# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 04:22:28 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 3,4-dimethoxy-N-(5-phenyl-1H-pyrazol-3-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC)C(=O)Nc2cc([nH]n2)c3ccccc3
#
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
 4Y0  4Y0  3,4-dimethoxy-N-(5-phenyl-1H-pyrazol-3-yl)benzamide  ligand  41  24  .  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_4Y0
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
 4Y0  N1    N  NR15  0  -0.511  -3.2838   1.6296   0.7976
 4Y0  C2    C  CR15  0  -0.550  -2.3270  -0.1502  -0.0204
 4Y0  C3    C  CR5   0   0.471  -1.3917   0.8091   0.4069
 4Y0  C4    C  CR5   0   0.439  -3.5525   0.4291   0.2546
 4Y0  N5    N  N     0  -0.307  -1.9822   1.8804   0.9046
 4Y0  N6    N  NH1   0  -0.746  -0.0053   0.8004   0.3617
 4Y0  C7    C  C     0   0.531   0.7748  -0.2442  -0.0114
 4Y0  C9    C  CR6   0  -0.048   2.2373   0.0256  -0.0420
 4Y0  C10   C  CR16  0  -0.411   3.0993  -1.0736   0.0630
 4Y0  C11   C  CR6   0   0.336   4.4683  -0.9066   0.0166
 4Y0  C12   C  CR6   0   0.322   5.0082   0.3873  -0.1642
 4Y0  C13   C  CR6   0   0.072  -4.9070  -0.0669   0.0287
 4Y0  C15   C  CR16  0  -0.308   2.7725   1.2903  -0.2199
 4Y0  C16   C  CR16  0  -0.373   4.1512   1.4692  -0.2830
 4Y0  O17   O  O2    0  -0.463   5.3701  -1.8967   0.1257
 4Y0  O18   O  O2    0  -0.455   6.3442   0.4542  -0.2108
 4Y0  C19   C  CR16  0  -0.302  -5.9891   0.8070  -0.0912
 4Y0  C20   C  CR16  0  -0.317  -5.1351  -1.4397  -0.0788
 4Y0  C21   C  CH3   0  -0.440   4.8942  -3.2108   0.3391
 4Y0  C22   C  CR16  0  -0.237  -6.4139  -1.9258  -0.3001
 4Y0  C23   C  CR16  0  -0.239  -7.2688   0.3172  -0.3045
 4Y0  O2    O  O     0  -0.467   0.3170  -1.3377  -0.3015
 4Y0  C     C  CH3   0  -0.441   6.9482   1.7206  -0.3953
 4Y0  C24   C  CR16  0  -0.261  -7.4866  -1.0499  -0.4112
 4Y0  H1    H  HNR5  0   0.424  -3.9421   2.3002   1.1611
 4Y0  H2    H  HCR5  0   0.277  -2.1469  -1.1042  -0.4797
 4Y0  H6    H  HNH1  0   0.415   0.4352   1.6388   0.7085
 4Y0  H10   H  HCR6  0   0.285   2.6728  -2.0591   0.1906
 4Y0  H15   H  HCR6  0   0.261   2.1432   2.1615  -0.3476
 4Y0  H16   H  HCR6  0   0.290   4.5384   2.4669  -0.4363
 4Y0  H19   H  HCR6  0   0.255  -5.8402   1.8785  -0.0385
 4Y0  H20   H  HCR6  0   0.258  -4.3105  -2.1339   0.0218
 4Y0  H211  H  HCH3  0   0.230   4.3110  -3.2863   1.2606
 4Y0  H212  H  HCH3  0   0.230   4.2824  -3.5642  -0.4952
 4Y0  H213  H  HCH3  0   0.263   5.7717  -3.8464   0.4254
 4Y0  HC1   H  HCH3  0   0.263   8.0213   1.5494  -0.4154
 4Y0  HC2   H  HCH3  0   0.233   6.6456   2.1814  -1.3389
 4Y0  HC3   H  HCH3  0   0.233   6.7145   2.4058   0.4234
 4Y0  H23   H  HCR6  0   0.263  -8.0956   1.0089  -0.3968
 4Y0  H22   H  HCR6  0   0.262  -6.5736  -2.9932  -0.3787
 4Y0  H24   H  HCR6  0   0.262  -8.4850  -1.4301  -0.5823

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
 4Y0  N1   C4    aromatic  1.345  0.020  1.345
 4Y0  N1   N5    aromatic  1.330  0.020  1.330
 4Y0  C2   C3    aromatic  1.406  0.020  1.406
 4Y0  C2   C4    aromatic  1.383  0.020  1.383
 4Y0  C3   N5    aromatic  1.321  0.020  1.321
 4Y0  C3   N6    single    1.387  0.020  1.387
 4Y0  C4   C13   single    1.460  0.020  1.460
 4Y0  N6   C7    single    1.356  0.020  1.356
 4Y0  C7   C9    single    1.488  0.020  1.488
 4Y0  C7   O2    double    1.220  0.020  1.220
 4Y0  C9   C10   aromatic  1.401  0.020  1.401
 4Y0  C9   C15   aromatic  1.385  0.020  1.385
 4Y0  C10  C11   aromatic  1.380  0.020  1.380
 4Y0  C11  C12   aromatic  1.414  0.020  1.414
 4Y0  C11  O17   single    1.344  0.020  1.344
 4Y0  C12  C16   aromatic  1.385  0.020  1.385
 4Y0  C12  O18   single    1.339  0.020  1.339
 4Y0  C13  C19   aromatic  1.396  0.020  1.396
 4Y0  C13  C20   aromatic  1.396  0.020  1.396
 4Y0  C15  C16   aromatic  1.392  0.020  1.392
 4Y0  O17  C21   single    1.414  0.020  1.414
 4Y0  O18  C     single    1.415  0.020  1.415
 4Y0  C19  C23   aromatic  1.387  0.020  1.387
 4Y0  C20  C22   aromatic  1.386  0.020  1.386
 4Y0  C22  C24   aromatic  1.389  0.020  1.389
 4Y0  C23  C24   aromatic  1.388  0.020  1.388
 4Y0  N1   H1    single    0.860  0.020  1.020
 4Y0  C2   H2    single    0.930  0.020  1.080
 4Y0  N6   H6    single    0.860  0.020  1.020
 4Y0  C10  H10   single    0.930  0.020  1.080
 4Y0  C15  H15   single    0.930  0.020  1.080
 4Y0  C16  H16   single    0.930  0.020  1.080
 4Y0  C19  H19   single    0.930  0.020  1.080
 4Y0  C20  H20   single    0.930  0.020  1.080
 4Y0  C21  H211  single    0.970  0.020  1.090
 4Y0  C21  H212  single    0.970  0.020  1.090
 4Y0  C21  H213  single    0.970  0.020  1.090
 4Y0  C    HC1   single    0.970  0.020  1.090
 4Y0  C    HC2   single    0.970  0.020  1.090
 4Y0  C    HC3   single    0.970  0.020  1.090
 4Y0  C23  H23   single    0.930  0.020  1.080
 4Y0  C22  H22   single    0.930  0.020  1.080
 4Y0  C24  H24   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
 4Y0  H1    N1   N5    119.00  3.000
 4Y0  H1    N1   C4    127.54  3.000
 4Y0  N5    N1   C4    113.36  3.000
 4Y0  H2    C2   C4    127.28  3.000
 4Y0  H2    C2   C3    128.63  3.000
 4Y0  C4    C2   C3    104.07  3.000
 4Y0  N6    C3   N5    117.66  3.000
 4Y0  N6    C3   C2    130.59  3.000
 4Y0  N5    C3   C2    111.75  3.000
 4Y0  C13   C4   C2    130.46  3.000
 4Y0  C13   C4   N1    123.45  3.000
 4Y0  C2    C4   N1    106.09  3.000
 4Y0  C3    N5   N1    104.73  3.000
 4Y0  H6    N6   C7    118.92  3.000
 4Y0  H6    N6   C3    114.85  3.000
 4Y0  C7    N6   C3    126.06  3.000
 4Y0  O2    C7   C9    121.76  3.000
 4Y0  O2    C7   N6    122.67  3.000
 4Y0  C9    C7   N6    115.56  3.000
 4Y0  C15   C9   C10   119.24  3.000
 4Y0  C15   C9   C7    123.25  3.000
 4Y0  C10   C9   C7    117.46  3.000
 4Y0  H10   C10  C11   120.36  3.000
 4Y0  H10   C10  C9    118.77  3.000
 4Y0  C11   C10  C9    120.86  3.000
 4Y0  O17   C11  C12   115.37  3.000
 4Y0  O17   C11  C10   125.03  3.000
 4Y0  C12   C11  C10   119.60  3.000
 4Y0  O18   C12  C16   125.14  3.000
 4Y0  O18   C12  C11   115.55  3.000
 4Y0  C16   C12  C11   119.31  3.000
 4Y0  C20   C13  C19   118.85  3.000
 4Y0  C20   C13  C4    119.84  3.000
 4Y0  C19   C13  C4    121.31  3.000
 4Y0  H15   C15  C16   117.86  3.000
 4Y0  H15   C15  C9    121.71  3.000
 4Y0  C16   C15  C9    120.40  3.000
 4Y0  H16   C16  C15   118.68  3.000
 4Y0  H16   C16  C12   120.75  3.000
 4Y0  C15   C16  C12   120.57  3.000
 4Y0  C21   O17  C11   118.11  3.000
 4Y0  C     O18  C12   118.37  3.000
 4Y0  H19   C19  C23   118.93  3.000
 4Y0  H19   C19  C13   120.57  3.000
 4Y0  C23   C19  C13   120.49  3.000
 4Y0  H20   C20  C22   119.52  3.000
 4Y0  H20   C20  C13   119.94  3.000
 4Y0  C22   C20  C13   120.53  3.000
 4Y0  H213  C21  H212  108.87  3.000
 4Y0  H213  C21  H211  108.87  3.000
 4Y0  H212  C21  H211  108.81  3.000
 4Y0  H213  C21  O17   106.48  3.000
 4Y0  H212  C21  O17   111.94  3.000
 4Y0  H211  C21  O17   111.78  3.000
 4Y0  H22   C22  C24   120.14  3.000
 4Y0  H22   C22  C20   119.59  3.000
 4Y0  C24   C22  C20   120.27  3.000
 4Y0  H23   C23  C24   120.20  3.000
 4Y0  H23   C23  C19   119.51  3.000
 4Y0  C24   C23  C19   120.29  3.000
 4Y0  HC3   C    HC2   108.86  3.000
 4Y0  HC3   C    HC1   108.89  3.000
 4Y0  HC2   C    HC1   108.89  3.000
 4Y0  HC3   C    O18   111.85  3.000
 4Y0  HC2   C    O18   111.82  3.000
 4Y0  HC1   C    O18   106.43  3.000
 4Y0  H24   C24  C23   120.20  3.000
 4Y0  H24   C24  C22   120.23  3.000
 4Y0  C23   C24  C22   119.58  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
 4Y0  CONST_01  C3    C2   C4   N1      0.00   0.0  0
 4Y0  CONST_04  C2    C3   N5   N1      0.00   0.0  0
 4Y0  CONST_05  N5    N1   C4   C2      0.00   0.0  0
 4Y0  CONST_08  C13   C4   C2   C3    180.00   0.0  0
 4Y0  CONST_09  C4    N1   N5   C3      0.00   0.0  0
 4Y0  CONST_10  N5    C3   C2   C4      0.00   0.0  0
 4Y0  CONST_11  C23   C19  C13  C4    180.00   0.0  0
 4Y0  CONST_12  C22   C20  C13  C4    180.00   0.0  0
 4Y0  CONST_13  C13   C4   N1   N5    180.00   0.0  0
 4Y0  CONST_14  C12   C11  C10  C9      0.00   0.0  0
 4Y0  CONST_15  C12   C16  C15  C9      0.00   0.0  0
 4Y0  CONST_16  C16   C15  C9   C10     0.00   0.0  0
 4Y0  CONST_17  C16   C12  C11  C10     0.00   0.0  0
 4Y0  CONST_18  C15   C9   C10  C11     0.00   0.0  0
 4Y0  CONST_19  C15   C16  C12  C11     0.00   0.0  0
 4Y0  CONST_20  C24   C23  C19  C13     0.00   0.0  0
 4Y0  CONST_21  C24   C22  C20  C13     0.00   0.0  0
 4Y0  CONST_22  C22   C20  C13  C19     0.00   0.0  0
 4Y0  CONST_23  C22   C24  C23  C19     0.00   0.0  0
 4Y0  CONST_24  C23   C19  C13  C20     0.00   0.0  0
 4Y0  CONST_25  C23   C24  C22  C20     0.00   0.0  0
 4Y0  CONST_26  N6    C3   N5   N1    180.00   0.0  0
 4Y0  CONST_27  N6    C3   C2   C4    180.00   0.0  0
 4Y0  CONST_28  C11   C10  C9   C7    180.00   0.0  0
 4Y0  CONST_29  C16   C15  C9   C7    180.00   0.0  0
 4Y0  CONST_30  O17   C11  C10  C9    180.00   0.0  0
 4Y0  CONST_31  O18   C12  C11  C10   180.00   0.0  0
 4Y0  CONST_32  O18   C12  C16  C15   180.00   0.0  0
 4Y0  CONST_33  O17   C11  C12  C16   180.00   0.0  0
 4Y0  CONST_34  H2    C2   C4   N1    180.00   0.0  0
 4Y0  CONST_35  H1    N1   C4   C2    180.00   0.0  0
 4Y0  CONST_36  H19   C19  C13  C4      0.00   0.0  0
 4Y0  CONST_37  H20   C20  C13  C4      0.00   0.0  0
 4Y0  CONST_38  H16   C16  C15  C9    180.00   0.0  0
 4Y0  CONST_39  H15   C15  C9   C10   180.00   0.0  0
 4Y0  CONST_40  H10   C10  C11  C12   180.00   0.0  0
 4Y0  CONST_41  H23   C23  C19  C13   180.00   0.0  0
 4Y0  CONST_42  H22   C22  C20  C13   180.00   0.0  0
 4Y0  CONST_43  H24   C24  C23  C19   180.00   0.0  0
 4Y0  CONST_44  C9    C7   N6   C3    180.00   0.0  0
 4Y0  CONST_45  C7    N6   C3   C2      0.00   0.0  0
 4Y0  CONST_46  C7    N6   C3   N5    180.00   0.0  0
 4Y0  CONST_47  H6    N6   C3   C2    180.00   0.0  0
 4Y0  CONST_48  O2    C7   N6   C3      0.00   0.0  0
 4Y0  Var_01    C10   C9   C7   N6    157.37  30.0  2
 4Y0  Var_02    H211  C21  O17  C11   -59.67  30.0  3
 4Y0  Var_03    HC1   C    O18  C12  -179.33  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
 4Y0  plan-1  N1   0.020
 4Y0  plan-1  C2   0.020
 4Y0  plan-1  C3   0.020
 4Y0  plan-1  C4   0.020
 4Y0  plan-1  N5   0.020
 4Y0  plan-1  N6   0.020
 4Y0  plan-1  C13  0.020
 4Y0  plan-1  H1   0.020
 4Y0  plan-1  H2   0.020
 4Y0  plan-2  C7   0.020
 4Y0  plan-2  C9   0.020
 4Y0  plan-2  C10  0.020
 4Y0  plan-2  C11  0.020
 4Y0  plan-2  C12  0.020
 4Y0  plan-2  C15  0.020
 4Y0  plan-2  C16  0.020
 4Y0  plan-2  O17  0.020
 4Y0  plan-2  O18  0.020
 4Y0  plan-2  H10  0.020
 4Y0  plan-2  H15  0.020
 4Y0  plan-2  H16  0.020
 4Y0  plan-3  C4   0.020
 4Y0  plan-3  C13  0.020
 4Y0  plan-3  C19  0.020
 4Y0  plan-3  C20  0.020
 4Y0  plan-3  C22  0.020
 4Y0  plan-3  C23  0.020
 4Y0  plan-3  C24  0.020
 4Y0  plan-3  H19  0.020
 4Y0  plan-3  H20  0.020
 4Y0  plan-3  H23  0.020
 4Y0  plan-3  H22  0.020
 4Y0  plan-3  H24  0.020
 4Y0  plan-4  C3   0.020
 4Y0  plan-4  N6   0.020
 4Y0  plan-4  C7   0.020
 4Y0  plan-4  C9   0.020
 4Y0  plan-4  O2   0.020
 4Y0  plan-4  H6   0.020

