# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 02:48:47 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-({4-[(3S)-3-cyano-3-cyclopropyl-2-oxopyrrolidin-1-yl]pyridin-2-yl}amino)-N,N-dimethylpyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)c1ccc(Nc2cc(ccn2)N3CC[C@@](C#N)(C4CC4)C3=O)nc1
#
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
 N9G  N9G  6-({4-[(3S)-3-cyano-3-cyclopropyl-2-oxopyrrolidin-1-yl]pyridin-2-yl}amino)-N,N-dimethylpyridine-3-carboxamide  ligand  51  29  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N9G
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
 N9G  C4   C  C     0   0.516   6.6234  -0.6250   0.3109
 N9G  C6   C  CR6   0  -0.173   5.1488  -0.6239   0.1041
 N9G  C7   C  CR16  0  -0.146   4.5030  -1.8048  -0.2702
 N9G  C8   C  CR16  0  -0.405   3.1345  -1.8265  -0.3794
 N9G  C13  C  CR6   0   0.480  -2.1702   0.9780   0.0691
 N9G  C15  C  CR16  0  -0.064  -0.4203   2.4823  -0.5287
 N9G  C20  C  CT    0  -0.371  -5.6438  -0.2116   0.4895
 N9G  C21  C  CSP   0   0.179  -6.2337  -1.2495   1.3257
 N9G  C24  C  CH2   0  -0.494  -5.6586   0.0741  -2.1562
 N9G  C26  C  C     0   0.600  -4.1393  -0.4664   0.3364
 N9G  N2   N  NT    0  -0.445   7.3269   0.4553  -0.0841
 N9G  C3   C  CH3   0  -0.536   6.8821   1.4260  -1.0649
 N9G  O5   O  O     0  -0.494   7.1484  -1.5868   0.8620
 N9G  C9   C  CR6   0   0.527   2.4164  -0.6594  -0.0670
 N9G  N10  N  NH1   0  -0.767   1.0458  -0.7090  -0.1474
 N9G  C11  C  CR6   0   0.533   0.1220   0.3191  -0.1644
 N9G  C12  C  CR16  0  -0.478  -1.2039  -0.0160   0.1350
 N9G  C14  C  CR16  0  -0.423  -1.7583   2.2733  -0.2687
 N9G  N16  N  N     0  -0.431   0.5134   1.5391  -0.4944
 N9G  N17  N  NT    0  -0.584  -3.5186   0.7464   0.3478
 N9G  C18  C  CH2   0  -0.305  -4.4539   1.8529   0.5459
 N9G  C19  C  CH2   0  -0.443  -5.6775   1.1741   1.1422
 N9G  N22  N  NS    0  -0.250  -6.7184  -2.0646   1.9759
 N9G  C23  C  CH1   0  -0.205  -6.3560  -0.2168  -0.8621
 N9G  C25  C  CH2   0  -0.481  -6.1671  -1.3048  -1.8693
 N9G  N28  N  N     0  -0.428   3.0160   0.4501   0.3389
 N9G  C29  C  CR16  0  -0.061   4.3403   0.4614   0.4072
 N9G  H1   H  HCR6  0   0.274   5.0753  -2.6952  -0.4959
 N9G  H2   H  HCR6  0   0.280   2.6178  -2.7220  -0.6989
 N9G  H3   H  HCR6  0   0.266  -0.0835   3.4775  -0.7959
 N9G  H4   H  HCH2  0   0.272  -6.1897   0.6879  -2.8715
 N9G  H5   H  HCH2  0   0.258  -4.5861   0.2250  -2.1665
 N9G  H6   H  HCH3  0   0.239   9.3666   0.1124  -0.5137
 N9G  H7   H  HCH3  0   0.246   8.9992   1.5972   0.3707
 N9G  H8   H  HCH3  0   0.254   8.9341   0.0414   1.2011
 N9G  H9   H  HCH3  0   0.264   5.9359   1.1397  -1.5122
 N9G  H10  H  HCH3  0   0.246   6.7760   2.4187  -0.6242
 N9G  H11  H  HCH3  0   0.255   7.6183   1.4898  -1.8681
 N9G  H12  H  HNH1  0   0.419   0.6556  -1.6362  -0.2094
 N9G  H13  H  HCR6  0   0.299  -1.4421  -1.0277   0.4185
 N9G  H14  H  HCR6  0   0.289  -2.4472   3.1007  -0.3464
 N9G  H15  H  HCH2  0   0.290  -4.0298   2.5907   1.2243
 N9G  H16  H  HCH2  0   0.275  -4.6814   2.3423  -0.4033
 N9G  H17  H  HCH2  0   0.289  -6.5985   1.7115   0.9280
 N9G  H18  H  HCH2  0   0.289  -5.5678   1.0913   2.2237
 N9G  H19  H  HCH1  0   0.293  -7.3640   0.1742  -0.7736
 N9G  H20  H  HCH2  0   0.268  -7.0483  -1.6538  -2.3907
 N9G  H21  H  HCH2  0   0.261  -5.4373  -2.0778  -1.6655
 N9G  H22  H  HCR6  0   0.269   4.7804   1.3911   0.7536
 N9G  O27  O  O     0  -0.421  -3.6356  -1.5563   0.2025
 N9G  C1   C  CH3   0  -0.525   8.7307   0.5470   0.2618

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
 N9G  O5   C4   double    1.227  0.020  1.227
 N9G  N16  C15  aromatic  1.328  0.020  1.328
 N9G  N16  C11  aromatic  1.323  0.020  1.323
 N9G  C15  C14  aromatic  1.379  0.020  1.379
 N9G  N10  C11  single    1.382  0.020  1.382
 N9G  N10  C9   single    1.374  0.020  1.374
 N9G  C11  C12  aromatic  1.400  0.020  1.400
 N9G  C9   C8   aromatic  1.406  0.020  1.406
 N9G  C9   N28  aromatic  1.325  0.020  1.325
 N9G  C8   C7   aromatic  1.373  0.020  1.373
 N9G  N28  C29  aromatic  1.326  0.020  1.326
 N9G  C14  C13  aromatic  1.401  0.020  1.401
 N9G  C7   C6   aromatic  1.397  0.020  1.397
 N9G  C29  C6   aromatic  1.387  0.020  1.387
 N9G  C6   C4   single    1.489  0.020  1.489
 N9G  C4   N2   single    1.348  0.020  1.348
 N9G  C12  C13  aromatic  1.388  0.020  1.388
 N9G  C13  N17  single    1.396  0.020  1.396
 N9G  N17  C18  single    1.462  0.020  1.462
 N9G  N17  C26  single    1.363  0.020  1.363
 N9G  C18  C19  single    1.521  0.020  1.521
 N9G  C19  C20  single    1.532  0.020  1.532
 N9G  N2   C1   single    1.449  0.020  1.449
 N9G  N2   C3   single    1.450  0.020  1.450
 N9G  C26  O27  double    1.208  0.020  1.208
 N9G  C26  C20  single    1.534  0.020  1.534
 N9G  C21  N22  triple    1.150  0.020  1.150
 N9G  C21  C20  single    1.458  0.020  1.458
 N9G  C20  C23  single    1.528  0.020  1.528
 N9G  C23  C25  single    1.495  0.020  1.495
 N9G  C23  C24  single    1.499  0.020  1.499
 N9G  C25  C24  single    1.497  0.020  1.497
 N9G  C7   H1   single    0.930  0.020  1.080
 N9G  C8   H2   single    0.930  0.020  1.080
 N9G  C15  H3   single    0.930  0.020  1.080
 N9G  C24  H4   single    0.970  0.020  1.090
 N9G  C24  H5   single    0.970  0.020  1.090
 N9G  C1   H6   single    0.970  0.020  1.090
 N9G  C1   H7   single    0.970  0.020  1.090
 N9G  C1   H8   single    0.970  0.020  1.090
 N9G  C3   H9   single    0.970  0.020  1.090
 N9G  C3   H10  single    0.970  0.020  1.090
 N9G  C3   H11  single    0.970  0.020  1.090
 N9G  N10  H12  single    0.860  0.020  1.020
 N9G  C12  H13  single    0.930  0.020  1.080
 N9G  C14  H14  single    0.930  0.020  1.080
 N9G  C18  H15  single    0.970  0.020  1.090
 N9G  C18  H16  single    0.970  0.020  1.090
 N9G  C19  H17  single    0.970  0.020  1.090
 N9G  C19  H18  single    0.970  0.020  1.090
 N9G  C23  H19  single    0.970  0.020  1.090
 N9G  C25  H20  single    0.970  0.020  1.090
 N9G  C25  H21  single    0.970  0.020  1.090
 N9G  C29  H22  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
 N9G  O5   C4   N2   122.45  3.000
 N9G  N2   C4   C6   118.39  3.000
 N9G  O5   C4   C6   119.13  3.000
 N9G  C29  C6   C7   116.78  3.000
 N9G  C29  C6   C4   123.20  3.000
 N9G  C7   C6   C4   119.62  3.000
 N9G  H1   C7   C8   119.83  3.000
 N9G  H1   C7   C6   120.46  3.000
 N9G  C8   C7   C6   119.70  3.000
 N9G  H2   C8   C9   120.59  3.000
 N9G  H2   C8   C7   120.83  3.000
 N9G  C9   C8   C7   118.58  3.000
 N9G  N17  C13  C14  119.05  3.000
 N9G  N17  C13  C12  122.96  3.000
 N9G  C14  C13  C12  117.98  3.000
 N9G  H3   C15  N16  116.11  3.000
 N9G  H3   C15  C14  119.15  3.000
 N9G  N16  C15  C14  124.74  3.000
 N9G  C23  C20  C19  111.70  3.000
 N9G  C23  C20  C26  111.62  3.000
 N9G  C19  C20  C26  102.38  3.000
 N9G  C23  C20  C21  108.45  3.000
 N9G  C26  C20  C21  109.63  3.000
 N9G  C19  C20  C21  113.00  3.000
 N9G  N22  C21  C20  180.00  3.000
 N9G  H5   C24  H4   113.63  3.000
 N9G  H5   C24  C25  117.80  3.000
 N9G  H4   C24  C25  118.84  3.000
 N9G  H5   C24  C23  119.74  3.000
 N9G  H4   C24  C23  116.91  3.000
 N9G  C25  C24  C23   59.85  3.000
 N9G  O27  C26  N17  127.88  3.000
 N9G  O27  C26  C20  124.75  3.000
 N9G  N17  C26  C20  107.35  3.000
 N9G  C3   N2   C1   114.61  3.000
 N9G  C3   N2   C4   125.06  3.000
 N9G  C1   N2   C4   119.10  3.000
 N9G  H11  C3   H10  108.04  3.000
 N9G  H11  C3   H9   107.47  3.000
 N9G  H10  C3   H9   108.77  3.000
 N9G  H11  C3   N2   109.27  3.000
 N9G  H10  C3   N2   111.45  3.000
 N9G  H9   C3   N2   111.70  3.000
 N9G  N28  C9   N10  119.98  3.000
 N9G  N28  C9   C8   122.16  3.000
 N9G  N10  C9   C8   117.82  3.000
 N9G  H12  N10  C11  115.13  3.000
 N9G  H12  N10  C9   115.03  3.000
 N9G  C11  N10  C9   129.84  3.000
 N9G  N16  C11  C12  123.66  3.000
 N9G  C12  C11  N10  116.90  3.000
 N9G  N16  C11  N10  119.42  3.000
 N9G  H13  C12  C11  119.37  3.000
 N9G  H13  C12  C13  122.08  3.000
 N9G  C11  C12  C13  118.54  3.000
 N9G  H14  C14  C15  119.31  3.000
 N9G  H14  C14  C13  122.58  3.000
 N9G  C15  C14  C13  118.10  3.000
 N9G  C11  N16  C15  116.97  3.000
 N9G  C18  N17  C26  112.53  3.000
 N9G  C26  N17  C13  125.87  3.000
 N9G  C18  N17  C13  121.28  3.000
 N9G  H16  C18  H15  108.61  3.000
 N9G  H16  C18  C19  111.92  3.000
 N9G  H15  C18  C19  111.81  3.000
 N9G  H16  C18  N17  110.77  3.000
 N9G  H15  C18  N17  110.37  3.000
 N9G  C19  C18  N17  103.30  3.000
 N9G  H18  C19  H17  108.55  3.000
 N9G  H18  C19  C18  109.99  3.000
 N9G  H17  C19  C18  112.55  3.000
 N9G  H18  C19  C20  110.59  3.000
 N9G  H17  C19  C20  112.43  3.000
 N9G  C18  C19  C20  102.65  3.000
 N9G  H19  C23  C25  115.77  3.000
 N9G  H19  C23  C24  115.66  3.000
 N9G  C25  C23  C24   60.03  3.000
 N9G  H19  C23  C20  111.08  3.000
 N9G  C24  C23  C20  123.12  3.000
 N9G  C25  C23  C20  122.67  3.000
 N9G  H21  C25  H20  114.18  3.000
 N9G  H21  C25  C23  118.57  3.000
 N9G  H20  C25  C23  117.18  3.000
 N9G  H21  C25  C24  117.69  3.000
 N9G  H20  C25  C24  118.78  3.000
 N9G  C23  C25  C24   60.12  3.000
 N9G  C29  N28  C9   118.35  3.000
 N9G  H22  C29  N28  115.38  3.000
 N9G  H22  C29  C6   120.24  3.000
 N9G  N28  C29  C6   124.35  3.000
 N9G  H8   C1   H7   108.43  3.000
 N9G  H8   C1   H6   108.64  3.000
 N9G  H7   C1   H6   108.11  3.000
 N9G  H8   C1   N2   111.01  3.000
 N9G  H7   C1   N2   108.88  3.000
 N9G  H6   C1   N2   111.67  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
 N9G  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 N9G  CONST_02  C9   N28  C29  C6      0.00   0.0  0
 N9G  CONST_03  N28  C9   C8   C7      0.00   0.0  0
 N9G  CONST_04  N28  C29  C6   C7      0.00   0.0  0
 N9G  CONST_05  C29  N28  C9   C8      0.00   0.0  0
 N9G  CONST_06  C29  C6   C7   C8      0.00   0.0  0
 N9G  CONST_07  N16  C15  C14  C13     0.00   0.0  0
 N9G  CONST_08  N16  C11  C12  C13     0.00   0.0  0
 N9G  CONST_09  C12  C11  N16  C15     0.00   0.0  0
 N9G  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 N9G  CONST_11  C14  C15  N16  C11     0.00   0.0  0
 N9G  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 N9G  CONST_13  N17  C13  C14  C15   180.00   0.0  0
 N9G  CONST_14  N17  C13  C12  C11   180.00   0.0  0
 N9G  CONST_15  C20  C26  N17  C13   180.00   0.0  0
 N9G  CONST_16  C18  N17  C26  C20     0.00   0.0  0
 N9G  CONST_17  C8   C7   C6   C4    180.00   0.0  0
 N9G  CONST_18  N28  C29  C6   C4    180.00   0.0  0
 N9G  CONST_19  N10  C9   C8   C7    180.00   0.0  0
 N9G  CONST_20  N10  C11  C12  C13   180.00   0.0  0
 N9G  CONST_21  N10  C11  N16  C15   180.00   0.0  0
 N9G  CONST_22  C29  N28  C9   N10   180.00   0.0  0
 N9G  CONST_23  O27  C26  N17  C13     0.00   0.0  0
 N9G  CONST_24  O27  C26  N17  C18   180.00   0.0  0
 N9G  CONST_25  H2   C8   C7   C6    180.00   0.0  0
 N9G  CONST_26  H22  C29  C6   C7    180.00   0.0  0
 N9G  CONST_27  H3   C15  C14  C13   180.00   0.0  0
 N9G  CONST_28  H1   C7   C8   C9    180.00   0.0  0
 N9G  CONST_29  H14  C14  C13  C12   180.00   0.0  0
 N9G  CONST_30  H13  C12  C13  C14   180.00   0.0  0
 N9G  CONST_31  C1   N2   C4   C6    180.00   0.0  0
 N9G  CONST_33  O5   C4   N2   C1      0.00   0.0  0
 N9G  Var_01    C19  C18  N17  C13  -166.80  30.0  1
 N9G  Var_02    N17  C18  C19  C20   -31.87  30.0  1
 N9G  Var_03    C24  C25  C23  C20  -112.30  30.0  1
 N9G  Var_04    C14  C13  N17  C26   161.23  30.0  2
 N9G  Var_05    C11  N10  C9   C8   -165.47  30.0  3
 N9G  Var_06    N16  C11  N10  C9     20.01  30.0  2
 N9G  Var_07    O5   C4   C6   C7    -39.57  30.0  2
 N9G  Var_08    H6   C1   N2   C4     90.93  30.0  3
 N9G  Var_09    H9   C3   N2   C4     -4.57  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
 N9G  chir_01  C20  C26  C19  C23  negativ
 N9G  chir_02  C23  C20  C25  C24  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
 N9G  plan-1  C4   0.020
 N9G  plan-1  C6   0.020
 N9G  plan-1  C7   0.020
 N9G  plan-1  C8   0.020
 N9G  plan-1  C9   0.020
 N9G  plan-1  N10  0.020
 N9G  plan-1  N28  0.020
 N9G  plan-1  C29  0.020
 N9G  plan-1  H1   0.020
 N9G  plan-1  H2   0.020
 N9G  plan-1  H22  0.020
 N9G  plan-2  C13  0.020
 N9G  plan-2  C15  0.020
 N9G  plan-2  N10  0.020
 N9G  plan-2  C11  0.020
 N9G  plan-2  C12  0.020
 N9G  plan-2  C14  0.020
 N9G  plan-2  N16  0.020
 N9G  plan-2  N17  0.020
 N9G  plan-2  H3   0.020
 N9G  plan-2  H13  0.020
 N9G  plan-2  H14  0.020
 N9G  plan-3  C13  0.020
 N9G  plan-3  C20  0.020
 N9G  plan-3  C26  0.020
 N9G  plan-3  N17  0.020
 N9G  plan-3  C18  0.020
 N9G  plan-3  O27  0.020
 N9G  plan-4  C4   0.020
 N9G  plan-4  C6   0.020
 N9G  plan-4  N2   0.020
 N9G  plan-4  C3   0.020
 N9G  plan-4  O5   0.020
 N9G  plan-4  C1   0.020

