# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:00:00 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: N-[4-(2-oxopyrrolidin-1-yl)phenyl]-2-(pyridin-2-yl)pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CCCN1c2ccc(NC(=O)c3cnc(nc3)c4ccccn4)cc2
#
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
 93C  93C  N-[4-(2-oxopyrrolidin-1-yl)phenyl]-2-(pyridin-2-yl)pyrimidine-5-carboxamide  ligand  44  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_93C
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
 93C  C5   C  CR16  0  -0.150   7.8282   1.7498   0.2644
 93C  C3   C  CR6   0   0.148   6.0033   0.2265   0.0289
 93C  C6   C  CR16  0  -0.309   8.6761   0.7184  -0.1036
 93C  C1   C  CR16  0  -0.080   8.1153  -0.5207  -0.3881
 93C  C17  C  CR16  0  -0.306  -2.5485  -1.0049   0.5226
 93C  C9   C  CR16  0   0.002   2.8804  -1.5956  -0.0615
 93C  C4   C  CR16  0  -0.292   6.4659   1.5044   0.3317
 93C  C13  C  C     0   0.539   0.4900  -0.9781   0.2594
 93C  C7   C  CR6   0   0.385   4.5530  -0.0829   0.0918
 93C  C18  C  CR16  0  -0.291  -3.9318  -0.9160   0.5075
 93C  C23  C  C     0   0.526  -6.8683  -0.7376  -0.1631
 93C  C24  C  CH2   0  -0.586  -8.2539  -0.1440  -0.2726
 93C  C25  C  CH2   0  -0.476  -8.0706   1.3064   0.1494
 93C  C26  C  CH2   0  -0.287  -6.6231   1.5957  -0.2312
 93C  N22  N  NT    0  -0.576  -5.9769   0.2946  -0.0872
 93C  C19  C  CR6   0   0.355  -4.5810   0.1705  -0.0783
 93C  C20  C  CR16  0  -0.315  -3.7959   1.1795  -0.6367
 93C  C21  C  CR16  0  -0.345  -2.4168   1.0958  -0.6175
 93C  C16  C  CR6   0   0.373  -1.7696   0.0026  -0.0446
 93C  N15  N  NH1   0  -0.759  -0.3690   0.0176  -0.0562
 93C  O14  O  O     0  -0.455   0.1582  -2.1061   0.5795
 93C  C10  C  CR6   0  -0.193   1.9308  -0.6086   0.1836
 93C  N8   N  N     0  -0.396   4.1740  -1.3394  -0.1169
 93C  C11  C  CR16  0  -0.012   2.4372   0.6652   0.4069
 93C  N12  N  N     0  -0.419   3.7318   0.9252   0.3616
 93C  N2   N  N     0  -0.404   6.8166  -0.7652  -0.3238
 93C  H1   H  HCR6  0   0.279   8.2178   2.7316   0.4980
 93C  H2   H  HCR6  0   0.277   9.7455   0.8621  -0.1704
 93C  H3   H  HCR6  0   0.266   8.7488  -1.3506  -0.6808
 93C  H4   H  HCR6  0   0.283  -2.0956  -1.8617   0.9925
 93C  H5   H  HCR6  0   0.286   2.5770  -2.6233  -0.2253
 93C  H6   H  HCR6  0   0.276   5.7748   2.2848   0.6143
 93C  H7   H  HCR6  0   0.274  -4.4945  -1.7069   0.9770
 93C  H8   H  HCH2  0   0.278  -8.5743  -0.2250  -1.3159
 93C  H9   H  HCH2  0   0.279  -8.9670  -0.7031   0.3317
 93C  H10  H  HCH2  0   0.261  -8.7633   1.9909  -0.3355
 93C  H11  H  HCH2  0   0.254  -8.1971   1.4054   1.2281
 93C  H12  H  HCH2  0   0.250  -6.5462   1.9544  -1.2618
 93C  H13  H  HCH2  0   0.264  -6.1514   2.3314   0.4198
 93C  H14  H  HCR6  0   0.280  -4.2505   2.0447  -1.0989
 93C  H15  H  HCR6  0   0.276  -1.8385   1.8985  -1.0595
 93C  H16  H  HNH1  0   0.426   0.0321   0.8648  -0.4291
 93C  H17  H  HCR6  0   0.285   1.7917   1.5027   0.6515
 93C  O27  O  O     0  -0.472  -6.5916  -1.9211  -0.1712

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
 93C  C24  C25  single    1.522  0.020  1.522
 93C  C24  C23  single    1.511  0.020  1.511
 93C  C25  C26  single    1.524  0.020  1.524
 93C  O27  C23  double    1.216  0.020  1.216
 93C  C23  N22  single    1.366  0.020  1.366
 93C  C26  N22  single    1.460  0.020  1.460
 93C  N22  C19  single    1.401  0.020  1.401
 93C  C18  C19  aromatic  1.395  0.020  1.395
 93C  C18  C17  aromatic  1.386  0.020  1.386
 93C  C19  C20  aromatic  1.395  0.020  1.395
 93C  C17  C16  aromatic  1.394  0.020  1.394
 93C  C20  C21  aromatic  1.382  0.020  1.382
 93C  C16  C21  aromatic  1.394  0.020  1.394
 93C  C16  N15  single    1.401  0.020  1.401
 93C  N15  C13  single    1.352  0.020  1.352
 93C  C11  N12  aromatic  1.321  0.020  1.321
 93C  C11  C10  aromatic  1.389  0.020  1.389
 93C  N12  C7   aromatic  1.328  0.020  1.328
 93C  C13  C10  single    1.489  0.020  1.489
 93C  C13  O14  double    1.219  0.020  1.219
 93C  C4   C5   aromatic  1.386  0.020  1.386
 93C  C4   C3   aromatic  1.392  0.020  1.392
 93C  C10  C9   aromatic  1.391  0.020  1.391
 93C  C5   C6   aromatic  1.385  0.020  1.385
 93C  C7   C3   single    1.484  0.020  1.484
 93C  C7   N8   aromatic  1.329  0.020  1.329
 93C  C3   N2   aromatic  1.330  0.020  1.330
 93C  C9   N8   aromatic  1.320  0.020  1.320
 93C  C6   C1   aromatic  1.390  0.020  1.390
 93C  N2   C1   aromatic  1.323  0.020  1.323
 93C  C5   H1   single    0.930  0.020  1.080
 93C  C6   H2   single    0.930  0.020  1.080
 93C  C1   H3   single    0.930  0.020  1.080
 93C  C17  H4   single    0.930  0.020  1.080
 93C  C9   H5   single    0.930  0.020  1.080
 93C  C4   H6   single    0.930  0.020  1.080
 93C  C18  H7   single    0.930  0.020  1.080
 93C  C24  H8   single    0.970  0.020  1.090
 93C  C24  H9   single    0.970  0.020  1.090
 93C  C25  H10  single    0.970  0.020  1.090
 93C  C25  H11  single    0.970  0.020  1.090
 93C  C26  H12  single    0.970  0.020  1.090
 93C  C26  H13  single    0.970  0.020  1.090
 93C  C20  H14  single    0.930  0.020  1.080
 93C  C21  H15  single    0.930  0.020  1.080
 93C  N15  H16  single    0.860  0.020  1.020
 93C  C11  H17  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
 93C  H1   C5   C4   120.28  3.000
 93C  H1   C5   C6   120.85  3.000
 93C  C4   C5   C6   118.87  3.000
 93C  N2   C3   C7   116.95  3.000
 93C  N2   C3   C4   122.61  3.000
 93C  C7   C3   C4   120.45  3.000
 93C  H2   C6   C1   120.34  3.000
 93C  H2   C6   C5   121.54  3.000
 93C  C1   C6   C5   118.13  3.000
 93C  H3   C1   N2   116.43  3.000
 93C  H3   C1   C6   120.13  3.000
 93C  N2   C1   C6   123.44  3.000
 93C  H4   C17  C16  121.16  3.000
 93C  H4   C17  C18  118.38  3.000
 93C  C16  C17  C18  120.45  3.000
 93C  H5   C9   N8   116.87  3.000
 93C  H5   C9   C10  120.54  3.000
 93C  N8   C9   C10  122.59  3.000
 93C  H6   C4   C3   120.50  3.000
 93C  H6   C4   C5   120.91  3.000
 93C  C3   C4   C5   118.59  3.000
 93C  C10  C13  O14  120.43  3.000
 93C  O14  C13  N15  124.74  3.000
 93C  C10  C13  N15  114.83  3.000
 93C  N12  C7   N8   124.99  3.000
 93C  N8   C7   C3   117.98  3.000
 93C  N12  C7   C3   117.04  3.000
 93C  H7   C18  C19  120.76  3.000
 93C  H7   C18  C17  117.97  3.000
 93C  C19  C18  C17  121.27  3.000
 93C  N22  C23  C24  107.79  3.000
 93C  N22  C23  O27  125.98  3.000
 93C  C24  C23  O27  126.21  3.000
 93C  H9   C24  H8   107.41  3.000
 93C  H9   C24  C25  114.47  3.000
 93C  H8   C24  C25  111.73  3.000
 93C  H9   C24  C23  111.00  3.000
 93C  H8   C24  C23  107.96  3.000
 93C  C25  C24  C23  104.11  3.000
 93C  H11  C25  H10  108.05  3.000
 93C  H11  C25  C26  109.87  3.000
 93C  H10  C25  C26  111.96  3.000
 93C  H11  C25  C24  110.30  3.000
 93C  H10  C25  C24  113.54  3.000
 93C  C26  C25  C24  103.06  3.000
 93C  H13  C26  H12  108.12  3.000
 93C  H13  C26  N22  110.55  3.000
 93C  H12  C26  N22  110.73  3.000
 93C  H13  C26  C25  112.96  3.000
 93C  H12  C26  C25  111.36  3.000
 93C  N22  C26  C25  103.10  3.000
 93C  C19  N22  C26  121.36  3.000
 93C  C19  N22  C23  125.70  3.000
 93C  C26  N22  C23  112.28  3.000
 93C  C20  C19  N22  119.60  3.000
 93C  C20  C19  C18  118.01  3.000
 93C  N22  C19  C18  122.36  3.000
 93C  H14  C20  C21  118.30  3.000
 93C  H14  C20  C19  120.88  3.000
 93C  C21  C20  C19  120.82  3.000
 93C  H15  C21  C16  120.06  3.000
 93C  H15  C21  C20  118.82  3.000
 93C  C16  C21  C20  121.11  3.000
 93C  N15  C16  C21  116.91  3.000
 93C  N15  C16  C17  124.73  3.000
 93C  C21  C16  C17  118.34  3.000
 93C  H16  N15  C16  114.18  3.000
 93C  H16  N15  C13  116.88  3.000
 93C  C16  N15  C13  128.70  3.000
 93C  C11  C10  C13  124.90  3.000
 93C  C13  C10  C9   119.55  3.000
 93C  C11  C10  C9   115.47  3.000
 93C  C7   N8   C9   117.16  3.000
 93C  H17  C11  N12  116.02  3.000
 93C  H17  C11  C10  121.81  3.000
 93C  N12  C11  C10  122.16  3.000
 93C  C11  N12  C7   117.61  3.000
 93C  C1   N2   C3   118.37  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
 93C  CONST_01  C7   C3   C4   C5    180.00   0.0  0
 93C  CONST_02  N2   C3   C4   C5      0.00   0.0  0
 93C  CONST_03  N2   C1   C6   C5      0.00   0.0  0
 93C  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 93C  CONST_05  C11  N12  C7   C3    180.00   0.0  0
 93C  CONST_06  C9   N8   C7   C3    180.00   0.0  0
 93C  CONST_07  C6   C1   N2   C3      0.00   0.0  0
 93C  CONST_08  C4   C5   C6   C1      0.00   0.0  0
 93C  CONST_09  C4   C3   N2   C1      0.00   0.0  0
 93C  CONST_10  C7   C3   N2   C1    180.00   0.0  0
 93C  CONST_11  C20  C19  C18  C17     0.00   0.0  0
 93C  CONST_12  C20  C21  C16  C17     0.00   0.0  0
 93C  CONST_13  N12  C11  C10  C9      0.00   0.0  0
 93C  CONST_14  N12  C7   N8   C9      0.00   0.0  0
 93C  CONST_15  N12  C7   C3   C4      0.00   0.0  0
 93C  CONST_16  N8   C7   C3   C4    180.00   0.0  0
 93C  CONST_17  C10  C11  N12  C7      0.00   0.0  0
 93C  CONST_18  C10  C9   N8   C7      0.00   0.0  0
 93C  CONST_19  C21  C20  C19  C18     0.00   0.0  0
 93C  CONST_20  C21  C16  C17  C18     0.00   0.0  0
 93C  CONST_21  C16  C17  C18  C19     0.00   0.0  0
 93C  CONST_22  C16  C21  C20  C19     0.00   0.0  0
 93C  CONST_23  C11  N12  C7   N8      0.00   0.0  0
 93C  CONST_24  N2   C3   C7   N8      0.00   0.0  0
 93C  CONST_25  C11  C10  C9   N8      0.00   0.0  0
 93C  CONST_26  N2   C3   C7   N12   180.00   0.0  0
 93C  CONST_27  N22  C19  C18  C17   180.00   0.0  0
 93C  CONST_28  C21  C20  C19  N22   180.00   0.0  0
 93C  CONST_29  C26  N22  C23  C24     0.00   0.0  0
 93C  CONST_30  C19  N22  C23  C24   180.00   0.0  0
 93C  CONST_31  N12  C11  C10  C13   180.00   0.0  0
 93C  CONST_32  N8   C9   C10  C13   180.00   0.0  0
 93C  CONST_33  N15  C16  C17  C18   180.00   0.0  0
 93C  CONST_34  N15  C16  C21  C20   180.00   0.0  0
 93C  CONST_35  C26  N22  C23  O27   180.00   0.0  0
 93C  CONST_36  C19  N22  C23  O27     0.00   0.0  0
 93C  CONST_37  H3   C1   C6   C5    180.00   0.0  0
 93C  CONST_38  H1   C5   C4   C3    180.00   0.0  0
 93C  CONST_39  H6   C4   C5   C6    180.00   0.0  0
 93C  CONST_40  H15  C21  C16  C17   180.00   0.0  0
 93C  CONST_41  H17  C11  C10  C9    180.00   0.0  0
 93C  CONST_42  H2   C6   C5   C4    180.00   0.0  0
 93C  CONST_43  H5   C9   N8   C7    180.00   0.0  0
 93C  CONST_44  H14  C20  C19  C18   180.00   0.0  0
 93C  CONST_45  H7   C18  C19  N22     0.00   0.0  0
 93C  CONST_46  H4   C17  C18  C19   180.00   0.0  0
 93C  CONST_47  C10  C13  N15  C16   180.00   0.0  0
 93C  CONST_48  C13  N15  C16  C17     0.00   0.0  0
 93C  CONST_49  C21  C16  N15  C13   180.00   0.0  0
 93C  CONST_50  H16  N15  C16  C17   180.00   0.0  0
 93C  CONST_51  O14  C13  N15  C16     0.00   0.0  0
 93C  Var_01    C23  N22  C19  C18   -33.21  30.0  3
 93C  Var_02    C26  C25  C24  C23    28.15  30.0  1
 93C  Var_03    C25  C26  N22  C23    22.09  30.0  1
 93C  Var_04    N22  C26  C25  C24   -30.20  30.0  1
 93C  Var_05    N22  C23  C24  C25   -15.74  30.0  1
 93C  Var_06    N15  C13  C10  C9   -153.66  30.0  2

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
 93C  plan-1  C5   0.020
 93C  plan-1  C3   0.020
 93C  plan-1  C6   0.020
 93C  plan-1  C1   0.020
 93C  plan-1  C4   0.020
 93C  plan-1  C7   0.020
 93C  plan-1  N2   0.020
 93C  plan-1  H1   0.020
 93C  plan-1  H2   0.020
 93C  plan-1  H3   0.020
 93C  plan-1  H6   0.020
 93C  plan-2  C17  0.020
 93C  plan-2  C18  0.020
 93C  plan-2  N22  0.020
 93C  plan-2  C19  0.020
 93C  plan-2  C20  0.020
 93C  plan-2  C21  0.020
 93C  plan-2  C16  0.020
 93C  plan-2  N15  0.020
 93C  plan-2  H4   0.020
 93C  plan-2  H7   0.020
 93C  plan-2  H14  0.020
 93C  plan-2  H15  0.020
 93C  plan-3  C3   0.020
 93C  plan-3  C9   0.020
 93C  plan-3  C13  0.020
 93C  plan-3  C7   0.020
 93C  plan-3  C10  0.020
 93C  plan-3  N8   0.020
 93C  plan-3  C11  0.020
 93C  plan-3  N12  0.020
 93C  plan-3  H5   0.020
 93C  plan-3  H17  0.020
 93C  plan-4  C13  0.020
 93C  plan-4  C16  0.020
 93C  plan-4  N15  0.020
 93C  plan-4  O14  0.020
 93C  plan-4  C10  0.020
 93C  plan-4  H16  0.020
 93C  plan-5  C23  0.020
 93C  plan-5  C24  0.020
 93C  plan-5  C26  0.020
 93C  plan-5  N22  0.020
 93C  plan-5  C19  0.020
 93C  plan-5  O27  0.020

