# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 14 14:18:49 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-acetamido-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-oxan-3-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1NC(C)=O
#
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
 8VZ  8VZ  ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-acetamido-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-oxan-3-yl]ethanamide  ligand  57  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8VZ
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
 8VZ  O26  O  O     0  -0.494   4.0507  -2.7489   0.6547
 8VZ  C24  C  C     0   0.523   3.9337  -2.5454  -0.5443
 8VZ  C25  C  CH3   0  -0.778   4.7021  -3.3332  -1.5731
 8VZ  N2   N  NH1   0  -0.642   3.0754  -1.6326  -1.0523
 8VZ  C2,  C  CH1   0  -0.186   2.2545  -0.7643  -0.2466
 8VZ  C1,  C  CH1   0   0.264   2.8581   0.6377  -0.1386
 8VZ  N1   N  NH1   0  -0.672   4.1285   0.5836   0.4997
 8VZ  C27  C  C     0   0.531   5.1552   1.4147   0.2036
 8VZ  C28  C  CH3   0  -0.782   6.4193   1.1713   0.9868
 8VZ  O29  O  O     0  -0.489   5.0775   2.2867  -0.6454
 8VZ  C3,  C  CH1   0   0.029   0.8417  -0.6916  -0.8355
 8VZ  O3,  O  OH1   0  -0.645   0.2118  -1.9400  -0.7956
 8VZ  C4,  C  CH1   0   0.026  -0.0033   0.3101  -0.0591
 8VZ  C5,  C  CH1   0  -0.007   0.7376   1.6528   0.0208
 8VZ  C6,  C  CH2   0  -0.168  -0.0020   2.6813   0.8515
 8VZ  O6,  O  OH1   0  -0.668   0.7260   3.8850   0.8197
 8VZ  O5,  O  O2    0  -0.484   2.0014   1.4574   0.6188
 8VZ  O1   O  O2    0  -0.514  -1.2316   0.4747  -0.7409
 8VZ  C1   C  CH1   0   0.290  -2.3845   0.3778   0.0148
 8VZ  C2   C  CH1   0  -0.032  -3.5237   1.0174  -0.7766
 8VZ  O2   O  OH1   0  -0.667  -3.3229   2.3986  -0.9596
 8VZ  C3   C  CH1   0   0.004  -4.8221   0.8434   0.0005
 8VZ  O3   O  OH1   0  -0.674  -5.9385   1.2967  -0.7242
 8VZ  C4   C  CH1   0  -0.001  -5.0487  -0.6269   0.3417
 8VZ  O4   O  OH1   0  -0.672  -5.2880  -1.3995  -0.8078
 8VZ  C5   C  CH1   0  -0.020  -3.8094  -1.1656   1.0474
 8VZ  O5   O  O2    0  -0.476  -2.6554  -0.9734   0.2544
 8VZ  C6   C  CH2   0  -0.150  -3.9297  -2.6371   1.3797
 8VZ  O6   O  OH1   0  -0.669  -2.8860  -2.9898   2.2550
 8VZ  H1   H  HCH3  0   0.275   4.1693  -4.2620  -1.7848
 8VZ  H2   H  HCH3  0   0.254   4.8268  -2.7996  -2.5139
 8VZ  H3   H  HCH3  0   0.265   5.6827  -3.5948  -1.1825
 8VZ  H4   H  HNH1  0   0.405   3.1116  -1.4462  -2.0433
 8VZ  H5   H  HCH1  0   0.280   2.1875  -1.1935   0.7571
 8VZ  H6   H  HCH1  0   0.230   2.9905   1.0581  -1.1447
 8VZ  H7   H  HNH1  0   0.400   4.2551  -0.0966   1.2332
 8VZ  H8   H  HCH3  0   0.250   6.3246   0.3937   1.7417
 8VZ  H9   H  HCH3  0   0.272   7.2158   0.8879   0.2983
 8VZ  H10  H  HCH3  0   0.270   6.7270   2.0952   1.4753
 8VZ  H11  H  HCH1  0   0.216   0.9249  -0.3220  -1.8722
 8VZ  H12  H  HOH1  0   0.450   0.7194  -2.5491  -1.3424
 8VZ  H13  H  HCH1  0   0.247  -0.1650  -0.0724   0.9580
 8VZ  H14  H  HCH1  0   0.226   0.8592   2.0444  -1.0028
 8VZ  H15  H  HCH2  0   0.206  -1.0071   2.8165   0.4383
 8VZ  H16  H  HCH2  0   0.201  -0.1174   2.2989   1.8756
 8VZ  H17  H  HOH1  0   0.457   0.2508   4.5318   1.3489
 8VZ  H18  H  HCH1  0   0.184  -2.2739   0.9089   0.9802
 8VZ  H19  H  HCH1  0   0.229  -3.6086   0.4957  -1.7399
 8VZ  H20  H  HOH1  0   0.461  -2.6861   2.5281  -1.6689
 8VZ  H21  H  HCH1  0   0.214  -4.7249   1.3921   0.9514
 8VZ  H22  H  HOH1  0   0.455  -5.7379   2.1695  -1.0793
 8VZ  H23  H  HCH1  0   0.233  -5.8915  -0.6892   1.0464
 8VZ  H24  H  HOH1  0   0.452  -5.9973  -0.9808  -1.3073
 8VZ  H25  H  HCH1  0   0.226  -3.7159  -0.6100   1.9951
 8VZ  H26  H  HCH2  0   0.201  -4.9142  -2.7976   1.8384
 8VZ  H27  H  HCH2  0   0.205  -3.9044  -3.2277   0.4568
 8VZ  H28  H  HOH1  0   0.456  -2.9629  -3.9287   2.4458

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
 8VZ  O6,  C6,  single  1.407  0.020  1.407
 8VZ  C6,  C5,  single  1.515  0.020  1.515
 8VZ  O29  C27  double  1.219  0.020  1.219
 8VZ  O2   C2   single  1.408  0.020  1.408
 8VZ  C5,  O5,  single  1.412  0.020  1.412
 8VZ  C5,  C4,  single  1.536  0.020  1.536
 8VZ  O5,  C1,  single  1.407  0.020  1.407
 8VZ  C27  C28  single  1.507  0.020  1.507
 8VZ  C27  N1   single  1.354  0.020  1.354
 8VZ  C3   O3   single  1.406  0.020  1.406
 8VZ  C3   C2   single  1.523  0.020  1.523
 8VZ  C3   C4   single  1.526  0.020  1.526
 8VZ  N1   C1,  single  1.423  0.020  1.423
 8VZ  C1   C2   single  1.528  0.020  1.528
 8VZ  C1   O1   single  1.382  0.020  1.382
 8VZ  C1   O5   single  1.399  0.020  1.399
 8VZ  C1,  C2,  single  1.530  0.020  1.530
 8VZ  C4,  O1   single  1.414  0.020  1.414
 8VZ  C4,  C3,  single  1.523  0.020  1.523
 8VZ  C5   C4   single  1.524  0.020  1.524
 8VZ  C5   O5   single  1.413  0.020  1.413
 8VZ  C5   C6   single  1.513  0.020  1.513
 8VZ  C4   O4   single  1.406  0.020  1.406
 8VZ  O6   C6   single  1.407  0.020  1.407
 8VZ  C2,  C3,  single  1.532  0.020  1.532
 8VZ  C2,  N2   single  1.441  0.020  1.441
 8VZ  C3,  O3,  single  1.399  0.020  1.399
 8VZ  N2   C24  single  1.352  0.020  1.352
 8VZ  O26  C24  double  1.222  0.020  1.222
 8VZ  C24  C25  single  1.507  0.020  1.507
 8VZ  C25  H1   single  0.970  0.020  1.090
 8VZ  C25  H2   single  0.970  0.020  1.090
 8VZ  C25  H3   single  0.970  0.020  1.090
 8VZ  N2   H4   single  0.860  0.020  1.020
 8VZ  C2,  H5   single  0.970  0.020  1.090
 8VZ  C1,  H6   single  0.970  0.020  1.090
 8VZ  N1   H7   single  0.860  0.020  1.020
 8VZ  C28  H8   single  0.970  0.020  1.090
 8VZ  C28  H9   single  0.970  0.020  1.090
 8VZ  C28  H10  single  0.970  0.020  1.090
 8VZ  C3,  H11  single  0.970  0.020  1.090
 8VZ  O3,  H12  single  0.850  0.020  0.980
 8VZ  C4,  H13  single  0.970  0.020  1.090
 8VZ  C5,  H14  single  0.970  0.020  1.090
 8VZ  C6,  H15  single  0.970  0.020  1.090
 8VZ  C6,  H16  single  0.970  0.020  1.090
 8VZ  O6,  H17  single  0.850  0.020  0.980
 8VZ  C1   H18  single  0.970  0.020  1.090
 8VZ  C2   H19  single  0.970  0.020  1.090
 8VZ  O2   H20  single  0.850  0.020  0.980
 8VZ  C3   H21  single  0.970  0.020  1.090
 8VZ  O3   H22  single  0.850  0.020  0.980
 8VZ  C4   H23  single  0.970  0.020  1.090
 8VZ  O4   H24  single  0.850  0.020  0.980
 8VZ  C5   H25  single  0.970  0.020  1.090
 8VZ  C6   H26  single  0.970  0.020  1.090
 8VZ  C6   H27  single  0.970  0.020  1.090
 8VZ  O6   H28  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
 8VZ  N2   C24  C25  114.85  3.000
 8VZ  C25  C24  O26  122.29  3.000
 8VZ  N2   C24  O26  122.82  3.000
 8VZ  H3   C25  H2   108.96  3.000
 8VZ  H3   C25  H1   107.77  3.000
 8VZ  H2   C25  H1   107.78  3.000
 8VZ  H3   C25  C24  109.90  3.000
 8VZ  H2   C25  C24  113.09  3.000
 8VZ  H1   C25  C24  109.18  3.000
 8VZ  H4   N2   C2,  117.27  3.000
 8VZ  H4   N2   C24  118.10  3.000
 8VZ  C2,  N2   C24  123.94  3.000
 8VZ  H5   C2,  C3,  108.35  3.000
 8VZ  H5   C2,  C1,  108.60  3.000
 8VZ  C3,  C2,  C1,  110.32  3.000
 8VZ  H5   C2,  N2   108.15  3.000
 8VZ  C3,  C2,  N2   109.81  3.000
 8VZ  C1,  C2,  N2   111.51  3.000
 8VZ  H6   C1,  O5,  110.09  3.000
 8VZ  H6   C1,  N1   108.54  3.000
 8VZ  O5,  C1,  N1   108.92  3.000
 8VZ  H6   C1,  C2,  109.49  3.000
 8VZ  N1   C1,  C2,  110.43  3.000
 8VZ  O5,  C1,  C2,  109.36  3.000
 8VZ  H7   N1   C27  118.56  3.000
 8VZ  H7   N1   C1,  117.66  3.000
 8VZ  C27  N1   C1,  123.76  3.000
 8VZ  O29  C27  C28  122.06  3.000
 8VZ  C28  C27  N1   115.05  3.000
 8VZ  O29  C27  N1   122.88  3.000
 8VZ  H10  C28  H9   107.29  3.000
 8VZ  H10  C28  H8   108.64  3.000
 8VZ  H9   C28  H8   108.42  3.000
 8VZ  H10  C28  C27  109.45  3.000
 8VZ  H9   C28  C27  109.06  3.000
 8VZ  H8   C28  C27  113.77  3.000
 8VZ  H11  C3,  C4,  107.48  3.000
 8VZ  H11  C3,  O3,  111.07  3.000
 8VZ  C4,  C3,  O3,  108.82  3.000
 8VZ  H11  C3,  C2,  107.90  3.000
 8VZ  O3,  C3,  C2,  111.21  3.000
 8VZ  C4,  C3,  C2,  110.29  3.000
 8VZ  H12  O3,  C3,  108.12  3.000
 8VZ  H13  C4,  O1   111.03  3.000
 8VZ  H13  C4,  C5,  109.10  3.000
 8VZ  O1   C4,  C5,  110.02  3.000
 8VZ  H13  C4,  C3,  108.94  3.000
 8VZ  O1   C4,  C3,  108.22  3.000
 8VZ  C5,  C4,  C3,  109.51  3.000
 8VZ  H14  C5,  O5,  110.10  3.000
 8VZ  H14  C5,  C6,  108.77  3.000
 8VZ  O5,  C5,  C6,  107.38  3.000
 8VZ  H14  C5,  C4,  108.38  3.000
 8VZ  O5,  C5,  C4,  109.45  3.000
 8VZ  C6,  C5,  C4,  112.75  3.000
 8VZ  H16  C6,  H15  107.34  3.000
 8VZ  H16  C6,  O6,  111.90  3.000
 8VZ  H15  C6,  O6,  111.14  3.000
 8VZ  H16  C6,  C5,  109.02  3.000
 8VZ  H15  C6,  C5,  108.97  3.000
 8VZ  O6,  C6,  C5,  108.41  3.000
 8VZ  H17  O6,  C6,  107.90  3.000
 8VZ  C5,  O5,  C1,  113.44  3.000
 8VZ  C1   O1   C4,  116.92  3.000
 8VZ  H18  C1   O5   109.48  3.000
 8VZ  H18  C1   C2   108.99  3.000
 8VZ  O5   C1   C2   110.41  3.000
 8VZ  H18  C1   O1   111.08  3.000
 8VZ  O5   C1   O1   108.85  3.000
 8VZ  C2   C1   O1   108.02  3.000
 8VZ  H19  C2   C3   109.10  3.000
 8VZ  H19  C2   O2   111.28  3.000
 8VZ  C3   C2   O2   107.46  3.000
 8VZ  H19  C2   C1   108.24  3.000
 8VZ  C3   C2   C1   108.87  3.000
 8VZ  O2   C2   C1   111.83  3.000
 8VZ  H20  O2   C2   108.80  3.000
 8VZ  H21  C3   C4   107.44  3.000
 8VZ  H21  C3   O3   110.74  3.000
 8VZ  C4   C3   O3   107.93  3.000
 8VZ  H21  C3   C2   107.95  3.000
 8VZ  C4   C3   C2   110.53  3.000
 8VZ  O3   C3   C2   112.15  3.000
 8VZ  H22  O3   C3   108.46  3.000
 8VZ  H23  C4   C5   107.83  3.000
 8VZ  H23  C4   O4   111.24  3.000
 8VZ  C5   C4   O4   108.83  3.000
 8VZ  H23  C4   C3   108.15  3.000
 8VZ  O4   C4   C3   111.84  3.000
 8VZ  C5   C4   C3   108.86  3.000
 8VZ  H24  O4   C4   108.09  3.000
 8VZ  H25  C5   C6   107.94  3.000
 8VZ  H25  C5   O5   110.15  3.000
 8VZ  C6   C5   O5   108.69  3.000
 8VZ  H25  C5   C4   106.78  3.000
 8VZ  C6   C5   C4   112.37  3.000
 8VZ  O5   C5   C4   110.85  3.000
 8VZ  C5   O5   C1   112.68  3.000
 8VZ  H27  C6   H26  107.08  3.000
 8VZ  H27  C6   O6   111.81  3.000
 8VZ  H26  C6   O6   111.63  3.000
 8VZ  H27  C6   C5   109.71  3.000
 8VZ  H26  C6   C5   107.77  3.000
 8VZ  O6   C6   C5   108.74  3.000
 8VZ  H28  O6   C6   108.00  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
 8VZ  CONST_01  C2,  N2   C24  O26    0.00   0.0  0
 8VZ  CONST_02  C2,  N2   C24  C25  180.00   0.0  0
 8VZ  CONST_03  O29  C27  N1   C1,    0.00   0.0  0
 8VZ  CONST_04  C28  C27  N1   C1,  180.00   0.0  0
 8VZ  CONST_05  H4   N2   C24  O26  180.00   0.0  0
 8VZ  CONST_06  H7   N1   C27  C28    0.00   0.0  0
 8VZ  Var_01    H1   C25  C24  O26   84.24  30.0  3
 8VZ  Var_02    H8   C28  C27  N1    -3.75  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
 8VZ  chir_01  C2,  C1,  C3,  N2   negativ
 8VZ  chir_02  C1,  O5,  N1   C2,  negativ
 8VZ  chir_03  C3,  O3,  C4,  C2,  negativ
 8VZ  chir_04  C4,  O1   C5,  C3,  positiv
 8VZ  chir_05  C5,  O5,  C4,  C6,  negativ
 8VZ  chir_06  C1   O5   O1   C2   negativ
 8VZ  chir_07  C2   O2   C1   C3   negativ
 8VZ  chir_08  C3   O3   C2   C4   positiv
 8VZ  chir_09  C4   O4   C5   C3   negativ
 8VZ  chir_10  C5   O5   C4   C6   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
 8VZ  plan-1  O26  0.020
 8VZ  plan-1  C24  0.020
 8VZ  plan-1  C25  0.020
 8VZ  plan-1  N2   0.020
 8VZ  plan-1  C2,  0.020
 8VZ  plan-1  H4   0.020
 8VZ  plan-2  C1,  0.020
 8VZ  plan-2  N1   0.020
 8VZ  plan-2  C27  0.020
 8VZ  plan-2  C28  0.020
 8VZ  plan-2  O29  0.020
 8VZ  plan-2  H7   0.020

