# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 08:59:37 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: (2R)-2-[(R)-{[(6S)-6-amino-6-carboxyhexanoyl]amino}(carboxy)methyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(N[C@H](SC1)[C@H](NC(=O)CCCC[C@H](N)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
 HJ2  HJ2  '(2R)-2-[(R)-{[(6S)-6-amino-6-carboxyhexanoyl]amino}(carboxy)methyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  49  26  .  2022-07-25  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HJ2
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
 HJ2  C7    C  CH1   0  -0.194  43.5147   6.8995  28.8761
 HJ2  H7    H  HCH1  0   0.315  42.4651   6.5902  28.7920
 HJ2  C6    C  CR16  0  -0.185  44.3219   5.6091  28.6859
 HJ2  S1    S  S2    0   0.017  46.1814   5.9451  28.7139
 HJ2  C2    C  C     0  -0.661  46.5894   4.6585  29.9381
 HJ2  N5    N  NR16  0  -0.637  43.9360   4.5699  29.5745
 HJ2  C4    C  CR6   0   0.051  44.6352   3.3459  29.4197
 HJ2  C13   C  C     0   0.414  43.7673   2.2066  29.0385
 HJ2  O14   O  OH1   0  -0.437  44.2875   1.0141  29.3126
 HJ2  O15   O  O     0  -0.564  42.6717   2.3432  28.5522
 HJ2  C3    C  CR6   0   0.269  45.9744   3.3432  29.5447
 HJ2  N2    N  NH1   0  -0.603  43.8596   7.7910  27.7885
 HJ2  H6    H  HCR6  0   0.330  44.1338   5.2675  27.6650
 HJ2  H2    H  H     0   0.304  47.6762   4.6015  29.9699
 HJ2  HN5   H  HNR6  0   0.406  43.8552   4.8829  30.5336
 HJ2  C81   C  CH3   0  -0.724  46.9436   2.2356  29.3037
 HJ2  H4    H  H     0   0.214  46.2485   4.9742  30.9257
 HJ2  H5    H  HNH1  0   0.354  44.0550   7.3629  26.8935
 HJ2  C9    C  C     0   0.420  43.7113   9.1317  27.7586
 HJ2  C10   C  CH2   0  -0.501  43.2969   9.8078  29.0393
 HJ2  O5    O  O     0  -0.537  43.9308   9.7729  26.7402
 HJ2  C11   C  CH2   0  -0.167  42.7411   8.8944  30.1283
 HJ2  H61   H  HCH2  0   0.331  44.1753  10.3415  29.4137
 HJ2  H71   H  HCH2  0   0.305  42.5632  10.5738  28.7824
 HJ2  C12   C  CH2   0  -0.372  42.6074   9.6884  31.4351
 HJ2  H8    H  HCH2  0   0.237  41.7434   8.5564  29.8256
 HJ2  H9    H  HCH2  0   0.807  45.6000   7.5549  30.0905
 HJ2  C131  C  CH2   0  -0.560  41.5266   9.1838  32.3924
 HJ2  H10   H  HCH2  0   0.239  43.5823   9.7462  31.9271
 HJ2  H11   H  HCH2  0   0.210  42.3504  10.7194  31.1687
 HJ2  C14   C  CH1   0  -0.101  41.3015  10.1514  33.5608
 HJ2  H12   H  HCH2  0   0.259  40.5973   9.0696  31.8317
 HJ2  H13   H  HCH2  0   0.315  41.7675   8.2009  32.8021
 HJ2  C15   C  C     0   0.499  40.1601   9.6733  34.4349
 HJ2  N3    N  NH2   0  -0.773  42.4991  10.2567  34.3676
 HJ2  H14   H  HCH1  0   0.244  40.9729  11.1144  33.1350
 HJ2  O6    O  OH1   0  -0.658  39.0168   9.5973  33.7585
 HJ2  O7    O  O     0  -0.522  40.2458   9.4089  35.6061
 HJ2  H15   H  HCH3  0   0.266  46.5268   1.3721  28.7998
 HJ2  H16   H  HCH3  0   0.225  47.7755   2.6140  28.7067
 HJ2  H17   H  HCH3  0   0.281  47.3702   1.9060  30.2542
 HJ2  H18   H  HNH2  0   0.368  43.2301  10.6943  33.8232
 HJ2  H19   H  HNH2  0   0.363  42.3379  10.8730  35.1534
 HJ2  H20   H  HOH1  0   0.460  38.3121   9.3037  34.3523
 HJ2  H21   H  HOH1  0   0.468  43.6794   0.3248  29.0110
 HJ2  C8    C  C     0  -0.188  43.6402   7.6506  30.2217
 HJ2  O4    O  OH1   0  -0.633  43.1851   6.7395  31.1917
 HJ2  O9    O  O     0  -0.429  44.9147   8.0917  30.5244
 HJ2  H22   H  HOH1  0   0.474  43.4321   7.0787  32.0590

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
 HJ2  C7    H7    single  0.970  0.020  1.090
 HJ2  C7    C6    single  1.534  0.020  1.534
 HJ2  C7    N2    single  1.448  0.020  1.448
 HJ2  C7    C8    single  1.546  0.020  1.546
 HJ2  C6    S1    single  1.890  0.020  1.890
 HJ2  C6    N5    single  1.421  0.020  1.421
 HJ2  C6    H6    single  0.970  0.020  1.090
 HJ2  S1    C2    single  1.822  0.020  1.822
 HJ2  C2    C3    single  1.504  0.020  1.504
 HJ2  C2    H2    single  0.970  0.020  1.090
 HJ2  C2    H4    single  0.970  0.020  1.090
 HJ2  N5    C4    single  1.418  0.020  1.418
 HJ2  N5    HN5   single  0.890  0.020  1.040
 HJ2  C4    C13   single  1.482  0.020  1.482
 HJ2  C4    C3    double  1.345  0.020  1.345
 HJ2  C13   O14   single  1.330  0.020  1.330
 HJ2  C13   O15   double  1.206  0.020  1.206
 HJ2  O14   H21   single  0.850  0.020  0.980
 HJ2  C3    C81   single  1.491  0.020  1.491
 HJ2  N2    H5    single  0.860  0.020  1.020
 HJ2  N2    C9    single  1.349  0.020  1.349
 HJ2  C81   H15   single  0.970  0.020  1.090
 HJ2  C81   H16   single  0.970  0.020  1.090
 HJ2  C81   H17   single  0.970  0.020  1.090
 HJ2  C9    C10   single  1.506  0.020  1.506
 HJ2  C9    O5    double  1.223  0.020  1.223
 HJ2  C10   C11   single  1.526  0.020  1.526
 HJ2  C10   H61   single  0.970  0.020  1.090
 HJ2  C10   H71   single  0.970  0.020  1.090
 HJ2  C11   C12   single  1.535  0.020  1.535
 HJ2  C11   H8    single  0.970  0.020  1.090
 HJ2  C11   H9    single  0.970  0.020  1.090
 HJ2  C12   C131  single  1.529  0.020  1.529
 HJ2  C12   H10   single  0.970  0.020  1.090
 HJ2  C12   H11   single  0.970  0.020  1.090
 HJ2  C131  C14   single  1.534  0.020  1.534
 HJ2  C131  H12   single  0.970  0.020  1.090
 HJ2  C131  H13   single  0.970  0.020  1.090
 HJ2  C14   C15   single  1.515  0.020  1.515
 HJ2  C14   N3    single  1.448  0.020  1.448
 HJ2  C14   H14   single  0.970  0.020  1.090
 HJ2  C15   O6    single  1.331  0.020  1.331
 HJ2  C15   O7    double  1.204  0.020  1.204
 HJ2  N3    H18   single  0.890  0.020  1.040
 HJ2  N3    H19   single  0.890  0.020  1.040
 HJ2  O6    H20   single  0.850  0.020  0.980
 HJ2  C8    O4    single  1.406  0.020  1.406
 HJ2  C8    O9    double  1.382  0.020  1.382
 HJ2  O4    H22   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
 HJ2  C8    C7    N2    109.59  3.000
 HJ2  C8    C7    C6    118.28  3.000
 HJ2  N2    C7    C6    107.42  3.000
 HJ2  C8    C7    H7    106.33  3.000
 HJ2  N2    C7    H7    110.11  3.000
 HJ2  C6    C7    H7    104.87  3.000
 HJ2  H6    C6    N5    107.99  3.000
 HJ2  H6    C6    S1    103.81  3.000
 HJ2  N5    C6    S1    112.83  3.000
 HJ2  H6    C6    C7    106.76  3.000
 HJ2  N5    C6    C7    113.26  3.000
 HJ2  S1    C6    C7    111.49  3.000
 HJ2  C2    S1    C6     96.02  3.000
 HJ2  H4    C2    H2    107.49  3.000
 HJ2  H4    C2    C3    111.21  3.000
 HJ2  H2    C2    C3    111.71  3.000
 HJ2  H4    C2    S1    109.50  3.000
 HJ2  H2    C2    S1    106.27  3.000
 HJ2  C3    C2    S1    110.49  3.000
 HJ2  HN5   N5    C4    114.19  3.000
 HJ2  HN5   N5    C6    112.84  3.000
 HJ2  C4    N5    C6    115.41  3.000
 HJ2  C3    C4    C13   127.26  3.000
 HJ2  C3    C4    N5    118.85  3.000
 HJ2  C13   C4    N5    113.76  3.000
 HJ2  O15   C13   O14   122.68  3.000
 HJ2  O15   C13   C4    123.26  3.000
 HJ2  O14   C13   C4    114.04  3.000
 HJ2  H21   O14   C13   109.19  3.000
 HJ2  C81   C3    C4    129.31  3.000
 HJ2  C81   C3    C2    115.21  3.000
 HJ2  C4    C3    C2    115.44  3.000
 HJ2  C9    N2    H5    114.98  3.000
 HJ2  C9    N2    C7    127.03  3.000
 HJ2  H5    N2    C7    116.76  3.000
 HJ2  H17   C81   H16   106.43  3.000
 HJ2  H17   C81   H15   108.32  3.000
 HJ2  H16   C81   H15   108.37  3.000
 HJ2  H17   C81   C3    109.70  3.000
 HJ2  H16   C81   C3    109.04  3.000
 HJ2  H15   C81   C3    114.65  3.000
 HJ2  O5    C9    C10   121.47  3.000
 HJ2  O5    C9    N2    121.30  3.000
 HJ2  C10   C9    N2    117.22  3.000
 HJ2  H71   C10   H61   106.14  3.000
 HJ2  H71   C10   C11   110.07  3.000
 HJ2  H61   C10   C11   109.89  3.000
 HJ2  H71   C10   C9    107.44  3.000
 HJ2  H61   C10   C9    106.80  3.000
 HJ2  C11   C10   C9    115.99  3.000
 HJ2  H9    C11   H8    133.64  3.000
 HJ2  H9    C11   C12   107.97  3.000
 HJ2  H8    C11   C12   108.38  3.000
 HJ2  H9    C11   C10    85.16  3.000
 HJ2  H8    C11   C10   108.61  3.000
 HJ2  C12   C11   C10   109.25  3.000
 HJ2  H11   C12   H10   105.60  3.000
 HJ2  H11   C12   C131  107.28  3.000
 HJ2  H10   C12   C131  111.46  3.000
 HJ2  H11   C12   C11   107.47  3.000
 HJ2  H10   C12   C11   109.43  3.000
 HJ2  C131  C12   C11   115.07  3.000
 HJ2  H13   C131  H12   106.64  3.000
 HJ2  H13   C131  C14   108.33  3.000
 HJ2  H12   C131  C14   109.42  3.000
 HJ2  H13   C131  C12   112.09  3.000
 HJ2  H12   C131  C12   108.34  3.000
 HJ2  C14   C131  C12   111.86  3.000
 HJ2  H14   C14   N3    113.46  3.000
 HJ2  H14   C14   C15   105.89  3.000
 HJ2  N3    C14   C15   108.94  3.000
 HJ2  H14   C14   C131  107.48  3.000
 HJ2  N3    C14   C131  110.42  3.000
 HJ2  C15   C14   C131  110.55  3.000
 HJ2  O7    C15   O6    122.91  3.000
 HJ2  O7    C15   C14   125.24  3.000
 HJ2  O6    C15   C14   111.84  3.000
 HJ2  H19   N3    H18   105.65  3.000
 HJ2  H19   N3    C14   110.20  3.000
 HJ2  H18   N3    C14   109.23  3.000
 HJ2  H20   O6    C15   109.35  3.000
 HJ2  O9    C8    O4    110.74  3.000
 HJ2  O9    C8    C7    114.86  3.000
 HJ2  O4    C8    C7    105.03  3.000
 HJ2  H22   O4    C8    108.04  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
 HJ2  CONST_01  H21   O14   C13  C4    180.00   0.0  0
 HJ2  CONST_02  C10   C9    N2   C7      0.00   0.0  0
 HJ2  CONST_03  O5    C9    N2   C7    180.00   0.0  0
 HJ2  CONST_04  C10   C9    N2   H5    180.00   0.0  0
 HJ2  CONST_05  H22   O4    C8   C7    180.00   0.0  0
 HJ2  CONST_06  H20   O6    C15  C14   180.00   0.0  0
 HJ2  Var_01    C3    C2    S1   C6     50.04  30.0  1
 HJ2  Var_02    C3    C4    N5   C6     58.12  30.0  1
 HJ2  Var_03    C4    C3    C2   S1    -58.88  30.0  1
 HJ2  Var_04    N5    C4    C3   C2      4.10  30.0  1
 HJ2  Var_05    O14   C13   C4   N5   -159.01  30.0  2
 HJ2  Var_06    H15   C81   C3   C2   -166.14  30.0  3
 HJ2  Var_07    C11   C10   C9   N2    -15.31  30.0  3
 HJ2  Var_08    C12   C11   C10  C9    169.92  30.0  3
 HJ2  Var_09    C131  C12   C11  C10   152.97  30.0  3
 HJ2  Var_10    C14   C131  C12  C11  -170.86  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
 HJ2  chir_01  C7   C6    N2   C8  positiv
 HJ2  chir_02  C6   S1    N5   C7  negativ
 HJ2  chir_03  C14  C131  C15  N3  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
 HJ2  plan-1  C7   0.020
 HJ2  plan-1  N2   0.020
 HJ2  plan-1  H5   0.020
 HJ2  plan-1  C9   0.020
 HJ2  plan-1  C10  0.020
 HJ2  plan-1  O5   0.020
 HJ2  plan-2  C6   0.020
 HJ2  plan-2  N5   0.020
 HJ2  plan-2  C4   0.020
 HJ2  plan-2  HN5  0.020
 HJ2  plan-3  C4   0.020
 HJ2  plan-3  C13  0.020
 HJ2  plan-3  O14  0.020
 HJ2  plan-3  O15  0.020
 HJ2  plan-3  H21  0.020
 HJ2  plan-4  C14  0.020
 HJ2  plan-4  C15  0.020
 HJ2  plan-4  O6   0.020
 HJ2  plan-4  O7   0.020
 HJ2  plan-4  H20  0.020
 HJ2  plan-5  C7   0.020
 HJ2  plan-5  C8   0.020
 HJ2  plan-5  O4   0.020
 HJ2  plan-5  O9   0.020
 HJ2  plan-5  H22  0.020

