# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 09:41:47 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(aminomethyl)-6-[(1~{R},2~{S},3~{S},4~{R},6~{S})-4,6-bis(azanyl)-3-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-cyclohexyl]oxy-oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)[C@H](O)[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
 CJX  CJX  (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(aminomethyl)-6-[(1~{R},2~{S},3~{S},4~{R},6~{S})-4,6-bis(azanyl)-3-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-cyclohexyl]oxy-oxane-3,4,5-triol  ligand  68  33  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CJX
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
 CJX  C4   C  CH1   0   0.018  48.4746  -3.9360  20.8116
 CJX  C5   C  CH1   0  -0.010  49.3003  -3.5904  22.0603
 CJX  C6   C  CH2   0  -0.200  50.2706  -2.4466  21.8577
 CJX  C3   C  CH1   0   0.012  47.4827  -5.0356  21.1566
 CJX  O2   O  OH1   0  -0.717  45.6988  -5.5854  22.6753
 CJX  C2   C  CH1   0   0.020  46.6380  -4.5979  22.3544
 CJX  O3   O  OH1   0  -0.670  46.6761  -5.2843  20.0298
 CJX  O4   O  OH1   0  -0.669  49.3136  -4.3929  19.7764
 CJX  O6   O  OH1   0  -0.667  49.5776  -1.2938  21.4421
 CJX  O5   O  O2    0  -0.494  48.4533  -3.2392  23.1427
 CJX  C1   C  CH1   0   0.201  47.5475  -4.2276  23.5267
 CJX  O1   O  O2    0  -0.509  48.1937  -5.3798  23.9736
 CJX  CBG  C  CH1   0   0.056  48.2709  -5.6054  25.3627
 CJX  CBA  C  CH1   0   0.022  49.6834  -6.0644  25.7033
 CJX  OAK  O  OH1   0  -0.693  50.5702  -5.0341  25.3566
 CJX  CAT  C  CH1   0  -0.095  47.2447  -6.6583  25.7772
 CJX  NAC  N  NH2   0  -0.818  45.9090  -6.2327  25.3756
 CJX  CAN  C  CH2   0  -0.465  47.3811  -6.9442  27.2684
 CJX  CAS  C  CH1   0  -0.100  48.7710  -7.4541  27.6243
 CJX  NAB  N  NH2   0  -0.808  48.8645  -7.6683  29.0597
 CJX  CBF  C  CH1   0   0.046  49.8122  -6.4330  27.1863
 CJX  OAQ  O  O2    0  -0.520  51.1003  -6.9911  27.4035
 CJX  CBD  C  CH1   0   0.238  52.1156  -6.1712  27.8935
 CJX  OAO  O  O2    0  -0.494  52.3669  -6.4067  29.2435
 CJX  CBB  C  CH1   0   0.020  52.8585  -7.7005  29.5709
 CJX  CAL  C  CH2   0  -0.345  52.9998  -7.7697  31.0845
 CJX  NAA  N  NH2   0  -0.803  54.0075  -6.8568  31.6025
 CJX  CAW  C  CH1   0  -0.003  54.1654  -7.9701  28.8210
 CJX  OAG  O  OH1   0  -0.671  54.6145  -9.2911  29.0288
 CJX  CAU  C  CH1   0   0.006  53.9530  -7.7896  27.3243
 CJX  OAE  O  OH1   0  -0.670  55.1568  -7.8903  26.6023
 CJX  CAY  C  CH1   0   0.016  53.3817  -6.4042  27.0651
 CJX  OAI  O  OH1   0  -0.676  53.0587  -6.2158  25.7048
 CJX  H1   H  HCH1  0   0.217  47.9069  -3.0495  20.4981
 CJX  H2   H  HCH1  0   0.222  49.9087  -4.4678  22.3194
 CJX  H3   H  HCH2  0   0.216  50.8072  -2.2820  22.8016
 CJX  H4   H  HCH2  0   0.205  51.0246  -2.7605  21.1255
 CJX  H5   H  HCH1  0   0.197  48.0457  -5.9402  21.4352
 CJX  H6   H  HOH1  0   0.468  45.7820  -5.8429  23.6292
 CJX  H7   H  HCH1  0   0.198  46.1144  -3.6726  22.0666
 CJX  H8   H  HOH1  0   0.445  46.0256  -5.9485  20.2815
 CJX  H9   H  HOH1  0   0.454  49.6880  -3.6320  19.3234
 CJX  H10  H  HOH1  0   0.456  50.2236  -0.6128  21.2352
 CJX  H11  H  HCH1  0   0.242  46.9535  -3.7789  24.3325
 CJX  H12  H  HCH1  0   0.222  48.0592  -4.6747  25.9133
 CJX  H13  H  HCH1  0   0.203  49.8874  -6.9767  25.1193
 CJX  H14  H  HOH1  0   0.459  51.4723  -5.3942  25.3376
 CJX  H15  H  HCH1  0   0.239  47.4649  -7.5772  25.2218
 CJX  H16  H  HNH2  0   0.372  45.2467  -6.9790  25.5546
 CJX  H17  H  HNH2  0   0.362  45.6045  -5.4490  25.9452
 CJX  H19  H  HCH2  0   0.227  47.1682  -6.0318  27.8379
 CJX  H20  H  HCH2  0   0.250  46.6327  -7.6841  27.5657
 CJX  H21  H  HCH1  0   0.207  48.9468  -8.3770  27.0464
 CJX  H22  H  HNH2  0   0.345  48.1670  -8.3480  29.3383
 CJX  H23  H  HNH2  0   0.353  49.7570  -8.0905  29.2828
 CJX  H25  H  HCH1  0   0.220  49.6831  -5.5263  27.7955
 CJX  H26  H  HCH1  0   0.247  51.8269  -5.1159  27.8317
 CJX  H27  H  HCH1  0   0.220  52.1299  -8.4716  29.2818
 CJX  H28  H  HCH2  0   0.243  52.0328  -7.5035  31.5170
 CJX  H29  H  HCH2  0   0.213  53.1679  -8.8189  31.3593
 CJX  H30  H  HNH2  0   0.353  53.8305  -6.6855  32.5829
 CJX  H31  H  HNH2  0   0.345  54.9228  -7.2865  31.5649
 CJX  H33  H  HCH1  0   0.221  54.9194  -7.2383  29.1446
 CJX  H34  H  HOH1  0   0.458  55.1312  -9.3260  29.8390
 CJX  H35  H  HCH1  0   0.213  53.2281  -8.5436  26.9806
 CJX  H36  H  HOH1  0   0.450  55.4991  -8.7830  26.7138
 CJX  H37  H  HCH1  0   0.235  54.1203  -5.6584  27.3902
 CJX  H38  H  HOH1  0   0.468  53.8696  -6.1219  25.1943

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
 CJX  O4   C4   single  1.409  0.020  1.409
 CJX  O3   C3   single  1.408  0.020  1.408
 CJX  C4   C3   single  1.521  0.020  1.521
 CJX  C4   C5   single  1.536  0.020  1.536
 CJX  C3   C2   single  1.530  0.020  1.530
 CJX  C5   C6   single  1.514  0.020  1.514
 CJX  C5   O5   single  1.419  0.020  1.419
 CJX  C6   O6   single  1.408  0.020  1.408
 CJX  C2   O2   single  1.400  0.020  1.400
 CJX  C2   C1   single  1.529  0.020  1.529
 CJX  O5   C1   single  1.395  0.020  1.395
 CJX  C1   O1   single  1.395  0.020  1.395
 CJX  O1   CBG  single  1.409  0.020  1.409
 CJX  OAK  CBA  single  1.403  0.020  1.403
 CJX  CBA  CBG  single  1.524  0.020  1.524
 CJX  CBA  CBF  single  1.534  0.020  1.534
 CJX  OAI  CAY  single  1.411  0.020  1.411
 CJX  CBG  CAT  single  1.528  0.020  1.528
 CJX  NAC  CAT  single  1.458  0.020  1.458
 CJX  CAT  CAN  single  1.524  0.020  1.524
 CJX  OAQ  CBF  single  1.420  0.020  1.420
 CJX  OAQ  CBD  single  1.394  0.020  1.394
 CJX  CBF  CAS  single  1.523  0.020  1.523
 CJX  CAY  CBD  single  1.531  0.020  1.531
 CJX  CAY  CAU  single  1.521  0.020  1.521
 CJX  CBD  OAO  single  1.393  0.020  1.393
 CJX  CAS  CAN  single  1.523  0.020  1.523
 CJX  CAS  NAB  single  1.454  0.020  1.454
 CJX  CAU  OAE  single  1.407  0.020  1.407
 CJX  CAU  CAW  single  1.522  0.020  1.522
 CJX  OAO  CBB  single  1.422  0.020  1.422
 CJX  CAW  CBB  single  1.531  0.020  1.531
 CJX  CAW  OAG  single  1.411  0.020  1.411
 CJX  CBB  CAL  single  1.522  0.020  1.522
 CJX  CAL  NAA  single  1.455  0.020  1.455
 CJX  C4   H1   single  0.970  0.020  1.090
 CJX  C5   H2   single  0.970  0.020  1.090
 CJX  C6   H3   single  0.970  0.020  1.090
 CJX  C6   H4   single  0.970  0.020  1.090
 CJX  C3   H5   single  0.970  0.020  1.090
 CJX  O2   H6   single  0.850  0.020  0.980
 CJX  C2   H7   single  0.970  0.020  1.090
 CJX  O3   H8   single  0.850  0.020  0.980
 CJX  O4   H9   single  0.850  0.020  0.980
 CJX  O6   H10  single  0.850  0.020  0.980
 CJX  C1   H11  single  0.970  0.020  1.090
 CJX  CBG  H12  single  0.970  0.020  1.090
 CJX  CBA  H13  single  0.970  0.020  1.090
 CJX  OAK  H14  single  0.850  0.020  0.980
 CJX  CAT  H15  single  0.970  0.020  1.090
 CJX  NAC  H16  single  0.890  0.020  1.040
 CJX  NAC  H17  single  0.890  0.020  1.040
 CJX  CAN  H19  single  0.970  0.020  1.090
 CJX  CAN  H20  single  0.970  0.020  1.090
 CJX  CAS  H21  single  0.970  0.020  1.090
 CJX  NAB  H22  single  0.890  0.020  1.040
 CJX  NAB  H23  single  0.890  0.020  1.040
 CJX  CBF  H25  single  0.970  0.020  1.090
 CJX  CBD  H26  single  0.970  0.020  1.090
 CJX  CBB  H27  single  0.970  0.020  1.090
 CJX  CAL  H28  single  0.970  0.020  1.090
 CJX  CAL  H29  single  0.970  0.020  1.090
 CJX  NAA  H30  single  0.890  0.020  1.040
 CJX  NAA  H31  single  0.890  0.020  1.040
 CJX  CAW  H33  single  0.970  0.020  1.090
 CJX  OAG  H34  single  0.850  0.020  0.980
 CJX  CAU  H35  single  0.970  0.020  1.090
 CJX  OAE  H36  single  0.850  0.020  0.980
 CJX  CAY  H37  single  0.970  0.020  1.090
 CJX  OAI  H38  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
 CJX  H1   C4   O4   111.09  3.000
 CJX  H1   C4   C3   108.13  3.000
 CJX  O4   C4   C3   108.70  3.000
 CJX  H1   C4   C5   109.16  3.000
 CJX  C3   C4   C5   109.20  3.000
 CJX  O4   C4   C5   110.50  3.000
 CJX  H2   C5   O5   110.39  3.000
 CJX  H2   C5   C6   106.27  3.000
 CJX  O5   C5   C6   107.33  3.000
 CJX  H2   C5   C4   108.04  3.000
 CJX  O5   C5   C4   110.79  3.000
 CJX  C6   C5   C4   113.94  3.000
 CJX  H4   C6   H3   106.30  3.000
 CJX  H4   C6   O6   112.07  3.000
 CJX  H3   C6   O6   111.81  3.000
 CJX  H4   C6   C5   108.28  3.000
 CJX  H3   C6   C5   108.15  3.000
 CJX  O6   C6   C5   110.05  3.000
 CJX  H5   C3   O3   110.50  3.000
 CJX  H5   C3   C2   108.61  3.000
 CJX  O3   C3   C2   111.16  3.000
 CJX  H5   C3   C4   108.53  3.000
 CJX  C2   C3   C4   109.33  3.000
 CJX  O3   C3   C4   108.66  3.000
 CJX  H6   O2   C2   110.33  3.000
 CJX  H7   C2   C1   106.24  3.000
 CJX  H7   C2   O2   109.48  3.000
 CJX  C1   C2   O2   113.21  3.000
 CJX  H7   C2   C3   107.35  3.000
 CJX  C1   C2   C3   109.95  3.000
 CJX  O2   C2   C3   110.37  3.000
 CJX  H8   O3   C3   107.44  3.000
 CJX  H9   O4   C4   108.75  3.000
 CJX  H10  O6   C6   108.23  3.000
 CJX  C1   O5   C5   114.99  3.000
 CJX  H11  C1   O1   110.70  3.000
 CJX  H11  C1   O5   105.31  3.000
 CJX  O1   C1   O5   111.89  3.000
 CJX  H11  C1   C2   109.88  3.000
 CJX  O1   C1   C2   108.73  3.000
 CJX  O5   C1   C2   110.30  3.000
 CJX  CBG  O1   C1   118.26  3.000
 CJX  H12  CBG  CAT  108.52  3.000
 CJX  H12  CBG  CBA  108.71  3.000
 CJX  CAT  CBG  CBA  110.76  3.000
 CJX  H12  CBG  O1   110.29  3.000
 CJX  CAT  CBG  O1   109.93  3.000
 CJX  CBA  CBG  O1   108.62  3.000
 CJX  H13  CBA  CBF  107.33  3.000
 CJX  H13  CBA  OAK  111.10  3.000
 CJX  CBF  CBA  OAK  111.25  3.000
 CJX  H13  CBA  CBG  107.60  3.000
 CJX  CBF  CBA  CBG  111.49  3.000
 CJX  OAK  CBA  CBG  108.03  3.000
 CJX  H14  OAK  CBA  108.64  3.000
 CJX  H15  CAT  CAN  108.69  3.000
 CJX  H15  CAT  NAC  106.80  3.000
 CJX  CAN  CAT  NAC  113.96  3.000
 CJX  H15  CAT  CBG  107.79  3.000
 CJX  CAN  CAT  CBG  109.55  3.000
 CJX  NAC  CAT  CBG  109.84  3.000
 CJX  H17  NAC  H16  105.85  3.000
 CJX  H17  NAC  CAT  110.21  3.000
 CJX  H16  NAC  CAT  109.57  3.000
 CJX  H20  CAN  H19  106.79  3.000
 CJX  H20  CAN  CAS  109.55  3.000
 CJX  H19  CAN  CAS  109.54  3.000
 CJX  H20  CAN  CAT  109.37  3.000
 CJX  H19  CAN  CAT  109.55  3.000
 CJX  CAS  CAN  CAT  111.91  3.000
 CJX  H21  CAS  CBF  107.54  3.000
 CJX  H21  CAS  NAB  112.56  3.000
 CJX  CBF  CAS  NAB  109.80  3.000
 CJX  H21  CAS  CAN  107.65  3.000
 CJX  NAB  CAS  CAN  109.80  3.000
 CJX  CBF  CAS  CAN  109.41  3.000
 CJX  H23  NAB  H22  105.46  3.000
 CJX  H23  NAB  CAS  109.61  3.000
 CJX  H22  NAB  CAS  109.03  3.000
 CJX  H25  CBF  OAQ  110.22  3.000
 CJX  H25  CBF  CAS  108.25  3.000
 CJX  OAQ  CBF  CAS  108.21  3.000
 CJX  H25  CBF  CBA  109.13  3.000
 CJX  CAS  CBF  CBA  112.45  3.000
 CJX  OAQ  CBF  CBA  108.57  3.000
 CJX  CBD  OAQ  CBF  118.89  3.000
 CJX  H26  CBD  CAY  109.51  3.000
 CJX  H26  CBD  OAO  105.37  3.000
 CJX  CAY  CBD  OAO  110.45  3.000
 CJX  H26  CBD  OAQ  110.78  3.000
 CJX  OAO  CBD  OAQ  111.87  3.000
 CJX  CAY  CBD  OAQ  108.82  3.000
 CJX  CBB  OAO  CBD  116.05  3.000
 CJX  H27  CBB  CAW  108.27  3.000
 CJX  H27  CBB  CAL  106.92  3.000
 CJX  CAW  CBB  CAL  113.58  3.000
 CJX  H27  CBB  OAO  110.39  3.000
 CJX  CAL  CBB  OAO  107.60  3.000
 CJX  CAW  CBB  OAO  110.03  3.000
 CJX  H29  CAL  H28  105.63  3.000
 CJX  H29  CAL  NAA  113.87  3.000
 CJX  H28  CAL  NAA  108.62  3.000
 CJX  H29  CAL  CBB  107.86  3.000
 CJX  H28  CAL  CBB  107.49  3.000
 CJX  NAA  CAL  CBB  112.94  3.000
 CJX  H31  NAA  H30  105.44  3.000
 CJX  H31  NAA  CAL  110.30  3.000
 CJX  H30  NAA  CAL  109.29  3.000
 CJX  H33  CAW  CAU  107.83  3.000
 CJX  H33  CAW  OAG  111.20  3.000
 CJX  CAU  CAW  OAG  107.47  3.000
 CJX  H33  CAW  CBB  108.91  3.000
 CJX  OAG  CAW  CBB  111.38  3.000
 CJX  CAU  CAW  CBB  109.97  3.000
 CJX  H34  OAG  CAW  109.21  3.000
 CJX  H35  CAU  CAY  108.87  3.000
 CJX  H35  CAU  OAE  110.74  3.000
 CJX  CAY  CAU  OAE  107.40  3.000
 CJX  H35  CAU  CAW  108.51  3.000
 CJX  OAE  CAU  CAW  112.12  3.000
 CJX  CAY  CAU  CAW  109.14  3.000
 CJX  H36  OAE  CAU  108.12  3.000
 CJX  H37  CAY  OAI  110.40  3.000
 CJX  H37  CAY  CAU  108.39  3.000
 CJX  OAI  CAY  CAU  111.84  3.000
 CJX  H37  CAY  CBD  107.01  3.000
 CJX  CAU  CAY  CBD  110.92  3.000
 CJX  OAI  CAY  CBD  108.18  3.000
 CJX  H38  OAI  CAY  109.35  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
 CJX  Var_01  H30  NAA  CAL  CBB  159.09  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
 CJX  chir_01  C4   O4   C3   C5   negativ
 CJX  chir_02  C5   O5   C4   C6   negativ
 CJX  chir_03  C3   O3   C4   C2   negativ
 CJX  chir_04  C2   O2   C3   C1   positiv
 CJX  chir_05  C1   O5   O1   C2   positiv
 CJX  chir_06  CBG  O1   CAT  CBA  negativ
 CJX  chir_07  CBA  OAK  CBG  CBF  positiv
 CJX  chir_08  CAT  NAC  CAN  CBG  positiv
 CJX  chir_09  CAS  NAB  CBF  CAN  positiv
 CJX  chir_10  CBF  OAQ  CBA  CAS  negativ
 CJX  chir_11  CBD  OAO  OAQ  CAY  positiv
 CJX  chir_12  CBB  OAO  CAL  CAW  positiv
 CJX  chir_13  CAW  OAG  CBB  CAU  positiv
 CJX  chir_14  CAU  OAE  CAY  CAW  positiv
 CJX  chir_15  CAY  OAI  CAU  CBD  positiv

