# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  2 22:10:34 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-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@@H]1N=C([C@@H](S[C@@H]2CN[C@@H](C2)C(=O)N(C)C)[C@@H]1C)C(O)=O)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
 LMP  LMP  '(2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid'  ligand  52  27  .  2022-07-25  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_LMP
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
 LMP  C1   C  CH1    0  -0.259   1.9787   0.9600  -0.5265
 LMP  C2   C  CH1    0  -0.459   0.7466   0.1321  -0.9279
 LMP  C3   C  C      0   0.185   1.2531  -1.2658  -0.6869
 LMP  C6A  C  C      0   0.522  -5.4188   0.4348  -0.2359
 LMP  N7A  N  NT     0  -0.441  -6.1030   0.6188   0.9110
 LMP  C9A  C  CH3    0  -0.524  -6.9974   1.7480   1.0647
 LMP  C8A  C  CH3    0  -0.528  -5.9344  -0.1762   2.1096
 LMP  C5A  C  CR15   0  -0.203  -4.3925  -0.7031  -0.2745
 LMP  C2A  C  CH2    0  -0.458  -3.1701  -0.3771   0.6245
 LMP  N3A  N  NR15   0  -0.603  -3.8366  -0.9059  -1.6028
 LMP  C4A  C  CH2    0  -0.256  -2.5683  -0.1984  -1.6676
 LMP  C1A  C  CR15   0  -0.386  -1.9720  -0.5396  -0.3139
 LMP  S21  S  S2     0   0.001  -0.6184   0.5281   0.2303
 LMP  C31  C  C      0   0.375   0.6997  -2.5050  -1.3787
 LMP  O31  O  O      0  -0.578   0.0688  -2.2768  -2.4280
 LMP  O32  O  OC    -1  -0.580   0.9492  -3.6001  -0.8540
 LMP  N4   N  N      0  -0.412   2.2389  -1.3179   0.1116
 LMP  C11  C  CH3    0  -0.677   2.8418   1.2160  -1.7569
 LMP  C5   C  CH1    0  -0.065   2.5888   0.0331   0.5500
 LMP  C6   C  CH1    0  -0.427   4.0680   0.1662   0.9659
 LMP  C61  C  CH1    0   0.082   5.0997  -0.4562   0.0135
 LMP  O62  O  OH1    0  -0.715   4.8550  -1.8461  -0.1699
 LMP  C62  C  CH3    0  -0.679   6.5136  -0.3380   0.5607
 LMP  C7   C  C      0   0.430   4.3014   1.6487   1.3407
 LMP  O71  O  O      0  -0.614   3.7313   2.0318   2.3828
 LMP  O72  O  OC    -1  -0.591   4.9922   2.3561   0.5808
 LMP  H1   H  HCH1   0   0.249   1.7009   1.9231  -0.0903
 LMP  H2   H  HCH1   0   0.292   0.4113   0.3110  -1.9489
 LMP  H3   H  HCH3   0   0.240  -8.0060   1.4031   1.2989
 LMP  H4   H  HCH3   0   0.239  -6.6604   2.3894   1.8816
 LMP  H5   H  HCH3   0   0.258  -7.0312   2.3350   0.1537
 LMP  H6   H  HCH3   0   0.243  -5.2587   0.3027   2.8219
 LMP  H7   H  HCH3   0   0.258  -6.9038  -0.2949   2.5938
 LMP  H8   H  HCH3   0   0.258  -5.5607  -1.1726   1.8953
 LMP  H9   H  HCR5   0   0.268  -4.8760  -1.6270   0.0582
 LMP  H12  H  HNR5   0   0.352  -4.4766  -0.5903  -2.3196
 LMP  H14  H  HCH2   0   0.245  -1.9547  -0.5635  -2.4908
 LMP  H15  H  HCH2   0   0.200  -2.6693   0.8916  -1.7642
 LMP  H16  H  HCR5   0   0.288  -1.6461  -1.5798  -0.3101
 LMP  H18  H  HCH3   0   0.236   2.2804   1.8032  -2.4854
 LMP  H19  H  HCH3   0   0.248   3.7378   1.7726  -1.4926
 LMP  H20  H  HCH3   0   0.220   3.1465   0.2896  -2.2473
 LMP  H21  H  HCH1   0   0.251   2.0251   0.2133   1.4745
 LMP  H22  H  HCH1   0   0.218   4.1460  -0.4115   1.8967
 LMP  H23  H  HCH1   0   0.184   5.0672   0.0565  -0.9548
 LMP  H24  H  HOH1   0   0.440   3.8925  -1.9861  -0.1117
 LMP  H25  H  HCH3   0   0.207   6.5783  -0.7443   1.5734
 LMP  H26  H  HCH3   0   0.220   7.2138  -0.8931  -0.0669
 LMP  H27  H  HCH3   0   0.226   6.8376   0.6988   0.5870
 LMP  H10  H  HCH2   0   0.253  -3.2245   0.6496   0.9983
 LMP  O7A  O  O      0  -0.500  -5.5884   1.1405  -1.2233
 LMP  H11  H  HCH2   0   0.268  -3.1056  -1.0322   1.4914

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
 LMP  O62  C61  single  1.423  0.020  1.423
 LMP  C62  C61  single  1.521  0.020  1.521
 LMP  C11  C1   single  1.525  0.020  1.525
 LMP  C61  C6   single  1.536  0.020  1.536
 LMP  O71  C7   deloc   1.248  0.020  1.248
 LMP  C7   C6   single  1.547  0.020  1.547
 LMP  C7   O72  deloc   1.247  0.020  1.247
 LMP  C1   C2   single  1.538  0.020  1.538
 LMP  C1   C5   single  1.546  0.020  1.546
 LMP  C2   C3   single  1.506  0.020  1.506
 LMP  C2   S21  single  1.833  0.020  1.833
 LMP  C6   C5   single  1.542  0.020  1.542
 LMP  C3   C31  single  1.523  0.020  1.523
 LMP  C3   N4   double  1.270  0.020  1.270
 LMP  O31  C31  deloc   1.245  0.020  1.245
 LMP  C5   N4   single  1.463  0.020  1.463
 LMP  C31  O32  deloc   1.240  0.020  1.240
 LMP  S21  C1A  single  1.808  0.020  1.808
 LMP  C1A  C2A  single  1.531  0.020  1.531
 LMP  C1A  C4A  single  1.518  0.020  1.518
 LMP  C2A  C5A  single  1.552  0.020  1.552
 LMP  C4A  N3A  single  1.454  0.020  1.454
 LMP  O7A  C6A  double  1.225  0.020  1.225
 LMP  N3A  C5A  single  1.454  0.020  1.454
 LMP  C5A  C6A  single  1.533  0.020  1.533
 LMP  C6A  N7A  single  1.348  0.020  1.348
 LMP  C8A  N7A  single  1.448  0.020  1.448
 LMP  N7A  C9A  single  1.449  0.020  1.449
 LMP  C1   H1   single  0.970  0.020  1.090
 LMP  C2   H2   single  0.970  0.020  1.090
 LMP  C9A  H3   single  0.970  0.020  1.090
 LMP  C9A  H4   single  0.970  0.020  1.090
 LMP  C9A  H5   single  0.970  0.020  1.090
 LMP  C8A  H6   single  0.970  0.020  1.090
 LMP  C8A  H7   single  0.970  0.020  1.090
 LMP  C8A  H8   single  0.970  0.020  1.090
 LMP  C5A  H9   single  0.970  0.020  1.090
 LMP  C2A  H10  single  0.970  0.020  1.090
 LMP  C2A  H11  single  0.970  0.020  1.090
 LMP  N3A  H12  single  0.890  0.020  1.040
 LMP  C4A  H14  single  0.970  0.020  1.090
 LMP  C4A  H15  single  0.970  0.020  1.090
 LMP  C1A  H16  single  0.970  0.020  1.090
 LMP  C11  H18  single  0.970  0.020  1.090
 LMP  C11  H19  single  0.970  0.020  1.090
 LMP  C11  H20  single  0.970  0.020  1.090
 LMP  C5   H21  single  0.970  0.020  1.090
 LMP  C6   H22  single  0.970  0.020  1.090
 LMP  C61  H23  single  0.970  0.020  1.090
 LMP  O62  H24  single  0.850  0.020  0.980
 LMP  C62  H25  single  0.970  0.020  1.090
 LMP  C62  H26  single  0.970  0.020  1.090
 LMP  C62  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
 LMP  H1   C1   C5   110.53  3.000
 LMP  H1   C1   C11  108.54  3.000
 LMP  C5   C1   C11  116.05  3.000
 LMP  H1   C1   C2   112.01  3.000
 LMP  C5   C1   C2   100.09  3.000
 LMP  C11  C1   C2   109.47  3.000
 LMP  H2   C2   S21  109.11  3.000
 LMP  H2   C2   C3   113.94  3.000
 LMP  S21  C2   C3   110.47  3.000
 LMP  H2   C2   C1   113.75  3.000
 LMP  S21  C2   C1   108.38  3.000
 LMP  C3   C2   C1   100.86  3.000
 LMP  N4   C3   C31  122.30  3.000
 LMP  N4   C3   C2   113.56  3.000
 LMP  C31  C3   C2   124.07  3.000
 LMP  C5A  C6A  N7A  117.56  3.000
 LMP  N7A  C6A  O7A  122.46  3.000
 LMP  C5A  C6A  O7A  119.99  3.000
 LMP  C8A  N7A  C9A  114.33  3.000
 LMP  C9A  N7A  C6A  120.66  3.000
 LMP  C8A  N7A  C6A  124.76  3.000
 LMP  H5   C9A  H4   108.67  3.000
 LMP  H5   C9A  H3   108.82  3.000
 LMP  H4   C9A  H3   108.08  3.000
 LMP  H5   C9A  N7A  110.62  3.000
 LMP  H4   C9A  N7A  110.28  3.000
 LMP  H3   C9A  N7A  110.30  3.000
 LMP  H8   C8A  H7   107.09  3.000
 LMP  H8   C8A  H6   108.55  3.000
 LMP  H7   C8A  H6   107.94  3.000
 LMP  H8   C8A  N7A  112.37  3.000
 LMP  H7   C8A  N7A  108.90  3.000
 LMP  H6   C8A  N7A  111.78  3.000
 LMP  H9   C5A  N3A  109.20  3.000
 LMP  H9   C5A  C2A  110.43  3.000
 LMP  N3A  C5A  C2A  104.91  3.000
 LMP  H9   C5A  C6A  108.86  3.000
 LMP  N3A  C5A  C6A  112.49  3.000
 LMP  C2A  C5A  C6A  110.90  3.000
 LMP  H11  C2A  H10  107.20  3.000
 LMP  H11  C2A  C1A  112.21  3.000
 LMP  H10  C2A  C1A  110.37  3.000
 LMP  H11  C2A  C5A  112.44  3.000
 LMP  H10  C2A  C5A  110.85  3.000
 LMP  C1A  C2A  C5A  103.83  3.000
 LMP  H12  N3A  C4A  111.63  3.000
 LMP  H12  N3A  C5A  111.22  3.000
 LMP  C4A  N3A  C5A  107.85  3.000
 LMP  H15  C4A  H14  108.52  3.000
 LMP  H15  C4A  C1A  109.72  3.000
 LMP  H14  C4A  C1A  112.16  3.000
 LMP  H15  C4A  N3A  113.98  3.000
 LMP  H14  C4A  N3A  111.22  3.000
 LMP  C1A  C4A  N3A  101.16  3.000
 LMP  H16  C1A  S21  109.79  3.000
 LMP  H16  C1A  C4A  109.57  3.000
 LMP  S21  C1A  C4A  115.45  3.000
 LMP  H16  C1A  C2A  109.46  3.000
 LMP  C4A  C1A  C2A  102.44  3.000
 LMP  S21  C1A  C2A  109.81  3.000
 LMP  C1A  S21  C2   103.87  3.000
 LMP  O32  C31  O31  128.35  3.000
 LMP  O32  C31  C3   116.95  3.000
 LMP  O31  C31  C3   114.68  3.000
 LMP  C5   N4   C3   109.65  3.000
 LMP  H20  C11  H19  108.27  3.000
 LMP  H20  C11  H18  107.48  3.000
 LMP  H19  C11  H18  108.10  3.000
 LMP  H20  C11  C1   112.21  3.000
 LMP  H19  C11  C1   110.87  3.000
 LMP  H18  C11  C1   109.75  3.000
 LMP  H21  C5   C6   104.55  3.000
 LMP  H21  C5   N4   106.33  3.000
 LMP  C6   C5   N4   112.95  3.000
 LMP  H21  C5   C1   106.58  3.000
 LMP  N4   C5   C1   104.51  3.000
 LMP  C6   C5   C1   120.97  3.000
 LMP  H22  C6   C7   106.74  3.000
 LMP  H22  C6   C61  105.35  3.000
 LMP  C7   C6   C61  115.93  3.000
 LMP  H22  C6   C5   104.55  3.000
 LMP  C7   C6   C5   107.02  3.000
 LMP  C61  C6   C5   116.24  3.000
 LMP  H23  C61  C62  108.00  3.000
 LMP  H23  C61  O62  109.75  3.000
 LMP  C62  C61  O62  106.39  3.000
 LMP  H23  C61  C6   109.77  3.000
 LMP  C62  C61  C6   111.71  3.000
 LMP  O62  C61  C6   111.12  3.000
 LMP  H24  O62  C61  107.61  3.000
 LMP  H27  C62  H26  107.93  3.000
 LMP  H27  C62  H25  108.33  3.000
 LMP  H26  C62  H25  107.79  3.000
 LMP  H27  C62  C61  111.11  3.000
 LMP  H26  C62  C61  110.48  3.000
 LMP  H25  C62  C61  111.07  3.000
 LMP  O72  C7   O71  125.99  3.000
 LMP  O72  C7   C6   118.66  3.000
 LMP  O71  C7   C6   115.32  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
 LMP  CONST_01  C5A  C6A  N7A  C9A  180.00   0.0  0
 LMP  CONST_02  C5A  C6A  N7A  C8A    0.00   0.0  0
 LMP  CONST_03  C8A  N7A  C6A  O7A  180.00   0.0  0
 LMP  CONST_04  C9A  N7A  C6A  O7A    0.00   0.0  0
 LMP  Var_01    C1A  C4A  N3A  C5A   42.15  30.0  1
 LMP  Var_02    O31  C31  C3   C2    19.60  30.0  2
 LMP  Var_03    H6   C8A  N7A  C6A   96.71  30.0  3
 LMP  Var_04    H3   C9A  N7A  C6A  122.34  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
 LMP  chir_01  C1   C11  C2   C5   negativ
 LMP  chir_02  C2   S21  C3   C1   positiv
 LMP  chir_03  C5A  N3A  C2A  C6A  negativ
 LMP  chir_04  C1A  S21  C4A  C2A  positiv
 LMP  chir_05  C5   N4   C6   C1   negativ
 LMP  chir_06  C6   C5   C7   C61  positiv
 LMP  chir_07  C61  O62  C6   C62  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
 LMP  plan-1  C6A  0.020
 LMP  plan-1  N7A  0.020
 LMP  plan-1  C9A  0.020
 LMP  plan-1  C8A  0.020
 LMP  plan-1  C5A  0.020
 LMP  plan-1  O7A  0.020
 LMP  plan-2  C3   0.020
 LMP  plan-2  C31  0.020
 LMP  plan-2  O31  0.020
 LMP  plan-2  O32  0.020
 LMP  plan-3  C6   0.020
 LMP  plan-3  C7   0.020
 LMP  plan-3  O71  0.020
 LMP  plan-3  O72  0.020

