# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 09:29:32 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2~{S},3~{R},4~{R})-4-(1~{H}-indol-3-ylsulfanyl)-3-methyl-2-[(2~{S},3~{S})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@@H](C=O)[C@@H]1N=C([C@H](Sc2c[nH]c3ccccc23)[C@@H]1C)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
 6QR  6QR  '(2~{S},3~{R},4~{R})-4-(1~{H}-indol-3-ylsulfanyl)-3-methyl-2-[(2~{S},3~{S})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid'  ligand  45  25  .  2021-08-05  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6QR
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
 6QR  C10  C  CR15  0   0.000  -3.2101   1.8800  -1.1201
 6QR  C11  C  CR56  0   0.349  -4.4990   0.0648  -1.2566
 6QR  C13  C  CR16  0  -0.356  -3.4441  -1.4491   0.3168
 6QR  C14  C  CR16  0  -0.267  -4.4090  -2.3847  -0.0016
 6QR  C15  C  CR16  0  -0.281  -5.4128  -2.0997  -0.9423
 6QR  C16  C  CR16  0  -0.302  -5.4745  -0.8756  -1.5810
 6QR  C18  C  CH3   0  -0.687   0.9204  -0.3574   2.2046
 6QR  C1   C  C1    0   0.207   4.0288  -0.0023   1.5949
 6QR  O1   O  O     0  -0.378   4.2003  -0.1030   2.7834
 6QR  N1   N  N     0  -0.327   2.3090   0.7488  -0.5251
 6QR  S1   S  S2    0   0.014  -1.3014   1.2226   0.8021
 6QR  C12  C  CR56  0   0.120  -3.4835  -0.2042  -0.3162
 6QR  C17  C  CR15  0  -0.244   0.8345  -0.6802   0.7203
 6QR  C2   C  CH1   0  -0.414   3.4540  -1.0805   0.7070
 6QR  O2   O  OH1   0  -0.671   5.7518  -1.5334   0.4430
 6QR  N2   N  NR15  0  -0.682  -4.3041   1.3397  -1.7159
 6QR  C3   C  CH1   0   0.069   4.5520  -1.4579  -0.3027
 6QR  C4   C  CH3   0  -0.692   4.2677  -2.7705  -1.0164
 6QR  C5   C  CR15  0  -0.134   2.1872  -0.6187  -0.0250
 6QR  C6   C  CR5   0   0.207   1.1521   1.2558  -0.5670
 6QR  C7   C  C     0   0.500   0.9191   2.5883  -1.1951
 6QR  C8   C  CR15  0  -0.452   0.0377   0.3622  -0.0926
 6QR  C9   C  CR5   0  -0.280  -2.6692   0.9723  -0.2482
 6QR  H1   H  HCR5  0   0.293  -2.8859   2.8803  -1.3544
 6QR  H2   H  HCR6  0   0.242  -2.6704  -1.6698   1.0430
 6QR  H3   H  HCR6  0   0.249  -4.3953  -3.3546   0.4784
 6QR  H4   H  HCR6  0   0.252  -6.1529  -2.8551  -1.1723
 6QR  H5   H  HCR6  0   0.263  -6.2502  -0.6598  -2.3046
 6QR  H7   H  HCH3  0   0.254  -0.0624  -0.4364   2.6668
 6QR  H8   H  HCH3  0   0.251   1.5722  -1.0621   2.7191
 6QR  H9   H  H     0   0.195   4.3090   0.9234   1.0617
 6QR  H12  H  HCR5  0   0.269   0.3928  -1.6701   0.5983
 6QR  H13  H  HCH1  0   0.273   3.2168  -1.9563   1.3190
 6QR  H14  H  HOH1  0   0.457   6.4848  -1.6586  -0.1684
 6QR  H15  H  HNR5  0   0.415  -4.8752   1.8106  -2.3982
 6QR  H16  H  HCH1  0   0.218   4.6199  -0.6546  -1.0499
 6QR  H17  H  HOH1  0   0.492   1.7610   4.2513  -1.4815
 6QR  H18  H  HCH3  0   0.232   4.1863  -3.5926  -0.3037
 6QR  H19  H  HCH3  0   0.236   3.3477  -2.7331  -1.6001
 6QR  H20  H  HCH3  0   0.244   5.0731  -3.0010  -1.7163
 6QR  H21  H  HCR5  0   0.291   2.0883  -1.2497  -0.9153
 6QR  H23  H  HCR5  0   0.334  -0.4278  -0.1111  -0.9626
 6QR  H6   H  HCH3  0   0.228   1.2955   0.6498   2.3971
 6QR  O3   O  OH1   0  -0.576   1.9345   3.4127  -1.0263
 6QR  O4   O  O     0  -0.412  -0.0854   2.8416  -1.8076

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
 6QR  C16  C15  aromatic  1.382  0.020  1.382
 6QR  C16  C11  aromatic  1.393  0.020  1.393
 6QR  C15  C14  aromatic  1.405  0.020  1.405
 6QR  C11  N2   aromatic  1.369  0.020  1.369
 6QR  C11  C12  aromatic  1.410  0.020  1.410
 6QR  N2   C10  aromatic  1.358  0.020  1.358
 6QR  C14  C13  aromatic  1.381  0.020  1.381
 6QR  C10  C9   aromatic  1.370  0.020  1.370
 6QR  C12  C13  aromatic  1.397  0.020  1.397
 6QR  C12  C9   aromatic  1.432  0.020  1.432
 6QR  O4   C7   double    1.203  0.020  1.203
 6QR  C9   S1   single    1.743  0.020  1.743
 6QR  O3   C7   single    1.319  0.020  1.319
 6QR  C7   C6   single    1.491  0.020  1.491
 6QR  C6   C8   single    1.505  0.020  1.505
 6QR  C6   N1   double    1.264  0.020  1.264
 6QR  S1   C8   single    1.826  0.020  1.826
 6QR  C8   C17  single    1.543  0.020  1.543
 6QR  N1   C5   single    1.461  0.020  1.461
 6QR  O1   C1   double    1.205  0.020  1.205
 6QR  C17  C5   single    1.546  0.020  1.546
 6QR  C17  C18  single    1.521  0.020  1.521
 6QR  C5   C2   single    1.534  0.020  1.534
 6QR  C1   C2   single    1.510  0.020  1.510
 6QR  C2   C3   single    1.539  0.020  1.539
 6QR  C3   C4   single    1.521  0.020  1.521
 6QR  C3   O2   single    1.415  0.020  1.415
 6QR  C10  H1   single    0.930  0.020  1.080
 6QR  C13  H2   single    0.930  0.020  1.080
 6QR  C14  H3   single    0.930  0.020  1.080
 6QR  C15  H4   single    0.930  0.020  1.080
 6QR  C16  H5   single    0.930  0.020  1.080
 6QR  C18  H6   single    0.970  0.020  1.090
 6QR  C18  H7   single    0.970  0.020  1.090
 6QR  C18  H8   single    0.970  0.020  1.090
 6QR  C1   H9   single    0.930  0.020  1.080
 6QR  C17  H12  single    0.970  0.020  1.090
 6QR  C2   H13  single    0.970  0.020  1.090
 6QR  O2   H14  single    0.850  0.020  0.980
 6QR  N2   H15  single    0.860  0.020  1.020
 6QR  C3   H16  single    0.970  0.020  1.090
 6QR  O3   H17  single    0.850  0.020  0.980
 6QR  C4   H18  single    0.970  0.020  1.090
 6QR  C4   H19  single    0.970  0.020  1.090
 6QR  C4   H20  single    0.970  0.020  1.090
 6QR  C5   H21  single    0.970  0.020  1.090
 6QR  C8   H23  single    0.970  0.020  1.090

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
 6QR  H1   C10  C9   129.41  3.000
 6QR  H1   C10  N2   121.09  3.000
 6QR  C9   C10  N2   109.50  3.000
 6QR  N2   C11  C12  107.39  3.000
 6QR  C12  C11  C16  122.06  3.000
 6QR  N2   C11  C16  130.55  3.000
 6QR  H2   C13  C12  120.34  3.000
 6QR  H2   C13  C14  121.01  3.000
 6QR  C12  C13  C14  118.65  3.000
 6QR  H3   C14  C15  119.19  3.000
 6QR  H3   C14  C13  119.73  3.000
 6QR  C15  C14  C13  121.07  3.000
 6QR  H4   C15  C16  119.31  3.000
 6QR  H4   C15  C14  119.30  3.000
 6QR  C16  C15  C14  121.39  3.000
 6QR  H5   C16  C15  121.16  3.000
 6QR  H5   C16  C11  121.52  3.000
 6QR  C15  C16  C11  117.32  3.000
 6QR  H8   C18  H7   107.02  3.000
 6QR  H8   C18  H6   107.94  3.000
 6QR  H7   C18  H6   107.59  3.000
 6QR  H8   C18  C17  110.94  3.000
 6QR  H7   C18  C17  110.35  3.000
 6QR  H6   C18  C17  112.77  3.000
 6QR  H9   C1   C2   114.28  3.000
 6QR  H9   C1   O1   120.67  3.000
 6QR  C2   C1   O1   125.05  3.000
 6QR  C6   N1   C5   108.09  3.000
 6QR  C9   S1   C8   102.28  3.000
 6QR  C9   C12  C13  133.97  3.000
 6QR  C9   C12  C11  106.52  3.000
 6QR  C13  C12  C11  119.50  3.000
 6QR  H12  C17  C8   110.18  3.000
 6QR  H12  C17  C5   109.67  3.000
 6QR  C8   C17  C5    99.84  3.000
 6QR  H12  C17  C18  108.94  3.000
 6QR  C5   C17  C18  114.37  3.000
 6QR  C8   C17  C18  113.56  3.000
 6QR  H13  C2   C5   109.19  3.000
 6QR  H13  C2   C3   108.98  3.000
 6QR  C5   C2   C3   110.48  3.000
 6QR  H13  C2   C1   108.97  3.000
 6QR  C3   C2   C1   106.82  3.000
 6QR  C5   C2   C1   112.32  3.000
 6QR  H14  O2   C3   108.53  3.000
 6QR  H15  N2   C11  125.61  3.000
 6QR  H15  N2   C10  124.63  3.000
 6QR  C11  N2   C10  109.76  3.000
 6QR  H16  C3   C4   108.86  3.000
 6QR  H16  C3   O2   110.18  3.000
 6QR  C4   C3   O2   111.09  3.000
 6QR  H16  C3   C2   108.11  3.000
 6QR  O2   C3   C2   105.81  3.000
 6QR  C4   C3   C2   112.72  3.000
 6QR  H20  C4   H19  106.65  3.000
 6QR  H20  C4   H18  108.34  3.000
 6QR  H19  C4   H18  108.22  3.000
 6QR  H20  C4   C3   110.19  3.000
 6QR  H19  C4   C3   112.30  3.000
 6QR  H18  C4   C3   110.96  3.000
 6QR  H21  C5   C2   106.79  3.000
 6QR  H21  C5   C17  106.85  3.000
 6QR  C2   C5   C17  118.72  3.000
 6QR  H21  C5   N1   105.57  3.000
 6QR  C2   C5   N1   112.10  3.000
 6QR  C17  C5   N1   105.98  3.000
 6QR  C8   C6   C7   123.20  3.000
 6QR  C8   C6   N1   115.41  3.000
 6QR  C7   C6   N1   121.02  3.000
 6QR  C6   C7   O4   122.19  3.000
 6QR  C6   C7   O3   112.60  3.000
 6QR  O4   C7   O3   125.19  3.000
 6QR  H23  C8   C6   108.73  3.000
 6QR  H23  C8   C17  110.26  3.000
 6QR  C6   C8   C17  100.65  3.000
 6QR  H23  C8   S1   106.34  3.000
 6QR  C17  C8   S1   116.03  3.000
 6QR  C6   C8   S1   114.69  3.000
 6QR  C12  C9   S1   126.35  3.000
 6QR  S1   C9   C10  126.75  3.000
 6QR  C12  C9   C10  106.83  3.000
 6QR  H17  O3   C7   110.04  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
 6QR  CONST_01  C16  C11  N2   C10  180.00   0.0  0
 6QR  CONST_02  C12  C11  N2   C10    0.00   0.0  0
 6QR  CONST_03  C11  C12  C9   C10    0.00   0.0  0
 6QR  CONST_04  C13  C12  C9   C10  180.00   0.0  0
 6QR  CONST_05  C14  C15  C16  C11    0.00   0.0  0
 6QR  CONST_06  C9   C10  N2   C11    0.00   0.0  0
 6QR  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 6QR  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 6QR  CONST_09  C16  C11  C12  C13    0.00   0.0  0
 6QR  CONST_10  N2   C11  C12  C13  180.00   0.0  0
 6QR  CONST_11  C9   C12  C13  C14  180.00   0.0  0
 6QR  CONST_12  N2   C11  C16  C15  180.00   0.0  0
 6QR  CONST_13  C12  C11  C16  C15    0.00   0.0  0
 6QR  CONST_14  C12  C13  C14  C15    0.00   0.0  0
 6QR  CONST_15  C9   C12  C11  C16  180.00   0.0  0
 6QR  CONST_16  N2   C10  C9   C12    0.00   0.0  0
 6QR  CONST_17  C9   C12  C11  N2     0.00   0.0  0
 6QR  CONST_18  S1   C9   C12  C11  180.00   0.0  0
 6QR  CONST_19  S1   C9   C12  C13    0.00   0.0  0
 6QR  CONST_20  N2   C10  C9   S1   180.00   0.0  0
 6QR  CONST_21  H4   C15  C16  C11  180.00   0.0  0
 6QR  CONST_22  H1   C10  N2   C11  180.00   0.0  0
 6QR  CONST_23  H2   C13  C12  C11  180.00   0.0  0
 6QR  CONST_24  H5   C16  C15  C14  180.00   0.0  0
 6QR  CONST_25  H3   C14  C15  C16  180.00   0.0  0
 6QR  CONST_26  H15  N2   C11  C16    0.00   0.0  0
 6QR  CONST_27  H17  O3   C7   C6   180.00   0.0  0
 6QR  Var_01    C8   C6   N1   C5     0.95  30.0  1
 6QR  Var_02    O4   C7   C6   N1   144.55  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
 6QR  chir_01  C17  C8  C5   C18  negativ
 6QR  chir_02  C2   C5  C1   C3   positiv
 6QR  chir_03  C3   O2  C2   C4   positiv
 6QR  chir_04  C5   N1  C17  C2   positiv
 6QR  chir_05  C8   S1  C17  C6   positiv

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
 6QR  plan-1  C10  0.020
 6QR  plan-1  C11  0.020
 6QR  plan-1  C13  0.020
 6QR  plan-1  C14  0.020
 6QR  plan-1  C15  0.020
 6QR  plan-1  C16  0.020
 6QR  plan-1  S1   0.020
 6QR  plan-1  C12  0.020
 6QR  plan-1  N2   0.020
 6QR  plan-1  C9   0.020
 6QR  plan-1  H1   0.020
 6QR  plan-1  H2   0.020
 6QR  plan-1  H3   0.020
 6QR  plan-1  H4   0.020
 6QR  plan-1  H5   0.020
 6QR  plan-1  H15  0.020
 6QR  plan-2  C6   0.020
 6QR  plan-2  C7   0.020
 6QR  plan-2  H17  0.020
 6QR  plan-2  O3   0.020
 6QR  plan-2  O4   0.020
 6QR  plan-3  C1   0.020
 6QR  plan-3  O1   0.020
 6QR  plan-3  C2   0.020
 6QR  plan-3  H9   0.020

