# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 04:56:24 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 3-fluoro-N-(naphthalen-2-ylcarbonyl)-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1cccc(F)c1)NC(=O)c2ccc3ccccc3c2
#
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
 GIA  GIA  3-fluoro-N-(naphthalen-2-ylcarbonyl)-D-phenylalanine  ligand  40  25  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GIA
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
 GIA  F1    F  F      0  -0.319  -2.0019  -3.7757  -1.4245
 GIA  C1    C  CR6    0   0.539  -2.5972  -2.8692  -0.6289
 GIA  C2    C  CR16   0  -0.429  -3.1179  -3.2826   0.5807
 GIA  C3    C  CR16   0  -0.226  -3.7318  -2.3275   1.3822
 GIA  C4    C  CR16   0  -0.317  -3.8107  -1.0043   0.9736
 GIA  C5    C  CR6    0   0.185  -3.2758  -0.6037  -0.2495
 GIA  C6    C  CR16   0  -0.487  -2.6645  -1.5575  -1.0578
 GIA  C7    C  CH2    0  -0.551  -3.3186   0.8390  -0.6649
 GIA  C8    C  CH1    0  -0.196  -2.2435   1.6750   0.0441
 GIA  C9    C  C      0   0.416  -2.3272   3.1657  -0.3817
 GIA  O10   O  OC    -1  -0.611  -3.4369   3.7010  -0.1939
 GIA  O11   O  O      0  -0.588  -1.3064   3.6846  -0.8602
 GIA  N12   N  NH1    0  -0.626  -0.9474   1.0904  -0.1891
 GIA  C13   C  C      0   0.535   0.0408   1.0950   0.7135
 GIA  O14   O  O      0  -0.499  -0.0686   1.5752   1.8360
 GIA  C15   C  CR6    0  -0.047   1.3163   0.4430   0.2794
 GIA  C16   C  CR16   0  -0.347   2.4897   0.8474   0.8639
 GIA  C17   C  CR66   0   0.140   3.7240   0.2630   0.5072
 GIA  C18   C  CR66   0   0.111   3.7429  -0.7774  -0.4576
 GIA  C19   C  CR16   0  -0.300   2.5200  -1.1923  -1.0336
 GIA  C20   C  CR16   0  -0.289   1.3411  -0.5991  -0.6798
 GIA  C21   C  CR16   0  -0.310   4.9428   0.6800   1.0936
 GIA  C22   C  CR16   0  -0.256   6.1235   0.0876   0.7390
 GIA  C23   C  CR16   0  -0.254   6.1411  -0.9488  -0.2195
 GIA  C24   C  CR16   0  -0.309   4.9786  -1.3711  -0.8048
 GIA  H2    H  HCR6   0   0.276  -3.0512  -4.3180   0.8875
 GIA  H3    H  HCR6   0   0.265  -4.1534  -2.6253   2.3331
 GIA  H4    H  HCR6   0   0.251  -4.2956  -0.2747   1.6110
 GIA  H6    H  HCR6   0   0.269  -2.2494  -1.2812  -2.0198
 GIA  H7    H  HCH2   0   0.252  -3.1927   0.9209  -1.7488
 GIA  H7A   H  HCH2   0   0.264  -4.2904   1.2696  -0.4250
 GIA  H8    H  HCH1   0   0.253  -2.4325   1.6278   1.1194
 GIA  HN12  H  HNH1   0   0.393  -0.7190   0.8604  -1.1431
 GIA  H16   H  HCR6   0   0.257   2.4808   1.6336   1.6090
 GIA  H19   H  HCR6   0   0.261   2.5251  -1.9980  -1.7572
 GIA  H20   H  HCR6   0   0.254   0.4199  -0.9608  -1.1196
 GIA  H21   H  HCR6   0   0.259   4.9265   1.4743   1.8297
 GIA  H22   H  HCR6   0   0.262   7.0510   0.4091   1.1944
 GIA  H23   H  HCR6   0   0.262   7.0824  -1.4102  -0.4880
 GIA  H24   H  HCR6   0   0.259   4.9919  -2.1661  -1.5402

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
 GIA  C1   F1    single    1.345  0.020  1.345
 GIA  C2   C1    aromatic  1.380  0.020  1.380
 GIA  C1   C6    aromatic  1.382  0.020  1.382
 GIA  C3   C2    aromatic  1.390  0.020  1.390
 GIA  C2   H2    single    0.930  0.020  1.080
 GIA  C3   C4    aromatic  1.387  0.020  1.387
 GIA  C3   H3    single    0.930  0.020  1.080
 GIA  C4   C5    aromatic  1.394  0.020  1.394
 GIA  C4   H4    single    0.930  0.020  1.080
 GIA  C5   C6    aromatic  1.392  0.020  1.392
 GIA  C5   C7    single    1.502  0.020  1.502
 GIA  C6   H6    single    0.930  0.020  1.080
 GIA  C8   C7    single    1.535  0.020  1.535
 GIA  C7   H7    single    0.970  0.020  1.090
 GIA  C7   H7A   single    0.970  0.020  1.090
 GIA  N12  C8    single    1.441  0.020  1.441
 GIA  C8   C9    single    1.553  0.020  1.553
 GIA  C8   H8    single    0.970  0.020  1.090
 GIA  O11  C9    deloc     1.241  0.020  1.241
 GIA  C9   O10   deloc     1.246  0.020  1.246
 GIA  C13  N12   single    1.338  0.020  1.338
 GIA  N12  HN12  single    0.860  0.020  1.020
 GIA  C15  C13   single    1.497  0.020  1.497
 GIA  C13  O14   double    1.226  0.020  1.226
 GIA  C20  C15   aromatic  1.417  0.020  1.417
 GIA  C16  C15   aromatic  1.372  0.020  1.372
 GIA  C17  C16   aromatic  1.412  0.020  1.412
 GIA  C16  H16   single    0.930  0.020  1.080
 GIA  C21  C17   aromatic  1.415  0.020  1.415
 GIA  C18  C17   aromatic  1.419  0.020  1.419
 GIA  C24  C18   aromatic  1.414  0.020  1.414
 GIA  C18  C19   aromatic  1.414  0.020  1.414
 GIA  C19  C20   aromatic  1.366  0.020  1.366
 GIA  C19  H19   single    0.930  0.020  1.080
 GIA  C20  H20   single    0.930  0.020  1.080
 GIA  C22  C21   aromatic  1.368  0.020  1.368
 GIA  C21  H21   single    0.930  0.020  1.080
 GIA  C23  C22   aromatic  1.412  0.020  1.412
 GIA  C22  H22   single    0.930  0.020  1.080
 GIA  C23  C24   aromatic  1.368  0.020  1.368
 GIA  C23  H23   single    0.930  0.020  1.080
 GIA  C24  H24   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
 GIA  C6    C1   C2   122.55  3.000
 GIA  C6    C1   F1   118.54  3.000
 GIA  C2    C1   F1   118.91  3.000
 GIA  H2    C2   C3   121.42  3.000
 GIA  H2    C2   C1   120.79  3.000
 GIA  C3    C2   C1   117.79  3.000
 GIA  H3    C3   C4   119.95  3.000
 GIA  H3    C3   C2   119.33  3.000
 GIA  C4    C3   C2   120.72  3.000
 GIA  H4    C4   C5   119.63  3.000
 GIA  H4    C4   C3   119.65  3.000
 GIA  C5    C4   C3   120.72  3.000
 GIA  C7    C5   C6   120.68  3.000
 GIA  C7    C5   C4   120.52  3.000
 GIA  C6    C5   C4   118.77  3.000
 GIA  H6    C6   C5   120.61  3.000
 GIA  H6    C6   C1   119.93  3.000
 GIA  C5    C6   C1   119.45  3.000
 GIA  H7A   C7   H7   106.92  3.000
 GIA  H7A   C7   C8   107.92  3.000
 GIA  H7    C7   C8   109.64  3.000
 GIA  H7A   C7   C5   110.13  3.000
 GIA  H7    C7   C5   110.03  3.000
 GIA  C8    C7   C5   112.04  3.000
 GIA  H8    C8   N12  107.30  3.000
 GIA  H8    C8   C9   107.58  3.000
 GIA  N12   C8   C9   113.18  3.000
 GIA  H8    C8   C7   108.04  3.000
 GIA  C9    C8   C7   111.00  3.000
 GIA  N12   C8   C7   109.52  3.000
 GIA  O11   C9   O10  127.66  3.000
 GIA  O10   C9   C8   114.78  3.000
 GIA  O11   C9   C8   117.57  3.000
 GIA  HN12  N12  C13  118.16  3.000
 GIA  HN12  N12  C8   116.73  3.000
 GIA  C13   N12  C8   123.61  3.000
 GIA  C15   C13  O14  120.82  3.000
 GIA  O14   C13  N12  123.57  3.000
 GIA  C15   C13  N12  115.60  3.000
 GIA  C20   C15  C16  119.37  3.000
 GIA  C16   C15  C13  118.48  3.000
 GIA  C20   C15  C13  122.12  3.000
 GIA  H16   C16  C17  118.79  3.000
 GIA  H16   C16  C15  120.00  3.000
 GIA  C17   C16  C15  121.21  3.000
 GIA  C21   C17  C18  119.09  3.000
 GIA  C18   C17  C16  119.15  3.000
 GIA  C21   C17  C16  121.75  3.000
 GIA  C24   C18  C19  122.18  3.000
 GIA  C19   C18  C17  118.72  3.000
 GIA  C24   C18  C17  119.10  3.000
 GIA  H19   C19  C20  120.01  3.000
 GIA  H19   C19  C18  119.10  3.000
 GIA  C20   C19  C18  120.89  3.000
 GIA  H20   C20  C19  118.93  3.000
 GIA  H20   C20  C15  120.39  3.000
 GIA  C19   C20  C15  120.65  3.000
 GIA  H21   C21  C22  120.46  3.000
 GIA  H21   C21  C17  118.99  3.000
 GIA  C22   C21  C17  120.55  3.000
 GIA  H22   C22  C23  119.55  3.000
 GIA  H22   C22  C21  120.14  3.000
 GIA  C23   C22  C21  120.31  3.000
 GIA  H23   C23  C24  120.08  3.000
 GIA  H23   C23  C22  119.49  3.000
 GIA  C24   C23  C22  120.42  3.000
 GIA  H24   C24  C23  120.44  3.000
 GIA  H24   C24  C18  119.05  3.000
 GIA  C23   C24  C18  120.52  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
 GIA  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 GIA  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 GIA  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 GIA  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 GIA  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 GIA  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 GIA  CONST_07  C18   C19  C20  C15    0.00   0.0  0
 GIA  CONST_08  C21   C17  C16  C15  180.00   0.0  0
 GIA  CONST_09  C18   C17  C16  C15    0.00   0.0  0
 GIA  CONST_10  C19   C20  C15  C16    0.00   0.0  0
 GIA  CONST_11  C22   C21  C17  C16  180.00   0.0  0
 GIA  CONST_12  C24   C18  C17  C16  180.00   0.0  0
 GIA  CONST_13  C19   C18  C17  C16    0.00   0.0  0
 GIA  CONST_14  C20   C15  C16  C17    0.00   0.0  0
 GIA  CONST_15  C23   C22  C21  C17    0.00   0.0  0
 GIA  CONST_16  C23   C24  C18  C17    0.00   0.0  0
 GIA  CONST_17  C20   C19  C18  C17    0.00   0.0  0
 GIA  CONST_18  C22   C21  C17  C18    0.00   0.0  0
 GIA  CONST_19  C22   C23  C24  C18    0.00   0.0  0
 GIA  CONST_20  C21   C17  C18  C19  180.00   0.0  0
 GIA  CONST_21  C23   C24  C18  C19  180.00   0.0  0
 GIA  CONST_22  C24   C18  C19  C20  180.00   0.0  0
 GIA  CONST_23  C24   C18  C17  C21    0.00   0.0  0
 GIA  CONST_24  C24   C23  C22  C21    0.00   0.0  0
 GIA  CONST_25  C3    C2   C1   F1   180.00   0.0  0
 GIA  CONST_26  C5    C6   C1   F1   180.00   0.0  0
 GIA  CONST_27  C7    C5   C6   C1   180.00   0.0  0
 GIA  CONST_28  C7    C5   C4   C3   180.00   0.0  0
 GIA  CONST_29  C19   C20  C15  C13  180.00   0.0  0
 GIA  CONST_30  C17   C16  C15  C13  180.00   0.0  0
 GIA  CONST_31  H3    C3   C2   C1   180.00   0.0  0
 GIA  CONST_32  H6    C6   C1   C2   180.00   0.0  0
 GIA  CONST_33  H4    C4   C3   C2   180.00   0.0  0
 GIA  CONST_34  H2    C2   C3   C4   180.00   0.0  0
 GIA  CONST_35  H19   C19  C20  C15  180.00   0.0  0
 GIA  CONST_36  H20   C20  C15  C16  180.00   0.0  0
 GIA  CONST_37  H21   C21  C17  C16    0.00   0.0  0
 GIA  CONST_38  H22   C22  C21  C17  180.00   0.0  0
 GIA  CONST_39  H24   C24  C18  C17  180.00   0.0  0
 GIA  CONST_40  H16   C16  C17  C18  180.00   0.0  0
 GIA  CONST_41  H23   C23  C24  C18  180.00   0.0  0
 GIA  CONST_42  C15   C13  N12  C8   180.00   0.0  0
 GIA  CONST_43  HN12  N12  C13  C15    0.00   0.0  0
 GIA  CONST_44  O14   C13  N12  C8     0.00   0.0  0
 GIA  Var_01    C8    C7   C5   C4    77.66  30.0  2
 GIA  Var_02    C20   C15  C13  N12  -27.74  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
 GIA  chir_01  C8  C7  N12  C9  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
 GIA  plan-1  F1    0.020
 GIA  plan-1  C1    0.020
 GIA  plan-1  C2    0.020
 GIA  plan-1  C3    0.020
 GIA  plan-1  C4    0.020
 GIA  plan-1  C5    0.020
 GIA  plan-1  C6    0.020
 GIA  plan-1  C7    0.020
 GIA  plan-1  H2    0.020
 GIA  plan-1  H3    0.020
 GIA  plan-1  H4    0.020
 GIA  plan-1  H6    0.020
 GIA  plan-2  C13   0.020
 GIA  plan-2  C15   0.020
 GIA  plan-2  C16   0.020
 GIA  plan-2  C17   0.020
 GIA  plan-2  C18   0.020
 GIA  plan-2  C19   0.020
 GIA  plan-2  C20   0.020
 GIA  plan-2  C21   0.020
 GIA  plan-2  C22   0.020
 GIA  plan-2  C23   0.020
 GIA  plan-2  C24   0.020
 GIA  plan-2  H16   0.020
 GIA  plan-2  H19   0.020
 GIA  plan-2  H20   0.020
 GIA  plan-2  H21   0.020
 GIA  plan-2  H22   0.020
 GIA  plan-2  H23   0.020
 GIA  plan-2  H24   0.020
 GIA  plan-3  C8    0.020
 GIA  plan-3  N12   0.020
 GIA  plan-3  C13   0.020
 GIA  plan-3  O14   0.020
 GIA  plan-3  C15   0.020
 GIA  plan-3  HN12  0.020
 GIA  plan-4  C8    0.020
 GIA  plan-4  C9    0.020
 GIA  plan-4  O10   0.020
 GIA  plan-4  O11   0.020

