# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:51:28 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 2-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}-4-methoxypyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1nc(ncc1C(N)=O)c2ccnc(NC(=O)C3CC3)c2
#
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
 2WG  2WG  2-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}-4-methoxypyrimidine-5-carboxamide  ligand  38  23  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2WG
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
 2WG  C1   C  CH3   0  -0.420   4.3021   2.6839   0.0307
 2WG  O2   O  O2    0  -0.440   4.5392   1.2831  -0.1131
 2WG  C3   C  CR6   0   0.584   3.5071   0.4703  -0.1487
 2WG  C4   C  CR6   0  -0.256   3.7421  -0.9140  -0.2490
 2WG  C5   C  CR16  0  -0.011   2.6094  -1.7013  -0.2575
 2WG  N6   N  N     0  -0.439   1.3754  -1.2111  -0.1783
 2WG  C7   C  CR6   0   0.418   1.2707   0.1021  -0.0811
 2WG  N8   N  N     0  -0.477   2.2875   0.9557  -0.0607
 2WG  C9   C  CR6   0   0.118  -0.0891   0.6792   0.0184
 2WG  C10  C  CR16  0  -0.375  -0.2801   2.0521   0.1757
 2WG  C11  C  CR16  0  -0.053  -1.5764   2.5182   0.2664
 2WG  N12  N  N     0  -0.420  -2.6558   1.7436   0.2075
 2WG  C13  C  CR6   0   0.555  -2.4712   0.4436   0.0622
 2WG  C14  C  CR16  0  -0.454  -1.2031  -0.1386  -0.0360
 2WG  N15  N  NH1   0  -0.751  -3.5666  -0.4080  -0.0188
 2WG  C16  C  C     0   0.587  -4.8880  -0.1527   0.2302
 2WG  O17  O  O     0  -0.454  -5.3220   0.9201   0.5977
 2WG  C18  C  CH1   0  -0.443  -5.7610  -1.3360   0.0070
 2WG  C19  C  CH2   0  -0.463  -7.1532  -1.0857  -0.5147
 2WG  C20  C  CH2   0  -0.464  -6.9664  -1.4965   0.8978
 2WG  C21  C  C     0   0.483   5.1105  -1.4912  -0.4068
 2WG  O22  O  O     0  -0.467   5.9135  -1.0236  -1.1974
 2WG  N23  N  NH2   0  -0.794   5.3505  -2.5643   0.3582
 2WG  H1   H  HCH3  0   0.256   5.2839   3.1476   0.0132
 2WG  H2   H  HCH3  0   0.243   3.6983   3.0723  -0.7886
 2WG  H3   H  HCH3  0   0.242   3.8087   2.9077   0.9760
 2WG  H4   H  HCR6  0   0.289   2.6936  -2.7789  -0.3463
 2WG  H5   H  HCR6  0   0.272   0.5549   2.7349   0.2264
 2WG  H6   H  HCR6  0   0.267  -1.7612   3.5793   0.3886
 2WG  H7   H  HCR6  0   0.280  -1.0940  -1.2088  -0.1490
 2WG  H8   H  HNH1  0   0.422  -3.3405  -1.3622  -0.2533
 2WG  H9   H  HCH1  0   0.285  -5.2774  -2.2480  -0.3231
 2WG  H10  H  HCH2  0   0.260  -7.4267  -0.0587  -0.7174
 2WG  H11  H  HCH2  0   0.266  -7.5432  -1.8085  -1.2188
 2WG  H12  H  HCH2  0   0.266  -7.2259  -2.5071   1.1825
 2WG  H13  H  HCH2  0   0.260  -7.1113  -0.7540   1.6712
 2WG  H14  H  HNH2  0   0.410   6.2441  -3.0278   0.3113
 2WG  H15  H  HNH2  0   0.416   4.7221  -2.8527   1.0888

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
 2WG  N23  C21  single    1.340  0.020  1.340
 2WG  C1   O2   single    1.428  0.020  1.428
 2WG  O2   C3   single    1.314  0.020  1.314
 2WG  C21  O22  double    1.220  0.020  1.220
 2WG  C21  C4   single    1.493  0.020  1.493
 2WG  C3   C4   aromatic  1.408  0.020  1.408
 2WG  C3   N8   aromatic  1.316  0.020  1.316
 2WG  C4   C5   aromatic  1.379  0.020  1.379
 2WG  N8   C7   aromatic  1.328  0.020  1.328
 2WG  C19  C20  single    1.483  0.020  1.483
 2WG  C19  C18  single    1.508  0.020  1.508
 2WG  O17  C16  double    1.214  0.020  1.214
 2WG  C5   N6   aromatic  1.330  0.020  1.330
 2WG  C20  C18  single    1.507  0.020  1.507
 2WG  C7   N6   aromatic  1.321  0.020  1.321
 2WG  C7   C9   single    1.481  0.020  1.481
 2WG  C16  C18  single    1.487  0.020  1.487
 2WG  C16  N15  single    1.369  0.020  1.369
 2WG  C14  C9   aromatic  1.383  0.020  1.383
 2WG  C14  C13  aromatic  1.399  0.020  1.399
 2WG  C9   C10  aromatic  1.395  0.020  1.395
 2WG  N15  C13  single    1.390  0.020  1.390
 2WG  C13  N12  aromatic  1.321  0.020  1.321
 2WG  C10  C11  aromatic  1.381  0.020  1.381
 2WG  N12  C11  aromatic  1.330  0.020  1.330
 2WG  C1   H1   single    0.970  0.020  1.090
 2WG  C1   H2   single    0.970  0.020  1.090
 2WG  C1   H3   single    0.970  0.020  1.090
 2WG  C5   H4   single    0.930  0.020  1.080
 2WG  C10  H5   single    0.930  0.020  1.080
 2WG  C11  H6   single    0.930  0.020  1.080
 2WG  C14  H7   single    0.930  0.020  1.080
 2WG  N15  H8   single    0.860  0.020  1.020
 2WG  C18  H9   single    0.970  0.020  1.090
 2WG  C19  H10  single    0.970  0.020  1.090
 2WG  C19  H11  single    0.970  0.020  1.090
 2WG  C20  H12  single    0.970  0.020  1.090
 2WG  C20  H13  single    0.970  0.020  1.090
 2WG  N23  H14  single    0.860  0.020  1.020
 2WG  N23  H15  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
 2WG  H3   C1   H2   109.17  3.000
 2WG  H3   C1   H1   109.62  3.000
 2WG  H2   C1   H1   109.68  3.000
 2WG  H3   C1   O2   111.35  3.000
 2WG  H2   C1   O2   111.47  3.000
 2WG  H1   C1   O2   105.49  3.000
 2WG  C3   O2   C1   118.62  3.000
 2WG  N8   C3   C4   121.49  3.000
 2WG  N8   C3   O2   119.87  3.000
 2WG  C4   C3   O2   118.62  3.000
 2WG  C21  C4   C5   122.08  3.000
 2WG  C5   C4   C3   115.12  3.000
 2WG  C21  C4   C3   122.72  3.000
 2WG  H4   C5   N6   116.30  3.000
 2WG  H4   C5   C4   120.25  3.000
 2WG  N6   C5   C4   123.44  3.000
 2WG  C7   N6   C5   116.38  3.000
 2WG  C9   C7   N8   116.85  3.000
 2WG  C9   C7   N6   117.73  3.000
 2WG  N8   C7   N6   125.42  3.000
 2WG  C7   N8   C3   118.14  3.000
 2WG  C14  C9   C10  118.43  3.000
 2WG  C10  C9   C7   121.12  3.000
 2WG  C14  C9   C7   120.44  3.000
 2WG  H5   C10  C11  120.63  3.000
 2WG  H5   C10  C9   121.45  3.000
 2WG  C11  C10  C9   117.92  3.000
 2WG  H6   C11  N12  115.89  3.000
 2WG  H6   C11  C10  119.87  3.000
 2WG  N12  C11  C10  124.23  3.000
 2WG  C13  N12  C11  117.68  3.000
 2WG  N15  C13  C14  117.09  3.000
 2WG  N15  C13  N12  119.95  3.000
 2WG  C14  C13  N12  122.96  3.000
 2WG  H7   C14  C13  120.70  3.000
 2WG  H7   C14  C9   120.52  3.000
 2WG  C13  C14  C9   118.77  3.000
 2WG  H8   N15  C16  115.80  3.000
 2WG  H8   N15  C13  114.63  3.000
 2WG  C16  N15  C13  129.50  3.000
 2WG  C18  C16  O17  122.59  3.000
 2WG  C18  C16  N15  113.02  3.000
 2WG  O17  C16  N15  124.40  3.000
 2WG  H9   C18  C20  116.57  3.000
 2WG  H9   C18  C19  116.51  3.000
 2WG  C20  C18  C19   58.92  3.000
 2WG  H9   C18  C16  116.95  3.000
 2WG  C20  C18  C16  117.74  3.000
 2WG  C19  C18  C16  117.50  3.000
 2WG  H11  C19  H10  114.90  3.000
 2WG  H11  C19  C20  118.71  3.000
 2WG  H10  C19  C20  118.24  3.000
 2WG  H11  C19  C18  116.57  3.000
 2WG  H10  C19  C18  117.12  3.000
 2WG  C20  C19  C18   60.53  3.000
 2WG  H13  C20  H12  114.90  3.000
 2WG  H13  C20  C19  118.29  3.000
 2WG  H12  C20  C19  118.65  3.000
 2WG  H13  C20  C18  117.16  3.000
 2WG  H12  C20  C18  116.54  3.000
 2WG  C19  C20  C18   60.55  3.000
 2WG  N23  C21  O22  124.00  3.000
 2WG  O22  C21  C4   121.56  3.000
 2WG  N23  C21  C4   114.42  3.000
 2WG  H15  N23  H14  117.12  3.000
 2WG  H15  N23  C21  122.18  3.000
 2WG  H14  N23  C21  120.05  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
 2WG  CONST_01  N6   C5   C4   C3      0.00   0.0  0
 2WG  CONST_02  N6   C7   N8   C3      0.00   0.0  0
 2WG  CONST_03  C9   C7   N8   C3    180.00   0.0  0
 2WG  CONST_04  C7   N8   C3   C4      0.00   0.0  0
 2WG  CONST_05  C7   N6   C5   C4      0.00   0.0  0
 2WG  CONST_06  N8   C3   C4   C5      0.00   0.0  0
 2WG  CONST_07  N8   C7   N6   C5      0.00   0.0  0
 2WG  CONST_08  C9   C7   N6   C5    180.00   0.0  0
 2WG  CONST_09  C14  C9   C7   N6      0.00   0.0  0
 2WG  CONST_10  C10  C9   C7   N6    180.00   0.0  0
 2WG  CONST_11  C13  C14  C9   C7    180.00   0.0  0
 2WG  CONST_12  C11  C10  C9   C7    180.00   0.0  0
 2WG  CONST_13  C14  C9   C7   N8    180.00   0.0  0
 2WG  CONST_14  C10  C9   C7   N8      0.00   0.0  0
 2WG  CONST_15  N12  C13  C14  C9      0.00   0.0  0
 2WG  CONST_16  N12  C11  C10  C9      0.00   0.0  0
 2WG  CONST_17  C13  C14  C9   C10     0.00   0.0  0
 2WG  CONST_18  C13  N12  C11  C10     0.00   0.0  0
 2WG  CONST_19  C14  C9   C10  C11     0.00   0.0  0
 2WG  CONST_20  C14  C13  N12  C11     0.00   0.0  0
 2WG  CONST_21  C5   C4   C3   O2    180.00   0.0  0
 2WG  CONST_22  C7   N8   C3   O2    180.00   0.0  0
 2WG  CONST_23  C21  C4   C5   N6    180.00   0.0  0
 2WG  CONST_24  C21  C4   C3   N8    180.00   0.0  0
 2WG  CONST_25  N15  C13  C14  C9    180.00   0.0  0
 2WG  CONST_26  N15  C13  N12  C11   180.00   0.0  0
 2WG  CONST_27  H4   C5   C4   C3    180.00   0.0  0
 2WG  CONST_28  H7   C14  C9   C7      0.00   0.0  0
 2WG  CONST_29  H5   C10  C9   C7      0.00   0.0  0
 2WG  CONST_30  H6   C11  C10  C9    180.00   0.0  0
 2WG  CONST_31  C18  C16  N15  C13   180.00   0.0  0
 2WG  CONST_32  C16  N15  C13  N12     0.00   0.0  0
 2WG  CONST_33  C16  N15  C13  C14   180.00   0.0  0
 2WG  CONST_34  H8   N15  C13  N12   180.00   0.0  0
 2WG  CONST_35  O17  C16  N15  C13     0.00   0.0  0
 2WG  CONST_36  H14  N23  C21  C4    180.00   0.0  0
 2WG  CONST_37  H15  N23  C21  C4      0.00   0.0  0
 2WG  Var_01    C20  C19  C18  C16  -107.39  30.0  1
 2WG  Var_02    H12  C20  C19  C18  -106.04  30.0  1
 2WG  Var_03    C4   C3   O2   C1   -178.07  30.0  2
 2WG  Var_04    N23  C21  C4   C3    136.26  30.0  2
 2WG  Var_05    C19  C18  C16  N15  -146.27  30.0  3
 2WG  Var_06    H1   C1   O2   C3   -178.82  30.0  3

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
 2WG  chir_01  C18  C19  C20  C16  both

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
 2WG  plan-1  O2   0.020
 2WG  plan-1  C3   0.020
 2WG  plan-1  C4   0.020
 2WG  plan-1  C5   0.020
 2WG  plan-1  N6   0.020
 2WG  plan-1  C7   0.020
 2WG  plan-1  N8   0.020
 2WG  plan-1  C9   0.020
 2WG  plan-1  C21  0.020
 2WG  plan-1  H4   0.020
 2WG  plan-2  C7   0.020
 2WG  plan-2  C9   0.020
 2WG  plan-2  C10  0.020
 2WG  plan-2  C11  0.020
 2WG  plan-2  N12  0.020
 2WG  plan-2  C13  0.020
 2WG  plan-2  C14  0.020
 2WG  plan-2  N15  0.020
 2WG  plan-2  H5   0.020
 2WG  plan-2  H6   0.020
 2WG  plan-2  H7   0.020
 2WG  plan-3  C4   0.020
 2WG  plan-3  C21  0.020
 2WG  plan-3  O22  0.020
 2WG  plan-3  N23  0.020
 2WG  plan-3  H14  0.020
 2WG  plan-3  H15  0.020
 2WG  plan-4  C13  0.020
 2WG  plan-4  N15  0.020
 2WG  plan-4  C16  0.020
 2WG  plan-4  O17  0.020
 2WG  plan-4  C18  0.020
 2WG  plan-4  H8   0.020

