# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 11:05:14 2020
#   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  46  26  .  2022-07-25  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_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  -0.197   1.5015  -0.8971   0.3318
 HJ2  H7    H  HCH1   0   0.261   1.4305  -1.7264  -0.3784
 HJ2  C6    C  CH1    0  -0.208   2.6089   0.0200  -0.1830
 HJ2  S1    S  S2     0  -0.063   2.8926   1.4227   0.9990
 HJ2  C2    C  CH2    0  -0.625   4.0078   2.2454  -0.1629
 HJ2  N5    N  NH1    0  -0.633   3.8059  -0.6809  -0.4443
 HJ2  C4    C  C      0   0.089   4.9754   0.0014  -0.7604
 HJ2  C13   C  C      0   0.375   6.1264  -0.9575  -1.0719
 HJ2  O14   O  OC    -1  -0.606   5.9064  -2.1553  -0.7985
 HJ2  O15   O  O      0  -0.581   7.1848  -0.4928  -1.5323
 HJ2  C3    C  C      0   0.018   5.0678   1.3499  -0.7540
 HJ2  N2    N  NH1    0  -0.638   0.2620  -0.1637   0.3136
 HJ2  H6    H  HCH1   0   0.278   2.2671   0.5086  -1.1025
 HJ2  H2    H  HCH2   0   0.269   3.4212   2.7501  -0.9376
 HJ2  HN5   H  HNH1   0   0.366   3.9428  -1.5184   0.1064
 HJ2  C81   C  CH3    0  -0.699   6.2322   2.1499  -1.2786
 HJ2  H4    H  HCH2   0   0.276   4.4997   3.0388   0.4070
 HJ2  H5    H  HNH1   0   0.387   0.3093   0.8403   0.4051
 HJ2  C9    C  C      0   0.569  -0.9183  -0.7656   0.5288
 HJ2  C10   C  CH2    0  -0.581  -2.1024   0.1660   0.6702
 HJ2  O5    O  O      0  -0.514  -1.0332  -1.9837   0.5885
 HJ2  C11   C  CH2    0  -0.413  -3.3732  -0.3883   0.0386
 HJ2  H61   H  HCH2   0   0.261  -2.2649   0.3332   1.7407
 HJ2  H71   H  HCH2   0   0.244  -1.8680   1.1448   0.2435
 HJ2  C12   C  CH2    0  -0.405  -4.5369   0.5923   0.1153
 HJ2  H8    H  HCH2   0   0.217  -3.1793  -0.6362  -1.0097
 HJ2  H9    H  HCH2   0   0.219  -3.6503  -1.3243   0.5296
 HJ2  C131  C  CH2    0  -0.417  -5.8050   0.0338  -0.5163
 HJ2  H10   H  HCH2   0   0.212  -4.7300   0.8590   1.1573
 HJ2  H11   H  HCH2   0   0.202  -4.2612   1.5241  -0.3921
 HJ2  C14   C  CH1    0  -0.214  -6.9817   1.0119  -0.5369
 HJ2  H12   H  HCH2   0   0.215  -5.5925  -0.2684  -1.5442
 HJ2  H13   H  HCH2   0   0.202  -6.1032  -0.8788   0.0157
 HJ2  C15   C  C      0   0.383  -8.1508   0.4011  -1.3510
 HJ2  N3    N  NH2    0  -0.785  -7.3149   1.4233   0.8189
 HJ2  H14   H  HCH1   0   0.206  -6.6469   1.9078  -1.0761
 HJ2  O6    O  OC    -1  -0.625  -7.9286   0.2053  -2.5652
 HJ2  O7    O  O      0  -0.609  -9.2081   0.1427  -0.7425
 HJ2  H15   H  HCH3   0   0.214   5.8989   3.1639  -1.5146
 HJ2  H16   H  HCH3   0   0.222   7.0326   2.2499  -0.5399
 HJ2  H17   H  HCH3   0   0.238   6.6727   1.7240  -2.1733
 HJ2  H18   H  HNH2   0   0.332  -8.0615   2.1066   0.7740
 HJ2  H19   H  HNH2   0   0.321  -7.7354   0.6299   1.2908
 HJ2  C8    C  C      0   0.423   1.8646  -1.4677   1.7290
 HJ2  O4    O  OC    -1  -0.604   2.7310  -2.3692   1.7175
 HJ2  O9    O  O      0  -0.580   1.3042  -0.9700   2.7144

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  1.527  0.020  1.527
 HJ2  C7    N2    single  1.440  0.020  1.440
 HJ2  C7    C8    single  1.552  0.020  1.552
 HJ2  C6    S1    single  1.856  0.020  1.856
 HJ2  C6    N5    single  1.411  0.020  1.411
 HJ2  C6    H6    single  0.970  0.020  1.090
 HJ2  S1    C2    single  1.808  0.020  1.808
 HJ2  C2    C3    single  1.508  0.020  1.508
 HJ2  C2    H2    single  0.970  0.020  1.090
 HJ2  C2    H4    single  0.970  0.020  1.090
 HJ2  N5    C4    single  1.390  0.020  1.390
 HJ2  N5    HN5   single  0.890  0.020  1.040
 HJ2  C4    C13   single  1.530  0.020  1.530
 HJ2  C4    C3    double  1.352  0.020  1.352
 HJ2  C13   O14   deloc   1.248  0.020  1.248
 HJ2  C13   O15   deloc   1.244  0.020  1.244
 HJ2  C3    C81   single  1.507  0.020  1.507
 HJ2  N2    H5    single  0.890  0.020  1.040
 HJ2  N2    C9    single  1.342  0.020  1.342
 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  1.513  0.020  1.513
 HJ2  C9    O5    double  1.225  0.020  1.225
 HJ2  C10   C11   single  1.524  0.020  1.524
 HJ2  C10   H61   single  0.970  0.020  1.090
 HJ2  C10   H71   single  0.970  0.020  1.090
 HJ2  C11   C12   single  1.524  0.020  1.524
 HJ2  C11   H8    single  0.970  0.020  1.090
 HJ2  C11   H9    single  0.970  0.020  1.090
 HJ2  C12   C131  single  1.523  0.020  1.523
 HJ2  C12   H10   single  0.970  0.020  1.090
 HJ2  C12   H11   single  0.970  0.020  1.090
 HJ2  C131  C14   single  1.530  0.020  1.530
 HJ2  C131  H12   single  0.970  0.020  1.090
 HJ2  C131  H13   single  0.970  0.020  1.090
 HJ2  C14   C15   single  1.550  0.020  1.550
 HJ2  C14   N3    single  1.456  0.020  1.456
 HJ2  C14   H14   single  0.970  0.020  1.090
 HJ2  C15   O6    deloc   1.250  0.020  1.250
 HJ2  C15   O7    deloc   1.247  0.020  1.247
 HJ2  N3    H18   single  0.890  0.020  1.040
 HJ2  N3    H19   single  0.890  0.020  1.040
 HJ2  C8    O4    deloc   1.250  0.020  1.250
 HJ2  C8    O9    deloc   1.238  0.020  1.238

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    113.57  3.000
 HJ2  C8    C7    C6    110.77  3.000
 HJ2  N2    C7    C6    108.30  3.000
 HJ2  C8    C7    H7    108.71  3.000
 HJ2  N2    C7    H7    108.78  3.000
 HJ2  C6    C7    H7    106.46  3.000
 HJ2  H6    C6    N5    109.30  3.000
 HJ2  H6    C6    S1    104.19  3.000
 HJ2  N5    C6    S1    111.32  3.000
 HJ2  H6    C6    C7    108.93  3.000
 HJ2  N5    C6    C7    112.28  3.000
 HJ2  S1    C6    C7    110.48  3.000
 HJ2  C2    S1    C6     91.66  3.000
 HJ2  H4    C2    H2    105.98  3.000
 HJ2  H4    C2    C3    108.59  3.000
 HJ2  H2    C2    C3    111.89  3.000
 HJ2  H4    C2    S1    105.82  3.000
 HJ2  H2    C2    S1    109.50  3.000
 HJ2  C3    C2    S1    114.52  3.000
 HJ2  HN5   N5    C4    114.59  3.000
 HJ2  HN5   N5    C6    115.16  3.000
 HJ2  C4    N5    C6    120.77  3.000
 HJ2  C3    C4    C13   125.08  3.000
 HJ2  C3    C4    N5    123.09  3.000
 HJ2  C13   C4    N5    111.81  3.000
 HJ2  O15   C13   O14   126.12  3.000
 HJ2  O15   C13   C4    118.76  3.000
 HJ2  O14   C13   C4    115.10  3.000
 HJ2  C81   C3    C4    125.51  3.000
 HJ2  C81   C3    C2    111.36  3.000
 HJ2  C4    C3    C2    123.10  3.000
 HJ2  C9    N2    H5    118.22  3.000
 HJ2  C9    N2    C7    121.76  3.000
 HJ2  H5    N2    C7    117.71  3.000
 HJ2  H17   C81   H16   107.21  3.000
 HJ2  H17   C81   H15   108.07  3.000
 HJ2  H16   C81   H15   106.51  3.000
 HJ2  H17   C81   C3    113.11  3.000
 HJ2  H16   C81   C3    112.26  3.000
 HJ2  H15   C81   C3    109.39  3.000
 HJ2  O5    C9    C10   122.29  3.000
 HJ2  O5    C9    N2    122.42  3.000
 HJ2  C10   C9    N2    115.28  3.000
 HJ2  H71   C10   H61   106.05  3.000
 HJ2  H71   C10   C11   110.04  3.000
 HJ2  H61   C10   C11   109.69  3.000
 HJ2  H71   C10   C9    110.30  3.000
 HJ2  H61   C10   C9    107.54  3.000
 HJ2  C11   C10   C9    112.95  3.000
 HJ2  H9    C11   H8    106.34  3.000
 HJ2  H9    C11   C12   109.57  3.000
 HJ2  H8    C11   C12   109.22  3.000
 HJ2  H9    C11   C10   109.69  3.000
 HJ2  H8    C11   C10   109.37  3.000
 HJ2  C12   C11   C10   112.46  3.000
 HJ2  H11   C12   H10   106.16  3.000
 HJ2  H11   C12   C131  109.22  3.000
 HJ2  H10   C12   C131  109.74  3.000
 HJ2  H11   C12   C11   109.37  3.000
 HJ2  H10   C12   C11   109.88  3.000
 HJ2  C131  C12   C11   112.28  3.000
 HJ2  H13   C131  H12   106.20  3.000
 HJ2  H13   C131  C14   109.21  3.000
 HJ2  H12   C131  C14   108.29  3.000
 HJ2  H13   C131  C12   109.28  3.000
 HJ2  H12   C131  C12   109.25  3.000
 HJ2  C14   C131  C12   114.29  3.000
 HJ2  H14   C14   N3    107.26  3.000
 HJ2  H14   C14   C15   107.07  3.000
 HJ2  N3    C14   C15   115.33  3.000
 HJ2  H14   C14   C131  107.08  3.000
 HJ2  N3    C14   C131  110.13  3.000
 HJ2  C15   C14   C131  109.58  3.000
 HJ2  O7    C15   O6    126.33  3.000
 HJ2  O7    C15   C14   117.70  3.000
 HJ2  O6    C15   C14   115.97  3.000
 HJ2  H19   N3    H18   104.04  3.000
 HJ2  H19   N3    C14   107.89  3.000
 HJ2  H18   N3    C14   108.55  3.000
 HJ2  O9    C8    O4    127.65  3.000
 HJ2  O9    C8    C7    117.57  3.000
 HJ2  O4    C8    C7    114.76  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  C10   C9    N2   C7    180.00   0.0  0
 HJ2  CONST_02  O5    C9    N2   C7      0.00   0.0  0
 HJ2  CONST_03  C10   C9    N2   H5      0.00   0.0  0
 HJ2  Var_01    C3    C2    S1   C6    -48.48  30.0  1
 HJ2  Var_02    C3    C4    N5   C6      4.37  30.0  1
 HJ2  Var_03    C4    C3    C2   S1     19.22  30.0  1
 HJ2  Var_04    N5    C4    C3   C2     11.77  30.0  1
 HJ2  Var_05    O14   C13   C4   N5    -10.54  30.0  2
 HJ2  Var_06    H15   C81   C3   C2    -24.19  30.0  3
 HJ2  Var_07    C11   C10   C9   N2    142.84  30.0  3
 HJ2  Var_08    C12   C11   C10  C9   -176.64  30.0  3
 HJ2  Var_09    C131  C12   C11  C10  -179.96  30.0  3
 HJ2  Var_10    C14   C131  C12  C11  -176.66  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-4  C14  0.020
 HJ2  plan-4  C15  0.020
 HJ2  plan-4  O6   0.020
 HJ2  plan-4  O7   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

