# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 07:38:27 2021
#   Inital geometry file: a 160 line input string
#   Ligand name: N-(4-fluorobenzoyl)-L-gamma-glutamyl-O-[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](N[P](O)(=O)OC[C@H](NC(=O)CC[C@H](NC(=O)c1ccc(F)cc1)C(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
 T01  T01  N-(4-fluorobenzoyl)-L-gamma-glutamyl-O-[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]-L-serine  ligand  63  38  .  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_T01
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
 T01  CAP  C  CR16  0  -0.267  25.1349  49.8761  41.6941
 T01  CAN  C  CR16  0  -0.398  24.9937  51.2513  41.5958
 T01  CBG  C  CR6   0   0.536  23.8558  51.8359  42.1175
 T01  FAM  F  F     0  -0.308  23.7075  53.1628  42.0188
 T01  CAO  C  CR16  0  -0.402  22.8680  51.0978  42.7426
 T01  CAQ  C  CR16  0  -0.258  23.0309  49.7266  42.8446
 T01  CBH  C  CR6   0  -0.049  24.1551  49.1003  42.3109
 T01  CBF  C  C     0   0.541  24.2886  47.6217  42.4640
 T01  OAF  O  O     0  -0.474  23.7782  47.0313  43.4071
 T01  N    N  NH1   0  -0.641  24.9938  47.0015  41.5005
 T01  CA   C  CH1   0  -0.223  25.3218  45.5998  41.5213
 T01  C    C  C     0   0.561  26.7735  45.4327  41.1086
 T01  O    O  O     0  -0.429  27.4492  46.3039  40.6248
 T01  OXT  O  OH1   0  -0.585  27.1987  44.2008  41.3323
 T01  CB   C  CH2   0  -0.427  24.4018  44.7713  40.6102
 T01  CG   C  CH2   0  -0.607  22.9469  44.8259  41.0502
 T01  CD   C  C     0   0.559  22.7070  44.0857  42.3510
 T01  OE1  O  O     0  -0.491  23.3858  43.1121  42.6444
 T01  NE2  N  NH1   0  -0.624  21.6767  44.4596  43.1420
 T01  CBK  C  CH1   0  -0.258  20.8704  45.6448  43.0635
 T01  CBD  C  C     0   0.585  20.9047  46.4844  44.3360
 T01  OAK  O  OH1   0  -0.574  21.5055  45.8948  45.3484
 T01  OAD  O  O     0  -0.448  20.3853  47.5708  44.3920
 T01  CAV  C  CH2   0  -0.152  19.4227  45.3297  42.7160
 T01  OAZ  O  O2    0  -0.594  18.8682  44.6209  43.8221
 T01  PBL  P  P     0   1.452  17.4977  43.7976  43.6541
 T01  OAL  O  O     0  -0.711  17.5089  42.7241  42.6354
 T01  OAG  O  OH1   0  -0.728  17.2662  43.3396  45.1690
 T01  NAY  N  NH1   0  -0.802  16.3345  44.9248  43.3567
 T01  CBJ  C  CH1   0  -0.158  15.1932  44.6134  42.5210
 T01  CBC  C  C     0   0.541  15.5786  44.3400  41.0764
 T01  OAJ  O  O     0  -0.444  14.9046  43.6487  40.3536
 T01  OAC  O  OH1   0  -0.574  16.6654  44.9792  40.6803
 T01  CAT  C  CH2   0  -0.490  14.1705  45.7544  42.5735
 T01  CAR  C  CH2   0  -0.589  14.6829  47.0854  42.0421
 T01  CBA  C  C     0   0.559  13.7158  48.2121  42.2830
 T01  OAH  O  O     0  -0.442  12.6558  48.1102  42.8481
 T01  OAA  O  OH1   0  -0.595  14.1694  49.3594  41.7899
 T01  H1   H  HCR6  0   0.269  26.0389  49.4254  41.3049
 T01  H2   H  HCR6  0   0.289  25.7592  51.8550  41.1272
 T01  H3   H  HCR6  0   0.287  21.9899  51.5842  43.1456
 T01  H4   H  HCR6  0   0.280  22.2653  49.1426  43.3364
 T01  H5   H  HNH1  0   0.408  25.2761  47.5238  40.6860
 T01  H6   H  HCH1  0   0.303  25.2248  45.2428  42.5489
 T01  H7   H  HOH1  0   0.489  28.1170  44.1019  41.0378
 T01  H8   H  HCH2  0   0.258  24.4765  45.1513  39.5889
 T01  H9   H  HCH2  0   0.260  24.7406  43.7367  40.5905
 T01  H10  H  HCH2  0   0.264  22.5981  45.8568  41.0642
 T01  H11  H  HCH2  0   0.302  22.3329  44.3256  40.2941
 T01  H12  H  HNH1  0   0.394  21.5311  43.8593  43.9417
 T01  H13  H  HCH1  0   0.311  21.2480  46.2918  42.2736
 T01  H14  H  HOH1  0   0.488  21.4808  46.4673  46.1305
 T01  H15  H  HCH2  0   0.254  18.8629  46.2481  42.5345
 T01  H16  H  HCH2  0   0.258  19.4027  44.7273  41.8058
 T01  H17  H  HOH1  0   0.498  17.8447  42.6249  45.4689
 T01  H18  H  HNH1  0   0.413  16.2150  45.6826  44.0141
 T01  H19  H  HCH1  0   0.296  14.6737  43.7153  42.8678
 T01  H20  H  HOH1  0   0.482  16.8362  44.7872  39.7456
 T01  H21  H  HCH2  0   0.272  13.8573  45.8572  43.6145
 T01  H22  H  HCH2  0   0.273  13.2857  45.4405  42.0185
 T01  H23  H  HCH2  0   0.289  14.8749  47.0399  40.9669
 T01  H24  H  HCH2  0   0.287  15.6394  47.3588  42.4964
 T01  H25  H  HOH1  0   0.480  13.5292  50.0675  41.9559

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
 T01  O    C    double    1.204  0.020  1.204
 T01  OXT  C    single    1.322  0.020  1.322
 T01  C    CA   single    1.518  0.020  1.518
 T01  OAJ  CBC  double    1.206  0.020  1.206
 T01  OAH  CBA  double    1.205  0.020  1.205
 T01  CAN  CAP  aromatic  1.386  0.020  1.386
 T01  CAN  CBG  aromatic  1.382  0.020  1.382
 T01  CAP  CBH  aromatic  1.394  0.020  1.394
 T01  CBA  OAA  single    1.329  0.020  1.329
 T01  CBA  CAR  single    1.504  0.020  1.504
 T01  CBC  OAC  single    1.322  0.020  1.322
 T01  CBC  CBJ  single    1.520  0.020  1.520
 T01  N    CA   single    1.440  0.020  1.440
 T01  N    CBF  single    1.346  0.020  1.346
 T01  CA   CB   single    1.537  0.020  1.537
 T01  CB   CG   single    1.521  0.020  1.521
 T01  CAR  CAT  single    1.522  0.020  1.522
 T01  CAT  CBJ  single    1.533  0.020  1.533
 T01  CBG  FAM  single    1.339  0.020  1.339
 T01  CBG  CAO  aromatic  1.383  0.020  1.383
 T01  CBH  CBF  single    1.492  0.020  1.492
 T01  CBH  CAQ  aromatic  1.393  0.020  1.393
 T01  CBJ  NAY  single    1.448  0.020  1.448
 T01  CBF  OAF  double    1.224  0.020  1.224
 T01  CG   CD   single    1.516  0.020  1.516
 T01  CAO  CAQ  aromatic  1.385  0.020  1.385
 T01  OAL  PBL  double    1.480  0.020  1.480
 T01  NAY  PBL  single    1.647  0.020  1.647
 T01  CD   OE1  double    1.223  0.020  1.223
 T01  CD   NE2  single    1.352  0.020  1.352
 T01  CAV  CBK  single    1.522  0.020  1.522
 T01  CAV  OAZ  single    1.426  0.020  1.426
 T01  PBL  OAZ  single    1.608  0.020  1.608
 T01  PBL  OAG  single    1.599  0.020  1.599
 T01  CBK  NE2  single    1.436  0.020  1.436
 T01  CBK  CBD  single    1.525  0.020  1.525
 T01  CBD  OAD  double    1.205  0.020  1.205
 T01  CBD  OAK  single    1.317  0.020  1.317
 T01  CAP  H1   single    0.930  0.020  1.080
 T01  CAN  H2   single    0.930  0.020  1.080
 T01  CAO  H3   single    0.930  0.020  1.080
 T01  CAQ  H4   single    0.930  0.020  1.080
 T01  N    H5   single    0.860  0.020  1.020
 T01  CA   H6   single    0.970  0.020  1.090
 T01  OXT  H7   single    0.850  0.020  0.980
 T01  CB   H8   single    0.970  0.020  1.090
 T01  CB   H9   single    0.970  0.020  1.090
 T01  CG   H10  single    0.970  0.020  1.090
 T01  CG   H11  single    0.970  0.020  1.090
 T01  NE2  H12  single    0.860  0.020  1.020
 T01  CBK  H13  single    0.970  0.020  1.090
 T01  OAK  H14  single    0.850  0.020  0.980
 T01  CAV  H15  single    0.970  0.020  1.090
 T01  CAV  H16  single    0.970  0.020  1.090
 T01  OAG  H17  single    0.850  0.020  0.980
 T01  NAY  H18  single    0.890  0.020  1.040
 T01  CBJ  H19  single    0.970  0.020  1.090
 T01  OAC  H20  single    0.850  0.020  0.980
 T01  CAT  H21  single    0.970  0.020  1.090
 T01  CAT  H22  single    0.970  0.020  1.090
 T01  CAR  H23  single    0.970  0.020  1.090
 T01  CAR  H24  single    0.970  0.020  1.090
 T01  OAA  H25  single    0.850  0.020  0.980

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
 T01  H1   CAP  CBH  120.96  3.000
 T01  H1   CAP  CAN  118.21  3.000
 T01  CBH  CAP  CAN  120.81  3.000
 T01  H2   CAN  CBG  120.69  3.000
 T01  H2   CAN  CAP  120.82  3.000
 T01  CBG  CAN  CAP  118.49  3.000
 T01  CAO  CBG  FAM  118.90  3.000
 T01  CAO  CBG  CAN  122.23  3.000
 T01  FAM  CBG  CAN  118.87  3.000
 T01  H3   CAO  CAQ  120.89  3.000
 T01  H3   CAO  CBG  120.56  3.000
 T01  CAQ  CAO  CBG  118.55  3.000
 T01  H4   CAQ  CBH  120.18  3.000
 T01  H4   CAQ  CAO  119.02  3.000
 T01  CBH  CAQ  CAO  120.79  3.000
 T01  CBF  CBH  CAQ  118.57  3.000
 T01  CAQ  CBH  CAP  119.12  3.000
 T01  CBF  CBH  CAP  122.28  3.000
 T01  N    CBF  OAF  123.22  3.000
 T01  OAF  CBF  CBH  121.30  3.000
 T01  N    CBF  CBH  115.47  3.000
 T01  H5   N    CA   116.90  3.000
 T01  H5   N    CBF  119.12  3.000
 T01  CA   N    CBF  123.90  3.000
 T01  H6   CA   CB   109.17  3.000
 T01  H6   CA   C    107.74  3.000
 T01  CB   CA   C    110.60  3.000
 T01  H6   CA   N    108.16  3.000
 T01  CB   CA   N    112.32  3.000
 T01  C    CA   N    108.72  3.000
 T01  OXT  C    O    124.17  3.000
 T01  OXT  C    CA   111.34  3.000
 T01  O    C    CA   124.48  3.000
 T01  H7   OXT  C    110.38  3.000
 T01  H9   CB   H8   107.00  3.000
 T01  H9   CB   CG   109.69  3.000
 T01  H8   CB   CG   108.87  3.000
 T01  H9   CB   CA   109.67  3.000
 T01  H8   CB   CA   109.02  3.000
 T01  CG   CB   CA   112.44  3.000
 T01  H11  CG   H10  105.19  3.000
 T01  H11  CG   CD   106.31  3.000
 T01  H10  CG   CD   113.63  3.000
 T01  H11  CG   CB   108.68  3.000
 T01  H10  CG   CB   110.14  3.000
 T01  CD   CG   CB   112.46  3.000
 T01  NE2  CD   OE1  120.20  3.000
 T01  NE2  CD   CG   119.19  3.000
 T01  OE1  CD   CG   120.46  3.000
 T01  H12  NE2  CBK  116.92  3.000
 T01  H12  NE2  CD   114.12  3.000
 T01  CBK  NE2  CD   128.64  3.000
 T01  H13  CBK  CAV  106.70  3.000
 T01  H13  CBK  CBD  105.70  3.000
 T01  CAV  CBK  CBD  109.03  3.000
 T01  H13  CBK  NE2  109.60  3.000
 T01  CBD  CBK  NE2  113.35  3.000
 T01  CAV  CBK  NE2  112.07  3.000
 T01  OAD  CBD  OAK  124.36  3.000
 T01  OAK  CBD  CBK  113.91  3.000
 T01  OAD  CBD  CBK  121.69  3.000
 T01  H14  OAK  CBD  110.14  3.000
 T01  H16  CAV  H15  108.45  3.000
 T01  H16  CAV  OAZ  111.43  3.000
 T01  H15  CAV  OAZ  110.37  3.000
 T01  H16  CAV  CBK  108.79  3.000
 T01  H15  CAV  CBK  110.60  3.000
 T01  OAZ  CAV  CBK  107.20  3.000
 T01  PBL  OAZ  CAV  120.34  3.000
 T01  NAY  PBL  OAG  105.36  3.000
 T01  OAG  PBL  OAL  116.45  3.000
 T01  NAY  PBL  OAL  112.18  3.000
 T01  OAG  PBL  OAZ   99.85  3.000
 T01  NAY  PBL  OAZ  105.69  3.000
 T01  OAL  PBL  OAZ  115.91  3.000
 T01  H17  OAG  PBL  114.76  3.000
 T01  H18  NAY  CBJ  116.33  3.000
 T01  H18  NAY  PBL  118.64  3.000
 T01  CBJ  NAY  PBL  120.90  3.000
 T01  H19  CBJ  CAT  106.46  3.000
 T01  H19  CBJ  CBC  105.91  3.000
 T01  CAT  CBJ  CBC  109.61  3.000
 T01  H19  CBJ  NAY  111.58  3.000
 T01  CAT  CBJ  NAY  110.23  3.000
 T01  CBC  CBJ  NAY  112.78  3.000
 T01  OAC  CBC  OAJ  123.86  3.000
 T01  OAC  CBC  CBJ  113.98  3.000
 T01  OAJ  CBC  CBJ  122.07  3.000
 T01  H20  OAC  CBC  109.76  3.000
 T01  H22  CAT  H21  106.24  3.000
 T01  H22  CAT  CAR  110.31  3.000
 T01  H21  CAT  CAR  110.31  3.000
 T01  H22  CAT  CBJ  108.03  3.000
 T01  H21  CAT  CBJ  107.10  3.000
 T01  CAR  CAT  CBJ  114.47  3.000
 T01  H24  CAR  H23  105.39  3.000
 T01  H24  CAR  CBA  107.97  3.000
 T01  H23  CAR  CBA  107.56  3.000
 T01  H24  CAR  CAT  111.59  3.000
 T01  H23  CAR  CAT  111.48  3.000
 T01  CBA  CAR  CAT  112.50  3.000
 T01  OAA  CBA  OAH  123.18  3.000
 T01  OAA  CBA  CAR  111.58  3.000
 T01  OAH  CBA  CAR  125.24  3.000
 T01  H25  OAA  CBA  109.99  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
 T01  CONST_01  CAO  CBG  CAN  CAP     0.00   0.0  0
 T01  CONST_02  CAO  CAQ  CBH  CAP     0.00   0.0  0
 T01  CONST_03  CAQ  CBH  CAP  CAN     0.00   0.0  0
 T01  CONST_04  CAQ  CAO  CBG  CAN     0.00   0.0  0
 T01  CONST_05  CBH  CAP  CAN  CBG     0.00   0.0  0
 T01  CONST_06  CBH  CAQ  CAO  CBG     0.00   0.0  0
 T01  CONST_07  FAM  CBG  CAN  CAP   180.00   0.0  0
 T01  CONST_08  CBF  CBH  CAP  CAN   180.00   0.0  0
 T01  CONST_09  CAQ  CAO  CBG  FAM   180.00   0.0  0
 T01  CONST_10  CBF  CBH  CAQ  CAO   180.00   0.0  0
 T01  CONST_11  H4   CAQ  CBH  CAP   180.00   0.0  0
 T01  CONST_12  H3   CAO  CBG  CAN   180.00   0.0  0
 T01  CONST_13  H1   CAP  CAN  CBG   180.00   0.0  0
 T01  CONST_14  H2   CAN  CBG  CAO   180.00   0.0  0
 T01  CONST_15  CA   N    CBF  CBH   180.00   0.0  0
 T01  CONST_16  H5   N    CBF  CBH     0.00   0.0  0
 T01  CONST_17  CA   N    CBF  OAF     0.00   0.0  0
 T01  CONST_18  CBK  NE2  CD   CG      0.00   0.0  0
 T01  CONST_19  CBK  NE2  CD   OE1   180.00   0.0  0
 T01  CONST_20  H12  NE2  CD   CG    180.00   0.0  0
 T01  CONST_21  H7   OXT  C    CA    180.00   0.0  0
 T01  CONST_22  H14  OAK  CBD  CBK   180.00   0.0  0
 T01  CONST_23  H20  OAC  CBC  CBJ   180.00   0.0  0
 T01  CONST_24  H25  OAA  CBA  CAR   180.00   0.0  0
 T01  Var_01    N    CBF  CBH  CAP   -30.38  30.0  2
 T01  Var_02    CD   CG   CB   CA    -69.68  30.0  3
 T01  Var_03    OE1  CD   CG   CB    -30.84  30.0  3
 T01  Var_04    OAL  PBL  OAZ  CAV    59.24  30.0  1
 T01  Var_05    CBJ  NAY  PBL  OAZ   148.36  30.0  1
 T01  Var_06    CBA  CAR  CAT  CBJ  -172.27  30.0  1
 T01  Var_07    OAH  CBA  CAR  CAT     1.07  30.0  2
 T01  Var_08    H15  CAV  OAZ  PBL    75.72  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
 T01  chir_01  CA   C    N    CB   negativ
 T01  chir_02  CBK  NE2  CAV  CBD  negativ
 T01  chir_04  CBJ  CBC  CAT  NAY  positiv
 T01  chir_05  PBL  NAY  OAZ  OAG  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
 T01  plan-1  CAP  0.020
 T01  plan-1  CAN  0.020
 T01  plan-1  CBG  0.020
 T01  plan-1  FAM  0.020
 T01  plan-1  CAO  0.020
 T01  plan-1  CAQ  0.020
 T01  plan-1  CBH  0.020
 T01  plan-1  CBF  0.020
 T01  plan-1  H1   0.020
 T01  plan-1  H2   0.020
 T01  plan-1  H3   0.020
 T01  plan-1  H4   0.020
 T01  plan-2  CBH  0.020
 T01  plan-2  CBF  0.020
 T01  plan-2  OAF  0.020
 T01  plan-2  N    0.020
 T01  plan-2  CA   0.020
 T01  plan-2  H5   0.020
 T01  plan-3  CG   0.020
 T01  plan-3  CD   0.020
 T01  plan-3  OE1  0.020
 T01  plan-3  NE2  0.020
 T01  plan-3  CBK  0.020
 T01  plan-3  H12  0.020
 T01  plan-4  CA   0.020
 T01  plan-4  C    0.020
 T01  plan-4  O    0.020
 T01  plan-4  OXT  0.020
 T01  plan-4  H7   0.020
 T01  plan-5  CBK  0.020
 T01  plan-5  CBD  0.020
 T01  plan-5  OAK  0.020
 T01  plan-5  OAD  0.020
 T01  plan-5  H14  0.020
 T01  plan-6  CBJ  0.020
 T01  plan-6  CBC  0.020
 T01  plan-6  OAJ  0.020
 T01  plan-6  OAC  0.020
 T01  plan-6  H20  0.020
 T01  plan-7  CAR  0.020
 T01  plan-7  CBA  0.020
 T01  plan-7  OAH  0.020
 T01  plan-7  OAA  0.020
 T01  plan-7  H25  0.020

