# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:03:39 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: methyl 4-fluoro-L-phenylalaninate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)Cc1ccc(F)cc1
#
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
 RQD  RQD  'methyl 4-fluoro-L-phenylalaninate'  ligand  26  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RQD
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
 RQD  C4   C  CR6   0   0.098  26.7607   2.0839  60.4939
 RQD  C5   C  CR16  0  -0.285  25.6376   2.7476  60.9803
 RQD  C6   C  CR16  0  -0.396  24.3984   2.1233  61.0372
 RQD  C7   C  CR6   0   0.509  24.2973   0.8196  60.5961
 RQD  C8   C  CR16  0  -0.395  25.3872   0.1242  60.1077
 RQD  C9   C  CR16  0  -0.288  26.6149   0.7675  60.0607
 RQD  F    F  F     0  -0.318  23.1028   0.2049  60.6471
 RQD  C3   C  CH2   0  -0.523  28.0879   2.7815  60.3931
 RQD  C2   C  CH1   0  -0.172  28.4313   3.1970  58.9542
 RQD  N    N  NH2   0  -0.797  29.6569   3.9731  58.9564
 RQD  C1   C  C     0   0.592  27.2918   4.0185  58.3757
 RQD  O1   O  O     0  -0.446  26.6020   3.6588  57.4544
 RQD  O    O  O2    0  -0.441  27.1238   5.1652  59.0130
 RQD  C    C  CH3   0  -0.424  26.0482   6.0022  58.5898
 RQD  H9   H  HCR6  0   0.262  25.7257   3.7696  61.3283
 RQD  H10  H  HCR6  0   0.278  23.5304   2.6441  61.4195
 RQD  H11  H  HCR6  0   0.278  25.2807  -0.8994  59.7729
 RQD  H12  H  HCR6  0   0.260  27.4751   0.2290  59.6807
 RQD  H7   H  HCH2  0   0.267  28.8860   2.1221  60.7447
 RQD  H8   H  HCH2  0   0.259  28.1037   3.6663  61.0314
 RQD  H    H  HCH1  0   0.243  28.4836   2.2884  58.3404
 RQD  H1   H  HNH2  0   0.357  30.3876   3.4317  59.4018
 RQD  H2   H  HNH2  0   0.356  29.9710   4.1283  58.0063
 RQD  H5   H  HCH3  0   0.251  26.0603   6.8623  59.2527
 RQD  H4   H  HCH3  0   0.240  26.1848   6.3373  57.5617
 RQD  H6   H  HCH3  0   0.236  25.0885   5.4928  58.6771

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
 RQD  C   O    single    1.427  0.020  1.427
 RQD  O1  C1   double    1.206  0.020  1.206
 RQD  C1  C2   single    1.519  0.020  1.519
 RQD  C1  O    single    1.323  0.020  1.323
 RQD  N   C2   single    1.451  0.020  1.451
 RQD  C2  C3   single    1.537  0.020  1.537
 RQD  C9  C8   aromatic  1.387  0.020  1.387
 RQD  C9  C4   aromatic  1.393  0.020  1.393
 RQD  C8  C7   aromatic  1.382  0.020  1.382
 RQD  C3  C4   single    1.503  0.020  1.503
 RQD  C4  C5   aromatic  1.392  0.020  1.392
 RQD  C7  F    single    1.344  0.020  1.344
 RQD  C7  C6   aromatic  1.380  0.020  1.380
 RQD  C5  C6   aromatic  1.389  0.020  1.389
 RQD  C5  H9   single    0.930  0.020  1.080
 RQD  C6  H10  single    0.930  0.020  1.080
 RQD  C8  H11  single    0.930  0.020  1.080
 RQD  C9  H12  single    0.930  0.020  1.080
 RQD  C3  H7   single    0.970  0.020  1.090
 RQD  C3  H8   single    0.970  0.020  1.090
 RQD  C2  H    single    0.970  0.020  1.090
 RQD  N   H1   single    0.890  0.020  1.040
 RQD  N   H2   single    0.890  0.020  1.040
 RQD  C   H5   single    0.970  0.020  1.090
 RQD  C   H4   single    0.970  0.020  1.090
 RQD  C   H6   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
 RQD  C3   C4  C9  120.67  3.000
 RQD  C3   C4  C5  120.97  3.000
 RQD  C9   C4  C5  118.33  3.000
 RQD  H9   C5  C6  118.91  3.000
 RQD  H9   C5  C4  119.76  3.000
 RQD  C6   C5  C4  121.32  3.000
 RQD  H10  C6  C7  120.58  3.000
 RQD  H10  C6  C5  120.93  3.000
 RQD  C7   C6  C5  118.49  3.000
 RQD  F    C7  C8  118.95  3.000
 RQD  F    C7  C6  119.01  3.000
 RQD  C8   C7  C6  122.04  3.000
 RQD  H11  C8  C9  121.02  3.000
 RQD  H11  C8  C7  120.51  3.000
 RQD  C9   C8  C7  118.47  3.000
 RQD  H12  C9  C8  118.95  3.000
 RQD  H12  C9  C4  119.70  3.000
 RQD  C8   C9  C4  121.36  3.000
 RQD  H8   C3  H7  106.88  3.000
 RQD  H8   C3  C2  108.98  3.000
 RQD  H7   C3  C2  107.53  3.000
 RQD  H8   C3  C4  110.48  3.000
 RQD  H7   C3  C4  110.08  3.000
 RQD  C2   C3  C4  112.68  3.000
 RQD  H    C2  C1  105.69  3.000
 RQD  H    C2  N   113.79  3.000
 RQD  C1   C2  N   110.17  3.000
 RQD  H    C2  C3  108.09  3.000
 RQD  N    C2  C3  109.39  3.000
 RQD  C1   C2  C3  109.59  3.000
 RQD  H2   N   H1  105.71  3.000
 RQD  H2   N   C2  110.04  3.000
 RQD  H1   N   C2  108.92  3.000
 RQD  O    C1  O1  123.65  3.000
 RQD  O    C1  C2  112.38  3.000
 RQD  O1   C1  C2  123.97  3.000
 RQD  C    O   C1  117.48  3.000
 RQD  H6   C   H4  109.24  3.000
 RQD  H6   C   H5  109.34  3.000
 RQD  H4   C   H5  109.32  3.000
 RQD  H6   C   O   111.45  3.000
 RQD  H4   C   O   111.44  3.000
 RQD  H5   C   O   105.96  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
 RQD  CONST_01  C7   C8  C9  C4     0.00   0.0  0
 RQD  CONST_02  C7   C6  C5  C4     0.00   0.0  0
 RQD  CONST_03  C8   C9  C4  C5     0.00   0.0  0
 RQD  CONST_04  C8   C7  C6  C5     0.00   0.0  0
 RQD  CONST_05  C9   C8  C7  C6     0.00   0.0  0
 RQD  CONST_06  C9   C4  C5  C6     0.00   0.0  0
 RQD  CONST_07  F    C7  C6  C5   180.00   0.0  0
 RQD  CONST_08  C3   C4  C5  C6   180.00   0.0  0
 RQD  CONST_09  C3   C4  C9  C8   180.00   0.0  0
 RQD  CONST_10  F    C7  C8  C9   180.00   0.0  0
 RQD  CONST_11  H11  C8  C9  C4   180.00   0.0  0
 RQD  CONST_12  H10  C6  C5  C4   180.00   0.0  0
 RQD  CONST_13  H12  C9  C4  C5   180.00   0.0  0
 RQD  CONST_14  H9   C5  C6  C7   180.00   0.0  0
 RQD  Var_01    C2   C3  C4  C5  -103.16  30.0  3
 RQD  Var_02    H5   C   O   C1   177.99  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
 RQD  chir_01  C2  C1  N  C3  negativ

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
 RQD  plan-1  C4   0.020
 RQD  plan-1  C5   0.020
 RQD  plan-1  C6   0.020
 RQD  plan-1  C7   0.020
 RQD  plan-1  C8   0.020
 RQD  plan-1  C9   0.020
 RQD  plan-1  F    0.020
 RQD  plan-1  C3   0.020
 RQD  plan-1  H9   0.020
 RQD  plan-1  H10  0.020
 RQD  plan-1  H11  0.020
 RQD  plan-1  H12  0.020
 RQD  plan-2  C2   0.020
 RQD  plan-2  C1   0.020
 RQD  plan-2  O1   0.020
 RQD  plan-2  O    0.020

