# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:59:44 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: 3-(alpha-D-galactopyranosyloxy)-N-(2-morpholin-4-ylethyl)-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2cc(cc(c2)[N+]([O-])=O)C(=O)NCCN3CCOCC3)[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
 A24  A24  3-(alpha-D-galactopyranosyloxy)-N-(2-morpholin-4-ylethyl)-5-nitrobenzamide  ligand  59  32  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A24
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
 A24  C1    C  CH1    0   0.202  -3.3171   0.9292   0.9433
 A24  O1    O  O2     0  -0.492  -3.0699  -0.4610   0.8682
 A24  C2    C  CH1    0  -0.015  -4.7557   1.0949   1.4403
 A24  O2    O  OH1    0  -0.665  -4.9937   0.3739   2.6208
 A24  C3    C  CH1    0   0.006  -5.7370   0.6239   0.3742
 A24  O3    O  OH1    0  -0.674  -7.0683   0.8970   0.7359
 A24  C4    C  CH1    0  -0.009  -5.4542   1.3515  -0.9387
 A24  O4    O  OH1    0  -0.671  -5.7032   2.7315  -0.8349
 A24  C5    C  CH1    0  -0.021  -3.9969   1.1414  -1.3219
 A24  O5    O  O2     0  -0.486  -3.1220   1.5535  -0.2760
 A24  C6    C  CH2    0  -0.158  -3.6088   1.9038  -2.5705
 A24  O6    O  OH1    0  -0.666  -2.3331   1.4726  -2.9794
 A24  C1'   C  CR6    0   0.443  -1.8379  -0.9174   0.5814
 A24  C2'   C  CR16   0  -0.381  -1.7429  -2.2968   0.4152
 A24  C3'   C  CR6    0   0.298  -0.5095  -2.8513   0.1377
 A24  C4'   C  CR16   0  -0.349   0.6390  -2.0872   0.0058
 A24  C5'   C  CR6    0  -0.006   0.5279  -0.7152   0.1690
 A24  C6'   C  CR16   0  -0.366  -0.6994  -0.1278   0.4627
 A24  N1'   N  N      1   0.328  -0.4144  -4.2987  -0.0186
 A24  O1'   O  O     -1  -0.371   0.6699  -4.7697  -0.2646
 A24  O2'   O  O      0  -0.370  -1.4232  -4.9502   0.1046
 A24  C7'   C  C      0   0.536   1.7272   0.1822   0.0913
 A24  O3'   O  O      0  -0.480   1.8004   1.1820   0.7906
 A24  N2'   N  NH1    0  -0.641   2.6715  -0.1840  -0.7859
 A24  O1B   O  O2     0  -0.485   8.7770   1.5860   0.6897
 A24  C2B   C  CH2    0  -0.188   8.7174   0.3578  -0.0016
 A24  C3B   C  CH2    0  -0.303   7.3921  -0.3446   0.2202
 A24  N4'   N  NT     0  -0.430   6.2958   0.5140  -0.1944
 A24  C5B   C  CH2    0  -0.310   6.3674   1.7758   0.5232
 A24  C6B   C  CH2    0  -0.185   7.7173   2.4307   0.3000
 A24  C7B   C  CH2    0  -0.267   5.0124  -0.1395  -0.0444
 A24  C8'   C  CH2    0  -0.303   3.9384   0.5003  -0.9217
 A24  H11   H  HCH1   0   0.266  -2.6199   1.3974   1.6477
 A24  H21   H  HCH1   0   0.244  -4.9060   2.1703   1.5950
 A24  HO21  H  HOH1   0   0.463  -4.7077   0.9024   3.3720
 A24  H31   H  HCH1   0   0.223  -5.5936  -0.4526   0.2005
 A24  HO31  H  HOH1   0   0.455  -7.2208   0.5565   1.6241
 A24  H41   H  HCH1   0   0.240  -6.0712   0.8950  -1.7269
 A24  HO41  H  HOH1   0   0.454  -6.6019   2.8499  -0.5091
 A24  H51   H  HCH1   0   0.243  -3.8666   0.0704  -1.5269
 A24  H61   H  HCH2   0   0.209  -3.6299   2.9809  -2.3711
 A24  H62   H  HCH2   0   0.203  -4.3709   1.7022  -3.3351
 A24  HO1   H  HOH1   0   0.456  -2.0652   2.0110  -3.7293
 A24  H2'1  H  HCR6   0   0.311  -2.6296  -2.9075   0.5117
 A24  H4'1  H  HCR6   0   0.297   1.5927  -2.5550  -0.1907
 A24  H6'1  H  HCR6   0   0.300  -0.7394   0.9446   0.5859
 A24  HN21  H  HNH1   0   0.414   2.5109  -0.9779  -1.3840
 A24  H2'2  H  HCH2   0   0.200   8.8664   0.5163  -1.0794
 A24  H3'1  H  HCH2   0   0.198   7.3042  -0.6410   1.2797
 A24  H3'2  H  HCH2   0   0.243   7.3780  -1.2612  -0.3744
 A24  H5'1  H  HCH2   0   0.243   5.5944   2.4597   0.1672
 A24  H5'2  H  HCH2   0   0.200   6.1982   1.6323   1.6048
 A24  H6A1  H  HCH2   0   0.236   7.7910   3.3426   0.8944
 A24  H6'2  H  HCH2   0   0.200   7.8160   2.7079  -0.7594
 A24  H7'1  H  HCH2   0   0.205   4.6737  -0.1516   1.0049
 A24  H7'2  H  HCH2   0   0.239   5.1226  -1.1832  -0.3493
 A24  H8'1  H  HCH2   0   0.256   4.2424   0.4495  -1.9669
 A24  H8'2  H  HCH2   0   0.248   3.7922   1.5508  -0.6740
 A24  H2A1  H  HCH2   0   0.236   9.5370  -0.2637   0.3627

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
 A24  C1   O1    single    1.414  0.020  1.414
 A24  C1   C2    single    1.531  0.020  1.531
 A24  C1   O5    single    1.384  0.020  1.384
 A24  C1   H11   single    0.970  0.020  1.090
 A24  O1   C1'   single    1.345  0.020  1.345
 A24  C2   O2    single    1.404  0.020  1.404
 A24  C2   C3    single    1.524  0.020  1.524
 A24  C2   H21   single    0.970  0.020  1.090
 A24  O2   HO21  single    0.850  0.020  0.980
 A24  C3   O3    single    1.406  0.020  1.406
 A24  C3   C4    single    1.527  0.020  1.527
 A24  C3   H31   single    0.970  0.020  1.090
 A24  O3   HO31  single    0.850  0.020  0.980
 A24  C4   O4    single    1.406  0.020  1.406
 A24  C4   C5    single    1.521  0.020  1.521
 A24  C4   H41   single    0.970  0.020  1.090
 A24  O4   HO41  single    0.850  0.020  0.980
 A24  C5   O5    single    1.424  0.020  1.424
 A24  C5   C6    single    1.514  0.020  1.514
 A24  C5   H51   single    0.970  0.020  1.090
 A24  C6   O6    single    1.407  0.020  1.407
 A24  C6   H61   single    0.970  0.020  1.090
 A24  C6   H62   single    0.970  0.020  1.090
 A24  O6   HO1   single    0.850  0.020  0.980
 A24  C1'  C2'   aromatic  1.393  0.020  1.393
 A24  C1'  C6'   aromatic  1.391  0.020  1.391
 A24  C2'  C3'   aromatic  1.380  0.020  1.380
 A24  C2'  H2'1  single    0.930  0.020  1.080
 A24  C3'  C4'   aromatic  1.386  0.020  1.386
 A24  C3'  N1'   single    1.459  0.020  1.459
 A24  C4'  C5'   aromatic  1.386  0.020  1.386
 A24  C4'  H4'1  single    0.930  0.020  1.080
 A24  C5'  C6'   aromatic  1.392  0.020  1.392
 A24  C5'  C7'   single    1.500  0.020  1.500
 A24  C6'  H6'1  single    0.930  0.020  1.080
 A24  N1'  O1'   single    1.207  0.020  1.207
 A24  N1'  O2'   double    1.207  0.020  1.207
 A24  C7'  O3'   double    1.222  0.020  1.222
 A24  C7'  N2'   single    1.340  0.020  1.340
 A24  N2'  C8'   single    1.446  0.020  1.446
 A24  N2'  HN21  single    0.860  0.020  1.020
 A24  O1B  C2B   single    1.411  0.020  1.411
 A24  O1B  C6B   single    1.410  0.020  1.410
 A24  C2B  C3B   single    1.516  0.020  1.516
 A24  C2B  H2A1  single    0.970  0.020  1.090
 A24  C2B  H2'2  single    0.970  0.020  1.090
 A24  C3B  N4'   single    1.453  0.020  1.453
 A24  C3B  H3'1  single    0.970  0.020  1.090
 A24  C3B  H3'2  single    0.970  0.020  1.090
 A24  N4'  C5B   single    1.453  0.020  1.453
 A24  N4'  C7B   single    1.448  0.020  1.448
 A24  C5B  C6B   single    1.517  0.020  1.517
 A24  C5B  H5'1  single    0.970  0.020  1.090
 A24  C5B  H5'2  single    0.970  0.020  1.090
 A24  C6B  H6A1  single    0.970  0.020  1.090
 A24  C6B  H6'2  single    0.970  0.020  1.090
 A24  C7B  C8'   single    1.527  0.020  1.527
 A24  C7B  H7'1  single    0.970  0.020  1.090
 A24  C7B  H7'2  single    0.970  0.020  1.090
 A24  C8'  H8'1  single    0.970  0.020  1.090
 A24  C8'  H8'2  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
 A24  H11   C1   O5    106.49  3.000
 A24  H11   C1   C2    110.05  3.000
 A24  O5    C1   C2    111.70  3.000
 A24  H11   C1   O1    110.06  3.000
 A24  O5    C1   O1    111.85  3.000
 A24  C2    C1   O1    106.73  3.000
 A24  C1'   O1   C1    120.34  3.000
 A24  H21   C2   C3    108.27  3.000
 A24  H21   C2   O2    111.21  3.000
 A24  C3    C2   O2    108.69  3.000
 A24  H21   C2   C1    106.30  3.000
 A24  C3    C2   C1    110.16  3.000
 A24  O2    C2   C1    112.13  3.000
 A24  HO21  O2   C2    108.91  3.000
 A24  H31   C3   C4    107.84  3.000
 A24  H31   C3   O3    110.74  3.000
 A24  C4    C3   O3    107.69  3.000
 A24  H31   C3   C2    109.21  3.000
 A24  C4    C3   C2    109.57  3.000
 A24  O3    C3   C2    111.70  3.000
 A24  HO31  O3   C3    108.56  3.000
 A24  H41   C4   C5    107.43  3.000
 A24  H41   C4   O4    111.15  3.000
 A24  C5    C4   O4    108.89  3.000
 A24  H41   C4   C3    108.32  3.000
 A24  C5    C4   C3    109.15  3.000
 A24  O4    C4   C3    111.79  3.000
 A24  HO41  O4   C4    108.11  3.000
 A24  H51   C5   C6    107.87  3.000
 A24  H51   C5   O5    110.26  3.000
 A24  C6    C5   O5    107.61  3.000
 A24  H51   C5   C4    107.18  3.000
 A24  C6    C5   C4    112.57  3.000
 A24  O5    C5   C4    111.31  3.000
 A24  C5    O5   C1    115.46  3.000
 A24  H62   C6   H61   107.09  3.000
 A24  H62   C6   O6    111.75  3.000
 A24  H61   C6   O6    111.81  3.000
 A24  H62   C6   C5    107.69  3.000
 A24  H61   C6   C5    109.88  3.000
 A24  O6    C6   C5    108.53  3.000
 A24  HO1   O6   C6    107.92  3.000
 A24  C6'   C1'  C2'   119.77  3.000
 A24  C6'   C1'  O1    125.14  3.000
 A24  C2'   C1'  O1    115.09  3.000
 A24  H2'1  C2'  C3'   121.59  3.000
 A24  H2'1  C2'  C1'   119.54  3.000
 A24  C3'   C2'  C1'   118.87  3.000
 A24  N1'   C3'  C4'   118.87  3.000
 A24  N1'   C3'  C2'   118.57  3.000
 A24  C4'   C3'  C2'   122.56  3.000
 A24  H4'1  C4'  C5'   121.39  3.000
 A24  H4'1  C4'  C3'   120.68  3.000
 A24  C5'   C4'  C3'   117.91  3.000
 A24  C7'   C5'  C6'   117.61  3.000
 A24  C7'   C5'  C4'   121.46  3.000
 A24  C6'   C5'  C4'   120.88  3.000
 A24  H6'1  C6'  C5'   118.41  3.000
 A24  H6'1  C6'  C1'   121.58  3.000
 A24  C5'   C6'  C1'   120.01  3.000
 A24  O2'   N1'  O1'   124.11  3.000
 A24  O2'   N1'  C3'   118.03  3.000
 A24  O1'   N1'  C3'   117.86  3.000
 A24  N2'   C7'  O3'   123.78  3.000
 A24  N2'   C7'  C5'   115.72  3.000
 A24  O3'   C7'  C5'   120.51  3.000
 A24  HN21  N2'  C8'   117.19  3.000
 A24  HN21  N2'  C7'   119.47  3.000
 A24  C8'   N2'  C7'   123.33  3.000
 A24  C6B   O1B  C2B   110.76  3.000
 A24  H2'2  C2B  H2A1  107.92  3.000
 A24  H2'2  C2B  C3B   109.19  3.000
 A24  H2A1  C2B  C3B   110.11  3.000
 A24  H2'2  C2B  O1B   110.44  3.000
 A24  H2A1  C2B  O1B   107.49  3.000
 A24  C3B   C2B  O1B   111.62  3.000
 A24  H3'2  C3B  H3'1  107.22  3.000
 A24  H3'2  C3B  N4'   109.31  3.000
 A24  H3'1  C3B  N4'   111.88  3.000
 A24  H3'2  C3B  C2B   108.68  3.000
 A24  H3'1  C3B  C2B   109.54  3.000
 A24  N4'   C3B  C2B   110.12  3.000
 A24  C7B   N4'  C5B   112.60  3.000
 A24  C7B   N4'  C3B   111.87  3.000
 A24  C5B   N4'  C3B   109.57  3.000
 A24  H5'2  C5B  H5'1  107.00  3.000
 A24  H5'2  C5B  C6B   109.67  3.000
 A24  H5'1  C5B  C6B   108.15  3.000
 A24  H5'2  C5B  N4'   111.31  3.000
 A24  H5'1  C5B  N4'   110.36  3.000
 A24  C6B   C5B  N4'   110.24  3.000
 A24  H6'2  C6B  H6A1  107.95  3.000
 A24  H6'2  C6B  C5B   109.30  3.000
 A24  H6A1  C6B  C5B   109.92  3.000
 A24  H6'2  C6B  O1B   110.48  3.000
 A24  H6A1  C6B  O1B   107.42  3.000
 A24  C5B   C6B  O1B   111.68  3.000
 A24  H7'2  C7B  H7'1  106.63  3.000
 A24  H7'2  C7B  C8'   108.10  3.000
 A24  H7'1  C7B  C8'   109.59  3.000
 A24  H7'2  C7B  N4'   108.22  3.000
 A24  H7'1  C7B  N4'   112.07  3.000
 A24  C8'   C7B  N4'   112.01  3.000
 A24  H8'2  C8'  H8'1  107.49  3.000
 A24  H8'2  C8'  C7B   111.58  3.000
 A24  H8'1  C8'  C7B   109.59  3.000
 A24  H8'2  C8'  N2'   108.51  3.000
 A24  H8'1  C8'  N2'   108.21  3.000
 A24  C7B   C8'  N2'   111.33  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
 A24  CONST_01  C4'   C3'  C2'  C1'     0.00   0.0  0
 A24  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 A24  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 A24  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 A24  CONST_05  C6'   C1'  C2'  C3'     0.00   0.0  0
 A24  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 A24  CONST_07  C3'   C2'  C1'  O1    180.00   0.0  0
 A24  CONST_08  C5'   C6'  C1'  O1    180.00   0.0  0
 A24  CONST_09  N1'   C3'  C2'  C1'   180.00   0.0  0
 A24  CONST_10  C7'   C5'  C6'  C1'   180.00   0.0  0
 A24  CONST_11  C7'   C5'  C4'  C3'   180.00   0.0  0
 A24  CONST_12  N1'   C3'  C4'  C5'   180.00   0.0  0
 A24  CONST_13  H6'1  C6'  C1'  C2'   180.00   0.0  0
 A24  CONST_14  H4'1  C4'  C3'  C2'   180.00   0.0  0
 A24  CONST_15  H2'1  C2'  C3'  C4'   180.00   0.0  0
 A24  CONST_16  O1'   N1'  C3'  C2'   180.00   0.0  0
 A24  CONST_17  O2'   N1'  C3'  C2'     0.00   0.0  0
 A24  CONST_18  O1'   N1'  C3'  C4'     0.00   0.0  0
 A24  CONST_19  O2'   N1'  C3'  C4'   180.00   0.0  0
 A24  CONST_20  C8'   N2'  C7'  C5'   180.00   0.0  0
 A24  CONST_21  HN21  N2'  C7'  C5'     0.00   0.0  0
 A24  CONST_22  C8'   N2'  C7'  O3'     0.00   0.0  0
 A24  Var_01    N4'   C3B  C2B  O1B    57.45  30.0  1
 A24  Var_02    N4'   C5B  C6B  O1B   -57.03  30.0  1
 A24  Var_03    C5B   C6B  O1B  C2B    57.08  30.0  1
 A24  Var_04    C5B   N4'  C3B  C2B   -56.51  30.0  1
 A24  Var_05    C6B   C5B  N4'  C3B    56.32  30.0  1
 A24  Var_06    C2'   C1'  O1   C1   -174.41  30.0  2
 A24  Var_07    O3'   C7'  C5'  C4'  -145.72  30.0  2
 A24  Var_08    C8'   C7B  N4'  C3B  -158.86  30.0  3
 A24  Var_09    N4'   C7B  C8'  N2'   178.57  30.0  1
 A24  Var_10    C7B   C8'  N2'  C7'    92.51  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
 A24  chir_01  C1  O1  C2  O5  positiv
 A24  chir_02  C2  O2  C1  C3  negativ
 A24  chir_03  C3  O3  C2  C4  positiv
 A24  chir_04  C4  O4  C5  C3  negativ
 A24  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
 A24  plan-1  O1    0.020
 A24  plan-1  C1'   0.020
 A24  plan-1  C2'   0.020
 A24  plan-1  C3'   0.020
 A24  plan-1  C4'   0.020
 A24  plan-1  C5'   0.020
 A24  plan-1  C6'   0.020
 A24  plan-1  N1'   0.020
 A24  plan-1  C7'   0.020
 A24  plan-1  H2'1  0.020
 A24  plan-1  H4'1  0.020
 A24  plan-1  H6'1  0.020
 A24  plan-2  C3'   0.020
 A24  plan-2  N1'   0.020
 A24  plan-2  O1'   0.020
 A24  plan-2  O2'   0.020
 A24  plan-3  C5'   0.020
 A24  plan-3  C7'   0.020
 A24  plan-3  O3'   0.020
 A24  plan-3  N2'   0.020
 A24  plan-3  C8'   0.020
 A24  plan-3  HN21  0.020

