# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 19:55:26 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  52  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  -1.2659   0.6979  -0.3090
 REX  C2    C  CH2    0  -0.412  -2.5509   0.0774   0.2234
 REX  C3    C  CH2    0  -0.581  -0.1347  -0.3169  -0.4005
 REX  C4    C  CH2    0  -0.456  -3.6747   1.0972   0.3586
 REX  C5    C  C      0   0.573   1.1479   0.2668  -0.9527
 REX  N1    N  NH1    0  -0.647   2.2738  -0.2841  -0.4684
 REX  O1    O  O      0  -0.505   1.1578   1.1624  -1.7872
 REX  C6    C  CH1    0  -0.199   3.5921   0.0734  -0.9262
 REX  C7    C  C      0   0.560   4.5946  -0.3289   0.1509
 REX  C8    C  CH3    0  -0.651   3.9574  -0.6105  -2.2474
 REX  O2    O  O      0  -0.486   4.3345  -1.1801   0.9882
 REX  N2    N  NH1    0  -0.631   5.7789   0.2911   0.0626
 REX  C9    C  CH1    0  -0.209   6.8892   0.0010   0.9338
 REX  C10   C  CH1    0  -0.206  -4.9886   0.5046   0.8612
 REX  C11   C  CH3    0  -0.651   6.9358   0.9465   2.1370
 REX  C12   C  C      0   0.553   8.1755   0.0776   0.1342
 REX  O3    O  O      0  -0.432   8.2571   0.4992  -0.9908
 REX  O4    O  OH1    0  -0.587   9.2052  -0.3601   0.8395
 REX  N3    N  NH1    0  -0.616  -5.5022  -0.4271  -0.1213
 REX  C13   C  C      0   0.422  -6.0240   1.6082   1.2173
 REX  C14   C  C      0   0.555  -6.4547  -1.3117   0.1628
 REX  C15   C  CH2    0  -0.437  -7.0779  -1.9665  -1.0599
 REX  O5    O  O      0  -0.496  -6.8224  -1.6230   1.2856
 REX  N4    N  NT3    1  -0.766  -7.9661  -3.0657  -0.6403
 REX  O6    O  O      0  -0.592  -7.1072   1.6016   0.6103
 REX  O7    O  OC    -1  -0.611  -5.6537   2.4032   2.1028
 REX  HC11  H  HCH2   0   0.223  -0.9635   1.5258   0.3392
 REX  HC12  H  HCH2   0   0.224  -1.4515   1.1299  -1.2950
 REX  HC21  H  HCH2   0   0.218  -2.8575  -0.7400  -0.4369
 REX  HC22  H  HCH2   0   0.215  -2.3633  -0.3770   1.2023
 REX  HC31  H  HCH2   0   0.267  -0.4304  -1.1394  -1.0616
 REX  HC32  H  HCH2   0   0.250   0.0467  -0.7694   0.5779
 REX  HC41  H  HCH2   0   0.239  -3.3711   1.8787   1.0563
 REX  HC42  H  HCH2   0   0.221  -3.8431   1.5955  -0.6040
 REX  HN1   H  HNH1   0   0.397   2.2116  -1.0324   0.2051
 REX  HC6   H  HCH1   0   0.278   3.6363   1.1567  -1.0647
 REX  HC81  H  HCH3   0   0.252   3.2317  -0.3473  -3.0153
 REX  HC82  H  HCH3   0   0.237   4.9416  -0.2970  -2.5959
 REX  HC83  H  HCH3   0   0.236   3.9622  -1.6947  -2.1339
 REX  HN2   H  HNH1   0   0.407   5.9025   1.0156  -0.6284
 REX  HC9   H  HCH1   0   0.299   6.7816  -1.0242   1.2950
 REX  H10   H  HCH1   0   0.245  -4.7779  -0.0565   1.7768
 REX  H111  H  HCH3   0   0.240   7.0616   1.9807   1.8159
 REX  H112  H  HCH3   0   0.254   6.0020   0.8715   2.6918
 REX  H113  H  HCH3   0   0.248   7.7487   0.6917   2.8144
 REX  HO4   H  HOH1   0   0.488  10.0243  -0.2759   0.3280
 REX  HN3   H  HNH1   0   0.399  -5.3665  -0.1835  -1.0916
 REX  H151  H  HCH2   0   0.331  -7.6795  -1.2482  -1.6146
 REX  H152  H  HCH2   0   0.328  -6.3263  -2.3777  -1.7310
 REX  HN41  H  HNT3   0   0.473  -7.4574  -3.8181  -0.1770
 REX  HN42  H  HNT3   0   0.471  -8.6851  -2.7473   0.0096
 REX  HN43  H  HNT3   0   0.483  -8.4418  -3.4752  -1.4434

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  1.522  0.020  1.522
 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  1.527  0.020  1.527
 REX  C4   HC41  single  0.970  0.020  1.090
 REX  C4   HC42  single  0.970  0.020  1.090
 REX  C5   N1    single  1.344  0.020  1.344
 REX  C5   O1    double  1.224  0.020  1.224
 REX  N1   C6    single  1.441  0.020  1.441
 REX  N1   HN1   single  0.860  0.020  1.020
 REX  C6   C7    single  1.525  0.020  1.525
 REX  C6   C8    single  1.532  0.020  1.532
 REX  C6   HC6   single  0.970  0.020  1.090
 REX  C7   O2    double  1.222  0.020  1.222
 REX  C7   N2    single  1.340  0.020  1.340
 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  1.441  0.020  1.441
 REX  N2   HN2   single  0.860  0.020  1.020
 REX  C9   C11   single  1.531  0.020  1.531
 REX  C9   C12   single  1.517  0.020  1.517
 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    double  1.204  0.020  1.204
 REX  C12  O4    single  1.323  0.020  1.323
 REX  O4   HO4   single  0.850  0.020  0.980
 REX  N3   C14   single  1.331  0.020  1.331
 REX  N3   HN3   single  0.890  0.020  1.040
 REX  C13  O6    double  1.242  0.020  1.242
 REX  C13  O7    single  1.246  0.020  1.246
 REX  C14  C15   single  1.521  0.020  1.521
 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  106.41  3.000
 REX  HC12  C1   C3    109.61  3.000
 REX  HC11  C1   C3    109.54  3.000
 REX  HC12  C1   C2    109.48  3.000
 REX  HC11  C1   C2    109.54  3.000
 REX  C3    C1   C2    112.11  3.000
 REX  HC22  C2   HC21  106.10  3.000
 REX  HC22  C2   C4    108.94  3.000
 REX  HC21  C2   C4    110.29  3.000
 REX  HC22  C2   C1    109.69  3.000
 REX  HC21  C2   C1    109.25  3.000
 REX  C4    C2   C1    112.37  3.000
 REX  HC32  C3   HC31  105.90  3.000
 REX  HC32  C3   C5    110.22  3.000
 REX  HC31  C3   C5    107.34  3.000
 REX  HC32  C3   C1    110.21  3.000
 REX  HC31  C3   C1    109.63  3.000
 REX  C5    C3   C1    113.24  3.000
 REX  HC42  C4   HC41  106.18  3.000
 REX  HC42  C4   C10   109.46  3.000
 REX  HC41  C4   C10   107.88  3.000
 REX  HC42  C4   C2    109.84  3.000
 REX  HC41  C4   C2    109.33  3.000
 REX  C10   C4   C2    113.85  3.000
 REX  O1    C5   N1    122.60  3.000
 REX  O1    C5   C3    122.53  3.000
 REX  N1    C5   C3    114.86  3.000
 REX  HN1   N1   C6    116.92  3.000
 REX  HN1   N1   C5    119.55  3.000
 REX  C6    N1   C5    123.40  3.000
 REX  HC6   C6   C8    108.88  3.000
 REX  HC6   C6   C7    108.92  3.000
 REX  C8    C6   C7    109.55  3.000
 REX  HC6   C6   N1    108.85  3.000
 REX  C8    C6   N1    112.43  3.000
 REX  C7    C6   N1    108.16  3.000
 REX  N2    C7   O2    123.76  3.000
 REX  N2    C7   C6    114.36  3.000
 REX  O2    C7   C6    121.84  3.000
 REX  HC83  C8   HC82  108.38  3.000
 REX  HC83  C8   HC81  108.47  3.000
 REX  HC82  C8   HC81  107.86  3.000
 REX  HC83  C8   C6    110.80  3.000
 REX  HC82  C8   C6    111.26  3.000
 REX  HC81  C8   C6    109.96  3.000
 REX  HN2   N2   C9    117.67  3.000
 REX  HN2   N2   C7    119.06  3.000
 REX  C9    N2   C7    123.25  3.000
 REX  HC9   C9   C12   107.78  3.000
 REX  HC9   C9   C11   108.83  3.000
 REX  C12   C9   C11   110.94  3.000
 REX  HC9   C9   N2    108.24  3.000
 REX  C12   C9   N2    108.94  3.000
 REX  C11   C9   N2    111.98  3.000
 REX  H10   C10  C13   107.49  3.000
 REX  H10   C10  N3    107.82  3.000
 REX  C13   C10  N3    112.09  3.000
 REX  H10   C10  C4    107.99  3.000
 REX  C13   C10  C4    111.91  3.000
 REX  N3    C10  C4    109.37  3.000
 REX  H113  C11  H112  107.89  3.000
 REX  H113  C11  H111  108.61  3.000
 REX  H112  C11  H111  108.32  3.000
 REX  H113  C11  C9    111.55  3.000
 REX  H112  C11  C9    109.38  3.000
 REX  H111  C11  C9    110.97  3.000
 REX  O4    C12  O3    124.14  3.000
 REX  O4    C12  C9    111.25  3.000
 REX  O3    C12  C9    124.60  3.000
 REX  HO4   O4   C12   110.35  3.000
 REX  HN3   N3   C14   117.51  3.000
 REX  HN3   N3   C10   116.69  3.000
 REX  C14   N3   C10   122.46  3.000
 REX  O7    C13  O6    127.59  3.000
 REX  O7    C13  C10   114.69  3.000
 REX  O6    C13  C10   117.73  3.000
 REX  O5    C14  C15   120.39  3.000
 REX  O5    C14  N3    125.53  3.000
 REX  C15   C14  N3    114.08  3.000
 REX  H152  C15  H151  108.46  3.000
 REX  H152  C15  N4    108.05  3.000
 REX  H151  C15  N4    107.70  3.000
 REX  H152  C15  C14   112.06  3.000
 REX  H151  C15  C14   110.61  3.000
 REX  N4    C15  C14   109.83  3.000
 REX  HN43  N4   HN42  107.36  3.000
 REX  HN43  N4   HN41  107.12  3.000
 REX  HN42  N4   HN41  107.01  3.000
 REX  HN43  N4   C15   110.88  3.000
 REX  HN42  N4   C15   111.92  3.000
 REX  HN41  N4   C15   112.27  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_05  C15   C14  N3   C10  180.00   0.0  0
 REX  CONST_06  O5    C14  N3   C10    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  CONST_10  HO4   O4   C12  C9   180.00   0.0  0
 REX  Var_01    C10   C4   C2   C1   178.74  30.0  3
 REX  Var_02    N1    C5   C3   C1   148.16  30.0  3
 REX  Var_03    C5    C3   C1   C2   178.87  30.0  3
 REX  Var_04    C4    C2   C1   C3   178.21  30.0  3
 REX  Var_05    N4    C15  C14  N3   171.48  30.0  3
 REX  Var_06    HN41  N4   C15  C14  -64.08  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-4  HO4  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

