# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 04:39:28 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2R)-2-[(R)-{[(6R)-6-amino-6-carboxyhexanoyl]amino}(carboxy)methyl]-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](CCCCC(=O)N[C@@H]([C@H]1SCC(=C)C(=N1)C(O)=O)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
 REC  REC  '(2R)-2-[(R)-{[(6R)-6-amino-6-carboxyhexanoyl]amino}(carboxy)methyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  44  26  .  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_REC
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
 REC  O14   O  O      0  -0.587  -3.5190  -3.5332   1.4006
 REC  C13   C  C      0   0.367  -3.7463  -3.0368   0.2866
 REC  O15   O  OC    -1  -0.599  -3.7649  -3.5945  -0.8243
 REC  C4    C  C      0   0.136  -4.0350  -1.5394   0.2622
 REC  N5    N  N      0  -0.386  -3.0298  -0.7725   0.3940
 REC  C3    C  C      0   0.111  -5.4414  -1.0953   0.1447
 REC  C16   C  C2     0  -0.561  -6.4123  -1.9057  -0.2782
 REC  C2    C  CH2    0  -0.637  -5.7073   0.3144   0.5615
 REC  S1    S  S2     0  -0.017  -4.5816   1.4110  -0.3442
 REC  C6    C  CH1    0  -0.265  -3.0563   0.6572   0.3304
 REC  C7    C  CH1    0  -0.123  -1.8665   1.1445  -0.5107
 REC  C8    C  C      0   0.406  -1.8404   2.6953  -0.4760
 REC  O9    O  O      0  -0.599  -1.3565   3.2211   0.5391
 REC  N10   N  NH1    0  -0.649  -0.6742   0.5542   0.0439
 REC  C11   C  C      0   0.561   0.5518   0.8357  -0.4217
 REC  O12   O  O      0  -0.508   0.7473   1.6643  -1.3015
 REC  CA1   C  CH2    0  -0.582   1.6725   0.0397   0.2199
 REC  CB1   C  CH2    0  -0.411   3.0644   0.5104  -0.1685
 REC  CG1   C  CH2    0  -0.407   4.1601  -0.3218   0.4862
 REC  CD1   C  CH2    0  -0.414   5.5559   0.1681   0.1267
 REC  CE1   C  CH1    0  -0.211   6.6874  -0.6828   0.7104
 REC  NZ1   N  NH2    0  -0.787   6.6287  -2.0297   0.1600
 REC  CZ1   C  C      0   0.383   8.0343   0.0537   0.5058
 REC  OH1   O  O      0  -0.610   8.8158  -0.3985  -0.3551
 REC  O     O  OC    -1  -0.625   8.2140   1.0741   1.2043
 REC  OXT   O  OC    -1  -0.602  -2.3688   3.2612  -1.4514
 REC  H6    H  HCH1   0   0.281  -2.9192   1.0333   1.3514
 REC  H161  H  H      0   0.253  -6.2198  -2.9180  -0.6043
 REC  H162  H  H      0   0.252  -7.4383  -1.5636  -0.3276
 REC  H2C1  H  HCH2   0   0.293  -6.7266   0.6188   0.3267
 REC  H2C2  H  HCH2   0   0.285  -5.5559   0.4488   1.6355
 REC  H7    H  HCH1   0   0.230  -2.0198   0.8070  -1.5424
 REC  H10   H  HNH1   0   0.389  -0.7959  -0.2479   0.6443
 REC  HA11  H  HCH2   0   0.254   1.5537   0.0710   1.3074
 REC  HA12  H  HCH2   0   0.260   1.5444  -1.0126  -0.0571
 REC  HB11  H  HCH2   0   0.216   3.1795   0.4673  -1.2549
 REC  HB12  H  HCH2   0   0.215   3.1890   1.5607   0.1103
 REC  HG11  H  HCH2   0   0.202   4.0411  -0.2952   1.5756
 REC  HG12  H  HCH2   0   0.212   4.0547  -1.3699   0.1939
 REC  HD11  H  HCH2   0   0.201   5.6620   0.1984  -0.9652
 REC  HD12  H  HCH2   0   0.214   5.6765   1.1979   0.4721
 REC  HE1   H  HCH1   0   0.203   6.5164  -0.7596   1.7910
 REC  HZ11  H  HNH2   0   0.321   6.9919  -1.9871  -0.7859
 REC  HZ12  H  HNH2   0   0.333   7.2941  -2.6122   0.6545

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
 REC  O14  C13   deloc   1.241  0.020  1.241
 REC  C13  O15   deloc   1.243  0.020  1.243
 REC  C13  C4    single  1.525  0.020  1.525
 REC  C4   N5    double  1.271  0.020  1.271
 REC  C4   C3    single  1.480  0.020  1.480
 REC  N5   C6    single  1.431  0.020  1.431
 REC  C3   C16   double  1.334  0.020  1.334
 REC  C3   C2    single  1.494  0.020  1.494
 REC  C2   S1    single  1.814  0.020  1.814
 REC  S1   C6    single  1.830  0.020  1.830
 REC  C6   C7    single  1.536  0.020  1.536
 REC  C7   C8    single  1.551  0.020  1.551
 REC  C7   N10   single  1.441  0.020  1.441
 REC  C8   O9    deloc   1.241  0.020  1.241
 REC  C8   OXT   deloc   1.245  0.020  1.245
 REC  N10  C11   single  1.341  0.020  1.341
 REC  C11  O12   double  1.224  0.020  1.224
 REC  C11  CA1   single  1.517  0.020  1.517
 REC  CA1  CB1   single  1.520  0.020  1.520
 REC  CB1  CG1   single  1.524  0.020  1.524
 REC  CG1  CD1   single  1.522  0.020  1.522
 REC  CD1  CE1   single  1.531  0.020  1.531
 REC  CE1  NZ1   single  1.456  0.020  1.456
 REC  CE1  CZ1   single  1.549  0.020  1.549
 REC  CZ1  OH1   deloc   1.248  0.020  1.248
 REC  CZ1  O     deloc   1.250  0.020  1.250
 REC  C6   H6    single  0.970  0.020  1.090
 REC  C16  H161  single  0.930  0.020  1.080
 REC  C16  H162  single  0.930  0.020  1.080
 REC  C2   H2C1  single  0.970  0.020  1.090
 REC  C2   H2C2  single  0.970  0.020  1.090
 REC  C7   H7    single  0.970  0.020  1.090
 REC  N10  H10   single  0.860  0.020  1.020
 REC  CA1  HA11  single  0.970  0.020  1.090
 REC  CA1  HA12  single  0.970  0.020  1.090
 REC  CB1  HB11  single  0.970  0.020  1.090
 REC  CB1  HB12  single  0.970  0.020  1.090
 REC  CG1  HG11  single  0.970  0.020  1.090
 REC  CG1  HG12  single  0.970  0.020  1.090
 REC  CD1  HD11  single  0.970  0.020  1.090
 REC  CD1  HD12  single  0.970  0.020  1.090
 REC  CE1  HE1   single  0.970  0.020  1.090
 REC  NZ1  HZ11  single  0.890  0.020  1.040
 REC  NZ1  HZ12  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
 REC  C4    C13  O15   115.04  3.000
 REC  C4    C13  O14   116.23  3.000
 REC  O15   C13  O14   128.73  3.000
 REC  C3    C4   N5    125.37  3.000
 REC  C3    C4   C13   118.42  3.000
 REC  N5    C4   C13   116.16  3.000
 REC  C6    N5   C4    125.69  3.000
 REC  C2    C3   C16   122.16  3.000
 REC  C2    C3   C4    115.48  3.000
 REC  C16   C3   C4    122.34  3.000
 REC  H162  C16  H161  116.81  3.000
 REC  H162  C16  C3    120.83  3.000
 REC  H161  C16  C3    122.36  3.000
 REC  H2C2  C2   H2C1  107.88  3.000
 REC  H2C2  C2   S1    109.30  3.000
 REC  H2C1  C2   S1    107.70  3.000
 REC  H2C2  C2   C3    111.44  3.000
 REC  H2C1  C2   C3    111.72  3.000
 REC  S1    C2   C3    108.70  3.000
 REC  C6    S1   C2     94.82  3.000
 REC  H6    C6   C7    107.70  3.000
 REC  H6    C6   S1    107.82  3.000
 REC  C7    C6   S1    108.24  3.000
 REC  H6    C6   N5    107.39  3.000
 REC  C7    C6   N5    109.08  3.000
 REC  S1    C6   N5    116.31  3.000
 REC  H7    C7   N10   110.59  3.000
 REC  H7    C7   C8    109.34  3.000
 REC  N10   C7   C8    112.76  3.000
 REC  H7    C7   C6    108.02  3.000
 REC  N10   C7   C6    107.46  3.000
 REC  C8    C7   C6    108.53  3.000
 REC  OXT   C8   O9    127.84  3.000
 REC  OXT   C8   C7    115.44  3.000
 REC  O9    C8   C7    116.63  3.000
 REC  H10   N10  C11   118.91  3.000
 REC  H10   N10  C7    117.04  3.000
 REC  C11   N10  C7    122.45  3.000
 REC  CA1   C11  O12   122.76  3.000
 REC  CA1   C11  N10   114.73  3.000
 REC  O12   C11  N10   122.51  3.000
 REC  HA12  CA1  HA11  105.43  3.000
 REC  HA12  CA1  CB1   109.87  3.000
 REC  HA11  CA1  CB1   110.15  3.000
 REC  HA12  CA1  C11   108.10  3.000
 REC  HA11  CA1  C11   108.97  3.000
 REC  CB1   CA1  C11   113.95  3.000
 REC  HB12  CB1  HB11  106.21  3.000
 REC  HB12  CB1  CG1   109.45  3.000
 REC  HB11  CB1  CG1   109.25  3.000
 REC  HB12  CB1  CA1   109.67  3.000
 REC  HB11  CB1  CA1   109.77  3.000
 REC  CG1   CB1  CA1   112.31  3.000
 REC  HG12  CG1  HG11  106.17  3.000
 REC  HG12  CG1  CD1   109.50  3.000
 REC  HG11  CG1  CD1   109.05  3.000
 REC  HG12  CG1  CB1   109.84  3.000
 REC  HG11  CG1  CB1   109.61  3.000
 REC  CD1   CG1  CB1   112.46  3.000
 REC  HD12  CD1  HD11  106.12  3.000
 REC  HD12  CD1  CE1   108.76  3.000
 REC  HD11  CD1  CE1   108.85  3.000
 REC  HD12  CD1  CG1   109.26  3.000
 REC  HD11  CD1  CG1   109.42  3.000
 REC  CE1   CD1  CG1   114.12  3.000
 REC  HE1   CE1  CZ1   107.40  3.000
 REC  HE1   CE1  NZ1   107.54  3.000
 REC  CZ1   CE1  NZ1   115.15  3.000
 REC  HE1   CE1  CD1   107.41  3.000
 REC  CZ1   CE1  CD1   109.15  3.000
 REC  NZ1   CE1  CD1   109.88  3.000
 REC  HZ12  NZ1  HZ11  104.14  3.000
 REC  HZ12  NZ1  CE1   108.71  3.000
 REC  HZ11  NZ1  CE1   107.41  3.000
 REC  O     CZ1  OH1   126.28  3.000
 REC  O     CZ1  CE1   116.08  3.000
 REC  OH1   CZ1  CE1   117.62  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
 REC  CONST_01  O12   C11  N10  C7      0.00   0.0  0
 REC  CONST_02  CA1   C11  N10  C7    180.00   0.0  0
 REC  CONST_03  H10   N10  C11  O12   180.00   0.0  0
 REC  Var_01    S1    C2   C3   C4     53.65  30.0  1
 REC  Var_02    C2    C3   C4   N5    -16.30  30.0  1
 REC  Var_03    N5    C4   C13  O14    76.24  30.0  2
 REC  Var_04    H161  C16  C3   C4     -3.02  30.0  2
 REC  Var_05    CB1   CA1  C11  N10  -171.52  30.0  3
 REC  Var_06    CG1   CB1  CA1  C11  -179.48  30.0  3
 REC  Var_07    CD1   CG1  CB1  CA1  -178.59  30.0  3
 REC  Var_08    CE1   CD1  CG1  CB1  -177.21  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
 REC  chir_01  C6   N5   S1   C7   positiv
 REC  chir_02  C7   N10  C6   C8   negativ
 REC  chir_03  CE1  CD1  NZ1  CZ1  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
 REC  plan-1  C7   0.020
 REC  plan-1  N10  0.020
 REC  plan-1  C11  0.020
 REC  plan-1  O12  0.020
 REC  plan-1  CA1  0.020
 REC  plan-1  H10  0.020
 REC  plan-2  O14  0.020
 REC  plan-2  C13  0.020
 REC  plan-2  O15  0.020
 REC  plan-2  C4   0.020
 REC  plan-3  C7   0.020
 REC  plan-3  C8   0.020
 REC  plan-3  O9   0.020
 REC  plan-3  OXT  0.020
 REC  plan-4  CE1  0.020
 REC  plan-4  CZ1  0.020
 REC  plan-4  OH1  0.020
 REC  plan-4  O    0.020

