# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 11:56:00 2021
#   Inital geometry file: a 93 line input string
#   Ligand name: 2-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxytetrahydrofuran-2-yl]-N-(pyridin-2-ylmethyl)acetamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1O[C@@H](CC(=O)NCc2ccccn2)[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
 D8M  D8M  '2-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxytetrahydrofuran-2-yl]-N-(pyridin-2-ylmethyl)acetamide (non-preferred name)'  ligand  39  20  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D8M
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
 D8M  O3   O  OH1   0  -0.663   4.4586   7.5333  10.2217
 D8M  C4   C  CR16  0  -0.334  -2.7610   3.2111  10.8509
 D8M  C5   C  CH2   0  -0.359  -2.1680   5.4246   9.7899
 D8M  C6   C  C     0   0.558   0.2040   5.8249  10.1862
 D8M  N1   N  NH1   0  -0.621  -0.8703   5.9037   9.3830
 D8M  C7   C  CH2   0  -0.597   1.5048   6.3010   9.5817
 D8M  C8   C  CR15  0   0.053   2.0618   7.4872  10.3573
 D8M  C9   C  CR15  0  -0.001   3.2986   8.1061   9.6948
 D8M  C10  C  CR15  0  -0.015   3.1045   9.6028   9.9541
 D8M  C11  C  CR15  0  -0.025   1.5868   9.7164   9.8457
 D8M  C12  C  CH2   0  -0.298   1.0838   9.8758   8.4180
 D8M  O    O  O     0  -0.496   0.1363   5.4192  11.3378
 D8M  C3   C  CR6   0   0.251  -2.2705   3.9192   9.7612
 D8M  N    N  N     0  -0.418  -1.8844   3.3209   8.6382
 D8M  C2   C  CR16  0  -0.081  -1.9744   1.9997   8.5635
 D8M  C1   C  CR16  0  -0.328  -2.4555   1.2056   9.5947
 D8M  C    C  CR16  0  -0.151  -2.8584   1.8305  10.7644
 D8M  O1   O  O     0  -0.505   1.0899   8.5160  10.4288
 D8M  O2   O  OH1   0  -0.670   3.5690   9.8858  11.2491
 D8M  H1   H  HOH1  0   0.458   5.2059   7.8003   9.6779
 D8M  H3   H  HCH2  0   0.261  -2.4069   5.8000  10.7849
 D8M  H4   H  HCH2  0   0.278  -2.9032   5.8485   9.1047
 D8M  H5   H  HNH1  0   0.403  -0.7437   6.1616   8.4193
 D8M  H6   H  HCH2  0   0.278   2.2260   5.4807   9.6221
 D8M  H7   H  HCH2  0   0.249   1.3842   6.5699   8.5293
 D8M  H8   H  HCR5  0   0.236   2.3156   7.1651  11.3743
 D8M  H12  H  HCR5  0   0.225   3.2453   7.9527   8.6085
 D8M  H13  H  HCR5  0   0.234   3.6114  10.2181   9.1985
 D8M  H14  H  HCR5  0   0.243   1.2051  10.5581  10.4341
 D8M  H15  H  HCH2  0   0.197   1.5285   9.1049   7.7701
 D8M  H16  H  HCH2  0   0.231   1.4425  10.8370   8.0405
 D8M  H17  H  HCR6  0   0.262  -1.6493   1.5462   7.6333
 D8M  H18  H  HCR6  0   0.269  -2.5089   0.1319   9.4788
 D8M  H19  H  HCR6  0   0.273  -3.2352   1.2540  11.5991
 D8M  H20  H  HOH1  0   0.453   3.4174  10.8196  11.4256
 D8M  N2   N  NH2   0  -0.798  -0.3687   9.8833   8.3999
 D8M  H2   H  HCR6  0   0.266  -3.0598   3.7335  11.7501
 D8M  H9   H  HNH2  0   0.351  -0.6926  10.0108   7.4503
 D8M  H10  H  HNH2  0   0.333  -0.7112   8.9760   8.6900

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
 D8M  N1   C5   single    1.442  0.020  1.442
 D8M  N1   C6   single    1.344  0.020  1.344
 D8M  C5   C3   single    1.509  0.020  1.509
 D8M  C7   C6   single    1.511  0.020  1.511
 D8M  C7   C8   single    1.523  0.020  1.523
 D8M  C6   O    double    1.223  0.020  1.223
 D8M  C9   O3   single    1.397  0.020  1.397
 D8M  C9   C8   single    1.534  0.020  1.534
 D8M  C9   C10  single    1.531  0.020  1.531
 D8M  C8   O1   single    1.417  0.020  1.417
 D8M  C3   N    aromatic  1.330  0.020  1.330
 D8M  C3   C4   aromatic  1.389  0.020  1.389
 D8M  C12  N2   single    1.453  0.020  1.453
 D8M  C12  C11  single    1.522  0.020  1.522
 D8M  N    C2   aromatic  1.326  0.020  1.326
 D8M  O1   C11  single    1.424  0.020  1.424
 D8M  C10  C11  single    1.526  0.020  1.526
 D8M  C10  O2   single    1.405  0.020  1.405
 D8M  C4   C    aromatic  1.387  0.020  1.387
 D8M  C2   C1   aromatic  1.388  0.020  1.388
 D8M  C    C1   aromatic  1.386  0.020  1.386
 D8M  O3   H1   single    0.850  0.020  0.980
 D8M  C4   H2   single    0.930  0.020  1.080
 D8M  C5   H3   single    0.970  0.020  1.090
 D8M  C5   H4   single    0.970  0.020  1.090
 D8M  N1   H5   single    0.860  0.020  1.020
 D8M  C7   H6   single    0.970  0.020  1.090
 D8M  C7   H7   single    0.970  0.020  1.090
 D8M  C8   H8   single    0.970  0.020  1.090
 D8M  N2   H9   single    0.890  0.020  1.040
 D8M  N2   H10  single    0.890  0.020  1.040
 D8M  C9   H12  single    0.970  0.020  1.090
 D8M  C10  H13  single    0.970  0.020  1.090
 D8M  C11  H14  single    0.970  0.020  1.090
 D8M  C12  H15  single    0.970  0.020  1.090
 D8M  C12  H16  single    0.970  0.020  1.090
 D8M  C2   H17  single    0.930  0.020  1.080
 D8M  C1   H18  single    0.930  0.020  1.080
 D8M  C    H19  single    0.930  0.020  1.080
 D8M  O2   H20  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
 D8M  H1   O3   C9   108.55  3.000
 D8M  H2   C4   C    120.87  3.000
 D8M  H2   C4   C3   120.22  3.000
 D8M  C    C4   C3   118.90  3.000
 D8M  H4   C5   H3   106.97  3.000
 D8M  H4   C5   C3   109.26  3.000
 D8M  H3   C5   C3   110.25  3.000
 D8M  H4   C5   N1   107.47  3.000
 D8M  H3   C5   N1   109.90  3.000
 D8M  C3   C5   N1   112.78  3.000
 D8M  O    C6   C7   121.93  3.000
 D8M  O    C6   N1   122.55  3.000
 D8M  C7   C6   N1   115.50  3.000
 D8M  H5   N1   C6   119.16  3.000
 D8M  H5   N1   C5   117.96  3.000
 D8M  C6   N1   C5   122.10  3.000
 D8M  H7   C7   H6   107.04  3.000
 D8M  H7   C7   C8   109.83  3.000
 D8M  H6   C7   C8   108.93  3.000
 D8M  H7   C7   C6   111.57  3.000
 D8M  H6   C7   C6   108.46  3.000
 D8M  C8   C7   C6   110.89  3.000
 D8M  H8   C8   O1   108.98  3.000
 D8M  H8   C8   C9   109.43  3.000
 D8M  O1   C8   C9   106.37  3.000
 D8M  H8   C8   C7   109.16  3.000
 D8M  O1   C8   C7   109.90  3.000
 D8M  C9   C8   C7   112.91  3.000
 D8M  H12  C9   C10  107.33  3.000
 D8M  H12  C9   C8   109.38  3.000
 D8M  C10  C9   C8   102.66  3.000
 D8M  H12  C9   O3   110.86  3.000
 D8M  C10  C9   O3   116.24  3.000
 D8M  C8   C9   O3   109.95  3.000
 D8M  H13  C10  O2   111.64  3.000
 D8M  H13  C10  C11  111.62  3.000
 D8M  O2   C10  C11  112.29  3.000
 D8M  H13  C10  C9   111.88  3.000
 D8M  O2   C10  C9   108.13  3.000
 D8M  C11  C10  C9   100.77  3.000
 D8M  H14  C11  O1   107.82  3.000
 D8M  H14  C11  C12  107.96  3.000
 D8M  O1   C11  C12  110.92  3.000
 D8M  H14  C11  C10  111.44  3.000
 D8M  O1   C11  C10  104.78  3.000
 D8M  C12  C11  C10  113.77  3.000
 D8M  H16  C12  H15  106.26  3.000
 D8M  H16  C12  C11  107.91  3.000
 D8M  H15  C12  C11  110.20  3.000
 D8M  H16  C12  N2   108.62  3.000
 D8M  H15  C12  N2   113.59  3.000
 D8M  C11  C12  N2   110.04  3.000
 D8M  N    C3   C5   116.44  3.000
 D8M  N    C3   C4   122.40  3.000
 D8M  C5   C3   C4   121.16  3.000
 D8M  C2   N    C3   118.43  3.000
 D8M  H17  C2   C1   120.13  3.000
 D8M  H17  C2   N    116.39  3.000
 D8M  C1   C2   N    123.48  3.000
 D8M  H18  C1   C    121.59  3.000
 D8M  H18  C1   C2   120.38  3.000
 D8M  C    C1   C2   118.03  3.000
 D8M  H19  C    C1   120.79  3.000
 D8M  H19  C    C4   120.45  3.000
 D8M  C1   C    C4   118.76  3.000
 D8M  C11  O1   C8   110.61  3.000
 D8M  H20  O2   C10  108.21  3.000
 D8M  H10  N2   H9   105.89  3.000
 D8M  H10  N2   C12  109.28  3.000
 D8M  H9   N2   C12  109.42  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
 D8M  CONST_01  C2   N   C3   C4     0.00   0.0  0
 D8M  CONST_02  C2   C1  C    C4     0.00   0.0  0
 D8M  CONST_03  C1   C2  N    C3     0.00   0.0  0
 D8M  CONST_04  C1   C   C4   C3     0.00   0.0  0
 D8M  CONST_05  C    C4  C3   N      0.00   0.0  0
 D8M  CONST_06  C    C1  C2   N      0.00   0.0  0
 D8M  CONST_07  C2   N   C3   C5   180.00   0.0  0
 D8M  CONST_08  C    C4  C3   C5   180.00   0.0  0
 D8M  CONST_09  H18  C1  C    C4   180.00   0.0  0
 D8M  CONST_10  H17  C2  N    C3   180.00   0.0  0
 D8M  CONST_11  H19  C   C4   C3   180.00   0.0  0
 D8M  CONST_12  H2   C4  C3   N    180.00   0.0  0
 D8M  CONST_13  C7   C6  N1   C5   180.00   0.0  0
 D8M  CONST_14  O    C6  N1   C5     0.00   0.0  0
 D8M  CONST_15  H5   N1  C6   C7     0.00   0.0  0
 D8M  Var_01    N1   C5  C3   C4   130.10  30.0  3
 D8M  Var_02    C3   C5  N1   C6   -75.27  30.0  3
 D8M  Var_03    C8   C7  C6   N1   118.15  30.0  1
 D8M  Var_04    H9   N2  C12  C11  178.71  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
 D8M  chir_01  C8   C7  C9   O1   negativ
 D8M  chir_02  C9   O3  C10  C8   positiv
 D8M  chir_03  C10  O2  C9   C11  negativ
 D8M  chir_04  C11  O1  C10  C12  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
 D8M  plan-1  C4   0.020
 D8M  plan-1  C5   0.020
 D8M  plan-1  C3   0.020
 D8M  plan-1  N    0.020
 D8M  plan-1  C2   0.020
 D8M  plan-1  C1   0.020
 D8M  plan-1  C    0.020
 D8M  plan-1  H17  0.020
 D8M  plan-1  H18  0.020
 D8M  plan-1  H19  0.020
 D8M  plan-1  H2   0.020
 D8M  plan-2  C5   0.020
 D8M  plan-2  C6   0.020
 D8M  plan-2  N1   0.020
 D8M  plan-2  C7   0.020
 D8M  plan-2  O    0.020
 D8M  plan-2  H5   0.020

