# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 17:58:10 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: (2R,3R,5R)-3-{[2-({N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)NCCS[C@@H]1C[C@H]2CC(=O)N2[C@@H]1C(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
 WCD  WCD  "(2R,3R,5R)-3-{[2-({N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid"  ligand  57  29  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_WCD
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
 WCD  C13  C  CH2    0  -0.126  30.7764  -23.9867  -21.4677
 WCD  C14  C  CH3    0  -0.659  29.6947  -24.1010  -19.2002
 WCD  C15  C  CH3    0  -0.680  30.7560  -26.1354  -20.2001
 WCD  C16  C  CT     0  -0.154  29.9636  -24.8571  -20.5020
 WCD  C18  C  CH1    0  -0.021  28.6321  -25.2757  -21.1960
 WCD  C19  C  C      0   0.513  27.7253  -24.0867  -21.4960
 WCD  C21  C  CH2    0  -0.287  25.8109  -22.7686  -20.7316
 WCD  C22  C  CH2    0  -0.585  26.3868  -21.5414  -20.0251
 WCD  C23  C  C      0   0.563  25.4367  -20.3648  -20.0789
 WCD  C01  C  C      0  -0.627  17.8744  -19.2604  -19.3547
 WCD  C02  C  C      0   0.481  18.1795  -20.4697  -20.2324
 WCD  C04  C  C      0  -0.044  19.3043  -19.4732  -18.8209
 WCD  C05  C  CH1    0  -0.188  20.6597  -20.9389  -20.2449
 WCD  C06  C  CH1    0  -0.410  21.5010  -19.7612  -19.6859
 WCD  C07  C  CH2    0  -0.446  20.4623  -18.6708  -19.3939
 WCD  C09  C  C      0   0.411  21.2943  -22.3306  -20.0223
 WCD  C24  C  CH2    0  -0.575  23.3522  -18.8368  -17.7641
 WCD  C26  C  CH2    0  -0.285  24.4759  -18.5291  -18.7479
 WCD  N03  N  N      0  -0.425  19.3711  -20.7132  -19.6058
 WCD  N20  N  NH1    0  -0.619  26.7048  -23.8990  -20.6499
 WCD  N27  N  NH1    0  -0.621  25.3671  -19.6412  -18.9483
 WCD  O10  O  O      0  -0.497  24.8117  -20.0949  -21.0964
 WCD  O11  O  O      0  -0.493  27.9431  -23.3598  -22.4575
 WCD  O12  O  OH1    0  -0.668  32.0353  -23.7013  -20.8967
 WCD  O17  O  OH1    0  -0.671  27.8921  -26.1922  -20.4264
 WCD  O28  O  OC    -1  -0.581  20.8377  -23.0243  -19.1021
 WCD  O29  O  O      0  -0.595  22.2282  -22.5996  -20.8031
 WCD  S25  S  S2     0  -0.016  22.3585  -20.2958  -18.1594
 WCD  H1   H  HCH2   0   0.211  30.2345  -23.0608  -21.6807
 WCD  H2   H  HCH2   0   0.191  30.8882  -24.5214  -22.4228
 WCD  H3   H  HCH3   0   0.229  29.0434  -24.6717  -18.5371
 WCD  H4   H  HCH3   0   0.236  30.6249  -23.9206  -18.6626
 WCD  H5   H  HCH3   0   0.230  29.2272  -23.1302  -19.3771
 WCD  H6   H  HCH3   0   0.228  30.2668  -26.7549  -19.4464
 WCD  H7   H  HCH3   0   0.229  30.8971  -26.7391  -21.1004
 WCD  H8   H  HCH3   0   0.249  31.7417  -25.8944  -19.8066
 WCD  H9   H  HCH1   0   0.242  28.8922  -25.7111  -22.1714
 WCD  H10  H  HCH2   0   0.245  25.6113  -22.5421  -21.7773
 WCD  H11  H  HCH2   0   0.260  24.8610  -23.0549  -20.2813
 WCD  H12  H  HCH2   0   0.254  26.6425  -21.7962  -18.9947
 WCD  H13  H  HCH2   0   0.274  27.3183  -21.2473  -20.5176
 WCD  H15  H  H      0   0.282  17.0672  -19.3943  -18.6349
 WCD  H16  H  H      0   0.249  19.3911  -19.6211  -17.7438
 WCD  H17  H  HCH1   0   0.253  20.5537  -20.7823  -21.3241
 WCD  H18  H  HCH1   0   0.298  22.2522  -19.4526  -20.4118
 WCD  H19  H  HCH2   0   0.263  20.8254  -17.8842  -18.7330
 WCD  H20  H  HCH2   0   0.251  20.1688  -18.1982  -20.3373
 WCD  H21  H  HCH2   0   0.281  23.7671  -19.0469  -16.7757
 WCD  H22  H  HCH2   0   0.274  22.7175  -17.9558  -17.6541
 WCD  H23  H  HCH2   0   0.260  25.0382  -17.6758  -18.3601
 WCD  H24  H  HCH2   0   0.257  24.0738  -18.2290  -19.7129
 WCD  H25  H  HNH1   0   0.404  26.6018  -24.5343  -19.8754
 WCD  H26  H  HNH1   0   0.398  25.8884  -19.9614  -18.1476
 WCD  H27  H  HOH1   0   0.452  32.4685  -23.0472  -21.4513
 WCD  H28  H  HOH1   0   0.465  28.3719  -27.0243  -20.3771
 WCD  O08  O  O      0  -0.437  17.6547  -21.0104  -21.1746
 WCD  H14  H  H      0   0.281  17.7116  -18.3386  -19.9135

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
 WCD  O11  C19  double  1.225  0.020  1.225
 WCD  C13  O12  single  1.411  0.020  1.411
 WCD  C13  C16  single  1.533  0.020  1.533
 WCD  C19  C18  single  1.525  0.020  1.525
 WCD  C19  N20  single  1.339  0.020  1.339
 WCD  C18  C16  single  1.559  0.020  1.559
 WCD  C18  O17  single  1.407  0.020  1.407
 WCD  O10  C23  double  1.224  0.020  1.224
 WCD  C21  N20  single  1.444  0.020  1.444
 WCD  C21  C22  single  1.529  0.020  1.529
 WCD  O08  C02  double  1.206  0.020  1.206
 WCD  C16  C15  single  1.534  0.020  1.534
 WCD  C16  C14  single  1.529  0.020  1.529
 WCD  C02  N03  single  1.368  0.020  1.368
 WCD  C02  C01  single  1.525  0.020  1.525
 WCD  C05  N03  single  1.456  0.020  1.456
 WCD  C05  C06  single  1.552  0.020  1.552
 WCD  C05  C09  single  1.546  0.020  1.546
 WCD  C23  C22  single  1.513  0.020  1.513
 WCD  C23  N27  single  1.344  0.020  1.344
 WCD  N03  C04  single  1.469  0.020  1.469
 WCD  O29  C09  deloc   1.247  0.020  1.247
 WCD  C07  C06  single  1.534  0.020  1.534
 WCD  C07  C04  single  1.521  0.020  1.521
 WCD  C06  S25  single  1.831  0.020  1.831
 WCD  C01  C04  single  1.541  0.020  1.541
 WCD  C09  O28  deloc   1.240  0.020  1.240
 WCD  N27  C26  single  1.439  0.020  1.439
 WCD  C26  C24  single  1.525  0.020  1.525
 WCD  S25  C24  single  1.809  0.020  1.809
 WCD  C13  H1   single  0.970  0.020  1.090
 WCD  C13  H2   single  0.970  0.020  1.090
 WCD  C14  H3   single  0.970  0.020  1.090
 WCD  C14  H4   single  0.970  0.020  1.090
 WCD  C14  H5   single  0.970  0.020  1.090
 WCD  C15  H6   single  0.970  0.020  1.090
 WCD  C15  H7   single  0.970  0.020  1.090
 WCD  C15  H8   single  0.970  0.020  1.090
 WCD  C18  H9   single  0.970  0.020  1.090
 WCD  C21  H10  single  0.970  0.020  1.090
 WCD  C21  H11  single  0.970  0.020  1.090
 WCD  C22  H12  single  0.970  0.020  1.090
 WCD  C22  H13  single  0.970  0.020  1.090
 WCD  C01  H14  single  0.970  0.020  1.090
 WCD  C01  H15  single  0.970  0.020  1.090
 WCD  C04  H16  single  0.970  0.020  1.090
 WCD  C05  H17  single  0.970  0.020  1.090
 WCD  C06  H18  single  0.970  0.020  1.090
 WCD  C07  H19  single  0.970  0.020  1.090
 WCD  C07  H20  single  0.970  0.020  1.090
 WCD  C24  H21  single  0.970  0.020  1.090
 WCD  C24  H22  single  0.970  0.020  1.090
 WCD  C26  H23  single  0.970  0.020  1.090
 WCD  C26  H24  single  0.970  0.020  1.090
 WCD  N20  H25  single  0.860  0.020  1.020
 WCD  N27  H26  single  0.860  0.020  1.020
 WCD  O12  H27  single  0.850  0.020  0.980
 WCD  O17  H28  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
 WCD  H2   C13  H1   107.02  3.000
 WCD  H2   C13  O12  111.03  3.000
 WCD  H1   C13  O12  110.45  3.000
 WCD  H2   C13  C16  108.95  3.000
 WCD  H1   C13  C16  109.91  3.000
 WCD  O12  C13  C16  109.44  3.000
 WCD  H5   C14  H4   107.35  3.000
 WCD  H5   C14  H3   107.94  3.000
 WCD  H4   C14  H3   107.25  3.000
 WCD  H5   C14  C16  112.14  3.000
 WCD  H4   C14  C16  110.60  3.000
 WCD  H3   C14  C16  111.34  3.000
 WCD  H8   C15  H7   107.65  3.000
 WCD  H8   C15  H6   106.38  3.000
 WCD  H7   C15  H6   108.25  3.000
 WCD  H8   C15  C16  110.76  3.000
 WCD  H7   C15  C16  111.40  3.000
 WCD  H6   C15  C16  112.17  3.000
 WCD  C18  C16  C15  107.76  3.000
 WCD  C15  C16  C14  109.59  3.000
 WCD  C18  C16  C14  111.19  3.000
 WCD  C14  C16  C13  110.41  3.000
 WCD  C15  C16  C13  108.86  3.000
 WCD  C18  C16  C13  108.96  3.000
 WCD  H9   C18  O17  110.59  3.000
 WCD  H9   C18  C19  105.96  3.000
 WCD  O17  C18  C19  107.62  3.000
 WCD  H9   C18  C16  107.41  3.000
 WCD  O17  C18  C16  112.37  3.000
 WCD  C19  C18  C16  112.71  3.000
 WCD  O11  C19  N20  123.26  3.000
 WCD  N20  C19  C18  115.99  3.000
 WCD  O11  C19  C18  120.75  3.000
 WCD  H11  C21  H10  106.97  3.000
 WCD  H11  C21  N20  108.10  3.000
 WCD  H10  C21  N20  109.32  3.000
 WCD  H11  C21  C22  110.39  3.000
 WCD  H10  C21  C22  110.25  3.000
 WCD  N20  C21  C22  111.67  3.000
 WCD  H13  C22  H12  106.75  3.000
 WCD  H13  C22  C23  108.03  3.000
 WCD  H12  C22  C23  111.22  3.000
 WCD  H13  C22  C21  109.18  3.000
 WCD  H12  C22  C21  109.70  3.000
 WCD  C23  C22  C21  111.79  3.000
 WCD  O10  C23  N27  123.64  3.000
 WCD  N27  C23  C22  114.91  3.000
 WCD  O10  C23  C22  121.43  3.000
 WCD  H15  C01  H14  109.38  3.000
 WCD  H15  C01  C04  116.20  3.000
 WCD  H14  C01  C04  115.65  3.000
 WCD  H15  C01  C02  115.52  3.000
 WCD  H14  C01  C02  113.91  3.000
 WCD  C04  C01  C02   84.51  3.000
 WCD  O08  C02  N03  131.05  3.000
 WCD  N03  C02  C01   92.97  3.000
 WCD  O08  C02  C01  135.88  3.000
 WCD  H16  C04  N03  114.18  3.000
 WCD  H16  C04  C07  112.52  3.000
 WCD  N03  C04  C07  102.09  3.000
 WCD  H16  C04  C01  115.76  3.000
 WCD  C07  C04  C01  120.20  3.000
 WCD  N03  C04  C01   88.49  3.000
 WCD  H17  C05  N03  108.94  3.000
 WCD  H17  C05  C09  108.08  3.000
 WCD  N03  C05  C09  116.09  3.000
 WCD  H17  C05  C06  107.39  3.000
 WCD  C09  C05  C06  114.14  3.000
 WCD  N03  C05  C06  101.78  3.000
 WCD  H18  C06  S25  108.39  3.000
 WCD  H18  C06  C07  113.10  3.000
 WCD  S25  C06  C07  111.47  3.000
 WCD  H18  C06  C05  110.42  3.000
 WCD  S25  C06  C05  109.44  3.000
 WCD  C07  C06  C05  103.94  3.000
 WCD  H20  C07  H19  107.47  3.000
 WCD  H20  C07  C06  108.92  3.000
 WCD  H19  C07  C06  113.76  3.000
 WCD  H20  C07  C04  110.38  3.000
 WCD  H19  C07  C04  113.96  3.000
 WCD  C06  C07  C04  102.25  3.000
 WCD  O29  C09  O28  128.32  3.000
 WCD  O28  C09  C05  117.36  3.000
 WCD  O29  C09  C05  114.31  3.000
 WCD  H22  C24  H21  106.56  3.000
 WCD  H22  C24  S25  110.70  3.000
 WCD  H21  C24  S25  104.55  3.000
 WCD  H22  C24  C26  109.31  3.000
 WCD  H21  C24  C26  110.04  3.000
 WCD  S25  C24  C26  115.25  3.000
 WCD  H24  C26  H23  106.83  3.000
 WCD  H24  C26  N27  108.58  3.000
 WCD  H23  C26  N27  109.52  3.000
 WCD  H24  C26  C24  110.84  3.000
 WCD  H23  C26  C24  107.92  3.000
 WCD  N27  C26  C24  112.97  3.000
 WCD  C05  N03  C04  113.93  3.000
 WCD  C04  N03  C02   93.14  3.000
 WCD  C05  N03  C02  126.69  3.000
 WCD  H25  N20  C21  118.31  3.000
 WCD  H25  N20  C19  118.40  3.000
 WCD  C21  N20  C19  123.09  3.000
 WCD  H26  N27  C26  117.08  3.000
 WCD  H26  N27  C23  118.07  3.000
 WCD  C26  N27  C23  124.42  3.000
 WCD  H27  O12  C13  107.84  3.000
 WCD  H28  O17  C18  109.22  3.000
 WCD  C24  S25  C06  101.77  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
 WCD  CONST_02  C04  N03  C02  C01     0.00   0.0  0
 WCD  CONST_03  O08  C02  N03  C04   180.00   0.0  0
 WCD  CONST_04  O08  C02  C01  C04   180.00   0.0  0
 WCD  CONST_06  C21  N20  C19  C18   180.00   0.0  0
 WCD  CONST_07  O11  C19  N20  C21     0.00   0.0  0
 WCD  CONST_08  C26  N27  C23  C22   180.00   0.0  0
 WCD  CONST_09  O10  C23  N27  C26     0.00   0.0  0
 WCD  CONST_10  H25  N20  C19  C18     0.00   0.0  0
 WCD  CONST_11  H26  N27  C23  C22     0.00   0.0  0
 WCD  CONST_12  H26  N27  C23  O10   180.00   0.0  0
 WCD  CONST_13  H25  N20  C19  O11   180.00   0.0  0
 WCD  Var_01    H14  C01  C02  N03   122.79  30.0  1
 WCD  Var_02    H15  C01  C02  N03  -109.34  30.0  1
 WCD  Var_03    H14  C01  C02  O08   -53.65  30.0  1
 WCD  Var_04    H15  C01  C02  O08    74.23  30.0  1
 WCD  Var_05    C26  C24  S25  C06   -67.51  30.0  3
 WCD  Var_06    H21  C24  S25  C06   171.57  30.0  3
 WCD  Var_07    H22  C24  S25  C06    57.18  30.0  3
 WCD  Var_08    O12  C13  C16  C14    62.83  30.0  3
 WCD  Var_09    O12  C13  C16  C15   -57.51  30.0  3
 WCD  Var_10    O12  C13  C16  C18  -174.78  30.0  3
 WCD  Var_11    C22  C21  N20  C19   -83.79  30.0  2
 WCD  Var_12    O10  C23  C22  C21   -41.53  30.0  2
 WCD  Var_13    N27  C23  C22  C21   139.99  30.0  2
 WCD  Var_14    N20  C21  C22  C23  -178.56  30.0  2
 WCD  Var_15    C24  C26  N27  C23   109.35  30.0  3
 WCD  Var_16    S25  C24  C26  N27   -54.81  30.0  3
 WCD  Var_17    H6   C15  C16  C13   174.86  30.0  3
 WCD  Var_18    H7   C15  C16  C13   -63.61  30.0  3
 WCD  Var_19    H8   C15  C16  C13    56.17  30.0  3
 WCD  Var_20    H3   C14  C16  C13   174.99  30.0  3
 WCD  Var_21    H4   C14  C16  C13   -65.88  30.0  3
 WCD  Var_22    H5   C14  C16  C13    53.91  30.0  3
 WCD  Var_23    H1   C13  C16  C14   -58.63  30.0  3
 WCD  Var_24    H2   C13  C16  C14  -175.60  30.0  3
 WCD  Var_25    H6   C15  C16  C14    54.01  30.0  3
 WCD  Var_26    H7   C15  C16  C14   175.54  30.0  3
 WCD  Var_27    H8   C15  C16  C14   -64.68  30.0  3
 WCD  Var_28    H1   C13  C16  C15  -178.97  30.0  3
 WCD  Var_29    H2   C13  C16  C15    64.06  30.0  3
 WCD  Var_30    H3   C14  C16  C15   -65.12  30.0  3
 WCD  Var_31    H4   C14  C16  C15    54.02  30.0  3
 WCD  Var_32    H5   C14  C16  C15   173.81  30.0  3
 WCD  Var_33    H1   C13  C16  C18    63.76  30.0  3
 WCD  Var_34    H2   C13  C16  C18   -53.21  30.0  3
 WCD  Var_35    H6   C15  C16  C18   -67.11  30.0  3
 WCD  Var_36    H7   C15  C16  C18    54.42  30.0  3
 WCD  Var_37    H8   C15  C16  C18   174.20  30.0  3
 WCD  Var_38    H3   C14  C16  C18    53.92  30.0  3
 WCD  Var_39    H4   C14  C16  C18   173.05  30.0  3
 WCD  Var_40    H5   C14  C16  C18   -67.15  30.0  3
 WCD  Var_41    H10  C21  N20  C19    38.48  30.0  2
 WCD  Var_42    H11  C21  N20  C19   154.59  30.0  2
 WCD  Var_43    H25  N20  C21  C22    91.01  30.0  3
 WCD  Var_44    H10  C21  C22  C23    59.70  30.0  2
 WCD  Var_45    H11  C21  C22  C23   -58.28  30.0  2
 WCD  Var_46    H23  C26  N27  C23  -130.33  30.0  3
 WCD  Var_47    H24  C26  N27  C23   -14.02  30.0  3
 WCD  Var_48    H26  N27  C26  C24   -62.92  30.0  2
 WCD  Var_49    H12  C22  C21  N20   -54.70  30.0  3
 WCD  Var_50    H13  C22  C21  N20    61.96  30.0  3
 WCD  Var_51    H12  C22  C23  N27    16.98  30.0  3
 WCD  Var_52    H13  C22  C23  N27   -99.86  30.0  3
 WCD  Var_53    H21  C24  C26  N27    63.08  30.0  3
 WCD  Var_54    H22  C24  C26  N27   179.78  30.0  3
 WCD  Var_55    H12  C22  C23  O10  -164.54  30.0  3
 WCD  Var_56    H13  C22  C23  O10    78.62  30.0  3
 WCD  Var_57    H23  C26  C24  S25  -176.04  30.0  2
 WCD  Var_58    H24  C26  C24  S25    67.31  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
 WCD  chir_01  C18  C19  C16  O17  negativ
 WCD  chir_02  C04  N03  C07  C01  negativ
 WCD  chir_03  C05  N03  C09  C06  positiv
 WCD  chir_04  C06  S25  C07  C05  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
 WCD  plan-1  C18  0.020
 WCD  plan-1  C19  0.020
 WCD  plan-1  C21  0.020
 WCD  plan-1  N20  0.020
 WCD  plan-1  O11  0.020
 WCD  plan-1  H25  0.020
 WCD  plan-2  C22  0.020
 WCD  plan-2  C23  0.020
 WCD  plan-2  C26  0.020
 WCD  plan-2  N27  0.020
 WCD  plan-2  O10  0.020
 WCD  plan-2  H26  0.020
 WCD  plan-3  C01  0.020
 WCD  plan-3  C02  0.020
 WCD  plan-3  C04  0.020
 WCD  plan-3  C05  0.020
 WCD  plan-3  N03  0.020
 WCD  plan-3  O08  0.020
 WCD  plan-4  C05  0.020
 WCD  plan-4  C09  0.020
 WCD  plan-4  O28  0.020
 WCD  plan-4  O29  0.020

