# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun 11 07:48:11 2020
#   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  58  33  .  2022-07-22  2022-07-26
;
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   0.387   0.3027   2.8509  -4.2275
 ZAF  O1A   O  O      0  -0.599  -0.6986   3.0535  -4.9327
 ZAF  O1B   O  OC    -1  -0.630   1.1074   3.7026  -3.7930
 ZAF  C2A   C  CH2    0  -0.550   1.8313   0.9310  -4.7572
 ZAF  C2    C  CH1    0  -0.036   0.6634   1.3923  -3.8814
 ZAF  CP1   C  C      0   0.161   2.2140  -0.4961  -4.4896
 ZAF  CP2   C  C1     0  -0.319   1.9249  -1.5011  -5.4075
 ZAF  CP3   C  C1     0  -0.247   2.2600  -2.8247  -5.1493
 ZAF  CP4   C  C1     0  -0.271   2.8830  -3.1648  -3.9566
 ZAF  CP5   C  C1     0  -0.237   3.1717  -2.1714  -3.0290
 ZAF  CP6   C  C1     0  -0.303   2.8424  -0.8507  -3.2969
 ZAF  O3    O  O2     0  -0.624  -0.4077   0.4982  -4.0858
 ZAF  P3    P  P      0   1.293  -1.5061   0.2798  -2.8831
 ZAF  O3A   O  O      0  -0.802  -2.6853  -0.3978  -3.5271
 ZAF  O3B   O  OP    -1  -0.790  -1.6863   1.5413  -2.0852
 ZAF  C4    C  CH1    0  -0.364  -0.6107  -0.9445  -1.8097
 ZAF  C4A   C  CH3    0  -0.665  -0.5278  -2.3361  -2.4107
 ZAF  N5    N  NH1    0  -0.621  -1.2617  -0.9682  -0.5118
 ZAF  C6    C  C      0   0.556  -0.8576  -0.2289   0.5261
 ZAF  O6    O  O      0  -0.497   0.2307   0.3260   0.5998
 ZAF  C7    C  CH1    0  -0.206  -1.8841  -0.0911   1.6455
 ZAF  C7A   C  CH3    0  -0.645  -2.8037   1.0916   1.3326
 ZAF  N8    N  NH1    0  -0.665  -1.1655   0.0797   2.8845
 ZAF  C9    C  C      0   0.766  -1.7326  -0.1282   4.0824
 ZAF  O9    O  O      0  -0.524  -2.8552  -0.5563   4.2647
 ZAF  O10   O  O2     0  -0.483  -0.8835   0.1842   5.0702
 ZAF  C11   C  CH2    0  -0.231  -1.3677   0.0589   6.4091
 ZAF  C1X   C  C      0   0.073  -0.2889   0.5601   7.3227
 ZAF  C2X   C  C1     0  -0.282   0.1263   1.8893   7.2577
 ZAF  C3X   C  C1     0  -0.242   1.1192   2.3581   8.1038
 ZAF  C4X   C  C1     0  -0.263   1.7064   1.5058   9.0319
 ZAF  C5X   C  C1     0  -0.241   1.2965   0.1825   9.1050
 ZAF  C6X   C  C1     0  -0.305   0.3062  -0.2873   8.2497
 ZAF  H2A1  H  HCH2   0   0.238   1.5641   1.0503  -5.8113
 ZAF  H2A2  H  HCH2   0   0.247   2.6778   1.5948  -4.5683
 ZAF  H2    H  HCH1   0   0.194   1.0002   1.3661  -2.8365
 ZAF  HP2   H  H      0   0.239   1.4342  -1.2425  -6.3387
 ZAF  HP3   H  H      0   0.248   2.0294  -3.5911  -5.8788
 ZAF  HP4   H  H      0   0.248   3.1414  -4.1953  -3.7494
 ZAF  HP5   H  H      0   0.247   3.6580  -2.4272  -2.0959
 ZAF  HP6   H  H      0   0.242   3.0751  -0.0830  -2.5667
 ZAF  H4    H  HCH1   0   0.259   0.4031  -0.5770  -1.6428
 ZAF  H4A1  H  HCH3   0   0.218  -1.5181  -2.7464  -2.6119
 ZAF  H4A2  H  HCH3   0   0.249   0.0241  -2.3048  -3.3497
 ZAF  H4A3  H  HCH3   0   0.222   0.0003  -3.0176  -1.7423
 ZAF  HN5   H  HNH1   0   0.393  -2.1956  -1.3490  -0.4795
 ZAF  H7    H  HCH1   0   0.271  -2.4816  -1.0037   1.7072
 ZAF  H7A1  H  HCH3   0   0.232  -2.2339   2.0201   1.3018
 ZAF  H7A2  H  HCH3   0   0.241  -3.2867   0.9653   0.3647
 ZAF  H7A3  H  HCH3   0   0.242  -3.5763   1.1814   2.0949
 ZAF  HN8   H  HNH1   0   0.396  -0.2579   0.5188   2.8316
 ZAF  H111  H  HCH2   0   0.247  -2.2791   0.6491   6.5328
 ZAF  H112  H  HCH2   0   0.248  -1.6083  -0.9826   6.6336
 ZAF  HP2'  H  H      0   0.254  -0.3308   2.5645   6.5440
 ZAF  HP3'  H  H      0   0.258   1.4335   3.3920   8.0429
 ZAF  HP4'  H  H      0   0.258   2.4794   1.8739   9.6942
 ZAF  HP5'  H  H      0   0.258   1.7492  -0.4877   9.8241
 ZAF  HP6'  H  H      0   0.256  -0.0052  -1.3234   8.3085

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   deloc     1.241  0.020  1.241
 ZAF  C1   O1B   deloc     1.250  0.020  1.250
 ZAF  C1   C2    single    1.542  0.020  1.542
 ZAF  C2A  C2    single    1.531  0.020  1.531
 ZAF  C2A  CP1   single    1.502  0.020  1.502
 ZAF  C2A  H2A1  single    0.970  0.020  1.090
 ZAF  C2A  H2A2  single    0.970  0.020  1.090
 ZAF  C2   O3    single    1.410  0.020  1.410
 ZAF  C2   H2    single    0.970  0.020  1.090
 ZAF  CP1  CP2   aromatic  1.391  0.020  1.391
 ZAF  CP1  CP6   aromatic  1.394  0.020  1.394
 ZAF  CP2  CP3   aromatic  1.390  0.020  1.390
 ZAF  CP2  HP2   single    0.930  0.020  1.080
 ZAF  CP3  CP4   aromatic  1.388  0.020  1.388
 ZAF  CP3  HP3   single    0.930  0.020  1.080
 ZAF  CP4  CP5   aromatic  1.390  0.020  1.390
 ZAF  CP4  HP4   single    0.930  0.020  1.080
 ZAF  CP5  CP6   aromatic  1.387  0.020  1.387
 ZAF  CP5  HP5   single    0.930  0.020  1.080
 ZAF  CP6  HP6   single    0.930  0.020  1.080
 ZAF  O3   P3    single    1.643  0.020  1.643
 ZAF  P3   O3A   deloc     1.505  0.020  1.505
 ZAF  P3   O3B   deloc     1.503  0.020  1.503
 ZAF  P3   C4    single    1.858  0.020  1.858
 ZAF  C4   C4A   single    1.518  0.020  1.518
 ZAF  C4   N5    single    1.452  0.020  1.452
 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    1.337  0.020  1.337
 ZAF  N5   HN5   single    0.860  0.020  1.020
 ZAF  C6   O6    double    1.224  0.020  1.224
 ZAF  C6   C7    single    1.525  0.020  1.525
 ZAF  C7   C7A   single    1.530  0.020  1.530
 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    1.342  0.020  1.342
 ZAF  N8   HN8   single    0.860  0.020  1.020
 ZAF  C9   O9    double    1.215  0.020  1.215
 ZAF  C9   O10   single    1.339  0.020  1.339
 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  1.390  0.020  1.390
 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   114.58  3.000
 ZAF  C2    C1   O1A   118.08  3.000
 ZAF  O1B   C1   O1A   127.28  3.000
 ZAF  H2A2  C2A  H2A1  106.84  3.000
 ZAF  H2A2  C2A  CP1   110.44  3.000
 ZAF  H2A1  C2A  CP1   109.73  3.000
 ZAF  H2A2  C2A  C2    108.01  3.000
 ZAF  H2A1  C2A  C2    109.39  3.000
 ZAF  CP1   C2A  C2    112.26  3.000
 ZAF  H2    C2   O3    110.84  3.000
 ZAF  H2    C2   C2A   107.65  3.000
 ZAF  O3    C2   C2A   107.79  3.000
 ZAF  H2    C2   C1    107.94  3.000
 ZAF  O3    C2   C1    112.93  3.000
 ZAF  C2A   C2   C1    109.58  3.000
 ZAF  CP6   CP1  CP2   118.32  3.000
 ZAF  CP6   CP1  C2A   120.60  3.000
 ZAF  CP2   CP1  C2A   121.06  3.000
 ZAF  HP2   CP2  CP3   119.74  3.000
 ZAF  HP2   CP2  CP1   119.24  3.000
 ZAF  CP3   CP2  CP1   121.02  3.000
 ZAF  HP3   CP3  CP4   120.07  3.000
 ZAF  HP3   CP3  CP2   119.84  3.000
 ZAF  CP4   CP3  CP2   120.09  3.000
 ZAF  HP4   CP4  CP5   120.22  3.000
 ZAF  HP4   CP4  CP3   120.33  3.000
 ZAF  CP5   CP4  CP3   119.46  3.000
 ZAF  HP5   CP5  CP6   119.86  3.000
 ZAF  HP5   CP5  CP4   119.98  3.000
 ZAF  CP6   CP5  CP4   120.16  3.000
 ZAF  HP6   CP6  CP5   119.53  3.000
 ZAF  HP6   CP6  CP1   119.52  3.000
 ZAF  CP5   CP6  CP1   120.96  3.000
 ZAF  P3    O3   C2    119.07  3.000
 ZAF  C4    P3   O3B   107.70  3.000
 ZAF  C4    P3   O3A   109.16  3.000
 ZAF  O3B   P3   O3A   120.73  3.000
 ZAF  C4    P3   O3    100.85  3.000
 ZAF  O3B   P3   O3    110.92  3.000
 ZAF  O3A   P3   O3    105.68  3.000
 ZAF  H4    C4   N5    106.57  3.000
 ZAF  H4    C4   C4A   108.57  3.000
 ZAF  N5    C4   C4A   111.31  3.000
 ZAF  H4    C4   P3    108.31  3.000
 ZAF  N5    C4   P3    108.12  3.000
 ZAF  C4A   C4   P3    113.68  3.000
 ZAF  H4A3  C4A  H4A2  107.50  3.000
 ZAF  H4A3  C4A  H4A1  108.51  3.000
 ZAF  H4A2  C4A  H4A1  108.17  3.000
 ZAF  H4A3  C4A  C4    110.88  3.000
 ZAF  H4A2  C4A  C4    110.03  3.000
 ZAF  H4A1  C4A  C4    111.61  3.000
 ZAF  HN5   N5   C6    117.62  3.000
 ZAF  HN5   N5   C4    116.72  3.000
 ZAF  C6    N5   C4    123.32  3.000
 ZAF  C7    C6   O6    120.89  3.000
 ZAF  C7    C6   N5    114.61  3.000
 ZAF  O6    C6   N5    124.50  3.000
 ZAF  H7    C7   N8    108.84  3.000
 ZAF  H7    C7   C7A   109.17  3.000
 ZAF  N8    C7   C7A   112.55  3.000
 ZAF  H7    C7   C6    109.52  3.000
 ZAF  N8    C7   C6    107.81  3.000
 ZAF  C7A   C7   C6    108.92  3.000
 ZAF  H7A3  C7A  H7A2  108.49  3.000
 ZAF  H7A3  C7A  H7A1  108.69  3.000
 ZAF  H7A2  C7A  H7A1  107.79  3.000
 ZAF  H7A3  C7A  C7    110.30  3.000
 ZAF  H7A2  C7A  C7    111.01  3.000
 ZAF  H7A1  C7A  C7    110.49  3.000
 ZAF  HN8   N8   C9    119.62  3.000
 ZAF  HN8   N8   C7    117.02  3.000
 ZAF  C9    N8   C7    122.55  3.000
 ZAF  O10   C9   O9    123.86  3.000
 ZAF  O10   C9   N8    110.75  3.000
 ZAF  O9    C9   N8    125.38  3.000
 ZAF  C11   O10  C9    117.11  3.000
 ZAF  H112  C11  H111  107.94  3.000
 ZAF  H112  C11  C1X   110.61  3.000
 ZAF  H111  C11  C1X   110.51  3.000
 ZAF  H112  C11  O10   110.53  3.000
 ZAF  H111  C11  O10   109.95  3.000
 ZAF  C1X   C11  O10   107.32  3.000
 ZAF  C6X   C1X  C2X   119.01  3.000
 ZAF  C6X   C1X  C11   120.70  3.000
 ZAF  C2X   C1X  C11   120.29  3.000
 ZAF  HP2'  C2X  C3X   119.57  3.000
 ZAF  HP2'  C2X  C1X   119.95  3.000
 ZAF  C3X   C2X  C1X   120.48  3.000
 ZAF  HP3'  C3X  C4X   120.03  3.000
 ZAF  HP3'  C3X  C2X   119.78  3.000
 ZAF  C4X   C3X  C2X   120.18  3.000
 ZAF  HP4'  C4X  C5X   120.21  3.000
 ZAF  HP4'  C4X  C3X   120.11  3.000
 ZAF  C5X   C4X  C3X   119.68  3.000
 ZAF  HP5'  C5X  C6X   119.83  3.000
 ZAF  HP5'  C5X  C4X   120.15  3.000
 ZAF  C6X   C5X  C4X   120.02  3.000
 ZAF  HP6'  C6X  C5X   119.64  3.000
 ZAF  HP6'  C6X  C1X   119.75  3.000
 ZAF  C5X   C6X  C1X   120.62  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_29  HN5   N5   C6   O6    180.00   0.0  0
 ZAF  Var_01    CP2   CP1  C2A  C2    107.69  30.0  2
 ZAF  Var_02    C2X   C1X  C11  O10    62.68  30.0  2
 ZAF  Var_03    C1X   C11  O10  C9   -175.68  30.0  3
 ZAF  Var_04    O3A   P3   O3   C2    164.64  30.0  3
 ZAF  Var_05    O9    C9   N8   C7      5.00  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

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-5  N8    0.020
 ZAF  plan-5  C9    0.020
 ZAF  plan-5  O9    0.020
 ZAF  plan-5  O10   0.020

