# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 06:27:03 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: N-{(6S)-6-[(ammonioacetyl)amino]-6-carboxylatohexanoyl}-D-alanyl-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)[C@@H](C)NC(=O)CCCC[C@H](NC(=O)C[NH3+])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
 REX  REX  N-{(6S)-6-[(ammonioacetyl)amino]-6-carboxylatohexanoyl}-D-alanyl-D-alanine  ligand  51  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_REX
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
 REX  C1    C  CH2    0  -0.415  -1.2224   0.6980  -0.3515
 REX  C2    C  CH2    0  -0.412  -2.5178   0.1309   0.2140
 REX  C3    C  CH2    0  -0.580  -0.1180  -0.3484  -0.4105
 REX  C4    C  CH2    0  -0.453  -3.6178   1.1803   0.3170
 REX  C5    C  C      0   0.570   1.1689   0.1727  -1.0141
 REX  N1    N  NH1    0  -0.645   2.2898  -0.3745  -0.5159
 REX  O1    O  O      0  -0.507   1.1832   1.0185  -1.8995
 REX  C6    C  CH1    0  -0.192   3.6097  -0.0885  -1.0241
 REX  C7    C  C      0   0.545   4.6218  -0.4296   0.0667
 REX  C8    C  CH3    0  -0.651   3.9319  -0.8939  -2.2849
 REX  O2    O  O      0  -0.509   4.4204  -1.3586   0.8426
 REX  N2    N  NH1    0  -0.630   5.7216   0.3178   0.0572
 REX  C9    C  CH1    0  -0.208   6.8835   0.1042   0.8934
 REX  C10   C  CH1    0  -0.213  -4.9433   0.6301   0.8364
 REX  C11   C  CH3    0  -0.657   6.6338   0.5314   2.3380
 REX  C12   C  C      0   0.421   8.0815   0.8832   0.2942
 REX  O3    O  O      0  -0.598   7.8511   1.6132  -0.6905
 REX  O4    O  OC    -1  -0.602   9.1697   0.7136   0.8690
 REX  N3    N  NH1    0  -0.611  -5.4753  -0.3194  -0.1181
 REX  C13   C  C      0   0.423  -5.9638   1.7574   1.1628
 REX  C14   C  C      0   0.558  -6.3972  -1.2231   0.2000
 REX  C15   C  CH2    0  -0.438  -7.0734  -1.8709  -0.9969
 REX  O5    O  O      0  -0.496  -6.7149  -1.5479   1.3348
 REX  N4    N  NT3    1  -0.767  -7.6769  -3.1530  -0.5904
 REX  O6    O  O      0  -0.592  -7.0697   1.7122   0.5998
 REX  O7    O  OC    -1  -0.610  -5.5629   2.6039   1.9844
 REX  HC11  H  HCH2   0   0.223  -0.8942   1.5441   0.2602
 REX  HC12  H  HCH2   0   0.224  -1.4054   1.0935  -1.3532
 REX  HC21  H  HCH2   0   0.217  -2.8482  -0.7038  -0.4126
 REX  HC22  H  HCH2   0   0.214  -2.3335  -0.2891   1.2086
 REX  HC31  H  HCH2   0   0.266  -0.4462  -1.1942  -1.0256
 REX  HC32  H  HCH2   0   0.249   0.0700  -0.7568   0.5858
 REX  HC41  H  HCH2   0   0.238  -3.2976   1.9767   0.9900
 REX  HC42  H  HCH2   0   0.220  -3.7755   1.6513  -0.6609
 REX  HN1   H  HNH1   0   0.395   2.2206  -1.0966   0.1852
 REX  HC6   H  HCH1   0   0.268   3.6711   0.9765  -1.2587
 REX  HC81  H  HCH3   0   0.247   3.2100  -0.6699  -3.0689
 REX  HC82  H  HCH3   0   0.237   4.9248  -0.6487  -2.6630
 REX  HC83  H  HCH3   0   0.232   3.8972  -1.9643  -2.0800
 REX  HN2   H  HNH1   0   0.389   5.8413   1.0453  -0.6352
 REX  HC9   H  HCH1   0   0.240   7.1360  -0.9613   0.8849
 REX  H10   H  HCH1   0   0.247  -4.7451   0.0895   1.7669
 REX  H111  H  HCH3   0   0.219   6.3925   1.5944   2.3943
 REX  H112  H  HCH3   0   0.232   5.8072  -0.0282   2.7737
 REX  H113  H  HCH3   0   0.229   7.5201   0.3502   2.9436
 REX  HN3   H  HNH1   0   0.400  -5.3757  -0.0803  -1.0938
 REX  H151  H  HCH2   0   0.332  -7.8757  -1.2275  -1.3565
 REX  H152  H  HCH2   0   0.322  -6.3880  -2.0612  -1.8193
 REX  HN41  H  HNT3   0   0.475  -6.9749  -3.8563  -0.3630
 REX  HN42  H  HNT3   0   0.468  -8.2646  -3.0416   0.2366
 REX  HN43  H  HNT3   0   0.483  -8.2587  -3.5389  -1.3329

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
 REX  C1   C2    single  1.523  0.020  1.523
 REX  C1   C3    single  1.523  0.020  1.523
 REX  C1   HC11  single  0.970  0.020  1.090
 REX  C1   HC12  single  0.970  0.020  1.090
 REX  C2   C4    single  1.524  0.020  1.524
 REX  C2   HC21  single  0.970  0.020  1.090
 REX  C2   HC22  single  0.970  0.020  1.090
 REX  C3   C5    single  1.514  0.020  1.514
 REX  C3   HC31  single  0.970  0.020  1.090
 REX  C3   HC32  single  0.970  0.020  1.090
 REX  C4   C10   single  1.526  0.020  1.526
 REX  C4   HC41  single  0.970  0.020  1.090
 REX  C4   HC42  single  0.970  0.020  1.090
 REX  C5   N1    single  1.343  0.020  1.343
 REX  C5   O1    double  1.225  0.020  1.225
 REX  N1   C6    single  1.443  0.020  1.443
 REX  N1   HN1   single  0.860  0.020  1.020
 REX  C6   C7    single  1.527  0.020  1.527
 REX  C6   C8    single  1.530  0.020  1.530
 REX  C6   HC6   single  0.970  0.020  1.090
 REX  C7   O2    double  1.227  0.020  1.227
 REX  C7   N2    single  1.330  0.020  1.330
 REX  C8   HC81  single  0.970  0.020  1.090
 REX  C8   HC82  single  0.970  0.020  1.090
 REX  C8   HC83  single  0.970  0.020  1.090
 REX  N2   C9    single  1.447  0.020  1.447
 REX  N2   HN2   single  0.860  0.020  1.020
 REX  C9   C11   single  1.527  0.020  1.527
 REX  C9   C12   single  1.550  0.020  1.550
 REX  C9   HC9   single  0.970  0.020  1.090
 REX  C10  N3    single  1.448  0.020  1.448
 REX  C10  C13   single  1.555  0.020  1.555
 REX  C10  H10   single  0.970  0.020  1.090
 REX  C11  H111  single  0.970  0.020  1.090
 REX  C11  H112  single  0.970  0.020  1.090
 REX  C11  H113  single  0.970  0.020  1.090
 REX  C12  O3    deloc   1.247  0.020  1.247
 REX  C12  O4    deloc   1.242  0.020  1.242
 REX  N3   C14   single  1.330  0.020  1.330
 REX  N3   HN3   single  0.890  0.020  1.040
 REX  C13  O6    deloc   1.242  0.020  1.242
 REX  C13  O7    deloc   1.246  0.020  1.246
 REX  C14  C15   single  1.520  0.020  1.520
 REX  C14  O5    double  1.222  0.020  1.222
 REX  C15  N4    single  1.474  0.020  1.474
 REX  C15  H151  single  0.970  0.020  1.090
 REX  C15  H152  single  0.970  0.020  1.090
 REX  N4   HN41  single  0.890  0.020  1.040
 REX  N4   HN42  single  0.890  0.020  1.040
 REX  N4   HN43  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
 REX  HC12  C1   HC11  106.43  3.000
 REX  HC12  C1   C3    109.57  3.000
 REX  HC11  C1   C3    109.60  3.000
 REX  HC12  C1   C2    109.43  3.000
 REX  HC11  C1   C2    109.60  3.000
 REX  C3    C1   C2    112.05  3.000
 REX  HC22  C2   HC21  106.15  3.000
 REX  HC22  C2   C4    108.91  3.000
 REX  HC21  C2   C4    110.24  3.000
 REX  HC22  C2   C1    109.68  3.000
 REX  HC21  C2   C1    109.15  3.000
 REX  C4    C2   C1    112.50  3.000
 REX  HC32  C3   HC31  105.94  3.000
 REX  HC32  C3   C5    110.23  3.000
 REX  HC31  C3   C5    107.24  3.000
 REX  HC32  C3   C1    110.26  3.000
 REX  HC31  C3   C1    109.57  3.000
 REX  C5    C3   C1    113.29  3.000
 REX  HC42  C4   HC41  106.18  3.000
 REX  HC42  C4   C10   109.47  3.000
 REX  HC41  C4   C10   107.95  3.000
 REX  HC42  C4   C2    109.83  3.000
 REX  HC41  C4   C2    109.43  3.000
 REX  C10   C4   C2    113.69  3.000
 REX  O1    C5   N1    122.67  3.000
 REX  O1    C5   C3    122.41  3.000
 REX  N1    C5   C3    114.92  3.000
 REX  HN1   N1   C6    116.70  3.000
 REX  HN1   N1   C5    119.48  3.000
 REX  C6    N1   C5    123.50  3.000
 REX  HC6   C6   C8    108.93  3.000
 REX  HC6   C6   C7    109.52  3.000
 REX  C8    C6   C7    109.36  3.000
 REX  HC6   C6   N1    108.68  3.000
 REX  C8    C6   N1    112.23  3.000
 REX  C7    C6   N1    108.09  3.000
 REX  N2    C7   O2    124.46  3.000
 REX  N2    C7   C6    114.68  3.000
 REX  O2    C7   C6    120.81  3.000
 REX  HC83  C8   HC82  108.36  3.000
 REX  HC83  C8   HC81  108.43  3.000
 REX  HC82  C8   HC81  107.92  3.000
 REX  HC83  C8   C6    110.80  3.000
 REX  HC82  C8   C6    111.04  3.000
 REX  HC81  C8   C6    110.19  3.000
 REX  HN2   N2   C9    113.99  3.000
 REX  HN2   N2   C7    120.47  3.000
 REX  C9    N2   C7    125.23  3.000
 REX  HC9   C9   C12   107.93  3.000
 REX  HC9   C9   C11   108.49  3.000
 REX  C12   C9   C11   110.58  3.000
 REX  HC9   C9   N2    108.92  3.000
 REX  C12   C9   N2    108.85  3.000
 REX  C11   C9   N2    111.96  3.000
 REX  H10   C10  C13   107.37  3.000
 REX  H10   C10  N3    107.65  3.000
 REX  C13   C10  N3    111.88  3.000
 REX  H10   C10  C4    108.07  3.000
 REX  C13   C10  C4    112.33  3.000
 REX  N3    C10  C4    109.35  3.000
 REX  H113  C11  H112  108.05  3.000
 REX  H113  C11  H111  108.27  3.000
 REX  H112  C11  H111  108.18  3.000
 REX  H113  C11  C9    110.28  3.000
 REX  H112  C11  C9    111.03  3.000
 REX  H111  C11  C9    110.94  3.000
 REX  O4    C12  O3    127.37  3.000
 REX  O4    C12  C9    115.45  3.000
 REX  O3    C12  C9    117.17  3.000
 REX  HN3   N3   C14   117.43  3.000
 REX  HN3   N3   C10   116.47  3.000
 REX  C14   N3   C10   122.88  3.000
 REX  O7    C13  O6    127.61  3.000
 REX  O7    C13  C10   114.82  3.000
 REX  O6    C13  C10   117.57  3.000
 REX  O5    C14  C15   120.15  3.000
 REX  O5    C14  N3    125.66  3.000
 REX  C15   C14  N3    114.19  3.000
 REX  H152  C15  H151  108.54  3.000
 REX  H152  C15  N4    108.32  3.000
 REX  H151  C15  N4    107.65  3.000
 REX  H152  C15  C14   112.95  3.000
 REX  H151  C15  C14   109.63  3.000
 REX  N4    C15  C14   109.62  3.000
 REX  HN43  N4   HN42  107.63  3.000
 REX  HN43  N4   HN41  107.12  3.000
 REX  HN42  N4   HN41  106.92  3.000
 REX  HN43  N4   C15   111.23  3.000
 REX  HN42  N4   C15   111.36  3.000
 REX  HN41  N4   C15   112.31  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
 REX  CONST_01  C6    N1   C5   C3   180.00   0.0  0
 REX  CONST_02  C6    N1   C5   O1     0.00   0.0  0
 REX  CONST_03  C9    N2   C7   C6   180.00   0.0  0
 REX  CONST_04  C9    N2   C7   O2     0.00   0.0  0
 REX  CONST_07  HN1   N1   C5   C3     0.00   0.0  0
 REX  CONST_08  HN2   N2   C7   C6     0.00   0.0  0
 REX  CONST_09  HN3   N3   C14  C15    0.00   0.0  0
 REX  Var_01    C10   C4   C2   C1   178.03  30.0  3
 REX  Var_02    N1    C5   C3   C1   147.73  30.0  3
 REX  Var_03    C5    C3   C1   C2   177.97  30.0  3
 REX  Var_04    C4    C2   C1   C3   178.26  30.0  3
 REX  Var_05    N4    C15  C14  N3   159.23  30.0  3
 REX  Var_06    HN41  N4   C15  C14  -68.77  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
 REX  chir_01  C6   N1  C7   C8   negativ
 REX  chir_02  C9   N2  C11  C12  positiv
 REX  chir_03  C10  C4  N3   C13  positiv

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
 REX  plan-1  C3   0.020
 REX  plan-1  C5   0.020
 REX  plan-1  N1   0.020
 REX  plan-1  O1   0.020
 REX  plan-1  C6   0.020
 REX  plan-1  HN1  0.020
 REX  plan-2  C6   0.020
 REX  plan-2  C7   0.020
 REX  plan-2  O2   0.020
 REX  plan-2  N2   0.020
 REX  plan-2  C9   0.020
 REX  plan-2  HN2  0.020
 REX  plan-3  C10  0.020
 REX  plan-3  N3   0.020
 REX  plan-3  C14  0.020
 REX  plan-3  C15  0.020
 REX  plan-3  O5   0.020
 REX  plan-3  HN3  0.020
 REX  plan-4  C9   0.020
 REX  plan-4  C12  0.020
 REX  plan-4  O3   0.020
 REX  plan-4  O4   0.020
 REX  plan-5  C10  0.020
 REX  plan-5  C13  0.020
 REX  plan-5  O6   0.020
 REX  plan-5  O7   0.020

