# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 07:43:12 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (2~{R},3~{R},4~{R})-4-methyl-3-(2-oxidanylidene-2-propoxy-ethyl)sulfanyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCOC(=O)CS[C@@H]1[C@H](C)C(=N[C@@H]1C(O)=O)[C@H](C=O)[C@@H](C)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
 6B7  6B7  '(2~{R},3~{R},4~{R})-4-methyl-3-(2-oxidanylidene-2-propoxy-ethyl)sulfanyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid'  ligand  46  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6B7
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
 6B7  C10  C  CH3   0  -0.682   1.4953   1.9105   1.4318
 6B7  CD   C  CR5   0   0.286   2.6692  -0.1063   0.3102
 6B7  C12  C  CH1   0  -0.475   3.8768   0.6892  -0.0803
 6B7  N    N  N     0  -0.334   2.3810  -1.2455  -0.1648
 6B7  C13  C  C1    0   0.203   3.5030   1.7002  -1.1533
 6B7  C14  C  CH1   0   0.065   5.0878  -0.1011  -0.6045
 6B7  C15  C  CH3   0  -0.696   5.5390  -1.2057   0.3352
 6B7  S1   S  S2    0   0.022  -0.6318   0.2968  -0.1650
 6B7  C1   C  C     0   0.615  -3.3160   0.5744  -0.2415
 6B7  O1   O  O     0  -0.442  -3.1104   1.2854  -1.1918
 6B7  O2   O  O2    0  -0.453  -4.5134   0.2379   0.1993
 6B7  C2   C  CH2   0  -0.162  -5.6618   0.7784  -0.4769
 6B7  C3   C  CH2   0  -0.469  -6.9006   0.1732   0.1455
 6B7  C4   C  CH3   0  -0.674  -8.1595   0.7314  -0.5044
 6B7  O5   O  O     0  -0.368   4.0984   2.7325  -1.3175
 6B7  C5   C  CH2   0  -0.681  -2.2335  -0.0423   0.6052
 6B7  O6   O  OH1   0  -0.664   4.7630  -0.5707  -1.8941
 6B7  CB   C  CR15  0  -0.425   0.4798  -0.4737   1.0651
 6B7  CA   C  CR15  0  -0.189   1.1789  -1.7215   0.4904
 6B7  C    C  C     0   0.531   0.3279  -2.5529  -0.4375
 6B7  CG   C  CR15  0  -0.298   1.7029   0.4078   1.3576
 6B7  H1   H  HCH3  0   0.256   0.7106   2.1472   2.1498
 6B7  H2   H  HCH3  0   0.248   2.4040   2.4092   1.7696
 6B7  H3   H  HCH3  0   0.234   1.2033   2.3457   0.4768
 6B7  H5   H  HCH1  0   0.307   4.2214   1.2486   0.7948
 6B7  H8   H  H     0   0.206   2.6551   1.4222  -1.8035
 6B7  H9   H  HCH1  0   0.227   5.9006   0.6356  -0.6669
 6B7  H10  H  HCH3  0   0.240   4.7959  -1.9965   0.4179
 6B7  H11  H  HCH3  0   0.238   6.4692  -1.6470  -0.0283
 6B7  H12  H  HCH3  0   0.229   5.7364  -0.8073   1.3314
 6B7  H13  H  HCH2  0   0.236  -5.6649   1.8663  -0.3721
 6B7  H14  H  HCH2  0   0.236  -5.6084   0.5429  -1.5423
 6B7  H15  H  HCH2  0   0.235  -6.8751  -0.9132   0.0311
 6B7  H16  H  HCH2  0   0.235  -6.9145   0.3821   1.2178
 6B7  H17  H  HOH1  0   0.486  -1.2720  -3.5699  -0.3971
 6B7  H18  H  HCH3  0   0.241  -9.0514   0.2870  -0.0645
 6B7  H19  H  HCH3  0   0.226  -8.2296   1.8124  -0.3738
 6B7  H20  H  HCH3  0   0.226  -8.1815   0.5254  -1.5757
 6B7  H21  H  HCH2  0   0.307  -2.4047  -1.1141   0.7064
 6B7  H22  H  HCH2  0   0.316  -2.2729   0.3926   1.6070
 6B7  H23  H  HOH1  0   0.454   5.5690  -0.8998  -2.3044
 6B7  H24  H  HCR5  0   0.317  -0.0947  -0.6902   1.9647
 6B7  H25  H  HCR5  0   0.308   1.4783  -2.3692   1.3269
 6B7  H26  H  HCR5  0   0.297   2.1042   0.0775   2.3267
 6B7  O    O  O     0  -0.424   0.5717  -2.7718  -1.5933
 6B7  OXT  O  OH1   0  -0.592  -0.7246  -3.0446   0.2062

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
 6B7  C4   C3   single  1.523  0.020  1.523
 6B7  C3   C2   single  1.513  0.020  1.513
 6B7  C2   O2   single  1.438  0.020  1.438
 6B7  O2   C1   single  1.320  0.020  1.320
 6B7  O    C    double  1.201  0.020  1.201
 6B7  C1   O1   double  1.205  0.020  1.205
 6B7  C1   C5   single  1.506  0.020  1.506
 6B7  C5   S1   single  1.809  0.020  1.809
 6B7  C    OXT  single  1.328  0.020  1.328
 6B7  C    CA   single  1.509  0.020  1.509
 6B7  S1   CB   single  1.828  0.020  1.828
 6B7  CA   CB   single  1.541  0.020  1.541
 6B7  CA   N    single  1.449  0.020  1.449
 6B7  CB   CG   single  1.536  0.020  1.536
 6B7  N    CD   double  1.267  0.020  1.267
 6B7  O5   C13  double  1.203  0.020  1.203
 6B7  CG   C10  single  1.519  0.020  1.519
 6B7  CG   CD   single  1.515  0.020  1.515
 6B7  CD   C12  single  1.498  0.020  1.498
 6B7  C13  C12  single  1.521  0.020  1.521
 6B7  C12  C14  single  1.538  0.020  1.538
 6B7  C14  O6   single  1.410  0.020  1.410
 6B7  C14  C15  single  1.519  0.020  1.519
 6B7  C10  H1   single  0.970  0.020  1.090
 6B7  C10  H2   single  0.970  0.020  1.090
 6B7  C10  H3   single  0.970  0.020  1.090
 6B7  C12  H5   single  0.970  0.020  1.090
 6B7  C13  H8   single  0.930  0.020  1.080
 6B7  C14  H9   single  0.970  0.020  1.090
 6B7  C15  H10  single  0.970  0.020  1.090
 6B7  C15  H11  single  0.970  0.020  1.090
 6B7  C15  H12  single  0.970  0.020  1.090
 6B7  C2   H13  single  0.970  0.020  1.090
 6B7  C2   H14  single  0.970  0.020  1.090
 6B7  C3   H15  single  0.970  0.020  1.090
 6B7  C3   H16  single  0.970  0.020  1.090
 6B7  OXT  H17  single  0.850  0.020  0.980
 6B7  C4   H18  single  0.970  0.020  1.090
 6B7  C4   H19  single  0.970  0.020  1.090
 6B7  C4   H20  single  0.970  0.020  1.090
 6B7  C5   H21  single  0.970  0.020  1.090
 6B7  C5   H22  single  0.970  0.020  1.090
 6B7  O6   H23  single  0.850  0.020  0.980
 6B7  CB   H24  single  0.970  0.020  1.090
 6B7  CA   H25  single  0.970  0.020  1.090
 6B7  CG   H26  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
 6B7  H3   C10  H2   108.20  3.000
 6B7  H3   C10  H1   107.33  3.000
 6B7  H2   C10  H1   107.26  3.000
 6B7  H3   C10  CG   112.89  3.000
 6B7  H2   C10  CG   110.72  3.000
 6B7  H1   C10  CG   110.22  3.000
 6B7  CG   CD   N    114.78  3.000
 6B7  CG   CD   C12  120.95  3.000
 6B7  N    CD   C12  124.26  3.000
 6B7  H5   C12  C14  106.69  3.000
 6B7  H5   C12  C13  107.56  3.000
 6B7  C14  C12  C13  107.13  3.000
 6B7  H5   C12  CD   108.47  3.000
 6B7  C14  C12  CD   116.79  3.000
 6B7  C13  C12  CD   109.81  3.000
 6B7  CA   N    CD   108.32  3.000
 6B7  H8   C13  O5   121.05  3.000
 6B7  H8   C13  C12  115.90  3.000
 6B7  O5   C13  C12  123.04  3.000
 6B7  H9   C14  O6   109.98  3.000
 6B7  H9   C14  C15  107.64  3.000
 6B7  O6   C14  C15  113.08  3.000
 6B7  H9   C14  C12  104.91  3.000
 6B7  C15  C14  C12  113.38  3.000
 6B7  O6   C14  C12  107.54  3.000
 6B7  H12  C15  H11  107.31  3.000
 6B7  H12  C15  H10  108.63  3.000
 6B7  H11  C15  H10  108.26  3.000
 6B7  H12  C15  C14  110.68  3.000
 6B7  H11  C15  C14  109.95  3.000
 6B7  H10  C15  C14  111.88  3.000
 6B7  CB   S1   C5    99.95  3.000
 6B7  C5   C1   O2   111.10  3.000
 6B7  C5   C1   O1   124.22  3.000
 6B7  O2   C1   O1   124.68  3.000
 6B7  C2   O2   C1   118.14  3.000
 6B7  H14  C2   H13  107.95  3.000
 6B7  H14  C2   C3   110.80  3.000
 6B7  H13  C2   C3   110.88  3.000
 6B7  H14  C2   O2   109.79  3.000
 6B7  H13  C2   O2   109.34  3.000
 6B7  C3   C2   O2   108.07  3.000
 6B7  H16  C3   H15  107.05  3.000
 6B7  H16  C3   C4   109.77  3.000
 6B7  H15  C3   C4   109.82  3.000
 6B7  H16  C3   C2   109.74  3.000
 6B7  H15  C3   C2   109.61  3.000
 6B7  C4   C3   C2   110.78  3.000
 6B7  H20  C4   H19  107.66  3.000
 6B7  H20  C4   H18  107.63  3.000
 6B7  H19  C4   H18  107.65  3.000
 6B7  H20  C4   C3   111.50  3.000
 6B7  H19  C4   C3   111.42  3.000
 6B7  H18  C4   C3   110.79  3.000
 6B7  H22  C5   H21  107.49  3.000
 6B7  H22  C5   C1   109.05  3.000
 6B7  H21  C5   C1   109.99  3.000
 6B7  H22  C5   S1   110.34  3.000
 6B7  H21  C5   S1   111.28  3.000
 6B7  C1   C5   S1   108.67  3.000
 6B7  H23  O6   C14  108.11  3.000
 6B7  H24  CB   CG   112.14  3.000
 6B7  H24  CB   CA   112.72  3.000
 6B7  CG   CB   CA   100.04  3.000
 6B7  H24  CB   S1   108.60  3.000
 6B7  CG   CB   S1   111.75  3.000
 6B7  CA   CB   S1   111.47  3.000
 6B7  H25  CA   C    107.26  3.000
 6B7  H25  CA   CB   108.47  3.000
 6B7  C    CA   CB   114.81  3.000
 6B7  H25  CA   N    108.15  3.000
 6B7  CB   CA   N    106.19  3.000
 6B7  C    CA   N    111.76  3.000
 6B7  CA   C    OXT  110.67  3.000
 6B7  CA   C    O    125.28  3.000
 6B7  OXT  C    O    124.03  3.000
 6B7  H26  CG   CB   106.62  3.000
 6B7  H26  CG   CD   105.94  3.000
 6B7  CB   CG   CD   100.46  3.000
 6B7  H26  CG   C10  107.70  3.000
 6B7  CD   CG   C10  117.18  3.000
 6B7  CB   CG   C10  117.92  3.000
 6B7  H17  OXT  C    110.28  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
 6B7  CONST_01  H17  OXT  C   CA  180.00   0.0  0
 6B7  Var_01    CG   CD   N   CA   -0.95  30.0  1
 6B7  Var_02    H21  C5   S1  CB  -61.07  30.0  1
 6B7  Var_03    O2   C1   C5  S1  173.41  30.0  2
 6B7  Var_04    C3   C2   O2  C1  176.04  30.0  2
 6B7  Var_05    C4   C3   C2  O2  178.61  30.0  2
 6B7  Var_06    C5   C1   O2  C2  178.17  30.0  3
 6B7  Var_07    H18  C4   C3  C2  179.33  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
 6B7  chir_01  C12  CD  C13  C14  positiv
 6B7  chir_02  C14  O6  C12  C15  negativ
 6B7  chir_03  CB   S1  CG   CA   positiv
 6B7  chir_04  CA   N   CB   C    negativ
 6B7  chir_05  CG   CB  C10  CD   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
 6B7  plan-1  CA   0.020
 6B7  plan-1  C    0.020
 6B7  plan-1  H17  0.020
 6B7  plan-1  O    0.020
 6B7  plan-1  OXT  0.020
 6B7  plan-2  C1   0.020
 6B7  plan-2  O1   0.020
 6B7  plan-2  O2   0.020
 6B7  plan-2  C5   0.020
 6B7  plan-3  C12  0.020
 6B7  plan-3  C13  0.020
 6B7  plan-3  O5   0.020
 6B7  plan-3  H8   0.020

