# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 11:46:06 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-nitrophenyl beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Oc2ccccc2[N+]([O-])=O)[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
 145  145  '2-nitrophenyl beta-D-galactopyranoside'  D-saccharide  36  21  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_145
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
 145  C1   C  CH1    0   0.264  -0.6642  -0.1290  -0.2660
 145  C2   C  CH1    0  -0.021  -1.4549  -1.4262  -0.1169
 145  O2   O  OH1    0  -0.664  -0.9006  -2.4606  -0.8890
 145  C3   C  CH1    0   0.002  -2.8788  -1.1801  -0.6072
 145  O3   O  OH1    0  -0.671  -3.7111  -2.2879  -0.3779
 145  C4   C  CH1    0   0.003  -3.4927   0.0230   0.1089
 145  O4   O  OH1    0  -0.668  -3.6933  -0.2275   1.4766
 145  C5   C  CH1    0  -0.023  -2.5544   1.2138  -0.0389
 145  C6   C  CH2    0  -0.155  -3.0438   2.4532   0.6766
 145  O6   O  OH1    0  -0.666  -2.2219   3.5315   0.2982
 145  O5   O  O2     0  -0.488  -1.2665   0.8940   0.4593
 145  O1'  O  O2     0  -0.480   0.6087  -0.3505   0.2709
 145  C1'  C  CR6    0   0.396   1.6334   0.4290  -0.1133
 145  C2'  C  CR6    0   0.152   2.9325  -0.0945  -0.0511
 145  C3'  C  CR16   0  -0.268   4.0326   0.6446  -0.4661
 145  C4'  C  CR16   0  -0.269   3.8589   1.9307  -0.9380
 145  C5'  C  CR16   0  -0.221   2.5774   2.4604  -1.0063
 145  C6'  C  CR16   0  -0.360   1.4757   1.7250  -0.6015
 145  N1'  N  N      1   0.334   3.1744  -1.4391   0.4339
 145  O2'  O  O     -1  -0.382   4.0803  -2.0590  -0.0763
 145  O3'  O  O      0  -0.371   2.4799  -1.8664   1.3239
 145  H1   H  HCH1   0   0.219  -0.5803   0.1416  -1.3336
 145  H2   H  HCH1   0   0.238  -1.4856  -1.6893   0.9489
 145  HO2  H  HOH1   0   0.457  -0.1463  -2.8281  -0.4185
 145  H3   H  HCH1   0   0.220  -2.8357  -0.9382  -1.6812
 145  HO3  H  HOH1   0   0.457  -3.3062  -3.0662  -0.7758
 145  H4   H  HCH1   0   0.239  -4.4375   0.2771  -0.3941
 145  HO4  H  HOH1   0   0.454  -4.2180  -1.0310   1.5592
 145  H5   H  HCH1   0   0.237  -2.4902   1.4445  -1.1142
 145  H61  H  HCH2   0   0.212  -3.0280   2.2893   1.7596
 145  H62  H  HCH2   0   0.203  -4.0906   2.6155   0.3878
 145  HO6  H  HOH1   0   0.458  -2.4518   4.2885   0.8442
 145  H3'  H  HCR6   0   0.297   5.0234   0.2168  -0.4069
 145  H4'  H  HCR6   0   0.276   4.7155   2.5133  -1.2456
 145  H5'  H  HCR6   0   0.281   2.4254   3.4664  -1.3736
 145  H6'  H  HCR6   0   0.306   0.4959   2.1794  -0.6451

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
 145  C1   C2   single    1.526  0.020  1.526
 145  C1   O5   single    1.391  0.020  1.391
 145  C1   O1'  single    1.399  0.020  1.399
 145  C1   H1   single    0.970  0.020  1.090
 145  C2   O2   single    1.405  0.020  1.405
 145  C2   C3   single    1.526  0.020  1.526
 145  C2   H2   single    0.970  0.020  1.090
 145  O2   HO2  single    0.850  0.020  0.980
 145  C3   O3   single    1.404  0.020  1.404
 145  C3   C4   single    1.529  0.020  1.529
 145  C3   H3   single    0.970  0.020  1.090
 145  O3   HO3  single    0.850  0.020  0.980
 145  C4   O4   single    1.405  0.020  1.405
 145  C4   C5   single    1.523  0.020  1.523
 145  C4   H4   single    0.970  0.020  1.090
 145  O4   HO4  single    0.850  0.020  0.980
 145  C5   C6   single    1.512  0.020  1.512
 145  C5   O5   single    1.417  0.020  1.417
 145  C5   H5   single    0.970  0.020  1.090
 145  C6   O6   single    1.408  0.020  1.408
 145  C6   H61  single    0.970  0.020  1.090
 145  C6   H62  single    0.970  0.020  1.090
 145  O6   HO6  single    0.850  0.020  0.980
 145  O1'  C1'  single    1.344  0.020  1.344
 145  C1'  C2'  aromatic  1.402  0.020  1.402
 145  C1'  C6'  aromatic  1.394  0.020  1.394
 145  C2'  C3'  aromatic  1.389  0.020  1.389
 145  C2'  N1'  single    1.450  0.020  1.450
 145  C3'  C4'  aromatic  1.381  0.020  1.381
 145  C3'  H3'  single    0.930  0.020  1.080
 145  C4'  C5'  aromatic  1.388  0.020  1.388
 145  C4'  H4'  single    0.930  0.020  1.080
 145  C5'  C6'  aromatic  1.385  0.020  1.385
 145  C5'  H5'  single    0.930  0.020  1.080
 145  C6'  H6'  single    0.930  0.020  1.080
 145  N1'  O2'  single    1.210  0.020  1.210
 145  N1'  O3'  double    1.207  0.020  1.207

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
 145  H1   C1   O1'  109.91  3.000
 145  H1   C1   O5   110.90  3.000
 145  O1'  C1   O5   108.07  3.000
 145  H1   C1   C2   110.00  3.000
 145  O1'  C1   C2   107.41  3.000
 145  O5   C1   C2   110.47  3.000
 145  H2   C2   C3   108.93  3.000
 145  H2   C2   O2   111.60  3.000
 145  C3   C2   O2   108.08  3.000
 145  H2   C2   C1   108.23  3.000
 145  C3   C2   C1   108.36  3.000
 145  O2   C2   C1   111.57  3.000
 145  HO2  O2   C2   108.78  3.000
 145  H3   C3   C4   107.43  3.000
 145  H3   C3   O3   110.82  3.000
 145  C4   C3   O3   107.84  3.000
 145  H3   C3   C2   108.18  3.000
 145  C4   C3   C2   110.56  3.000
 145  O3   C3   C2   111.92  3.000
 145  HO3  O3   C3   108.71  3.000
 145  H4   C4   C5   107.71  3.000
 145  H4   C4   O4   111.32  3.000
 145  C5   C4   O4   108.77  3.000
 145  H4   C4   C3   108.21  3.000
 145  C5   C4   C3   108.81  3.000
 145  O4   C4   C3   111.90  3.000
 145  HO4  O4   C4   108.07  3.000
 145  H5   C5   O5   109.72  3.000
 145  H5   C5   C6   108.00  3.000
 145  O5   C5   C6   108.22  3.000
 145  H5   C5   C4   107.11  3.000
 145  O5   C5   C4   110.44  3.000
 145  C6   C5   C4   113.29  3.000
 145  H62  C6   H61  107.22  3.000
 145  H62  C6   O6   111.88  3.000
 145  H61  C6   O6   111.83  3.000
 145  H62  C6   C5   107.77  3.000
 145  H61  C6   C5   109.90  3.000
 145  O6   C6   C5   108.16  3.000
 145  HO6  O6   C6   108.12  3.000
 145  C5   O5   C1   112.09  3.000
 145  C1'  O1'  C1   119.49  3.000
 145  C6'  C1'  C2'  117.88  3.000
 145  C6'  C1'  O1'  123.59  3.000
 145  C2'  C1'  O1'  118.52  3.000
 145  N1'  C2'  C3'  117.48  3.000
 145  N1'  C2'  C1'  121.05  3.000
 145  C3'  C2'  C1'  121.47  3.000
 145  H3'  C3'  C4'  120.17  3.000
 145  H3'  C3'  C2'  119.94  3.000
 145  C4'  C3'  C2'  119.88  3.000
 145  H4'  C4'  C5'  120.80  3.000
 145  H4'  C4'  C3'  119.98  3.000
 145  C5'  C4'  C3'  119.22  3.000
 145  H5'  C5'  C6'  118.77  3.000
 145  H5'  C5'  C4'  120.08  3.000
 145  C6'  C5'  C4'  121.15  3.000
 145  H6'  C6'  C5'  119.08  3.000
 145  H6'  C6'  C1'  120.50  3.000
 145  C5'  C6'  C1'  120.40  3.000
 145  O3'  N1'  O2'  124.05  3.000
 145  O3'  N1'  C2'  118.62  3.000
 145  O2'  N1'  C2'  117.32  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
 145  CONST_01  C4'  C3'  C2'  C1'     0.00   0.0  0
 145  CONST_02  C4'  C5'  C6'  C1'     0.00   0.0  0
 145  CONST_03  C5'  C6'  C1'  C2'     0.00   0.0  0
 145  CONST_04  C5'  C4'  C3'  C2'     0.00   0.0  0
 145  CONST_05  C6'  C1'  C2'  C3'     0.00   0.0  0
 145  CONST_06  C6'  C5'  C4'  C3'     0.00   0.0  0
 145  CONST_07  C3'  C2'  C1'  O1'   180.00   0.0  0
 145  CONST_08  C5'  C6'  C1'  O1'   180.00   0.0  0
 145  CONST_09  N1'  C2'  C3'  C4'   180.00   0.0  0
 145  CONST_10  N1'  C2'  C1'  C6'   180.00   0.0  0
 145  CONST_11  H3'  C3'  C2'  C1'   180.00   0.0  0
 145  CONST_12  H5'  C5'  C6'  C1'   180.00   0.0  0
 145  CONST_13  H6'  C6'  C1'  C2'   180.00   0.0  0
 145  CONST_14  H4'  C4'  C3'  C2'   180.00   0.0  0
 145  Var_01    C2'  C1'  O1'  C1   -153.44  30.0  2

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
 145  chir_01  C1  C2  O5  O1'  negativ
 145  chir_02  C2  O2  C1  C3   negativ
 145  chir_03  C3  O3  C2  C4   positiv
 145  chir_04  C4  O4  C5  C3   negativ
 145  chir_05  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
 145  plan-1  O1'  0.020
 145  plan-1  C1'  0.020
 145  plan-1  C2'  0.020
 145  plan-1  C3'  0.020
 145  plan-1  C4'  0.020
 145  plan-1  C5'  0.020
 145  plan-1  C6'  0.020
 145  plan-1  N1'  0.020
 145  plan-1  H3'  0.020
 145  plan-1  H4'  0.020
 145  plan-1  H5'  0.020
 145  plan-1  H6'  0.020
 145  plan-2  C2'  0.020
 145  plan-2  N1'  0.020
 145  plan-2  O2'  0.020
 145  plan-2  O3'  0.020

