# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 12 10:40:50 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-xylopyranosyl)oxy]-2-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C[C@@H](N)[C@H](O[C@H]2OC[C@@H](O)[C@H](N)[C@H]2O)[C@@H](O)[C@@H]1O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N
#
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
 7XP  7XP  '(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-xylopyranosyl)oxy]-2-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside'  ligand  65  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7XP
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
 7XP  C4   C  CH1   0   0.002  -5.5279  -0.8099   0.2229
 7XP  C5   C  CH1   0  -0.025  -4.8634   0.4993   0.6529
 7XP  C6   C  CH2   0  -0.166  -5.7830   1.3635   1.4860
 7XP  N2   N  NH2   0  -0.808  -2.2755  -2.6223  -0.4131
 7XP  C3   C  CH1   0   0.049  -4.5120  -1.6619  -0.5243
 7XP  OAH  O  OH1   0  -0.669   4.5764  -1.4977  -1.7996
 7XP  CAX  C  CH1   0   0.001   4.8860  -0.3297  -1.0851
 7XP  CAU  C  CH1   0  -0.155   6.2000  -0.5450  -0.3265
 7XP  NAC  N  NH2   0  -0.805   6.6860   0.7580   0.1019
 7XP  CAT  C  CH1   0   0.031   6.0090  -1.4152   0.9208
 7XP  OAF  O  OH1   0  -0.666   5.8788  -2.7564   0.5119
 7XP  CAL  C  CH2   0  -0.215   4.8079  -0.9355   1.7227
 7XP  OAN  O  O2    0  -0.496   3.6435  -0.8700   0.9283
 7XP  CBC  C  CH1   0   0.316   3.7738   0.0632  -0.1154
 7XP  OAQ  O  O2    0  -0.532   2.5800   0.0689  -0.8126
 7XP  CBE  C  CH1   0   0.039   1.5479   0.9194  -0.3421
 7XP  CAZ  C  CH1   0   0.046   0.2604   0.0981  -0.3808
 7XP  OAJ  O  OH1   0  -0.669   0.3473  -0.9938   0.5056
 7XP  CAS  C  CH1   0  -0.112   1.4485   2.1723  -1.2012
 7XP  NAB  N  NH2   0  -0.777   2.7059   2.9000  -1.1635
 7XP  CAM  C  CH2   0  -0.463   0.2392   2.9818  -0.7432
 7XP  CAR  C  CH1   0  -0.100  -1.0679   2.2027  -0.8142
 7XP  NAA  N  NH2   0  -0.811  -2.1371   3.0374  -0.2901
 7XP  CBD  C  CH1   0   0.037  -0.9696   0.9172   0.0022
 7XP  O1   O  O2    0  -0.512  -2.1359   0.1481  -0.2491
 7XP  C1   C  CH1   0   0.266  -2.7143  -0.5361   0.8174
 7XP  O5   O  O2    0  -0.500  -3.7147   0.2247   1.4371
 7XP  O6   O  OH1   0  -0.665  -5.1514   2.5960   1.7356
 7XP  O4   O  OH1   0  -0.675  -6.6147  -0.5824  -0.6494
 7XP  O3   O  OH1   0  -0.675  -5.0390  -2.9266  -0.8503
 7XP  C2   C  CH1   0  -0.138  -3.2729  -1.8780   0.3327
 7XP  H1   H  HCH1  0   0.220  -5.8526  -1.3564   1.1205
 7XP  H2   H  HCH1  0   0.217  -4.5928   1.0554  -0.2564
 7XP  H3   H  HCH2  0   0.199  -6.7216   1.5002   0.9363
 7XP  H4   H  HCH2  0   0.198  -6.0302   0.8322   2.4159
 7XP  H5   H  HNH2  0   0.350  -1.3765  -2.5615   0.0472
 7XP  H6   H  HNH2  0   0.344  -2.5299  -3.6005  -0.4243
 7XP  H8   H  HCH1  0   0.201  -4.2120  -1.1214  -1.4357
 7XP  H9   H  HOH1  0   0.445   3.7264  -1.3618  -2.2307
 7XP  H11  H  HCH1  0   0.233   6.8992  -1.0636  -0.9990
 7XP  H12  H  HNH2  0   0.352   7.5762   0.6512   0.5719
 7XP  H13  H  HNH2  0   0.351   6.8729   1.3348  -0.7087
 7XP  H15  H  HCH1  0   0.215   6.8971  -1.2908   1.5596
 7XP  H16  H  HOH1  0   0.448   5.8628  -3.3073   1.3005
 7XP  H17  H  HCH2  0   0.244   4.5985  -1.6210   2.5475
 7XP  H18  H  HCH2  0   0.208   5.0380   0.0438   2.1616
 7XP  H19  H  HCH1  0   0.196   4.0045   1.0555   0.2984
 7XP  H20  H  HCH1  0   0.225   1.7442   1.2163   0.6990
 7XP  H21  H  HCH1  0   0.206   0.1184  -0.2523  -1.4157
 7XP  H22  H  HOH1  0   0.449   1.1454  -1.4893   0.2912
 7XP  H23  H  HCH1  0   0.229   1.2895   1.8564  -2.2392
 7XP  H24  H  HNH2  0   0.349   2.6837   3.6430  -1.8509
 7XP  H25  H  HNH2  0   0.337   2.8059   3.3606  -0.2654
 7XP  H27  H  HCH2  0   0.220   0.3970   3.3239   0.2867
 7XP  H28  H  HCH2  0   0.245   0.1555   3.8810  -1.3606
 7XP  H29  H  HCH1  0   0.206  -1.2310   1.9090  -1.8646
 7XP  H30  H  HNH2  0   0.345  -2.2832   3.8197  -0.9156
 7XP  H31  H  HNH2  0   0.357  -3.0105   2.5291  -0.2760
 7XP  H33  H  HCH1  0   0.223  -0.9060   1.1900   1.0660
 7XP  H34  H  HCH1  0   0.240  -1.9763  -0.7160   1.6051
 7XP  H35  H  HOH1  0   0.455  -5.7644   3.1474   2.2299
 7XP  H36  H  HOH1  0   0.460  -7.4188  -0.4858  -0.1325
 7XP  H37  H  HOH1  0   0.448  -5.8254  -2.7871  -1.3880
 7XP  H38  H  HCH1  0   0.220  -3.5955  -2.3998   1.2484
 7XP  H10  H  HCH1  0   0.213   5.0222   0.5224  -1.7704

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
 7XP  NAB  CAS  single  1.453  0.020  1.453
 7XP  OAH  CAX  single  1.404  0.020  1.404
 7XP  CAS  CAM  single  1.526  0.020  1.526
 7XP  CAS  CBE  single  1.522  0.020  1.522
 7XP  CAM  CAR  single  1.523  0.020  1.523
 7XP  CAX  CBC  single  1.527  0.020  1.527
 7XP  CAX  CAU  single  1.532  0.020  1.532
 7XP  CBC  OAQ  single  1.383  0.020  1.383
 7XP  CBC  OAN  single  1.406  0.020  1.406
 7XP  NAC  CAU  single  1.455  0.020  1.455
 7XP  OAQ  CBE  single  1.418  0.020  1.418
 7XP  CBE  CAZ  single  1.528  0.020  1.528
 7XP  CAU  CAT  single  1.533  0.020  1.533
 7XP  CAR  NAA  single  1.454  0.020  1.454
 7XP  CAR  CBD  single  1.526  0.020  1.526
 7XP  OAN  CAL  single  1.411  0.020  1.411
 7XP  CAZ  CBD  single  1.527  0.020  1.527
 7XP  CAZ  OAJ  single  1.409  0.020  1.409
 7XP  CAT  CAL  single  1.522  0.020  1.522
 7XP  CAT  OAF  single  1.408  0.020  1.408
 7XP  CBD  O1   single  1.419  0.020  1.419
 7XP  O6   C6   single  1.407  0.020  1.407
 7XP  O1   C1   single  1.393  0.020  1.393
 7XP  O5   C1   single  1.401  0.020  1.401
 7XP  O5   C5   single  1.418  0.020  1.418
 7XP  C6   C5   single  1.512  0.020  1.512
 7XP  C1   C2   single  1.532  0.020  1.532
 7XP  C5   C4   single  1.530  0.020  1.530
 7XP  C2   N2   single  1.451  0.020  1.451
 7XP  C2   C3   single  1.522  0.020  1.522
 7XP  C4   C3   single  1.522  0.020  1.522
 7XP  C4   O4   single  1.412  0.020  1.412
 7XP  C3   O3   single  1.408  0.020  1.408
 7XP  C4   H1   single  0.970  0.020  1.090
 7XP  C5   H2   single  0.970  0.020  1.090
 7XP  C6   H3   single  0.970  0.020  1.090
 7XP  C6   H4   single  0.970  0.020  1.090
 7XP  N2   H5   single  0.890  0.020  1.040
 7XP  N2   H6   single  0.890  0.020  1.040
 7XP  C3   H8   single  0.970  0.020  1.090
 7XP  OAH  H9   single  0.850  0.020  0.980
 7XP  CAX  H10  single  0.970  0.020  1.090
 7XP  CAU  H11  single  0.970  0.020  1.090
 7XP  NAC  H12  single  0.890  0.020  1.040
 7XP  NAC  H13  single  0.890  0.020  1.040
 7XP  CAT  H15  single  0.970  0.020  1.090
 7XP  OAF  H16  single  0.850  0.020  0.980
 7XP  CAL  H17  single  0.970  0.020  1.090
 7XP  CAL  H18  single  0.970  0.020  1.090
 7XP  CBC  H19  single  0.970  0.020  1.090
 7XP  CBE  H20  single  0.970  0.020  1.090
 7XP  CAZ  H21  single  0.970  0.020  1.090
 7XP  OAJ  H22  single  0.850  0.020  0.980
 7XP  CAS  H23  single  0.970  0.020  1.090
 7XP  NAB  H24  single  0.890  0.020  1.040
 7XP  NAB  H25  single  0.890  0.020  1.040
 7XP  CAM  H27  single  0.970  0.020  1.090
 7XP  CAM  H28  single  0.970  0.020  1.090
 7XP  CAR  H29  single  0.970  0.020  1.090
 7XP  NAA  H30  single  0.890  0.020  1.040
 7XP  NAA  H31  single  0.890  0.020  1.040
 7XP  CBD  H33  single  0.970  0.020  1.090
 7XP  C1   H34  single  0.970  0.020  1.090
 7XP  O6   H35  single  0.850  0.020  0.980
 7XP  O4   H36  single  0.850  0.020  0.980
 7XP  O3   H37  single  0.850  0.020  0.980
 7XP  C2   H38  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
 7XP  H1   C4   O4   110.91  3.000
 7XP  H1   C4   C3   108.64  3.000
 7XP  O4   C4   C3   107.50  3.000
 7XP  H1   C4   C5   108.91  3.000
 7XP  O4   C4   C5   111.72  3.000
 7XP  C3   C4   C5   109.10  3.000
 7XP  H2   C5   O5   110.85  3.000
 7XP  H2   C5   C6   108.43  3.000
 7XP  O5   C5   C6   107.38  3.000
 7XP  H2   C5   C4   107.89  3.000
 7XP  C6   C5   C4   112.33  3.000
 7XP  O5   C5   C4   109.97  3.000
 7XP  H4   C6   H3   106.97  3.000
 7XP  H4   C6   O6   111.98  3.000
 7XP  H3   C6   O6   111.35  3.000
 7XP  H4   C6   C5   109.06  3.000
 7XP  H3   C6   C5   108.40  3.000
 7XP  O6   C6   C5   108.99  3.000
 7XP  H6   N2   H5   106.66  3.000
 7XP  H6   N2   C2   109.22  3.000
 7XP  H5   N2   C2   110.25  3.000
 7XP  H8   C3   C2   108.29  3.000
 7XP  H8   C3   O3   110.55  3.000
 7XP  C2   C3   O3   107.91  3.000
 7XP  H8   C3   C4   108.27  3.000
 7XP  O3   C3   C4   111.50  3.000
 7XP  C2   C3   C4   110.27  3.000
 7XP  H9   OAH  CAX  107.77  3.000
 7XP  H10  CAX  CBC  106.62  3.000
 7XP  H10  CAX  CAU  108.09  3.000
 7XP  CBC  CAX  CAU  110.26  3.000
 7XP  H10  CAX  OAH  110.74  3.000
 7XP  CAU  CAX  OAH  108.92  3.000
 7XP  CBC  CAX  OAH  112.13  3.000
 7XP  H11  CAU  CAT  108.00  3.000
 7XP  H11  CAU  NAC  112.94  3.000
 7XP  CAT  CAU  NAC  108.08  3.000
 7XP  H11  CAU  CAX  107.98  3.000
 7XP  CAT  CAU  CAX  112.07  3.000
 7XP  NAC  CAU  CAX  107.84  3.000
 7XP  H13  NAC  H12  105.64  3.000
 7XP  H13  NAC  CAU  109.64  3.000
 7XP  H12  NAC  CAU  109.63  3.000
 7XP  H15  CAT  CAL  107.17  3.000
 7XP  H15  CAT  OAF  110.53  3.000
 7XP  CAL  CAT  OAF  112.35  3.000
 7XP  H15  CAT  CAU  107.90  3.000
 7XP  OAF  CAT  CAU  108.42  3.000
 7XP  CAL  CAT  CAU  110.38  3.000
 7XP  H16  OAF  CAT  107.99  3.000
 7XP  H18  CAL  H17  107.34  3.000
 7XP  H18  CAL  OAN  110.89  3.000
 7XP  H17  CAL  OAN  107.22  3.000
 7XP  H18  CAL  CAT  109.06  3.000
 7XP  H17  CAL  CAT  110.56  3.000
 7XP  OAN  CAL  CAT  111.67  3.000
 7XP  CBC  OAN  CAL  111.85  3.000
 7XP  H19  CBC  OAQ  111.55  3.000
 7XP  H19  CBC  OAN  109.82  3.000
 7XP  OAQ  CBC  OAN  107.28  3.000
 7XP  H19  CBC  CAX  108.56  3.000
 7XP  OAN  CBC  CAX  111.60  3.000
 7XP  OAQ  CBC  CAX  108.04  3.000
 7XP  CBE  OAQ  CBC  117.62  3.000
 7XP  H20  CBE  CAS  108.88  3.000
 7XP  H20  CBE  CAZ  108.63  3.000
 7XP  CAS  CBE  CAZ  111.91  3.000
 7XP  H20  CBE  OAQ  110.24  3.000
 7XP  CAZ  CBE  OAQ  106.41  3.000
 7XP  CAS  CBE  OAQ  110.73  3.000
 7XP  H21  CAZ  CBD  107.60  3.000
 7XP  H21  CAZ  OAJ  110.63  3.000
 7XP  CBD  CAZ  OAJ  107.92  3.000
 7XP  H21  CAZ  CBE  107.67  3.000
 7XP  OAJ  CAZ  CBE  110.41  3.000
 7XP  CBD  CAZ  CBE  112.60  3.000
 7XP  H22  OAJ  CAZ  108.04  3.000
 7XP  H23  CAS  CAM  108.79  3.000
 7XP  H23  CAS  NAB  107.11  3.000
 7XP  CAM  CAS  NAB  114.35  3.000
 7XP  H23  CAS  CBE  107.85  3.000
 7XP  CAM  CAS  CBE  108.60  3.000
 7XP  NAB  CAS  CBE  109.93  3.000
 7XP  H25  NAB  H24  105.67  3.000
 7XP  H25  NAB  CAS  109.61  3.000
 7XP  H24  NAB  CAS  109.32  3.000
 7XP  H28  CAM  H27  106.54  3.000
 7XP  H28  CAM  CAR  109.17  3.000
 7XP  H27  CAM  CAR  109.07  3.000
 7XP  H28  CAM  CAS  109.11  3.000
 7XP  H27  CAM  CAS  109.48  3.000
 7XP  CAR  CAM  CAS  113.25  3.000
 7XP  H29  CAR  CBD  107.14  3.000
 7XP  H29  CAR  NAA  112.79  3.000
 7XP  CBD  CAR  NAA  109.76  3.000
 7XP  H29  CAR  CAM  107.91  3.000
 7XP  CBD  CAR  CAM  110.53  3.000
 7XP  NAA  CAR  CAM  108.70  3.000
 7XP  H31  NAA  H30  105.81  3.000
 7XP  H31  NAA  CAR  110.60  3.000
 7XP  H30  NAA  CAR  109.09  3.000
 7XP  H33  CBD  O1   110.67  3.000
 7XP  H33  CBD  CAR  108.19  3.000
 7XP  O1   CBD  CAR  107.99  3.000
 7XP  H33  CBD  CAZ  109.21  3.000
 7XP  O1   CBD  CAZ  109.08  3.000
 7XP  CAR  CBD  CAZ  111.70  3.000
 7XP  C1   O1   CBD  118.15  3.000
 7XP  H34  C1   C2   109.24  3.000
 7XP  H34  C1   O5   104.62  3.000
 7XP  C2   C1   O5   110.80  3.000
 7XP  H34  C1   O1   110.60  3.000
 7XP  C2   C1   O1   109.84  3.000
 7XP  O5   C1   O1   111.62  3.000
 7XP  C1   O5   C5   116.04  3.000
 7XP  H35  O6   C6   107.90  3.000
 7XP  H36  O4   C4   109.15  3.000
 7XP  H37  O3   C3   107.75  3.000
 7XP  H38  C2   C1   104.98  3.000
 7XP  H38  C2   C3   107.26  3.000
 7XP  C1   C2   C3   110.52  3.000
 7XP  H38  C2   N2   112.67  3.000
 7XP  C3   C2   N2   110.06  3.000
 7XP  C1   C2   N2   111.18  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
 7XP  Var_01  H17  CAL  OAN  CBC  175.82  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
 7XP  chir_01  C4   C5   C3   O4   positiv
 7XP  chir_02  C5   O5   C4   C6   negativ
 7XP  chir_03  C3   O3   C4   C2   negativ
 7XP  chir_04  CAX  OAH  CBC  CAU  negativ
 7XP  chir_05  CAU  NAC  CAT  CAX  negativ
 7XP  chir_06  CAT  OAF  CAU  CAL  negativ
 7XP  chir_07  CBC  OAN  OAQ  CAX  positiv
 7XP  chir_08  CBE  OAQ  CAS  CAZ  negativ
 7XP  chir_09  CAZ  OAJ  CBE  CBD  positiv
 7XP  chir_10  CAS  NAB  CAM  CBE  positiv
 7XP  chir_11  CAR  NAA  CBD  CAM  positiv
 7XP  chir_12  CBD  O1   CAZ  CAR  negativ
 7XP  chir_13  C1   O1   O5   C2   negativ
 7XP  chir_14  C2   N2   C3   C1   positiv

