# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:46:59 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: (2S)-7-amino-2-{[(R)-hydroxy{(1R)-2-methyl-1-[(3-phenylpropanoyl)amino]propyl}phosphoryl]methyl}heptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)CCc1ccccc1)[P](O)(=O)C[C@@H](CCCCCN)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
 EF1  EF1  '(2S)-7-amino-2-{[(R)-hydroxy{(1R)-2-methyl-1-[(3-phenylpropanoyl)amino]propyl}phosphoryl]methyl}heptanoic acid'  ligand  64  29  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EF1
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
 EF1  O23  O  O     0  -0.445   -3.6020  -1.9348   1.5154
 EF1  C21  C  C     0   0.541   -3.3212  -0.7604   1.5294
 EF1  O22  O  OH1   0  -0.582   -3.3785  -0.0103   2.6190
 EF1  C20  C  CH1   0  -0.356   -2.9096   0.0170   0.2976
 EF1  C24  C  CH2   0  -0.412   -4.1452   0.2351  -0.5902
 EF1  C25  C  CH2   0  -0.428   -5.2663   1.0227   0.0768
 EF1  C26  C  CH2   0  -0.419   -6.4430   1.2610  -0.8609
 EF1  C27  C  CH2   0  -0.427   -7.5748   2.0380  -0.2011
 EF1  C28  C  CH2   0  -0.273   -8.7627   2.2476  -1.1265
 EF1  N29  N  NH2   0  -0.800   -9.8195   2.9966  -0.4600
 EF1  C17  C  CH2   0  -0.745   -1.8365  -0.7469  -0.4818
 EF1  P13  P  P     0   1.240   -0.2453  -0.8399   0.3901
 EF1  O18  O  O     0  -0.697    0.2844   0.5039   0.7567
 EF1  O19  O  OH1   0  -0.754   -0.4755  -1.6892   1.7524
 EF1  C12  C  CH1   0  -0.314    0.9457  -1.8107  -0.6542
 EF1  C14  C  CH1   0  -0.272    0.8646  -3.3427  -0.5523
 EF1  C16  C  CH3   0  -0.674   -0.5182  -3.8813  -0.9096
 EF1  C15  C  CH3   0  -0.646    1.9080  -3.9795  -1.4683
 EF1  N10  N  NH1   0  -0.637    2.2657  -1.3439  -0.3143
 EF1  C9   C  C     0   0.585    2.8346  -0.2600  -0.8837
 EF1  O11  O  O     0  -0.492    2.3477   0.3128  -1.8449
 EF1  C8   C  CH2   0  -0.587    4.1267   0.1791  -0.2312
 EF1  C7   C  CH2   0  -0.505    5.0086   1.0246  -1.1449
 EF1  C1   C  CR6   0   0.127    6.2773   1.4284  -0.4454
 EF1  C6   C  CR16  0  -0.307    6.3167   2.5678   0.3559
 EF1  C2   C  CR16  0  -0.311    7.4284   0.6510  -0.5495
 EF1  C3   C  CR16  0  -0.240    8.5900   1.0019   0.1265
 EF1  C4   C  CR16  0  -0.273    8.6165   2.1391   0.9230
 EF1  C5   C  CR16  0  -0.240    7.4746   2.9225   1.0349
 EF1  H1   H  HOH1  0   0.481   -3.6803  -0.5406   3.3728
 EF1  H2   H  HCH1  0   0.280   -2.5188   0.9920   0.5973
 EF1  H3   H  HCH2  0   0.245   -3.8162   0.7662  -1.4876
 EF1  H4   H  HCH2  0   0.233   -4.5198  -0.7366  -0.9261
 EF1  H5   H  HCH2  0   0.222   -5.6274   0.4922   0.9638
 EF1  H6   H  HCH2  0   0.222   -4.8776   1.9830   0.4307
 EF1  H7   H  HCH2  0   0.214   -6.1004   1.8009  -1.7502
 EF1  H8   H  HCH2  0   0.213   -6.8209   0.2966  -1.2173
 EF1  H9   H  HCH2  0   0.211   -7.9042   1.5014   0.6963
 EF1  H10  H  HCH2  0   0.214   -7.2080   3.0115   0.1387
 EF1  H11  H  HCH2  0   0.211   -8.4377   2.8190  -2.0009
 EF1  H12  H  HCH2  0   0.186   -9.0926   1.2693  -1.5066
 EF1  H13  H  HNH2  0   0.345  -10.5878   3.1392  -1.1031
 EF1  H15  H  HNH2  0   0.336  -10.1987   2.4332   0.2916
 EF1  H16  H  HCH2  0   0.295   -2.2001  -1.7346  -0.7673
 EF1  H17  H  HCH2  0   0.303   -1.6260  -0.2179  -1.4157
 EF1  H18  H  HOH1  0   0.487   -0.9176  -2.5441   1.6740
 EF1  H19  H  HCH1  0   0.291    0.7421  -1.5189  -1.6895
 EF1  H20  H  HCH1  0   0.244    1.0964  -3.6338   0.4785
 EF1  H21  H  HCH3  0   0.257   -0.4959  -4.9706  -0.9332
 EF1  H22  H  HCH3  0   0.212   -1.2985  -3.6099  -0.1972
 EF1  H23  H  HCH3  0   0.236   -0.8331  -3.5371  -1.8968
 EF1  H24  H  HCH3  0   0.238    2.9220  -3.6753  -1.2136
 EF1  H25  H  HCH3  0   0.237    1.8585  -5.0663  -1.3919
 EF1  H26  H  HCH3  0   0.224    1.7272  -3.7097  -2.5112
 EF1  H27  H  HNH1  0   0.404    2.6933  -1.7249   0.5164
 EF1  H28  H  HCH2  0   0.282    3.8614   0.7511   0.6646
 EF1  H29  H  HCH2  0   0.267    4.6790  -0.6943   0.1258
 EF1  H30  H  HCH2  0   0.250    5.2500   0.4590  -2.0473
 EF1  H31  H  HCH2  0   0.252    4.4612   1.9125  -1.4653
 EF1  H32  H  HCR6  0   0.247    5.4309   3.1861   0.4464
 EF1  H33  H  HCR6  0   0.246    7.4193  -0.2369  -1.1715
 EF1  H34  H  HCR6  0   0.253    9.4759   0.3875   0.0279
 EF1  H35  H  HCR6  0   0.253    9.5205   2.4144   1.4509
 EF1  H36  H  HCR6  0   0.253    7.4860   3.8136   1.6498

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
 EF1  C27  C28  single    1.520  0.020  1.520
 EF1  C27  C26  single    1.523  0.020  1.523
 EF1  C28  N29  single    1.457  0.020  1.457
 EF1  C26  C25  single    1.523  0.020  1.523
 EF1  C24  C25  single    1.524  0.020  1.524
 EF1  C24  C20  single    1.537  0.020  1.537
 EF1  C16  C14  single    1.526  0.020  1.526
 EF1  C17  C20  single    1.531  0.020  1.531
 EF1  C17  P13  single    1.817  0.020  1.817
 EF1  C20  C21  single    1.514  0.020  1.514
 EF1  O18  P13  double    1.490  0.020  1.490
 EF1  C14  C15  single    1.528  0.020  1.528
 EF1  C14  C12  single    1.538  0.020  1.538
 EF1  P13  C12  single    1.858  0.020  1.858
 EF1  P13  O19  single    1.622  0.020  1.622
 EF1  C21  O23  double    1.208  0.020  1.208
 EF1  C21  O22  single    1.324  0.020  1.324
 EF1  C5   C4   aromatic  1.389  0.020  1.389
 EF1  C5   C6   aromatic  1.388  0.020  1.388
 EF1  C4   C3   aromatic  1.389  0.020  1.389
 EF1  C12  N10  single    1.441  0.020  1.441
 EF1  N10  C9   single    1.350  0.020  1.350
 EF1  C6   C1   aromatic  1.393  0.020  1.393
 EF1  C3   C2   aromatic  1.389  0.020  1.389
 EF1  C9   C8   single    1.513  0.020  1.513
 EF1  C9   O11  double    1.220  0.020  1.220
 EF1  C1   C2   aromatic  1.393  0.020  1.393
 EF1  C1   C7   single    1.504  0.020  1.504
 EF1  C8   C7   single    1.526  0.020  1.526
 EF1  O22  H1   single    0.850  0.020  0.980
 EF1  C20  H2   single    0.970  0.020  1.090
 EF1  C24  H3   single    0.970  0.020  1.090
 EF1  C24  H4   single    0.970  0.020  1.090
 EF1  C25  H5   single    0.970  0.020  1.090
 EF1  C25  H6   single    0.970  0.020  1.090
 EF1  C26  H7   single    0.970  0.020  1.090
 EF1  C26  H8   single    0.970  0.020  1.090
 EF1  C27  H9   single    0.970  0.020  1.090
 EF1  C27  H10  single    0.970  0.020  1.090
 EF1  C28  H11  single    0.970  0.020  1.090
 EF1  C28  H12  single    0.970  0.020  1.090
 EF1  N29  H13  single    0.890  0.020  1.040
 EF1  N29  H15  single    0.890  0.020  1.040
 EF1  C17  H16  single    0.970  0.020  1.090
 EF1  C17  H17  single    0.970  0.020  1.090
 EF1  O19  H18  single    0.850  0.020  0.980
 EF1  C12  H19  single    0.970  0.020  1.090
 EF1  C14  H20  single    0.970  0.020  1.090
 EF1  C16  H21  single    0.970  0.020  1.090
 EF1  C16  H22  single    0.970  0.020  1.090
 EF1  C16  H23  single    0.970  0.020  1.090
 EF1  C15  H24  single    0.970  0.020  1.090
 EF1  C15  H25  single    0.970  0.020  1.090
 EF1  C15  H26  single    0.970  0.020  1.090
 EF1  N10  H27  single    0.860  0.020  1.020
 EF1  C8   H28  single    0.970  0.020  1.090
 EF1  C8   H29  single    0.970  0.020  1.090
 EF1  C7   H30  single    0.970  0.020  1.090
 EF1  C7   H31  single    0.970  0.020  1.090
 EF1  C6   H32  single    0.930  0.020  1.080
 EF1  C2   H33  single    0.930  0.020  1.080
 EF1  C3   H34  single    0.930  0.020  1.080
 EF1  C4   H35  single    0.930  0.020  1.080
 EF1  C5   H36  single    0.930  0.020  1.080

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
 EF1  C20  C21  O22  112.99  3.000
 EF1  O22  C21  O23  123.40  3.000
 EF1  C20  C21  O23  123.59  3.000
 EF1  H1   O22  C21  110.08  3.000
 EF1  H2   C20  C17  109.54  3.000
 EF1  H2   C20  C24  108.63  3.000
 EF1  C17  C20  C24  109.89  3.000
 EF1  H2   C20  C21  109.42  3.000
 EF1  C17  C20  C21  110.41  3.000
 EF1  C24  C20  C21  108.92  3.000
 EF1  H4   C24  H3   106.40  3.000
 EF1  H4   C24  C25  109.96  3.000
 EF1  H3   C24  C25  109.24  3.000
 EF1  H4   C24  C20  109.06  3.000
 EF1  H3   C24  C20  107.52  3.000
 EF1  C25  C24  C20  114.33  3.000
 EF1  H6   C25  H5   106.27  3.000
 EF1  H6   C25  C26  109.63  3.000
 EF1  H5   C25  C26  108.65  3.000
 EF1  H6   C25  C24  109.49  3.000
 EF1  H5   C25  C24  110.30  3.000
 EF1  C26  C25  C24  112.32  3.000
 EF1  H8   C26  H7   106.12  3.000
 EF1  H8   C26  C27  109.49  3.000
 EF1  H7   C26  C27  109.43  3.000
 EF1  H8   C26  C25  109.21  3.000
 EF1  H7   C26  C25  109.59  3.000
 EF1  C27  C26  C25  112.78  3.000
 EF1  H10  C27  H9   106.38  3.000
 EF1  H10  C27  C28  109.16  3.000
 EF1  H9   C27  C28  109.33  3.000
 EF1  H10  C27  C26  109.83  3.000
 EF1  H9   C27  C26  109.16  3.000
 EF1  C28  C27  C26  112.78  3.000
 EF1  H12  C28  H11  106.10  3.000
 EF1  H12  C28  N29  113.44  3.000
 EF1  H11  C28  N29  108.23  3.000
 EF1  H12  C28  C27  108.78  3.000
 EF1  H11  C28  C27  109.05  3.000
 EF1  N29  C28  C27  111.05  3.000
 EF1  H15  N29  H13  105.40  3.000
 EF1  H15  N29  C28  108.97  3.000
 EF1  H13  N29  C28  109.42  3.000
 EF1  H17  C17  H16  106.18  3.000
 EF1  H17  C17  P13  105.43  3.000
 EF1  H16  C17  P13  111.79  3.000
 EF1  H17  C17  C20  109.17  3.000
 EF1  H16  C17  C20  110.59  3.000
 EF1  P13  C17  C20  113.28  3.000
 EF1  C12  P13  O19  106.82  3.000
 EF1  O19  P13  O18  108.42  3.000
 EF1  C12  P13  O18  112.43  3.000
 EF1  O19  P13  C17  107.80  3.000
 EF1  C12  P13  C17  108.57  3.000
 EF1  O18  P13  C17  112.54  3.000
 EF1  H18  O19  P13  117.41  3.000
 EF1  H19  C12  N10  107.89  3.000
 EF1  H19  C12  C14  108.57  3.000
 EF1  N10  C12  C14  110.83  3.000
 EF1  H19  C12  P13  105.84  3.000
 EF1  N10  C12  P13  106.58  3.000
 EF1  C14  C12  P13  116.72  3.000
 EF1  H20  C14  C15  107.99  3.000
 EF1  H20  C14  C16  108.55  3.000
 EF1  C15  C14  C16  109.35  3.000
 EF1  H20  C14  C12  108.41  3.000
 EF1  C15  C14  C12  109.85  3.000
 EF1  C16  C14  C12  112.57  3.000
 EF1  H23  C16  H22  107.80  3.000
 EF1  H23  C16  H21  107.54  3.000
 EF1  H22  C16  H21  106.11  3.000
 EF1  H23  C16  C14  111.20  3.000
 EF1  H22  C16  C14  114.03  3.000
 EF1  H21  C16  C14  109.83  3.000
 EF1  H26  C15  H25  107.79  3.000
 EF1  H26  C15  H24  107.97  3.000
 EF1  H25  C15  H24  107.72  3.000
 EF1  H26  C15  C14  110.88  3.000
 EF1  H25  C15  C14  110.02  3.000
 EF1  H24  C15  C14  112.29  3.000
 EF1  H27  N10  C9   118.15  3.000
 EF1  H27  N10  C12  117.40  3.000
 EF1  C9   N10  C12  123.14  3.000
 EF1  C8   C9   O11  122.98  3.000
 EF1  O11  C9   N10  122.74  3.000
 EF1  C8   C9   N10  114.27  3.000
 EF1  H29  C8   H28  105.82  3.000
 EF1  H29  C8   C7   110.26  3.000
 EF1  H28  C8   C7   109.90  3.000
 EF1  H29  C8   C9   109.90  3.000
 EF1  H28  C8   C9   107.30  3.000
 EF1  C7   C8   C9   113.35  3.000
 EF1  H31  C7   H30  106.84  3.000
 EF1  H31  C7   C1   109.95  3.000
 EF1  H30  C7   C1   109.69  3.000
 EF1  H31  C7   C8   109.69  3.000
 EF1  H30  C7   C8   109.61  3.000
 EF1  C1   C7   C8   110.97  3.000
 EF1  C2   C1   C6   118.42  3.000
 EF1  C2   C1   C7   120.83  3.000
 EF1  C6   C1   C7   120.72  3.000
 EF1  H32  C6   C5   119.66  3.000
 EF1  H32  C6   C1   119.42  3.000
 EF1  C5   C6   C1   120.92  3.000
 EF1  H33  C2   C3   119.55  3.000
 EF1  H33  C2   C1   119.54  3.000
 EF1  C3   C2   C1   120.91  3.000
 EF1  H34  C3   C4   120.09  3.000
 EF1  H34  C3   C2   119.78  3.000
 EF1  C4   C3   C2   120.13  3.000
 EF1  H35  C4   C5   120.24  3.000
 EF1  H35  C4   C3   120.26  3.000
 EF1  C5   C4   C3   119.49  3.000
 EF1  H36  C5   C4   120.08  3.000
 EF1  H36  C5   C6   119.79  3.000
 EF1  C4   C5   C6   120.13  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
 EF1  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 EF1  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 EF1  CONST_03  C3   C4   C5   C6      0.00   0.0  0
 EF1  CONST_04  C3   C2   C1   C6      0.00   0.0  0
 EF1  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 EF1  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 EF1  CONST_07  C5   C6   C1   C7    180.00   0.0  0
 EF1  CONST_08  C3   C2   C1   C7    180.00   0.0  0
 EF1  CONST_09  H36  C5   C6   C1    180.00   0.0  0
 EF1  CONST_10  H34  C3   C2   C1    180.00   0.0  0
 EF1  CONST_11  H35  C4   C5   C6    180.00   0.0  0
 EF1  CONST_12  H33  C2   C1   C6    180.00   0.0  0
 EF1  CONST_13  H32  C6   C1   C2    180.00   0.0  0
 EF1  CONST_14  C8   C9   N10  C12   180.00   0.0  0
 EF1  CONST_15  O11  C9   N10  C12     0.00   0.0  0
 EF1  CONST_16  H27  N10  C9   O11   180.00   0.0  0
 EF1  CONST_17  H1   O22  C21  O23     0.00   0.0  0
 EF1  Var_01    C6   C1   C7   C8    -85.88  30.0  2
 EF1  Var_02    C1   C7   C8   C9   -179.87  30.0  3
 EF1  Var_03    C26  C25  C24  C20   177.66  30.0  3
 EF1  Var_04    O18  P13  C17  C20   -55.74  30.0  3
 EF1  Var_05    C27  C26  C25  C24   179.54  30.0  1
 EF1  Var_06    C28  C27  C26  C25  -178.65  30.0  1
 EF1  Var_07    N29  C28  C27  C26  -179.83  30.0  3
 EF1  Var_08    C7   C8   C9   N10   158.40  30.0  3
 EF1  Var_09    H13  N29  C28  C27   178.78  30.0  3
 EF1  Var_10    H21  C16  C14  C12   173.61  30.0  3
 EF1  Var_11    H24  C15  C14  C12    59.56  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
 EF1  chir_01  C20  C24  C17  C21  positiv
 EF1  chir_03  C12  C14  P13  N10  negativ
 EF1  chir_04  P13  O18  C12  O19  both

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
 EF1  plan-1  C7   0.020
 EF1  plan-1  C1   0.020
 EF1  plan-1  C6   0.020
 EF1  plan-1  C2   0.020
 EF1  plan-1  C3   0.020
 EF1  plan-1  C4   0.020
 EF1  plan-1  C5   0.020
 EF1  plan-1  H32  0.020
 EF1  plan-1  H33  0.020
 EF1  plan-1  H34  0.020
 EF1  plan-1  H35  0.020
 EF1  plan-1  H36  0.020
 EF1  plan-2  C12  0.020
 EF1  plan-2  N10  0.020
 EF1  plan-2  C9   0.020
 EF1  plan-2  O11  0.020
 EF1  plan-2  C8   0.020
 EF1  plan-2  H27  0.020
 EF1  plan-3  O23  0.020
 EF1  plan-3  C21  0.020
 EF1  plan-3  O22  0.020
 EF1  plan-3  C20  0.020
 EF1  plan-3  H1   0.020

