# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 19:05:20 2021
#   Inital geometry file: a 151 line input string
#   Ligand name: (2S)-2-{[(R)-[(1R)-1-({N-[(benzyloxy)carbonyl]-L-alanyl}amino)ethyl](hydroxy)phosphoryl]oxy}-3-phenylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](C)[P@](O)(=O)O[C@@H](Cc2ccccc2)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
 ZAF  ZAF  '(2S)-2-{[(R)-[(1R)-1-({N-[(benzyloxy)carbonyl]-L-alanyl}amino)ethyl](hydroxy)phosphoryl]oxy}-3-phenylpropanoic acid'  ligand  60  33  .  2022-07-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ZAF
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
 ZAF  C1    C  C     0   0.544  44.4613  21.6944  33.9655
 ZAF  O1A   O  O     0  -0.412  43.4394  21.8192  33.3513
 ZAF  O1B   O  OH1   0  -0.577  45.1889  20.5897  33.8495
 ZAF  C2A   C  CH2   0  -0.549  46.1042  23.5967  34.0681
 ZAF  C2    C  CH1   0  -0.116  45.0452  22.8005  34.8365
 ZAF  CP1   C  CR6   0   0.110  45.5800  24.1519  32.7732
 ZAF  CP2   C  CR16  0  -0.302  44.7730  25.2869  32.7644
 ZAF  CP3   C  CR16  0  -0.239  44.2719  25.7896  31.5722
 ZAF  CP4   C  CR16  0  -0.267  44.5745  25.1623  30.3697
 ZAF  CP5   C  CR16  0  -0.240  45.3800  24.0320  30.3682
 ZAF  CP6   C  CR16  0  -0.299  45.8787  23.5316  31.5638
 ZAF  O3    O  O2    0  -0.612  45.6909  22.2466  35.9816
 ZAF  P3    P  P     0   1.399  44.7782  21.6922  37.1999
 ZAF  O3A   O  O     0  -0.683  43.5860  20.9347  36.7521
 ZAF  O3B   O  OH1   0  -0.736  44.4836  23.0431  38.0118
 ZAF  C4    C  CH1   0  -0.353  46.0134  20.7537  38.1552
 ZAF  C4A   C  CH3   0  -0.685  47.2521  21.5520  38.5336
 ZAF  N5    N  NH1   0  -0.647  46.3583  19.5785  37.3893
 ZAF  C6    C  C     0   0.566  45.7781  18.3770  37.5783
 ZAF  O6    O  O     0  -0.471  44.8955  18.1720  38.3892
 ZAF  C7    C  CH1   0  -0.192  46.2722  17.2823  36.6324
 ZAF  C7A   C  CH3   0  -0.687  45.2533  17.1027  35.5129
 ZAF  N8    N  NH1   0  -0.661  46.4298  16.0358  37.3402
 ZAF  C9    C  C     0   0.748  47.2277  15.8634  38.4112
 ZAF  O9    O  O     0  -0.519  47.3378  14.8298  39.0385
 ZAF  O10   O  O2    0  -0.473  47.8909  16.9866  38.6933
 ZAF  C11   C  CH2   0  -0.221  48.7801  16.9704  39.8115
 ZAF  C1X   C  CR6   0   0.073  49.3927  18.3349  39.9228
 ZAF  C2X   C  CR16  0  -0.274  50.1639  18.8508  38.8823
 ZAF  C3X   C  CR16  0  -0.241  50.7576  20.0979  38.9989
 ZAF  C4X   C  CR16  0  -0.263  50.5903  20.8452  40.1596
 ZAF  C5X   C  CR16  0  -0.243  49.8204  20.3413  41.1972
 ZAF  C6X   C  CR16  0  -0.303  49.2206  19.0930  41.0750
 ZAF  HOB1  H  HOH1  0   0.480  45.9766  20.6103  34.4101
 ZAF  H2A1  H  HCH2  0   0.291  46.4403  24.4055  34.7203
 ZAF  H2A2  H  HCH2  0   0.273  46.9703  22.9576  33.8802
 ZAF  H2    H  HCH1  0   0.294  44.2243  23.4627  35.1245
 ZAF  HP2   H  HCR6  0   0.253  44.5389  25.7854  33.6982
 ZAF  HP3   H  HCR6  0   0.257  43.6482  26.6741  31.5809
 ZAF  HP4   H  HCR6  0   0.257  44.1877  25.5555  29.4385
 ZAF  HP5   H  HCR6  0   0.257  45.6222  23.5390  29.4356
 ZAF  HP6   H  HCR6  0   0.253  46.5112  22.6514  31.5532
 ZAF  HOB3  H  HOH1  0   0.501  43.6752  23.0184  38.5422
 ZAF  H4    H  HCH1  0   0.308  45.5022  20.4310  39.0655
 ZAF  H4A1  H  HCH3  0   0.279  47.9103  20.9261  39.1339
 ZAF  H4A2  H  HCH3  0   0.243  47.8070  21.8859  37.6569
 ZAF  H4A3  H  HCH3  0   0.255  46.9856  22.4282  39.1211
 ZAF  HN5   H  HNH1  0   0.407  47.1679  19.6393  36.7914
 ZAF  H7    H  HCH1  0   0.271  47.2262  17.5797  36.1852
 ZAF  H7A1  H  HCH3  0   0.261  45.5970  16.3502  34.8036
 ZAF  H7A2  H  HCH3  0   0.247  44.2858  16.7942  35.9096
 ZAF  H7A3  H  HCH3  0   0.247  45.1156  18.0356  34.9693
 ZAF  HN8   H  HNH1  0   0.410  45.8462  15.2556  37.0829
 ZAF  H111  H  HCH2  0   0.251  48.2386  16.7163  40.7249
 ZAF  H112  H  HCH2  0   0.249  49.5526  16.2129  39.6579
 ZAF  HP2'  H  HCR6  0   0.252  50.3066  18.2726  37.9770
 ZAF  HP3'  H  HCR6  0   0.257  51.3548  20.4883  38.1851
 ZAF  HP4'  H  HCR6  0   0.258  51.0570  21.8173  40.2521
 ZAF  HP5'  H  HCR6  0   0.258  49.6807  20.9199  42.1012
 ZAF  HP6'  H  HCR6  0   0.255  48.6169  18.7062  41.8875

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
 ZAF  C1   O1A   double    1.199  0.020  1.199
 ZAF  C1   O1B   single    1.328  0.020  1.328
 ZAF  C1   C2    single    1.524  0.020  1.524
 ZAF  O1B  HOB1  single    0.850  0.020  0.980
 ZAF  C2A  C2    single    1.532  0.020  1.532
 ZAF  C2A  CP1   single    1.503  0.020  1.503
 ZAF  C2A  H2A1  single    0.970  0.020  1.090
 ZAF  C2A  H2A2  single    0.970  0.020  1.090
 ZAF  C2   O3    single    1.426  0.020  1.426
 ZAF  C2   H2    single    0.970  0.020  1.090
 ZAF  CP1  CP2   aromatic  1.393  0.020  1.393
 ZAF  CP1  CP6   aromatic  1.392  0.020  1.392
 ZAF  CP2  CP3   aromatic  1.387  0.020  1.387
 ZAF  CP2  HP2   single    0.930  0.020  1.080
 ZAF  CP3  CP4   aromatic  1.390  0.020  1.390
 ZAF  CP3  HP3   single    0.930  0.020  1.080
 ZAF  CP4  CP5   aromatic  1.388  0.020  1.388
 ZAF  CP4  HP4   single    0.930  0.020  1.080
 ZAF  CP5  CP6   aromatic  1.389  0.020  1.389
 ZAF  CP5  HP5   single    0.930  0.020  1.080
 ZAF  CP6  HP6   single    0.930  0.020  1.080
 ZAF  O3   P3    single    1.620  0.020  1.620
 ZAF  P3   O3A   double    1.482  0.020  1.482
 ZAF  P3   O3B   single    1.603  0.020  1.603
 ZAF  P3   C4    single    1.822  0.020  1.822
 ZAF  O3B  HOB3  single    0.850  0.020  0.980
 ZAF  C4   C4A   single    1.521  0.020  1.521
 ZAF  C4   N5    single    1.445  0.020  1.445
 ZAF  C4   H4    single    0.970  0.020  1.090
 ZAF  C4A  H4A1  single    0.970  0.020  1.090
 ZAF  C4A  H4A2  single    0.970  0.020  1.090
 ZAF  C4A  H4A3  single    0.970  0.020  1.090
 ZAF  N5   C6    single    1.348  0.020  1.348
 ZAF  N5   HN5   single    0.860  0.020  1.020
 ZAF  C6   O6    double    1.216  0.020  1.216
 ZAF  C6   C7    single    1.529  0.020  1.529
 ZAF  C7   C7A   single    1.524  0.020  1.524
 ZAF  C7   N8    single    1.442  0.020  1.442
 ZAF  C7   H7    single    0.970  0.020  1.090
 ZAF  C7A  H7A1  single    0.970  0.020  1.090
 ZAF  C7A  H7A2  single    0.970  0.020  1.090
 ZAF  C7A  H7A3  single    0.970  0.020  1.090
 ZAF  N8   C9    single    1.347  0.020  1.347
 ZAF  N8   HN8   single    0.860  0.020  1.020
 ZAF  C9   O9    double    1.214  0.020  1.214
 ZAF  C9   O10   single    1.335  0.020  1.335
 ZAF  O10  C11   single    1.429  0.020  1.429
 ZAF  C11  C1X   single    1.500  0.020  1.500
 ZAF  C11  H111  single    0.970  0.020  1.090
 ZAF  C11  H112  single    0.970  0.020  1.090
 ZAF  C1X  C2X   aromatic  1.394  0.020  1.394
 ZAF  C1X  C6X   aromatic  1.390  0.020  1.390
 ZAF  C2X  C3X   aromatic  1.386  0.020  1.386
 ZAF  C2X  HP2'  single    0.930  0.020  1.080
 ZAF  C3X  C4X   aromatic  1.391  0.020  1.391
 ZAF  C3X  HP3'  single    0.930  0.020  1.080
 ZAF  C4X  C5X   aromatic  1.387  0.020  1.387
 ZAF  C4X  HP4'  single    0.930  0.020  1.080
 ZAF  C5X  C6X   aromatic  1.390  0.020  1.390
 ZAF  C5X  HP5'  single    0.930  0.020  1.080
 ZAF  C6X  HP6'  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
 ZAF  C2    C1   O1B   116.34  3.000
 ZAF  C2    C1   O1A   122.94  3.000
 ZAF  O1B   C1   O1A   120.60  3.000
 ZAF  HOB1  O1B  C1    112.20  3.000
 ZAF  H2A2  C2A  H2A1  106.97  3.000
 ZAF  H2A2  C2A  CP1   110.14  3.000
 ZAF  H2A1  C2A  CP1   110.38  3.000
 ZAF  H2A2  C2A  C2    109.28  3.000
 ZAF  H2A1  C2A  C2    107.35  3.000
 ZAF  CP1   C2A  C2    112.53  3.000
 ZAF  H2    C2   O3    111.32  3.000
 ZAF  H2    C2   C2A   109.66  3.000
 ZAF  O3    C2   C2A   106.96  3.000
 ZAF  H2    C2   C1    107.60  3.000
 ZAF  O3    C2   C1    110.51  3.000
 ZAF  C2A   C2   C1    110.82  3.000
 ZAF  CP6   CP1  CP2   118.83  3.000
 ZAF  CP6   CP1  C2A   120.61  3.000
 ZAF  CP2   CP1  C2A   120.56  3.000
 ZAF  HP2   CP2  CP3   119.71  3.000
 ZAF  HP2   CP2  CP1   119.63  3.000
 ZAF  CP3   CP2  CP1   120.66  3.000
 ZAF  HP3   CP3  CP4   120.09  3.000
 ZAF  HP3   CP3  CP2   119.82  3.000
 ZAF  CP4   CP3  CP2   120.09  3.000
 ZAF  HP4   CP4  CP5   120.15  3.000
 ZAF  HP4   CP4  CP3   120.18  3.000
 ZAF  CP5   CP4  CP3   119.66  3.000
 ZAF  HP5   CP5  CP6   119.82  3.000
 ZAF  HP5   CP5  CP4   120.12  3.000
 ZAF  CP6   CP5  CP4   120.06  3.000
 ZAF  HP6   CP6  CP5   119.59  3.000
 ZAF  HP6   CP6  CP1   119.72  3.000
 ZAF  CP5   CP6  CP1   120.70  3.000
 ZAF  P3    O3   C2    118.79  3.000
 ZAF  C4    P3   O3B   107.04  3.000
 ZAF  C4    P3   O3A   116.14  3.000
 ZAF  O3B   P3   O3A   115.84  3.000
 ZAF  C4    P3   O3    100.88  3.000
 ZAF  O3B   P3   O3    101.30  3.000
 ZAF  O3A   P3   O3    113.64  3.000
 ZAF  HOB3  O3B  P3    114.19  3.000
 ZAF  H4    C4   N5    108.25  3.000
 ZAF  H4    C4   C4A   109.19  3.000
 ZAF  N5    C4   C4A   111.37  3.000
 ZAF  H4    C4   P3    105.77  3.000
 ZAF  N5    C4   P3    107.63  3.000
 ZAF  C4A   C4   P3    114.33  3.000
 ZAF  H4A3  C4A  H4A2  108.20  3.000
 ZAF  H4A3  C4A  H4A1  108.26  3.000
 ZAF  H4A2  C4A  H4A1  108.17  3.000
 ZAF  H4A3  C4A  C4    110.94  3.000
 ZAF  H4A2  C4A  C4    112.04  3.000
 ZAF  H4A1  C4A  C4    109.13  3.000
 ZAF  HN5   N5   C6    118.86  3.000
 ZAF  HN5   N5   C4    117.20  3.000
 ZAF  C6    N5   C4    123.24  3.000
 ZAF  C7    C6   O6    121.77  3.000
 ZAF  C7    C6   N5    114.36  3.000
 ZAF  O6    C6   N5    123.81  3.000
 ZAF  H7    C7   N8    109.88  3.000
 ZAF  H7    C7   C7A   108.33  3.000
 ZAF  N8    C7   C7A   109.37  3.000
 ZAF  H7    C7   C6    109.87  3.000
 ZAF  N8    C7   C6    110.52  3.000
 ZAF  C7A   C7   C6    108.83  3.000
 ZAF  H7A3  C7A  H7A2  108.18  3.000
 ZAF  H7A3  C7A  H7A1  107.86  3.000
 ZAF  H7A2  C7A  H7A1  108.74  3.000
 ZAF  H7A3  C7A  C7    110.51  3.000
 ZAF  H7A2  C7A  C7    111.06  3.000
 ZAF  H7A1  C7A  C7    110.40  3.000
 ZAF  HN8   N8   C9    116.56  3.000
 ZAF  HN8   N8   C7    118.73  3.000
 ZAF  C9    N8   C7    124.46  3.000
 ZAF  O10   C9   O9    124.22  3.000
 ZAF  O10   C9   N8    110.78  3.000
 ZAF  O9    C9   N8    125.00  3.000
 ZAF  C11   O10  C9    117.72  3.000
 ZAF  H112  C11  H111  107.87  3.000
 ZAF  H112  C11  C1X   110.63  3.000
 ZAF  H111  C11  C1X   110.62  3.000
 ZAF  H112  C11  O10   109.75  3.000
 ZAF  H111  C11  O10   110.41  3.000
 ZAF  C1X   C11  O10   107.57  3.000
 ZAF  C6X   C1X  C2X   119.04  3.000
 ZAF  C6X   C1X  C11   120.47  3.000
 ZAF  C2X   C1X  C11   120.48  3.000
 ZAF  HP2'  C2X  C3X   119.60  3.000
 ZAF  HP2'  C2X  C1X   119.93  3.000
 ZAF  C3X   C2X  C1X   120.47  3.000
 ZAF  HP3'  C3X  C4X   120.01  3.000
 ZAF  HP3'  C3X  C2X   119.84  3.000
 ZAF  C4X   C3X  C2X   120.15  3.000
 ZAF  HP4'  C4X  C5X   120.12  3.000
 ZAF  HP4'  C4X  C3X   120.14  3.000
 ZAF  C5X   C4X  C3X   119.74  3.000
 ZAF  HP5'  C5X  C6X   119.85  3.000
 ZAF  HP5'  C5X  C4X   120.15  3.000
 ZAF  C6X   C5X  C4X   120.00  3.000
 ZAF  HP6'  C6X  C5X   119.67  3.000
 ZAF  HP6'  C6X  C1X   119.72  3.000
 ZAF  C5X   C6X  C1X   120.61  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
 ZAF  CONST_01  CP4   CP3  CP2  CP1     0.00   0.0  0
 ZAF  CONST_02  CP4   CP5  CP6  CP1     0.00   0.0  0
 ZAF  CONST_03  CP5   CP6  CP1  CP2     0.00   0.0  0
 ZAF  CONST_04  CP5   CP4  CP3  CP2     0.00   0.0  0
 ZAF  CONST_05  CP6   CP1  CP2  CP3     0.00   0.0  0
 ZAF  CONST_06  CP6   CP5  CP4  CP3     0.00   0.0  0
 ZAF  CONST_07  C4X   C3X  C2X  C1X     0.00   0.0  0
 ZAF  CONST_08  C4X   C5X  C6X  C1X     0.00   0.0  0
 ZAF  CONST_09  C5X   C6X  C1X  C2X     0.00   0.0  0
 ZAF  CONST_10  C5X   C4X  C3X  C2X     0.00   0.0  0
 ZAF  CONST_11  C6X   C1X  C2X  C3X     0.00   0.0  0
 ZAF  CONST_12  C6X   C5X  C4X  C3X     0.00   0.0  0
 ZAF  CONST_13  CP3   CP2  CP1  C2A   180.00   0.0  0
 ZAF  CONST_14  CP5   CP6  CP1  C2A   180.00   0.0  0
 ZAF  CONST_15  C3X   C2X  C1X  C11   180.00   0.0  0
 ZAF  CONST_16  C5X   C6X  C1X  C11   180.00   0.0  0
 ZAF  CONST_17  HP3   CP3  CP2  CP1   180.00   0.0  0
 ZAF  CONST_18  HP5   CP5  CP6  CP1   180.00   0.0  0
 ZAF  CONST_19  HP6   CP6  CP1  CP2   180.00   0.0  0
 ZAF  CONST_20  HP4   CP4  CP3  CP2   180.00   0.0  0
 ZAF  CONST_21  HP2   CP2  CP3  CP4   180.00   0.0  0
 ZAF  CONST_22  HP3'  C3X  C2X  C1X   180.00   0.0  0
 ZAF  CONST_23  HP5'  C5X  C6X  C1X   180.00   0.0  0
 ZAF  CONST_24  HP6'  C6X  C1X  C2X   180.00   0.0  0
 ZAF  CONST_25  HP4'  C4X  C3X  C2X   180.00   0.0  0
 ZAF  CONST_26  HP2'  C2X  C3X  C4X   180.00   0.0  0
 ZAF  CONST_27  O6    C6   N5   C4      0.00   0.0  0
 ZAF  CONST_28  C7    C6   N5   C4    180.00   0.0  0
 ZAF  CONST_29  HN5   N5   C6   O6    180.00   0.0  0
 ZAF  CONST_30  HOB1  O1B  C1   O1A   180.00   0.0  0
 ZAF  Var_01    CP2   CP1  C2A  C2     77.76  30.0  2
 ZAF  Var_02    C2X   C1X  C11  O10   -61.09  30.0  2
 ZAF  Var_03    C1X   C11  O10  C9   -179.77  30.0  3
 ZAF  Var_04    O3A   P3   O3   C2     41.50  30.0  3
 ZAF  Var_05    O9    C9   N8   C7    177.70  30.0  2

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
 ZAF  chir_01  C2  C1   C2A  O3   positiv
 ZAF  chir_03  C4  P3   N5   C4A  negativ
 ZAF  chir_04  C7  N8   C6   C7A  positiv
 ZAF  chir_05  P3  O3A  O3B  C4   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
 ZAF  plan-1  C2A   0.020
 ZAF  plan-1  CP1   0.020
 ZAF  plan-1  CP2   0.020
 ZAF  plan-1  CP3   0.020
 ZAF  plan-1  CP4   0.020
 ZAF  plan-1  CP5   0.020
 ZAF  plan-1  CP6   0.020
 ZAF  plan-1  HP2   0.020
 ZAF  plan-1  HP3   0.020
 ZAF  plan-1  HP4   0.020
 ZAF  plan-1  HP5   0.020
 ZAF  plan-1  HP6   0.020
 ZAF  plan-2  C11   0.020
 ZAF  plan-2  C1X   0.020
 ZAF  plan-2  C2X   0.020
 ZAF  plan-2  C3X   0.020
 ZAF  plan-2  C4X   0.020
 ZAF  plan-2  C5X   0.020
 ZAF  plan-2  C6X   0.020
 ZAF  plan-2  HP2'  0.020
 ZAF  plan-2  HP3'  0.020
 ZAF  plan-2  HP4'  0.020
 ZAF  plan-2  HP5'  0.020
 ZAF  plan-2  HP6'  0.020
 ZAF  plan-3  C4    0.020
 ZAF  plan-3  N5    0.020
 ZAF  plan-3  C6    0.020
 ZAF  plan-3  O6    0.020
 ZAF  plan-3  C7    0.020
 ZAF  plan-3  HN5   0.020
 ZAF  plan-4  C1    0.020
 ZAF  plan-4  O1A   0.020
 ZAF  plan-4  O1B   0.020
 ZAF  plan-4  C2    0.020
 ZAF  plan-4  HOB1  0.020
 ZAF  plan-5  N8    0.020
 ZAF  plan-5  C9    0.020
 ZAF  plan-5  O9    0.020
 ZAF  plan-5  O10   0.020

