# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 00:31:47 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (2~{S},3~{R},4~{R})-4-(2-cyclohexyloxy-2-oxidanylidene-ethyl)sulfanyl-3-methyl-2-[(2~{S},3~{R})-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](SCC(=O)OC2CCCCC2)[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
 T8G  T8G  '(2~{S},3~{R},4~{R})-4-(2-cyclohexyloxy-2-oxidanylidene-ethyl)sulfanyl-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid'  ligand  53  26  .  2021-08-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T8G
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
 T8G  C18  C  CH3   0  -0.701  -5.3951   1.6947  -2.4070
 T8G  C10  C  CR5   0   0.178  -2.4742  -1.4467   0.2141
 T8G  C11  C  C     0   0.495  -2.5184  -2.8422   0.7384
 T8G  C12  C  CR15  0  -0.255  -1.6795   0.6788  -0.3533
 T8G  N1   N  N     0  -0.303  -3.5324  -0.7667   0.0868
 T8G  C13  C  CH3   0  -0.690  -1.3545   1.4325   0.9280
 T8G  C14  C  CR15  0  -0.134  -3.1969   0.4832  -0.5861
 T8G  C15  C  CH1   0  -0.401  -4.1027   1.6489  -0.1955
 T8G  S1   S  S2    0   0.039   0.2778  -1.2022   0.5873
 T8G  C1   C  C     0   0.619   2.8451  -0.5533   0.0880
 T8G  O1   O  O     0  -0.442   3.0768  -1.2445   1.0472
 T8G  C16  C  C1    0   0.194  -4.3590   1.7170   1.2941
 T8G  C17  C  CH1   0   0.047  -5.4770   1.6735  -0.8894
 T8G  O2   O  O2    0  -0.467   3.7511   0.0825  -0.6297
 T8G  C2   C  CH1   0   0.050   5.1442  -0.0153  -0.2569
 T8G  O3   O  OH1   0  -0.575  -3.5925  -3.0775   1.4653
 T8G  C3   C  CH2   0  -0.456   5.9592   0.2490  -1.5109
 T8G  O4   O  O     0  -0.413  -1.6577  -3.6481   0.4944
 T8G  C4   C  CH2   0  -0.447   7.4511   0.1926  -1.1883
 T8G  O5   O  O     0  -0.385  -4.7567   2.7121   1.8474
 T8G  C5   C  CH2   0  -0.432   7.8172   1.1695  -0.0756
 T8G  O6   O  OH1   0  -0.662  -6.2140   0.5712  -0.4073
 T8G  C6   C  CH2   0  -0.444   6.9671   0.9254   1.1669
 T8G  C7   C  CH2   0  -0.461   5.4753   0.9819   0.8430
 T8G  C8   C  CH2   0  -0.688   1.4574  -0.3005  -0.4437
 T8G  C9   C  CR15  0  -0.449  -1.2271  -0.7960  -0.3359
 T8G  H1   H  HCH3  0   0.246  -6.3879   1.8588  -2.8305
 T8G  H2   H  HCH3  0   0.234  -4.7552   2.5076  -2.7523
 T8G  H3   H  HCH3  0   0.233  -5.0144   0.7595  -2.8182
 T8G  H4   H  HCR5  0   0.273  -1.2405   1.2058  -1.2020
 T8G  H5   H  HCH3  0   0.232  -1.7384   0.9344   1.8200
 T8G  H6   H  HCH3  0   0.258  -0.2787   1.5332   1.0651
 T8G  H7   H  HCH3  0   0.252  -1.7580   2.4448   0.8942
 T8G  H8   H  HCR5  0   0.294  -3.3359   0.2899  -1.6558
 T8G  H9   H  HCH1  0   0.299  -3.6073   2.5790  -0.4927
 T8G  H10  H  H     0   0.201  -4.1977   0.7871   1.8655
 T8G  H11  H  HCH1  0   0.223  -5.9461   2.6156  -0.5739
 T8G  H12  H  HCH1  0   0.236   5.3452  -1.0320   0.0958
 T8G  H13  H  HOH1  0   0.492  -3.5905  -3.9976   1.7711
 T8G  H14  H  HCH2  0   0.245   5.7095  -0.4836  -2.2820
 T8G  H15  H  HCH2  0   0.227   5.7083   1.2390  -1.9062
 T8G  H16  H  HCH2  0   0.219   7.7174  -0.8240  -0.8805
 T8G  H17  H  HCH2  0   0.239   8.0280   0.4058  -2.0904
 T8G  H18  H  HCH2  0   0.233   8.8777   1.0792   0.1705
 T8G  H19  H  HCH2  0   0.214   7.6623   2.1953  -0.4267
 T8G  H20  H  HOH1  0   0.453  -7.1135   0.6426  -0.7424
 T8G  H21  H  HCH2  0   0.219   7.2091  -0.0579   1.5844
 T8G  H22  H  HCH2  0   0.238   7.2003   1.6575   1.9425
 T8G  H23  H  HCH2  0   0.226   5.2105   1.9889   0.5040
 T8G  H24  H  HCH2  0   0.246   4.8886   0.7737   1.7400
 T8G  H25  H  HCH2  0   0.315   1.3904  -0.6307  -1.4834
 T8G  H26  H  HCH2  0   0.305   1.2641   0.7747  -0.4329
 T8G  H27  H  HCR5  0   0.329  -1.0922  -1.1497  -1.3665

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
 T8G  C5   C4   single  1.525  0.020  1.525
 T8G  C5   C6   single  1.525  0.020  1.525
 T8G  C4   C3   single  1.527  0.020  1.527
 T8G  C6   C7   single  1.528  0.020  1.528
 T8G  C3   C2   single  1.519  0.020  1.519
 T8G  C7   C2   single  1.521  0.020  1.521
 T8G  C2   O2   single  1.445  0.020  1.445
 T8G  O4   C11  double  1.204  0.020  1.204
 T8G  O2   C1   single  1.319  0.020  1.319
 T8G  O3   C11  single  1.318  0.020  1.318
 T8G  C11  C10  single  1.491  0.020  1.491
 T8G  O1   C1   double  1.205  0.020  1.205
 T8G  C1   C8   single  1.507  0.020  1.507
 T8G  S1   C8   single  1.808  0.020  1.808
 T8G  S1   C9   single  1.812  0.020  1.812
 T8G  C10  C9   single  1.510  0.020  1.510
 T8G  C10  N1   double  1.264  0.020  1.264
 T8G  C9   C12  single  1.543  0.020  1.543
 T8G  N1   C14  single  1.459  0.020  1.459
 T8G  C12  C14  single  1.548  0.020  1.548
 T8G  C12  C13  single  1.522  0.020  1.522
 T8G  O5   C16  double  1.206  0.020  1.206
 T8G  C14  C15  single  1.527  0.020  1.527
 T8G  C16  C15  single  1.513  0.020  1.513
 T8G  C15  C17  single  1.540  0.020  1.540
 T8G  C17  C18  single  1.520  0.020  1.520
 T8G  C17  O6   single  1.411  0.020  1.411
 T8G  C18  H1   single  0.970  0.020  1.090
 T8G  C18  H2   single  0.970  0.020  1.090
 T8G  C18  H3   single  0.970  0.020  1.090
 T8G  C12  H4   single  0.970  0.020  1.090
 T8G  C13  H5   single  0.970  0.020  1.090
 T8G  C13  H6   single  0.970  0.020  1.090
 T8G  C13  H7   single  0.970  0.020  1.090
 T8G  C14  H8   single  0.970  0.020  1.090
 T8G  C15  H9   single  0.970  0.020  1.090
 T8G  C16  H10  single  0.930  0.020  1.080
 T8G  C17  H11  single  0.970  0.020  1.090
 T8G  C2   H12  single  0.970  0.020  1.090
 T8G  O3   H13  single  0.850  0.020  0.980
 T8G  C3   H14  single  0.970  0.020  1.090
 T8G  C3   H15  single  0.970  0.020  1.090
 T8G  C4   H16  single  0.970  0.020  1.090
 T8G  C4   H17  single  0.970  0.020  1.090
 T8G  C5   H18  single  0.970  0.020  1.090
 T8G  C5   H19  single  0.970  0.020  1.090
 T8G  O6   H20  single  0.850  0.020  0.980
 T8G  C6   H21  single  0.970  0.020  1.090
 T8G  C6   H22  single  0.970  0.020  1.090
 T8G  C7   H23  single  0.970  0.020  1.090
 T8G  C7   H24  single  0.970  0.020  1.090
 T8G  C8   H25  single  0.970  0.020  1.090
 T8G  C8   H26  single  0.970  0.020  1.090
 T8G  C9   H27  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
 T8G  H3   C18  H2   108.37  3.000
 T8G  H3   C18  H1   107.46  3.000
 T8G  H2   C18  H1   107.38  3.000
 T8G  H3   C18  C17  112.54  3.000
 T8G  H2   C18  C17  110.99  3.000
 T8G  H1   C18  C17  109.90  3.000
 T8G  C9   C10  N1   115.01  3.000
 T8G  N1   C10  C11  120.93  3.000
 T8G  C9   C10  C11  123.75  3.000
 T8G  O4   C11  O3   125.08  3.000
 T8G  O3   C11  C10  112.65  3.000
 T8G  O4   C11  C10  122.27  3.000
 T8G  H4   C12  C9   110.64  3.000
 T8G  H4   C12  C14  109.79  3.000
 T8G  C9   C12  C14   99.69  3.000
 T8G  H4   C12  C13  109.25  3.000
 T8G  C14  C12  C13  113.50  3.000
 T8G  C9   C12  C13  113.66  3.000
 T8G  C14  N1   C10  108.35  3.000
 T8G  H7   C13  H6   106.48  3.000
 T8G  H7   C13  H5   108.59  3.000
 T8G  H6   C13  H5   106.67  3.000
 T8G  H7   C13  C12  110.78  3.000
 T8G  H6   C13  C12  111.27  3.000
 T8G  H5   C13  C12  112.77  3.000
 T8G  H8   C14  C15  108.00  3.000
 T8G  H8   C14  N1   105.66  3.000
 T8G  C15  C14  N1   113.56  3.000
 T8G  H8   C14  C12  107.07  3.000
 T8G  C15  C14  C12  116.53  3.000
 T8G  N1   C14  C12  105.34  3.000
 T8G  H9   C15  C17  105.54  3.000
 T8G  H9   C15  C16  107.80  3.000
 T8G  C17  C15  C16  106.96  3.000
 T8G  H9   C15  C14  108.10  3.000
 T8G  C17  C15  C14  115.23  3.000
 T8G  C16  C15  C14  112.74  3.000
 T8G  C9   S1   C8    98.02  3.000
 T8G  C8   C1   O2   111.07  3.000
 T8G  C8   C1   O1   123.64  3.000
 T8G  O2   C1   O1   125.29  3.000
 T8G  H10  C16  O5   120.41  3.000
 T8G  H10  C16  C15  116.56  3.000
 T8G  O5   C16  C15  123.00  3.000
 T8G  H11  C17  O6   110.41  3.000
 T8G  H11  C17  C15  105.39  3.000
 T8G  O6   C17  C15  107.45  3.000
 T8G  H11  C17  C18  107.32  3.000
 T8G  O6   C17  C18  112.35  3.000
 T8G  C15  C17  C18  113.71  3.000
 T8G  C2   O2   C1   119.27  3.000
 T8G  H12  C2   C7   109.63  3.000
 T8G  H12  C2   C3   109.21  3.000
 T8G  C7   C2   C3   111.48  3.000
 T8G  H12  C2   O2   108.84  3.000
 T8G  C7   C2   O2   110.61  3.000
 T8G  C3   C2   O2   107.01  3.000
 T8G  H13  O3   C11  109.98  3.000
 T8G  H15  C3   H14  107.39  3.000
 T8G  H15  C3   C4   109.48  3.000
 T8G  H14  C3   C4   110.34  3.000
 T8G  H15  C3   C2   109.41  3.000
 T8G  H14  C3   C2   110.09  3.000
 T8G  C4   C3   C2   110.08  3.000
 T8G  H17  C4   H16  106.56  3.000
 T8G  H17  C4   C5   110.53  3.000
 T8G  H16  C4   C5   109.34  3.000
 T8G  H17  C4   C3   109.54  3.000
 T8G  H16  C4   C3   109.34  3.000
 T8G  C5   C4   C3   111.40  3.000
 T8G  H19  C5   H18  106.67  3.000
 T8G  H19  C5   C6   109.40  3.000
 T8G  H18  C5   C6   110.15  3.000
 T8G  H19  C5   C4   109.39  3.000
 T8G  H18  C5   C4   110.15  3.000
 T8G  C6   C5   C4   110.98  3.000
 T8G  H20  O6   C17  108.14  3.000
 T8G  H22  C6   H21  106.50  3.000
 T8G  H22  C6   C7   109.54  3.000
 T8G  H21  C6   C7   109.25  3.000
 T8G  H22  C6   C5   110.64  3.000
 T8G  H21  C6   C5   109.33  3.000
 T8G  C7   C6   C5   111.45  3.000
 T8G  H24  C7   H23  107.44  3.000
 T8G  H24  C7   C6   110.09  3.000
 T8G  H23  C7   C6   109.62  3.000
 T8G  H24  C7   C2   110.61  3.000
 T8G  H23  C7   C2   109.05  3.000
 T8G  C6   C7   C2   109.98  3.000
 T8G  H26  C8   H25  107.21  3.000
 T8G  H26  C8   C1   108.93  3.000
 T8G  H25  C8   C1   109.96  3.000
 T8G  H26  C8   S1   111.70  3.000
 T8G  H25  C8   S1   110.60  3.000
 T8G  C1   C8   S1   108.42  3.000
 T8G  H27  C9   S1   107.71  3.000
 T8G  H27  C9   C12  109.47  3.000
 T8G  S1   C9   C12  117.62  3.000
 T8G  H27  C9   C10  107.73  3.000
 T8G  C12  C9   C10  100.01  3.000
 T8G  S1   C9   C10  113.81  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
 T8G  CONST_01  H13  O3   C11  C10  180.00   0.0  0
 T8G  Var_01    C9   C10  N1   C14    0.25  30.0  1
 T8G  Var_02    C5   C4   C3   C2   -56.13  30.0  1
 T8G  Var_03    C5   C6   C7   C2    56.11  30.0  1
 T8G  Var_04    C6   C5   C4   C3    55.12  30.0  1
 T8G  Var_05    C7   C6   C5   C4   -55.17  30.0  1
 T8G  Var_06    O4   C11  C10  N1   156.17  30.0  2
 T8G  Var_07    C8   C1   O2   C2   178.74  30.0  3
 T8G  Var_08    H25  C8   S1   C9   -56.09  30.0  3
 T8G  Var_09    O2   C1   C8   S1   179.97  30.0  2

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
 T8G  chir_01  C12  C9   C14  C13  negativ
 T8G  chir_02  C14  N1   C12  C15  positiv
 T8G  chir_03  C15  C14  C16  C17  positiv
 T8G  chir_04  C17  O6   C15  C18  negativ
 T8G  chir_05  C2   C3   C7   O2   negativ
 T8G  chir_06  C9   S1   C10  C12  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
 T8G  plan-1  C10  0.020
 T8G  plan-1  C11  0.020
 T8G  plan-1  O3   0.020
 T8G  plan-1  O4   0.020
 T8G  plan-1  H13  0.020
 T8G  plan-2  C1   0.020
 T8G  plan-2  O1   0.020
 T8G  plan-2  O2   0.020
 T8G  plan-2  C8   0.020
 T8G  plan-3  C15  0.020
 T8G  plan-3  C16  0.020
 T8G  plan-3  O5   0.020
 T8G  plan-3  H10  0.020

