# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 00:34:13 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: (2R)-2-[(R)-carboxy{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}methoxymethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-oxazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@](NC(=O)[C@H](C(O)=O)c1ccc(O)cc1)([C@@H]2NC(=C(CO2)CSc3nnnn3C)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
 XQP  XQP  "(2R)-2-[(R)-carboxy{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}methoxymethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-oxazine-4-carboxylic acid"  ligand  56  37  .  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
;

data_comp_XQP
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
 XQP  C1   C  C      0   0.412  32.3826   2.9981  16.4323
 XQP  O1   O  OC    -1  -0.572  31.4606   2.5385  17.1328
 XQP  C2   C  C      0   0.116  32.4693   6.1277  16.9210
 XQP  N2   N  NH1    0  -0.703  30.7392   2.8647  14.6372
 XQP  C3   C  C      0   0.007  31.1627   6.0919  17.2673
 XQP  C5   C  CH1    0   0.132  31.9530   5.0324  14.8113
 XQP  C6   C  CT     0   0.304  32.0038   3.4621  14.9752
 XQP  C7   C  CH3    0  -0.415  33.2812   1.7206  13.9512
 XQP  C8   C  C      0   0.551  30.0713   3.0178  13.4861
 XQP  C9   C  CH1    0  -0.561  28.7132   2.3197  13.3948
 XQP  C10  C  CR6    0   0.112  28.8978   0.9891  12.6983
 XQP  C11  C  CR16   0  -0.314  28.2815   0.7400  11.4753
 XQP  C12  C  CR16   0  -0.323  28.4316  -0.4708  10.8154
 XQP  C13  C  CR6    0   0.335  29.2176  -1.4733  11.3750
 XQP  C14  C  CR16   0  -0.368  29.8404  -1.2416  12.5992
 XQP  C15  C  CR16   0  -0.266  29.6750  -0.0279  13.2488
 XQP  C16  C  C      0   0.452  27.8928   2.1013  14.6954
 XQP  C18  C  CR5    0   0.331  28.4547   4.7947  18.9360
 XQP  C4   C  CH2    0  -0.195  30.1707   5.5797  16.2632
 XQP  N1   N  NH1    0  -0.658  32.8530   5.7620  15.6538
 XQP  N3   N  N      0  -0.333  27.5580   5.6556  18.5044
 XQP  N4   N  N      0  -0.137  26.5344   4.9302  18.0631
 XQP  N5   N  N      0  -0.085  26.7500   3.6838  18.2183
 XQP  N6   N  NR5    0  -0.293  27.9557   3.5652  18.7571
 XQP  O10  O  O      0  -0.576  33.5776   3.1148  16.7366
 XQP  O2   O  O2     0  -0.477  30.6732   5.5643  14.9456
 XQP  O3   O  O2     0  -0.496  33.0229   3.0964  14.0771
 XQP  O5   O  OH1    0  -0.633  29.3439  -2.6333  10.6953
 XQP  O6   O  OC    -1  -0.575  26.6734   2.2974  14.6018
 XQP  O7   O  O      0  -0.583  28.5138   1.7017  15.7070
 XQP  O8   O  O      0  -0.586  34.7654   6.5217  17.2408
 XQP  O9   O  OC    -1  -0.568  33.4163   6.9916  18.9460
 XQP  S1   S  S2     0   0.044  30.0043   5.1286  19.6375
 XQP  H2   H  HNH1   0   0.418  30.2396   2.3785  15.3833
 XQP  H4   H  HCH1   0   0.241  32.2416   5.2164  13.7744
 XQP  H5   H  HCH3   0   0.227  34.1045   1.6160  13.2446
 XQP  H6   H  HCH3   0   0.204  33.5844   1.2538  14.8928
 XQP  H7   H  HCH3   0   0.207  32.4242   1.1668  13.5560
 XQP  H8   H  HCH1   0   0.253  28.1181   2.9503  12.7314
 XQP  H9   H  HCR6   0   0.246  27.6699   1.5103  11.0206
 XQP  H10  H  HCR6   0   0.255  27.9423  -0.6383   9.8637
 XQP  H11  H  HCR6   0   0.264  30.4557  -2.0121  13.0514
 XQP  H12  H  HCR6   0   0.247  30.1681   0.1243  14.2000
 XQP  H15  H  HCH3   0   0.278  28.0741   1.5358  18.4247
 XQP  H16  H  HCH3   0   0.277  29.6006   2.3099  18.8668
 XQP  H17  H  HCH3   0   0.269  28.3608   2.0271  20.1124
 XQP  H18  H  HCH2   0   0.228  29.2902   6.2293  16.2412
 XQP  H19  H  HCH2   0   0.207  29.8119   4.5792  16.5441
 XQP  H20  H  HOH1   0   0.470  29.9185  -3.2427  11.1726
 XQP  H3   H  HNH1   0   0.366  33.8359   5.5553  15.5721
 XQP  C17  C  CH2    0  -0.684  30.5884   6.5298  18.5592
 XQP  O4   O  O      0  -0.504  30.4884   3.6283  12.5090
 XQP  C19  C  CH3    0  -0.534  28.5336   2.2774  19.0684
 XQP  H13  H  HCH2   0   0.318  31.3244   7.0319  19.1771
 XQP  H14  H  HCH2   0   0.284  29.7213   7.1796  18.4320
 XQP  C20  C  C      0   0.386  33.6500   6.5951  17.7900

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
 XQP  O5   C13  single    1.350  0.020  1.350
 XQP  C12  C13  aromatic  1.391  0.020  1.391
 XQP  C12  C11  aromatic  1.387  0.020  1.387
 XQP  C13  C14  aromatic  1.393  0.020  1.393
 XQP  C11  C10  aromatic  1.392  0.020  1.392
 XQP  C14  C15  aromatic  1.387  0.020  1.387
 XQP  C10  C15  aromatic  1.393  0.020  1.393
 XQP  C10  C9   single    1.513  0.020  1.513
 XQP  C7   O3   single    1.405  0.020  1.405
 XQP  O4   C8   double    1.225  0.020  1.225
 XQP  O3   C6   single    1.407  0.020  1.407
 XQP  C8   C9   single    1.530  0.020  1.530
 XQP  C8   N2   single    1.340  0.020  1.340
 XQP  C9   C16  single    1.553  0.020  1.553
 XQP  N2   C6   single    1.439  0.020  1.439
 XQP  C6   C5   single    1.580  0.020  1.580
 XQP  C6   C1   single    1.575  0.020  1.575
 XQP  C16  O7   deloc     1.253  0.020  1.253
 XQP  C16  O6   deloc     1.239  0.020  1.239
 XQP  C5   O2   single    1.392  0.020  1.392
 XQP  C5   N1   single    1.433  0.020  1.433
 XQP  O10  C1   deloc     1.239  0.020  1.239
 XQP  C1   O1   deloc     1.246  0.020  1.246
 XQP  O2   C4   single    1.410  0.020  1.410
 XQP  N1   C2   single    1.374  0.020  1.374
 XQP  C4   C3   single    1.502  0.020  1.502
 XQP  C2   C3   double    1.352  0.020  1.352
 XQP  C2   C20  single    1.539  0.020  1.539
 XQP  O8   C20  deloc     1.245  0.020  1.245
 XQP  C3   C17  single    1.480  0.020  1.480
 XQP  C20  O9   deloc     1.244  0.020  1.244
 XQP  N4   N3   aromatic  1.330  0.020  1.330
 XQP  N4   N5   aromatic  1.274  0.020  1.274
 XQP  N3   C18  aromatic  1.316  0.020  1.316
 XQP  N5   N6   aromatic  1.326  0.020  1.326
 XQP  C17  S1   single    1.862  0.020  1.862
 XQP  C18  N6   aromatic  1.339  0.020  1.339
 XQP  C18  S1   single    1.733  0.020  1.733
 XQP  N6   C19  single    1.445  0.020  1.445
 XQP  N2   H2   single    0.860  0.020  1.020
 XQP  C5   H4   single    0.970  0.020  1.090
 XQP  C7   H5   single    0.970  0.020  1.090
 XQP  C7   H6   single    0.970  0.020  1.090
 XQP  C7   H7   single    0.970  0.020  1.090
 XQP  C9   H8   single    0.970  0.020  1.090
 XQP  C11  H9   single    0.930  0.020  1.080
 XQP  C12  H10  single    0.930  0.020  1.080
 XQP  C14  H11  single    0.930  0.020  1.080
 XQP  C15  H12  single    0.930  0.020  1.080
 XQP  C17  H13  single    0.970  0.020  1.090
 XQP  C17  H14  single    0.970  0.020  1.090
 XQP  C19  H15  single    0.970  0.020  1.090
 XQP  C19  H16  single    0.970  0.020  1.090
 XQP  C19  H17  single    0.970  0.020  1.090
 XQP  C4   H18  single    0.970  0.020  1.090
 XQP  C4   H19  single    0.970  0.020  1.090
 XQP  O5   H20  single    0.850  0.020  0.980
 XQP  N1   H3   single    0.890  0.020  1.040

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
 XQP  O10  C1   C6   115.56  3.000
 XQP  O10  C1   O1   127.63  3.000
 XQP  C6   C1   O1   116.80  3.000
 XQP  N1   C2   C20  112.80  3.000
 XQP  C20  C2   C3   127.22  3.000
 XQP  N1   C2   C3   119.95  3.000
 XQP  H2   N2   C8   116.00  3.000
 XQP  H2   N2   C6   117.13  3.000
 XQP  C8   N2   C6   126.34  3.000
 XQP  C4   C3   C17  115.36  3.000
 XQP  C17  C3   C2   126.21  3.000
 XQP  C4   C3   C2   118.43  3.000
 XQP  H4   C5   O2   105.67  3.000
 XQP  H4   C5   N1   107.86  3.000
 XQP  O2   C5   N1   109.03  3.000
 XQP  H4   C5   C6   104.93  3.000
 XQP  N1   C5   C6   115.15  3.000
 XQP  O2   C5   C6   113.53  3.000
 XQP  O3   C6   C5   102.44  3.000
 XQP  C5   C6   N2   111.10  3.000
 XQP  O3   C6   N2   112.26  3.000
 XQP  C5   C6   C1   113.36  3.000
 XQP  N2   C6   C1   107.84  3.000
 XQP  O3   C6   C1   109.86  3.000
 XQP  H7   C7   H6   108.18  3.000
 XQP  H7   C7   H5   107.99  3.000
 XQP  H6   C7   H5   107.92  3.000
 XQP  H7   C7   O3   112.57  3.000
 XQP  H6   C7   O3   113.05  3.000
 XQP  H5   C7   O3   106.91  3.000
 XQP  C9   C8   O4   118.81  3.000
 XQP  C9   C8   N2   116.22  3.000
 XQP  O4   C8   N2   124.92  3.000
 XQP  H8   C9   C16  107.59  3.000
 XQP  H8   C9   C10  107.14  3.000
 XQP  C16  C9   C10  109.04  3.000
 XQP  H8   C9   C8   104.87  3.000
 XQP  C16  C9   C8   118.89  3.000
 XQP  C10  C9   C8   108.69  3.000
 XQP  C15  C10  C11  117.62  3.000
 XQP  C15  C10  C9   121.87  3.000
 XQP  C11  C10  C9   120.51  3.000
 XQP  H9   C11  C12  118.81  3.000
 XQP  H9   C11  C10  119.44  3.000
 XQP  C12  C11  C10  121.75  3.000
 XQP  H10  C12  C13  119.81  3.000
 XQP  H10  C12  C11  120.28  3.000
 XQP  C13  C12  C11  119.92  3.000
 XQP  O5   C13  C14  122.91  3.000
 XQP  C14  C13  C12  119.09  3.000
 XQP  O5   C13  C12  118.00  3.000
 XQP  H11  C14  C15  119.61  3.000
 XQP  H11  C14  C13  120.12  3.000
 XQP  C15  C14  C13  120.27  3.000
 XQP  H12  C15  C14  118.73  3.000
 XQP  H12  C15  C10  119.92  3.000
 XQP  C14  C15  C10  121.35  3.000
 XQP  O7   C16  O6   126.85  3.000
 XQP  O6   C16  C9   115.75  3.000
 XQP  O7   C16  C9   117.34  3.000
 XQP  S1   C18  N6   124.34  3.000
 XQP  S1   C18  N3   128.02  3.000
 XQP  N6   C18  N3   107.64  3.000
 XQP  H19  C4   H18  106.42  3.000
 XQP  H19  C4   O2   110.19  3.000
 XQP  H18  C4   O2   105.93  3.000
 XQP  H19  C4   C3   110.80  3.000
 XQP  H18  C4   C3   110.02  3.000
 XQP  O2   C4   C3   113.15  3.000
 XQP  H3   N1   C5   117.43  3.000
 XQP  H3   N1   C2   113.70  3.000
 XQP  C5   N1   C2   120.18  3.000
 XQP  N4   N3   C18  106.05  3.000
 XQP  N5   N4   N3   111.27  3.000
 XQP  N6   N5   N4   106.91  3.000
 XQP  N5   N6   C19  122.06  3.000
 XQP  C19  N6   C18  129.82  3.000
 XQP  N5   N6   C18  108.12  3.000
 XQP  C4   O2   C5   114.95  3.000
 XQP  C7   O3   C6   116.41  3.000
 XQP  H20  O5   C13  110.46  3.000
 XQP  C18  S1   C17  101.01  3.000
 XQP  H14  C17  H13  109.27  3.000
 XQP  H14  C17  S1   105.45  3.000
 XQP  H13  C17  S1   103.38  3.000
 XQP  H14  C17  C3   112.51  3.000
 XQP  H13  C17  C3   111.78  3.000
 XQP  S1   C17  C3   113.87  3.000
 XQP  H17  C19  H16  109.95  3.000
 XQP  H17  C19  H15  110.20  3.000
 XQP  H16  C19  H15  109.06  3.000
 XQP  H17  C19  N6   110.39  3.000
 XQP  H16  C19  N6   109.03  3.000
 XQP  H15  C19  N6   108.18  3.000
 XQP  O9   C20  O8   126.63  3.000
 XQP  O9   C20  C2   118.51  3.000
 XQP  O8   C20  C2   114.85  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
 XQP  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 XQP  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 XQP  CONST_03  C14  C13  C12  C11     0.00   0.0  0
 XQP  CONST_04  C14  C15  C10  C11     0.00   0.0  0
 XQP  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 XQP  CONST_06  C15  C10  C11  C12     0.00   0.0  0
 XQP  CONST_07  N5   N4   N3   C18     0.00   0.0  0
 XQP  CONST_08  N4   N5   N6   C18     0.00   0.0  0
 XQP  CONST_09  N6   N5   N4   N3      0.00   0.0  0
 XQP  CONST_10  N5   N6   C18  N3      0.00   0.0  0
 XQP  CONST_11  N6   C18  N3   N4      0.00   0.0  0
 XQP  CONST_12  C12  C11  C10  C9    180.00   0.0  0
 XQP  CONST_13  C14  C15  C10  C9    180.00   0.0  0
 XQP  CONST_14  O5   C13  C12  C11   180.00   0.0  0
 XQP  CONST_15  O5   C13  C14  C15   180.00   0.0  0
 XQP  CONST_16  N4   N5   N6   C19   180.00   0.0  0
 XQP  CONST_17  N3   C18  N6   C19   180.00   0.0  0
 XQP  CONST_18  S1   C18  N3   N4    180.00   0.0  0
 XQP  CONST_19  S1   C18  N6   N5    180.00   0.0  0
 XQP  CONST_20  H10  C12  C11  C10   180.00   0.0  0
 XQP  CONST_21  H11  C14  C15  C10   180.00   0.0  0
 XQP  CONST_22  H12  C15  C10  C11   180.00   0.0  0
 XQP  CONST_23  H11  C14  C13  C12   180.00   0.0  0
 XQP  CONST_24  H9   C11  C12  C13   180.00   0.0  0
 XQP  CONST_25  H12  C15  C14  C13   180.00   0.0  0
 XQP  CONST_26  H10  C12  C13  C14   180.00   0.0  0
 XQP  CONST_27  H9   C11  C10  C15   180.00   0.0  0
 XQP  CONST_28  C6   N2   C8   O4      0.00   0.0  0
 XQP  CONST_29  C9   C8   N2   C6    180.00   0.0  0
 XQP  CONST_30  H2   N2   C8   O4    180.00   0.0  0
 XQP  CONST_31  H2   N2   C8   C9      0.00   0.0  0
 XQP  Var_01    O2   C4   C3   C2    -17.66  30.0  1
 XQP  Var_02    C5   O2   C4   C3     46.09  30.0  1
 XQP  Var_03    C5   N1   C2   C3    -15.78  30.0  1
 XQP  Var_04    N1   C2   C3   C4      3.12  30.0  1
 XQP  Var_05    C20  C2   N1   C5    166.26  30.0  1
 XQP  Var_06    O2   C4   C3   C17   161.65  30.0  1
 XQP  Var_07    N1   C2   C3   C17  -176.11  30.0  1
 XQP  Var_08    C4   C3   C2   C20  -179.24  30.0  1
 XQP  Var_09    H18  C4   C3   C2   -135.92  30.0  1
 XQP  Var_10    H19  C4   C3   C2    106.67  30.0  1
 XQP  Var_11    H3   N1   C2   C3   -162.62  30.0  1
 XQP  Var_12    H18  C4   O2   C5    166.70  30.0  1
 XQP  Var_13    H19  C4   O2   C5    -78.57  30.0  1
 XQP  Var_14    S1   C17  C3   C2   -108.36  30.0  3
 XQP  Var_15    O8   C20  C2   C3    179.50  30.0  2
 XQP  Var_16    O9   C20  C2   C3     -0.01  30.0  2
 XQP  Var_17    C18  S1   C17  C3    -80.99  30.0  3
 XQP  Var_18    C20  C2   C3   C17     1.53  30.0  1
 XQP  Var_19    N3   C18  S1   C17   -40.72  30.0  2
 XQP  Var_20    N6   C18  S1   C17   140.21  30.0  2
 XQP  Var_21    S1   C17  C3   C4     72.39  30.0  3
 XQP  Var_22    O8   C20  C2   N1     -2.72  30.0  2
 XQP  Var_23    O9   C20  C2   N1    177.77  30.0  2
 XQP  Var_24    H13  C17  C3   C2      8.34  30.0  3
 XQP  Var_25    H14  C17  C3   C2    131.73  30.0  3
 XQP  Var_26    H18  C4   C3   C17    43.40  30.0  1
 XQP  Var_27    H19  C4   C3   C17   -74.02  30.0  1
 XQP  Var_28    H15  C19  N6   C18  -155.79  30.0  2
 XQP  Var_29    H16  C19  N6   C18   -37.32  30.0  2
 XQP  Var_30    H17  C19  N6   C18    83.56  30.0  2
 XQP  Var_31    H3   N1   C2   C20    19.43  30.0  1
 XQP  Var_32    H13  C17  C3   C4   -170.91  30.0  3
 XQP  Var_33    H14  C17  C3   C4    -47.52  30.0  3
 XQP  Var_34    H15  C19  N6   N5     24.78  30.0  2
 XQP  Var_35    H16  C19  N6   N5    143.25  30.0  2
 XQP  Var_36    H17  C19  N6   N5    -95.87  30.0  2
 XQP  Var_37    H13  C17  S1   C18   157.53  30.0  1
 XQP  Var_38    H14  C17  S1   C18    42.84  30.0  1
 XQP  Var_39    H5   C7   O3   C6   -178.62  30.0  3
 XQP  Var_40    H6   C7   O3   C6    -60.01  30.0  3
 XQP  Var_41    H7   C7   O3   C6     62.96  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
 XQP  chir_01  C5  C6   O2  N1   negativ
 XQP  chir_02  C6  N2   C1  C5   positiv
 XQP  chir_03  C9  C16  C8  C10  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
 XQP  plan-1  C18  0.020
 XQP  plan-1  N3   0.020
 XQP  plan-1  N4   0.020
 XQP  plan-1  N5   0.020
 XQP  plan-1  N6   0.020
 XQP  plan-1  S1   0.020
 XQP  plan-1  C19  0.020
 XQP  plan-2  C9   0.020
 XQP  plan-2  C10  0.020
 XQP  plan-2  C11  0.020
 XQP  plan-2  C12  0.020
 XQP  plan-2  C13  0.020
 XQP  plan-2  C14  0.020
 XQP  plan-2  C15  0.020
 XQP  plan-2  O5   0.020
 XQP  plan-2  H9   0.020
 XQP  plan-2  H10  0.020
 XQP  plan-2  H11  0.020
 XQP  plan-2  H12  0.020
 XQP  plan-3  N2   0.020
 XQP  plan-3  C6   0.020
 XQP  plan-3  C8   0.020
 XQP  plan-3  C9   0.020
 XQP  plan-3  H2   0.020
 XQP  plan-3  O4   0.020
 XQP  plan-4  C2   0.020
 XQP  plan-4  C5   0.020
 XQP  plan-4  N1   0.020
 XQP  plan-4  H3   0.020
 XQP  plan-5  C1   0.020
 XQP  plan-5  O1   0.020
 XQP  plan-5  C6   0.020
 XQP  plan-5  O10  0.020
 XQP  plan-6  C9   0.020
 XQP  plan-6  C16  0.020
 XQP  plan-6  O6   0.020
 XQP  plan-6  O7   0.020
 XQP  plan-7  C2   0.020
 XQP  plan-7  O8   0.020
 XQP  plan-7  O9   0.020
 XQP  plan-7  C20  0.020

