# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:07:07 2022
#   Inital geometry file: a 134 line input string
#   Ligand name: (2R,4S)-5-([1,1'-biphenyl]-4-yl)-4-[(3-carboxypropanoyl)amino]-2-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C[C@@H](Cc1ccc(cc1)c2ccccc2)NC(=O)CCC(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
 6LD  6LD  '(2R,4S)-5-([1,1'-biphenyl]-4-yl)-4-[(3-carboxypropanoyl)amino]-2-methylpentanoic acid'  ligand  51  28  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6LD
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
 6LD  C1   C  CR6    0   0.072  -2.9963   0.8423  -0.2229
 6LD  C2   C  CR6    0   0.090  -4.4083   0.4855   0.0219
 6LD  C3   C  CR16   0  -0.299  -2.3209   1.7284   0.6184
 6LD  C11  C  CR6    0   0.150  -0.2964   1.5236  -0.6908
 6LD  C12  C  CR16   0  -0.269  -7.0885  -0.1975   0.4870
 6LD  C13  C  CH2    0  -0.531   1.1543   1.8441  -0.8968
 6LD  C14  C  CH1    0  -0.071   2.0779   0.9203  -0.0830
 6LD  C16  C  CH2    0  -0.399   3.5587   1.2020  -0.3425
 6LD  C18  C  CH1    0  -0.405   4.0102   2.6315  -0.0514
 6LD  C19  C  CH2    0  -0.573   0.6805  -2.6054  -0.2457
 6LD  C21  C  C      0   0.437   5.5084   2.8592  -0.3793
 6LD  C22  C  CH3    0  -0.662   3.6979   3.0557   1.3821
 6LD  C23  C  CH2    0  -0.584   0.7130  -3.7682   0.7320
 6LD  C26  C  C      0   0.417   0.2124  -5.1082   0.1634
 6LD  C4   C  CR16   0  -0.297  -2.2963   0.3076  -1.3046
 6LD  C5   C  CR16   0  -0.314  -5.2938   0.2918  -1.0407
 6LD  C6   C  CR16   0  -0.313  -4.8933   0.3304   1.3225
 6LD  C7   C  CR16   0  -0.281  -0.9960   2.0589   0.3873
 6LD  C8   C  CR16   0  -0.295  -0.9715   0.6454  -1.5335
 6LD  C9   C  CR16   0  -0.240  -6.6192  -0.0474  -0.8114
 6LD  C10  C  CR16   0  -0.240  -6.2190  -0.0065   1.5530
 6LD  N15  N  NH1    0  -0.639   1.7883  -0.4660  -0.3880
 6LD  O20  O  O      0  -0.504   0.6856  -0.9769   1.5171
 6LD  O24  O  OC    -1  -0.619   5.9917   3.9528  -0.0196
 6LD  O25  O  O      0  -0.604   6.1156   1.9584  -0.9918
 6LD  O27  O  OC    -1  -0.631   0.3235  -6.0934   0.9227
 6LD  O28  O  O      0  -0.608  -0.2663  -5.1122  -0.9876
 6LD  H1   H  HCR6   0   0.247  -2.8406   2.1829   1.4529
 6LD  H2   H  HCR6   0   0.256  -8.1229  -0.4598   0.6673
 6LD  H3   H  HCH2   0   0.241   1.4167   1.7627  -1.9565
 6LD  H4   H  HCH2   0   0.254   1.3457   2.8795  -0.6072
 6LD  H5   H  HCH1   0   0.247   1.8552   1.0522   0.9763
 6LD  H6   H  HCH2   0   0.219   4.1434   0.5052   0.2657
 6LD  H7   H  HCH2   0   0.213   3.7802   0.9575  -1.3857
 6LD  H8   H  HCH1   0   0.225   3.4627   3.3110  -0.7187
 6LD  H9   H  HCH2   0   0.254  -0.3317  -2.4893  -0.6466
 6LD  H10  H  HCH2   0   0.236   1.3193  -2.8111  -1.1074
 6LD  H11  H  HCH3   0   0.211   4.1921   2.4011   2.1047
 6LD  H12  H  HCH3   0   0.228   4.0407   4.0715   1.5660
 6LD  H13  H  HCH3   0   0.213   2.6281   3.0305   1.5984
 6LD  H14  H  HCH2   0   0.227   1.7307  -3.9120   1.1093
 6LD  H15  H  HCH2   0   0.232   0.1123  -3.5249   1.6131
 6LD  H16  H  HCR6   0   0.248  -2.7830  -0.3961  -1.9690
 6LD  H17  H  HCR6   0   0.252  -4.9500   0.4262  -2.0587
 6LD  H18  H  HCR6   0   0.252  -4.2241   0.4540   2.1649
 6LD  H19  H  HCR6   0   0.241  -0.4987   2.7533   1.0557
 6LD  H20  H  HCR6   0   0.243  -0.4539   0.2109  -2.3804
 6LD  H21  H  HCR6   0   0.256  -7.2886  -0.1868  -1.6505
 6LD  H22  H  HCR6   0   0.256  -6.5709  -0.1284   2.5694
 6LD  H23  H  HNH1   0   0.385   2.0284  -0.7879  -1.3130
 6LD  C17  C  C      0   0.570   1.0492  -1.2819   0.3886

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
 6LD  C9   C12  aromatic  1.389  0.020  1.389
 6LD  C9   C5   aromatic  1.387  0.020  1.387
 6LD  C12  C10  aromatic  1.389  0.020  1.389
 6LD  C5   C2   aromatic  1.397  0.020  1.397
 6LD  C10  C6   aromatic  1.387  0.020  1.387
 6LD  C2   C6   aromatic  1.397  0.020  1.397
 6LD  C2   C1   single    1.477  0.020  1.477
 6LD  C1   C4   aromatic  1.395  0.020  1.395
 6LD  C1   C3   aromatic  1.396  0.020  1.396
 6LD  C4   C8   aromatic  1.386  0.020  1.386
 6LD  C3   C7   aromatic  1.385  0.020  1.385
 6LD  C8   C11  aromatic  1.392  0.020  1.392
 6LD  C7   C11  aromatic  1.392  0.020  1.392
 6LD  C11  C13  single    1.500  0.020  1.500
 6LD  C13  C14  single    1.539  0.020  1.539
 6LD  C14  N15  single    1.449  0.020  1.449
 6LD  C14  C16  single    1.529  0.020  1.529
 6LD  O20  C17  double    1.224  0.020  1.224
 6LD  N15  C17  single    1.347  0.020  1.347
 6LD  C16  C18  single    1.527  0.020  1.527
 6LD  C17  C19  single    1.513  0.020  1.513
 6LD  O25  C21  deloc     1.247  0.020  1.247
 6LD  C19  C23  single    1.520  0.020  1.520
 6LD  C21  C18  single    1.550  0.020  1.550
 6LD  C21  O24  deloc     1.249  0.020  1.249
 6LD  C18  C22  single    1.527  0.020  1.527
 6LD  C23  C26  single    1.539  0.020  1.539
 6LD  C26  O28  deloc     1.247  0.020  1.247
 6LD  C26  O27  deloc     1.249  0.020  1.249
 6LD  C3   H1   single    0.930  0.020  1.080
 6LD  C12  H2   single    0.930  0.020  1.080
 6LD  C13  H3   single    0.970  0.020  1.090
 6LD  C13  H4   single    0.970  0.020  1.090
 6LD  C14  H5   single    0.970  0.020  1.090
 6LD  C16  H6   single    0.970  0.020  1.090
 6LD  C16  H7   single    0.970  0.020  1.090
 6LD  C18  H8   single    0.970  0.020  1.090
 6LD  C19  H9   single    0.970  0.020  1.090
 6LD  C19  H10  single    0.970  0.020  1.090
 6LD  C22  H11  single    0.970  0.020  1.090
 6LD  C22  H12  single    0.970  0.020  1.090
 6LD  C22  H13  single    0.970  0.020  1.090
 6LD  C23  H14  single    0.970  0.020  1.090
 6LD  C23  H15  single    0.970  0.020  1.090
 6LD  C4   H16  single    0.930  0.020  1.080
 6LD  C5   H17  single    0.930  0.020  1.080
 6LD  C6   H18  single    0.930  0.020  1.080
 6LD  C7   H19  single    0.930  0.020  1.080
 6LD  C8   H20  single    0.930  0.020  1.080
 6LD  C9   H21  single    0.930  0.020  1.080
 6LD  C10  H22  single    0.930  0.020  1.080
 6LD  N15  H23  single    0.860  0.020  1.020

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
 6LD  C4   C1   C3   117.89  3.000
 6LD  C3   C1   C2   121.07  3.000
 6LD  C4   C1   C2   121.04  3.000
 6LD  C6   C2   C5   118.22  3.000
 6LD  C6   C2   C1   120.87  3.000
 6LD  C5   C2   C1   120.90  3.000
 6LD  H1   C3   C7   119.18  3.000
 6LD  H1   C3   C1   119.90  3.000
 6LD  C7   C3   C1   120.91  3.000
 6LD  C8   C11  C7   117.89  3.000
 6LD  C7   C11  C13  120.68  3.000
 6LD  C8   C11  C13  121.39  3.000
 6LD  H2   C12  C10  120.26  3.000
 6LD  H2   C12  C9   120.32  3.000
 6LD  C10  C12  C9   119.42  3.000
 6LD  H4   C13  H3   106.56  3.000
 6LD  H4   C13  C14  108.89  3.000
 6LD  H3   C13  C14  108.86  3.000
 6LD  H4   C13  C11  109.61  3.000
 6LD  H3   C13  C11  110.42  3.000
 6LD  C14  C13  C11  112.31  3.000
 6LD  H5   C14  N15  106.23  3.000
 6LD  H5   C14  C16  109.89  3.000
 6LD  N15  C14  C16  109.52  3.000
 6LD  H5   C14  C13  108.57  3.000
 6LD  C16  C14  C13  112.38  3.000
 6LD  N15  C14  C13  110.06  3.000
 6LD  H7   C16  H6   106.22  3.000
 6LD  H7   C16  C18  109.33  3.000
 6LD  H6   C16  C18  109.39  3.000
 6LD  H7   C16  C14  108.46  3.000
 6LD  H6   C16  C14  107.81  3.000
 6LD  C18  C16  C14  115.23  3.000
 6LD  H8   C18  C22  107.25  3.000
 6LD  H8   C18  C21  105.20  3.000
 6LD  C22  C18  C21  110.82  3.000
 6LD  H8   C18  C16  108.41  3.000
 6LD  C22  C18  C16  112.24  3.000
 6LD  C21  C18  C16  112.51  3.000
 6LD  H10  C19  H9   105.77  3.000
 6LD  H10  C19  C23  110.55  3.000
 6LD  H9   C19  C23  109.66  3.000
 6LD  H10  C19  C17  110.67  3.000
 6LD  H9   C19  C17  106.62  3.000
 6LD  C23  C19  C17  113.22  3.000
 6LD  O25  C21  O24  125.85  3.000
 6LD  O24  C21  C18  116.21  3.000
 6LD  O25  C21  C18  117.92  3.000
 6LD  H13  C22  H12  107.27  3.000
 6LD  H13  C22  H11  107.35  3.000
 6LD  H12  C22  H11  107.76  3.000
 6LD  H13  C22  C18  112.33  3.000
 6LD  H12  C22  C18  110.71  3.000
 6LD  H11  C22  C18  111.21  3.000
 6LD  H15  C23  H14  105.20  3.000
 6LD  H15  C23  C26  108.21  3.000
 6LD  H14  C23  C26  108.37  3.000
 6LD  H15  C23  C19  109.66  3.000
 6LD  H14  C23  C19  110.01  3.000
 6LD  C26  C23  C19  114.93  3.000
 6LD  O28  C26  O27  126.37  3.000
 6LD  O27  C26  C23  115.67  3.000
 6LD  O28  C26  C23  117.95  3.000
 6LD  H16  C4   C8   119.10  3.000
 6LD  H16  C4   C1   119.94  3.000
 6LD  C8   C4   C1   120.95  3.000
 6LD  H17  C5   C9   119.28  3.000
 6LD  H17  C5   C2   119.79  3.000
 6LD  C9   C5   C2   120.93  3.000
 6LD  H18  C6   C10  119.27  3.000
 6LD  H18  C6   C2   119.81  3.000
 6LD  C10  C6   C2   120.90  3.000
 6LD  H19  C7   C11  119.54  3.000
 6LD  H19  C7   C3   119.24  3.000
 6LD  C11  C7   C3   121.21  3.000
 6LD  H20  C8   C4   119.20  3.000
 6LD  H20  C8   C11  119.64  3.000
 6LD  C4   C8   C11  121.15  3.000
 6LD  H21  C9   C5   119.62  3.000
 6LD  H21  C9   C12  120.12  3.000
 6LD  C5   C9   C12  120.25  3.000
 6LD  H22  C10  C6   119.61  3.000
 6LD  H22  C10  C12  120.11  3.000
 6LD  C6   C10  C12  120.27  3.000
 6LD  H23  N15  C17  117.78  3.000
 6LD  H23  N15  C14  116.81  3.000
 6LD  C17  N15  C14  124.60  3.000
 6LD  O20  C17  N15  122.91  3.000
 6LD  N15  C17  C19  114.94  3.000
 6LD  O20  C17  C19  122.14  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
 6LD  CONST_01  C9   C5   C2   C1   180.00   0.0  0
 6LD  CONST_02  C10  C6   C2   C1   180.00   0.0  0
 6LD  CONST_03  C11  C8   C4   C1     0.00   0.0  0
 6LD  CONST_04  C11  C7   C3   C1     0.00   0.0  0
 6LD  CONST_05  C12  C9   C5   C2     0.00   0.0  0
 6LD  CONST_06  C12  C10  C6   C2     0.00   0.0  0
 6LD  CONST_07  C8   C4   C1   C2   180.00   0.0  0
 6LD  CONST_08  C7   C3   C1   C2   180.00   0.0  0
 6LD  CONST_11  C8   C4   C1   C3     0.00   0.0  0
 6LD  CONST_12  C8   C11  C7   C3     0.00   0.0  0
 6LD  CONST_15  C7   C3   C1   C4     0.00   0.0  0
 6LD  CONST_16  C7   C11  C8   C4     0.00   0.0  0
 6LD  CONST_17  C10  C12  C9   C5     0.00   0.0  0
 6LD  CONST_18  C10  C6   C2   C5     0.00   0.0  0
 6LD  CONST_19  C9   C12  C10  C6     0.00   0.0  0
 6LD  CONST_20  C9   C5   C2   C6     0.00   0.0  0
 6LD  CONST_21  C13  C11  C7   C3   180.00   0.0  0
 6LD  CONST_22  C4   C8   C11  C13  180.00   0.0  0
 6LD  CONST_23  H17  C5   C2   C1     0.00   0.0  0
 6LD  CONST_24  H18  C6   C2   C1     0.00   0.0  0
 6LD  CONST_25  H20  C8   C4   C1   180.00   0.0  0
 6LD  CONST_26  H19  C7   C3   C1   180.00   0.0  0
 6LD  CONST_27  H21  C9   C5   C2   180.00   0.0  0
 6LD  CONST_28  H22  C10  C6   C2   180.00   0.0  0
 6LD  CONST_29  H16  C4   C1   C2     0.00   0.0  0
 6LD  CONST_30  H1   C3   C1   C2     0.00   0.0  0
 6LD  CONST_31  H2   C12  C9   C5   180.00   0.0  0
 6LD  CONST_32  O20  C17  N15  C14    0.00   0.0  0
 6LD  CONST_33  C19  C17  N15  C14  180.00   0.0  0
 6LD  CONST_34  H23  N15  C17  C19    0.00   0.0  0
 6LD  Var_01    C8   C11  C13  C14  -92.52  30.0  2
 6LD  Var_02    C26  C23  C19  C17  174.29  30.0  3
 6LD  Var_03    O28  C26  C23  C19   -5.45  30.0  3
 6LD  Var_04    O20  C17  C19  C23  -38.87  30.0  1

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
 6LD  chir_01  C14  C13  N15  C16  negativ
 6LD  chir_02  C18  C22  C21  C16  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
 6LD  plan-1  C1   0.020
 6LD  plan-1  C2   0.020
 6LD  plan-1  C3   0.020
 6LD  plan-1  C11  0.020
 6LD  plan-1  C13  0.020
 6LD  plan-1  C4   0.020
 6LD  plan-1  C7   0.020
 6LD  plan-1  C8   0.020
 6LD  plan-1  H1   0.020
 6LD  plan-1  H16  0.020
 6LD  plan-1  H19  0.020
 6LD  plan-1  H20  0.020
 6LD  plan-2  C1   0.020
 6LD  plan-2  C2   0.020
 6LD  plan-2  C12  0.020
 6LD  plan-2  C5   0.020
 6LD  plan-2  C6   0.020
 6LD  plan-2  C9   0.020
 6LD  plan-2  C10  0.020
 6LD  plan-2  H2   0.020
 6LD  plan-2  H17  0.020
 6LD  plan-2  H18  0.020
 6LD  plan-2  H21  0.020
 6LD  plan-2  H22  0.020
 6LD  plan-3  C14  0.020
 6LD  plan-3  C19  0.020
 6LD  plan-3  N15  0.020
 6LD  plan-3  O20  0.020
 6LD  plan-3  H23  0.020
 6LD  plan-3  C17  0.020
 6LD  plan-4  C18  0.020
 6LD  plan-4  C21  0.020
 6LD  plan-4  O24  0.020
 6LD  plan-4  O25  0.020
 6LD  plan-5  C23  0.020
 6LD  plan-5  C26  0.020
 6LD  plan-5  O27  0.020
 6LD  plan-5  O28  0.020

