# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 07:11:46 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (2R)-2-[(1R)-2-[(2S)-2-amino-2-carboxyethoxy]-2-oxo-1-{[(2R)-tetrahydrothiophen-2-ylacetyl]amino}ethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](COC(=O)[C@@H](NC(=O)C[C@H]1CCCS1)[C@H]2SCC(=C)C(=N2)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
 SE0  SE0  '(2R)-2-[(1R)-2-[(2S)-2-amino-2-carboxyethoxy]-2-oxo-1-{[(2R)-tetrahydrothiophen-2-ylacetyl]amino}ethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  52  29  .  2022-07-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SE0
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
 SE0  N     N  NH2   0  -0.773   4.7487  -1.4183  -2.2170
 SE0  CA    C  CH1   0  -0.256   5.1119  -0.7658  -0.9878
 SE0  C     C  C     0   0.521   6.5770  -0.9492  -0.5937
 SE0  O     O  O     0  -0.431   7.3554  -1.6483  -1.1881
 SE0  CB    C  CH2   0  -0.201   4.2183  -1.2401   0.1529
 SE0  OG    O  O2    0  -0.436   2.8851  -0.8410  -0.1754
 SE0  OXT   O  OH1   0  -0.593   6.8965  -0.2324   0.4755
 SE0  S1    S  S2    0   0.019   1.9055   1.9822   0.4997
 SE0  C2    C  CH2   0  -0.631   1.1909   3.4973   1.2032
 SE0  C3    C  C     0   0.135  -0.1216   3.7702   0.5419
 SE0  C3'   C  C2    0  -0.530  -0.3857   4.9302  -0.0593
 SE0  C4    C  C     0   0.140  -1.0700   2.6409   0.5540
 SE0  C4'   C  C     0   0.499  -2.5503   2.9106   0.3968
 SE0  O4A   O  O     0  -0.422  -3.0894   3.8977   0.8283
 SE0  O4B   O  OH1   0  -0.544  -3.1610   1.9213  -0.2172
 SE0  N5    N  N     0  -0.298  -0.7913   1.4272   0.7778
 SE0  C6    C  CH1   0  -0.246   0.5143   0.9163   1.0150
 SE0  C7    C  CH1   0  -0.215   0.6184  -0.4553   0.2990
 SE0  C8    C  C     0   0.604   1.9295  -1.1145   0.6900
 SE0  O9    O  O     0  -0.435   2.0710  -1.7650   1.6926
 SE0  N10   N  NH1   0  -0.629  -0.4831  -1.2947   0.6623
 SE0  C11   C  C     0   0.608  -1.5851  -1.4112  -0.1195
 SE0  O12   O  O     0  -0.466  -1.6127  -1.0683  -1.2869
 SE0  C13   C  CH2   0  -0.572  -2.7763  -2.0252   0.5759
 SE0  C14   C  CH1   0  -0.357  -3.8419  -2.5196  -0.3821
 SE0  C15   C  CH2   0  -0.414  -4.9898  -3.2264   0.3318
 SE0  C16   C  CH2   0  -0.425  -6.1836  -3.2067  -0.6095
 SE0  C17   C  CH2   0  -0.533  -6.3300  -1.7638  -1.0737
 SE0  S19   S  S2    0  -0.011  -4.6260  -1.1414  -1.3132
 SE0  HN    H  HNH2  0   0.358   5.2435  -1.0028  -2.9949
 SE0  HNA   H  HNH2  0   0.347   5.0181  -2.3942  -2.1933
 SE0  HA    H  HCH1  0   0.286   4.9587   0.3127  -1.1080
 SE0  HXT   H  HOH1  0   0.489   7.8289  -0.3654   0.7047
 SE0  HB    H  HCH2  0   0.287   4.2724  -2.3274   0.2528
 SE0  HBA   H  HCH2  0   0.289   4.5089  -0.7906   1.1028
 SE0  H2    H  HCH2  0   0.294   1.0783   3.3709   2.2822
 SE0  H2A   H  HCH2  0   0.298   1.9018   4.3036   1.0316
 SE0  H3'   H  H     0   0.257   0.3520   5.7219  -0.0748
 SE0  H3'A  H  H     0   0.261  -1.3203   5.1372  -0.5597
 SE0  HO4B  H  HOH1  0   0.469  -4.1179   2.0710  -0.2443
 SE0  H6    H  HCH1  0   0.296   0.5951   0.7431   2.0951
 SE0  H7    H  HCH1  0   0.316   0.5859  -0.2888  -0.7775
 SE0  HN10  H  HNH1  0   0.385  -0.5676  -1.5496   1.6351
 SE0  H13   H  HCH2  0   0.265  -2.4437  -2.8544   1.2083
 SE0  H13A  H  HCH2  0   0.281  -3.2008  -1.2725   1.2482
 SE0  H14   H  HCH1  0   0.272  -3.3889  -3.2013  -1.1056
 SE0  H15   H  HCH2  0   0.255  -4.6955  -4.2400   0.6112
 SE0  H15A  H  HCH2  0   0.231  -5.2383  -2.6903   1.2529
 SE0  H16   H  HCH2  0   0.223  -5.9960  -3.8589  -1.4656
 SE0  H16A  H  HCH2  0   0.239  -7.0957  -3.5567  -0.1234
 SE0  H17   H  HCH2  0   0.254  -6.8842  -1.6776  -2.0078
 SE0  H17A  H  HCH2  0   0.241  -6.8410  -1.1623  -0.3209

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
 SE0  N    CA    single  1.438  0.020  1.438
 SE0  N    HN    single  0.890  0.020  1.040
 SE0  N    HNA   single  0.890  0.020  1.040
 SE0  C    CA    single  1.528  0.020  1.528
 SE0  CA   CB    single  1.525  0.020  1.525
 SE0  CA   HA    single  0.970  0.020  1.090
 SE0  O    C     double  1.203  0.020  1.203
 SE0  C    OXT   single  1.326  0.020  1.326
 SE0  OXT  HXT   single  0.850  0.020  0.980
 SE0  CB   OG    single  1.430  0.020  1.430
 SE0  CB   HB    single  0.970  0.020  1.090
 SE0  CB   HBA   single  0.970  0.020  1.090
 SE0  C8   OG    single  1.318  0.020  1.318
 SE0  C6   S1    single  1.827  0.020  1.827
 SE0  S1   C2    single  1.817  0.020  1.817
 SE0  C3   C2    single  1.495  0.020  1.495
 SE0  C2   H2    single  0.970  0.020  1.090
 SE0  C2   H2A   single  0.970  0.020  1.090
 SE0  C4   C3    single  1.475  0.020  1.475
 SE0  C3   C3'   double  1.333  0.020  1.333
 SE0  C3'  H3'   single  0.930  0.020  1.080
 SE0  C3'  H3'A  single  0.930  0.020  1.080
 SE0  N5   C4    double  1.265  0.020  1.265
 SE0  C4'  C4    single  1.513  0.020  1.513
 SE0  O4A  C4'   double  1.205  0.020  1.205
 SE0  C4'  O4B   single  1.315  0.020  1.315
 SE0  O4B  HO4B  single  0.850  0.020  0.980
 SE0  N5   C6    single  1.422  0.020  1.422
 SE0  C7   C6    single  1.551  0.020  1.551
 SE0  C6   H6    single  0.970  0.020  1.090
 SE0  C8   C7    single  1.519  0.020  1.519
 SE0  N10  C7    single  1.432  0.020  1.432
 SE0  C7   H7    single  0.970  0.020  1.090
 SE0  O9   C8    double  1.203  0.020  1.203
 SE0  C11  N10   single  1.356  0.020  1.356
 SE0  N10  HN10  single  0.890  0.020  1.040
 SE0  C13  C11   single  1.510  0.020  1.510
 SE0  C11  O12   double  1.217  0.020  1.217
 SE0  C13  C14   single  1.516  0.020  1.516
 SE0  C13  H13   single  0.970  0.020  1.090
 SE0  C13  H13A  single  0.970  0.020  1.090
 SE0  C14  S19   single  1.839  0.020  1.839
 SE0  C14  C15   single  1.525  0.020  1.525
 SE0  C14  H14   single  0.970  0.020  1.090
 SE0  C15  C16   single  1.520  0.020  1.520
 SE0  C15  H15   single  0.970  0.020  1.090
 SE0  C15  H15A  single  0.970  0.020  1.090
 SE0  C16  C17   single  1.523  0.020  1.523
 SE0  C16  H16   single  0.970  0.020  1.090
 SE0  C16  H16A  single  0.970  0.020  1.090
 SE0  S19  C17   single  1.830  0.020  1.830
 SE0  C17  H17   single  0.970  0.020  1.090
 SE0  C17  H17A  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
 SE0  HNA   N    HN   106.49  3.000
 SE0  HNA   N    CA   110.49  3.000
 SE0  HN    N    CA   110.34  3.000
 SE0  HA    CA   CB   107.83  3.000
 SE0  HA    CA   C    106.28  3.000
 SE0  CB    CA   C    109.37  3.000
 SE0  HA    CA   N    108.51  3.000
 SE0  CB    CA   N    110.51  3.000
 SE0  C     CA   N    114.08  3.000
 SE0  OXT   C    O    123.81  3.000
 SE0  OXT   C    CA   111.96  3.000
 SE0  O     C    CA   124.23  3.000
 SE0  HBA   CB   HB   108.50  3.000
 SE0  HBA   CB   OG   109.48  3.000
 SE0  HB    CB   OG   110.16  3.000
 SE0  HBA   CB   CA   111.56  3.000
 SE0  HB    CB   CA   110.41  3.000
 SE0  OG    CB   CA   106.73  3.000
 SE0  C8    OG   CB   117.86  3.000
 SE0  HXT   OXT  C    110.37  3.000
 SE0  C6    S1   C2    94.46  3.000
 SE0  H2A   C2   H2   107.99  3.000
 SE0  H2A   C2   C3   111.63  3.000
 SE0  H2    C2   C3   111.57  3.000
 SE0  H2A   C2   S1   107.44  3.000
 SE0  H2    C2   S1   109.06  3.000
 SE0  C3    C2   S1   109.04  3.000
 SE0  C4    C3   C3'  122.86  3.000
 SE0  C3'   C3   C2   122.16  3.000
 SE0  C4    C3   C2   114.92  3.000
 SE0  H3'A  C3'  H3'  116.29  3.000
 SE0  H3'A  C3'  C3   123.17  3.000
 SE0  H3'   C3'  C3   120.54  3.000
 SE0  N5    C4   C4'  113.88  3.000
 SE0  C4'   C4   C3   119.47  3.000
 SE0  N5    C4   C3   126.47  3.000
 SE0  O4B   C4'  O4A  125.17  3.000
 SE0  O4B   C4'  C4   111.64  3.000
 SE0  O4A   C4'  C4   123.14  3.000
 SE0  HO4B  O4B  C4'  110.82  3.000
 SE0  C6    N5   C4   125.20  3.000
 SE0  H6    C6   C7   108.06  3.000
 SE0  H6    C6   N5   106.78  3.000
 SE0  C7    C6   N5   107.61  3.000
 SE0  H6    C6   S1   108.28  3.000
 SE0  C7    C6   S1   109.56  3.000
 SE0  N5    C6   S1   116.27  3.000
 SE0  H7    C7   N10  108.50  3.000
 SE0  H7    C7   C8   110.26  3.000
 SE0  N10   C7   C8   110.14  3.000
 SE0  H7    C7   C6   108.59  3.000
 SE0  N10   C7   C6   110.47  3.000
 SE0  C8    C7   C6   108.85  3.000
 SE0  O9    C8   C7   123.40  3.000
 SE0  O9    C8   OG   125.03  3.000
 SE0  C7    C8   OG   111.52  3.000
 SE0  HN10  N10  C11  117.77  3.000
 SE0  HN10  N10  C7   117.20  3.000
 SE0  C11   N10  C7   121.95  3.000
 SE0  C13   C11  O12  122.58  3.000
 SE0  O12   C11  N10  123.17  3.000
 SE0  C13   C11  N10  114.24  3.000
 SE0  H13A  C13  H13  106.49  3.000
 SE0  H13A  C13  C14  109.86  3.000
 SE0  H13   C13  C14  109.37  3.000
 SE0  H13A  C13  C11  108.01  3.000
 SE0  H13   C13  C11  109.53  3.000
 SE0  C14   C13  C11  113.34  3.000
 SE0  H14   C14  S19  108.01  3.000
 SE0  H14   C14  C15  109.44  3.000
 SE0  S19   C14  C15  105.27  3.000
 SE0  H14   C14  C13  109.31  3.000
 SE0  C15   C14  C13  112.60  3.000
 SE0  S19   C14  C13  112.05  3.000
 SE0  H15A  C15  H15  107.49  3.000
 SE0  H15A  C15  C16  109.66  3.000
 SE0  H15   C15  C16  112.47  3.000
 SE0  H15A  C15  C14  109.75  3.000
 SE0  H15   C15  C14  110.31  3.000
 SE0  C16   C15  C14  107.16  3.000
 SE0  H16A  C16  H16  107.52  3.000
 SE0  H16A  C16  C17  111.06  3.000
 SE0  H16   C16  C17  110.08  3.000
 SE0  H16A  C16  C15  112.11  3.000
 SE0  H16   C16  C15  110.04  3.000
 SE0  C17   C16  C15  106.05  3.000
 SE0  H17A  C17  H17  108.05  3.000
 SE0  H17A  C17  S19  109.82  3.000
 SE0  H17   C17  S19  109.55  3.000
 SE0  H17A  C17  C16  110.93  3.000
 SE0  H17   C17  C16  112.65  3.000
 SE0  S19   C17  C16  105.82  3.000
 SE0  C17   S19  C14   94.35  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
 SE0  CONST_01  HO4B  O4B  C4'  C4    180.00   0.0  0
 SE0  CONST_04  HN10  N10  C11  O12   180.00   0.0  0
 SE0  CONST_05  HXT   OXT  C    CA    180.00   0.0  0
 SE0  Var_01    C4    C3   C2   S1     52.67  30.0  1
 SE0  Var_02    N5    C4   C3   C2    -17.10  30.0  1
 SE0  Var_03    C16   C17  S19  C14   -15.10  30.0  1
 SE0  Var_04    C17   C16  C15  C14   -49.94  30.0  1
 SE0  Var_05    S19   C17  C16  C15    38.75  30.0  1
 SE0  Var_06    O4A   C4'  C4   C3    -33.82  30.0  2
 SE0  Var_07    H3'   C3'  C3   C2     -0.69  30.0  2
 SE0  Var_08    C14   C13  C11  N10  -163.07  30.0  1
 SE0  Var_09    C7    C8   OG   CB    171.68  30.0  1
 SE0  Var_10    HB    CB   OG   C8     61.84  30.0  1

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
 SE0  chir_01  CA   N    C    CB   positiv
 SE0  chir_02  C6   S1   N5   C7   negativ
 SE0  chir_03  C7   N10  C6   C8   negativ
 SE0  chir_04  C14  S19  C13  C15  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
 SE0  plan-1  C7    0.020
 SE0  plan-1  N10   0.020
 SE0  plan-1  C11   0.020
 SE0  plan-1  O12   0.020
 SE0  plan-1  C13   0.020
 SE0  plan-1  HN10  0.020
 SE0  plan-2  CA    0.020
 SE0  plan-2  C     0.020
 SE0  plan-2  O     0.020
 SE0  plan-2  OXT   0.020
 SE0  plan-2  HXT   0.020
 SE0  plan-3  C4    0.020
 SE0  plan-3  C4'   0.020
 SE0  plan-3  O4A   0.020
 SE0  plan-3  O4B   0.020
 SE0  plan-3  HO4B  0.020
 SE0  plan-4  OG    0.020
 SE0  plan-4  C7    0.020
 SE0  plan-4  C8    0.020
 SE0  plan-4  O9    0.020

