# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 20:45:06 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: methyl 3-O-[(1-beta-D-galactopyranosyl-1H-1,2,3-triazol-4-yl)methyl]-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO)[C@H](O)[C@H](OCc2cn(nn2)[C@@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)[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
 P8J  P8J  'methyl 3-O-[(1-beta-D-galactopyranosyl-1H-1,2,3-triazol-4-yl)methyl]-beta-D-galactopyranoside'  ligand  57  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P8J
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
 P8J  C2   C  CR15  0  -0.044  -21.0476  -10.7221   2.3667
 P8J  C3   C  CH2   0  -0.263  -21.7777  -13.1853   2.1171
 P8J  C4   C  CH2   0  -0.155  -20.7215   -6.0914  -0.1793
 P8J  C5   C  CH1   0  -0.020  -20.0283   -6.6642   1.0374
 P8J  C6   C  CH1   0   0.226  -19.6157   -8.6951   2.1162
 P8J  C7   C  CH1   0  -0.028  -18.1152   -8.4276   2.2495
 P8J  C11  C  CR16  0  -0.015  -23.1716  -14.4578  -1.9791
 P8J  C12  C  CR16  0   0.314  -23.9779  -12.2522  -2.0699
 P8J  C14  C  CR16  0  -0.045  -22.9045  -13.0245   0.0234
 P8J  O11  O  O2    0  -0.489  -24.9973  -11.4915  -2.5918
 P8J  C13  C  CR16  0   0.003  -23.9658  -12.0910  -0.5527
 P8J  O9   O  OH1   0  -0.665  -23.6832  -10.7470  -0.2614
 P8J  O8   O  O     0  -0.494  -24.2029  -13.5953  -2.4073
 P8J  C15  C  CR16  0   0.017  -23.0856  -14.4652  -0.4587
 P8J  O10  O  OH1   0  -0.670  -24.2532  -15.0442   0.0665
 P8J  O6   O  O2    0  -0.502  -22.9938  -12.9500   1.4328
 P8J  C1   C  CR5   0   0.105  -20.8468  -12.0270   2.0002
 P8J  N3   N  N     0  -0.288  -19.6142  -12.1136   1.4493
 P8J  N2   N  N     0  -0.105  -19.0587  -10.9556   1.4600
 P8J  N1   N  NR5   0  -0.311  -19.9097  -10.1035   2.0127
 P8J  O2   O  O2    0  -0.474  -20.1312   -8.0786   0.9767
 P8J  O1   O  OH1   0  -0.666  -22.0955   -6.3779  -0.0842
 P8J  C9   C  CH1   0  -0.002  -18.5742   -6.2249   1.1510
 P8J  O5   O  OH1   0  -0.668  -17.9061   -6.5408  -0.0438
 P8J  C8   C  CH1   0   0.009  -17.9386   -6.9158   2.3570
 P8J  O4   O  OH1   0  -0.670  -16.5856   -6.5475   2.4017
 P8J  O3   O  OH1   0  -0.666  -17.5860   -9.0198   3.4064
 P8J  H1   H  HCR5  0   0.322  -21.8709  -10.2138   2.8401
 P8J  H2   H  HCH2  0   0.264  -22.0482  -13.3556   3.1598
 P8J  H3   H  HCH2  0   0.243  -21.2735  -14.0900   1.7606
 P8J  H4   H  HCH2  0   0.210  -20.2800   -6.5112  -1.0898
 P8J  H5   H  HCH2  0   0.205  -20.5297   -5.0107  -0.1953
 P8J  H6   H  HCH1  0   0.238  -20.5455   -6.2939   1.9369
 P8J  H7   H  HCH1  0   0.249  -20.1267   -8.3387   3.0227
 P8J  H8   H  HCH1  0   0.247  -17.6077   -8.7791   1.3448
 P8J  H11  H  HCR6  0   0.228  -22.1978  -14.1012  -2.3555
 P8J  H12  H  HCR6  0   0.180  -22.9992  -11.9323  -2.4812
 P8J  H13  H  HCR6  0   0.239  -21.9217  -12.6677  -0.3200
 P8J  H14  H  HCH3  0   0.238  -25.6918  -10.5829  -4.2642
 P8J  H15  H  HCH3  0   0.211  -23.9684  -10.9923  -4.3307
 P8J  H16  H  HCH3  0   0.220  -25.1918  -12.2620  -4.5257
 P8J  H17  H  HCR6  0   0.221  -24.9530  -12.3885  -0.1693
 P8J  H18  H  HOH1  0   0.452  -23.6497  -10.6483   0.6954
 P8J  H19  H  HOH1  0   0.456  -23.5176  -16.6237  -4.3182
 P8J  H20  H  HCR6  0   0.228  -22.1929  -15.0440  -0.1752
 P8J  H21  H  HOH1  0   0.451  -24.2529  -14.8982   1.0188
 P8J  H22  H  HOH1  0   0.457  -22.5244   -6.0428  -0.8764
 P8J  H23  H  HCH1  0   0.241  -18.5690   -5.1406   1.3369
 P8J  H24  H  HOH1  0   0.454  -16.9732   -6.3292   0.0685
 P8J  H25  H  HCH1  0   0.219  -18.4723   -6.5719   3.2575
 P8J  H26  H  HOH1  0   0.457  -16.1506   -7.0597   3.0921
 P8J  H27  H  HOH1  0   0.460  -17.3238   -9.9221   3.1978
 P8J  C16  C  CH3   0  -0.410  -24.9530  -11.3364  -3.9970
 P8J  C10  C  CH2   0  -0.155  -23.4206  -15.8354  -2.5552
 P8J  O7   O  OH1   0  -0.669  -23.2644  -15.7716  -3.9529
 P8J  H9   H  HCH2  0   0.209  -24.4219  -16.1810  -2.2749
 P8J  H10  H  HCH2  0   0.201  -22.7008  -16.5268  -2.0972

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
 P8J  C16  O11  single    1.414  0.020  1.414
 P8J  O7   C10  single    1.408  0.020  1.408
 P8J  O11  C12  single    1.375  0.020  1.375
 P8J  O8   C12  single    1.403  0.020  1.403
 P8J  O8   C11  single    1.411  0.020  1.411
 P8J  C10  C11  single    1.514  0.020  1.514
 P8J  C12  C13  single    1.526  0.020  1.526
 P8J  C11  C15  single    1.523  0.020  1.523
 P8J  C13  O9   single    1.404  0.020  1.404
 P8J  C13  C14  single    1.526  0.020  1.526
 P8J  O5   C9   single    1.405  0.020  1.405
 P8J  C15  O10  single    1.405  0.020  1.405
 P8J  C15  C14  single    1.530  0.020  1.530
 P8J  C14  O6   single    1.414  0.020  1.414
 P8J  C4   O1   single    1.407  0.020  1.407
 P8J  C4   C5   single    1.513  0.020  1.513
 P8J  C9   C5   single    1.523  0.020  1.523
 P8J  C9   C8   single    1.528  0.020  1.528
 P8J  O2   C5   single    1.419  0.020  1.419
 P8J  O2   C6   single    1.394  0.020  1.394
 P8J  N2   N3   aromatic  1.284  0.020  1.284
 P8J  N2   N1   aromatic  1.325  0.020  1.325
 P8J  N3   C1   aromatic  1.353  0.020  1.353
 P8J  O6   C3   single    1.415  0.020  1.415
 P8J  O4   C8   single    1.403  0.020  1.403
 P8J  C7   C8   single    1.526  0.020  1.526
 P8J  C7   C6   single    1.530  0.020  1.530
 P8J  C7   O3   single    1.403  0.020  1.403
 P8J  N1   C6   single    1.442  0.020  1.442
 P8J  N1   C2   aromatic  1.343  0.020  1.343
 P8J  C1   C3   single    1.491  0.020  1.491
 P8J  C1   C2   aromatic  1.370  0.020  1.370
 P8J  C2   H1   single    0.930  0.020  1.080
 P8J  C3   H2   single    0.970  0.020  1.090
 P8J  C3   H3   single    0.970  0.020  1.090
 P8J  C4   H4   single    0.970  0.020  1.090
 P8J  C4   H5   single    0.970  0.020  1.090
 P8J  C5   H6   single    0.970  0.020  1.090
 P8J  C6   H7   single    0.970  0.020  1.090
 P8J  C7   H8   single    0.970  0.020  1.090
 P8J  C10  H9   single    0.970  0.020  1.090
 P8J  C10  H10  single    0.970  0.020  1.090
 P8J  C11  H11  single    0.970  0.020  1.090
 P8J  C12  H12  single    0.970  0.020  1.090
 P8J  C14  H13  single    0.970  0.020  1.090
 P8J  C16  H14  single    0.970  0.020  1.090
 P8J  C16  H15  single    0.970  0.020  1.090
 P8J  C16  H16  single    0.970  0.020  1.090
 P8J  C13  H17  single    0.970  0.020  1.090
 P8J  O9   H18  single    0.850  0.020  0.980
 P8J  O7   H19  single    0.850  0.020  0.980
 P8J  C15  H20  single    0.970  0.020  1.090
 P8J  O10  H21  single    0.850  0.020  0.980
 P8J  O1   H22  single    0.850  0.020  0.980
 P8J  C9   H23  single    0.970  0.020  1.090
 P8J  O5   H24  single    0.850  0.020  0.980
 P8J  C8   H25  single    0.970  0.020  1.090
 P8J  O4   H26  single    0.850  0.020  0.980
 P8J  O3   H27  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
 P8J  H1   C2   N1   123.11  3.000
 P8J  H1   C2   C1   132.76  3.000
 P8J  N1   C2   C1   104.13  3.000
 P8J  H3   C3   H2   107.23  3.000
 P8J  H3   C3   C1   109.20  3.000
 P8J  H2   C3   C1   110.57  3.000
 P8J  H3   C3   O6   112.06  3.000
 P8J  H2   C3   O6   105.97  3.000
 P8J  C1   C3   O6   111.69  3.000
 P8J  H5   C4   H4   107.15  3.000
 P8J  H5   C4   O1   111.85  3.000
 P8J  H4   C4   O1   111.82  3.000
 P8J  H5   C4   C5   107.72  3.000
 P8J  H4   C4   C5   109.79  3.000
 P8J  O1   C4   C5   108.42  3.000
 P8J  H6   C5   C9   106.88  3.000
 P8J  H6   C5   O2   109.62  3.000
 P8J  C9   C5   O2   111.09  3.000
 P8J  H6   C5   C4   108.32  3.000
 P8J  O2   C5   C4   108.04  3.000
 P8J  C9   C5   C4   112.84  3.000
 P8J  H7   C6   O2   111.01  3.000
 P8J  H7   C6   N1   106.31  3.000
 P8J  O2   C6   N1   107.32  3.000
 P8J  H7   C6   C7   109.09  3.000
 P8J  N1   C6   C7   112.14  3.000
 P8J  O2   C6   C7   110.88  3.000
 P8J  H8   C7   O3   111.77  3.000
 P8J  H8   C7   C8   108.82  3.000
 P8J  O3   C7   C8   108.45  3.000
 P8J  H8   C7   C6   109.05  3.000
 P8J  O3   C7   C6   111.58  3.000
 P8J  C8   C7   C6   107.03  3.000
 P8J  H11  C11  C15  107.00  3.000
 P8J  H11  C11  O8   110.12  3.000
 P8J  C15  C11  O8   110.32  3.000
 P8J  H11  C11  C10  108.03  3.000
 P8J  C15  C11  C10  112.63  3.000
 P8J  O8   C11  C10  108.70  3.000
 P8J  H12  C12  O8   109.18  3.000
 P8J  H12  C12  C13  109.35  3.000
 P8J  O8   C12  C13  109.97  3.000
 P8J  H12  C12  O11  110.73  3.000
 P8J  C13  C12  O11  108.96  3.000
 P8J  O8   C12  O11  108.64  3.000
 P8J  H13  C14  O6   110.50  3.000
 P8J  H13  C14  C15  108.22  3.000
 P8J  O6   C14  C15  110.87  3.000
 P8J  H13  C14  C13  107.75  3.000
 P8J  O6   C14  C13  107.46  3.000
 P8J  C15  C14  C13  112.00  3.000
 P8J  C16  O11  C12  114.49  3.000
 P8J  H17  C13  O9   111.54  3.000
 P8J  H17  C13  C14  109.09  3.000
 P8J  O9   C13  C14  111.54  3.000
 P8J  H17  C13  C12  108.11  3.000
 P8J  C14  C13  C12  108.43  3.000
 P8J  O9   C13  C12  108.01  3.000
 P8J  H18  O9   C13  108.15  3.000
 P8J  C12  O8   C11  113.27  3.000
 P8J  H20  C15  O10  111.15  3.000
 P8J  H20  C15  C14  108.54  3.000
 P8J  O10  C15  C14  111.63  3.000
 P8J  H20  C15  C11  107.79  3.000
 P8J  C14  C15  C11  108.47  3.000
 P8J  O10  C15  C11  109.16  3.000
 P8J  H21  O10  C15  107.87  3.000
 P8J  C14  O6   C3   114.77  3.000
 P8J  N3   C1   C3   123.45  3.000
 P8J  C3   C1   C2   128.87  3.000
 P8J  N3   C1   C2   107.66  3.000
 P8J  N2   N3   C1   109.45  3.000
 P8J  N1   N2   N3   107.78  3.000
 P8J  N2   N1   C6   121.79  3.000
 P8J  C6   N1   C2   127.13  3.000
 P8J  N2   N1   C2   110.98  3.000
 P8J  C6   O2   C5   112.26  3.000
 P8J  H22  O1   C4   108.00  3.000
 P8J  H23  C9   C8   108.08  3.000
 P8J  H23  C9   O5   111.29  3.000
 P8J  C8   C9   O5   111.82  3.000
 P8J  H23  C9   C5   107.53  3.000
 P8J  C8   C9   C5   109.00  3.000
 P8J  O5   C9   C5   109.01  3.000
 P8J  H24  O5   C9   108.18  3.000
 P8J  H25  C8   O4   111.05  3.000
 P8J  H25  C8   C9   107.60  3.000
 P8J  O4   C8   C9   107.91  3.000
 P8J  H25  C8   C7   108.10  3.000
 P8J  O4   C8   C7   111.96  3.000
 P8J  C9   C8   C7   110.13  3.000
 P8J  H26  O4   C8   108.59  3.000
 P8J  H27  O3   C7   108.64  3.000
 P8J  H16  C16  H15  108.38  3.000
 P8J  H16  C16  H14  108.63  3.000
 P8J  H15  C16  H14  108.54  3.000
 P8J  H16  C16  O11  112.40  3.000
 P8J  H15  C16  O11  111.43  3.000
 P8J  H14  C16  O11  107.37  3.000
 P8J  H10  C10  H9   107.08  3.000
 P8J  H10  C10  O7   111.71  3.000
 P8J  H9   C10  O7   111.70  3.000
 P8J  H10  C10  C11  107.85  3.000
 P8J  H9   C10  C11  109.87  3.000
 P8J  O7   C10  C11  108.56  3.000
 P8J  H19  O7   C10  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
 P8J  CONST_01  N3   N2   N1   C2      0.00   0.0  0
 P8J  CONST_02  N2   N3   C1   C2      0.00   0.0  0
 P8J  CONST_03  N1   N2   N3   C1      0.00   0.0  0
 P8J  CONST_04  N2   N1   C2   C1      0.00   0.0  0
 P8J  CONST_05  N1   C2   C1   N3      0.00   0.0  0
 P8J  CONST_06  N3   N2   N1   C6    180.00   0.0  0
 P8J  CONST_07  C1   C2   N1   C6    180.00   0.0  0
 P8J  CONST_08  N2   N3   C1   C3    180.00   0.0  0
 P8J  CONST_09  N1   C2   C1   C3    180.00   0.0  0
 P8J  CONST_10  H1   C2   N1   C6      0.00   0.0  0
 P8J  Var_01    O6   C3   C1   C2     57.68  30.0  2
 P8J  Var_02    C1   C3   O6   C14    74.08  30.0  3
 P8J  Var_03    H14  C16  O11  C12  -170.12  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
 P8J  chir_01  C5   C4   C9   O2   positiv
 P8J  chir_02  C6   O2   N1   C7   negativ
 P8J  chir_03  C7   O3   C6   C8   negativ
 P8J  chir_04  C11  O8   C10  C15  positiv
 P8J  chir_05  C12  O11  O8   C13  positiv
 P8J  chir_06  C14  O6   C13  C15  positiv
 P8J  chir_07  C13  O9   C12  C14  negativ
 P8J  chir_08  C15  O10  C14  C11  positiv
 P8J  chir_09  C9   O5   C5   C8   negativ
 P8J  chir_10  C8   O4   C9   C7   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
 P8J  plan-1  C2  0.020
 P8J  plan-1  C3  0.020
 P8J  plan-1  C6  0.020
 P8J  plan-1  C1  0.020
 P8J  plan-1  N3  0.020
 P8J  plan-1  N2  0.020
 P8J  plan-1  N1  0.020
 P8J  plan-1  H1  0.020

