# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 10:10:53 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: (3~{R})-1-pyrrolo[1,2-a]quinoxalin-4-ylpiperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCCN(C1)c2nc3ccccc3n4cccc24
#
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
 ER6  ER6  '(3~{R})-1-pyrrolo[1,2-a]quinoxalin-4-ylpiperidine-3-carboxylic acid'  ligand  38  22  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ER6
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
 ER6  C4   C  CR16   0  -0.331  32.6012  -21.9313  6.3544
 ER6  C14  C  CH2    0  -0.417  33.6113  -15.4913  3.6076
 ER6  C5   C  CR6    0   0.186  33.6838  -21.3262  5.6976
 ER6  C6   C  CR6    0   0.365  34.7382  -22.1539  5.2831
 ER6  C11  C  CR15   0  -0.052  37.0249  -22.0252  4.3547
 ER6  C7   C  C      0   0.464  34.6280  -19.3933  4.8321
 ER6  C8   C  CR5    0   0.278  35.8252  -20.1335  4.4734
 ER6  C9   C  CR15   0  -0.389  37.0967  -19.8060  4.0289
 ER6  C10  C  CR15   0  -0.345  37.8385  -20.9959  3.9503
 ER6  C12  C  CH2    0  -0.309  35.3266  -17.3435  3.6089
 ER6  C13  C  CH2    0  -0.429  34.4780  -16.4066  2.7588
 ER6  N1   N  N      0  -0.507  33.6490  -19.9841  5.4617
 ER6  N2   N  NR5    0  -0.596  35.8137  -21.5054  4.6822
 ER6  C3   C  CR16   0  -0.257  32.5711  -23.2923  6.5779
 ER6  N3   N  NT     0  -0.501  34.5113  -18.0676  4.5657
 ER6  C1   C  CR16   0  -0.324  34.7086  -23.5283  5.5010
 ER6  C15  C  CH1    0  -0.394  32.7530  -16.3026  4.5699
 ER6  C16  C  CH2    0  -0.289  33.6525  -17.2223  5.3894
 ER6  C17  C  C      0   0.422  31.5653  -17.0562  3.9131
 ER6  C2   C  CR16   0  -0.275  33.6260  -24.0966  6.1466
 ER6  O1   O  OC    -1  -0.611  30.9168  -17.8101  4.6672
 ER6  O2   O  O      0  -0.594  31.3195  -16.8245  2.7130
 ER6  H1   H  HCR6   0   0.251  31.7837  -21.2982  6.6767
 ER6  H4   H  HCR5   0   0.291  37.2369  -23.0766  4.4451
 ER6  H5   H  HCR5   0   0.266  37.4736  -18.8241  3.8041
 ER6  H6   H  HCR5   0   0.255  38.8651  -21.0940  3.6357
 ER6  H7   H  HCH2   0   0.254  35.8224  -18.0440  2.9447
 ER6  H8   H  HCH2   0   0.218  36.1029  -16.7675  4.1299
 ER6  H9   H  HCH2   0   0.223  33.8437  -16.9989  2.0979
 ER6  H10  H  HCH2   0   0.227  35.1530  -15.8276  2.1240
 ER6  H11  H  HCR6   0   0.252  31.7244  -23.7364  7.0850
 ER6  H12  H  HCR6   0   0.272  35.5234  -24.1594  5.1721
 ER6  H13  H  HCH1   0   0.234  32.3011  -15.6141  5.2958
 ER6  H14  H  HCH2   0   0.222  34.3072  -16.6073  6.0219
 ER6  H15  H  HCH2   0   0.259  33.0595  -17.8545  6.0396
 ER6  H16  H  HCR6   0   0.255  33.6049  -25.1647  6.3154
 ER6  H2   H  HCH2   0   0.203  34.2580  -14.8193  4.1838
 ER6  H3   H  HCH2   0   0.222  32.9916  -14.8575  2.9733

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
 ER6  C13  C14  single    1.520  0.020  1.520
 ER6  C13  C12  single    1.523  0.020  1.523
 ER6  O2   C17  deloc     1.247  0.020  1.247
 ER6  C14  C15  single    1.523  0.020  1.523
 ER6  C12  N3   single    1.451  0.020  1.451
 ER6  C10  C9   aromatic  1.404  0.020  1.404
 ER6  C10  C11  aromatic  1.373  0.020  1.373
 ER6  C9   C8   aromatic  1.386  0.020  1.386
 ER6  C17  C15  single    1.552  0.020  1.552
 ER6  C17  O1   deloc     1.248  0.020  1.248
 ER6  C11  N2   aromatic  1.358  0.020  1.358
 ER6  C8   N2   aromatic  1.388  0.020  1.388
 ER6  C8   C7   aromatic  1.452  0.020  1.452
 ER6  C15  C16  single    1.525  0.020  1.525
 ER6  N2   C6   aromatic  1.392  0.020  1.392
 ER6  N3   C7   single    1.357  0.020  1.357
 ER6  N3   C16  single    1.460  0.020  1.460
 ER6  C7   N1   aromatic  1.305  0.020  1.305
 ER6  C6   C1   aromatic  1.392  0.020  1.392
 ER6  C6   C5   aromatic  1.403  0.020  1.403
 ER6  C1   C2   aromatic  1.383  0.020  1.383
 ER6  N1   C5   aromatic  1.363  0.020  1.363
 ER6  C5   C4   aromatic  1.403  0.020  1.403
 ER6  C2   C3   aromatic  1.395  0.020  1.395
 ER6  C4   C3   aromatic  1.380  0.020  1.380
 ER6  C4   H1   single    0.930  0.020  1.080
 ER6  C14  H2   single    0.970  0.020  1.090
 ER6  C14  H3   single    0.970  0.020  1.090
 ER6  C11  H4   single    0.930  0.020  1.080
 ER6  C9   H5   single    0.930  0.020  1.080
 ER6  C10  H6   single    0.930  0.020  1.080
 ER6  C12  H7   single    0.970  0.020  1.090
 ER6  C12  H8   single    0.970  0.020  1.090
 ER6  C13  H9   single    0.970  0.020  1.090
 ER6  C13  H10  single    0.970  0.020  1.090
 ER6  C3   H11  single    0.930  0.020  1.080
 ER6  C1   H12  single    0.930  0.020  1.080
 ER6  C15  H13  single    0.970  0.020  1.090
 ER6  C16  H14  single    0.970  0.020  1.090
 ER6  C16  H15  single    0.970  0.020  1.090
 ER6  C2   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
 ER6  H1   C4   C3   120.80  3.000
 ER6  H1   C4   C5   118.00  3.000
 ER6  C3   C4   C5   121.20  3.000
 ER6  H3   C14  H2   106.55  3.000
 ER6  H3   C14  C15  110.91  3.000
 ER6  H2   C14  C15  109.07  3.000
 ER6  H3   C14  C13  110.45  3.000
 ER6  H2   C14  C13  109.05  3.000
 ER6  C15  C14  C13  110.69  3.000
 ER6  N1   C5   C6   123.29  3.000
 ER6  N1   C5   C4   119.06  3.000
 ER6  C6   C5   C4   117.62  3.000
 ER6  C1   C6   N2   122.95  3.000
 ER6  C1   C6   C5   121.35  3.000
 ER6  N2   C6   C5   115.67  3.000
 ER6  H4   C11  N2   121.96  3.000
 ER6  H4   C11  C10  129.81  3.000
 ER6  N2   C11  C10  108.22  3.000
 ER6  N3   C7   N1   118.18  3.000
 ER6  N1   C7   C8   120.44  3.000
 ER6  N3   C7   C8   121.34  3.000
 ER6  N2   C8   C9   106.82  3.000
 ER6  N2   C8   C7   117.38  3.000
 ER6  C9   C8   C7   135.63  3.000
 ER6  H5   C9   C10  125.22  3.000
 ER6  H5   C9   C8   127.16  3.000
 ER6  C10  C9   C8   107.60  3.000
 ER6  H6   C10  C9   126.61  3.000
 ER6  H6   C10  C11  125.60  3.000
 ER6  C9   C10  C11  107.79  3.000
 ER6  H8   C12  H7   107.81  3.000
 ER6  H8   C12  N3   110.25  3.000
 ER6  H7   C12  N3   109.77  3.000
 ER6  H8   C12  C13  109.63  3.000
 ER6  H7   C12  C13  108.06  3.000
 ER6  N3   C12  C13  111.23  3.000
 ER6  H10  C13  H9   107.16  3.000
 ER6  H10  C13  C12  107.82  3.000
 ER6  H9   C13  C12  109.16  3.000
 ER6  H10  C13  C14  110.95  3.000
 ER6  H9   C13  C14  109.49  3.000
 ER6  C12  C13  C14  112.11  3.000
 ER6  C7   N1   C5   120.66  3.000
 ER6  C8   N2   C11  109.56  3.000
 ER6  C8   N2   C6   122.13  3.000
 ER6  C11  N2   C6   127.93  3.000
 ER6  H11  C3   C2   120.00  3.000
 ER6  H11  C3   C4   119.86  3.000
 ER6  C2   C3   C4   120.15  3.000
 ER6  C16  N3   C12  114.44  3.000
 ER6  C16  N3   C7   120.36  3.000
 ER6  C12  N3   C7   124.66  3.000
 ER6  H12  C1   C2   119.46  3.000
 ER6  H12  C1   C6   120.83  3.000
 ER6  C2   C1   C6   119.71  3.000
 ER6  H13  C15  C17  105.62  3.000
 ER6  H13  C15  C16  105.41  3.000
 ER6  C17  C15  C16  112.69  3.000
 ER6  H13  C15  C14  108.40  3.000
 ER6  C16  C15  C14  109.16  3.000
 ER6  C17  C15  C14  114.98  3.000
 ER6  H15  C16  H14  107.90  3.000
 ER6  H15  C16  C15  110.57  3.000
 ER6  H14  C16  C15  108.85  3.000
 ER6  H15  C16  N3   108.83  3.000
 ER6  H14  C16  N3   107.37  3.000
 ER6  C15  C16  N3   113.14  3.000
 ER6  O2   C17  O1   126.26  3.000
 ER6  O1   C17  C15  115.79  3.000
 ER6  O2   C17  C15  117.90  3.000
 ER6  H16  C2   C1   119.61  3.000
 ER6  H16  C2   C3   120.42  3.000
 ER6  C1   C2   C3   119.97  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
 ER6  CONST_01  N2   C6   C5   C4    180.00   0.0  0
 ER6  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 ER6  CONST_03  C7   N1   C5   C4    180.00   0.0  0
 ER6  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 ER6  CONST_05  C11  N2   C6   C5    180.00   0.0  0
 ER6  CONST_06  C8   N2   C6   C5      0.00   0.0  0
 ER6  CONST_07  C2   C1   C6   C5      0.00   0.0  0
 ER6  CONST_08  C8   C7   N1   C5      0.00   0.0  0
 ER6  CONST_09  C2   C3   C4   C5      0.00   0.0  0
 ER6  CONST_10  C10  C11  N2   C6    180.00   0.0  0
 ER6  CONST_11  C9   C8   N2   C6    180.00   0.0  0
 ER6  CONST_12  C7   C8   N2   C6      0.00   0.0  0
 ER6  CONST_13  C3   C2   C1   C6      0.00   0.0  0
 ER6  CONST_14  C7   N1   C5   C6      0.00   0.0  0
 ER6  CONST_15  C3   C4   C5   C6      0.00   0.0  0
 ER6  CONST_16  C8   C9   C10  C11     0.00   0.0  0
 ER6  CONST_17  C9   C8   N2   C11     0.00   0.0  0
 ER6  CONST_18  C7   C8   N2   C11   180.00   0.0  0
 ER6  CONST_19  C1   C6   N2   C11     0.00   0.0  0
 ER6  CONST_20  C10  C9   C8   C7    180.00   0.0  0
 ER6  CONST_21  C10  C11  N2   C8      0.00   0.0  0
 ER6  CONST_22  C1   C6   N2   C8    180.00   0.0  0
 ER6  CONST_23  N2   C11  C10  C9      0.00   0.0  0
 ER6  CONST_24  N1   C7   C8   C9    180.00   0.0  0
 ER6  CONST_25  N2   C8   C9   C10     0.00   0.0  0
 ER6  CONST_26  N2   C8   C7   N1      0.00   0.0  0
 ER6  CONST_27  N2   C6   C5   N1      0.00   0.0  0
 ER6  CONST_28  C1   C6   C5   N1    180.00   0.0  0
 ER6  CONST_29  C3   C4   C5   N1    180.00   0.0  0
 ER6  CONST_30  C2   C1   C6   N2    180.00   0.0  0
 ER6  CONST_31  N3   C7   N1   C5    180.00   0.0  0
 ER6  CONST_32  N3   C7   C8   C9      0.00   0.0  0
 ER6  CONST_33  N3   C7   C8   N2    180.00   0.0  0
 ER6  CONST_34  H16  C2   C3   C4    180.00   0.0  0
 ER6  CONST_35  H12  C1   C6   C5    180.00   0.0  0
 ER6  CONST_36  H11  C3   C4   C5    180.00   0.0  0
 ER6  CONST_37  H4   C11  N2   C6      0.00   0.0  0
 ER6  CONST_38  H1   C4   C5   C6    180.00   0.0  0
 ER6  CONST_39  H5   C9   C10  C11   180.00   0.0  0
 ER6  CONST_40  H6   C10  C9   C8    180.00   0.0  0
 ER6  Var_01    N3   C12  C13  C14    52.60  30.0  1
 ER6  Var_02    C13  C12  N3   C7    136.08  30.0  1
 ER6  Var_03    C15  C16  N3   C7   -133.53  30.0  1
 ER6  Var_04    C12  N3   C7   C8     18.16  30.0  2
 ER6  Var_05    C15  C14  C13  C12   -54.83  30.0  1

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
 ER6  chir_01  C15  C14  C17  C16  negativ

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
 ER6  plan-1  C4   0.020
 ER6  plan-1  C5   0.020
 ER6  plan-1  C6   0.020
 ER6  plan-1  C11  0.020
 ER6  plan-1  C7   0.020
 ER6  plan-1  C8   0.020
 ER6  plan-1  C9   0.020
 ER6  plan-1  C10  0.020
 ER6  plan-1  N1   0.020
 ER6  plan-1  N2   0.020
 ER6  plan-1  C3   0.020
 ER6  plan-1  N3   0.020
 ER6  plan-1  C1   0.020
 ER6  plan-1  C2   0.020
 ER6  plan-1  H1   0.020
 ER6  plan-1  H4   0.020
 ER6  plan-1  H5   0.020
 ER6  plan-1  H6   0.020
 ER6  plan-1  H11  0.020
 ER6  plan-1  H12  0.020
 ER6  plan-1  H16  0.020
 ER6  plan-2  C15  0.020
 ER6  plan-2  C17  0.020
 ER6  plan-2  O1   0.020
 ER6  plan-2  O2   0.020

