# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 15:13:00 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: O-[(S)-(cyclohexyloxy)(methyl)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[P@](=O)(OC[C@H](N)C(O)=O)OC1CCCCC1
#
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
 GFT  GFT  O-[(S)-(cyclohexyloxy)(methyl)phosphoryl]-L-serine  L-peptide  36  17  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_GFT
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
 GFT  N     N  NH2    0  -0.799   7.5096   4.8610  -37.5847
 GFT  CA    C  CH1    0  -0.240   8.4827   3.9047  -37.0638
 GFT  C     C  C      0   0.392   9.9445   4.1979  -37.4834
 GFT  O     O  O      0  -0.601  10.8054   4.2421  -36.5855
 GFT  CB    C  CH2    0  -0.163   8.0556   2.5416  -37.5824
 GFT  OG    O  O2     0  -0.605   8.9716   1.5435  -37.1088
 GFT  CAA   C  CH3    0  -0.955  10.4948  -0.5958  -36.9719
 GFT  OAC   O  O      0  -0.702   9.4795   0.3565  -39.3810
 GFT  CAD   C  CH2    0  -0.433   5.2174  -2.9977  -37.1771
 GFT  CAE   C  CH2    0  -0.432   6.6983  -3.3639  -37.1476
 GFT  CAF   C  CH2    0  -0.433   5.0180  -1.5201  -37.5022
 GFT  CAG   C  CH2    0  -0.443   7.4690  -2.4709  -36.1794
 GFT  CAH   C  CH2    0  -0.446   5.7933  -0.6338  -36.5322
 GFT  OAI   O  O2     0  -0.600   7.8590  -0.6808  -37.7568
 GFT  CAJ   C  CH1    0  -0.007   7.2712  -0.9912  -36.4748
 GFT  PAK   P  P      0   1.367   9.1980   0.1849  -37.9352
 GFT  OXT   O  OC    -1  -0.612  10.1217   4.3630  -38.7091
 GFT  HN1   H  HNH2   0   0.345   7.6192   5.7433  -37.1007
 GFT  HN2   H  HNH2   0   0.330   7.7523   5.0516  -38.5510
 GFT  HA    H  HCH1   0   0.214   8.4036   3.9046  -35.9727
 GFT  HB1C  H  HCH2   0   0.215   8.0404   2.5583  -38.6761
 GFT  HB2C  H  HCH2   0   0.237   7.0490   2.3044  -37.2304
 GFT  HAA1  H  HCH3   0   0.280  10.6952  -1.5867  -37.3769
 GFT  HAA2  H  HCH3   0   0.288  11.4076  -0.0048  -37.0386
 GFT  HAA3  H  HCH3   0   0.279  10.2240  -0.6973  -35.9218
 GFT  HAE1  H  HCH2   0   0.230   6.8243  -4.4092  -36.8569
 GFT  HAE2  H  HCH2   0   0.216   7.1182  -3.2727  -38.1534
 GFT  HAF1  H  HCH2   0   0.216   5.3447  -1.3232  -38.5272
 GFT  HAF2  H  HCH2   0   0.231   3.9573  -1.2625  -37.4630
 GFT  HAG1  H  HCH2   0   0.226   7.1130  -2.6479  -35.1596
 GFT  HAG2  H  HCH2   0   0.243   8.5334  -2.7189  -36.1804
 GFT  HAH1  H  HCH2   0   0.247   5.6746   0.4227  -36.7848
 GFT  HAH2  H  HCH2   0   0.226   5.3901  -0.7578  -35.5226
 GFT  HAJ   H  HCH1   0   0.249   7.7517  -0.3949  -35.6920
 GFT  HAD1  H  HCH2   0   0.228   4.6894  -3.6191  -37.9041
 GFT  HAD2  H  HCH2   0   0.210   4.7726  -3.2154  -36.1999

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
 GFT  N    CA    single  1.458  0.019  1.458
 GFT  C    O     deloc   1.231  0.020  1.231
 GFT  C    OXT   deloc   1.249  0.020  1.249
 GFT  CB   OG    single  1.435  0.020  1.435
 GFT  CB   CA    single  1.530  0.020  1.530
 GFT  OG   PAK   single  1.606  0.020  1.606
 GFT  CAA  PAK   single  1.794  0.020  1.794
 GFT  OAC  PAK   double  1.483  0.020  1.483
 GFT  CAD  CAE   single  1.526  0.020  1.526
 GFT  CAD  CAF   single  1.526  0.020  1.526
 GFT  CAE  CAG   single  1.526  0.020  1.526
 GFT  CAF  CAH   single  1.526  0.020  1.526
 GFT  CAG  CAJ   single  1.522  0.020  1.522
 GFT  CAH  CAJ   single  1.522  0.020  1.522
 GFT  OAI  CAJ   single  1.444  0.020  1.444
 GFT  OAI  PAK   single  1.604  0.020  1.604
 GFT  N    HN1   single  0.890  0.020  1.040
 GFT  N    HN2   single  0.890  0.020  1.040
 GFT  CA   HA    single  0.970  0.020  0.970
 GFT  C    CA    single  1.525  0.021  1.525
 GFT  CB   HB1C  single  0.970  0.020  1.090
 GFT  CB   HB2C  single  0.970  0.020  1.090
 GFT  CAA  HAA1  single  0.970  0.020  1.090
 GFT  CAA  HAA2  single  0.970  0.020  1.090
 GFT  CAA  HAA3  single  0.970  0.020  1.090
 GFT  CAD  HAD1  single  0.970  0.020  1.090
 GFT  CAD  HAD2  single  0.970  0.020  1.090
 GFT  CAE  HAE1  single  0.970  0.020  1.090
 GFT  CAE  HAE2  single  0.970  0.020  1.090
 GFT  CAF  HAF1  single  0.970  0.020  1.090
 GFT  CAF  HAF2  single  0.970  0.020  1.090
 GFT  CAG  HAG1  single  0.970  0.020  1.090
 GFT  CAG  HAG2  single  0.970  0.020  1.090
 GFT  CAH  HAH1  single  0.970  0.020  1.090
 GFT  CAH  HAH2  single  0.970  0.020  1.090
 GFT  CAJ  HAJ   single  0.970  0.020  1.090

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
 GFT  HN2   N    HN1   105.42  3.000
 GFT  HN2   N    CA    107.66  3.000
 GFT  HN1   N    CA    109.15  3.000
 GFT  HA    CA   CB    109.00  3.000
 GFT  HA    CA   C     109.00  3.000
 GFT  CB    CA   C     110.10  1.900
 GFT  C     CA   N     111.00  2.800
 GFT  HA    CA   N     110.00  3.000
 GFT  CB    CA   N     110.50  1.700
 GFT  OXT   C    O     127.23  3.000
 GFT  OXT   C    CA    115.13  3.000
 GFT  O     C    CA    120.80  1.700
 GFT  HB2C  CB   HB1C  108.22  3.000
 GFT  HB2C  CB   OG    109.32  3.000
 GFT  HB1C  CB   OG    110.45  3.000
 GFT  HB2C  CB   CA    110.11  3.000
 GFT  HB1C  CB   CA    109.35  3.000
 GFT  OG    CB   CA    109.38  3.000
 GFT  PAK   OG   CB    120.56  3.000
 GFT  HAA3  CAA  HAA2  108.54  3.000
 GFT  HAA3  CAA  HAA1  108.63  3.000
 GFT  HAA2  CAA  HAA1  108.46  3.000
 GFT  HAA3  CAA  PAK   112.24  3.000
 GFT  HAA2  CAA  PAK   109.67  3.000
 GFT  HAA1  CAA  PAK   109.22  3.000
 GFT  HAD2  CAD  HAD1  106.52  3.000
 GFT  HAD2  CAD  CAF   109.23  3.000
 GFT  HAD1  CAD  CAF   110.24  3.000
 GFT  HAD2  CAD  CAE   109.21  3.000
 GFT  HAD1  CAD  CAE   110.20  3.000
 GFT  CAF   CAD  CAE   111.31  3.000
 GFT  HAE2  CAE  HAE1  106.28  3.000
 GFT  HAE2  CAE  CAG   109.92  3.000
 GFT  HAE1  CAE  CAG   109.44  3.000
 GFT  HAE2  CAE  CAD   109.56  3.000
 GFT  HAE1  CAE  CAD   110.30  3.000
 GFT  CAG   CAE  CAD   111.22  3.000
 GFT  HAF2  CAF  HAF1  106.34  3.000
 GFT  HAF2  CAF  CAH   109.49  3.000
 GFT  HAF1  CAF  CAH   109.84  3.000
 GFT  HAF2  CAF  CAD   110.34  3.000
 GFT  HAF1  CAF  CAD   109.57  3.000
 GFT  CAH   CAF  CAD   111.14  3.000
 GFT  HAG2  CAG  HAG1  106.31  3.000
 GFT  HAG2  CAG  CAJ   110.31  3.000
 GFT  HAG1  CAG  CAJ   107.21  3.000
 GFT  HAG2  CAG  CAE   111.01  3.000
 GFT  HAG1  CAG  CAE   109.40  3.000
 GFT  CAJ   CAG  CAE   112.35  3.000
 GFT  HAH2  CAH  HAH1  106.43  3.000
 GFT  HAH2  CAH  CAJ   107.25  3.000
 GFT  HAH1  CAH  CAJ   109.95  3.000
 GFT  HAH2  CAH  CAF   109.48  3.000
 GFT  HAH1  CAH  CAF   111.07  3.000
 GFT  CAJ   CAH  CAF   112.40  3.000
 GFT  PAK   OAI  CAJ   123.67  3.000
 GFT  HAJ   CAJ  OAI   109.81  3.000
 GFT  HAJ   CAJ  CAH   108.98  3.000
 GFT  OAI   CAJ  CAH   108.14  3.000
 GFT  HAJ   CAJ  CAG   109.49  3.000
 GFT  OAI   CAJ  CAG   109.17  3.000
 GFT  CAH   CAJ  CAG   111.22  3.000
 GFT  OAI   PAK  OAC   109.22  3.000
 GFT  OAI   PAK  CAA   107.98  3.000
 GFT  OAC   PAK  CAA   115.89  3.000
 GFT  OAI   PAK  OG    106.35  3.000
 GFT  OAC   PAK  OG    115.50  3.000
 GFT  CAA   PAK  OG    101.17  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
 GFT  Var_01  CAJ   CAG  CAE  CAD  -54.48  30.0  1
 GFT  Var_02  CAJ   CAH  CAF  CAD   54.57  30.0  1
 GFT  Var_03  CAH   CAF  CAD  CAE  -55.10  30.0  1
 GFT  Var_04  CAG   CAE  CAD  CAF   55.09  30.0  1
 GFT  Var_05  CAA   PAK  OG   CB   175.93  30.0  3
 GFT  Var_06  HAA1  CAA  PAK  OG   175.18  30.0  3
 GFT  Var_07  HB1C  CB   OG   PAK  -32.94  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
 GFT  chir_01  CA   N    CB   C    negativ
 GFT  chir_02  CAJ  OAI  CAG  CAH  positiv
 GFT  chir_03  PAK  CAA  OAC  OAI  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
 GFT  plan-1  CA   0.020
 GFT  plan-1  C    0.020
 GFT  plan-1  O    0.020
 GFT  plan-1  OXT  0.020

