# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 04:08:30 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  50  29  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.782   4.5067  -1.5393  -2.3127
 SE0  CA    C  CH1    0  -0.268   4.9870  -0.8656  -1.1204
 SE0  C     C  C      0   0.386   6.4660  -1.1466  -0.7253
 SE0  O     O  O      0  -0.597   7.1194  -1.9068  -1.4612
 SE0  CB    C  CH2    0  -0.168   4.1000  -1.2006   0.0633
 SE0  OG    O  O2     0  -0.437   2.7634  -0.7575  -0.2322
 SE0  OXT   O  OC    -1  -0.615   6.8700  -0.5698   0.3053
 SE0  S1    S  S2     0  -0.018   1.9095   2.1166   0.5226
 SE0  C2    C  C      0  -0.634   1.2675   3.6511   1.2456
 SE0  C3    C  CR6    0   0.114  -0.0113   4.0094   0.5586
 SE0  C3'   C  C2     0  -0.557  -0.2299   5.2370   0.0851
 SE0  C4    C  CR6    0   0.124  -1.0303   2.9376   0.4696
 SE0  C4'   C  C      0   0.379  -2.4644   3.3281   0.1264
 SE0  O4A   O  O      0  -0.590  -3.2612   3.3652   1.0766
 SE0  O4B   O  OC    -1  -0.601  -2.6751   3.5700  -1.0742
 SE0  N5    N  N      0  -0.347  -0.8289   1.7037   0.6994
 SE0  C6    C  CR16   0  -0.227   0.4400   1.1304   0.9989
 SE0  C7    C  CH1    0  -0.206   0.5295  -0.2496   0.3092
 SE0  C8    C  C      0   0.596   1.8428  -0.9144   0.6917
 SE0  O9    O  O      0  -0.447   2.0024  -1.4867   1.7416
 SE0  N10   N  NH1    0  -0.631  -0.5644  -1.0848   0.7103
 SE0  C11   C  C      0   0.594  -1.6253  -1.3479  -0.0827
 SE0  O12   O  O      0  -0.477  -1.6656  -1.0653  -1.2678
 SE0  C13   C  CH2    0  -0.576  -2.7652  -2.0469   0.6241
 SE0  C14   C  CH1    0  -0.354  -3.7792  -2.6524  -0.3247
 SE0  C15   C  CH2    0  -0.416  -4.8897  -3.4027   0.4055
 SE0  C16   C  CH2    0  -0.441  -6.0785  -3.4811  -0.5392
 SE0  C17   C  CH2    0  -0.549  -6.3028  -2.0653  -1.0528
 SE0  S19   S  S2     0  -0.029  -4.6345  -1.3643  -1.3194
 SE0  HN    H  HNH2   0   0.340   5.0298  -1.1946  -3.1080
 SE0  HNA   H  HNH2   0   0.327   4.7636  -2.5183  -2.2506
 SE0  HA    H  HCH1   0   0.236   4.9074   0.2148  -1.2926
 SE0  HB    H  HCH2   0   0.233   4.0907  -2.2788   0.2493
 SE0  HBA   H  HCH2   0   0.243   4.4565  -0.6982   0.9618
 SE0  H2    H  H      0   0.291   1.1201   3.5022   2.3181
 SE0  H2A   H  H      0   0.298   2.0248   4.4230   1.1169
 SE0  H3'   H  H      0   0.255   0.5184   6.0129   0.1856
 SE0  H3'A  H  H      0   0.256  -1.1435   5.5067  -0.4250
 SE0  H6    H  HCR6   0   0.286   0.4932   0.9677   2.0826
 SE0  H7    H  HCH1   0   0.297   0.4757  -0.1050  -0.7694
 SE0  HN10  H  HNH1   0   0.402  -0.6310  -1.3228   1.6883
 SE0  H13   H  HCH2   0   0.275  -2.3606  -2.8293   1.2741
 SE0  H13A  H  HCH2   0   0.279  -3.2584  -1.3239   1.2821
 SE0  H14   H  HCH1   0   0.269  -3.2737  -3.3319  -1.0148
 SE0  H15   H  HCH2   0   0.253  -4.5400  -4.3891   0.7165
 SE0  H15A  H  HCH2   0   0.231  -5.1726  -2.8546   1.3093
 SE0  H16   H  HCH2   0   0.234  -5.8510  -4.1495  -1.3729
 SE0  H16A  H  HCH2   0   0.249  -6.9717  -3.8655  -0.0440
 SE0  H17   H  HCH2   0   0.265  -6.8605  -2.0424  -1.9885
 SE0  H17A  H  HCH2   0   0.253  -6.8450  -1.4654  -0.3208

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  1.451  0.020  1.451
 SE0  N    HN    single  0.890  0.020  1.040
 SE0  N    HNA   single  0.890  0.020  1.040
 SE0  C    CA    single  1.557  0.020  1.557
 SE0  CA   CB    single  1.517  0.020  1.517
 SE0  CA   HA    single  0.970  0.020  1.090
 SE0  O    C     deloc   1.244  0.020  1.244
 SE0  C    OXT   deloc   1.248  0.020  1.248
 SE0  CB   OG    single  1.439  0.020  1.439
 SE0  CB   HB    single  0.970  0.020  1.090
 SE0  CB   HBA   single  0.970  0.020  1.090
 SE0  C8   OG    single  1.314  0.020  1.314
 SE0  C6   S1    single  1.833  0.020  1.833
 SE0  S1   C2    single  1.814  0.020  1.814
 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  1.482  0.020  1.482
 SE0  C3   C3'   double  1.334  0.020  1.334
 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  1.271  0.020  1.271
 SE0  C4'  C4    single  1.525  0.020  1.525
 SE0  O4A  C4'   deloc   1.241  0.020  1.241
 SE0  C4'  O4B   deloc   1.243  0.020  1.243
 SE0  N5   C6    single  1.424  0.020  1.424
 SE0  C7   C6    single  1.545  0.020  1.545
 SE0  C6   H6    single  0.970  0.020  1.090
 SE0  C8   C7    single  1.521  0.020  1.521
 SE0  N10  C7    single  1.434  0.020  1.434
 SE0  C7   H7    single  0.970  0.020  1.090
 SE0  O9   C8    double  1.206  0.020  1.206
 SE0  C11  N10   single  1.350  0.020  1.350
 SE0  N10  HN10  single  0.860  0.020  1.020
 SE0  C13  C11   single  1.512  0.020  1.512
 SE0  C11  O12   double  1.219  0.020  1.219
 SE0  C13  C14   single  1.515  0.020  1.515
 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  1.526  0.020  1.526
 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  1.829  0.020  1.829
 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   104.24  3.000
 SE0  HNA   N    CA   108.30  3.000
 SE0  HN    N    CA   108.44  3.000
 SE0  HA    CA   CB   107.31  3.000
 SE0  HA    CA   C    106.66  3.000
 SE0  CB    CA   C    108.53  3.000
 SE0  HA    CA   N    107.71  3.000
 SE0  CB    CA   N    110.19  3.000
 SE0  C     CA   N    116.05  3.000
 SE0  OXT   C    O    126.95  3.000
 SE0  OXT   C    CA   115.70  3.000
 SE0  O     C    CA   117.35  3.000
 SE0  HBA   CB   HB   108.48  3.000
 SE0  HBA   CB   OG   109.35  3.000
 SE0  HB    CB   OG   109.30  3.000
 SE0  HBA   CB   CA   110.52  3.000
 SE0  HB    CB   CA   110.81  3.000
 SE0  OG    CB   CA   108.36  3.000
 SE0  C8    OG   CB   118.02  3.000
 SE0  C6    S1   C2    93.89  3.000
 SE0  H2A   C2   H2   107.84  3.000
 SE0  H2A   C2   C3   111.75  3.000
 SE0  H2    C2   C3   111.61  3.000
 SE0  H2A   C2   S1   107.84  3.000
 SE0  H2    C2   S1   108.89  3.000
 SE0  C3    C2   S1   108.80  3.000
 SE0  C4    C3   C3'  122.13  3.000
 SE0  C3'   C3   C2   121.59  3.000
 SE0  C4    C3   C2   116.26  3.000
 SE0  H3'A  C3'  H3'  116.70  3.000
 SE0  H3'A  C3'  C3   122.40  3.000
 SE0  H3'   C3'  C3   120.90  3.000
 SE0  N5    C4   C4'  115.98  3.000
 SE0  C4'   C4   C3   118.36  3.000
 SE0  N5    C4   C3   125.62  3.000
 SE0  O4B   C4'  O4A  128.70  3.000
 SE0  O4B   C4'  C4   115.25  3.000
 SE0  O4A   C4'  C4   116.05  3.000
 SE0  C6    N5   C4   124.75  3.000
 SE0  H6    C6   C7   107.80  3.000
 SE0  H6    C6   N5   108.09  3.000
 SE0  C7    C6   N5   108.50  3.000
 SE0  H6    C6   S1   107.31  3.000
 SE0  C7    C6   S1   108.55  3.000
 SE0  N5    C6   S1   116.30  3.000
 SE0  H7    C7   N10  108.46  3.000
 SE0  H7    C7   C8   110.47  3.000
 SE0  N10   C7   C8   109.50  3.000
 SE0  H7    C7   C6   108.69  3.000
 SE0  N10   C7   C6   110.56  3.000
 SE0  C8    C7   C6   109.15  3.000
 SE0  O9    C8   C7   122.72  3.000
 SE0  O9    C8   OG   125.18  3.000
 SE0  C7    C8   OG   112.09  3.000
 SE0  HN10  N10  C11  118.13  3.000
 SE0  HN10  N10  C7   117.33  3.000
 SE0  C11   N10  C7   123.28  3.000
 SE0  C13   C11  O12  122.45  3.000
 SE0  O12   C11  N10  123.48  3.000
 SE0  C13   C11  N10  114.06  3.000
 SE0  H13A  C13  H13  106.35  3.000
 SE0  H13A  C13  C14  109.80  3.000
 SE0  H13   C13  C14  109.49  3.000
 SE0  H13A  C13  C11  108.37  3.000
 SE0  H13   C13  C11  109.23  3.000
 SE0  C14   C13  C11  113.36  3.000
 SE0  H14   C14  S19  108.02  3.000
 SE0  H14   C14  C15  109.46  3.000
 SE0  S19   C14  C15  105.36  3.000
 SE0  H14   C14  C13  109.54  3.000
 SE0  C15   C14  C13  112.57  3.000
 SE0  S19   C14  C13  111.73  3.000
 SE0  H15A  C15  H15  107.46  3.000
 SE0  H15A  C15  C16  109.69  3.000
 SE0  H15   C15  C16  112.39  3.000
 SE0  H15A  C15  C14  109.70  3.000
 SE0  H15   C15  C14  110.33  3.000
 SE0  C16   C15  C14  107.27  3.000
 SE0  H16A  C16  H16  107.53  3.000
 SE0  H16A  C16  C17  111.10  3.000
 SE0  H16   C16  C17  110.01  3.000
 SE0  H16A  C16  C15  112.10  3.000
 SE0  H16   C16  C15  110.05  3.000
 SE0  C17   C16  C15  106.07  3.000
 SE0  H17A  C17  H17  108.08  3.000
 SE0  H17A  C17  S19  109.90  3.000
 SE0  H17   C17  S19  109.48  3.000
 SE0  H17A  C17  C16  111.00  3.000
 SE0  H17   C17  C16  112.62  3.000
 SE0  S19   C17  C16  105.73  3.000
 SE0  C17   S19  C14   94.41  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  C13   C11  N10  C7    180.00   0.0  0
 SE0  CONST_02  O12   C11  N10  C7      0.00   0.0  0
 SE0  CONST_03  HN10  N10  C11  O12   180.00   0.0  0
 SE0  Var_01    C4    C3   C2   S1     50.92  30.0  1
 SE0  Var_02    N5    C4   C3   C2    -13.50  30.0  1
 SE0  Var_03    C16   C17  S19  C14   -15.82  30.0  1
 SE0  Var_04    C17   C16  C15  C14   -49.70  30.0  1
 SE0  Var_05    S19   C17  C16  C15    39.14  30.0  1
 SE0  Var_06    O4A   C4'  C4   C3   -102.08  30.0  2
 SE0  Var_07    H3'   C3'  C3   C2      0.04  30.0  2
 SE0  Var_08    C14   C13  C11  N10  -165.03  30.0  1
 SE0  Var_09    C7    C8   OG   CB    172.95  30.0  1
 SE0  Var_10    HB    CB   OG   C8     61.43  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-3  C4    0.020
 SE0  plan-3  C4'   0.020
 SE0  plan-3  O4A   0.020
 SE0  plan-3  O4B   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

