# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 03:30:05 2021
#   Inital geometry file: a 145 line input string
#   Ligand name: (2S)-2-{[(R)-[({N-[(benzyloxy)carbonyl]-L-alanyl}amino)methyl](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)NC[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
 AGF  AGF  '(2S)-2-{[(R)-[({N-[(benzyloxy)carbonyl]-L-alanyl}amino)methyl](hydroxy)phosphoryl]oxy}-3-phenylpropanoic acid'  ligand  57  32  .  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_AGF
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
 AGF  C1    C  C     0   0.740  46.8145  16.9873  39.7990
 AGF  O1    O  O     0  -0.519  47.0378  15.9904  40.4551
 AGF  O1A   O  O2    0  -0.470  47.3819  18.1746  40.0133
 AGF  CB1   C  CH2   0  -0.232  48.2189  18.3492  41.1589
 AGF  CG1   C  CR6   0   0.087  48.3338  19.8284  41.3788
 AGF  CDB   C  CR16  0  -0.293  47.6067  20.4509  42.3871
 AGF  CDL   C  CR16  0  -0.274  49.1395  20.6033  40.5479
 AGF  CEB   C  CR16  0  -0.243  47.6870  21.8256  42.5714
 AGF  CEL   C  CR16  0  -0.245  49.2163  21.9772  40.7233
 AGF  CZ1   C  CR16  0  -0.267  48.4901  22.5912  41.7376
 AGF  C2    C  C     0   0.562  45.1483  19.3443  38.9994
 AGF  O2    O  O     0  -0.483  44.2623  19.1059  39.8014
 AGF  CA2   C  CH1   0  -0.177  45.6593  18.2721  38.0341
 AGF  CB2   C  CH3   0  -0.695  44.5886  17.9827  36.9910
 AGF  N2    N  NH1   0  -0.660  45.9656  17.0568  38.7548
 AGF  CA3   C  CH2   0  -0.572  45.3653  21.6949  39.6346
 AGF  P3    P  P     0   1.385  44.3558  22.8090  38.6250
 AGF  O1P   O  O     0  -0.698  43.1658  22.2315  37.9551
 AGF  O2P   O  OH1   0  -0.729  44.0954  24.0064  39.6540
 AGF  O3P   O  O2    0  -0.602  45.4432  23.3756  37.5665
 AGF  CA4   C  CH1   0  -0.018  45.0886  23.5809  36.2074
 AGF  C4    C  C     0   0.522  44.8511  22.2383  35.5327
 AGF  O41   O  O     0  -0.429  45.5274  21.2652  35.7458
 AGF  O42   O  OH1   0  -0.576  43.8707  22.2922  34.6512
 AGF  CB4   C  CH2   0  -0.557  46.2721  24.2883  35.5425
 AGF  CG4   C  CR6   0   0.104  46.0297  24.5562  34.0828
 AGF  CDE   C  CR16  0  -0.302  45.2441  25.6339  33.6805
 AGF  CDO   C  CR16  0  -0.298  46.5654  23.7182  33.1090
 AGF  CEE   C  CR16  0  -0.239  44.9972  25.8669  32.3350
 AGF  CEO   C  CR16  0  -0.239  46.3203  23.9473  31.7615
 AGF  CZ4   C  CR16  0  -0.268  45.5345  25.0228  31.3708
 AGF  HB11  H  HCH2  0   0.251  47.7835  17.8598  42.0311
 AGF  HB12  H  HCH2  0   0.246  49.1959  17.8997  40.9670
 AGF  HD11  H  HCR6  0   0.254  46.9745  19.8577  43.0371
 AGF  HD12  H  HCR6  0   0.254  49.7138  20.1294  39.7602
 AGF  HE11  H  HCR6  0   0.258  47.1205  22.2981  43.3633
 AGF  HE12  H  HCR6  0   0.258  49.8463  22.5705  40.0734
 AGF  HZ1   H  HCR6  0   0.259  48.5537  23.6626  41.8783
 AGF  HA2   H  HCH1  0   0.265  46.5547  18.6335  37.5187
 AGF  HB21  H  HCH3  0   0.255  44.9408  17.2312  36.2844
 AGF  HB22  H  HCH3  0   0.242  43.6737  17.6199  37.4596
 AGF  HB23  H  HCH3  0   0.259  44.3558  18.8861  36.4304
 AGF  HN2   H  HNH1  0   0.409  45.4528  16.2184  38.5317
 AGF  HA31  H  HCH2  0   0.301  44.7878  21.3846  40.5046
 AGF  HA32  H  HCH2  0   0.306  46.2560  22.2069  40.0036
 AGF  HN3   H  HNH1  0   0.405  46.4760  20.6494  38.1910
 AGF  HOP2  H  HOH1  0   0.499  43.4133  24.6370  39.3835
 AGF  HA4   H  HCH1  0   0.277  44.1956  24.2065  36.1248
 AGF  HO4   H  HOH1  0   0.484  43.7957  21.4480  34.1797
 AGF  HB41  H  HCH2  0   0.283  46.4384  25.2261  36.0767
 AGF  HB42  H  HCH2  0   0.271  47.1664  23.6747  35.6714
 AGF  HD41  H  HCR6  0   0.252  44.8243  26.3009  34.4253
 AGF  HD42  H  HCR6  0   0.252  47.1808  22.8769  33.4059
 AGF  HE41  H  HCR6  0   0.256  44.3892  26.7119  32.0382
 AGF  HE42  H  HCR6  0   0.256  46.7458  23.2859  31.0176
 AGF  HZ4   H  HCR6  0   0.256  45.3447  25.2061  30.3212
 AGF  N3    N  NH1   0  -0.621  45.7321  20.5448  38.8607

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
 AGF  C1   O1    double    1.214  0.020  1.214
 AGF  C1   O1A   single    1.333  0.020  1.333
 AGF  C1   N2    single    1.347  0.020  1.347
 AGF  O1A  CB1   single    1.429  0.020  1.429
 AGF  CB1  CG1   single    1.500  0.020  1.500
 AGF  CB1  HB11  single    0.970  0.020  1.090
 AGF  CB1  HB12  single    0.970  0.020  1.090
 AGF  CG1  CDB   aromatic  1.390  0.020  1.390
 AGF  CG1  CDL   aromatic  1.393  0.020  1.393
 AGF  CDB  CEB   aromatic  1.389  0.020  1.389
 AGF  CDB  HD11  single    0.930  0.020  1.080
 AGF  CDL  CEL   aromatic  1.387  0.020  1.387
 AGF  CDL  HD12  single    0.930  0.020  1.080
 AGF  CEB  CZ1   aromatic  1.388  0.020  1.388
 AGF  CEB  HE11  single    0.930  0.020  1.080
 AGF  CEL  CZ1   aromatic  1.390  0.020  1.390
 AGF  CEL  HE12  single    0.930  0.020  1.080
 AGF  CZ1  HZ1   single    0.930  0.020  1.080
 AGF  C2   O2    double    1.219  0.020  1.219
 AGF  C2   CA2   single    1.531  0.020  1.531
 AGF  C2   N3    single    1.342  0.020  1.342
 AGF  CA2  CB2   single    1.523  0.020  1.523
 AGF  CA2  N2    single    1.446  0.020  1.446
 AGF  CA2  HA2   single    0.970  0.020  1.090
 AGF  CB2  HB21  single    0.970  0.020  1.090
 AGF  CB2  HB22  single    0.970  0.020  1.090
 AGF  CB2  HB23  single    0.970  0.020  1.090
 AGF  N2   HN2   single    0.860  0.020  1.020
 AGF  CA3  N3    single    1.434  0.020  1.434
 AGF  CA3  P3    single    1.811  0.020  1.811
 AGF  CA3  HA31  single    0.970  0.020  1.090
 AGF  CA3  HA32  single    0.970  0.020  1.090
 AGF  N3   HN3   single    0.860  0.020  1.020
 AGF  P3   O1P   double    1.483  0.020  1.483
 AGF  P3   O2P   single    1.600  0.020  1.600
 AGF  P3   O3P   single    1.620  0.020  1.620
 AGF  O2P  HOP2  single    0.850  0.020  0.980
 AGF  O3P  CA4   single    1.419  0.020  1.419
 AGF  CA4  C4    single    1.521  0.020  1.521
 AGF  CA4  CB4   single    1.531  0.020  1.531
 AGF  CA4  HA4   single    0.970  0.020  1.090
 AGF  C4   O41   double    1.204  0.020  1.204
 AGF  C4   O42   single    1.320  0.020  1.320
 AGF  O42  HO4   single    0.850  0.020  0.980
 AGF  CB4  CG4   single    1.504  0.020  1.504
 AGF  CB4  HB41  single    0.970  0.020  1.090
 AGF  CB4  HB42  single    0.970  0.020  1.090
 AGF  CG4  CDE   aromatic  1.393  0.020  1.393
 AGF  CG4  CDO   aromatic  1.392  0.020  1.392
 AGF  CDE  CEE   aromatic  1.388  0.020  1.388
 AGF  CDE  HD41  single    0.930  0.020  1.080
 AGF  CDO  CEO   aromatic  1.389  0.020  1.389
 AGF  CDO  HD42  single    0.930  0.020  1.080
 AGF  CEE  CZ4   aromatic  1.390  0.020  1.390
 AGF  CEE  HE41  single    0.930  0.020  1.080
 AGF  CEO  CZ4   aromatic  1.388  0.020  1.388
 AGF  CEO  HE42  single    0.930  0.020  1.080
 AGF  CZ4  HZ4   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
 AGF  N2    C1   O1A   110.28  3.000
 AGF  N2    C1   O1    125.24  3.000
 AGF  O1A   C1   O1    124.48  3.000
 AGF  CB1   O1A  C1    119.13  3.000
 AGF  HB12  CB1  HB11  108.22  3.000
 AGF  HB12  CB1  CG1   111.29  3.000
 AGF  HB11  CB1  CG1   110.85  3.000
 AGF  HB12  CB1  O1A   109.43  3.000
 AGF  HB11  CB1  O1A   110.63  3.000
 AGF  CG1   CB1  O1A   106.43  3.000
 AGF  CDL   CG1  CDB   119.08  3.000
 AGF  CDL   CG1  CB1   120.37  3.000
 AGF  CDB   CG1  CB1   120.52  3.000
 AGF  HD11  CDB  CEB   119.73  3.000
 AGF  HD11  CDB  CG1   119.67  3.000
 AGF  CEB   CDB  CG1   120.60  3.000
 AGF  HD12  CDL  CEL   119.70  3.000
 AGF  HD12  CDL  CG1   119.79  3.000
 AGF  CEL   CDL  CG1   120.51  3.000
 AGF  HE11  CEB  CZ1   120.11  3.000
 AGF  HE11  CEB  CDB   119.92  3.000
 AGF  CZ1   CEB  CDB   119.97  3.000
 AGF  HE12  CEL  CZ1   120.00  3.000
 AGF  HE12  CEL  CDL   119.96  3.000
 AGF  CZ1   CEL  CDL   120.04  3.000
 AGF  HZ1   CZ1  CEL   120.09  3.000
 AGF  HZ1   CZ1  CEB   120.12  3.000
 AGF  CEL   CZ1  CEB   119.79  3.000
 AGF  N3    C2   CA2   114.60  3.000
 AGF  N3    C2   O2    124.01  3.000
 AGF  CA2   C2   O2    121.38  3.000
 AGF  HA2   CA2  N2    109.82  3.000
 AGF  HA2   CA2  CB2   108.39  3.000
 AGF  N2    CA2  CB2   109.31  3.000
 AGF  HA2   CA2  C2    109.80  3.000
 AGF  N2    CA2  C2    110.20  3.000
 AGF  CB2   CA2  C2    109.29  3.000
 AGF  HB23  CB2  HB22  108.55  3.000
 AGF  HB23  CB2  HB21  107.91  3.000
 AGF  HB22  CB2  HB21  108.69  3.000
 AGF  HB23  CB2  CA2   110.21  3.000
 AGF  HB22  CB2  CA2   111.04  3.000
 AGF  HB21  CB2  CA2   110.36  3.000
 AGF  HN2   N2   CA2   118.76  3.000
 AGF  HN2   N2   C1    116.69  3.000
 AGF  CA2   N2   C1    124.27  3.000
 AGF  HA32  CA3  HA31  107.23  3.000
 AGF  HA32  CA3  P3    110.77  3.000
 AGF  HA31  CA3  P3    108.96  3.000
 AGF  HA32  CA3  N3    110.49  3.000
 AGF  HA31  CA3  N3    109.77  3.000
 AGF  P3    CA3  N3    109.58  3.000
 AGF  O3P   P3   O2P   105.53  3.000
 AGF  O3P   P3   O1P   112.32  3.000
 AGF  O2P   P3   O1P   116.84  3.000
 AGF  O3P   P3   CA3   101.84  3.000
 AGF  O2P   P3   CA3   101.10  3.000
 AGF  O1P   P3   CA3   117.37  3.000
 AGF  HOP2  O2P  P3    115.00  3.000
 AGF  CA4   O3P  P3    120.56  3.000
 AGF  HA4   CA4  CB4   109.52  3.000
 AGF  HA4   CA4  C4    110.12  3.000
 AGF  CB4   CA4  C4    109.63  3.000
 AGF  HA4   CA4  O3P   111.04  3.000
 AGF  CB4   CA4  O3P   106.83  3.000
 AGF  C4    CA4  O3P   109.63  3.000
 AGF  O42   C4   O41   124.65  3.000
 AGF  O42   C4   CA4   112.10  3.000
 AGF  O41   C4   CA4   123.17  3.000
 AGF  HO4   O42  C4    110.29  3.000
 AGF  HB42  CB4  HB41  107.46  3.000
 AGF  HB42  CB4  CG4   110.28  3.000
 AGF  HB41  CB4  CG4   110.27  3.000
 AGF  HB42  CB4  CA4   108.79  3.000
 AGF  HB41  CB4  CA4   107.59  3.000
 AGF  CG4   CB4  CA4   112.29  3.000
 AGF  CDO   CG4  CDE   118.74  3.000
 AGF  CDO   CG4  CB4   120.66  3.000
 AGF  CDE   CG4  CB4   120.60  3.000
 AGF  HD41  CDE  CEE   119.59  3.000
 AGF  HD41  CDE  CG4   119.73  3.000
 AGF  CEE   CDE  CG4   120.68  3.000
 AGF  HD42  CDO  CEO   119.61  3.000
 AGF  HD42  CDO  CG4   119.61  3.000
 AGF  CEO   CDO  CG4   120.77  3.000
 AGF  HE41  CEE  CZ4   120.08  3.000
 AGF  HE41  CEE  CDE   119.79  3.000
 AGF  CZ4   CEE  CDE   120.13  3.000
 AGF  HE42  CEO  CZ4   120.17  3.000
 AGF  HE42  CEO  CDO   119.78  3.000
 AGF  CZ4   CEO  CDO   120.06  3.000
 AGF  HZ4   CZ4  CEO   120.23  3.000
 AGF  HZ4   CZ4  CEE   120.14  3.000
 AGF  CEO   CZ4  CEE   119.62  3.000
 AGF  HN3   N3   CA3   117.70  3.000
 AGF  HN3   N3   C2    118.90  3.000
 AGF  CA3   N3   C2    123.40  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
 AGF  CONST_01  CZ1   CEB  CDB  CG1     0.00   0.0  0
 AGF  CONST_02  CZ1   CEL  CDL  CG1     0.00   0.0  0
 AGF  CONST_03  CEL   CDL  CG1  CDB     0.00   0.0  0
 AGF  CONST_04  CEL   CZ1  CEB  CDB     0.00   0.0  0
 AGF  CONST_05  CEB   CDB  CG1  CDL     0.00   0.0  0
 AGF  CONST_06  CEB   CZ1  CEL  CDL     0.00   0.0  0
 AGF  CONST_07  CZ4   CEE  CDE  CG4     0.00   0.0  0
 AGF  CONST_08  CZ4   CEO  CDO  CG4     0.00   0.0  0
 AGF  CONST_09  CEO   CDO  CG4  CDE     0.00   0.0  0
 AGF  CONST_10  CEO   CZ4  CEE  CDE     0.00   0.0  0
 AGF  CONST_11  CEE   CDE  CG4  CDO     0.00   0.0  0
 AGF  CONST_12  CEE   CZ4  CEO  CDO     0.00   0.0  0
 AGF  CONST_13  CEB   CDB  CG1  CB1   180.00   0.0  0
 AGF  CONST_14  CEL   CDL  CG1  CB1   180.00   0.0  0
 AGF  CONST_15  CEE   CDE  CG4  CB4   180.00   0.0  0
 AGF  CONST_16  CEO   CDO  CG4  CB4   180.00   0.0  0
 AGF  CONST_17  HE11  CEB  CDB  CG1   180.00   0.0  0
 AGF  CONST_18  HE12  CEL  CDL  CG1   180.00   0.0  0
 AGF  CONST_19  HD12  CDL  CG1  CDB   180.00   0.0  0
 AGF  CONST_20  HZ1   CZ1  CEB  CDB   180.00   0.0  0
 AGF  CONST_21  HD11  CDB  CG1  CDL   180.00   0.0  0
 AGF  CONST_22  HE41  CEE  CDE  CG4   180.00   0.0  0
 AGF  CONST_23  HE42  CEO  CDO  CG4   180.00   0.0  0
 AGF  CONST_24  HD42  CDO  CG4  CDE   180.00   0.0  0
 AGF  CONST_25  HZ4   CZ4  CEE  CDE   180.00   0.0  0
 AGF  CONST_26  HD41  CDE  CG4  CDO   180.00   0.0  0
 AGF  CONST_27  CA3   N3   C2   O2      0.00   0.0  0
 AGF  CONST_28  CA3   N3   C2   CA2   180.00   0.0  0
 AGF  CONST_29  HN3   N3   C2   O2    180.00   0.0  0
 AGF  CONST_30  HO4   O42  C4   CA4   180.00   0.0  0
 AGF  Var_01    CDB   CG1  CB1  O1A   103.01  30.0  2
 AGF  Var_02    CDE   CG4  CB4  CA4    79.43  30.0  2
 AGF  Var_03    CG1   CB1  O1A  C1   -161.97  30.0  3
 AGF  Var_04    CA2   N2   C1   O1    176.43  30.0  2
 AGF  Var_05    N2    C1   O1A  CB1   173.96  30.0  1
 AGF  Var_06    P3    CA3  N3   C2   -103.30  30.0  2
 AGF  Var_07    O1P   P3   CA3  N3     52.87  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
 AGF  chir_01  CA2  C2   CB2  N2   positiv
 AGF  chir_03  CA4  O3P  C4   CB4  positiv
 AGF  chir_04  P3   O1P  O2P  O3P  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
 AGF  plan-1  CB1   0.020
 AGF  plan-1  CG1   0.020
 AGF  plan-1  CDB   0.020
 AGF  plan-1  CDL   0.020
 AGF  plan-1  CEB   0.020
 AGF  plan-1  CEL   0.020
 AGF  plan-1  CZ1   0.020
 AGF  plan-1  HD11  0.020
 AGF  plan-1  HD12  0.020
 AGF  plan-1  HE11  0.020
 AGF  plan-1  HE12  0.020
 AGF  plan-1  HZ1   0.020
 AGF  plan-2  CB4   0.020
 AGF  plan-2  CG4   0.020
 AGF  plan-2  CDE   0.020
 AGF  plan-2  CDO   0.020
 AGF  plan-2  CEE   0.020
 AGF  plan-2  CEO   0.020
 AGF  plan-2  CZ4   0.020
 AGF  plan-2  HD41  0.020
 AGF  plan-2  HD42  0.020
 AGF  plan-2  HE41  0.020
 AGF  plan-2  HE42  0.020
 AGF  plan-2  HZ4   0.020
 AGF  plan-3  C2    0.020
 AGF  plan-3  O2    0.020
 AGF  plan-3  CA2   0.020
 AGF  plan-3  CA3   0.020
 AGF  plan-3  HN3   0.020
 AGF  plan-3  N3    0.020
 AGF  plan-4  CA4   0.020
 AGF  plan-4  C4    0.020
 AGF  plan-4  O41   0.020
 AGF  plan-4  O42   0.020
 AGF  plan-4  HO4   0.020
 AGF  plan-5  C1    0.020
 AGF  plan-5  O1    0.020
 AGF  plan-5  O1A   0.020
 AGF  plan-5  N2    0.020

