# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:01:47 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (2S)-amino(4,4-difluorocyclohexyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C1CCC(F)(F)CC1)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
 1Y2  1Y2  '(2S)-amino(4,4-difluorocyclohexyl)ethanoic acid'  ligand  25  13  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1Y2
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
 1Y2  C30  C  C      0   0.407  -2.8902   0.2889   0.1157
 1Y2  O31  O  O      0  -0.606  -3.3672   0.3782  -1.0332
 1Y2  C32  C  CH1    0  -0.195  -1.8173  -0.7959   0.3631
 1Y2  N34  N  NH2    0  -0.805  -1.8747  -1.8212  -0.6644
 1Y2  C42  C  CH1    0  -0.249  -0.4421  -0.1135   0.5420
 1Y2  C43  C  CH2    0  -0.446   0.6064  -1.0900   1.0784
 1Y2  C44  C  CH2    0  -0.554   1.9599  -0.4151   1.2914
 1Y2  C45  C  CT     0   0.756   2.4287   0.2667   0.0289
 1Y2  F46  F  F      0  -0.358   3.6143   0.9213   0.2616
 1Y2  F47  F  F      0  -0.360   2.7352  -0.6859  -0.9172
 1Y2  C48  C  CH2    0  -0.553   1.4127   1.2271  -0.5394
 1Y2  C49  C  CH2    0  -0.447   0.0624   0.5427  -0.7433
 1Y2  H28  H  HCH1   0   0.208  -2.0519  -1.2667   1.3265
 1Y2  H29  H  HNH2   0   0.333  -1.9337  -1.3744  -1.5699
 1Y2  H39  H  HCH1   0   0.216  -0.5769   0.6688   1.2990
 1Y2  H40  H  HCH2   0   0.242   0.2690  -1.5118   2.0282
 1Y2  H41  H  HCH2   0   0.216   0.7249  -1.9356   0.3928
 1Y2  H42  H  HCH2   0   0.247   1.8658   0.3475   2.0689
 1Y2  H43  H  HCH2   0   0.262   2.7095  -1.1350   1.6293
 1Y2  H44  H  HCH2   0   0.246   1.3029   2.0556   0.1655
 1Y2  H45  H  HCH2   0   0.261   1.7837   1.6481  -1.4775
 1Y2  H46  H  HCH2   0   0.217   0.1530  -0.2122  -1.5302
 1Y2  H47  H  HCH2   0   0.245  -0.6510   1.2840  -1.1081
 1Y2  H2   H  HNH2   0   0.332  -1.0340  -2.3849  -0.6634
 1Y2  OXT  O  OC    -1  -0.616  -3.1675   1.0137   1.0925

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
 1Y2  N34  C32  single  1.453  0.020  1.453
 1Y2  C49  C48  single  1.528  0.020  1.528
 1Y2  C49  C42  single  1.529  0.020  1.529
 1Y2  C32  C42  single  1.546  0.020  1.546
 1Y2  C32  C30  single  1.546  0.020  1.546
 1Y2  C48  C45  single  1.509  0.020  1.509
 1Y2  C42  C43  single  1.530  0.020  1.530
 1Y2  C30  O31  deloc   1.247  0.020  1.247
 1Y2  F47  C45  single  1.377  0.020  1.377
 1Y2  C45  F46  single  1.374  0.020  1.374
 1Y2  C45  C44  single  1.509  0.020  1.509
 1Y2  C43  C44  single  1.527  0.020  1.527
 1Y2  C32  H28  single  0.970  0.020  1.090
 1Y2  N34  H29  single  0.890  0.020  1.040
 1Y2  C42  H39  single  0.970  0.020  1.090
 1Y2  C43  H40  single  0.970  0.020  1.090
 1Y2  C43  H41  single  0.970  0.020  1.090
 1Y2  C44  H42  single  0.970  0.020  1.090
 1Y2  C44  H43  single  0.970  0.020  1.090
 1Y2  C48  H44  single  0.970  0.020  1.090
 1Y2  C48  H45  single  0.970  0.020  1.090
 1Y2  C49  H46  single  0.970  0.020  1.090
 1Y2  C49  H47  single  0.970  0.020  1.090
 1Y2  N34  H2   single  0.890  0.020  1.040
 1Y2  C30  OXT  deloc   1.248  0.020  1.248

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
 1Y2  OXT  C30  C32  115.89  3.000
 1Y2  OXT  C30  O31  126.49  3.000
 1Y2  C32  C30  O31  117.59  3.000
 1Y2  H28  C32  C42  106.14  3.000
 1Y2  H28  C32  N34  108.03  3.000
 1Y2  C42  C32  N34  115.39  3.000
 1Y2  H28  C32  C30  107.04  3.000
 1Y2  C42  C32  C30  109.04  3.000
 1Y2  N34  C32  C30  110.77  3.000
 1Y2  H2   N34  H29  107.18  3.000
 1Y2  H2   N34  C32  111.07  3.000
 1Y2  H29  N34  C32  108.88  3.000
 1Y2  H39  C42  C49  108.34  3.000
 1Y2  H39  C42  C43  107.31  3.000
 1Y2  C49  C42  C43  110.04  3.000
 1Y2  H39  C42  C32  106.58  3.000
 1Y2  C43  C42  C32  111.62  3.000
 1Y2  C49  C42  C32  112.69  3.000
 1Y2  H41  C43  H40  106.23  3.000
 1Y2  H41  C43  C44  109.43  3.000
 1Y2  H40  C43  C44  108.85  3.000
 1Y2  H41  C43  C42  110.34  3.000
 1Y2  H40  C43  C42  109.85  3.000
 1Y2  C44  C43  C42  111.97  3.000
 1Y2  H43  C44  H42  107.38  3.000
 1Y2  H43  C44  C45  110.06  3.000
 1Y2  H42  C44  C45  107.85  3.000
 1Y2  H43  C44  C43  111.09  3.000
 1Y2  H42  C44  C43  109.34  3.000
 1Y2  C45  C44  C43  110.99  3.000
 1Y2  C48  C45  F47  109.35  3.000
 1Y2  F47  C45  F46  104.71  3.000
 1Y2  C48  C45  F46  109.97  3.000
 1Y2  F46  C45  C44  109.97  3.000
 1Y2  F47  C45  C44  109.35  3.000
 1Y2  C48  C45  C44  113.16  3.000
 1Y2  H45  C48  H44  107.19  3.000
 1Y2  H45  C48  C49  110.98  3.000
 1Y2  H44  C48  C49  109.68  3.000
 1Y2  H45  C48  C45  109.86  3.000
 1Y2  H44  C48  C45  107.88  3.000
 1Y2  C49  C48  C45  111.11  3.000
 1Y2  H47  C49  H46  106.39  3.000
 1Y2  H47  C49  C48  108.55  3.000
 1Y2  H46  C49  C48  109.39  3.000
 1Y2  H47  C49  C42  110.91  3.000
 1Y2  H46  C49  C42  109.62  3.000
 1Y2  C48  C49  C42  111.83  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
 1Y2  Var_01  C45  C48  C49  C42   54.61  30.0  1
 1Y2  Var_02  C45  C44  C43  C42  -54.51  30.0  1
 1Y2  Var_03  C48  C45  C44  C43   53.65  30.0  1
 1Y2  Var_04  C49  C48  C45  C44  -53.77  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
 1Y2  chir_01  C32  N34  C42  C30  negativ
 1Y2  chir_02  C42  C49  C32  C43  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
 1Y2  plan-1  C30  0.020
 1Y2  plan-1  O31  0.020
 1Y2  plan-1  C32  0.020
 1Y2  plan-1  OXT  0.020

