# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 18 15:40:42 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 3-(alpha-D-galactopyranosyloxy)-N-(3-morpholin-4-ylpropyl)-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)NCCCN3CCOCC3)[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
 A32  A32  3-(alpha-D-galactopyranosyloxy)-N-(3-morpholin-4-ylpropyl)-5-nitrobenzamide  ligand  62  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A32
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
 A32  C1    C  CH1    0   0.202  -3.9501   0.8664   0.8375
 A32  O1    O  O2     0  -0.491  -3.5643  -0.4840   0.6792
 A32  C2    C  CH1    0  -0.013  -5.3870   0.8592   1.3668
 A32  O2    O  OH1    0  -0.665  -5.5282   0.0528   2.5067
 A32  C3    C  CH1    0   0.002  -6.3403   0.3524   0.2917
 A32  O3    O  OH1    0  -0.674  -7.6841   0.4737   0.6897
 A32  C4    C  CH1    0  -0.008  -6.1601   1.1747  -0.9825
 A32  O4    O  OH1    0  -0.672  -6.5514   2.5127  -0.7957
 A32  C5    C  CH1    0  -0.020  -4.6974   1.1393  -1.4005
 A32  O5    O  O2     0  -0.487  -3.8452   1.5753  -0.3462
 A32  C6    C  CH2    0  -0.158  -4.4169   2.0119  -2.6050
 A32  O6    O  OH1    0  -0.664  -3.1115   1.7432  -3.0566
 A32  C1'   C  CR6    0   0.441  -2.2807  -0.7958   0.4268
 A32  C2'   C  CR16   0  -0.380  -2.0124  -2.1579   0.3171
 A32  C3'   C  CR6    0   0.298  -0.7150  -2.5643   0.0762
 A32  C4'   C  CR16   0  -0.350   0.3367  -1.6701  -0.0462
 A32  C5'   C  CR6    0  -0.011   0.0547  -0.3177   0.0691
 A32  C6'   C  CR16   0  -0.367  -1.2490   0.1246   0.2750
 A32  N1'   N  N      1   0.328  -0.4445  -3.9916  -0.0609
 A32  O1'   O  O     -1  -0.371   0.6867  -4.3294  -0.3149
 A32  O2'   O  O      0  -0.370  -1.3634  -4.7603   0.0866
 A32  C7'   C  C      0   0.548   1.1226   0.7266  -0.0750
 A32  O3'   O  O      0  -0.481   0.8571   1.8368  -0.5118
 A32  N2'   N  NH1    0  -0.654   2.3532   0.3560   0.3037
 A32  O1B   O  O2     0  -0.485   9.9704   0.0670  -0.1266
 A32  C2B   C  CH2    0  -0.188   9.6288   0.8565   0.9913
 A32  C3B   C  CH2    0  -0.303   8.3340   1.6116   0.7633
 A32  N4'   N  NT     0  -0.428   7.2569   0.6850   0.4640
 A32  C5B   C  CH2    0  -0.310   7.6173  -0.1217  -0.6891
 A32  C6B   C  CH2    0  -0.185   8.9322  -0.8353  -0.4370
 A32  C7B   C  CH2    0  -0.254   5.9958   1.3803   0.2957
 A32  C8'   C  CH2    0  -0.493   4.7901   0.4506   0.3084
 A32  C9'   C  CH2    0  -0.243   3.4951   1.2458   0.2483
 A32  H11   H  HCH1   0   0.267  -3.2860   1.3615   1.5556
 A32  H21   H  HCH1   0   0.243  -5.6391   1.9040   1.5858
 A32  HO21  H  HOH1   0   0.463  -5.2653   0.5582   3.2819
 A32  H31   H  HCH1   0   0.225  -6.0966  -0.6941   0.0568
 A32  HO31  H  HOH1   0   0.456  -7.7833   0.0669   1.5572
 A32  H41   H  HCH1   0   0.239  -6.7435   0.6995  -1.7851
 A32  HO41  H  HOH1   0   0.453  -7.4333   2.5115  -0.4080
 A32  H51   H  HCH1   0   0.243  -4.4642   0.1014  -1.6738
 A32  H61   H  HCH2   0   0.208  -4.5472   3.0668  -2.3387
 A32  H62   H  HCH2   0   0.202  -5.1687   1.7767  -3.3702
 A32  HO1   H  HOH1   0   0.455  -2.9164   2.3511  -3.7752
 A32  H2'1  H  HCR6   0   0.311  -2.8202  -2.8691   0.4174
 A32  H4'1  H  HCR6   0   0.296   1.3363  -2.0214  -0.2562
 A32  H6'1  H  HCR6   0   0.300  -1.4266   1.1891   0.3134
 A32  HN21  H  HNH1   0   0.409   2.4652  -0.4968   0.8291
 A32  H2'2  H  HCH2   0   0.199   9.5319   0.2301   1.8898
 A32  H3'1  H  HCH2   0   0.196   8.4768   2.3492  -0.0459
 A32  H3'2  H  HCH2   0   0.241   8.0888   2.1718   1.6691
 A32  H5'1  H  HCH2   0   0.243   6.8537  -0.8800  -0.8710
 A32  H5'2  H  HCH2   0   0.196   7.6911   0.4909  -1.6052
 A32  H6A1  H  HCH2   0   0.236   9.2341  -1.3876  -1.3282
 A32  H6'2  H  HCH2   0   0.199   8.7963  -1.5587   0.3794
 A32  H7'1  H  HCH2   0   0.195   5.9861   1.9857  -0.6277
 A32  H7'2  H  HCH2   0   0.233   5.8953   2.0863   1.1255
 A32  H8'1  H  HCH2   0   0.235   4.8182  -0.1529   1.2208
 A32  H8'2  H  HCH2   0   0.243   4.8153  -0.2411  -0.5368
 A32  H9'1  H  HCH2   0   0.245   3.4506   1.8190  -0.6788
 A32  H9'2  H  HCH2   0   0.237   3.4553   1.9660   1.0723
 A32  H2A1  H  HCH2   0   0.235  10.4473   1.5585   1.1583

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
 A32  C1   O1    single    1.413  0.020  1.413
 A32  C1   C2    single    1.531  0.020  1.531
 A32  C1   O5    single    1.384  0.020  1.384
 A32  C1   H11   single    0.970  0.020  1.090
 A32  O1   C1'   single    1.345  0.020  1.345
 A32  C2   O2    single    1.403  0.020  1.403
 A32  C2   C3    single    1.524  0.020  1.524
 A32  C2   H21   single    0.970  0.020  1.090
 A32  O2   HO21  single    0.850  0.020  0.980
 A32  C3   O3    single    1.407  0.020  1.407
 A32  C3   C4    single    1.527  0.020  1.527
 A32  C3   H31   single    0.970  0.020  1.090
 A32  O3   HO31  single    0.850  0.020  0.980
 A32  C4   O4    single    1.406  0.020  1.406
 A32  C4   C5    single    1.522  0.020  1.522
 A32  C4   H41   single    0.970  0.020  1.090
 A32  O4   HO41  single    0.850  0.020  0.980
 A32  C5   O5    single    1.424  0.020  1.424
 A32  C5   C6    single    1.514  0.020  1.514
 A32  C5   H51   single    0.970  0.020  1.090
 A32  C6   O6    single    1.407  0.020  1.407
 A32  C6   H61   single    0.970  0.020  1.090
 A32  C6   H62   single    0.970  0.020  1.090
 A32  O6   HO1   single    0.850  0.020  0.980
 A32  C1'  C2'   aromatic  1.393  0.020  1.393
 A32  C1'  C6'   aromatic  1.391  0.020  1.391
 A32  C2'  C3'   aromatic  1.381  0.020  1.381
 A32  C2'  H2'1  single    0.930  0.020  1.080
 A32  C3'  C4'   aromatic  1.386  0.020  1.386
 A32  C3'  N1'   single    1.459  0.020  1.459
 A32  C4'  C5'   aromatic  1.386  0.020  1.386
 A32  C4'  H4'1  single    0.930  0.020  1.080
 A32  C5'  C6'   aromatic  1.392  0.020  1.392
 A32  C5'  C7'   single    1.501  0.020  1.501
 A32  C6'  H6'1  single    0.930  0.020  1.080
 A32  N1'  O1'   single    1.208  0.020  1.208
 A32  N1'  O2'   double    1.207  0.020  1.207
 A32  C7'  O3'   double    1.222  0.020  1.222
 A32  C7'  N2'   single    1.340  0.020  1.340
 A32  N2'  C9'   single    1.449  0.020  1.449
 A32  N2'  HN21  single    0.860  0.020  1.020
 A32  O1B  C2B   single    1.411  0.020  1.411
 A32  O1B  C6B   single    1.410  0.020  1.410
 A32  C2B  C3B   single    1.516  0.020  1.516
 A32  C2B  H2A1  single    0.970  0.020  1.090
 A32  C2B  H2'2  single    0.970  0.020  1.090
 A32  C3B  N4'   single    1.452  0.020  1.452
 A32  C3B  H3'1  single    0.970  0.020  1.090
 A32  C3B  H3'2  single    0.970  0.020  1.090
 A32  N4'  C5B   single    1.453  0.020  1.453
 A32  N4'  C7B   single    1.450  0.020  1.450
 A32  C5B  C6B   single    1.517  0.020  1.517
 A32  C5B  H5'1  single    0.970  0.020  1.090
 A32  C5B  H5'2  single    0.970  0.020  1.090
 A32  C6B  H6A1  single    0.970  0.020  1.090
 A32  C6B  H6'2  single    0.970  0.020  1.090
 A32  C7B  C8'   single    1.523  0.020  1.523
 A32  C7B  H7'1  single    0.970  0.020  1.090
 A32  C7B  H7'2  single    0.970  0.020  1.090
 A32  C8'  C9'   single    1.521  0.020  1.521
 A32  C8'  H8'1  single    0.970  0.020  1.090
 A32  C8'  H8'2  single    0.970  0.020  1.090
 A32  C9'  H9'1  single    0.970  0.020  1.090
 A32  C9'  H9'2  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
 A32  H11   C1   O5    106.44  3.000
 A32  H11   C1   C2    110.13  3.000
 A32  O5    C1   C2    111.67  3.000
 A32  H11   C1   O1    109.85  3.000
 A32  O5    C1   O1    111.90  3.000
 A32  C2    C1   O1    106.88  3.000
 A32  C1'   O1   C1    120.21  3.000
 A32  H21   C2   C3    108.30  3.000
 A32  H21   C2   O2    111.22  3.000
 A32  C3    C2   O2    108.60  3.000
 A32  H21   C2   C1    106.27  3.000
 A32  C3    C2   C1    110.17  3.000
 A32  O2    C2   C1    112.20  3.000
 A32  HO21  O2   C2    108.97  3.000
 A32  H31   C3   C4    107.93  3.000
 A32  H31   C3   O3    110.74  3.000
 A32  C4    C3   O3    107.60  3.000
 A32  H31   C3   C2    109.18  3.000
 A32  C4    C3   C2    109.62  3.000
 A32  O3    C3   C2    111.68  3.000
 A32  HO31  O3   C3    108.47  3.000
 A32  H41   C4   C5    107.41  3.000
 A32  H41   C4   O4    111.12  3.000
 A32  C5    C4   O4    109.03  3.000
 A32  H41   C4   C3    108.28  3.000
 A32  C5    C4   C3    109.27  3.000
 A32  O4    C4   C3    111.63  3.000
 A32  HO41  O4   C4    107.88  3.000
 A32  H51   C5   C6    107.90  3.000
 A32  H51   C5   O5    110.28  3.000
 A32  C6    C5   O5    107.56  3.000
 A32  H51   C5   C4    107.12  3.000
 A32  C6    C5   C4    112.54  3.000
 A32  O5    C5   C4    111.39  3.000
 A32  C5    O5   C1    115.54  3.000
 A32  H62   C6   H61   107.10  3.000
 A32  H62   C6   O6    111.75  3.000
 A32  H61   C6   O6    111.84  3.000
 A32  H62   C6   C5    107.71  3.000
 A32  H61   C6   C5    109.85  3.000
 A32  O6    C6   C5    108.50  3.000
 A32  HO1   O6   C6    107.91  3.000
 A32  C6'   C1'  C2'   119.72  3.000
 A32  C6'   C1'  O1    125.10  3.000
 A32  C2'   C1'  O1    115.18  3.000
 A32  H2'1  C2'  C3'   121.65  3.000
 A32  H2'1  C2'  C1'   119.48  3.000
 A32  C3'   C2'  C1'   118.86  3.000
 A32  N1'   C3'  C4'   118.82  3.000
 A32  N1'   C3'  C2'   118.59  3.000
 A32  C4'   C3'  C2'   122.59  3.000
 A32  H4'1  C4'  C5'   121.44  3.000
 A32  H4'1  C4'  C3'   120.64  3.000
 A32  C5'   C4'  C3'   117.89  3.000
 A32  C7'   C5'  C6'   117.36  3.000
 A32  C7'   C5'  C4'   121.75  3.000
 A32  C6'   C5'  C4'   120.85  3.000
 A32  H6'1  C6'  C5'   118.19  3.000
 A32  H6'1  C6'  C1'   121.76  3.000
 A32  C5'   C6'  C1'   120.04  3.000
 A32  O2'   N1'  O1'   124.10  3.000
 A32  O2'   N1'  C3'   118.05  3.000
 A32  O1'   N1'  C3'   117.85  3.000
 A32  N2'   C7'  O3'   123.49  3.000
 A32  N2'   C7'  C5'   115.72  3.000
 A32  O3'   C7'  C5'   120.79  3.000
 A32  HN21  N2'  C9'   116.88  3.000
 A32  HN21  N2'  C7'   118.91  3.000
 A32  C9'   N2'  C7'   122.91  3.000
 A32  C6B   O1B  C2B   110.75  3.000
 A32  H2'2  C2B  H2A1  107.91  3.000
 A32  H2'2  C2B  C3B   109.35  3.000
 A32  H2A1  C2B  C3B   110.08  3.000
 A32  H2'2  C2B  O1B   110.50  3.000
 A32  H2A1  C2B  O1B   107.44  3.000
 A32  C3B   C2B  O1B   111.49  3.000
 A32  H3'2  C3B  H3'1  107.10  3.000
 A32  H3'2  C3B  N4'   109.36  3.000
 A32  H3'1  C3B  N4'   111.79  3.000
 A32  H3'2  C3B  C2B   108.80  3.000
 A32  H3'1  C3B  C2B   109.42  3.000
 A32  N4'   C3B  C2B   110.28  3.000
 A32  C7B   N4'  C5B   112.95  3.000
 A32  C7B   N4'  C3B   111.29  3.000
 A32  C5B   N4'  C3B   109.51  3.000
 A32  H5'2  C5B  H5'1  107.09  3.000
 A32  H5'2  C5B  C6B   109.92  3.000
 A32  H5'1  C5B  C6B   107.90  3.000
 A32  H5'2  C5B  N4'   111.53  3.000
 A32  H5'1  C5B  N4'   110.16  3.000
 A32  C6B   C5B  N4'   110.14  3.000
 A32  H6'2  C6B  H6A1  107.92  3.000
 A32  H6'2  C6B  C5B   109.01  3.000
 A32  H6A1  C6B  C5B   110.01  3.000
 A32  H6'2  C6B  O1B   110.40  3.000
 A32  H6A1  C6B  O1B   107.46  3.000
 A32  C5B   C6B  O1B   111.95  3.000
 A32  H7'2  C7B  H7'1  106.24  3.000
 A32  H7'2  C7B  C8'   108.36  3.000
 A32  H7'1  C7B  C8'   109.56  3.000
 A32  H7'2  C7B  N4'   107.53  3.000
 A32  H7'1  C7B  N4'   111.57  3.000
 A32  C8'   C7B  N4'   113.27  3.000
 A32  H8'2  C8'  H8'1  107.18  3.000
 A32  H8'2  C8'  C9'   108.67  3.000
 A32  H8'1  C8'  C9'   110.07  3.000
 A32  H8'2  C8'  C7B   111.22  3.000
 A32  H8'1  C8'  C7B   108.86  3.000
 A32  C9'   C8'  C7B   110.77  3.000
 A32  H9'2  C9'  H9'1  107.00  3.000
 A32  H9'2  C9'  C8'   110.19  3.000
 A32  H9'1  C9'  C8'   110.07  3.000
 A32  H9'2  C9'  N2'   110.27  3.000
 A32  H9'1  C9'  N2'   108.85  3.000
 A32  C8'   C9'  N2'   110.40  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
 A32  CONST_01  C4'   C3'  C2'  C1'     0.00   0.0  0
 A32  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 A32  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 A32  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 A32  CONST_05  C6'   C1'  C2'  C3'     0.00   0.0  0
 A32  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 A32  CONST_07  C3'   C2'  C1'  O1    180.00   0.0  0
 A32  CONST_08  C5'   C6'  C1'  O1    180.00   0.0  0
 A32  CONST_09  N1'   C3'  C2'  C1'   180.00   0.0  0
 A32  CONST_10  C7'   C5'  C6'  C1'   180.00   0.0  0
 A32  CONST_11  C7'   C5'  C4'  C3'   180.00   0.0  0
 A32  CONST_12  N1'   C3'  C4'  C5'   180.00   0.0  0
 A32  CONST_13  H6'1  C6'  C1'  C2'   180.00   0.0  0
 A32  CONST_14  H4'1  C4'  C3'  C2'   180.00   0.0  0
 A32  CONST_15  H2'1  C2'  C3'  C4'   180.00   0.0  0
 A32  CONST_16  O1'   N1'  C3'  C2'   180.00   0.0  0
 A32  CONST_17  O2'   N1'  C3'  C2'     0.00   0.0  0
 A32  CONST_18  O1'   N1'  C3'  C4'     0.00   0.0  0
 A32  CONST_19  O2'   N1'  C3'  C4'   180.00   0.0  0
 A32  CONST_20  C9'   N2'  C7'  C5'   180.00   0.0  0
 A32  CONST_21  HN21  N2'  C7'  C5'     0.00   0.0  0
 A32  CONST_22  C9'   N2'  C7'  O3'     0.00   0.0  0
 A32  Var_01    N4'   C3B  C2B  O1B    57.58  30.0  1
 A32  Var_02    N4'   C5B  C6B  O1B   -56.86  30.0  1
 A32  Var_03    C5B   C6B  O1B  C2B    56.88  30.0  1
 A32  Var_04    C5B   N4'  C3B  C2B   -56.75  30.0  1
 A32  Var_05    C6B   C5B  N4'  C3B    56.22  30.0  1
 A32  Var_06    C2'   C1'  O1   C1    178.74  30.0  2
 A32  Var_07    O3'   C7'  C5'  C4'   149.78  30.0  2
 A32  Var_08    C8'   C7B  N4'  C3B  -166.39  30.0  3
 A32  Var_09    C9'   C8'  C7B  N4'   175.14  30.0  3
 A32  Var_10    C8'   C9'  N2'  C7'  -162.03  30.0  3
 A32  Var_11    C7B   C8'  C9'  N2'  -178.19  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
 A32  chir_01  C1  O1  C2  O5  positiv
 A32  chir_02  C2  O2  C1  C3  negativ
 A32  chir_03  C3  O3  C2  C4  positiv
 A32  chir_04  C4  O4  C5  C3  negativ
 A32  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
 A32  plan-1  O1    0.020
 A32  plan-1  C1'   0.020
 A32  plan-1  C2'   0.020
 A32  plan-1  C3'   0.020
 A32  plan-1  C4'   0.020
 A32  plan-1  C5'   0.020
 A32  plan-1  C6'   0.020
 A32  plan-1  N1'   0.020
 A32  plan-1  C7'   0.020
 A32  plan-1  H2'1  0.020
 A32  plan-1  H4'1  0.020
 A32  plan-1  H6'1  0.020
 A32  plan-2  C3'   0.020
 A32  plan-2  N1'   0.020
 A32  plan-2  O1'   0.020
 A32  plan-2  O2'   0.020
 A32  plan-3  C5'   0.020
 A32  plan-3  C7'   0.020
 A32  plan-3  O3'   0.020
 A32  plan-3  N2'   0.020
 A32  plan-3  C9'   0.020
 A32  plan-3  HN21  0.020

