# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 22:00:21 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: (2R,4S,5R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-oxoethyl]-5-(sulfanylmethyl)-1,3-thiazinane-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO/N=C(C(=O)N[C@H](C=O)[C@@H]1N[C@@H]([C@H](CS)CS1)C(O)=O)/c2csc(N)n2
#
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
 LD0  LD0  "(2R,4S,5R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-oxoethyl]-5-(sulfanylmethyl)-1,3-thiazinane-4-carboxylic acid"  ligand  45  27  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LD0
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
 LD0  C15  C  C1     0   0.188  -50.3016  14.9975  36.5504
 LD0  C17  C  CH1    0  -0.209  -51.7363  14.4850  34.5279
 LD0  C20  C  CH1    0  -0.152  -53.1289  12.0996  33.0447
 LD0  C21  C  CH2    0  -0.582  -51.8673  11.8341  33.9036
 LD0  C01  C  CH3    0  -0.386  -53.2848  17.4602  40.4019
 LD0  C04  C  C      0   0.024  -54.7331  15.5730  37.9362
 LD0  C05  C  CR5    0   0.348  -56.0242  15.3769  37.2784
 LD0  C06  C  CR15   0  -0.548  -57.1717  16.0442  37.5641
 LD0  C08  C  CR5    0   0.267  -57.2998  14.3777  35.7890
 LD0  C11  C  C      0   0.508  -53.6043  14.6658  37.5075
 LD0  C14  C  CH1    0  -0.187  -51.6436  14.4931  36.0731
 LD0  C19  C  CH1    0  -0.228  -53.2924  13.6104  32.8494
 LD0  C23  C  CH2    0  -0.573  -54.2739  11.4351  33.8061
 LD0  C25  C  C      0   0.431  -54.6159  14.0371  32.1802
 LD0  N03  N  N      0  -0.101  -54.6197  16.4333  38.8659
 LD0  N09  N  N      0  -0.466  -56.1001  14.4424  36.2792
 LD0  N10  N  NH2    0  -0.832  -57.6991  13.5112  34.8383
 LD0  N13  N  NH1    0  -0.601  -52.7250  15.2259  36.6654
 LD0  N18  N  NH1    0  -0.596  -53.1023  14.2381  34.1399
 LD0  O02  O  O2     0  -0.389  -53.3663  16.4791  39.3839
 LD0  O12  O  O      0  -0.455  -53.5543  13.5216  37.9181
 LD0  O16  O  O      0  -0.356  -50.1621  15.8332  37.4038
 LD0  O26  O  O      0  -0.592  -54.8907  13.4332  31.1274
 LD0  O27  O  OC    -1  -0.585  -55.2507  14.9693  32.7108
 LD0  S07  S  S2     0   0.186  -58.4321  15.4823  36.5335
 LD0  S22  S  S2     0  -0.011  -50.6512  13.1776  33.8446
 LD0  S24  S  S2     0  -0.239  -55.8250  11.2194  32.8527
 LD0  H1   H  H      0   0.201  -49.4352  14.5257  36.0568
 LD0  H2   H  HCH1   0   0.276  -51.3326  15.4272  34.1270
 LD0  H3   H  HCH1   0   0.242  -53.0050  11.6218  32.0706
 LD0  H4   H  HCH2   0   0.275  -52.1399  11.6721  34.9487
 LD0  H5   H  HCH2   0   0.291  -51.3488  10.9343  33.5721
 LD0  H6   H  HCH3   0   0.242  -52.2616  17.4256  40.7697
 LD0  H7   H  HCH3   0   0.225  -53.4909  18.4599  40.0146
 LD0  H8   H  HCH3   0   0.225  -53.9680  17.2434  41.2252
 LD0  H9   H  HCR5   0   0.301  -57.3431  16.8131  38.2997
 LD0  H10  H  HCH1   0   0.301  -51.7276  13.4543  36.4091
 LD0  H11  H  HCH1   0   0.230  -52.5179  13.9241  32.1322
 LD0  H12  H  HCH2   0   0.262  -54.4879  12.0092  34.7094
 LD0  H13  H  HCH2   0   0.279  -53.9618  10.4368  34.1142
 LD0  H14  H  HNH2   0   0.404  -58.5608  13.6893  34.3500
 LD0  H15  H  HNH2   0   0.405  -56.9835  13.0663  34.2751
 LD0  H16  H  HNH1   0   0.415  -52.8365  16.1992  36.4211
 LD0  H17  H  HNH1   0   0.356  -53.6633  15.0789  34.1861
 LD0  H20  H  HSH1   0   0.206  -56.3430  10.3057  33.6856

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
 LD0  O26  C25  deloc     1.244  0.020  1.244
 LD0  C25  O27  deloc     1.246  0.020  1.246
 LD0  C25  C19  single    1.543  0.020  1.543
 LD0  S24  C23  single    1.833  0.020  1.833
 LD0  C19  C20  single    1.532  0.020  1.532
 LD0  C19  N18  single    1.448  0.020  1.448
 LD0  C20  C21  single    1.549  0.020  1.549
 LD0  C20  C23  single    1.527  0.020  1.527
 LD0  S22  C21  single    1.813  0.020  1.813
 LD0  S22  C17  single    1.831  0.020  1.831
 LD0  N18  C17  single    1.441  0.020  1.441
 LD0  C17  C14  single    1.548  0.020  1.548
 LD0  N10  C08  single    1.347  0.020  1.347
 LD0  C08  S07  aromatic  1.748  0.020  1.748
 LD0  C08  N09  aromatic  1.298  0.020  1.298
 LD0  C14  N13  single    1.434  0.020  1.434
 LD0  C14  C15  single    1.511  0.020  1.511
 LD0  S07  C06  aromatic  1.722  0.020  1.722
 LD0  N09  C05  aromatic  1.370  0.020  1.370
 LD0  N13  C11  single    1.340  0.020  1.340
 LD0  O16  C15  double    1.203  0.020  1.203
 LD0  C06  C05  aromatic  1.358  0.020  1.358
 LD0  C05  C04  single    1.462  0.020  1.462
 LD0  C11  C04  single    1.510  0.020  1.510
 LD0  C11  O12  double    1.217  0.020  1.217
 LD0  C04  N03  double    1.272  0.020  1.272
 LD0  N03  O02  single    1.357  0.020  1.357
 LD0  O02  C01  single    1.416  0.020  1.416
 LD0  C15  H1   single    0.930  0.020  1.080
 LD0  C17  H2   single    0.970  0.020  1.090
 LD0  C20  H3   single    0.970  0.020  1.090
 LD0  C21  H4   single    0.970  0.020  1.090
 LD0  C21  H5   single    0.970  0.020  1.090
 LD0  C01  H6   single    0.970  0.020  1.090
 LD0  C01  H7   single    0.970  0.020  1.090
 LD0  C01  H8   single    0.970  0.020  1.090
 LD0  C06  H9   single    0.930  0.020  1.080
 LD0  C14  H10  single    0.970  0.020  1.090
 LD0  C19  H11  single    0.970  0.020  1.090
 LD0  C23  H12  single    0.970  0.020  1.090
 LD0  C23  H13  single    0.970  0.020  1.090
 LD0  N10  H14  single    0.890  0.020  1.040
 LD0  N10  H15  single    0.890  0.020  1.040
 LD0  N13  H16  single    0.860  0.020  1.020
 LD0  N18  H17  single    0.890  0.020  1.040
 LD0  S24  H20  single    1.200  0.020  1.300

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
 LD0  H1   C15  O16  121.58  3.000
 LD0  H1   C15  C14  114.42  3.000
 LD0  O16  C15  C14  124.00  3.000
 LD0  H2   C17  S22  104.94  3.000
 LD0  H2   C17  N18  113.34  3.000
 LD0  S22  C17  N18  109.80  3.000
 LD0  H2   C17  C14  109.71  3.000
 LD0  N18  C17  C14  109.04  3.000
 LD0  S22  C17  C14  109.92  3.000
 LD0  H3   C20  C23  109.84  3.000
 LD0  H3   C20  C19  109.25  3.000
 LD0  C23  C20  C19  114.37  3.000
 LD0  H3   C20  C21  109.10  3.000
 LD0  C23  C20  C21  105.05  3.000
 LD0  C19  C20  C21  109.06  3.000
 LD0  H5   C21  H4   106.70  3.000
 LD0  H5   C21  S22  106.42  3.000
 LD0  H4   C21  S22  107.97  3.000
 LD0  H5   C21  C20  111.11  3.000
 LD0  H4   C21  C20  110.66  3.000
 LD0  S22  C21  C20  113.65  3.000
 LD0  H8   C01  H7   109.34  3.000
 LD0  H8   C01  H6   109.11  3.000
 LD0  H7   C01  H6   109.07  3.000
 LD0  H8   C01  O02  111.63  3.000
 LD0  H7   C01  O02  111.62  3.000
 LD0  H6   C01  O02  105.97  3.000
 LD0  N03  C04  C11  123.18  3.000
 LD0  N03  C04  C05  119.89  3.000
 LD0  C11  C04  C05  116.85  3.000
 LD0  N09  C05  C06  116.21  3.000
 LD0  C06  C05  C04  125.85  3.000
 LD0  N09  C05  C04  117.93  3.000
 LD0  H9   C06  S07  121.65  3.000
 LD0  H9   C06  C05  128.94  3.000
 LD0  S07  C06  C05  109.41  3.000
 LD0  S07  C08  N10  121.00  3.000
 LD0  S07  C08  N09  113.98  3.000
 LD0  N10  C08  N09  124.95  3.000
 LD0  O12  C11  N13  125.32  3.000
 LD0  O12  C11  C04  119.99  3.000
 LD0  N13  C11  C04  114.69  3.000
 LD0  H10  C14  N13  107.47  3.000
 LD0  H10  C14  C17  107.26  3.000
 LD0  N13  C14  C17  111.70  3.000
 LD0  H10  C14  C15  106.73  3.000
 LD0  N13  C14  C15  111.63  3.000
 LD0  C17  C14  C15  111.73  3.000
 LD0  H11  C19  N18  111.39  3.000
 LD0  H11  C19  C25  104.01  3.000
 LD0  N18  C19  C25  112.29  3.000
 LD0  H11  C19  C20  106.79  3.000
 LD0  N18  C19  C20  107.45  3.000
 LD0  C25  C19  C20  114.80  3.000
 LD0  H13  C23  H12  107.69  3.000
 LD0  H13  C23  S24  106.34  3.000
 LD0  H12  C23  S24  109.05  3.000
 LD0  H13  C23  C20  108.95  3.000
 LD0  H12  C23  C20  109.31  3.000
 LD0  S24  C23  C20  115.23  3.000
 LD0  O27  C25  O26  127.64  3.000
 LD0  O27  C25  C19  117.32  3.000
 LD0  O26  C25  C19  114.96  3.000
 LD0  O02  N03  C04  112.59  3.000
 LD0  C08  N09  C05  111.14  3.000
 LD0  H15  N10  H14  114.37  3.000
 LD0  H15  N10  C08  117.73  3.000
 LD0  H14  N10  C08  118.85  3.000
 LD0  H16  N13  C14  118.41  3.000
 LD0  H16  N13  C11  118.85  3.000
 LD0  C14  N13  C11  122.73  3.000
 LD0  H17  N18  C19  109.16  3.000
 LD0  H17  N18  C17  111.76  3.000
 LD0  C19  N18  C17  116.02  3.000
 LD0  N03  O02  C01  110.54  3.000
 LD0  C08  S07  C06   89.25  3.000
 LD0  C21  S22  C17   96.86  3.000
 LD0  H20  S24  C23   94.82  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
 LD0  CONST_01  S07  C08  N09  C05     0.00   0.0  0
 LD0  CONST_02  C08  S07  C06  C05     0.00   0.0  0
 LD0  CONST_03  N09  C08  S07  C06     0.00   0.0  0
 LD0  CONST_04  C08  N09  C05  C06     0.00   0.0  0
 LD0  CONST_05  S07  C06  C05  N09     0.00   0.0  0
 LD0  CONST_06  C08  N09  C05  C04   180.00   0.0  0
 LD0  CONST_07  S07  C06  C05  C04   180.00   0.0  0
 LD0  CONST_08  N10  C08  N09  C05   180.00   0.0  0
 LD0  CONST_09  N10  C08  S07  C06   180.00   0.0  0
 LD0  CONST_10  H9   C06  S07  C08   180.00   0.0  0
 LD0  CONST_11  H9   C06  C05  N09   180.00   0.0  0
 LD0  CONST_16  C14  N13  C11  C04   180.00   0.0  0
 LD0  CONST_17  O12  C11  N13  C14     0.00   0.0  0
 LD0  CONST_18  H16  N13  C11  C04     0.00   0.0  0
 LD0  CONST_19  H16  N13  C11  O12   180.00   0.0  0
 LD0  Var_01    C20  C21  S22  C17    60.64  30.0  1
 LD0  Var_02    H4   C21  S22  C17   -62.52  30.0  1
 LD0  Var_03    H5   C21  S22  C17  -176.75  30.0  1
 LD0  Var_04    C11  C04  C05  C06   176.79  30.0  2
 LD0  Var_05    N03  C04  C05  C06     0.00  30.0  2
 LD0  Var_06    N09  C05  C04  C11    -3.40  30.0  2
 LD0  Var_07    N09  C05  C04  N03   179.81  30.0  2
 LD0  Var_08    O02  N03  C04  C05   179.11   0.0  2
 LD0  Var_09    N13  C11  C04  C05   101.67  30.0  2
 LD0  Var_10    O12  C11  C04  C05   -77.76  30.0  2
 LD0  Var_11    O02  N03  C04  C11     2.53   0.0  2
 LD0  Var_12    C04  N03  O02  C01   179.29  30.0  1
 LD0  Var_13    N13  C11  C04  N03   -81.65  30.0  2
 LD0  Var_14    O12  C11  C04  N03    98.91  30.0  2
 LD0  Var_15    H6   C01  O02  N03   179.35  30.0  3
 LD0  Var_16    H7   C01  O02  N03   -62.04  30.0  3
 LD0  Var_17    H8   C01  O02  N03    60.68  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
 LD0  chir_01  C17  S22  N18  C14  negativ
 LD0  chir_02  C20  C19  C21  C23  negativ
 LD0  chir_03  C14  N13  C17  C15  negativ
 LD0  chir_04  C19  N18  C25  C20  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
 LD0  plan-1  C04  0.020
 LD0  plan-1  C05  0.020
 LD0  plan-1  C06  0.020
 LD0  plan-1  C08  0.020
 LD0  plan-1  N09  0.020
 LD0  plan-1  N10  0.020
 LD0  plan-1  S07  0.020
 LD0  plan-1  H9   0.020
 LD0  plan-2  C04  0.020
 LD0  plan-2  C05  0.020
 LD0  plan-2  C11  0.020
 LD0  plan-2  N03  0.020
 LD0  plan-2  O02  0.020
 LD0  plan-3  C04  0.020
 LD0  plan-3  C11  0.020
 LD0  plan-3  C14  0.020
 LD0  plan-3  N13  0.020
 LD0  plan-3  O12  0.020
 LD0  plan-3  H16  0.020
 LD0  plan-4  C08  0.020
 LD0  plan-4  N10  0.020
 LD0  plan-4  H14  0.020
 LD0  plan-4  H15  0.020
 LD0  plan-5  C19  0.020
 LD0  plan-5  C25  0.020
 LD0  plan-5  O26  0.020
 LD0  plan-5  O27  0.020
 LD0  plan-6  C15  0.020
 LD0  plan-6  C14  0.020
 LD0  plan-6  O16  0.020
 LD0  plan-6  H1   0.020

