# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 23:35:46 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (1R,2S,3S,4R,5R)-4-[(4-bromobenzyl)amino]-5-(hydroxymethyl)cyclopentane-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1NCc2ccc(Br)cc2
#
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
 LR1  LR1  (1R,2S,3S,4R,5R)-4-[(4-bromobenzyl)amino]-5-(hydroxymethyl)cyclopentane-1,2,3-triol  ligand  37  19  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LR1
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
 LR1  CAH   C   CR16  0  -0.302  -2.1316  -1.7170   0.2874
 LR1  CAF   C   CR16  0  -0.214  -3.4698  -1.3538   0.3333
 LR1  CAM   C   CR6   0  -0.126  -3.7980  -0.0295   0.5825
 LR1  BR    BR  BR    0  -0.058  -5.6168   0.4853   0.6372
 LR1  CAG   C   CR16  0  -0.212  -2.8108   0.9228   0.7845
 LR1  CAI   C   CR16  0  -0.298  -1.4781   0.5366   0.7393
 LR1  CAN   C   CR6   0   0.082  -1.1184  -0.7849   0.4941
 LR1  CAK   C   CH2   0  -0.297   0.3252  -1.2249   0.4764
 LR1  NAL   N   NH1   0  -0.614   1.2136  -0.1429   0.1157
 LR1  CAS   C   CH1   0  -0.092   2.6075  -0.3117   0.4514
 LR1  CAQ   C   CH1   0   0.026   3.4448  -1.2333  -0.4359
 LR1  OAD   O   OH1   0  -0.665   3.1024  -2.5812  -0.2356
 LR1  CAO   C   CH1   0  -0.014   4.8634  -0.8613  -0.0240
 LR1  OAB   O   OH1   0  -0.676   5.8868  -1.3351  -0.8664
 LR1  CAP   C   CH1   0   0.067   4.8216   0.6604  -0.0394
 LR1  OAC   O   OH1   0  -0.673   5.8202   1.2734   0.7381
 LR1  CAR   C   CH1   0  -0.308   3.4170   1.0192   0.4796
 LR1  CAJ   C   CH2   0  -0.152   2.7712   2.1370  -0.3212
 LR1  OAA   O   OH1   0  -0.671   3.6012   3.2747  -0.2475
 LR1  HAH   H   HCR6  0   0.258  -1.8790  -2.7506   0.0814
 LR1  HAF   H   HCR6  0   0.276  -4.2369  -2.0985   0.1680
 LR1  HAG   H   HCR6  0   0.275  -3.0643   1.9574   0.9744
 LR1  HAI   H   HCR6  0   0.264  -0.7053   1.2792   0.8874
 LR1  HAK1  H   HCH2  0   0.244   0.5976  -1.5603   1.4824
 LR1  HAK2  H   HCH2  0   0.223   0.4133  -2.1100  -0.1653
 LR1  HAL   H   HNH1  0   0.347   1.0979   0.0823  -0.8646
 LR1  HAS   H   HCH1  0   0.245   2.6326  -0.7306   1.4634
 LR1  HAQ   H   HCH1  0   0.199   3.2992  -0.9421  -1.4893
 LR1  HAR   H   HCH1  0   0.250   3.5037   1.3559   1.5170
 LR1  HAD   H   HOH1  0   0.452   3.4822  -3.1057  -0.9466
 LR1  HAO   H   HCH1  0   0.208   5.0189  -1.2003   1.0118
 LR1  HAB   H   HOH1  0   0.454   6.0731  -2.2521  -0.6451
 LR1  HAP   H   HCH1  0   0.203   4.9065   0.9770  -1.0915
 LR1  HAC   H   HOH1  0   0.447   6.6752   1.0430   0.3607
 LR1  HAJ1  H   HCH2  0   0.184   2.6368   1.8144  -1.3646
 LR1  HAJ2  H   HCH2  0   0.215   1.7730   2.3420   0.0810
 LR1  HAA   H   HOH1  0   0.453   3.2058   3.9650  -0.7870

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
 LR1  CAH  CAF   aromatic  1.387  0.020  1.387
 LR1  CAH  CAN   aromatic  1.392  0.020  1.392
 LR1  CAF  CAM   aromatic  1.387  0.020  1.387
 LR1  CAM  BR    single    1.891  0.020  1.891
 LR1  CAM  CAG   aromatic  1.386  0.020  1.386
 LR1  CAG  CAI   aromatic  1.388  0.020  1.388
 LR1  CAI  CAN   aromatic  1.391  0.020  1.391
 LR1  CAN  CAK   single    1.509  0.020  1.509
 LR1  CAK  NAL   single    1.446  0.020  1.446
 LR1  NAL  CAS   single    1.444  0.020  1.444
 LR1  CAS  CAQ   single    1.529  0.020  1.529
 LR1  CAS  CAR   single    1.558  0.020  1.558
 LR1  CAQ  OAD   single    1.405  0.020  1.405
 LR1  CAQ  CAO   single    1.523  0.020  1.523
 LR1  CAO  OAB   single    1.408  0.020  1.408
 LR1  CAO  CAP   single    1.522  0.020  1.522
 LR1  CAP  OAC   single    1.406  0.020  1.406
 LR1  CAP  CAR   single    1.540  0.020  1.540
 LR1  CAR  CAJ   single    1.519  0.020  1.519
 LR1  CAJ  OAA   single    1.410  0.020  1.410
 LR1  CAH  HAH   single    0.930  0.020  1.080
 LR1  CAF  HAF   single    0.930  0.020  1.080
 LR1  CAG  HAG   single    0.930  0.020  1.080
 LR1  CAI  HAI   single    0.930  0.020  1.080
 LR1  CAK  HAK1  single    0.970  0.020  1.090
 LR1  CAK  HAK2  single    0.970  0.020  1.090
 LR1  NAL  HAL   single    0.890  0.020  1.040
 LR1  CAS  HAS   single    0.970  0.020  1.090
 LR1  CAQ  HAQ   single    0.970  0.020  1.090
 LR1  CAR  HAR   single    0.970  0.020  1.090
 LR1  OAD  HAD   single    0.850  0.020  0.980
 LR1  CAO  HAO   single    0.970  0.020  1.090
 LR1  OAB  HAB   single    0.850  0.020  0.980
 LR1  CAP  HAP   single    0.970  0.020  1.090
 LR1  OAC  HAC   single    0.850  0.020  0.980
 LR1  CAJ  HAJ1  single    0.970  0.020  1.090
 LR1  CAJ  HAJ2  single    0.970  0.020  1.090
 LR1  OAA  HAA   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
 LR1  HAH   CAH  CAN   119.81  3.000
 LR1  HAH   CAH  CAF   118.73  3.000
 LR1  CAN   CAH  CAF   121.45  3.000
 LR1  HAF   CAF  CAM   121.13  3.000
 LR1  HAF   CAF  CAH   119.92  3.000
 LR1  CAM   CAF  CAH   118.96  3.000
 LR1  CAG   CAM  BR    119.58  3.000
 LR1  CAG   CAM  CAF   120.90  3.000
 LR1  BR    CAM  CAF   119.52  3.000
 LR1  HAG   CAG  CAI   119.78  3.000
 LR1  HAG   CAG  CAM   121.03  3.000
 LR1  CAI   CAG  CAM   119.19  3.000
 LR1  HAI   CAI  CAN   119.43  3.000
 LR1  HAI   CAI  CAG   119.36  3.000
 LR1  CAN   CAI  CAG   121.21  3.000
 LR1  CAK   CAN  CAI   121.75  3.000
 LR1  CAK   CAN  CAH   119.94  3.000
 LR1  CAI   CAN  CAH   118.29  3.000
 LR1  HAK2  CAK  HAK1  105.69  3.000
 LR1  HAK2  CAK  NAL   114.12  3.000
 LR1  HAK1  CAK  NAL   107.79  3.000
 LR1  HAK2  CAK  CAN   108.60  3.000
 LR1  HAK1  CAK  CAN   108.45  3.000
 LR1  NAL   CAK  CAN   111.87  3.000
 LR1  HAL   NAL  CAS   111.19  3.000
 LR1  HAL   NAL  CAK   109.74  3.000
 LR1  CAS   NAL  CAK   116.60  3.000
 LR1  HAS   CAS  CAR   107.34  3.000
 LR1  HAS   CAS  CAQ   107.04  3.000
 LR1  CAR   CAS  CAQ   103.94  3.000
 LR1  HAS   CAS  NAL   106.36  3.000
 LR1  CAR   CAS  NAL   113.95  3.000
 LR1  CAQ   CAS  NAL   117.66  3.000
 LR1  HAQ   CAQ  CAO   108.47  3.000
 LR1  HAQ   CAQ  OAD   110.94  3.000
 LR1  CAO   CAQ  OAD   115.00  3.000
 LR1  HAQ   CAQ  CAS   108.84  3.000
 LR1  CAO   CAQ  CAS   101.88  3.000
 LR1  OAD   CAQ  CAS   111.23  3.000
 LR1  HAD   OAD  CAQ   108.76  3.000
 LR1  HAO   CAO  CAP   108.73  3.000
 LR1  HAO   CAO  OAB   110.90  3.000
 LR1  CAP   CAO  OAB   110.51  3.000
 LR1  HAO   CAO  CAQ   108.10  3.000
 LR1  CAP   CAO  CAQ   102.46  3.000
 LR1  OAB   CAO  CAQ   115.66  3.000
 LR1  HAB   OAB  CAO   108.91  3.000
 LR1  HAP   CAP  CAR   108.97  3.000
 LR1  HAP   CAP  OAC   110.36  3.000
 LR1  CAR   CAP  OAC   111.09  3.000
 LR1  HAP   CAP  CAO   107.14  3.000
 LR1  CAR   CAP  CAO   104.75  3.000
 LR1  OAC   CAP  CAO   114.25  3.000
 LR1  HAC   OAC  CAP   108.04  3.000
 LR1  HAR   CAR  CAJ   107.89  3.000
 LR1  HAR   CAR  CAP   108.60  3.000
 LR1  CAJ   CAR  CAP   112.43  3.000
 LR1  HAR   CAR  CAS   108.73  3.000
 LR1  CAJ   CAR  CAS   113.46  3.000
 LR1  CAP   CAR  CAS   105.59  3.000
 LR1  HAJ2  CAJ  HAJ1  106.96  3.000
 LR1  HAJ2  CAJ  OAA   111.47  3.000
 LR1  HAJ1  CAJ  OAA   110.98  3.000
 LR1  HAJ2  CAJ  CAR   109.36  3.000
 LR1  HAJ1  CAJ  CAR   109.64  3.000
 LR1  OAA   CAJ  CAR   108.41  3.000
 LR1  HAA   OAA  CAJ   107.94  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
 LR1  CONST_01  CAG  CAM  CAF  CAH    0.00   0.0  0
 LR1  CONST_02  CAG  CAI  CAN  CAH    0.00   0.0  0
 LR1  CONST_03  CAI  CAN  CAH  CAF    0.00   0.0  0
 LR1  CONST_04  CAI  CAG  CAM  CAF    0.00   0.0  0
 LR1  CONST_05  CAN  CAH  CAF  CAM    0.00   0.0  0
 LR1  CONST_06  CAN  CAI  CAG  CAM    0.00   0.0  0
 LR1  CONST_07  BR   CAM  CAF  CAH  180.00   0.0  0
 LR1  CONST_08  CAK  CAN  CAH  CAF  180.00   0.0  0
 LR1  CONST_09  CAI  CAG  CAM  BR   180.00   0.0  0
 LR1  CONST_10  CAK  CAN  CAI  CAG  180.00   0.0  0
 LR1  CONST_11  HAI  CAI  CAN  CAH  180.00   0.0  0
 LR1  CONST_12  HAG  CAG  CAM  CAF  180.00   0.0  0
 LR1  CONST_13  HAH  CAH  CAF  CAM  180.00   0.0  0
 LR1  CONST_14  HAF  CAF  CAM  CAG  180.00   0.0  0
 LR1  Var_01    NAL  CAK  CAN  CAH  154.43  30.0  2
 LR1  Var_02    CAS  NAL  CAK  CAN  161.75  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
 LR1  chir_01  CAS  NAL  CAQ  CAR  negativ
 LR1  chir_02  CAQ  OAD  CAO  CAS  positiv
 LR1  chir_03  CAO  OAB  CAP  CAQ  negativ
 LR1  chir_04  CAP  OAC  CAR  CAO  positiv
 LR1  chir_05  CAR  CAS  CAP  CAJ  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
 LR1  plan-1  CAH  0.020
 LR1  plan-1  CAF  0.020
 LR1  plan-1  CAM  0.020
 LR1  plan-1  BR   0.020
 LR1  plan-1  CAG  0.020
 LR1  plan-1  CAI  0.020
 LR1  plan-1  CAN  0.020
 LR1  plan-1  CAK  0.020
 LR1  plan-1  HAH  0.020
 LR1  plan-1  HAF  0.020
 LR1  plan-1  HAG  0.020
 LR1  plan-1  HAI  0.020

