# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 23:44:10 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (2S)-2-[(ammonioacetyl)amino]-7-{[(1R)-1-carboxyethyl]amino}-7-oxoheptanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](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
 REY  REY  (2S)-2-[(ammonioacetyl)amino]-7-{[(1R)-1-carboxyethyl]amino}-7-oxoheptanoate  ligand  42  21  .  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_REY
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
 REY  C1    C  CH2    0  -0.414   0.5607   0.8838  -0.2556
 REY  C2    C  CH2    0  -0.412  -0.7846   0.2450   0.0676
 REY  C3    C  CH2    0  -0.585   1.6909  -0.1349  -0.2517
 REY  C4    C  CH2    0  -0.457  -1.9252   1.2555   0.0165
 REY  C5    C  C      0   0.575   3.0465   0.4660  -0.5545
 REY  N1    N  NH1    0  -0.644   4.0908  -0.2198  -0.0524
 REY  O1    O  O      0  -0.500   3.1867   1.4835  -1.2182
 REY  C6    C  CH1    0  -0.198   5.4601   0.1408  -0.3144
 REY  C7    C  C      0   0.548   6.3196  -0.3176   0.8460
 REY  C8    C  CH3    0  -0.653   5.9763  -0.4428  -1.6340
 REY  O2    O  OH1    0  -0.587   7.5485   0.1638   0.7556
 REY  C9    C  CH1    0  -0.206  -3.2619   0.7155   0.5166
 REY  N3    N  NH1    0  -0.617  -3.6444  -0.4477  -0.2563
 REY  C10   C  C      0   0.421  -4.3612   1.8141   0.4979
 REY  C11   C  C      0   0.560  -4.6011  -1.2788   0.1480
 REY  C12   C  CH2    0  -0.436  -5.0992  -2.2355  -0.9230
 REY  O3    O  O      0  -0.496  -5.0746  -1.3182   1.2742
 REY  N4    N  NT3    1  -0.768  -5.8370  -3.3415  -0.2856
 REY  O4    O  O      0  -0.592  -5.3660   1.6123  -0.2035
 REY  O5    O  OC    -1  -0.611  -4.1152   2.8107   1.2043
 REY  O6    O  O      0  -0.434   5.9455  -1.0453   1.7303
 REY  HC11  H  HCH2   0   0.224   0.7693   1.6700   0.4757
 REY  HC12  H  HCH2   0   0.224   0.5101   1.3736  -1.2310
 REY  HC21  H  HCH2   0   0.217  -0.9725  -0.5751  -0.6318
 REY  HC22  H  HCH2   0   0.215  -0.7447  -0.2074   1.0645
 REY  HC31  H  HCH2   0   0.270   1.4995  -0.9024  -1.0099
 REY  HC32  H  HCH2   0   0.253   1.7221  -0.6630   0.7053
 REY  HC41  H  HCH2   0   0.238  -1.6704   2.1197   0.6319
 REY  HC42  H  HCH2   0   0.223  -2.0373   1.6315  -1.0073
 REY  HN1   H  HNH1   0   0.400   3.9163  -1.0688   0.4628
 REY  HC6   H  HCH1   0   0.293   5.5260   1.2305  -0.3666
 REY  HC81  H  HCH3   0   0.246   6.9967  -0.1246  -1.8394
 REY  HC82  H  HCH3   0   0.237   5.9473  -1.5325  -1.6176
 REY  HC83  H  HCH3   0   0.252   5.3461  -0.0956  -2.4511
 REY  HO2   H  HOH1   0   0.488   8.0950  -0.1731   1.4815
 REY  HC9   H  HCH1   0   0.246  -3.1296   0.3935   1.5538
 REY  HN3   H  HNH1   0   0.401  -3.4091  -0.4464  -1.2380
 REY  H121  H  HCH2   0   0.332  -5.7856  -1.7173  -1.5914
 REY  H122  H  HCH2   0   0.323  -4.2927  -2.6602  -1.5163
 REY  HN41  H  HNT3   0   0.476  -5.2183  -3.9715   0.2242
 REY  HN42  H  HNT3   0   0.468  -6.5239  -2.9918   0.3839
 REY  HN43  H  HNT3   0   0.483  -6.3341  -3.9027  -0.9756

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
 REY  C1   C2    single  1.524  0.020  1.524
 REY  C1   C3    single  1.522  0.020  1.522
 REY  C1   HC11  single  0.970  0.020  1.090
 REY  C1   HC12  single  0.970  0.020  1.090
 REY  C2   C4    single  1.525  0.020  1.525
 REY  C2   HC21  single  0.970  0.020  1.090
 REY  C2   HC22  single  0.970  0.020  1.090
 REY  C3   C5    single  1.513  0.020  1.513
 REY  C3   HC31  single  0.970  0.020  1.090
 REY  C3   HC32  single  0.970  0.020  1.090
 REY  C4   C9    single  1.526  0.020  1.526
 REY  C4   HC41  single  0.970  0.020  1.090
 REY  C4   HC42  single  0.970  0.020  1.090
 REY  C5   N1    single  1.346  0.020  1.346
 REY  C5   O1    double  1.223  0.020  1.223
 REY  N1   C6    single  1.440  0.020  1.440
 REY  N1   HN1   single  0.860  0.020  1.020
 REY  C6   C7    single  1.515  0.020  1.515
 REY  C6   C8    single  1.532  0.020  1.532
 REY  C6   HC6   single  0.970  0.020  1.090
 REY  C7   O2    single  1.323  0.020  1.323
 REY  C7   O6    double  1.205  0.020  1.205
 REY  C8   HC81  single  0.970  0.020  1.090
 REY  C8   HC82  single  0.970  0.020  1.090
 REY  C8   HC83  single  0.970  0.020  1.090
 REY  O2   HO2   single  0.850  0.020  0.980
 REY  C9   N3    single  1.448  0.020  1.448
 REY  C9   C10   single  1.554  0.020  1.554
 REY  C9   HC9   single  0.970  0.020  1.090
 REY  N3   C11   single  1.330  0.020  1.330
 REY  N3   HN3   single  0.890  0.020  1.040
 REY  C10  O4    double  1.242  0.020  1.242
 REY  C10  O5    single  1.246  0.020  1.246
 REY  C11  C12   single  1.520  0.020  1.520
 REY  C11  O3    double  1.222  0.020  1.222
 REY  C12  N4    single  1.474  0.020  1.474
 REY  C12  H121  single  0.970  0.020  1.090
 REY  C12  H122  single  0.970  0.020  1.090
 REY  N4   HN41  single  0.890  0.020  1.040
 REY  N4   HN42  single  0.890  0.020  1.040
 REY  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
 REY  HC12  C1   HC11  106.46  3.000
 REY  HC12  C1   C3    109.68  3.000
 REY  HC11  C1   C3    109.74  3.000
 REY  HC12  C1   C2    109.66  3.000
 REY  HC11  C1   C2    109.14  3.000
 REY  C3    C1   C2    112.00  3.000
 REY  HC22  C2   HC21  106.17  3.000
 REY  HC22  C2   C4    109.36  3.000
 REY  HC21  C2   C4    110.30  3.000
 REY  HC22  C2   C1    109.51  3.000
 REY  HC21  C2   C1    109.28  3.000
 REY  C4    C2   C1    112.05  3.000
 REY  HC32  C3   HC31  105.80  3.000
 REY  HC32  C3   C5    109.95  3.000
 REY  HC31  C3   C5    107.23  3.000
 REY  HC32  C3   C1    110.29  3.000
 REY  HC31  C3   C1    109.72  3.000
 REY  C5    C3   C1    113.52  3.000
 REY  HC42  C4   HC41  106.20  3.000
 REY  HC42  C4   C9    109.74  3.000
 REY  HC41  C4   C9    107.46  3.000
 REY  HC42  C4   C2    109.57  3.000
 REY  HC41  C4   C2    109.35  3.000
 REY  C9    C4   C2    114.19  3.000
 REY  O1    C5   N1    122.49  3.000
 REY  O1    C5   C3    122.79  3.000
 REY  N1    C5   C3    114.70  3.000
 REY  HN1   N1   C6    117.94  3.000
 REY  HN1   N1   C5    119.02  3.000
 REY  C6    N1   C5    122.83  3.000
 REY  HC6   C6   C8    108.56  3.000
 REY  HC6   C6   C7    107.70  3.000
 REY  C8    C6   C7    110.68  3.000
 REY  HC6   C6   N1    108.41  3.000
 REY  C8    C6   N1    112.43  3.000
 REY  C7    C6   N1    108.92  3.000
 REY  O6    C7   O2    123.95  3.000
 REY  O6    C7   C6    124.67  3.000
 REY  O2    C7   C6    111.37  3.000
 REY  HC83  C8   HC82  108.34  3.000
 REY  HC83  C8   HC81  107.92  3.000
 REY  HC82  C8   HC81  108.66  3.000
 REY  HC83  C8   C6    109.26  3.000
 REY  HC82  C8   C6    111.03  3.000
 REY  HC81  C8   C6    111.53  3.000
 REY  HO2   O2   C7    110.25  3.000
 REY  HC9   C9   C10   107.75  3.000
 REY  HC9   C9   N3    107.55  3.000
 REY  C10   C9   N3    112.00  3.000
 REY  HC9   C9   C4    107.99  3.000
 REY  C10   C9   C4    111.44  3.000
 REY  N3    C9   C4    109.92  3.000
 REY  HN3   N3   C11   117.65  3.000
 REY  HN3   N3   C9    117.16  3.000
 REY  C11   N3   C9    121.98  3.000
 REY  O5    C10  O4    127.58  3.000
 REY  O5    C10  C9    114.77  3.000
 REY  O4    C10  C9    117.66  3.000
 REY  O3    C11  C12   120.13  3.000
 REY  O3    C11  N3    125.36  3.000
 REY  C12   C11  N3    114.51  3.000
 REY  H122  C12  H121  108.56  3.000
 REY  H122  C12  N4    108.30  3.000
 REY  H121  C12  N4    107.87  3.000
 REY  H122  C12  C11   112.78  3.000
 REY  H121  C12  C11   109.84  3.000
 REY  N4    C12  C11   109.36  3.000
 REY  HN43  N4   HN42  107.73  3.000
 REY  HN43  N4   HN41  107.12  3.000
 REY  HN42  N4   HN41  106.98  3.000
 REY  HN43  N4   C12   111.37  3.000
 REY  HN42  N4   C12   111.30  3.000
 REY  HN41  N4   C12   112.08  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
 REY  CONST_01  C6    N1   C5   C3    180.00   0.0  0
 REY  CONST_02  C6    N1   C5   O1      0.00   0.0  0
 REY  CONST_03  C12   C11  N3   C9    180.00   0.0  0
 REY  CONST_04  O3    C11  N3   C9      0.00   0.0  0
 REY  CONST_05  HN1   N1   C5   C3      0.00   0.0  0
 REY  CONST_06  HN3   N3   C11  C12     0.00   0.0  0
 REY  CONST_07  HO2   O2   C7   C6    180.00   0.0  0
 REY  Var_01    C9    C4   C2   C1   -172.04  30.0  3
 REY  Var_02    N1    C5   C3   C1    154.41  30.0  3
 REY  Var_03    C5    C3   C1   C2   -179.38  30.0  3
 REY  Var_04    C4    C2   C1   C3   -178.02  30.0  3
 REY  Var_05    N4    C12  C11  N3    163.35  30.0  3
 REY  Var_06    HN41  N4   C12  C11   -70.84  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
 REY  chir_01  C6  N1  C7  C8   negativ
 REY  chir_02  C9  C4  N3  C10  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
 REY  plan-1  C3   0.020
 REY  plan-1  C5   0.020
 REY  plan-1  N1   0.020
 REY  plan-1  O1   0.020
 REY  plan-1  C6   0.020
 REY  plan-1  HN1  0.020
 REY  plan-2  C9   0.020
 REY  plan-2  N3   0.020
 REY  plan-2  C11  0.020
 REY  plan-2  C12  0.020
 REY  plan-2  O3   0.020
 REY  plan-2  HN3  0.020
 REY  plan-3  C6   0.020
 REY  plan-3  C7   0.020
 REY  plan-3  O2   0.020
 REY  plan-3  O6   0.020
 REY  plan-3  HO2  0.020
 REY  plan-4  C9   0.020
 REY  plan-4  C10  0.020
 REY  plan-4  O4   0.020
 REY  plan-4  O5   0.020

