# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:07:46 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: (2R)-5-[(carbamoyloxy)methyl]-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@](NC(=O)Cc1sccc1)(C=O)[C@@H]2NC(=C(COC(N)=O)CS2)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
 1QL  1QL  '(2R)-5-[(carbamoyloxy)methyl]-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  46  28  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1QL
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
 1QL  C4   C  CR5    0  -0.119   5.4329   1.0062  -0.2158
 1QL  C2   C  C      0   0.586   3.1486  -0.0260   0.0006
 1QL  N2   N  NH1    0  -0.660  -1.4782  -1.3768   0.0992
 1QL  C6   C  CR15   0  -0.185   7.4953   1.0506  -1.2866
 1QL  O6   O  OC    -1  -0.568  -4.7701  -2.5473  -0.0770
 1QL  C5   C  CR15   0  -0.234   6.1266   1.4377  -1.3065
 1QL  C8   C  CH1    0  -0.267  -0.5396  -0.3063   0.0987
 1QL  O5   O  O      0  -0.591  -3.0390  -3.1151   1.2012
 1QL  C13  C  C      0   0.140  -2.8311  -1.1320  -0.0334
 1QL  C10  C  C      0  -0.033  -3.3330   0.0311  -0.4996
 1QL  C11  C  CH2    0  -0.238  -4.7919   0.3194  -0.6412
 1QL  C9   C  CH2    0  -0.610  -2.4610   1.1897  -0.9169
 1QL  S1   S  S2     0   0.023  -0.7852   0.6984  -1.4016
 1QL  C14  C  C1     0   0.169   1.0981  -1.8364  -1.0109
 1QL  O4   O  O      0  -0.353   1.2304  -1.4426  -2.1348
 1QL  C1   C  CT     0   0.356   0.8837  -0.8865   0.1792
 1QL  O    O  O2     0  -0.484   1.0217  -1.7111   1.3009
 1QL  C    C  CH3    0  -0.431   0.9137  -1.0995   2.5728
 1QL  N    N  NH1    0  -0.688   1.8212   0.1937   0.1450
 1QL  O1   O  O      0  -0.456   3.6051  -1.1376  -0.1801
 1QL  C3   C  CH2    0  -0.681   3.9965   1.2298   0.0983
 1QL  S    S  S2     0   0.210   6.4569   0.1165   0.8441
 1QL  C7   C  CR15   0  -0.471   7.8161   0.3299  -0.1779
 1QL  H1   H  HCR5   0   0.265   8.2060   1.2997  -2.0615
 1QL  H3   H  HCR5   0   0.263   5.6730   2.0169  -2.0992
 1QL  H4   H  HCH1   0   0.300  -0.6885   0.3872   0.9406
 1QL  H5   H  HCH2   0   0.224  -5.0272   0.5864  -1.6765
 1QL  H6   H  HCH2   0   0.262  -5.4060  -0.5273  -0.3536
 1QL  H7   H  HCH2   0   0.278  -2.8858   1.6748  -1.8003
 1QL  H8   H  HCH2   0   0.281  -2.3949   1.9572  -0.1425
 1QL  H9   H  H      0   0.222   1.0811  -2.9070  -0.7502
 1QL  H10  H  HCH3   0   0.225   1.6037  -0.2604   2.6885
 1QL  H11  H  HCH3   0   0.226  -0.1009  -0.7526   2.7851
 1QL  H12  H  HCH3   0   0.254   1.1737  -1.8610   3.3046
 1QL  H13  H  HNH1   0   0.416   1.4900   1.1341   0.3050
 1QL  H14  H  HCH2   0   0.310   3.8712   1.6419   1.1047
 1QL  H15  H  HCH2   0   0.308   3.5937   1.9838  -0.5822
 1QL  H16  H  HCR5   0   0.294   8.7729  -0.0909   0.0898
 1QL  O2   O  O2     0  -0.482  -5.0736   1.4537   0.2063
 1QL  C16  C  C      0   0.720  -6.2991   1.9756   0.1413
 1QL  H17  H  HNH1   0   0.382  -1.3107  -2.1342   0.7516
 1QL  O3   O  O      0  -0.530  -7.1815   1.5557  -0.5829
 1QL  N1   N  NH2    0  -0.833  -6.4240   3.0256   0.9709
 1QL  H24  H  HNH2   0   0.403  -5.6841   3.3041   1.5913
 1QL  H25  H  HNH2   0   0.405  -7.3150   3.4797   1.0642
 1QL  C15  C  C      0   0.393  -3.6384  -2.3715   0.3992

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
 1QL  C9   S1   single    1.812  0.020  1.812
 1QL  C9   C10  single    1.509  0.020  1.509
 1QL  C11  C10  single    1.494  0.020  1.494
 1QL  S1   C8   single    1.822  0.020  1.822
 1QL  C10  C13  double    1.350  0.020  1.350
 1QL  O4   C14  double    1.198  0.020  1.198
 1QL  C8   N2   single    1.424  0.020  1.424
 1QL  C8   C1   single    1.539  0.020  1.539
 1QL  C14  C1   single    1.538  0.020  1.538
 1QL  C13  N2   single    1.381  0.020  1.381
 1QL  C13  C15  single    1.541  0.020  1.541
 1QL  C1   O    single    1.399  0.020  1.399
 1QL  C1   N    single    1.431  0.020  1.431
 1QL  O    C    single    1.415  0.020  1.415
 1QL  C15  O5   deloc     1.247  0.020  1.247
 1QL  C15  O6   deloc     1.240  0.020  1.240
 1QL  N    C2   single    1.353  0.020  1.353
 1QL  O1   C2   double    1.215  0.020  1.215
 1QL  C2   C3   single    1.518  0.020  1.518
 1QL  C5   C4   aromatic  1.363  0.020  1.363
 1QL  C5   C6   aromatic  1.422  0.020  1.422
 1QL  C3   C4   single    1.487  0.020  1.487
 1QL  C4   S    aromatic  1.721  0.020  1.721
 1QL  C6   C7   aromatic  1.361  0.020  1.361
 1QL  C7   S    aromatic  1.714  0.020  1.714
 1QL  C6   H1   single    0.930  0.020  1.080
 1QL  C5   H3   single    0.930  0.020  1.080
 1QL  C8   H4   single    0.970  0.020  1.090
 1QL  C11  H5   single    0.970  0.020  1.090
 1QL  C11  H6   single    0.970  0.020  1.090
 1QL  C9   H7   single    0.970  0.020  1.090
 1QL  C9   H8   single    0.970  0.020  1.090
 1QL  C14  H9   single    0.930  0.020  1.080
 1QL  C    H10  single    0.970  0.020  1.090
 1QL  C    H11  single    0.970  0.020  1.090
 1QL  C    H12  single    0.970  0.020  1.090
 1QL  N    H13  single    0.860  0.020  1.020
 1QL  C3   H14  single    0.970  0.020  1.090
 1QL  C3   H15  single    0.970  0.020  1.090
 1QL  C7   H16  single    0.930  0.020  1.080
 1QL  C11  O2   single    1.444  0.020  1.444
 1QL  O2   C16  single    1.334  0.020  1.334
 1QL  N2   H17  single    0.890  0.020  1.040
 1QL  C16  O3   double    1.216  0.020  1.216
 1QL  C16  N1   single    1.344  0.020  1.344
 1QL  N1   H24  single    0.860  0.020  1.020
 1QL  N1   H25  single    0.860  0.020  1.020

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
 1QL  S    C4   C3   121.48  3.000
 1QL  S    C4   C5   110.71  3.000
 1QL  C3   C4   C5   127.81  3.000
 1QL  C3   C2   O1   123.80  3.000
 1QL  C3   C2   N    113.99  3.000
 1QL  O1   C2   N    122.20  3.000
 1QL  H17  N2   C13  110.86  3.000
 1QL  H17  N2   C8   116.94  3.000
 1QL  C13  N2   C8   120.83  3.000
 1QL  H1   C6   C7   123.46  3.000
 1QL  H1   C6   C5   124.06  3.000
 1QL  C7   C6   C5   112.48  3.000
 1QL  H3   C5   C6   124.02  3.000
 1QL  H3   C5   C4   122.87  3.000
 1QL  C6   C5   C4   113.10  3.000
 1QL  H4   C8   C1   108.82  3.000
 1QL  H4   C8   S1   105.31  3.000
 1QL  C1   C8   S1   112.06  3.000
 1QL  H4   C8   N2   112.59  3.000
 1QL  C1   C8   N2   109.04  3.000
 1QL  S1   C8   N2   109.02  3.000
 1QL  C10  C13  C15  126.52  3.000
 1QL  C15  C13  N2   110.10  3.000
 1QL  C10  C13  N2   123.37  3.000
 1QL  C9   C10  C11  112.96  3.000
 1QL  C11  C10  C13  124.21  3.000
 1QL  C9   C10  C13  122.83  3.000
 1QL  O2   C11  H6   110.32  3.000
 1QL  O2   C11  H5   108.76  3.000
 1QL  H6   C11  H5   108.62  3.000
 1QL  O2   C11  C10  106.65  3.000
 1QL  H6   C11  C10  112.15  3.000
 1QL  H5   C11  C10  110.28  3.000
 1QL  H8   C9   H7   106.52  3.000
 1QL  H8   C9   S1   108.91  3.000
 1QL  H7   C9   S1   105.27  3.000
 1QL  H8   C9   C10  112.24  3.000
 1QL  H7   C9   C10  109.85  3.000
 1QL  S1   C9   C10  113.59  3.000
 1QL  C9   S1   C8    93.09  3.000
 1QL  H9   C14  C1   114.51  3.000
 1QL  H9   C14  O4   122.88  3.000
 1QL  C1   C14  O4   122.57  3.000
 1QL  N    C1   O    113.55  3.000
 1QL  N    C1   C14  110.89  3.000
 1QL  O    C1   C14  104.05  3.000
 1QL  N    C1   C8   108.67  3.000
 1QL  O    C1   C8   110.81  3.000
 1QL  C14  C1   C8   108.74  3.000
 1QL  C    O    C1   117.27  3.000
 1QL  H12  C    H11  108.25  3.000
 1QL  H12  C    H10  108.39  3.000
 1QL  H11  C    H10  108.78  3.000
 1QL  H12  C    O    106.49  3.000
 1QL  H11  C    O    112.49  3.000
 1QL  H10  C    O    112.27  3.000
 1QL  H13  N    C1   118.97  3.000
 1QL  H13  N    C2   119.34  3.000
 1QL  C1   N    C2   121.51  3.000
 1QL  H15  C3   H14  105.70  3.000
 1QL  H15  C3   C2   108.95  3.000
 1QL  H14  C3   C2   107.85  3.000
 1QL  H15  C3   C4   109.16  3.000
 1QL  H14  C3   C4   111.18  3.000
 1QL  C2   C3   C4   113.67  3.000
 1QL  C7   S    C4    92.31  3.000
 1QL  H16  C7   S    120.44  3.000
 1QL  H16  C7   C6   128.16  3.000
 1QL  S    C7   C6   111.40  3.000
 1QL  C16  O2   C11  117.27  3.000
 1QL  N1   C16  O3   124.74  3.000
 1QL  N1   C16  O2   111.17  3.000
 1QL  O3   C16  O2   124.10  3.000
 1QL  H25  N1   H24  118.06  3.000
 1QL  H25  N1   C16  119.54  3.000
 1QL  H24  N1   C16  121.95  3.000
 1QL  C13  C15  O5   114.10  3.000
 1QL  O5   C15  O6   126.93  3.000
 1QL  C13  C15  O6   118.96  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
 1QL  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 1QL  CONST_02  C6   C7   S    C4      0.00   0.0  0
 1QL  CONST_03  S    C4   C5   C6      0.00   0.0  0
 1QL  CONST_04  C7   S    C4   C5      0.00   0.0  0
 1QL  CONST_05  S    C7   C6   C5      0.00   0.0  0
 1QL  CONST_06  C3   C4   C5   C6    180.00   0.0  0
 1QL  CONST_07  C7   S    C4   C3    180.00   0.0  0
 1QL  CONST_08  H1   C6   C5   C4    180.00   0.0  0
 1QL  CONST_09  H16  C7   S    C4    180.00   0.0  0
 1QL  CONST_10  H3   C5   C4   S     180.00   0.0  0
 1QL  CONST_11  O1   C2   N    C1      0.00   0.0  0
 1QL  CONST_12  C3   C2   N    C1    180.00   0.0  0
 1QL  CONST_13  H13  N    C2   O1    180.00   0.0  0
 1QL  Var_01    C9   C10  C13  N2     -0.38  30.0  1
 1QL  Var_02    C10  C9   S1   C8    -49.47  30.0  1
 1QL  Var_03    C10  C13  N2   C8     17.28  30.0  1
 1QL  Var_04    S1   C9   C10  C13    24.26  30.0  1
 1QL  Var_05    C5   C4   C3   C2    110.09  30.0  2
 1QL  Var_06    O5   C15  C13  N2     24.77  30.0  2
 1QL  Var_07    O2   C11  C10  C13   119.13  30.0  2
 1QL  Var_08    N    C2   C3   C4   -173.35  30.0  1
 1QL  Var_09    O3   C16  O2   C11    -0.03  30.0  3
 1QL  Var_10    H10  C    O    C1    -54.38  30.0  3
 1QL  Var_11    H24  N1   C16  O2     -4.09  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
 1QL  chir_01  C8  S1  N2  C1   negativ
 1QL  chir_02  C1  N   C8  C14  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
 1QL  plan-1  C4   0.020
 1QL  plan-1  C6   0.020
 1QL  plan-1  C5   0.020
 1QL  plan-1  C3   0.020
 1QL  plan-1  S    0.020
 1QL  plan-1  C7   0.020
 1QL  plan-1  H1   0.020
 1QL  plan-1  H3   0.020
 1QL  plan-1  H16  0.020
 1QL  plan-2  C2   0.020
 1QL  plan-2  C1   0.020
 1QL  plan-2  N    0.020
 1QL  plan-2  O1   0.020
 1QL  plan-2  C3   0.020
 1QL  plan-2  H13  0.020
 1QL  plan-3  N2   0.020
 1QL  plan-3  C8   0.020
 1QL  plan-3  C13  0.020
 1QL  plan-3  H17  0.020
 1QL  plan-4  O6   0.020
 1QL  plan-4  O5   0.020
 1QL  plan-4  C13  0.020
 1QL  plan-4  C15  0.020
 1QL  plan-5  C14  0.020
 1QL  plan-5  O4   0.020
 1QL  plan-5  C1   0.020
 1QL  plan-5  H9   0.020
 1QL  plan-6  O2   0.020
 1QL  plan-6  C16  0.020
 1QL  plan-6  O3   0.020
 1QL  plan-6  N1   0.020

