# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:50:17 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: N-{[(2R,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]methyl}-4-(dimethylamino)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccc(cc1)C(=O)NC[C@H]2N[C@H](CO)[C@@H](O)[C@@H]2O
#
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
 MNI  MNI  N-{[(2R,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]methyl}-4-(dimethylamino)benzamide  ligand  45  22  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MNI
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
 MNI  O1B   O  O     0  -0.504  -0.4178  0.3584   3.2659
 MNI  C1B   C  C     0   0.532  -0.7845  1.5019   3.5208
 MNI  C2B   C  CR6   0  -0.074  -0.8837  1.9919   4.9178
 MNI  C3B   C  CR16  0  -0.257  -1.0385  1.0684   5.9514
 MNI  C4B   C  CR16  0  -0.347  -1.1230  1.4603   7.2711
 MNI  C5B   C  CR6   0   0.398  -1.0241  2.8207   7.6342
 MNI  N5B   N  NT    0  -0.501  -1.0789  3.2161   8.9346
 MNI  C8B   C  CH3   0  -0.538  -1.3561  2.2521   9.9742
 MNI  C9B   C  CH3   0  -0.537  -1.0806  4.6231   9.2625
 MNI  C6B   C  CR16  0  -0.346  -0.8559  3.7507   6.5871
 MNI  C7B   C  CR16  0  -0.277  -0.7867  3.3381   5.2714
 MNI  N1B   N  NH1   0  -0.652  -1.1367  2.3675   2.5520
 MNI  C1A   C  CH2   0  -0.294  -0.9165  2.1060   1.1483
 MNI  C2A   C  CH1   0  -0.132   0.5561  2.1876   0.7529
 MNI  N5A   N  NH1   0  -0.611   0.6833  2.1153  -0.7102
 MNI  C5M   C  CH1   0  -0.185   1.1050  3.4436  -1.1515
 MNI  C6A   C  CH2   0  -0.158   1.7199  3.4029  -2.5338
 MNI  O6A   O  OH1   0  -0.665   0.8035  3.0041  -3.5271
 MNI  C4A   C  CH1   0   0.032   2.0256  3.9311  -0.0324
 MNI  O4A   O  OH1   0  -0.667   2.2851  5.3094  -0.0095
 MNI  C3A   C  CH1   0   0.015   1.2225  3.5105   1.1965
 MNI  O3A   O  OH1   0  -0.657   1.9385  3.4433   2.3997
 MNI  H3B   H  HCR6  0   0.250  -1.1075  0.0130   5.7200
 MNI  H4B   H  HCR6  0   0.268  -1.2611  0.6968   8.0230
 MNI  H8B1  H  HCH3  0   0.258  -1.3012  2.7437  10.9413
 MNI  H8B2  H  HCH3  0   0.240  -0.6252  1.4409   9.9789
 MNI  H8B3  H  HCH3  0   0.233  -2.3518  1.8069   9.8816
 MNI  H9B1  H  HCH3  0   0.240  -0.1855  5.1256   8.8889
 MNI  H9B2  H  HCH3  0   0.258  -1.0897  4.7381  10.3426
 MNI  H9B3  H  HCH3  0   0.233  -1.9540  5.1478   8.8618
 MNI  H6B   H  HCR6  0   0.270  -0.7659  4.8074   6.7935
 MNI  H7B   H  HCR6  0   0.246  -0.6231  4.0999   4.5187
 MNI  HN1B  H  HNH1  0   0.401  -1.4987  3.2696   2.8067
 MNI  H1A1  H  HCH2  0   0.249  -1.3157  1.1267   0.8785
 MNI  H1A2  H  HCH2  0   0.250  -1.4826  2.8505   0.5871
 MNI  H2A   H  HCH1  0   0.252   1.0854  1.3445   1.2052
 MNI  HN5A  H  HNH1  0   0.352   1.4107  1.4472  -0.9407
 MNI  H5M   H  HCH1  0   0.234   0.2269  4.1039  -1.1790
 MNI  H6A1  H  HCH2  0   0.192   2.6053  2.7492  -2.5122
 MNI  H6A2  H  HCH2  0   0.225   2.0676  4.4009  -2.8085
 MNI  HO6A  H  HOH1  0   0.446   0.4218  2.1635  -3.2536
 MNI  H4A   H  HCH1  0   0.205   2.9595  3.3453  -0.0693
 MNI  HO4A  H  HOH1  0   0.454   2.9763  5.5066  -0.6478
 MNI  H3A   H  HCH1  0   0.231   0.4535  4.2765   1.3568
 MNI  HO3A  H  HOH1  0   0.441   2.5892  2.7370   2.3291

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
 MNI  O1B  C1B   double    1.228  0.020  1.228
 MNI  C1B  N1B   single    1.346  0.020  1.346
 MNI  C1B  C2B   single    1.484  0.020  1.484
 MNI  C2B  C3B   aromatic  1.395  0.020  1.395
 MNI  C2B  C7B   aromatic  1.395  0.020  1.395
 MNI  C3B  C4B   aromatic  1.379  0.020  1.379
 MNI  C3B  H3B   single    0.930  0.020  1.080
 MNI  C4B  C5B   aromatic  1.412  0.020  1.412
 MNI  C4B  H4B   single    0.930  0.020  1.080
 MNI  C5B  C6B   aromatic  1.411  0.020  1.411
 MNI  C5B  N5B   single    1.360  0.020  1.360
 MNI  N5B  C8B   single    1.445  0.020  1.445
 MNI  N5B  C9B   single    1.445  0.020  1.445
 MNI  C8B  H8B1  single    0.970  0.020  1.090
 MNI  C8B  H8B2  single    0.970  0.020  1.090
 MNI  C8B  H8B3  single    0.970  0.020  1.090
 MNI  C9B  H9B1  single    0.970  0.020  1.090
 MNI  C9B  H9B2  single    0.970  0.020  1.090
 MNI  C9B  H9B3  single    0.970  0.020  1.090
 MNI  C6B  C7B   aromatic  1.381  0.020  1.381
 MNI  C6B  H6B   single    0.930  0.020  1.080
 MNI  C7B  H7B   single    0.930  0.020  1.080
 MNI  N1B  C1A   single    1.445  0.020  1.445
 MNI  N1B  HN1B  single    0.860  0.020  1.020
 MNI  C1A  C2A   single    1.527  0.020  1.527
 MNI  C1A  H1A1  single    0.970  0.020  1.090
 MNI  C1A  H1A2  single    0.970  0.020  1.090
 MNI  C2A  N5A   single    1.470  0.020  1.470
 MNI  C2A  C3A   single    1.546  0.020  1.546
 MNI  C2A  H2A   single    0.970  0.020  1.090
 MNI  N5A  C5M   single    1.462  0.020  1.462
 MNI  N5A  HN5A  single    0.890  0.020  1.040
 MNI  C5M  C6A   single    1.513  0.020  1.513
 MNI  C5M  C4A   single    1.529  0.020  1.529
 MNI  C5M  H5M   single    0.970  0.020  1.090
 MNI  C6A  O6A   single    1.409  0.020  1.409
 MNI  C6A  H6A1  single    0.970  0.020  1.090
 MNI  C6A  H6A2  single    0.970  0.020  1.090
 MNI  O6A  HO6A  single    0.850  0.020  0.980
 MNI  C4A  O4A   single    1.403  0.020  1.403
 MNI  C4A  C3A   single    1.527  0.020  1.527
 MNI  C4A  H4A   single    0.970  0.020  1.090
 MNI  O4A  HO4A  single    0.850  0.020  0.980
 MNI  C3A  O3A   single    1.402  0.020  1.402
 MNI  C3A  H3A   single    0.970  0.020  1.090
 MNI  O3A  HO3A  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
 MNI  N1B   C1B  C2B   116.60  3.000
 MNI  C2B   C1B  O1B   121.53  3.000
 MNI  N1B   C1B  O1B   121.85  3.000
 MNI  C7B   C2B  C3B   117.31  3.000
 MNI  C7B   C2B  C1B   123.54  3.000
 MNI  C3B   C2B  C1B   119.11  3.000
 MNI  H3B   C3B  C4B   118.53  3.000
 MNI  H3B   C3B  C2B   119.62  3.000
 MNI  C4B   C3B  C2B   121.85  3.000
 MNI  H4B   C4B  C5B   120.73  3.000
 MNI  H4B   C4B  C3B   118.22  3.000
 MNI  C5B   C4B  C3B   121.05  3.000
 MNI  C6B   C5B  N5B   121.52  3.000
 MNI  N5B   C5B  C4B   121.55  3.000
 MNI  C6B   C5B  C4B   116.92  3.000
 MNI  C9B   N5B  C8B   119.10  3.000
 MNI  C9B   N5B  C5B   120.01  3.000
 MNI  C8B   N5B  C5B   120.11  3.000
 MNI  H8B3  C8B  H8B2  107.88  3.000
 MNI  H8B3  C8B  H8B1  107.77  3.000
 MNI  H8B2  C8B  H8B1  107.37  3.000
 MNI  H8B3  C8B  N5B   112.65  3.000
 MNI  H8B2  C8B  N5B   111.74  3.000
 MNI  H8B1  C8B  N5B   109.21  3.000
 MNI  H9B3  C9B  H9B2  107.85  3.000
 MNI  H9B3  C9B  H9B1  107.95  3.000
 MNI  H9B2  C9B  H9B1  107.35  3.000
 MNI  H9B3  C9B  N5B   112.62  3.000
 MNI  H9B2  C9B  N5B   109.19  3.000
 MNI  H9B1  C9B  N5B   111.68  3.000
 MNI  H6B   C6B  C7B   118.05  3.000
 MNI  H6B   C6B  C5B   120.86  3.000
 MNI  C7B   C6B  C5B   121.09  3.000
 MNI  H7B   C7B  C6B   117.36  3.000
 MNI  H7B   C7B  C2B   120.86  3.000
 MNI  C6B   C7B  C2B   121.76  3.000
 MNI  HN1B  N1B  C1A   117.62  3.000
 MNI  HN1B  N1B  C1B   119.28  3.000
 MNI  C1A   N1B  C1B   122.89  3.000
 MNI  H1A2  C1A  H1A1  107.19  3.000
 MNI  H1A2  C1A  C2A   109.32  3.000
 MNI  H1A1  C1A  C2A   109.67  3.000
 MNI  H1A2  C1A  N1B   107.30  3.000
 MNI  H1A1  C1A  N1B   110.29  3.000
 MNI  C2A   C1A  N1B   112.88  3.000
 MNI  H2A   C2A  C3A   109.41  3.000
 MNI  H2A   C2A  N5A   109.38  3.000
 MNI  C3A   C2A  N5A   106.87  3.000
 MNI  H2A   C2A  C1A   108.58  3.000
 MNI  C3A   C2A  C1A   112.78  3.000
 MNI  N5A   C2A  C1A   109.78  3.000
 MNI  HN5A  N5A  C5M   108.85  3.000
 MNI  HN5A  N5A  C2A   108.70  3.000
 MNI  C5M   N5A  C2A   106.30  3.000
 MNI  H5M   C5M  C4A   107.93  3.000
 MNI  H5M   C5M  C6A   108.54  3.000
 MNI  C4A   C5M  C6A   115.63  3.000
 MNI  H5M   C5M  N5A   108.84  3.000
 MNI  C4A   C5M  N5A   104.03  3.000
 MNI  C6A   C5M  N5A   111.62  3.000
 MNI  H6A2  C6A  H6A1  106.95  3.000
 MNI  H6A2  C6A  O6A   106.76  3.000
 MNI  H6A1  C6A  O6A   111.65  3.000
 MNI  H6A2  C6A  C5M   109.55  3.000
 MNI  H6A1  C6A  C5M   108.96  3.000
 MNI  O6A   C6A  C5M   112.79  3.000
 MNI  HO6A  O6A  C6A   107.74  3.000
 MNI  H4A   C4A  C3A   109.02  3.000
 MNI  H4A   C4A  O4A   111.45  3.000
 MNI  C3A   C4A  O4A   110.78  3.000
 MNI  H4A   C4A  C5M   108.42  3.000
 MNI  C3A   C4A  C5M   100.63  3.000
 MNI  O4A   C4A  C5M   115.89  3.000
 MNI  HO4A  O4A  C4A   108.89  3.000
 MNI  H3A   C3A  O3A   105.42  3.000
 MNI  H3A   C3A  C4A   107.09  3.000
 MNI  O3A   C3A  C4A   115.81  3.000
 MNI  H3A   C3A  C2A   109.70  3.000
 MNI  O3A   C3A  C2A   115.17  3.000
 MNI  C4A   C3A  C2A   103.39  3.000
 MNI  HO3A  O3A  C3A   108.50  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
 MNI  CONST_01  C5B   C4B  C3B  C2B    0.00   0.0  0
 MNI  CONST_02  C5B   C6B  C7B  C2B    0.00   0.0  0
 MNI  CONST_03  C6B   C7B  C2B  C3B    0.00   0.0  0
 MNI  CONST_04  C6B   C5B  C4B  C3B    0.00   0.0  0
 MNI  CONST_05  C7B   C2B  C3B  C4B    0.00   0.0  0
 MNI  CONST_06  C7B   C6B  C5B  C4B    0.00   0.0  0
 MNI  CONST_07  C4B   C3B  C2B  C1B  180.00   0.0  0
 MNI  CONST_08  C6B   C7B  C2B  C1B  180.00   0.0  0
 MNI  CONST_09  N5B   C5B  C4B  C3B  180.00   0.0  0
 MNI  CONST_10  C7B   C6B  C5B  N5B  180.00   0.0  0
 MNI  CONST_11  H4B   C4B  C3B  C2B  180.00   0.0  0
 MNI  CONST_12  H6B   C6B  C7B  C2B  180.00   0.0  0
 MNI  CONST_13  H7B   C7B  C2B  C3B  180.00   0.0  0
 MNI  CONST_14  H3B   C3B  C4B  C5B  180.00   0.0  0
 MNI  CONST_15  C8B   N5B  C5B  C4B    0.00   0.0  0
 MNI  CONST_16  C9B   N5B  C5B  C4B  180.00   0.0  0
 MNI  CONST_17  C6B   C5B  N5B  C8B  180.00   0.0  0
 MNI  CONST_18  C6B   C5B  N5B  C9B    0.00   0.0  0
 MNI  CONST_19  C1A   N1B  C1B  C2B  180.00   0.0  0
 MNI  CONST_20  HN1B  N1B  C1B  C2B    0.00   0.0  0
 MNI  CONST_21  C1A   N1B  C1B  O1B    0.00   0.0  0
 MNI  Var_01    C3B   C2B  C1B  O1B  -23.23  30.0  2
 MNI  Var_02    C2A   C1A  N1B  C1B  -71.71  30.0  3
 MNI  Var_03    H8B1  C8B  N5B  C5B  176.74  30.0  3
 MNI  Var_04    H9B1  C9B  N5B  C5B  -59.29  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
 MNI  chir_01  C2A  C1A  N5A  C3A  negativ
 MNI  chir_02  C5M  N5A  C4A  C6A  negativ
 MNI  chir_03  C4A  O4A  C5M  C3A  positiv
 MNI  chir_04  C3A  O3A  C4A  C2A  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
 MNI  plan-1  C1B   0.020
 MNI  plan-1  C2B   0.020
 MNI  plan-1  C3B   0.020
 MNI  plan-1  C4B   0.020
 MNI  plan-1  C5B   0.020
 MNI  plan-1  N5B   0.020
 MNI  plan-1  C6B   0.020
 MNI  plan-1  C7B   0.020
 MNI  plan-1  H3B   0.020
 MNI  plan-1  H4B   0.020
 MNI  plan-1  H6B   0.020
 MNI  plan-1  H7B   0.020
 MNI  plan-2  C5B   0.020
 MNI  plan-2  N5B   0.020
 MNI  plan-2  C8B   0.020
 MNI  plan-2  C9B   0.020
 MNI  plan-3  O1B   0.020
 MNI  plan-3  C1B   0.020
 MNI  plan-3  C2B   0.020
 MNI  plan-3  N1B   0.020
 MNI  plan-3  C1A   0.020
 MNI  plan-3  HN1B  0.020

