# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:35:37 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 6-[(cyclopropanecarbonyl)amino]-N-methyl-4-{[2-(methylsulfonyl)phenyl]amino}pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cnc(NC(=O)C2CC2)cc1Nc3ccccc3[S](C)(=O)=O
#
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
 L9A  L9A  6-[(cyclopropanecarbonyl)amino]-N-methyl-4-{[2-(methylsulfonyl)phenyl]amino}pyridine-3-carboxamide  ligand  47  27  .  2022-08-10  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_L9A
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
 L9A  C13  C  CR6   0  -0.263   2.7866   1.3321  -1.0242
 L9A  C18  C  CH3   0  -0.790   2.4190   1.5945   1.7520
 L9A  C17  C  CH2   0  -0.462  -6.4657   2.3278   0.3211
 L9A  C16  C  CH2   0  -0.463  -6.8432   1.5234  -0.8658
 L9A  C15  C  CH1   0  -0.445  -5.3852   1.7298  -0.5435
 L9A  C11  C  CR16  0  -0.249   2.5863   2.5003  -3.1100
 L9A  C12  C  CR16  0  -0.249   3.2181   2.3287  -1.8900
 L9A  C1   C  CR6   0  -0.230  -0.2725  -2.0827   0.4536
 L9A  C2   C  CR16  0  -0.095  -1.6167  -2.3300   0.6978
 L9A  N1   N  N     0  -0.442  -2.6206  -1.5120   0.4307
 L9A  C3   C  CR6   0   0.549  -2.3041  -0.3379  -0.1019
 L9A  C4   C  CR16  0  -0.500  -1.0044   0.0301  -0.4264
 L9A  C5   C  CR6   0   0.493   0.0443  -0.8575  -0.1907
 L9A  N2   N  NH1   0  -0.639   0.4657  -4.0022   1.7164
 L9A  C7   C  CH3   0  -0.513   1.4013  -5.0305   2.1095
 L9A  O1   O  O     0  -0.514   1.8974  -3.0371   0.2903
 L9A  N4   N  NH1   0  -0.751  -3.3080   0.5740  -0.3871
 L9A  C8   C  CR6   0   0.347   1.7286   0.4824  -1.3661
 L9A  C9   C  CR16  0  -0.270   1.1128   0.6645  -2.6020
 L9A  C10  C  CR16  0  -0.237   1.5324   1.6676  -3.4598
 L9A  C14  C  C     0   0.588  -4.6251   0.5716  -0.0039
 L9A  O2   O  O     0  -0.450  -5.1321  -0.2738   0.7033
 L9A  S1   S  S     0   1.222   3.6329   1.1542   0.5312
 L9A  O3   O  OS    0  -0.666   4.0074  -0.2471   0.7117
 L9A  O4   O  OS    0  -0.664   4.6952   2.1569   0.5733
 L9A  H18  H  HCH3  0   0.292   1.5964   0.8851   1.7364
 L9A  H19  H  HCH3  0   0.315   2.9184   1.5595   2.7200
 L9A  H20  H  HCH3  0   0.298   2.0613   2.6020   1.5538
 L9A  H17  H  HCH2  0   0.261  -6.6132   1.8938   1.3013
 L9A  H14  H  HCH2  0   0.261  -7.2497   0.5337  -0.7032
 L9A  H15  H  HCH2  0   0.267  -7.2216   2.0329  -1.7415
 L9A  H13  H  HCH1  0   0.286  -4.8413   2.4167  -1.1810
 L9A  H11  H  HCR6  0   0.275   2.9204   3.2764  -3.7844
 L9A  H12  H  HCR6  0   0.288   4.0394   2.9744  -1.6127
 L9A  H1   H  HCR6  0   0.263  -1.9186  -3.2833   1.1181
 L9A  H2   H  HCR6  0   0.298  -0.8153   1.0052  -0.8540
 L9A  H3   H  HNH1  0   0.413  -0.3912  -3.9343   2.2372
 L9A  H6   H  HCH3  0   0.244   1.7661  -5.5836   1.2449
 L9A  H5   H  HCH3  0   0.240   2.2602  -4.6214   2.6438
 L9A  H4   H  HCH3  0   0.253   0.8860  -5.7245   2.7669
 L9A  H8   H  HNH1  0   0.424  -3.0079   1.3794  -0.9152
 L9A  H9   H  HCR6  0   0.293   0.3084   0.0046  -2.8997
 L9A  H10  H  HCR6  0   0.278   1.0425   1.7862  -4.4168
 L9A  N3   N  NH1   0  -0.820   1.3321  -0.5432  -0.4996
 L9A  C6   C  C     0   0.569   0.7786  -3.0704   0.8083
 L9A  H16  H  HCH2  0   0.266  -6.5787   3.4026   0.2785
 L9A  H7   H  HNH1  0   0.432   2.0141  -1.2611  -0.2665

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
 L9A  O4   S1   double    1.461  0.020  1.461
 L9A  C18  S1   single    1.777  0.020  1.777
 L9A  C12  C11  aromatic  1.385  0.020  1.385
 L9A  C12  C13  aromatic  1.389  0.020  1.389
 L9A  S1   C13  single    1.780  0.020  1.780
 L9A  S1   O3   double    1.462  0.020  1.462
 L9A  C11  C10  aromatic  1.388  0.020  1.388
 L9A  C13  C8   aromatic  1.399  0.020  1.399
 L9A  C10  C9   aromatic  1.385  0.020  1.385
 L9A  C8   C9   aromatic  1.393  0.020  1.393
 L9A  C8   N3   single    1.400  0.020  1.400
 L9A  N3   C5   single    1.361  0.020  1.361
 L9A  O1   C6   double    1.233  0.020  1.233
 L9A  C5   C4   aromatic  1.394  0.020  1.394
 L9A  C5   C1   aromatic  1.420  0.020  1.420
 L9A  C4   C3   aromatic  1.389  0.020  1.389
 L9A  C6   C1   single    1.485  0.020  1.485
 L9A  C6   N2   single    1.338  0.020  1.338
 L9A  O2   C14  double    1.213  0.020  1.213
 L9A  C1   C2   aromatic  1.388  0.020  1.388
 L9A  C7   N2   single    1.445  0.020  1.445
 L9A  C16  C15  single    1.507  0.020  1.507
 L9A  C16  C17  single    1.483  0.020  1.483
 L9A  C3   N4   single    1.386  0.020  1.386
 L9A  C3   N1   aromatic  1.327  0.020  1.327
 L9A  C14  N4   single    1.372  0.020  1.372
 L9A  C14  C15  single    1.487  0.020  1.487
 L9A  C2   N1   aromatic  1.322  0.020  1.322
 L9A  C15  C17  single    1.508  0.020  1.508
 L9A  C18  H18  single    0.970  0.020  1.090
 L9A  C18  H19  single    0.970  0.020  1.090
 L9A  C18  H20  single    0.970  0.020  1.090
 L9A  C17  H16  single    0.970  0.020  1.090
 L9A  C17  H17  single    0.970  0.020  1.090
 L9A  C16  H14  single    0.970  0.020  1.090
 L9A  C16  H15  single    0.970  0.020  1.090
 L9A  C15  H13  single    0.970  0.020  1.090
 L9A  C11  H11  single    0.930  0.020  1.080
 L9A  C12  H12  single    0.930  0.020  1.080
 L9A  C2   H1   single    0.930  0.020  1.080
 L9A  C4   H2   single    0.930  0.020  1.080
 L9A  N2   H3   single    0.860  0.020  1.020
 L9A  C7   H6   single    0.970  0.020  1.090
 L9A  C7   H5   single    0.970  0.020  1.090
 L9A  C7   H4   single    0.970  0.020  1.090
 L9A  N3   H7   single    0.860  0.020  1.020
 L9A  N4   H8   single    0.860  0.020  1.020
 L9A  C9   H9   single    0.930  0.020  1.080
 L9A  C10  H10  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
 L9A  S1   C13  C8   120.82  3.000
 L9A  C8   C13  C12  121.22  3.000
 L9A  S1   C13  C12  117.96  3.000
 L9A  H20  C18  H19  110.03  3.000
 L9A  H20  C18  H18  110.69  3.000
 L9A  H19  C18  H18  109.81  3.000
 L9A  H20  C18  S1   109.21  3.000
 L9A  H19  C18  S1   106.81  3.000
 L9A  H18  C18  S1   110.22  3.000
 L9A  H17  C17  H16  114.84  3.000
 L9A  H17  C17  C15  117.26  3.000
 L9A  H16  C17  C15  116.52  3.000
 L9A  H17  C17  C16  118.22  3.000
 L9A  H16  C17  C16  118.75  3.000
 L9A  C15  C17  C16   60.54  3.000
 L9A  H15  C16  H14  114.91  3.000
 L9A  H15  C16  C15  116.55  3.000
 L9A  H14  C16  C15  117.15  3.000
 L9A  H15  C16  C17  118.79  3.000
 L9A  H14  C16  C17  118.13  3.000
 L9A  C15  C16  C17   60.55  3.000
 L9A  H13  C15  C14  116.79  3.000
 L9A  H13  C15  C16  116.52  3.000
 L9A  C14  C15  C16  117.74  3.000
 L9A  H13  C15  C17  116.47  3.000
 L9A  C14  C15  C17  117.86  3.000
 L9A  C16  C15  C17   58.91  3.000
 L9A  H11  C11  C10  120.54  3.000
 L9A  H11  C11  C12  119.84  3.000
 L9A  C10  C11  C12  119.61  3.000
 L9A  H12  C12  C11  119.91  3.000
 L9A  H12  C12  C13  120.32  3.000
 L9A  C11  C12  C13  119.76  3.000
 L9A  C6   C1   C5   121.62  3.000
 L9A  C6   C1   C2   121.65  3.000
 L9A  C5   C1   C2   116.71  3.000
 L9A  H1   C2   N1   114.25  3.000
 L9A  H1   C2   C1   119.61  3.000
 L9A  N1   C2   C1   126.11  3.000
 L9A  C3   N1   C2   116.56  3.000
 L9A  N4   C3   C4   117.08  3.000
 L9A  N4   C3   N1   119.46  3.000
 L9A  C4   C3   N1   123.44  3.000
 L9A  H2   C4   C5   120.63  3.000
 L9A  H2   C4   C3   119.66  3.000
 L9A  C5   C4   C3   119.71  3.000
 L9A  N3   C5   C4   121.76  3.000
 L9A  C4   C5   C1   117.28  3.000
 L9A  N3   C5   C1   120.88  3.000
 L9A  H3   N2   C7   117.34  3.000
 L9A  H3   N2   C6   120.26  3.000
 L9A  C7   N2   C6   121.92  3.000
 L9A  H4   C7   H5   108.46  3.000
 L9A  H4   C7   H6   108.35  3.000
 L9A  H5   C7   H6   108.39  3.000
 L9A  H4   C7   N2   108.19  3.000
 L9A  H5   C7   N2   112.10  3.000
 L9A  H6   C7   N2   111.25  3.000
 L9A  H8   N4   C14  115.67  3.000
 L9A  H8   N4   C3   114.69  3.000
 L9A  C14  N4   C3   129.56  3.000
 L9A  C9   C8   N3   121.32  3.000
 L9A  N3   C8   C13  120.51  3.000
 L9A  C9   C8   C13  118.15  3.000
 L9A  H9   C9   C10  119.77  3.000
 L9A  H9   C9   C8   119.54  3.000
 L9A  C10  C9   C8   120.68  3.000
 L9A  H10  C10  C9   119.35  3.000
 L9A  H10  C10  C11  120.07  3.000
 L9A  C9   C10  C11  120.57  3.000
 L9A  O2   C14  N4   124.43  3.000
 L9A  N4   C14  C15  112.84  3.000
 L9A  O2   C14  C15  122.73  3.000
 L9A  O4   S1   O3   117.91  3.000
 L9A  O3   S1   C18  109.13  3.000
 L9A  O4   S1   C18  107.86  3.000
 L9A  O3   S1   C13  109.00  3.000
 L9A  C18  S1   C13  104.53  3.000
 L9A  O4   S1   C13  107.60  3.000
 L9A  H7   N3   C8   117.96  3.000
 L9A  H7   N3   C5   114.80  3.000
 L9A  C8   N3   C5   125.29  3.000
 L9A  O1   C6   N2   121.06  3.000
 L9A  N2   C6   C1   117.36  3.000
 L9A  O1   C6   C1   121.58  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
 L9A  CONST_01  C10  C11  C12  C13    0.00   0.0  0
 L9A  CONST_02  C10  C9   C8   C13    0.00   0.0  0
 L9A  CONST_03  C8   C13  C12  C11    0.00   0.0  0
 L9A  CONST_04  C8   C9   C10  C11    0.00   0.0  0
 L9A  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 L9A  CONST_06  C9   C8   C13  C12    0.00   0.0  0
 L9A  CONST_07  C3   C4   C5   C1     0.00   0.0  0
 L9A  CONST_08  C3   N1   C2   C1     0.00   0.0  0
 L9A  CONST_09  C4   C5   C1   C2     0.00   0.0  0
 L9A  CONST_10  C4   C3   N1   C2     0.00   0.0  0
 L9A  CONST_11  C5   C4   C3   N1     0.00   0.0  0
 L9A  CONST_12  C5   C1   C2   N1     0.00   0.0  0
 L9A  CONST_13  S1   C13  C12  C11  180.00   0.0  0
 L9A  CONST_14  N3   C8   C13  C12  180.00   0.0  0
 L9A  CONST_15  N3   C5   C1   C2   180.00   0.0  0
 L9A  CONST_16  N4   C3   N1   C2   180.00   0.0  0
 L9A  CONST_17  C6   C1   C2   N1   180.00   0.0  0
 L9A  CONST_18  N3   C5   C4   C3   180.00   0.0  0
 L9A  CONST_19  C6   C1   C5   C4   180.00   0.0  0
 L9A  CONST_20  N4   C3   C4   C5   180.00   0.0  0
 L9A  CONST_21  C10  C9   C8   N3   180.00   0.0  0
 L9A  CONST_22  S1   C13  C8   C9   180.00   0.0  0
 L9A  CONST_23  H11  C11  C12  C13  180.00   0.0  0
 L9A  CONST_24  H9   C9   C8   C13  180.00   0.0  0
 L9A  CONST_25  H10  C10  C11  C12  180.00   0.0  0
 L9A  CONST_26  H2   C4   C5   C1   180.00   0.0  0
 L9A  CONST_27  H1   C2   N1   C3   180.00   0.0  0
 L9A  CONST_28  H12  C12  C13  C8   180.00   0.0  0
 L9A  CONST_29  C3   N4   C14  C15  180.00   0.0  0
 L9A  CONST_30  C14  N4   C3   N1     0.00   0.0  0
 L9A  CONST_31  C14  N4   C3   C4   180.00   0.0  0
 L9A  CONST_32  H8   N4   C3   N1   180.00   0.0  0
 L9A  CONST_33  C7   N2   C6   C1   180.00   0.0  0
 L9A  CONST_34  O2   C14  N4   C3     0.00   0.0  0
 L9A  CONST_35  H3   N2   C6   C1     0.00   0.0  0
 L9A  CONST_36  O1   C6   N2   C7     0.00   0.0  0
 L9A  Var_01    C5   N3   C8   C13  136.11  30.0  2
 L9A  Var_02    C14  C15  C16  C17  107.43  30.0  1
 L9A  Var_03    C8   N3   C5   C1   165.93  30.0  1
 L9A  Var_04    C12  C13  S1   C18  113.81  30.0  2
 L9A  Var_05    O2   C14  C15  C17   34.87  30.0  1
 L9A  Var_06    O1   C6   C1   C2   160.16  30.0  2
 L9A  Var_07    H18  C18  S1   C13   64.29  30.0  3
 L9A  Var_08    H6   C7   N2   C6   -54.89  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
 L9A  chir_01  C15  C16  C14  C17  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
 L9A  plan-1  C13  0.020
 L9A  plan-1  C11  0.020
 L9A  plan-1  C12  0.020
 L9A  plan-1  C8   0.020
 L9A  plan-1  C9   0.020
 L9A  plan-1  C10  0.020
 L9A  plan-1  S1   0.020
 L9A  plan-1  H11  0.020
 L9A  plan-1  H12  0.020
 L9A  plan-1  H9   0.020
 L9A  plan-1  H10  0.020
 L9A  plan-1  N3   0.020
 L9A  plan-2  C1   0.020
 L9A  plan-2  C2   0.020
 L9A  plan-2  N1   0.020
 L9A  plan-2  C3   0.020
 L9A  plan-2  C4   0.020
 L9A  plan-2  C5   0.020
 L9A  plan-2  N4   0.020
 L9A  plan-2  H1   0.020
 L9A  plan-2  H2   0.020
 L9A  plan-2  N3   0.020
 L9A  plan-2  C6   0.020
 L9A  plan-3  C1   0.020
 L9A  plan-3  N2   0.020
 L9A  plan-3  C7   0.020
 L9A  plan-3  O1   0.020
 L9A  plan-3  H3   0.020
 L9A  plan-3  C6   0.020
 L9A  plan-4  C15  0.020
 L9A  plan-4  C3   0.020
 L9A  plan-4  N4   0.020
 L9A  plan-4  C14  0.020
 L9A  plan-4  O2   0.020
 L9A  plan-4  H8   0.020

