# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:26:29 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 1-[(3R)-3-hydroxy-2-methylbutan-2-yl]-L-tryptophan
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)C(C)(C)n1cc(C[C@H](N)C(O)=O)c2ccccc12
#
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
 F7P  F7P  1-[(3R)-3-hydroxy-2-methylbutan-2-yl]-L-tryptophan  L-peptide  43  21  .  2022-07-25  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_F7P
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
 F7P  CB   C  CH2   0  -0.563  -2.1532   0.4443  -0.7917
 F7P  CA   C  CH1   0  -0.202  -2.9543   0.6356   0.5217
 F7P  C    C  C     0   0.536  -4.3489   1.1205   0.1857
 F7P  O    O  O     0  -0.437  -5.3514   0.4609   0.2940
 F7P  N    N  NH2   0  -0.785  -3.0473  -0.5281   1.3719
 F7P  C5   C  CH3   0  -0.696   4.0790   2.6964   0.7223
 F7P  C4   C  CH1   0   0.017   2.8083   2.0576   0.1744
 F7P  C2   C  CH3   0  -0.674   3.1655   0.0754   1.6453
 F7P  CG   C  CR5   0   0.017  -0.7595  -0.0244  -0.5379
 F7P  CD1  C  CR15  0  -0.057   0.3369   0.7613  -0.3396
 F7P  CD2  C  CR56  0   0.003  -0.3014  -1.3715  -0.4231
 F7P  NE1  N  NR5   0  -0.566   1.4613   0.0055  -0.1055
 F7P  CE2  C  CR56  0   0.376   1.0870  -1.3213  -0.1510
 F7P  CE3  C  CR16  0  -0.377  -0.9533  -2.6047  -0.5317
 F7P  CZ2  C  CR16  0  -0.307   1.8115  -2.5065   0.0245
 F7P  CZ3  C  CR16  0  -0.271  -0.2295  -3.7668  -0.3665
 F7P  CH2  C  CR16  0  -0.284   1.1432  -3.7110  -0.0857
 F7P  C1   C  CT    0   0.099   2.8152   0.5139   0.2208
 F7P  C3   C  CH3   0  -0.661   3.8270  -0.0353  -0.7883
 F7P  O6   O  OH1   0  -0.669   2.5905   2.4454  -1.1653
 F7P  O1   O  OH1   0  -0.595  -4.3403   2.3641  -0.2804
 F7P  H1   H  HCH2  0   0.248  -2.6800  -0.2753  -1.4272
 F7P  H2   H  HCH2  0   0.259  -2.1316   1.3865  -1.3432
 F7P  H3   H  HCH1  0   0.275  -2.4569   1.4260   1.0920
 F7P  H4   H  HNH2  0   0.342  -3.4493  -1.3078   0.8657
 F7P  H5   H  HNH2  0   0.361  -2.1161  -0.8129   1.6468
 F7P  H8   H  HCH3  0   0.234   4.9820   2.3315   0.2323
 F7P  H9   H  HCH3  0   0.244   4.0297   3.7755   0.5643
 F7P  H10  H  HCH1  0   0.226   1.9841   2.4016   0.8175
 F7P  H11  H  HCH3  0   0.241   2.5450   0.5939   2.3782
 F7P  H12  H  HCH3  0   0.253   3.0181  -0.9927   1.7860
 F7P  H13  H  HCH3  0   0.245   4.2087   0.2875   1.8719
 F7P  H14  H  HCR5  0   0.282   0.3737   1.8359  -0.3749
 F7P  H15  H  HCR6  0   0.235  -2.0154  -2.6468  -0.7423
 F7P  H16  H  HCR6  0   0.256   2.8688  -2.5168   0.2423
 F7P  H17  H  HCR6  0   0.245  -0.7200  -4.7280  -0.4496
 F7P  H18  H  HCR6  0   0.248   1.6979  -4.6303   0.0501
 F7P  H19  H  HCH3  0   0.242   3.9419  -1.1133  -0.7056
 F7P  H20  H  HCH3  0   0.246   3.5371   0.1949  -1.8115
 F7P  H21  H  HCH3  0   0.238   4.8120   0.3948  -0.6080
 F7P  H22  H  HOH1  0   0.454   2.5153   3.4044  -1.1942
 F7P  H23  H  HOH1  0   0.482  -5.2382   2.6355  -0.5231
 F7P  H7   H  HCH3  0   0.240   4.1824   2.5431   1.7949

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
 F7P  C3   C1   single    1.531  0.020  1.531
 F7P  O6   C4   single    1.412  0.020  1.412
 F7P  C2   C1   single    1.531  0.020  1.531
 F7P  C5   C4   single    1.524  0.020  1.524
 F7P  C1   C4   single    1.544  0.020  1.544
 F7P  C1   NE1  single    1.483  0.020  1.483
 F7P  O    C    double    1.231  0.020  1.231
 F7P  NE1  CD1  aromatic  1.375  0.020  1.375
 F7P  NE1  CE2  aromatic  1.379  0.020  1.379
 F7P  CD1  CG   aromatic  1.363  0.020  1.363
 F7P  C    CA   single    1.525  0.021  1.525
 F7P  CG   CB   single    1.492  0.020  1.492
 F7P  CG   CD2  aromatic  1.428  0.020  1.428
 F7P  CE2  CZ2  aromatic  1.400  0.020  1.400
 F7P  CE2  CD2  aromatic  1.416  0.020  1.416
 F7P  CA   CB   single    1.521  0.033  1.521
 F7P  CA   N    single    1.458  0.019  1.458
 F7P  CZ2  CH2  aromatic  1.382  0.020  1.382
 F7P  CD2  CE3  aromatic  1.399  0.020  1.399
 F7P  CH2  CZ3  aromatic  1.402  0.020  1.402
 F7P  CE3  CZ3  aromatic  1.379  0.020  1.379
 F7P  C    O1   single    1.328  0.020  1.328
 F7P  CB   H1   single    0.970  0.020  1.090
 F7P  CB   H2   single    0.970  0.020  1.090
 F7P  CA   H3   single    0.970  0.020  1.090
 F7P  N    H4   single    0.890  0.020  1.040
 F7P  N    H5   single    0.890  0.020  1.040
 F7P  C5   H7   single    0.970  0.020  1.090
 F7P  C5   H8   single    0.970  0.020  1.090
 F7P  C5   H9   single    0.970  0.020  1.090
 F7P  C4   H10  single    0.970  0.020  1.090
 F7P  C2   H11  single    0.970  0.020  1.090
 F7P  C2   H12  single    0.970  0.020  1.090
 F7P  C2   H13  single    0.970  0.020  1.090
 F7P  CD1  H14  single    0.930  0.020  1.080
 F7P  CE3  H15  single    0.930  0.020  1.080
 F7P  CZ2  H16  single    0.930  0.020  1.080
 F7P  CZ3  H17  single    0.930  0.020  1.080
 F7P  CH2  H18  single    0.930  0.020  1.080
 F7P  C3   H19  single    0.970  0.020  1.090
 F7P  C3   H20  single    0.970  0.020  1.090
 F7P  C3   H21  single    0.970  0.020  1.090
 F7P  O6   H22  single    0.850  0.020  0.980
 F7P  O1   H23  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
 F7P  H2   CB   H1   106.47  3.000
 F7P  H2   CB   CG   109.78  3.000
 F7P  H1   CB   CG   109.98  3.000
 F7P  H2   CB   CA   109.37  3.000
 F7P  H1   CB   CA   108.91  3.000
 F7P  CG   CB   CA   112.16  3.000
 F7P  H3   CA   N    107.73  3.000
 F7P  H3   CA   C    107.63  3.000
 F7P  N    CA   C    111.00  2.800
 F7P  H3   CA   CB   107.20  3.000
 F7P  N    CA   CB   110.40  1.500
 F7P  C    CA   CB   110.50  1.500
 F7P  O1   C    O    123.33  3.000
 F7P  O1   C    CA   111.82  3.000
 F7P  O    C    CA   120.80  1.700
 F7P  H5   N    H4   106.52  3.000
 F7P  H5   N    CA   109.12  3.000
 F7P  H4   N    CA   110.59  3.000
 F7P  H9   C5   H8   107.64  3.000
 F7P  H9   C5   H7   106.63  3.000
 F7P  H8   C5   H7   108.49  3.000
 F7P  H9   C5   C4   108.95  3.000
 F7P  H8   C5   C4   112.87  3.000
 F7P  H7   C5   C4   112.00  3.000
 F7P  H10  C4   O6   110.68  3.000
 F7P  H10  C4   C1   107.35  3.000
 F7P  O6   C4   C1   107.69  3.000
 F7P  H10  C4   C5   106.45  3.000
 F7P  C1   C4   C5   113.85  3.000
 F7P  O6   C4   C5   110.77  3.000
 F7P  H13  C2   H12  107.12  3.000
 F7P  H13  C2   H11  108.21  3.000
 F7P  H12  C2   H11  107.62  3.000
 F7P  H13  C2   C1   110.93  3.000
 F7P  H12  C2   C1   111.76  3.000
 F7P  H11  C2   C1   111.02  3.000
 F7P  CD2  CG   CD1  105.91  3.000
 F7P  CD2  CG   CB   127.58  3.000
 F7P  CD1  CG   CB   126.50  3.000
 F7P  H14  CD1  NE1  121.78  3.000
 F7P  H14  CD1  CG   126.76  3.000
 F7P  NE1  CD1  CG   111.45  3.000
 F7P  CE3  CD2  CE2  120.21  3.000
 F7P  CE3  CD2  CG   132.53  3.000
 F7P  CE2  CD2  CG   107.26  3.000
 F7P  C1   NE1  CE2  125.80  3.000
 F7P  CE2  NE1  CD1  107.53  3.000
 F7P  C1   NE1  CD1  126.57  3.000
 F7P  CZ2  CE2  NE1  132.04  3.000
 F7P  CZ2  CE2  CD2  120.10  3.000
 F7P  NE1  CE2  CD2  107.85  3.000
 F7P  H15  CE3  CZ3  120.33  3.000
 F7P  H15  CE3  CD2  120.40  3.000
 F7P  CZ3  CE3  CD2  119.27  3.000
 F7P  H16  CZ2  CH2  118.78  3.000
 F7P  H16  CZ2  CE2  122.69  3.000
 F7P  CH2  CZ2  CE2  118.52  3.000
 F7P  H17  CZ3  CH2  119.63  3.000
 F7P  H17  CZ3  CE3  120.09  3.000
 F7P  CH2  CZ3  CE3  120.28  3.000
 F7P  H18  CH2  CZ3  119.54  3.000
 F7P  H18  CH2  CZ2  118.85  3.000
 F7P  CZ3  CH2  CZ2  121.61  3.000
 F7P  C3   C1   NE1  109.60  3.000
 F7P  NE1  C1   C2   108.39  3.000
 F7P  C3   C1   C2   111.06  3.000
 F7P  NE1  C1   C4   109.39  3.000
 F7P  C2   C1   C4   108.38  3.000
 F7P  C3   C1   C4   109.98  3.000
 F7P  H21  C3   H20  108.23  3.000
 F7P  H21  C3   H19  106.46  3.000
 F7P  H20  C3   H19  108.02  3.000
 F7P  H21  C3   C1   110.29  3.000
 F7P  H20  C3   C1   111.58  3.000
 F7P  H19  C3   C1   112.05  3.000
 F7P  H22  O6   C4   108.31  3.000
 F7P  H23  O1   C    110.14  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
 F7P  CONST_01  CE2  NE1  CD1  CG     0.00   0.0  0
 F7P  CONST_02  NE1  CE2  CD2  CG     0.00   0.0  0
 F7P  CONST_03  CZ2  CE2  CD2  CG   180.00   0.0  0
 F7P  CONST_04  CZ3  CE3  CD2  CG   180.00   0.0  0
 F7P  CONST_05  CZ2  CE2  NE1  CD1  180.00   0.0  0
 F7P  CONST_06  CD2  CE2  NE1  CD1    0.00   0.0  0
 F7P  CONST_07  CE2  CD2  CG   CD1    0.00   0.0  0
 F7P  CONST_08  CE3  CD2  CG   CD1  180.00   0.0  0
 F7P  CONST_09  NE1  CD1  CG   CD2    0.00   0.0  0
 F7P  CONST_10  CH2  CZ2  CE2  CD2    0.00   0.0  0
 F7P  CONST_11  CH2  CZ3  CE3  CD2    0.00   0.0  0
 F7P  CONST_12  CH2  CZ2  CE2  NE1  180.00   0.0  0
 F7P  CONST_13  CE3  CD2  CE2  NE1  180.00   0.0  0
 F7P  CONST_14  CZ3  CH2  CZ2  CE2    0.00   0.0  0
 F7P  CONST_15  CZ3  CE3  CD2  CE2    0.00   0.0  0
 F7P  CONST_16  CZ2  CE2  CD2  CE3    0.00   0.0  0
 F7P  CONST_17  CZ2  CH2  CZ3  CE3    0.00   0.0  0
 F7P  CONST_18  NE1  CD1  CG   CB   180.00   0.0  0
 F7P  CONST_19  CE2  CD2  CG   CB   180.00   0.0  0
 F7P  CONST_20  CE3  CD2  CG   CB     0.00   0.0  0
 F7P  CONST_21  C1   NE1  CD1  CG   180.00   0.0  0
 F7P  CONST_22  C1   NE1  CE2  CD2  180.00   0.0  0
 F7P  CONST_23  C1   NE1  CE2  CZ2    0.00   0.0  0
 F7P  CONST_24  H15  CE3  CD2  CG     0.00   0.0  0
 F7P  CONST_25  H14  CD1  CG   CD2  180.00   0.0  0
 F7P  CONST_26  H16  CZ2  CE2  CD2  180.00   0.0  0
 F7P  CONST_27  H17  CZ3  CE3  CD2  180.00   0.0  0
 F7P  CONST_28  H18  CH2  CZ2  CE2  180.00   0.0  0
 F7P  CONST_29  H23  O1   C    CA   180.00   0.0  0
 F7P  Var_01    CD1  CG   CB   CA   -89.76  30.0  2
 F7P  Var_02    CD1  NE1  C1   C4    -3.57  30.0  2
 F7P  Var_03    H19  C3   C1   NE1  -66.17  30.0  3
 F7P  Var_04    H11  C2   C1   NE1  -68.70  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
 F7P  chir_01  CA  C   CB  N   positiv
 F7P  chir_02  C4  O6  C5  C1  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
 F7P  plan-1  CB   0.020
 F7P  plan-1  CG   0.020
 F7P  plan-1  CD1  0.020
 F7P  plan-1  CD2  0.020
 F7P  plan-1  NE1  0.020
 F7P  plan-1  CE2  0.020
 F7P  plan-1  CE3  0.020
 F7P  plan-1  CZ2  0.020
 F7P  plan-1  CZ3  0.020
 F7P  plan-1  CH2  0.020
 F7P  plan-1  C1   0.020
 F7P  plan-1  H14  0.020
 F7P  plan-1  H15  0.020
 F7P  plan-1  H16  0.020
 F7P  plan-1  H17  0.020
 F7P  plan-1  H18  0.020
 F7P  plan-2  CA   0.020
 F7P  plan-2  C    0.020
 F7P  plan-2  O    0.020
 F7P  plan-2  O1   0.020
 F7P  plan-2  H23  0.020

