# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 12:53:17 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (1r,3R,4S)-N-(2-chloro-3-fluorobenzyl)-3,4-dihydroxycyclopentanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@H](C[C@H]1O)C(=O)NCc2cccc(F)c2Cl
#
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
 43Z  43Z  (1r,3R,4S)-N-(2-chloro-3-fluorobenzyl)-3,4-dihydroxycyclopentanecarboxamide  ligand  34  19  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_43Z
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
 43Z  CL   CL  CL    0  -0.114  -1.8280  -1.8248   0.1066
 43Z  CAP  C   CR6   0  -0.216  -2.6477  -0.3152   0.2410
 43Z  CAN  C   CR6   0   0.547  -3.8872  -0.1806  -0.3619
 43Z  FAD  F   F     0  -0.290  -4.3961  -1.2204  -1.0271
 43Z  CAG  C   CR16  0  -0.424  -4.6041   0.9965  -0.2880
 43Z  CAF  C   CR16  0  -0.198  -4.0602   2.0596   0.4149
 43Z  CAH  C   CR16  0  -0.279  -2.8203   1.9339   1.0255
 43Z  CAO  C   CR6   0   0.095  -2.0958   0.7493   0.9510
 43Z  CAI  C   CH2   0  -0.304  -0.7445   0.6418   1.6061
 43Z  NAL  N   NH1   0  -0.584   0.3094   0.5559   0.6234
 43Z  CAM  C   C     0   0.524   1.2683  -0.3934   0.6138
 43Z  OAA  O   O     0  -0.387   1.3494  -1.2589   1.4698
 43Z  CAS  C   CR15  0  -0.372   2.2303  -0.2698  -0.5542
 43Z  CAJ  C   CH2   0  -0.462   3.2332  -1.4361  -0.6851
 43Z  CAQ  C   CR15  0   0.028   4.6175  -0.8293  -0.5143
 43Z  OAB  O   OH1   0  -0.631   4.9507  -0.8099   0.8558
 43Z  CAR  C   CR15  0   0.058   4.4234   0.5956  -1.0448
 43Z  OAC  O   OH1   0  -0.634   5.4429   1.4920  -0.6746
 43Z  CAK  C   CH2   0  -0.489   3.0880   1.0110  -0.4445
 43Z  H1   H   HCR6  0   0.299  -5.5687   1.0730  -0.7724
 43Z  H2   H   HCR6  0   0.256  -4.6059   2.9906   0.4822
 43Z  H3   H   HCR6  0   0.249  -2.4009   2.7698   1.5709
 43Z  H4   H   HCH2  0   0.292  -0.5964   1.5082   2.2548
 43Z  H5   H   HCH2  0   0.208  -0.6919  -0.2433   2.2388
 43Z  H6   H   HNH1  0   0.351   0.3129   1.2495  -0.1076
 43Z  H7   H   HCR5  0   0.294   1.6259  -0.2131  -1.4638
 43Z  H8   H   HCH2  0   0.245   3.0531  -2.2303   0.0384
 43Z  H9   H   HCH2  0   0.247   3.1522  -1.8827  -1.6767
 43Z  H10  H   HCR5  0   0.130   5.3752  -1.3755  -1.0935
 43Z  H11  H   HOH1  0   0.439   5.6530  -0.1600   0.9740
 43Z  H12  H   HCR5  0   0.182   4.3216   0.5393  -2.1377
 43Z  H13  H   HOH1  0   0.461   6.2132   1.3246  -1.2267
 43Z  H14  H   HCH2  0   0.205   2.6419   1.8601  -0.9627
 43Z  H15  H   HCH2  0   0.272   3.2307   1.3002   0.5999

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
 43Z  FAD  CAN  single    1.335  0.020  1.335
 43Z  CAN  CAG  aromatic  1.380  0.020  1.380
 43Z  CAN  CAP  aromatic  1.385  0.020  1.385
 43Z  CL   CAP  single    1.723  0.020  1.723
 43Z  CAG  CAF  aromatic  1.386  0.020  1.386
 43Z  CAP  CAO  aromatic  1.394  0.020  1.394
 43Z  CAF  CAH  aromatic  1.388  0.020  1.388
 43Z  CAO  CAH  aromatic  1.391  0.020  1.391
 43Z  CAO  CAI  single    1.506  0.020  1.506
 43Z  CAI  NAL  single    1.444  0.020  1.444
 43Z  NAL  CAM  single    1.349  0.020  1.349
 43Z  CAM  OAA  double    1.220  0.020  1.220
 43Z  CAM  CAS  single    1.518  0.020  1.518
 43Z  CAK  CAS  single    1.545  0.020  1.545
 43Z  CAK  CAR  single    1.522  0.020  1.522
 43Z  OAC  CAR  single    1.407  0.020  1.407
 43Z  CAS  CAJ  single    1.544  0.020  1.544
 43Z  CAR  CAQ  single    1.533  0.020  1.533
 43Z  CAJ  CAQ  single    1.521  0.020  1.521
 43Z  OAB  CAQ  single    1.410  0.020  1.410
 43Z  CAG  H1   single    0.930  0.020  1.080
 43Z  CAF  H2   single    0.930  0.020  1.080
 43Z  CAH  H3   single    0.930  0.020  1.080
 43Z  CAI  H4   single    0.970  0.020  1.090
 43Z  CAI  H5   single    0.970  0.020  1.090
 43Z  NAL  H6   single    0.860  0.020  1.020
 43Z  CAS  H7   single    0.970  0.020  1.090
 43Z  CAJ  H8   single    0.970  0.020  1.090
 43Z  CAJ  H9   single    0.970  0.020  1.090
 43Z  CAQ  H10  single    0.970  0.020  1.090
 43Z  OAB  H11  single    0.850  0.020  0.980
 43Z  CAR  H12  single    0.970  0.020  1.090
 43Z  OAC  H13  single    0.850  0.020  0.980
 43Z  CAK  H14  single    0.970  0.020  1.090
 43Z  CAK  H15  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
 43Z  CAO  CAP  CAN  120.13  3.000
 43Z  CAO  CAP  CL   121.38  3.000
 43Z  CAN  CAP  CL   118.49  3.000
 43Z  CAG  CAN  FAD  119.53  3.000
 43Z  CAG  CAN  CAP  121.64  3.000
 43Z  FAD  CAN  CAP  118.84  3.000
 43Z  H1   CAG  CAF  121.51  3.000
 43Z  H1   CAG  CAN  119.96  3.000
 43Z  CAF  CAG  CAN  118.52  3.000
 43Z  H2   CAF  CAH  120.10  3.000
 43Z  H2   CAF  CAG  119.61  3.000
 43Z  CAH  CAF  CAG  120.29  3.000
 43Z  H3   CAH  CAO  118.87  3.000
 43Z  H3   CAH  CAF  119.86  3.000
 43Z  CAO  CAH  CAF  121.27  3.000
 43Z  CAI  CAO  CAH  120.34  3.000
 43Z  CAI  CAO  CAP  121.51  3.000
 43Z  CAH  CAO  CAP  118.15  3.000
 43Z  H5   CAI  H4   107.04  3.000
 43Z  H5   CAI  NAL  108.17  3.000
 43Z  H4   CAI  NAL  110.64  3.000
 43Z  H5   CAI  CAO  110.74  3.000
 43Z  H4   CAI  CAO  108.87  3.000
 43Z  NAL  CAI  CAO  111.30  3.000
 43Z  H6   NAL  CAM  118.46  3.000
 43Z  H6   NAL  CAI  117.09  3.000
 43Z  CAM  NAL  CAI  124.44  3.000
 43Z  CAS  CAM  OAA  123.74  3.000
 43Z  CAS  CAM  NAL  113.48  3.000
 43Z  OAA  CAM  NAL  122.77  3.000
 43Z  H7   CAS  CAK  108.83  3.000
 43Z  H7   CAS  CAJ  109.13  3.000
 43Z  CAK  CAS  CAJ  105.76  3.000
 43Z  H7   CAS  CAM  107.09  3.000
 43Z  CAJ  CAS  CAM  114.54  3.000
 43Z  CAK  CAS  CAM  111.38  3.000
 43Z  H9   CAJ  H8   107.04  3.000
 43Z  H9   CAJ  CAQ  109.45  3.000
 43Z  H8   CAJ  CAQ  111.51  3.000
 43Z  H9   CAJ  CAS  109.77  3.000
 43Z  H8   CAJ  CAS  112.78  3.000
 43Z  CAQ  CAJ  CAS  106.28  3.000
 43Z  H10  CAQ  CAR  111.53  3.000
 43Z  H10  CAQ  OAB  110.85  3.000
 43Z  CAR  CAQ  OAB  110.70  3.000
 43Z  H10  CAQ  CAJ  111.72  3.000
 43Z  OAB  CAQ  CAJ  109.24  3.000
 43Z  CAR  CAQ  CAJ  102.52  3.000
 43Z  H11  OAB  CAQ  107.49  3.000
 43Z  H12  CAR  CAK  108.96  3.000
 43Z  H12  CAR  OAC  111.18  3.000
 43Z  CAK  CAR  OAC  110.98  3.000
 43Z  H12  CAR  CAQ  107.96  3.000
 43Z  OAC  CAR  CAQ  114.17  3.000
 43Z  CAK  CAR  CAQ  103.20  3.000
 43Z  H13  OAC  CAR  108.55  3.000
 43Z  H15  CAK  H14  107.55  3.000
 43Z  H15  CAK  CAR  109.55  3.000
 43Z  H14  CAK  CAR  112.60  3.000
 43Z  H15  CAK  CAS  111.07  3.000
 43Z  H14  CAK  CAS  112.62  3.000
 43Z  CAR  CAK  CAS  103.46  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
 43Z  CONST_01  CAF  CAG  CAN  CAP     0.00   0.0  0
 43Z  CONST_02  CAF  CAH  CAO  CAP     0.00   0.0  0
 43Z  CONST_03  CAH  CAF  CAG  CAN     0.00   0.0  0
 43Z  CONST_04  CAH  CAO  CAP  CAN     0.00   0.0  0
 43Z  CONST_05  CAO  CAP  CAN  CAG     0.00   0.0  0
 43Z  CONST_06  CAO  CAH  CAF  CAG     0.00   0.0  0
 43Z  CONST_07  CAG  CAN  CAP  CL    180.00   0.0  0
 43Z  CONST_08  CAH  CAO  CAP  CL    180.00   0.0  0
 43Z  CONST_09  CAI  CAO  CAP  CAN   180.00   0.0  0
 43Z  CONST_10  CAF  CAG  CAN  FAD   180.00   0.0  0
 43Z  CONST_11  CAO  CAP  CAN  FAD   180.00   0.0  0
 43Z  CONST_12  CAI  CAO  CAH  CAF   180.00   0.0  0
 43Z  CONST_13  H1   CAG  CAN  CAP   180.00   0.0  0
 43Z  CONST_14  H3   CAH  CAO  CAP   180.00   0.0  0
 43Z  CONST_15  H2   CAF  CAG  CAN   180.00   0.0  0
 43Z  CONST_16  CAS  CAM  NAL  CAI   180.00   0.0  0
 43Z  CONST_17  H6   NAL  CAM  CAS     0.00   0.0  0
 43Z  CONST_18  OAA  CAM  NAL  CAI     0.00   0.0  0
 43Z  Var_01    NAL  CAI  CAO  CAP    68.36  30.0  2
 43Z  Var_02    CAM  NAL  CAI  CAO  -128.62  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
 43Z  chir_01  CAS  CAM  CAK  CAJ  negativ
 43Z  chir_02  CAQ  OAB  CAR  CAJ  positiv
 43Z  chir_03  CAR  OAC  CAK  CAQ  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
 43Z  plan-1  CL   0.020
 43Z  plan-1  CAP  0.020
 43Z  plan-1  CAN  0.020
 43Z  plan-1  FAD  0.020
 43Z  plan-1  CAG  0.020
 43Z  plan-1  CAF  0.020
 43Z  plan-1  CAH  0.020
 43Z  plan-1  CAO  0.020
 43Z  plan-1  CAI  0.020
 43Z  plan-1  H1   0.020
 43Z  plan-1  H2   0.020
 43Z  plan-1  H3   0.020
 43Z  plan-2  CAI  0.020
 43Z  plan-2  NAL  0.020
 43Z  plan-2  CAM  0.020
 43Z  plan-2  OAA  0.020
 43Z  plan-2  CAS  0.020
 43Z  plan-2  H6   0.020

