254  -2.2533   0.3327  -0.6655
 GZA  C09   C  CR15  0   0.026  -1.3893  -0.4960  -0.0532
 GZA  C10   C  CR5   0   0.048  -0.5324   0.3221   0.6390
 GZA  C11   C  CR15  0  -0.067  -0.9602   1.6301   0.3890
 GZA  N12   N  N     0  -0.270  -2.0145   1.6121  -0.4048
 GZA  O13   O  O2    0  -0.484   0.5010  -0.0820   1.4439
 GZA  C14   C  CR6   0   0.710   1.7382  -0.0073   0.9600
 GZA  N15   N  NR16  0  -0.718   2.6608  -0.4082   1.8747
 GZA  C16   C  CR6   0   0.572   4.0180  -0.4216   1.6278
 GZA  C17   C  CR66  0  -0.037   4.3553   0.0406   0.2803
 GZA  C18   C  CR16  0  -0.340   5.6731   0.1080  -0.1669
 GZA  C19   C  CR16  0  -0.075   5.9054   0.5542  -1.4494
 GZA  N20   N  N     0  -0.381   4.9243   0.9228  -2.2818
 GZA  C21   C  CR16  0  -0.115   3.6807   0.8607  -1.8633
 GZA  C22   C  CR66  0   0.189   3.3221   0.4247  -0.5768
 GZA  N23   N  N     0  -0.491   1.9984   0.3959  -0.2217
 GZA  O24   O  O     0  -0.427   4.8139  -0.7858   2.4668
 GZA  H01   H  HCH2  0   0.289  -3.2202  -1.0069  -1.8994
 GZA  H01A  H  HCH2  0   0.292  -3.5459   0.6912  -2.2232
 GZA  H03   H  HCR6  0   0.255  -4.9804   2.0009  -0.5532
 GZA  H04   H  HCR6  0   0.258  -6.9785   1.8812   0.8824
 GZA  H05   H  HCR6  0   0.259  -7.7979  -0.3102   1.6913
 GZA  H06   H  HCR6  0   0.259  -6.6095  -2.3823   1.0408
 GZA  H07   H  HCR6  0   0.256  -4.6132  -2.2612  -0.3971
 GZA  H09   H  HCR5  0   0.309  -1.4364  -1.5685  -0.1499
 GZA  H11   H  HCR5  0   0.280  -0.5400   2.5592   0.7422
 GZA  HN15  H  HNR6  0   0.439   2.3465  -0.7162   2.7883
 GZA  H18   H  HCR6  0   0.284   6.4949  -0.1806   0.4739
 GZA  H19   H  HCR6  0   0.273   6.9162   0.6229  -1.8319
 GZA  H21   H  HCR6  0   0.276   2.8984   1.1639  -2.5516

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
 GZA  C01  C02   single    1.506  0.020  1.506
 GZA  C01  N08   single    1.451  0.020  1.451
 GZA  C02  C03   aromatic  1.393  0.020  1.393
 GZA  C02  C07   aromatic  1.391  0.020  1.391
 GZA  C03  C04   aromatic  1.387  0.020  1.387
 GZA  C04  C05   aromatic  1.390  0.020  1.390
 GZA  C05  C06   aromatic  1.388  0.020  1.388
 GZA  C06  C07   aromatic  1.389  0.020  1.389
 GZA  N08  C09   aromatic  1.345  0.020  1.345
 GZA  N08  N12   aromatic  1.327  0.020  1.327
 GZA  C09  C10   aromatic  1.372  0.020  1.372
 GZA  C10  C11   aromatic  1.399  0.020  1.399
 GZA  C10  O13   single    1.371  0.020  1.371
 GZA  C11  N12   aromatic  1.320  0.020  1.320
 GZA  O13  C14   single    1.331  0.020  1.331
 GZA  C14  N15   single    1.360  0.020  1.360
 GZA  C14  N23   double    1.275  0.020  1.275
 GZA  N15  C16   single    1.380  0.020  1.380
 GZA  C16  C17   single    1.464  0.020  1.464
 GZA  C16  O24   double    1.212  0.020  1.212
 GZA  C17  C18   aromatic  1.393  0.020  1.393
 GZA  C17  C22   aromatic  1.396  0.020  1.396
 GZA  C18  C19   aromatic  1.378  0.020  1.378
 GZA  C19  N20   aromatic  1.338  0.020  1.338
 GZA  N20  C21   aromatic  1.314  0.020  1.314
 GZA  C21  C22   aromatic  1.405  0.020  1.405
 GZA  C22  N23   single    1.371  0.020  1.371
 GZA  C01  H01   single    0.970  0.020  1.090
 GZA  C01  H01A  single    0.970  0.020  1.090
 GZA  C03  H03   single    0.930  0.020  1.080
 GZA  C04  H04   single    0.930  0.020  1.080
 GZA  C05  H05   single    0.930  0.020  1.080
 GZA  C06  H06   single    0.930  0.020  1.080
 GZA  C07  H07   single    0.930  0.020  1.080
 GZA  C09  H09   single    0.930  0.020  1.080
 GZA  C11  H11   single    0.930  0.020  1.080
 GZA  N15  HN15  single    0.860  0.020  1.020
 GZA  C18  H18   single    0.930  0.020  1.080
 GZA  C19  H19   single    0.930  0.020  1.080
 GZA  C21  H21   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
 GZA  H01A  C01  H01  107.70  3.000
 GZA  H01A  C01  N08  107.21  3.000
 GZA  H01   C01  N08  107.70  3.000
 GZA  H01A  C01  C02  111.15  3.000
 GZA  H01   C01  C02  110.88  3.000
 GZA  N08   C01  C02  111.99  3.000
 GZA  C07   C02  C03  119.15  3.000
 GZA  C07   C02  C01  120.50  3.000
 GZA  C03   C02  C01  120.34  3.000
 GZA  H03   C03  C04  119.79  3.000
 GZA  H03   C03  C02  119.78  3.000
 GZA  C04   C03  C02  120.43  3.000
 GZA  H04   C04  C05  120.10  3.000
 GZA  H04   C04  C03  119.78  3.000
 GZA  C05   C04  C03  120.12  3.000
 GZA  H05   C05  C06  120.14  3.000
 GZA  H05   C05  C04  120.10  3.000
 GZA  C06   C05  C04  119.76  3.000
 GZA  H06   C06  C07  119.79  3.000
 GZA  H06   C06  C05  120.20  3.000
 GZA  C07   C06  C05  120.01  3.000
 GZA  H07   C07  C06  119.66  3.000
 GZA  H07   C07  C02  119.80  3.000
 GZA  C06   C07  C02  120.54  3.000
 GZA  N12   N08  C09  112.89  3.000
 GZA  N12   N08  C01  120.03  3.000
 GZA  C09   N08  C01  126.79  3.000
 GZA  H09   C09  C10  131.74  3.000
 GZA  H09   C09  N08  122.98  3.000
 GZA  C10   C09  N08  105.28  3.000
 GZA  O13   C10  C11  127.67  3.000
 GZA  O13   C10  C09  126.25  3.000
 GZA  C11   C10  C09  106.04  3.000
 GZA  H11   C11  N12  121.31  3.000
 GZA  H11   C11  C10  128.87  3.000
 GZA  N12   C11  C10  109.82  3.000
 GZA  C11   N12  N08  105.96  3.000
 GZA  C14   O13  C10  118.09  3.000
 GZA  N23   C14  N15  125.32  3.000
 GZA  N23   C14  O13  122.98  3.000
 GZA  N15   C14  O13  111.70  3.000
 GZA  HN15  N15  C16  117.59  3.000
 GZA  HN15  N15  C14  119.04  3.000
 GZA  C16   N15  C14  123.37  3.000
 GZA  O24   C16  C17  125.49  3.000
 GZA  O24   C16  N15  121.66  3.000
 GZA  C17   C16  N15  112.85  3.000
 GZA  C22   C17  C18  119.31  3.000
 GZA  C22   C17  C16  118.77  3.000
 GZA  C18   C17  C16  121.92  3.000
 GZA  H18   C18  C19  120.66  3.000
 GZA  H18   C18  C17  121.04  3.000
 GZA  C19   C18  C17  118.30  3.000
 GZA  H19   C19  N20  116.56  3.000
 GZA  H19   C19  C18  120.45  3.000
 GZA  N20   C19  C18  122.99  3.000
 GZA  C21   N20  C19  118.87  3.000
 GZA  H21   C21  C22  118.91  3.000
 GZA  H21   C21  N20  117.85  3.000
 GZA  C22   C21  N20  123.24  3.000
 GZA  N23   C22  C21  119.36  3.000
 GZA  N23   C22  C17  123.35  3.000
 GZA  C21   C22  C17  117.29  3.000
 GZA  C22   N23  C14  116.34  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
 GZA  CONST_01  C05   C04  C03  C02    0.00   0.0  0
 GZA  CONST_02  C05   C06  C07  C02    0.00   0.0  0
 GZA  CONST_03  C06   C07  C02  C03    0.00   0.0  0
 GZA  CONST_04  C06   C05  C04  C03    0.00   0.0  0
 GZA  CONST_05  C07   C02  C03  C04    0.00   0.0  0
 GZA  CONST_06  C07   C06  C05  C04    0.00   0.0  0
 GZA  CONST_07  C11   C10  C09  N08    0.00   0.0  0
 GZA  CONST_08  C10   C11  N12  N08    0.00   0.0  0
 GZA  CONST_09  C11   N12  N08  C09    0.00   0.0  0
 GZA  CONST_10  N12   C11  C10  C09    0.00   0.0  0
 GZA  CONST_11  N12   N08  C09  C10    0.00   0.0  0
 GZA  CONST_12  N20   C19  C18  C17    0.00   0.0  0
 GZA  CONST_13  N20   C21  C22  C17    0.00   0.0  0
 GZA  CONST_14  C21   C22  C17  C18    0.00   0.0  0
 GZA  CONST_15  C21   N20  C19  C18    0.00   0.0  0
 GZA  CONST_16  C22   C17  C18  C19    0.00   0.0  0
 GZA  CONST_17  C22   C21  N20  C19    0.00   0.0  0
 GZA  CONST_18  C17   C16  N15  C14    0.00   0.0  0
 GZA  CONST_19  C22   N23  C14  N15    0.00   0.0  0
 GZA  CONST_20  N23   C14  N15  C16    0.00   0.0  0
 GZA  CONST_21  C04   C03  C02  C01  180.00   0.0  0
 GZA  CONST_22  C06   C07  C02  C01  180.00   0.0  0
 GZA  CONST_23  C10   C09  N08  C01  180.00   0.0  0
 GZA  CONST_24  C11   N12  N08  C01  180.00   0.0  0
 GZA  CONST_25  O13   C10  C09  N08  180.00   0.0  0
 GZA  CONST_26  O13   C10  C11  N12  180.00   0.0  0
 GZA  CONST_27  C16   N15  C14  O13  180.00   0.0  0
 GZA  CONST_28  C22   N23  C14  O13  180.00   0.0  0
 GZA  CONST_29  O24   C16  N15  C14  180.00   0.0  0
 GZA  CONST_30  H04   C04  C03  C02  180.00   0.0  0
 GZA  CONST_31  H06   C06  C07  C02  180.00   0.0  0
 GZA  CONST_32  H07   C07  C02  C03  180.00   0.0  0
 GZA  CONST_33  H05   C05  C04  C03  180.00   0.0  0
 GZA  CONST_34  H03   C03  C04  C05  180.00   0.0  0
 GZA  CONST_35  H11   C11  N12  N08  180.00   0.0  0
 GZA  CONST_36  H09   C09  C10  C11  180.00   0.0  0
 GZA  CONST_37  H18   C18  C17  C16    0.00   0.0  0
 GZA  CONST_38  H19   C19  C18  C17  180.00   0.0  0
 GZA  CONST_39  H21   C21  C22  C17  180.00   0.0  0
 GZA  CONST_40  HN15  N15  C16  C17  180.00   0.0  0
 GZA  Var_01    C09   N08  C01  C02   90.81  30.0  2
 GZA  Var_02    N08   C01  C02  C03   78.91  30.0  2
 GZA  Var_03    N15   C14  O13  C10  178.50  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
 GZA  plan-1  C01   0.020
 GZA  plan-1  N08   0.020
 GZA  plan-1  C09   0.020
 GZA  plan-1  C10   0.020
 GZA  plan-1  C11   0.020
 GZA  plan-1  N12   0.020
 GZA  plan-1  O13   0.020
 GZA  plan-1  H09   0.020
 GZA  plan-1  H11   0.020
 GZA  plan-2  C01   0.020
 GZA  plan-2  C02   0.020
 GZA  plan-2  C03   0.020
 GZA  plan-2  C04   0.020
 GZA  plan-2  C05   0.020
 GZA  plan-2  C06   0.020
 GZA  plan-2  C07   0.020
 GZA  plan-2  H03   0.020
 GZA  plan-2  H04   0.020
 GZA  plan-2  H05   0.020
 GZA  plan-2  H06   0.020
 GZA  plan-2  H07   0.020
 GZA  plan-3  O13   0.020
 GZA  plan-3  C14   0.020
 GZA  plan-3  N15   0.020
 GZA  plan-3  C16   0.020
 GZA  plan-3  C17   0.020
 GZA  plan-3  C18   0.020
 GZA  plan-3  C19   0.020
 GZA  plan-3  N20   0.020
 GZA  plan-3  C21   0.020
 GZA  plan-3  C22   0.020
 GZA  plan-3  N23   0.020
 GZA  plan-3  O24   0.020
 GZA  plan-3  HN15  0.020
 GZA  plan-3  H18   0.020
 GZA  plan-3  H19   0.020
 GZA  plan-3  H21   0.020

