# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jul  6 19:22:59 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: methyl 3-O-beta-D-xylopyranosyl-alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O[C@@H]2OC[C@@H](O)[C@H](O)[C@H]2O)[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
 XLM  XLM  'methyl 3-O-beta-D-xylopyranosyl-alpha-D-mannopyranoside'  ligand  44  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XLM
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
 XLM  C1    C  CH1   0   0.287   0.2675   0.2423  -1.5954
 XLM  C2    C  CH1   0  -0.013  -0.7481  -0.2212  -2.6444
 XLM  C3    C  CH1   0   0.010  -0.0309  -0.5251  -3.9477
 XLM  C4    C  CH1   0  -0.006   0.8082   0.6817  -4.3538
 XLM  C5    C  CH2   0  -0.230   1.7323   1.0772  -3.2048
 XLM  O2    O  OH1   0  -0.674  -1.4103  -1.3788  -2.2096
 XLM  O3    O  OH1   0  -0.669  -0.9871  -0.8565  -4.9217
 XLM  O4    O  OH1   0  -0.671   1.5449   0.3207  -5.4996
 XLM  O5    O  O2    0  -0.482   0.9880   1.3596  -2.0388
 XLM  C1'   C  CH1   0   0.256   0.0424  -1.5446   2.5593
 XLM  C2'   C  CH1   0  -0.030  -0.3380  -1.2085   1.1156
 XLM  C3'   C  CH1   0   0.003   0.0811   0.2233   0.7848
 XLM  C4'   C  CH1   0   0.012  -0.4426   1.2053   1.8234
 XLM  C5'   C  CH1   0  -0.018  -0.0448   0.7317   3.2280
 XLM  C6'   C  CH2   0  -0.165  -0.6791   1.5855   4.3043
 XLM  O2'   O  OH1   0  -0.668  -1.7321  -1.2997   0.9375
 XLM  O3'   O  O2    0  -0.507  -0.4365   0.6160  -0.4682
 XLM  O4'   O  OH1   0  -0.666   0.1204   2.4660   1.5507
 XLM  O5'   O  O2    0  -0.497  -0.4699  -0.6028   3.4510
 XLM  O6'   O  OH1   0  -0.667  -0.1964   1.1711   5.5594
 XLM  H1    H  HCH1  0   0.195   0.9671  -0.5881  -1.3862
 XLM  H2    H  HCH1  0   0.215  -1.4533   0.6083  -2.8158
 XLM  H3    H  HCH1  0   0.207   0.6583  -1.3686  -3.7703
 XLM  H4    H  HCH1  0   0.222   0.1309   1.5208  -4.5669
 XLM  H5C1  H  HCH2  0   0.252   2.2919   1.9800  -3.4538
 XLM  H5C2  H  HCH2  0   0.215   2.4587   0.2711  -3.0243
 XLM  HA    H  HOH1  0   0.448  -1.8093  -1.1945  -1.3489
 XLM  HB    H  HOH1  0   0.449  -0.5221  -0.9968  -5.7532
 XLM  HC    H  HOH1  0   0.461   1.8184   1.1215  -5.9564
 XLM  H1'   H  HCH1  0   0.237  -0.4240  -2.4969   2.8544
 XLM  H2'   H  HCH1  0   0.242   0.1876  -1.9085   0.4526
 XLM  H3'   H  HCH1  0   0.251   1.1779   0.2724   0.7846
 XLM  H4'   H  HCH1  0   0.231  -1.5385   1.2385   1.7586
 XLM  H5'   H  HCH1  0   0.226   1.0480   0.8116   3.3193
 XLM  H6'1  H  HCH2  0   0.205  -0.4304   2.6342   4.1067
 XLM  H6'2  H  HCH2  0   0.197  -1.7728   1.4953   4.2350
 XLM  H7'1  H  HCH3  0   0.238   2.9908  -2.2993   3.7203
 XLM  H7'2  H  HCH3  0   0.220   1.8316  -1.3216   4.6352
 XLM  H7'3  H  HCH3  0   0.213   1.4310  -2.9938   4.1963
 XLM  HD    H  HOH1  0   0.463  -1.9971  -2.2200   1.0405
 XLM  HE    H  HOH1  0   0.460  -0.5175   3.1487   1.7742
 XLM  H6'   H  HOH1  0   0.456  -0.5283   1.7841   6.2210
 XLM  O1'   O  O2    0  -0.500   1.4278  -1.6468   2.6102
 XLM  C7'   C  CH3   0  -0.409   1.9332  -2.0819   3.8568

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
 XLM  C1   C2    single  1.532  0.020  1.532
 XLM  C1   O5    single  1.401  0.020  1.401
 XLM  C1   O3'   single  1.381  0.020  1.381
 XLM  C1   H1    single  0.970  0.020  1.090
 XLM  C2   C3    single  1.518  0.020  1.518
 XLM  C2   O2    single  1.403  0.020  1.403
 XLM  C2   H2    single  0.970  0.020  1.090
 XLM  C3   C4    single  1.525  0.020  1.525
 XLM  C3   O3    single  1.405  0.020  1.405
 XLM  C3   H3    single  0.970  0.020  1.090
 XLM  C4   C5    single  1.527  0.020  1.527
 XLM  C4   O4    single  1.409  0.020  1.409
 XLM  C4   H4    single  0.970  0.020  1.090
 XLM  C5   O5    single  1.412  0.020  1.412
 XLM  C5   H5C1  single  0.970  0.020  1.090
 XLM  C5   H5C2  single  0.970  0.020  1.090
 XLM  O2   HA    single  0.850  0.020  0.980
 XLM  O3   HB    single  0.850  0.020  0.980
 XLM  O4   HC    single  0.850  0.020  0.980
 XLM  C1'  C2'   single  1.530  0.020  1.530
 XLM  C1'  O1'   single  1.390  0.020  1.390
 XLM  C1'  O5'   single  1.394  0.020  1.394
 XLM  C1'  H1'   single  0.970  0.020  1.090
 XLM  C2'  C3'   single  1.528  0.020  1.528
 XLM  C2'  O2'   single  1.408  0.020  1.408
 XLM  C2'  H2'   single  0.970  0.020  1.090
 XLM  C3'  C4'   single  1.522  0.020  1.522
 XLM  C3'  O3'   single  1.412  0.020  1.412
 XLM  C3'  H3'   single  0.970  0.020  1.090
 XLM  C4'  C5'   single  1.535  0.020  1.535
 XLM  C4'  O4'   single  1.407  0.020  1.407
 XLM  C4'  H4'   single  0.970  0.020  1.090
 XLM  C5'  C6'   single  1.513  0.020  1.513
 XLM  C5'  O5'   single  1.418  0.020  1.418
 XLM  C5'  H5'   single  0.970  0.020  1.090
 XLM  C6'  O6'   single  1.407  0.020  1.407
 XLM  C6'  H6'1  single  0.970  0.020  1.090
 XLM  C6'  H6'2  single  0.970  0.020  1.090
 XLM  C7'  O1'   single  1.414  0.020  1.414
 XLM  C7'  H7'1  single  0.970  0.020  1.090
 XLM  C7'  H7'2  single  0.970  0.020  1.090
 XLM  C7'  H7'3  single  0.970  0.020  1.090
 XLM  O2'  HD    single  0.850  0.020  0.980
 XLM  O4'  HE    single  0.850  0.020  0.980
 XLM  O6'  H6'   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
 XLM  H1    C1   O3'   111.81  3.000
 XLM  H1    C1   O5    109.46  3.000
 XLM  O3'   C1   O5    107.74  3.000
 XLM  H1    C1   C2    108.77  3.000
 XLM  O3'   C1   C2    107.63  3.000
 XLM  O5    C1   C2    111.43  3.000
 XLM  H2    C2   O2    111.54  3.000
 XLM  H2    C2   C3    108.63  3.000
 XLM  O2    C2   C3    108.90  3.000
 XLM  H2    C2   C1    107.64  3.000
 XLM  O2    C2   C1    110.51  3.000
 XLM  C3    C2   C1    109.59  3.000
 XLM  H3    C3   O3    110.87  3.000
 XLM  H3    C3   C4    107.70  3.000
 XLM  O3    C3   C4    112.13  3.000
 XLM  H3    C3   C2    108.06  3.000
 XLM  O3    C3   C2    108.72  3.000
 XLM  C4    C3   C2    109.27  3.000
 XLM  H4    C4   O4    111.11  3.000
 XLM  H4    C4   C5    108.73  3.000
 XLM  O4    C4   C5    111.21  3.000
 XLM  H4    C4   C3    108.47  3.000
 XLM  O4    C4   C3    107.55  3.000
 XLM  C5    C4   C3    109.73  3.000
 XLM  H5C2  C5   H5C1  107.77  3.000
 XLM  H5C2  C5   O5    111.05  3.000
 XLM  H5C1  C5   O5    107.06  3.000
 XLM  H5C2  C5   C4    109.47  3.000
 XLM  H5C1  C5   C4    110.68  3.000
 XLM  O5    C5   C4    110.75  3.000
 XLM  HA    O2   C2    108.27  3.000
 XLM  HB    O3   C3    107.72  3.000
 XLM  HC    O4   C4    108.76  3.000
 XLM  C5    O5   C1    111.89  3.000
 XLM  H1'   C1'  O5'   104.91  3.000
 XLM  H1'   C1'  O1'   110.42  3.000
 XLM  O5'   C1'  O1'   113.10  3.000
 XLM  H1'   C1'  C2'   109.73  3.000
 XLM  O5'   C1'  C2'   111.32  3.000
 XLM  O1'   C1'  C2'   107.36  3.000
 XLM  H2'   C2'  O2'   110.87  3.000
 XLM  H2'   C2'  C3'   109.59  3.000
 XLM  O2'   C2'  C3'   107.75  3.000
 XLM  H2'   C2'  C1'   108.09  3.000
 XLM  O2'   C2'  C1'   110.56  3.000
 XLM  C3'   C2'  C1'   109.99  3.000
 XLM  H3'   C3'  O3'   110.72  3.000
 XLM  H3'   C3'  C4'   108.36  3.000
 XLM  O3'   C3'  C4'   107.46  3.000
 XLM  H3'   C3'  C2'   108.42  3.000
 XLM  O3'   C3'  C2'   110.62  3.000
 XLM  C4'   C3'  C2'   111.24  3.000
 XLM  H4'   C4'  O4'   111.13  3.000
 XLM  H4'   C4'  C5'   108.78  3.000
 XLM  O4'   C4'  C5'   110.49  3.000
 XLM  H4'   C4'  C3'   108.82  3.000
 XLM  O4'   C4'  C3'   107.94  3.000
 XLM  C5'   C4'  C3'   109.65  3.000
 XLM  H5'   C5'  O5'   110.68  3.000
 XLM  H5'   C5'  C6'   108.46  3.000
 XLM  O5'   C5'  C6'   107.07  3.000
 XLM  H5'   C5'  C4'   108.13  3.000
 XLM  O5'   C5'  C4'   110.89  3.000
 XLM  C6'   C5'  C4'   111.61  3.000
 XLM  H6'2  C6'  H6'1  107.03  3.000
 XLM  H6'2  C6'  O6'   111.92  3.000
 XLM  H6'1  C6'  O6'   111.39  3.000
 XLM  H6'2  C6'  C5'   109.02  3.000
 XLM  H6'1  C6'  C5'   108.46  3.000
 XLM  O6'   C6'  C5'   108.93  3.000
 XLM  HD    O2'  C2'   108.71  3.000
 XLM  C3'   O3'  C1    117.55  3.000
 XLM  HE    O4'  C4'   109.02  3.000
 XLM  C5'   O5'  C1'   115.15  3.000
 XLM  H6'   O6'  C6'   107.92  3.000
 XLM  C7'   O1'  C1'   114.28  3.000
 XLM  H7'3  C7'  H7'2  108.42  3.000
 XLM  H7'3  C7'  H7'1  108.56  3.000
 XLM  H7'2  C7'  H7'1  108.58  3.000
 XLM  H7'3  C7'  O1'   111.45  3.000
 XLM  H7'2  C7'  O1'   112.38  3.000
 XLM  H7'1  C7'  O1'   107.36  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
 XLM  Var_01  C4    C5   O5   C1    61.67  30.0  1
 XLM  Var_02  H7'1  C7'  O1'  C1'  169.66  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
 XLM  chir_01  C1   C2   O5   O3'  negativ
 XLM  chir_02  C2   O2   C1   C3   negativ
 XLM  chir_03  C3   O3   C2   C4   positiv
 XLM  chir_04  C4   O4   C3   C5   negativ
 XLM  chir_05  C1'  C2'  O1'  O5'  negativ
 XLM  chir_06  C2'  O2'  C1'  C3'  positiv
 XLM  chir_07  C3'  O3'  C4'  C2'  negativ
 XLM  chir_08  C4'  O4'  C5'  C3'  positiv
 XLM  chir_09  C5'  O5'  C4'  C6'  negativ

