# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:14:19 2021
#   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  39  22  .  2022-08-10  2022-11-17
;
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  -0.329  32.4861  -21.5673  6.0689
 ER6  C14  C  CH2   0  -0.439  33.3302  -15.9903  3.3309
 ER6  C5   C  CR66  0   0.192  33.6754  -21.0330  5.5557
 ER6  C6   C  CR66  0   0.375  34.6699  -21.9286  5.1324
 ER6  C11  C  CR15  0  -0.056  37.0195  -21.9697  4.3495
 ER6  C7   C  CR6   0   0.444  34.8867  -19.1576  4.9634
 ER6  C8   C  CR56  0   0.315  36.0148  -19.9832  4.5946
 ER6  C9   C  CR15  0  -0.398  37.3303  -19.7466  4.2383
 ER6  C10  C  CR15  0  -0.341  37.9516  -20.9972  4.0781
 ER6  C12  C  CH2   0  -0.339  35.5434  -17.1344  3.7077
 ER6  C13  C  CH2   0  -0.432  34.4488  -16.8091  2.6972
 ER6  N1   N  N     0  -0.495  33.8021  -19.6744  5.4537
 ER6  N2   N  N     0  -0.598  35.8501  -21.3565  4.6693
 ER6  C3   C  CR16  0  -0.258  32.2933  -22.9312  6.1455
 ER6  N3   N  NT    0  -0.487  34.9849  -17.7962  4.8818
 ER6  C1   C  CR16  0  -0.326  34.4765  -23.3053  5.2029
 ER6  C15  C  CH1   0  -0.379  32.7965  -16.6062  4.6250
 ER6  C16  C  CH2   0  -0.328  33.9743  -16.9890  5.5379
 ER6  C17  C  C     0   0.577  31.8441  -17.7531  4.3893
 ER6  C2   C  CR16  0  -0.272  33.2897  -23.8036  5.7070
 ER6  O1   O  OH1   0  -0.601  31.1090  -18.0064  5.4694
 ER6  O2   O  O     0  -0.446  31.6988  -18.3440  3.3479
 ER6  H1   H  HCR6  0   0.252  31.7201  -20.8795  6.4030
 ER6  H3   H  HCH2  0   0.247  32.5203  -15.8292  2.6175
 ER6  H4   H  HCR5  0   0.294  37.1224  -23.0413  4.3538
 ER6  H5   H  HCR5  0   0.264  37.8071  -18.7881  4.1202
 ER6  H6   H  HCR5  0   0.260  38.9785  -21.1747  3.8015
 ER6  H7   H  HCH2  0   0.264  36.2974  -17.7577  3.2405
 ER6  H8   H  HCH2  0   0.241  36.0399  -16.2171  4.0383
 ER6  H9   H  HCH2  0   0.233  34.0566  -17.7399  2.2823
 ER6  H10  H  HCH2  0   0.241  34.8887  -16.2520  1.8670
 ER6  H11  H  HCR6  0   0.258  31.3673  -23.3237  6.5440
 ER6  H12  H  HCR6  0   0.276  35.2445  -23.9897  4.8676
 ER6  H13  H  HCH1  0   0.285  32.2287  -15.8441  5.1684
 ER6  H14  H  HCH2  0   0.264  34.4599  -16.0558  5.8369
 ER6  H15  H  HCH2  0   0.273  33.6377  -17.4868  6.4435
 ER6  H16  H  HCR6  0   0.261  33.1401  -24.8736  5.7598
 ER6  H17  H  HOH1  0   0.472  30.5211  -18.7557  5.2961
 ER6  H2   H  HCH2  0   0.237  33.7215  -14.9996  3.5804

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    1.524  0.020  1.524
 ER6  C13  C12  single    1.525  0.020  1.525
 ER6  O2   C17  double    1.206  0.020  1.206
 ER6  C14  C15  single    1.529  0.020  1.529
 ER6  C12  N3   single    1.459  0.020  1.459
 ER6  C10  C9   aromatic  1.406  0.020  1.406
 ER6  C10  C11  aromatic  1.374  0.020  1.374
 ER6  C9   C8   aromatic  1.383  0.020  1.383
 ER6  C17  C15  single    1.509  0.020  1.509
 ER6  C17  O1   single    1.331  0.020  1.331
 ER6  C11  N2   aromatic  1.359  0.020  1.359
 ER6  C8   N2   aromatic  1.385  0.020  1.385
 ER6  C8   C7   aromatic  1.446  0.020  1.446
 ER6  C15  C16  single    1.539  0.020  1.539
 ER6  N2   C6   aromatic  1.391  0.020  1.391
 ER6  N3   C7   single    1.367  0.020  1.367
 ER6  N3   C16  single    1.450  0.020  1.450
 ER6  C7   N1   aromatic  1.298  0.020  1.298
 ER6  C6   C1   aromatic  1.392  0.020  1.392
 ER6  C6   C5   aromatic  1.404  0.020  1.404
 ER6  C1   C2   aromatic  1.382  0.020  1.382
 ER6  N1   C5   aromatic  1.368  0.020  1.368
 ER6  C5   C4   aromatic  1.401  0.020  1.401
 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
 ER6  O1   H17  single    0.850  0.020  0.980

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   120.81  3.000
 ER6  H1   C4   C5   118.13  3.000
 ER6  C3   C4   C5   121.06  3.000
 ER6  H3   C14  H2   106.31  3.000
 ER6  H3   C14  C15  110.71  3.000
 ER6  H2   C14  C15  107.25  3.000
 ER6  H3   C14  C13  110.62  3.000
 ER6  H2   C14  C13  108.59  3.000
 ER6  C15  C14  C13  113.05  3.000
 ER6  N1   C5   C6   123.06  3.000
 ER6  N1   C5   C4   118.98  3.000
 ER6  C6   C5   C4   117.93  3.000
 ER6  C1   C6   N2   122.79  3.000
 ER6  C1   C6   C5   121.16  3.000
 ER6  N2   C6   C5   116.05  3.000
 ER6  H4   C11  N2   122.04  3.000
 ER6  H4   C11  C10  129.83  3.000
 ER6  N2   C11  C10  108.11  3.000
 ER6  N3   C7   N1   118.63  3.000
 ER6  N1   C7   C8   121.41  3.000
 ER6  N3   C7   C8   119.82  3.000
 ER6  N2   C8   C9   107.25  3.000
 ER6  N2   C8   C7   117.36  3.000
 ER6  C9   C8   C7   135.24  3.000
 ER6  H5   C9   C10  125.71  3.000
 ER6  H5   C9   C8   126.97  3.000
 ER6  C10  C9   C8   107.31  3.000
 ER6  H6   C10  C9   126.63  3.000
 ER6  H6   C10  C11  125.47  3.000
 ER6  C9   C10  C11  107.90  3.000
 ER6  H8   C12  H7   107.26  3.000
 ER6  H8   C12  N3   108.11  3.000
 ER6  H7   C12  N3   110.62  3.000
 ER6  H8   C12  C13  110.31  3.000
 ER6  H7   C12  C13  109.65  3.000
 ER6  N3   C12  C13  110.81  3.000
 ER6  H10  C13  H9   106.89  3.000
 ER6  H10  C13  C12  108.87  3.000
 ER6  H9   C13  C12  109.14  3.000
 ER6  H10  C13  C14  109.73  3.000
 ER6  H9   C13  C14  110.63  3.000
 ER6  C12  C13  C14  111.46  3.000
 ER6  C7   N1   C5   120.07  3.000
 ER6  C8   N2   C11  109.42  3.000
 ER6  C8   N2   C6   121.78  3.000
 ER6  C11  N2   C6   128.54  3.000
 ER6  H11  C3   C2   120.01  3.000
 ER6  H11  C3   C4   119.92  3.000
 ER6  C2   C3   C4   120.07  3.000
 ER6  C16  N3   C12  112.23  3.000
 ER6  C16  N3   C7   118.50  3.000
 ER6  C12  N3   C7   121.82  3.000
 ER6  H12  C1   C2   119.63  3.000
 ER6  H12  C1   C6   120.75  3.000
 ER6  C2   C1   C6   119.62  3.000
 ER6  H13  C15  C17  106.22  3.000
 ER6  H13  C15  C16  106.01  3.000
 ER6  C17  C15  C16  112.75  3.000
 ER6  H13  C15  C14  108.70  3.000
 ER6  C16  C15  C14  109.58  3.000
 ER6  C17  C15  C14  113.21  3.000
 ER6  H15  C16  H14  107.49  3.000
 ER6  H15  C16  C15  111.79  3.000
 ER6  H14  C16  C15  106.85  3.000
 ER6  H15  C16  N3   109.74  3.000
 ER6  H14  C16  N3   106.81  3.000
 ER6  C15  C16  N3   113.80  3.000
 ER6  O2   C17  O1   122.75  3.000
 ER6  O1   C17  C15  111.49  3.000
 ER6  O2   C17  C15  125.67  3.000
 ER6  H16  C2   C1   119.55  3.000
 ER6  H16  C2   C3   120.30  3.000
 ER6  C1   C2   C3   120.15  3.000
 ER6  H17  O1   C17  109.72  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  CONST_41  H17  O1   C17  C15  180.00   0.0  0
 ER6  Var_01    N3   C12  C13  C14   54.77  30.0  1
 ER6  Var_02    C13  C12  N3   C7    90.95  30.0  1
 ER6  Var_03    C15  C16  N3   C7   -92.54  30.0  1
 ER6  Var_04    C12  N3   C7   C8    46.53  30.0  3
 ER6  Var_05    C15  C14  C13  C12  -50.95  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
 ER6  plan-2  H17  0.020

