# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 17:33:42 2021
#   Inital geometry file: a 157 line input string
#   Ligand name: N-(4-fluorobenzoyl)-L-valyl-O-[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)c1ccc(F)cc1)C(=O)N[C@@H](CO[P](O)(=O)N[C@@H](CCC(O)=O)C(O)=O)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
 2F9  2F9  N-(4-fluorobenzoyl)-L-valyl-O-[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]-L-serine  ligand  63  36  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2F9
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
 2F9  OE1  O  OH1   0  -0.595  15.5027  48.9554  39.4567
 2F9  CD   C  C     0   0.560  14.8228  47.9899  40.0655
 2F9  OE2  O  O     0  -0.442  13.6333  48.0397  40.2551
 2F9  CG   C  CH2   0  -0.586  15.7188  46.8521  40.4728
 2F9  CB   C  CH2   0  -0.488  14.9504  45.7268  41.1505
 2F9  CA   C  CH1   0  -0.169  15.8246  44.6003  41.7127
 2F9  C    C  C     0   0.547  16.6009  43.9386  40.5864
 2F9  OXT  O  OH1   0  -0.575  17.8175  44.4256  40.4133
 2F9  O    O  O     0  -0.443  16.1114  43.0903  39.8833
 2F9  N    N  NH1   0  -0.795  16.6846  45.1055  42.7664
 2F9  PBJ  P  P     0   1.442  17.4842  44.0523  43.7506
 2F9  OAL  O  O     0  -0.709  17.7716  42.7685  43.0727
 2F9  OAH  O  OH1   0  -0.726  16.6217  43.9728  45.0939
 2F9  OAX  O  O2    0  -0.589  18.7606  44.8671  44.2887
 2F9  CAT  C  CH2   0  -0.211  19.8305  45.1969  43.4173
 2F9  CBH  C  CH1   0  -0.171  20.2848  46.6131  43.7605
 2F9  CBA  C  C     0   0.542  20.5415  46.7028  45.2622
 2F9  OAK  O  O     0  -0.431  21.5054  46.2198  45.7966
 2F9  OAE  O  OH1   0  -0.577  19.5634  47.3218  45.8970
 2F9  NAV  N  NH1   0  -0.658  21.4930  46.8884  43.0292
 2F9  CBC  C  C     0   0.584  22.1458  48.0488  43.1965
 2F9  OAG  O  O     0  -0.478  21.7389  48.9137  43.9564
 2F9  CBI  C  CH1   0  -0.219  23.4431  48.1869  42.4108
 2F9  CBF  C  CH1   0  -0.221  24.5412  47.2709  43.0006
 2F9  CAB  C  CH3   0  -0.680  24.8177  47.5657  44.4702
 2F9  CAA  C  CH3   0  -0.659  25.8181  47.3663  42.1748
 2F9  NAU  N  NH1   0  -0.650  23.8303  49.5726  42.3957
 2F9  CBB  C  C     0   0.542  24.2053  50.2320  41.2830
 2F9  OAF  O  O     0  -0.481  24.2255  49.7247  40.1711
 2F9  CBE  C  CR6   0  -0.046  24.6035  51.6563  41.4894
 2F9  CAP  C  CR16  0  -0.272  25.1639  52.1102  42.6817
 2F9  CAN  C  CR16  0  -0.398  25.5441  53.4351  42.8280
 2F9  CBD  C  CR6   0   0.533  25.3502  54.2974  41.7664
 2F9  FAM  F  F     0  -0.308  25.7093  55.5804  41.9011
 2F9  CAO  C  CR16  0  -0.399  24.8053  53.8794  40.5663
 2F9  CAQ  C  CR16  0  -0.251  24.4441  52.5496  40.4321
 2F9  H1   H  HOH1  0   0.480  14.9030  49.6737  39.2053
 2F9  H2   H  HCH2  0   0.289  16.2351  46.5028  39.5747
 2F9  H3   H  HCH2  0   0.284  16.5015  47.2560  41.1215
 2F9  H4   H  HCH2  0   0.273  14.3615  46.1191  41.9824
 2F9  H5   H  HCH2  0   0.273  14.2395  45.2822  40.4534
 2F9  H6   H  HCH1  0   0.298  15.1346  43.8390  42.0890
 2F9  H7   H  HOH1  0   0.483  18.2455  43.9821  39.6652
 2F9  H8   H  HNH1  0   0.412  16.4262  46.0050  43.1487
 2F9  H9   H  HOH1  0   0.498  16.9716  43.3668  45.7619
 2F9  H10  H  HCH2  0   0.277  19.5326  45.1623  42.3668
 2F9  H11  H  HCH2  0   0.262  20.6499  44.4900  43.5673
 2F9  H12  H  HCH1  0   0.291  19.4976  47.3192  43.4815
 2F9  H13  H  HOH1  0   0.484  19.7297  47.3182  46.8520
 2F9  H14  H  HNH1  0   0.418  21.8501  46.2012  42.3835
 2F9  H15  H  HCH1  0   0.297  23.2626  47.8745  41.3790
 2F9  H16  H  HCH1  0   0.237  24.1676  46.2453  42.9203
 2F9  H17  H  HCH3  0   0.243  23.9502  47.3784  45.1027
 2F9  H18  H  HCH3  0   0.240  25.6267  46.9310  44.8330
 2F9  H19  H  HCH3  0   0.220  25.1287  48.6014  44.6195
 2F9  H20  H  HCH3  0   0.238  26.5460  46.6327  42.5233
 2F9  H21  H  HCH3  0   0.233  25.6323  47.1792  41.1165
 2F9  H22  H  HCH3  0   0.222  26.2802  48.3503  42.2684
 2F9  H23  H  HNH1  0   0.403  23.6673  50.0996  43.2394
 2F9  H24  H  HCR6  0   0.271  25.3405  51.4325  43.5073
 2F9  H25  H  HCR6  0   0.289  25.9892  53.7865  43.7489
 2F9  H26  H  HCR6  0   0.287  24.6687  54.5788  39.7522
 2F9  H27  H  HCR6  0   0.273  24.0235  52.2079  39.4962

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
 2F9  O    C    double    1.206  0.020  1.206
 2F9  OE2  CD   double    1.206  0.020  1.206
 2F9  CD   OE1  single    1.329  0.020  1.329
 2F9  CD   CG   single    1.504  0.020  1.504
 2F9  OAF  CBB  double    1.222  0.020  1.222
 2F9  CAQ  CAO  aromatic  1.384  0.020  1.384
 2F9  CAQ  CBE  aromatic  1.393  0.020  1.393
 2F9  C    OXT  single    1.322  0.020  1.322
 2F9  C    CA   single    1.520  0.020  1.520
 2F9  CAO  CBD  aromatic  1.383  0.020  1.383
 2F9  CG   CB   single    1.522  0.020  1.522
 2F9  CB   CA   single    1.533  0.020  1.533
 2F9  CBB  CBE  single    1.493  0.020  1.493
 2F9  CBB  NAU  single    1.347  0.020  1.347
 2F9  CBE  CAP  aromatic  1.393  0.020  1.393
 2F9  CA   N    single    1.451  0.020  1.451
 2F9  CBD  FAM  single    1.339  0.020  1.339
 2F9  CBD  CAN  aromatic  1.381  0.020  1.381
 2F9  CAA  CBF  single    1.524  0.020  1.524
 2F9  NAU  CBI  single    1.439  0.020  1.439
 2F9  CBI  CBF  single    1.547  0.020  1.547
 2F9  CBI  CBC  single    1.523  0.020  1.523
 2F9  CAP  CAN  aromatic  1.386  0.020  1.386
 2F9  OAL  PBJ  double    1.480  0.020  1.480
 2F9  N    PBJ  single    1.648  0.020  1.648
 2F9  CBF  CAB  single    1.524  0.020  1.524
 2F9  CBC  NAV  single    1.342  0.020  1.342
 2F9  CBC  OAG  double    1.221  0.020  1.221
 2F9  CAT  CBH  single    1.526  0.020  1.526
 2F9  CAT  OAX  single    1.419  0.020  1.419
 2F9  NAV  CBH  single    1.439  0.020  1.439
 2F9  PBJ  OAX  single    1.607  0.020  1.607
 2F9  PBJ  OAH  single    1.598  0.020  1.598
 2F9  CBH  CBA  single    1.526  0.020  1.526
 2F9  CBA  OAK  double    1.203  0.020  1.203
 2F9  CBA  OAE  single    1.320  0.020  1.320
 2F9  OE1  H1   single    0.850  0.020  0.980
 2F9  CG   H2   single    0.970  0.020  1.090
 2F9  CG   H3   single    0.970  0.020  1.090
 2F9  CB   H4   single    0.970  0.020  1.090
 2F9  CB   H5   single    0.970  0.020  1.090
 2F9  CA   H6   single    0.970  0.020  1.090
 2F9  OXT  H7   single    0.850  0.020  0.980
 2F9  N    H8   single    0.890  0.020  1.040
 2F9  OAH  H9   single    0.850  0.020  0.980
 2F9  CAT  H10  single    0.970  0.020  1.090
 2F9  CAT  H11  single    0.970  0.020  1.090
 2F9  CBH  H12  single    0.970  0.020  1.090
 2F9  OAE  H13  single    0.850  0.020  0.980
 2F9  NAV  H14  single    0.860  0.020  1.020
 2F9  CBI  H15  single    0.970  0.020  1.090
 2F9  CBF  H16  single    0.970  0.020  1.090
 2F9  CAB  H17  single    0.970  0.020  1.090
 2F9  CAB  H18  single    0.970  0.020  1.090
 2F9  CAB  H19  single    0.970  0.020  1.090
 2F9  CAA  H20  single    0.970  0.020  1.090
 2F9  CAA  H21  single    0.970  0.020  1.090
 2F9  CAA  H22  single    0.970  0.020  1.090
 2F9  NAU  H23  single    0.860  0.020  1.020
 2F9  CAP  H24  single    0.930  0.020  1.080
 2F9  CAN  H25  single    0.930  0.020  1.080
 2F9  CAO  H26  single    0.930  0.020  1.080
 2F9  CAQ  H27  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
 2F9  H1   OE1  CD   109.93  3.000
 2F9  CG   CD   OE2  125.19  3.000
 2F9  CG   CD   OE1  111.65  3.000
 2F9  OE2  CD   OE1  123.16  3.000
 2F9  H3   CG   H2   105.50  3.000
 2F9  H3   CG   CB   111.73  3.000
 2F9  H2   CG   CB   111.60  3.000
 2F9  H3   CG   CD   107.90  3.000
 2F9  H2   CG   CD   107.48  3.000
 2F9  CB   CG   CD   112.28  3.000
 2F9  H5   CB   H4   106.37  3.000
 2F9  H5   CB   CA   107.85  3.000
 2F9  H4   CB   CA   106.99  3.000
 2F9  H5   CB   CG   110.25  3.000
 2F9  H4   CB   CG   110.24  3.000
 2F9  CA   CB   CG   114.76  3.000
 2F9  H6   CA   N    111.49  3.000
 2F9  H6   CA   C    105.91  3.000
 2F9  N    CA   C    112.77  3.000
 2F9  H6   CA   CB   106.13  3.000
 2F9  N    CA   CB   110.39  3.000
 2F9  C    CA   CB   109.85  3.000
 2F9  O    C    OXT  123.82  3.000
 2F9  OXT  C    CA   114.01  3.000
 2F9  O    C    CA   122.08  3.000
 2F9  H7   OXT  C    109.81  3.000
 2F9  H8   N    PBJ  117.82  3.000
 2F9  H8   N    CA   115.66  3.000
 2F9  PBJ  N    CA   119.91  3.000
 2F9  OAX  PBJ  OAH   99.93  3.000
 2F9  OAH  PBJ  OAL  116.53  3.000
 2F9  OAX  PBJ  OAL  116.04  3.000
 2F9  OAH  PBJ  N    105.77  3.000
 2F9  OAX  PBJ  N    105.14  3.000
 2F9  OAL  PBJ  N    112.02  3.000
 2F9  H9   OAH  PBJ  114.60  3.000
 2F9  CAT  OAX  PBJ  120.74  3.000
 2F9  H11  CAT  H10  108.42  3.000
 2F9  H11  CAT  CBH  110.25  3.000
 2F9  H10  CAT  CBH  109.07  3.000
 2F9  H11  CAT  OAX  109.33  3.000
 2F9  H10  CAT  OAX  112.19  3.000
 2F9  CBH  CAT  OAX  107.58  3.000
 2F9  H12  CBH  NAV  110.56  3.000
 2F9  H12  CBH  CBA  109.52  3.000
 2F9  NAV  CBH  CBA  110.34  3.000
 2F9  H12  CBH  CAT  109.11  3.000
 2F9  CBA  CBH  CAT  109.01  3.000
 2F9  NAV  CBH  CAT  108.25  3.000
 2F9  OAE  CBA  OAK  124.62  3.000
 2F9  OAE  CBA  CBH  112.09  3.000
 2F9  OAK  CBA  CBH  123.24  3.000
 2F9  H13  OAE  CBA  110.18  3.000
 2F9  H14  NAV  CBC  119.79  3.000
 2F9  H14  NAV  CBH  119.50  3.000
 2F9  CBC  NAV  CBH  120.70  3.000
 2F9  CBI  CBC  OAG  122.73  3.000
 2F9  OAG  CBC  NAV  121.87  3.000
 2F9  CBI  CBC  NAV  115.37  3.000
 2F9  H15  CBI  NAU  108.04  3.000
 2F9  H15  CBI  CBF  107.93  3.000
 2F9  NAU  CBI  CBF  112.53  3.000
 2F9  H15  CBI  CBC  108.69  3.000
 2F9  CBF  CBI  CBC  110.75  3.000
 2F9  NAU  CBI  CBC  108.78  3.000
 2F9  H16  CBF  CAA  107.76  3.000
 2F9  H16  CBF  CAB  108.29  3.000
 2F9  CAA  CBF  CAB  111.00  3.000
 2F9  H16  CBF  CBI  106.54  3.000
 2F9  CAB  CBF  CBI  112.45  3.000
 2F9  CAA  CBF  CBI  110.56  3.000
 2F9  H19  CAB  H18  107.18  3.000
 2F9  H19  CAB  H17  108.09  3.000
 2F9  H18  CAB  H17  107.31  3.000
 2F9  H19  CAB  CBF  111.53  3.000
 2F9  H18  CAB  CBF  110.05  3.000
 2F9  H17  CAB  CBF  112.45  3.000
 2F9  H22  CAA  H21  108.06  3.000
 2F9  H22  CAA  H20  107.25  3.000
 2F9  H21  CAA  H20  107.96  3.000
 2F9  H22  CAA  CBF  111.40  3.000
 2F9  H21  CAA  CBF  111.87  3.000
 2F9  H20  CAA  CBF  110.13  3.000
 2F9  H23  NAU  CBB  118.73  3.000
 2F9  H23  NAU  CBI  116.82  3.000
 2F9  CBB  NAU  CBI  123.72  3.000
 2F9  CBE  CBB  OAF  121.14  3.000
 2F9  CBE  CBB  NAU  115.28  3.000
 2F9  OAF  CBB  NAU  123.58  3.000
 2F9  CAQ  CBE  CAP  119.11  3.000
 2F9  CAP  CBE  CBB  122.42  3.000
 2F9  CAQ  CBE  CBB  118.43  3.000
 2F9  H24  CAP  CAN  118.24  3.000
 2F9  H24  CAP  CBE  120.95  3.000
 2F9  CAN  CAP  CBE  120.79  3.000
 2F9  H25  CAN  CBD  120.62  3.000
 2F9  H25  CAN  CAP  120.89  3.000
 2F9  CBD  CAN  CAP  118.50  3.000
 2F9  CAO  CBD  FAM  118.85  3.000
 2F9  FAM  CBD  CAN  118.89  3.000
 2F9  CAO  CBD  CAN  122.25  3.000
 2F9  H26  CAO  CAQ  121.00  3.000
 2F9  H26  CAO  CBD  120.49  3.000
 2F9  CAQ  CAO  CBD  118.51  3.000
 2F9  H27  CAQ  CAO  119.26  3.000
 2F9  H27  CAQ  CBE  119.91  3.000
 2F9  CAO  CAQ  CBE  120.83  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
 2F9  CONST_01  CBD  CAO  CAQ  CBE     0.00   0.0  0
 2F9  CONST_02  CBD  CAN  CAP  CBE     0.00   0.0  0
 2F9  CONST_03  CAO  CAQ  CBE  CAP     0.00   0.0  0
 2F9  CONST_04  CAO  CBD  CAN  CAP     0.00   0.0  0
 2F9  CONST_05  CAQ  CAO  CBD  CAN     0.00   0.0  0
 2F9  CONST_06  CAQ  CBE  CAP  CAN     0.00   0.0  0
 2F9  CONST_07  CAO  CAQ  CBE  CBB   180.00   0.0  0
 2F9  CONST_08  CAN  CAP  CBE  CBB   180.00   0.0  0
 2F9  CONST_09  FAM  CBD  CAN  CAP   180.00   0.0  0
 2F9  CONST_10  CAQ  CAO  CBD  FAM   180.00   0.0  0
 2F9  CONST_11  H26  CAO  CAQ  CBE   180.00   0.0  0
 2F9  CONST_12  H25  CAN  CAP  CBE   180.00   0.0  0
 2F9  CONST_13  H27  CAQ  CBE  CAP   180.00   0.0  0
 2F9  CONST_14  H24  CAP  CAN  CBD   180.00   0.0  0
 2F9  CONST_15  CBE  CBB  NAU  CBI   180.00   0.0  0
 2F9  CONST_16  H23  NAU  CBB  CBE     0.00   0.0  0
 2F9  CONST_17  CBI  CBC  NAV  CBH   180.00   0.0  0
 2F9  CONST_18  OAG  CBC  NAV  CBH     0.00   0.0  0
 2F9  CONST_19  OAF  CBB  NAU  CBI     0.00   0.0  0
 2F9  CONST_20  H14  NAV  CBC  OAG   180.00   0.0  0
 2F9  CONST_21  H1   OE1  CD   OE2     0.00   0.0  0
 2F9  CONST_22  H7   OXT  C    CA    180.00   0.0  0
 2F9  CONST_23  H13  OAE  CBA  CBH   180.00   0.0  0
 2F9  Var_01    CAQ  CBE  CBB  NAU  -152.57  30.0  2
 2F9  Var_02    CB   CG   CD   OE1  -179.02  30.0  3
 2F9  Var_03    CA   CB   CG   CD   -174.26  30.0  3
 2F9  Var_04    OAL  PBJ  N    CA     28.44  30.0  3
 2F9  Var_05    CBH  CAT  OAX  PBJ   140.01  30.0  1
 2F9  Var_06    H20  CAA  CBF  CBI  -173.29  30.0  3
 2F9  Var_07    H17  CAB  CBF  CBI    62.99  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
 2F9  chir_01  CA   C    CB   N    positiv
 2F9  chir_03  CBH  CAT  NAV  CBA  positiv
 2F9  chir_04  CBI  NAU  CBC  CBF  positiv
 2F9  chir_05  PBJ  N    OAX  OAH  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
 2F9  plan-1  CBB  0.020
 2F9  plan-1  CBE  0.020
 2F9  plan-1  CAP  0.020
 2F9  plan-1  CAN  0.020
 2F9  plan-1  CBD  0.020
 2F9  plan-1  FAM  0.020
 2F9  plan-1  CAO  0.020
 2F9  plan-1  CAQ  0.020
 2F9  plan-1  H24  0.020
 2F9  plan-1  H25  0.020
 2F9  plan-1  H26  0.020
 2F9  plan-1  H27  0.020
 2F9  plan-2  CBH  0.020
 2F9  plan-2  NAV  0.020
 2F9  plan-2  CBC  0.020
 2F9  plan-2  OAG  0.020
 2F9  plan-2  CBI  0.020
 2F9  plan-2  H14  0.020
 2F9  plan-3  CBI  0.020
 2F9  plan-3  NAU  0.020
 2F9  plan-3  CBB  0.020
 2F9  plan-3  OAF  0.020
 2F9  plan-3  CBE  0.020
 2F9  plan-3  H23  0.020
 2F9  plan-4  OE1  0.020
 2F9  plan-4  CD   0.020
 2F9  plan-4  OE2  0.020
 2F9  plan-4  CG   0.020
 2F9  plan-4  H1   0.020
 2F9  plan-5  CA   0.020
 2F9  plan-5  C    0.020
 2F9  plan-5  OXT  0.020
 2F9  plan-5  O    0.020
 2F9  plan-5  H7   0.020
 2F9  plan-6  CBH  0.020
 2F9  plan-6  CBA  0.020
 2F9  plan-6  OAK  0.020
 2F9  plan-6  OAE  0.020
 2F9  plan-6  H13  0.020

