# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 00:36:26 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  47  26  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.416  -4.3965  -3.7403   1.1540
 REC  C13   C  C     0   0.496  -3.7586  -2.9955   0.4574
 REC  O15   O  OH1   0  -0.569  -2.7074  -3.3417  -0.2564
 REC  C4    C  C     0   0.163  -4.0597  -1.5184   0.3424
 REC  N5    N  N     0  -0.343  -3.0369  -0.7736   0.3922
 REC  C3    C  C     0   0.126  -5.4654  -1.0819   0.2811
 REC  C16   C  C2    0  -0.536  -6.4501  -1.8889  -0.1147
 REC  C2    C  CH2   0  -0.637  -5.7096   0.3491   0.6367
 REC  S1    S  S2    0   0.015  -4.5855   1.3991  -0.3273
 REC  C6    C  CH1   0  -0.275  -3.0728   0.6549   0.3644
 REC  C7    C  CH1   0  -0.131  -1.8568   1.1455  -0.4432
 REC  C8    C  C     0   0.529  -1.7830   2.6640  -0.3229
 REC  O9    O  O     0  -0.429  -1.4284   3.2331   0.6749
 REC  N10   N  NH1   0  -0.658  -0.6734   0.5471   0.1089
 REC  C11   C  C     0   0.579   0.5498   0.8896  -0.3440
 REC  O12   O  O     0  -0.490   0.6968   1.8089  -1.1354
 REC  CA1   C  CH2   0  -0.584   1.6879   0.0634   0.2078
 REC  CB1   C  CH2   0  -0.416   3.0669   0.5497  -0.2061
 REC  CG1   C  CH2   0  -0.413   4.1674  -0.3172   0.3929
 REC  CD1   C  CH2   0  -0.431   5.5580   0.1674   0.0080
 REC  CE1   C  CH1   0  -0.207   6.6728  -0.7366   0.5531
 REC  NZ1   N  NH2   0  -0.776   6.5906  -2.0514  -0.0356
 REC  CZ1   C  C     0   0.520   8.0201  -0.0596   0.3402
 REC  OH1   O  O     0  -0.442   8.8336  -0.3951  -0.4846
 REC  O     O  OH1   0  -0.594   8.2023   0.9653   1.1664
 REC  OXT   O  OH1   0  -0.579  -2.2268   3.2639  -1.4140
 REC  H15   H  HOH1  0   0.492  -2.5106  -4.2824  -0.1253
 REC  H6    H  HCH1  0   0.322  -2.9535   0.9981   1.3989
 REC  H161  H  H     0   0.267  -6.2983  -2.9227  -0.3891
 REC  H162  H  H     0   0.272  -7.4654  -1.5207  -0.1825
 REC  H2C1  H  HCH2  0   0.311  -6.7268   0.6525   0.3950
 REC  H2C2  H  HCH2  0   0.304  -5.5445   0.5320   1.7006
 REC  H7    H  HCH1  0   0.298  -1.9953   0.8638  -1.4924
 REC  H10   H  HNH1  0   0.409  -0.7955  -0.3051   0.6361
 REC  HOT   H  HOH1  0   0.486  -2.2326   4.2257  -1.2900
 REC  HA11  H  HCH2  0   0.268   1.6040   0.0446   1.2988
 REC  HA12  H  HCH2  0   0.271   1.5420  -0.9732  -0.1142
 REC  HB11  H  HCH2  0   0.225   3.1524   0.5443  -1.2958
 REC  HB12  H  HCH2  0   0.224   3.2040   1.5872   0.1102
 REC  HG11  H  HCH2  0   0.216   4.0786  -0.3188   1.4848
 REC  HG12  H  HCH2  0   0.225   4.0390  -1.3536   0.0722
 REC  HD11  H  HCH2  0   0.228   5.6473   0.2168  -1.0830
 REC  HD12  H  HCH2  0   0.240   5.6979   1.1873   0.3738
 REC  HE1   H  HCH1  0   0.264   6.5288  -0.8346   1.6345
 REC  HZ11  H  HNH2  0   0.343   6.7896  -2.0014  -1.0272
 REC  HZ12  H  HNH2  0   0.354   7.2894  -2.6646   0.3637
 REC  H     H  HOH1  0   0.480   9.0577   1.3853   0.9910

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   double  1.203  0.020  1.203
 REC  C13  O15   single  1.317  0.020  1.317
 REC  C13  C4    single  1.512  0.020  1.512
 REC  C4   N5    double  1.266  0.020  1.266
 REC  C4   C3    single  1.473  0.020  1.473
 REC  N5   C6    single  1.429  0.020  1.429
 REC  C3   C16   double  1.333  0.020  1.333
 REC  C3   C2    single  1.495  0.020  1.495
 REC  C2   S1    single  1.815  0.020  1.815
 REC  S1   C6    single  1.822  0.020  1.822
 REC  C6   C7    single  1.540  0.020  1.540
 REC  C7   C8    single  1.525  0.020  1.525
 REC  C7   N10   single  1.436  0.020  1.436
 REC  C8   O9    double  1.202  0.020  1.202
 REC  C8   OXT   single  1.322  0.020  1.322
 REC  N10  C11   single  1.349  0.020  1.349
 REC  C11  O12   double  1.222  0.020  1.222
 REC  C11  CA1   single  1.511  0.020  1.511
 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  1.535  0.020  1.535
 REC  CE1  NZ1   single  1.443  0.020  1.443
 REC  CE1  CZ1   single  1.523  0.020  1.523
 REC  CZ1  OH1   double  1.206  0.020  1.206
 REC  CZ1  O     single  1.329  0.020  1.329
 REC  O15  H15   single  0.850  0.020  0.980
 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  OXT  HOT   single  0.850  0.020  0.980
 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
 REC  O    H     single  0.850  0.020  0.980

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   112.00  3.000
 REC  C4    C13  O14   122.91  3.000
 REC  O15   C13  O14   125.06  3.000
 REC  H15   O15  C13   110.10  3.000
 REC  C3    C4   N5    126.73  3.000
 REC  C3    C4   C13   118.86  3.000
 REC  N5    C4   C13   114.26  3.000
 REC  C6    N5   C4    124.53  3.000
 REC  C2    C3   C16   121.97  3.000
 REC  C2    C3   C4    115.45  3.000
 REC  C16   C3   C4    122.53  3.000
 REC  H162  C16  H161  116.20  3.000
 REC  H162  C16  C3    120.37  3.000
 REC  H161  C16  C3    123.43  3.000
 REC  H2C2  C2   H2C1  108.12  3.000
 REC  H2C2  C2   S1    109.08  3.000
 REC  H2C1  C2   S1    107.43  3.000
 REC  H2C2  C2   C3    111.56  3.000
 REC  H2C1  C2   C3    111.51  3.000
 REC  S1    C2   C3    109.04  3.000
 REC  C6    S1   C2     94.37  3.000
 REC  H6    C6   C7    108.01  3.000
 REC  H6    C6   S1    108.70  3.000
 REC  C7    C6   S1    109.05  3.000
 REC  H6    C6   N5    106.96  3.000
 REC  C7    C6   N5    107.98  3.000
 REC  S1    C6   N5    115.88  3.000
 REC  H7    C7   N10   111.43  3.000
 REC  H7    C7   C8    109.74  3.000
 REC  N10   C7   C8    110.16  3.000
 REC  H7    C7   C6    108.70  3.000
 REC  N10   C7   C6    108.44  3.000
 REC  C8    C7   C6    108.30  3.000
 REC  OXT   C8   O9    124.70  3.000
 REC  OXT   C8   C7    111.75  3.000
 REC  O9    C8   C7    123.44  3.000
 REC  H10   N10  C11   119.97  3.000
 REC  H10   N10  C7    116.92  3.000
 REC  C11   N10  C7    120.82  3.000
 REC  CA1   C11  O12   123.88  3.000
 REC  CA1   C11  N10   114.94  3.000
 REC  O12   C11  N10   121.18  3.000
 REC  HA12  CA1  HA11  105.47  3.000
 REC  HA12  CA1  CB1   110.10  3.000
 REC  HA11  CA1  CB1   110.27  3.000
 REC  HA12  CA1  C11   108.06  3.000
 REC  HA11  CA1  C11   108.41  3.000
 REC  CB1   CA1  C11   114.15  3.000
 REC  HB12  CB1  HB11  106.46  3.000
 REC  HB12  CB1  CG1   109.61  3.000
 REC  HB11  CB1  CG1   109.43  3.000
 REC  HB12  CB1  CA1   109.80  3.000
 REC  HB11  CB1  CA1   109.93  3.000
 REC  CG1   CB1  CA1   111.49  3.000
 REC  HG12  CG1  HG11  106.36  3.000
 REC  HG12  CG1  CD1   109.58  3.000
 REC  HG11  CG1  CD1   109.06  3.000
 REC  HG12  CG1  CB1   109.84  3.000
 REC  HG11  CG1  CB1   109.52  3.000
 REC  CD1   CG1  CB1   112.29  3.000
 REC  HD12  CD1  HD11  106.31  3.000
 REC  HD12  CD1  CE1   109.75  3.000
 REC  HD11  CD1  CE1   108.71  3.000
 REC  HD12  CD1  CG1   109.24  3.000
 REC  HD11  CD1  CG1   109.91  3.000
 REC  CE1   CD1  CG1   112.71  3.000
 REC  HE1   CE1  CZ1   107.10  3.000
 REC  HE1   CE1  NZ1   108.29  3.000
 REC  CZ1   CE1  NZ1   113.49  3.000
 REC  HE1   CE1  CD1   107.92  3.000
 REC  CZ1   CE1  CD1   109.33  3.000
 REC  NZ1   CE1  CD1   110.51  3.000
 REC  HZ12  NZ1  HZ11  106.30  3.000
 REC  HZ12  NZ1  CE1   110.60  3.000
 REC  HZ11  NZ1  CE1   110.08  3.000
 REC  O     CZ1  OH1   123.17  3.000
 REC  O     CZ1  CE1   112.17  3.000
 REC  OH1   CZ1  CE1   124.66  3.000
 REC  H     O    CZ1   110.05  3.000
 REC  HOT   OXT  C8    110.28  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  H15   O15  C13  C4    180.00   0.0  0
 REC  CONST_02  O12   C11  N10  C7      0.00   0.0  0
 REC  CONST_03  CA1   C11  N10  C7    180.00   0.0  0
 REC  CONST_04  H10   N10  C11  O12   180.00   0.0  0
 REC  CONST_05  HOT   OXT  C8   C7    180.00   0.0  0
 REC  CONST_06  H     O    CZ1  CE1   180.00   0.0  0
 REC  Var_01    S1    C2   C3   C4     50.97  30.0  1
 REC  Var_02    C2    C3   C4   N5    -15.44  30.0  1
 REC  Var_03    N5    C4   C13  O14   135.57  30.0  2
 REC  Var_04    H161  C16  C3   C4      1.90  30.0  2
 REC  Var_05    CB1   CA1  C11  N10  -174.29  30.0  3
 REC  Var_06    CG1   CB1  CA1  C11   179.48  30.0  3
 REC  Var_07    CD1   CG1  CB1  CA1  -179.08  30.0  3
 REC  Var_08    CE1   CD1  CG1  CB1  -177.36  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-2  H15  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-3  HOT  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
 REC  plan-4  H    0.020

