# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 19:06:51 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (2~{S})-2-azanyl-3-(2-fluorophenyl)-2-methyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](N)(Cc1ccccc1F)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
 9DT  9DT  '(2~{S})-2-azanyl-3-(2-fluorophenyl)-2-methyl-propanoic acid'  ligand  26  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9DT
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
 9DT  C36  C  C     0   0.562   2.7933  -0.1813  -0.2610
 9DT  C38  C  CT    0  -0.043   1.3662  -0.1756   0.3063
 9DT  C39  C  CH3   0  -0.659   1.2356  -1.4470   1.1516
 9DT  C40  C  CH2   0  -0.509   0.3863  -0.1954  -0.8851
 9DT  C41  C  CR6   0  -0.043  -1.0569  -0.2530  -0.4781
 9DT  C42  C  CR16  0  -0.285  -1.7150  -1.4735  -0.3345
 9DT  C43  C  CR16  0  -0.259  -3.0474  -1.5485   0.0466
 9DT  C44  C  CR16  0  -0.255  -3.7623  -0.3831   0.2839
 9DT  C45  C  CR16  0  -0.406  -3.1426   0.8493   0.1325
 9DT  C46  C  CR6   0   0.509  -1.8130   0.8868  -0.2428
 9DT  F47  F  F     0  -0.314  -1.2445   2.0937  -0.4122
 9DT  N48  N  NH2   0  -0.771   1.0733   0.9613   1.1529
 9DT  O37  O  O     0  -0.443   3.1048  -0.6069  -1.3465
 9DT  H2   H  HCH3  0   0.249   1.9720  -1.4629   1.9566
 9DT  H3   H  HCH3  0   0.254   0.2460  -1.4813   1.6062
 9DT  H4   H  HCH3  0   0.240   1.3687  -2.3466   0.5503
 9DT  H5   H  HCH2  0   0.263   0.5680   0.6813  -1.5118
 9DT  H6   H  HCH2  0   0.263   0.6036  -1.0626  -1.5090
 9DT  H7   H  HCR6  0   0.259  -1.1662  -2.3864  -0.5327
 9DT  H8   H  HCR6  0   0.257  -3.5252  -2.5133   0.1525
 9DT  H9   H  HCR6  0   0.264  -4.8030  -0.4267   0.5765
 9DT  H10  H  HCR6  0   0.274  -3.6837   1.7718   0.2994
 9DT  H11  H  HNH2  0   0.352   1.6610   0.9616   1.9768
 9DT  H12  H  HNH2  0   0.349   1.2427   1.8347   0.6704
 9DT  OXT  O  OH1   0  -0.592   3.6794   0.3022   0.6002
 9DT  H1   H  HOH1  0   0.481   4.5704   0.2423   0.2243

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
 9DT  O37  C36  double    1.207  0.020  1.207
 9DT  C36  C38  single    1.536  0.020  1.536
 9DT  N48  C38  single    1.447  0.020  1.447
 9DT  C38  C39  single    1.532  0.020  1.532
 9DT  C38  C40  single    1.543  0.020  1.543
 9DT  C43  C42  aromatic  1.388  0.020  1.388
 9DT  C43  C44  aromatic  1.388  0.020  1.388
 9DT  C42  C41  aromatic  1.394  0.020  1.394
 9DT  C44  C45  aromatic  1.388  0.020  1.388
 9DT  C41  C40  single    1.501  0.020  1.501
 9DT  C41  C46  aromatic  1.388  0.020  1.388
 9DT  C45  C46  aromatic  1.382  0.020  1.382
 9DT  C46  F47  single    1.345  0.020  1.345
 9DT  C39  H2   single    0.970  0.020  1.090
 9DT  C39  H3   single    0.970  0.020  1.090
 9DT  C39  H4   single    0.970  0.020  1.090
 9DT  C40  H5   single    0.970  0.020  1.090
 9DT  C40  H6   single    0.970  0.020  1.090
 9DT  C42  H7   single    0.930  0.020  1.080
 9DT  C43  H8   single    0.930  0.020  1.080
 9DT  C44  H9   single    0.930  0.020  1.080
 9DT  C45  H10  single    0.930  0.020  1.080
 9DT  N48  H11  single    0.890  0.020  1.040
 9DT  N48  H12  single    0.890  0.020  1.040
 9DT  C36  OXT  single    1.327  0.020  1.327
 9DT  OXT  H1   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
 9DT  OXT  C36  O37  122.68  3.000
 9DT  OXT  C36  C38  112.30  3.000
 9DT  O37  C36  C38  124.99  3.000
 9DT  N48  C38  C40  109.47  3.000
 9DT  C40  C38  C39  111.17  3.000
 9DT  N48  C38  C39  108.16  3.000
 9DT  C40  C38  C36  107.75  3.000
 9DT  C39  C38  C36  106.26  3.000
 9DT  N48  C38  C36  114.02  3.000
 9DT  H4   C39  H3   108.37  3.000
 9DT  H4   C39  H2   108.21  3.000
 9DT  H3   C39  H2   107.74  3.000
 9DT  H4   C39  C38  111.72  3.000
 9DT  H3   C39  C38  109.49  3.000
 9DT  H2   C39  C38  111.19  3.000
 9DT  H6   C40  H5   106.07  3.000
 9DT  H6   C40  C41  108.44  3.000
 9DT  H5   C40  C41  110.25  3.000
 9DT  H6   C40  C38  109.00  3.000
 9DT  H5   C40  C38  109.08  3.000
 9DT  C41  C40  C38  113.70  3.000
 9DT  C46  C41  C42  116.39  3.000
 9DT  C46  C41  C40  122.58  3.000
 9DT  C42  C41  C40  121.03  3.000
 9DT  H7   C42  C43  119.41  3.000
 9DT  H7   C42  C41  118.67  3.000
 9DT  C43  C42  C41  121.92  3.000
 9DT  H8   C43  C44  120.32  3.000
 9DT  H8   C43  C42  119.94  3.000
 9DT  C44  C43  C42  119.74  3.000
 9DT  H9   C44  C45  119.66  3.000
 9DT  H9   C44  C43  120.52  3.000
 9DT  C45  C44  C43  119.81  3.000
 9DT  H10  C45  C46  119.98  3.000
 9DT  H10  C45  C44  121.12  3.000
 9DT  C46  C45  C44  118.90  3.000
 9DT  F47  C46  C45  117.72  3.000
 9DT  F47  C46  C41  119.04  3.000
 9DT  C45  C46  C41  123.22  3.000
 9DT  H12  N48  H11  106.89  3.000
 9DT  H12  N48  C38  111.41  3.000
 9DT  H11  N48  C38  111.04  3.000
 9DT  H1   OXT  C36  109.86  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
 9DT  CONST_01  C44  C43  C42  C41    0.00   0.0  0
 9DT  CONST_02  C44  C45  C46  C41    0.00   0.0  0
 9DT  CONST_03  C45  C44  C43  C42    0.00   0.0  0
 9DT  CONST_04  C45  C46  C41  C42    0.00   0.0  0
 9DT  CONST_05  C46  C41  C42  C43    0.00   0.0  0
 9DT  CONST_06  C46  C45  C44  C43    0.00   0.0  0
 9DT  CONST_07  C43  C42  C41  C40  180.00   0.0  0
 9DT  CONST_08  C45  C46  C41  C40  180.00   0.0  0
 9DT  CONST_09  F47  C46  C41  C42  180.00   0.0  0
 9DT  CONST_10  F47  C46  C45  C44  180.00   0.0  0
 9DT  CONST_11  H8   C43  C42  C41  180.00   0.0  0
 9DT  CONST_12  H10  C45  C46  C41  180.00   0.0  0
 9DT  CONST_13  H9   C44  C43  C42  180.00   0.0  0
 9DT  CONST_14  H7   C42  C43  C44  180.00   0.0  0
 9DT  CONST_15  H1   OXT  C36  C38  180.00   0.0  0
 9DT  Var_01    C42  C41  C40  C38  -91.78  30.0  2

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
 9DT  chir_01  C38  N48  C39  C40  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
 9DT  plan-1  C40  0.020
 9DT  plan-1  C41  0.020
 9DT  plan-1  C42  0.020
 9DT  plan-1  C43  0.020
 9DT  plan-1  C44  0.020
 9DT  plan-1  C45  0.020
 9DT  plan-1  C46  0.020
 9DT  plan-1  F47  0.020
 9DT  plan-1  H7   0.020
 9DT  plan-1  H8   0.020
 9DT  plan-1  H9   0.020
 9DT  plan-1  H10  0.020
 9DT  plan-2  C36  0.020
 9DT  plan-2  C38  0.020
 9DT  plan-2  O37  0.020
 9DT  plan-2  OXT  0.020
 9DT  plan-2  H1   0.020

