# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 08:00:59 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (2S,3S,4R,5S,2'S,3'S,4'R,5'S)-2,2'-(butane-1,4-diyl)bis(5-methylpyrrolidine-3,4-diol)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@@H](CCCC[C@@H]2N[C@@H](C)[C@@H](O)[C@H]2O)[C@H](O)[C@@H]1O
#
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
 68F  68F  (2S,3S,4R,5S,2'S,3'S,4'R,5'S)-2,2'-(butane-1,4-diyl)bis(5-methylpyrrolidine-3,4-diol)  ligand  48  20  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_68F
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
 68F  OAG  O  OH1   0  -0.669   4.5292   1.7150   1.5309
 68F  CAC  C  CH1   0   0.040   4.3238   0.4030   1.0884
 68F  CAB  C  CH1   0  -0.028   5.4825  -0.2478   0.3371
 68F  OAH  O  OH1   0  -0.672   5.9986   0.6903  -0.5766
 68F  CAA  C  CH1   0  -0.070   4.7580  -1.4172  -0.3335
 68F  CAI  C  CH3   0  -0.684   5.4832  -2.0306  -1.5177
 68F  NAE  N  NH1   0  -0.636   3.4573  -0.8557  -0.7204
 68F  CAD  C  CH1   0  -0.049   3.1814   0.3456   0.0711
 68F  CAF  C  CH2   0  -0.451   1.8036   0.3464   0.7156
 68F  CAJ  C  CH2   0  -0.419   0.6523   0.3721  -0.2835
 68F  CAK  C  CH2   0  -0.419  -0.7140   0.3913   0.3907
 68F  CAL  C  CH2   0  -0.452  -1.8613   0.4210  -0.6128
 68F  CAM  C  CR15  0  -0.046  -3.2433   0.4426   0.0227
 68F  NAQ  N  NR15  0  -0.635  -3.5882  -0.7933   0.7296
 68F  CAP  C  CR15  0  -0.070  -4.8881  -1.2873   0.2598
 68F  CAR  C  CH3   0  -0.685  -5.6638  -1.9817   1.3644
 68F  CAO  C  CR15  0  -0.025  -5.5612  -0.0454  -0.3264
 68F  OAS  O  OH1   0  -0.672  -6.0670   0.8326   0.6501
 68F  CAN  C  CR15  0   0.035  -4.3669   0.6245  -1.0009
 68F  OAT  O  OH1   0  -0.669  -4.5193   1.9761  -1.3324
 68F  H1   H  HOH1  0   0.451   5.1393   1.6976   2.2740
 68F  H2   H  HCH1  0   0.204   4.0697  -0.2645   1.9264
 68F  H3   H  HCH1  0   0.224   6.2681  -0.6147   1.0116
 68F  H4   H  HOH1  0   0.453   6.7060   0.2688  -1.0737
 68F  H5   H  HCH1  0   0.213   4.6431  -2.1971   0.4314
 68F  H6   H  HCH3  0   0.222   6.4669  -2.4091  -1.2317
 68F  H7   H  HCH3  0   0.236   4.9158  -2.8725  -1.9160
 68F  H8   H  HCH3  0   0.219   5.6077  -1.3086  -2.3257
 68F  H9   H  HNH1  0   0.348   2.7281  -1.5469  -0.6105
 68F  H11  H  HCH1  0   0.203   3.2548   1.2349  -0.5722
 68F  H12  H  HCH2  0   0.212   1.7108  -0.5324   1.3651
 68F  H13  H  HCH2  0   0.227   1.7271   1.2207   1.3699
 68F  H14  H  HCH2  0   0.213   0.7539   1.2507  -0.9302
 68F  H15  H  HCH2  0   0.215   0.7080  -0.4980  -0.9460
 68F  H16  H  HCH2  0   0.214  -0.8027  -0.4855   1.0411
 68F  H17  H  HCH2  0   0.214  -0.7871   1.2645   1.0483
 68F  H18  H  HCH2  0   0.226  -1.7566   1.3084  -1.2454
 68F  H19  H  HCH2  0   0.213  -1.7890  -0.4439  -1.2831
 68F  H20  H  HCR5  0   0.202  -3.2827   1.2909   0.7220
 68F  H21  H  HNR5  0   0.348  -2.8748  -1.5002   0.6148
 68F  H23  H  HCR5  0   0.210  -4.7721  -2.0014  -0.5681
 68F  H24  H  HCH3  0   0.219  -5.7893  -1.3334   2.2324
 68F  H25  H  HCH3  0   0.223  -6.6497  -2.2993   1.0189
 68F  H26  H  HCH3  0   0.237  -5.1339  -2.8745   1.6984
 68F  H27  H  HCR5  0   0.223  -6.3421  -0.3266  -1.0460
 68F  H28  H  HOH1  0   0.453  -6.8028   0.3994   1.0929
 68F  H29  H  HCR5  0   0.205  -4.1217   0.0238  -1.8904
 68F  H30  H  HOH1  0   0.452  -5.0993   2.0421  -2.0964

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
 68F  OAH  CAB  single  1.407  0.020  1.407
 68F  OAG  CAC  single  1.400  0.020  1.400
 68F  CAB  CAC  single  1.527  0.020  1.527
 68F  CAB  CAA  single  1.530  0.020  1.530
 68F  CAC  CAD  single  1.531  0.020  1.531
 68F  CAD  NAE  single  1.465  0.020  1.465
 68F  CAD  CAF  single  1.521  0.020  1.521
 68F  CAI  CAA  single  1.518  0.020  1.518
 68F  NAE  CAA  single  1.469  0.020  1.469
 68F  CAF  CAJ  single  1.525  0.020  1.525
 68F  CAJ  CAK  single  1.524  0.020  1.524
 68F  CAK  CAL  single  1.524  0.020  1.524
 68F  CAN  OAT  single  1.400  0.020  1.400
 68F  CAN  CAO  single  1.526  0.020  1.526
 68F  CAN  CAM  single  1.531  0.020  1.531
 68F  CAL  CAM  single  1.521  0.020  1.521
 68F  CAO  CAP  single  1.529  0.020  1.529
 68F  CAO  OAS  single  1.407  0.020  1.407
 68F  CAM  NAQ  single  1.465  0.020  1.465
 68F  CAP  NAQ  single  1.468  0.020  1.468
 68F  CAP  CAR  single  1.518  0.020  1.518
 68F  OAG  H1   single  0.850  0.020  0.980
 68F  CAC  H2   single  0.970  0.020  1.090
 68F  CAB  H3   single  0.970  0.020  1.090
 68F  OAH  H4   single  0.850  0.020  0.980
 68F  CAA  H5   single  0.970  0.020  1.090
 68F  CAI  H6   single  0.970  0.020  1.090
 68F  CAI  H7   single  0.970  0.020  1.090
 68F  CAI  H8   single  0.970  0.020  1.090
 68F  NAE  H9   single  0.890  0.020  1.040
 68F  CAD  H11  single  0.970  0.020  1.090
 68F  CAF  H12  single  0.970  0.020  1.090
 68F  CAF  H13  single  0.970  0.020  1.090
 68F  CAJ  H14  single  0.970  0.020  1.090
 68F  CAJ  H15  single  0.970  0.020  1.090
 68F  CAK  H16  single  0.970  0.020  1.090
 68F  CAK  H17  single  0.970  0.020  1.090
 68F  CAL  H18  single  0.970  0.020  1.090
 68F  CAL  H19  single  0.970  0.020  1.090
 68F  CAM  H20  single  0.970  0.020  1.090
 68F  NAQ  H21  single  0.890  0.020  1.040
 68F  CAP  H23  single  0.970  0.020  1.090
 68F  CAR  H24  single  0.970  0.020  1.090
 68F  CAR  H25  single  0.970  0.020  1.090
 68F  CAR  H26  single  0.970  0.020  1.090
 68F  CAO  H27  single  0.970  0.020  1.090
 68F  OAS  H28  single  0.850  0.020  0.980
 68F  CAN  H29  single  0.970  0.020  1.090
 68F  OAT  H30  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
 68F  H1   OAG  CAC  108.69  3.000
 68F  H2   CAC  CAD  108.11  3.000
 68F  H2   CAC  CAB  106.93  3.000
 68F  CAD  CAC  CAB  102.91  3.000
 68F  H2   CAC  OAG  111.19  3.000
 68F  CAD  CAC  OAG  110.78  3.000
 68F  CAB  CAC  OAG  116.35  3.000
 68F  H3   CAB  CAA  110.64  3.000
 68F  H3   CAB  OAH  111.04  3.000
 68F  CAA  CAB  OAH  113.48  3.000
 68F  H3   CAB  CAC  112.52  3.000
 68F  CAA  CAB  CAC  100.49  3.000
 68F  OAH  CAB  CAC  108.27  3.000
 68F  H4   OAH  CAB  108.25  3.000
 68F  H5   CAA  NAE  111.24  3.000
 68F  H5   CAA  CAI  107.83  3.000
 68F  NAE  CAA  CAI  111.85  3.000
 68F  H5   CAA  CAB  106.67  3.000
 68F  NAE  CAA  CAB  104.04  3.000
 68F  CAI  CAA  CAB  115.11  3.000
 68F  H8   CAI  H7   107.45  3.000
 68F  H8   CAI  H6   108.70  3.000
 68F  H7   CAI  H6   107.26  3.000
 68F  H8   CAI  CAA  111.40  3.000
 68F  H7   CAI  CAA  110.39  3.000
 68F  H6   CAI  CAA  111.47  3.000
 68F  H9   NAE  CAD  111.48  3.000
 68F  H9   NAE  CAA  110.42  3.000
 68F  CAD  NAE  CAA  109.76  3.000
 68F  H11  CAD  CAF  107.92  3.000
 68F  H11  CAD  NAE  109.54  3.000
 68F  CAF  CAD  NAE  113.58  3.000
 68F  H11  CAD  CAC  107.97  3.000
 68F  CAF  CAD  CAC  113.23  3.000
 68F  NAE  CAD  CAC  104.44  3.000
 68F  H13  CAF  H12  106.27  3.000
 68F  H13  CAF  CAJ  108.99  3.000
 68F  H12  CAF  CAJ  109.74  3.000
 68F  H13  CAF  CAD  108.48  3.000
 68F  H12  CAF  CAD  109.09  3.000
 68F  CAJ  CAF  CAD  113.97  3.000
 68F  H15  CAJ  H14  105.99  3.000
 68F  H15  CAJ  CAK  108.86  3.000
 68F  H14  CAJ  CAK  109.52  3.000
 68F  H15  CAJ  CAF  110.16  3.000
 68F  H14  CAJ  CAF  109.29  3.000
 68F  CAK  CAJ  CAF  112.79  3.000
 68F  H17  CAK  H16  106.03  3.000
 68F  H17  CAK  CAL  109.24  3.000
 68F  H16  CAK  CAL  110.21  3.000
 68F  H17  CAK  CAJ  109.60  3.000
 68F  H16  CAK  CAJ  108.98  3.000
 68F  CAL  CAK  CAJ  112.57  3.000
 68F  H19  CAL  H18  106.24  3.000
 68F  H19  CAL  CAM  109.05  3.000
 68F  H18  CAL  CAM  108.46  3.000
 68F  H19  CAL  CAK  109.72  3.000
 68F  H18  CAL  CAK  108.91  3.000
 68F  CAM  CAL  CAK  114.14  3.000
 68F  H20  CAM  CAN  107.89  3.000
 68F  H20  CAM  NAQ  109.59  3.000
 68F  CAN  CAM  NAQ  104.48  3.000
 68F  H20  CAM  CAL  108.00  3.000
 68F  NAQ  CAM  CAL  113.80  3.000
 68F  CAN  CAM  CAL  112.91  3.000
 68F  H21  NAQ  CAP  110.68  3.000
 68F  H21  NAQ  CAM  111.65  3.000
 68F  CAP  NAQ  CAM  109.75  3.000
 68F  H23  CAP  CAO  106.57  3.000
 68F  H23  CAP  CAR  107.75  3.000
 68F  CAO  CAP  CAR  115.18  3.000
 68F  H23  CAP  NAQ  111.48  3.000
 68F  CAR  CAP  NAQ  111.94  3.000
 68F  CAO  CAP  NAQ  103.84  3.000
 68F  H26  CAR  H25  107.30  3.000
 68F  H26  CAR  H24  107.39  3.000
 68F  H25  CAR  H24  108.71  3.000
 68F  H26  CAR  CAP  110.43  3.000
 68F  H25  CAR  CAP  111.36  3.000
 68F  H24  CAR  CAP  111.48  3.000
 68F  H27  CAO  CAN  112.28  3.000
 68F  H27  CAO  OAS  111.03  3.000
 68F  CAN  CAO  OAS  108.30  3.000
 68F  H27  CAO  CAP  110.86  3.000
 68F  OAS  CAO  CAP  113.51  3.000
 68F  CAN  CAO  CAP  100.45  3.000
 68F  H28  OAS  CAO  108.26  3.000
 68F  H29  CAN  OAT  111.08  3.000
 68F  H29  CAN  CAO  106.97  3.000
 68F  OAT  CAN  CAO  116.30  3.000
 68F  H29  CAN  CAM  108.17  3.000
 68F  CAO  CAN  CAM  103.10  3.000
 68F  OAT  CAN  CAM  110.67  3.000
 68F  H30  OAT  CAN  108.67  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
 68F  Var_01  CAK  CAJ  CAF  CAD  -179.23  30.0  3
 68F  Var_02  CAM  CAL  CAK  CAJ  -179.93  30.0  3
 68F  Var_03  CAL  CAK  CAJ  CAF   179.84  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
 68F  chir_01  CAC  OAG  CAB  CAD  positiv
 68F  chir_02  CAB  OAH  CAC  CAA  negativ
 68F  chir_03  CAA  NAE  CAB  CAI  positiv
 68F  chir_04  CAD  NAE  CAF  CAC  negativ
 68F  chir_05  CAM  NAQ  CAN  CAL  positiv
 68F  chir_06  CAP  NAQ  CAO  CAR  positiv
 68F  chir_07  CAO  OAS  CAP  CAN  positiv
 68F  chir_08  CAN  OAT  CAO  CAM  positiv

