# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 20:54:08 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}indolizine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(F)cc(c1)[S](=O)(=O)c2ccc(CNC(=O)c3ccc4cccn4c3)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
 2RM  2RM  N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}indolizine-6-carboxamide  ligand  46  30  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2RM
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
 2RM  C1   C  CR15  0  -0.348  -8.1301  -0.1848  -2.5379
 2RM  C2   C  CR15  0  -0.395  -8.1492   0.7950  -1.5239
 2RM  C3   C  CR56  0   0.401  -7.0015   0.6276  -0.7747
 2RM  C4   C  CR16  0  -0.356  -6.4374   1.2694   0.3510
 2RM  C5   C  CR16  0  -0.207  -5.2554   0.8406   0.8643
 2RM  C6   C  CR6   0  -0.206  -4.5681  -0.2664   0.2710
 2RM  C7   C  CR16  0   0.064  -5.1132  -0.8731  -0.8183
 2RM  N8   N  N     0  -0.535  -6.2950  -0.4435  -1.3300
 2RM  C9   C  CR15  0  -0.061  -6.9868  -0.9335  -2.4035
 2RM  C10  C  C     0   0.548  -3.2735  -0.8185   0.7610
 2RM  O11  O  O     0  -0.481  -2.6992  -1.7240   0.1706
 2RM  N12  N  NH1   0  -0.675  -2.7698  -0.2719   1.8834
 2RM  C13  C  CH2   0  -0.331  -1.5440  -0.7284   2.4787
 2RM  C14  C  CR6   0   0.101  -0.2867  -0.1214   1.9027
 2RM  C15  C  CR16  0  -0.270   0.9341  -0.4522   2.4931
 2RM  C16  C  CR16  0  -0.207   2.1197   0.0714   2.0168
 2RM  C17  C  CR6   0  -0.190   2.0851   0.9253   0.9191
 2RM  C18  C  CR16  0  -0.225   0.8863   1.2692   0.3167
 2RM  C19  C  CR16  0  -0.281  -0.2973   0.7448   0.8178
 2RM  S20  S  S     0   1.228   3.6013   1.5953   0.3062
 2RM  O21  O  OS    0  -0.642   3.2875   2.6357  -0.6657
 2RM  O22  O  OS    0  -0.642   4.4643   1.8965   1.4421
 2RM  C23  C  CR6   0  -0.142   4.3319   0.2288  -0.5723
 2RM  C24  C  CR16  0  -0.396   3.9384  -0.0057  -1.8812
 2RM  C25  C  CR6   0   0.568   4.5134  -1.0816  -2.5283
 2RM  C26  C  CR16  0  -0.540   5.4477  -1.9037  -1.9265
 2RM  C27  C  CR6   0   0.572   5.8027  -1.6180  -0.6231
 2RM  C28  C  CR16  0  -0.416   5.2658  -0.5576   0.0820
 2RM  F29  F  F     0  -0.297   6.7055  -2.3958  -0.0240
 2RM  F30  F  F     0  -0.297   4.1602  -1.3390  -3.7884
 2RM  H1   H  HCR5  0   0.258  -8.8822  -0.3345  -3.2965
 2RM  H2   H  HCR5  0   0.254  -8.9094   1.5396  -1.3508
 2RM  H3   H  HCR6  0   0.274  -6.9660   2.1047   0.7896
 2RM  H4   H  HCR6  0   0.256  -4.8506   1.3627   1.7200
 2RM  H5   H  HCR6  0   0.306  -4.6485  -1.7091  -1.3206
 2RM  H6   H  HCR5  0   0.287  -6.6095  -1.7663  -2.9735
 2RM  H7   H  HNH1  0   0.419  -3.2731   0.4482   2.3714
 2RM  H8   H  HCH2  0   0.287  -1.5899  -0.5008   3.5442
 2RM  H9   H  HCH2  0   0.275  -1.4775  -1.8153   2.3996
 2RM  H10  H  HCR6  0   0.270   0.9562  -1.1216   3.3444
 2RM  H11  H  HCR6  0   0.285   3.0534  -0.1879   2.4986
 2RM  H12  H  HCR6  0   0.286   0.8600   1.9394  -0.5314
 2RM  H13  H  HCR6  0   0.260  -1.2307   1.0341   0.3550
 2RM  H14  H  HCR6  0   0.311   3.2155   0.6185  -2.3890
 2RM  H15  H  HCR6  0   0.321   5.8863  -2.7380  -2.4579
 2RM  H16  H  HCR6  0   0.312   5.5747  -0.3612   1.0995

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
 2RM  F29  C27  single    1.334  0.020  1.334
 2RM  C27  C28  aromatic  1.382  0.020  1.382
 2RM  C27  C26  aromatic  1.381  0.020  1.381
 2RM  C28  C23  aromatic  1.385  0.020  1.385
 2RM  C26  C25  aromatic  1.382  0.020  1.382
 2RM  O22  S20  double    1.458  0.020  1.458
 2RM  C23  C24  aromatic  1.387  0.020  1.387
 2RM  C23  S20  single    1.781  0.020  1.781
 2RM  C25  C24  aromatic  1.381  0.020  1.381
 2RM  C25  F30  single    1.334  0.020  1.334
 2RM  S20  O21  double    1.458  0.020  1.458
 2RM  S20  C17  single    1.767  0.020  1.767
 2RM  C18  C17  aromatic  1.385  0.020  1.385
 2RM  C18  C19  aromatic  1.388  0.020  1.388
 2RM  C17  C16  aromatic  1.391  0.020  1.391
 2RM  C19  C14  aromatic  1.388  0.020  1.388
 2RM  C16  C15  aromatic  1.381  0.020  1.381
 2RM  C14  C15  aromatic  1.396  0.020  1.396
 2RM  C14  C13  single    1.510  0.020  1.510
 2RM  C13  N12  single    1.437  0.020  1.437
 2RM  O11  C10  double    1.224  0.020  1.224
 2RM  N12  C10  single    1.346  0.020  1.346
 2RM  C10  C6   single    1.490  0.020  1.490
 2RM  C6   C5   aromatic  1.432  0.020  1.432
 2RM  C6   C7   aromatic  1.361  0.020  1.361
 2RM  C5   C4   aromatic  1.358  0.020  1.358
 2RM  C7   N8   aromatic  1.358  0.020  1.358
 2RM  C4   C3   aromatic  1.413  0.020  1.413
 2RM  N8   C3   aromatic  1.398  0.020  1.398
 2RM  N8   C9   aromatic  1.368  0.020  1.368
 2RM  C3   C2   aromatic  1.381  0.020  1.381
 2RM  C9   C1   aromatic  1.373  0.020  1.373
 2RM  C2   C1   aromatic  1.410  0.020  1.410
 2RM  C1   H1   single    0.930  0.020  1.080
 2RM  C2   H2   single    0.930  0.020  1.080
 2RM  C4   H3   single    0.930  0.020  1.080
 2RM  C5   H4   single    0.930  0.020  1.080
 2RM  C7   H5   single    0.930  0.020  1.080
 2RM  C9   H6   single    0.930  0.020  1.080
 2RM  N12  H7   single    0.860  0.020  1.020
 2RM  C13  H8   single    0.970  0.020  1.090
 2RM  C13  H9   single    0.970  0.020  1.090
 2RM  C15  H10  single    0.930  0.020  1.080
 2RM  C16  H11  single    0.930  0.020  1.080
 2RM  C18  H12  single    0.930  0.020  1.080
 2RM  C19  H13  single    0.930  0.020  1.080
 2RM  C24  H14  single    0.930  0.020  1.080
 2RM  C26  H15  single    0.930  0.020  1.080
 2RM  C28  H16  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
 2RM  H1   C1   C9   125.00  3.000
 2RM  H1   C1   C2   126.35  3.000
 2RM  C9   C1   C2   108.65  3.000
 2RM  H2   C2   C3   125.64  3.000
 2RM  H2   C2   C1   127.22  3.000
 2RM  C3   C2   C1   107.14  3.000
 2RM  N8   C3   C4   117.56  3.000
 2RM  N8   C3   C2   107.30  3.000
 2RM  C4   C3   C2   135.14  3.000
 2RM  H3   C4   C5   121.07  3.000
 2RM  H3   C4   C3   118.60  3.000
 2RM  C5   C4   C3   120.33  3.000
 2RM  H4   C5   C6   121.44  3.000
 2RM  H4   C5   C4   118.20  3.000
 2RM  C6   C5   C4   120.36  3.000
 2RM  C10  C6   C7   116.49  3.000
 2RM  C7   C6   C5   118.95  3.000
 2RM  C10  C6   C5   124.56  3.000
 2RM  H5   C7   N8   116.36  3.000
 2RM  H5   C7   C6   123.02  3.000
 2RM  N8   C7   C6   120.62  3.000
 2RM  C9   N8   C7   128.52  3.000
 2RM  C9   N8   C3   109.30  3.000
 2RM  C7   N8   C3   122.18  3.000
 2RM  H6   C9   N8   121.00  3.000
 2RM  H6   C9   C1   131.39  3.000
 2RM  N8   C9   C1   107.61  3.000
 2RM  N12  C10  O11  121.80  3.000
 2RM  N12  C10  C6   116.67  3.000
 2RM  O11  C10  C6   121.53  3.000
 2RM  H7   N12  C13  116.98  3.000
 2RM  H7   N12  C10  120.55  3.000
 2RM  C13  N12  C10  122.38  3.000
 2RM  H9   C13  H8   106.33  3.000
 2RM  H9   C13  C14  108.77  3.000
 2RM  H8   C13  C14  108.89  3.000
 2RM  H9   C13  N12  109.76  3.000
 2RM  H8   C13  N12  107.61  3.000
 2RM  C14  C13  N12  115.12  3.000
 2RM  C19  C14  C15  119.02  3.000
 2RM  C15  C14  C13  118.13  3.000
 2RM  C19  C14  C13  122.85  3.000
 2RM  H10  C15  C16  119.20  3.000
 2RM  H10  C15  C14  119.79  3.000
 2RM  C16  C15  C14  121.01  3.000
 2RM  H11  C16  C17  121.31  3.000
 2RM  H11  C16  C15  119.77  3.000
 2RM  C17  C16  C15  118.92  3.000
 2RM  S20  C17  C18  119.84  3.000
 2RM  C18  C17  C16  121.14  3.000
 2RM  S20  C17  C16  119.02  3.000
 2RM  H12  C18  C19  119.77  3.000
 2RM  H12  C18  C17  121.07  3.000
 2RM  C19  C18  C17  119.16  3.000
 2RM  H13  C19  C18  118.72  3.000
 2RM  H13  C19  C14  120.53  3.000
 2RM  C18  C19  C14  120.75  3.000
 2RM  C23  S20  O22  107.45  3.000
 2RM  C23  S20  O21  107.88  3.000
 2RM  O22  S20  O21  119.96  3.000
 2RM  O21  S20  C17  108.49  3.000
 2RM  C23  S20  C17  103.42  3.000
 2RM  O22  S20  C17  108.41  3.000
 2RM  C28  C23  C24  122.76  3.000
 2RM  C24  C23  S20  118.61  3.000
 2RM  C28  C23  S20  118.63  3.000
 2RM  H14  C24  C25  120.53  3.000
 2RM  H14  C24  C23  122.35  3.000
 2RM  C25  C24  C23  117.12  3.000
 2RM  F30  C25  C26  118.40  3.000
 2RM  F30  C25  C24  118.87  3.000
 2RM  C26  C25  C24  122.74  3.000
 2RM  H15  C26  C27  121.26  3.000
 2RM  H15  C26  C25  121.25  3.000
 2RM  C27  C26  C25  117.50  3.000
 2RM  F29  C27  C28  118.77  3.000
 2RM  C28  C27  C26  122.72  3.000
 2RM  F29  C27  C26  118.51  3.000
 2RM  H16  C28  C27  120.56  3.000
 2RM  H16  C28  C23  122.28  3.000
 2RM  C27  C28  C23  117.16  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
 2RM  CONST_01  C7   N8   C9   C1    180.00   0.0  0
 2RM  CONST_02  C3   N8   C9   C1      0.00   0.0  0
 2RM  CONST_03  C4   C3   C2   C1    180.00   0.0  0
 2RM  CONST_04  N8   C3   C2   C1      0.00   0.0  0
 2RM  CONST_05  C5   C4   C3   C2    180.00   0.0  0
 2RM  CONST_06  C7   N8   C3   C2    180.00   0.0  0
 2RM  CONST_07  C9   N8   C3   C2      0.00   0.0  0
 2RM  CONST_08  N8   C9   C1   C2      0.00   0.0  0
 2RM  CONST_09  C6   C5   C4   C3      0.00   0.0  0
 2RM  CONST_10  C6   C7   N8   C3      0.00   0.0  0
 2RM  CONST_11  C9   C1   C2   C3      0.00   0.0  0
 2RM  CONST_12  C7   C6   C5   C4      0.00   0.0  0
 2RM  CONST_13  C7   N8   C3   C4      0.00   0.0  0
 2RM  CONST_14  C9   N8   C3   C4    180.00   0.0  0
 2RM  CONST_15  N8   C7   C6   C5      0.00   0.0  0
 2RM  CONST_16  N8   C3   C4   C5      0.00   0.0  0
 2RM  CONST_17  C9   N8   C7   C6    180.00   0.0  0
 2RM  CONST_18  C17  C18  C19  C14     0.00   0.0  0
 2RM  CONST_19  C17  C16  C15  C14     0.00   0.0  0
 2RM  CONST_20  C18  C17  C16  C15     0.00   0.0  0
 2RM  CONST_21  C18  C19  C14  C15     0.00   0.0  0
 2RM  CONST_22  C19  C18  C17  C16     0.00   0.0  0
 2RM  CONST_23  C19  C14  C15  C16     0.00   0.0  0
 2RM  CONST_24  C26  C27  C28  C23     0.00   0.0  0
 2RM  CONST_25  C26  C25  C24  C23     0.00   0.0  0
 2RM  CONST_26  C27  C28  C23  C24     0.00   0.0  0
 2RM  CONST_27  C27  C26  C25  C24     0.00   0.0  0
 2RM  CONST_28  C28  C27  C26  C25     0.00   0.0  0
 2RM  CONST_29  C28  C23  C24  C25     0.00   0.0  0
 2RM  CONST_30  C10  C6   C5   C4    180.00   0.0  0
 2RM  CONST_31  C10  C6   C7   N8    180.00   0.0  0
 2RM  CONST_32  C18  C19  C14  C13   180.00   0.0  0
 2RM  CONST_33  C16  C15  C14  C13   180.00   0.0  0
 2RM  CONST_34  S20  C17  C16  C15   180.00   0.0  0
 2RM  CONST_35  S20  C17  C18  C19   180.00   0.0  0
 2RM  CONST_36  C27  C28  C23  S20   180.00   0.0  0
 2RM  CONST_37  C25  C24  C23  S20   180.00   0.0  0
 2RM  CONST_38  F29  C27  C28  C23   180.00   0.0  0
 2RM  CONST_39  F30  C25  C24  C23   180.00   0.0  0
 2RM  CONST_40  F29  C27  C26  C25   180.00   0.0  0
 2RM  CONST_41  F30  C25  C26  C27   180.00   0.0  0
 2RM  CONST_42  H3   C4   C3   C2      0.00   0.0  0
 2RM  CONST_43  H6   C9   C1   C2    180.00   0.0  0
 2RM  CONST_44  H4   C5   C4   C3    180.00   0.0  0
 2RM  CONST_45  H5   C7   N8   C3    180.00   0.0  0
 2RM  CONST_46  H1   C1   C2   C3    180.00   0.0  0
 2RM  CONST_47  H2   C2   C3   C4      0.00   0.0  0
 2RM  CONST_48  H12  C18  C19  C14   180.00   0.0  0
 2RM  CONST_49  H11  C16  C15  C14   180.00   0.0  0
 2RM  CONST_50  H13  C19  C14  C15   180.00   0.0  0
 2RM  CONST_51  H10  C15  C16  C17   180.00   0.0  0
 2RM  CONST_52  H16  C28  C23  C24   180.00   0.0  0
 2RM  CONST_53  H15  C26  C25  C24   180.00   0.0  0
 2RM  CONST_54  H14  C24  C25  C26   180.00   0.0  0
 2RM  CONST_55  C13  N12  C10  C6    180.00   0.0  0
 2RM  CONST_56  H7   N12  C10  C6      0.00   0.0  0
 2RM  CONST_57  C13  N12  C10  O11     0.00   0.0  0
 2RM  Var_01    C23  S20  C17  C16    76.09  30.0  1
 2RM  Var_02    C28  C23  S20  C17   -95.93  30.0  2
 2RM  Var_03    O11  C10  C6   C5   -176.21  30.0  2
 2RM  Var_04    C19  C14  C13  N12    -4.22  30.0  2
 2RM  Var_05    C14  C13  N12  C10    84.70  30.0  1

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
 2RM  plan-1  C13  0.020
 2RM  plan-1  C14  0.020
 2RM  plan-1  C15  0.020
 2RM  plan-1  C16  0.020
 2RM  plan-1  C17  0.020
 2RM  plan-1  C18  0.020
 2RM  plan-1  C19  0.020
 2RM  plan-1  S20  0.020
 2RM  plan-1  H10  0.020
 2RM  plan-1  H11  0.020
 2RM  plan-1  H12  0.020
 2RM  plan-1  H13  0.020
 2RM  plan-2  S20  0.020
 2RM  plan-2  C23  0.020
 2RM  plan-2  C24  0.020
 2RM  plan-2  C25  0.020
 2RM  plan-2  C26  0.020
 2RM  plan-2  C27  0.020
 2RM  plan-2  C28  0.020
 2RM  plan-2  F29  0.020
 2RM  plan-2  F30  0.020
 2RM  plan-2  H14  0.020
 2RM  plan-2  H15  0.020
 2RM  plan-2  H16  0.020
 2RM  plan-3  C1   0.020
 2RM  plan-3  C2   0.020
 2RM  plan-3  C3   0.020
 2RM  plan-3  C4   0.020
 2RM  plan-3  C5   0.020
 2RM  plan-3  C6   0.020
 2RM  plan-3  C7   0.020
 2RM  plan-3  N8   0.020
 2RM  plan-3  C9   0.020
 2RM  plan-3  C10  0.020
 2RM  plan-3  H1   0.020
 2RM  plan-3  H2   0.020
 2RM  plan-3  H3   0.020
 2RM  plan-3  H4   0.020
 2RM  plan-3  H5   0.020
 2RM  plan-3  H6   0.020
 2RM  plan-4  C6   0.020
 2RM  plan-4  C10  0.020
 2RM  plan-4  O11  0.020
 2RM  plan-4  N12  0.020
 2RM  plan-4  C13  0.020
 2RM  plan-4  H7   0.020

