# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 16:59:30 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 6-{[(1R,3S,4R)-3-hydroxy-4-(hydroxymethyl)cyclopentyl]amino}pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(N[C@H]2C[C@H](O)[C@@H](CO)C2)nc1
#
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
 4H3  4H3  6-{[(1R,3S,4R)-3-hydroxy-4-(hydroxymethyl)cyclopentyl]amino}pyridine-3-carboxamide  ligand  35  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4H3
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
 4H3  C5   C  CR16  0  -0.152   2.7660   0.8470   0.7312
 4H3  C6   C  CR16  0  -0.390   1.4306   0.5388   0.7984
 4H3  C18  C  CR16  0  -0.074   3.1145  -1.1577  -0.4811
 4H3  C4   C  CR6   0  -0.165   3.6571   0.0020   0.0620
 4H3  C7   C  CR6   0   0.506   0.9851  -0.6594   0.2007
 4H3  C2   C  C     0   0.482   5.0951   0.3599  -0.0016
 4H3  C16  C  CH2   0  -0.471  -2.6824  -1.0450   0.8434
 4H3  C10  C  CH2   0  -0.495  -1.7768   0.9356  -0.2765
 4H3  C13  C  CR15  0  -0.305  -3.8155  -0.1162   0.4111
 4H3  C9   C  CR15  0  -0.076  -1.3965  -0.2181   0.6827
 4H3  C11  C  CR15  0   0.093  -3.1848   0.6019  -0.7794
 4H3  C14  C  CH2   0  -0.132  -5.0894  -0.8887   0.1395
 4H3  N17  N  N     0  -0.464   1.8369  -1.4866  -0.4189
 4H3  N1   N  NH2   0  -0.821   5.8347  -0.2718  -0.9302
 4H3  N8   N  NH1   0  -0.659  -0.3051  -1.0506   0.2336
 4H3  O3   O  O     0  -0.491   5.5735   1.1890   0.7644
 4H3  O12  O  OH1   0  -0.662  -3.9293   1.7227  -1.1820
 4H3  O15  O  OH1   0  -0.667  -6.1448  -0.0093  -0.1728
 4H3  H1   H  HCR6  0   0.269   3.1250   1.7599   1.1881
 4H3  H2   H  HCR6  0   0.274   0.7463   1.2064   1.3020
 4H3  H3   H  HCR6  0   0.256   3.7471  -1.8829  -0.9841
 4H3  H4   H  HCH2  0   0.262  -2.8050  -1.4296   1.8554
 4H3  H5   H  HCH2  0   0.234  -2.6563  -1.9113   0.1723
 4H3  H6   H  HCH2  0   0.237  -1.8155   1.8804   0.2722
 4H3  H7   H  HCH2  0   0.248  -1.0525   1.0548  -1.0844
 4H3  H8   H  HCR5  0   0.236  -3.9976   0.6199   1.2045
 4H3  H9   H  HCR5  0   0.263  -1.1219   0.1944   1.6553
 4H3  H10  H  HCR5  0   0.188  -3.1039  -0.1279  -1.6016
 4H3  H11  H  HCH2  0   0.182  -4.8995  -1.5995  -0.6786
 4H3  H12  H  HCH2  0   0.200  -5.3261  -1.4909   1.0275
 4H3  H13  H  HNH2  0   0.409   5.4258  -0.8192  -1.6670
 4H3  H14  H  HNH2  0   0.403   6.8098  -0.0407  -1.0261
 4H3  H15  H  HNH1  0   0.383  -0.5272  -1.8545  -0.3341
 4H3  H16  H  HOH1  0   0.447  -3.4724   2.1308  -1.9238
 4H3  H17  H  HOH1  0   0.451  -6.9500  -0.5300  -0.2391

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
 4H3  O12  C11  single    1.404  0.020  1.404
 4H3  C14  C13  single    1.514  0.020  1.514
 4H3  C14  O15  single    1.409  0.020  1.409
 4H3  C11  C13  single    1.527  0.020  1.527
 4H3  C11  C10  single    1.532  0.020  1.532
 4H3  C13  C16  single    1.528  0.020  1.528
 4H3  C10  C9   single    1.548  0.020  1.548
 4H3  C16  C9   single    1.537  0.020  1.537
 4H3  C9   N8   single    1.444  0.020  1.444
 4H3  N8   C7   single    1.349  0.020  1.349
 4H3  C6   C7   aromatic  1.411  0.020  1.411
 4H3  C6   C5   aromatic  1.372  0.020  1.372
 4H3  C7   N17  aromatic  1.339  0.020  1.339
 4H3  C5   C4   aromatic  1.399  0.020  1.399
 4H3  N17  C18  aromatic  1.321  0.020  1.321
 4H3  C4   C18  aromatic  1.391  0.020  1.391
 4H3  C4   C2   single    1.483  0.020  1.483
 4H3  O3   C2   double    1.226  0.020  1.226
 4H3  C2   N1   single    1.345  0.020  1.345
 4H3  C5   H1   single    0.930  0.020  1.080
 4H3  C6   H2   single    0.930  0.020  1.080
 4H3  C18  H3   single    0.930  0.020  1.080
 4H3  C16  H4   single    0.970  0.020  1.090
 4H3  C16  H5   single    0.970  0.020  1.090
 4H3  C10  H6   single    0.970  0.020  1.090
 4H3  C10  H7   single    0.970  0.020  1.090
 4H3  C13  H8   single    0.970  0.020  1.090
 4H3  C9   H9   single    0.970  0.020  1.090
 4H3  C11  H10  single    0.970  0.020  1.090
 4H3  C14  H11  single    0.970  0.020  1.090
 4H3  C14  H12  single    0.970  0.020  1.090
 4H3  N1   H13  single    0.860  0.020  1.020
 4H3  N1   H14  single    0.860  0.020  1.020
 4H3  N8   H15  single    0.860  0.020  1.020
 4H3  O12  H16  single    0.850  0.020  0.980
 4H3  O15  H17  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
 4H3  H1   C5   C4   120.03  3.000
 4H3  H1   C5   C6   119.44  3.000
 4H3  C4   C5   C6   120.52  3.000
 4H3  H2   C6   C7   121.47  3.000
 4H3  H2   C6   C5   120.03  3.000
 4H3  C7   C6   C5   118.50  3.000
 4H3  H3   C18  N17  114.77  3.000
 4H3  H3   C18  C4   120.70  3.000
 4H3  N17  C18  C4   124.52  3.000
 4H3  C2   C4   C18  124.24  3.000
 4H3  C2   C4   C5   119.50  3.000
 4H3  C18  C4   C5   116.24  3.000
 4H3  N8   C7   N17  116.14  3.000
 4H3  N17  C7   C6   121.30  3.000
 4H3  N8   C7   C6   122.55  3.000
 4H3  O3   C2   N1   122.32  3.000
 4H3  N1   C2   C4   116.71  3.000
 4H3  O3   C2   C4   120.98  3.000
 4H3  H5   C16  H4   107.00  3.000
 4H3  H5   C16  C9   109.95  3.000
 4H3  H4   C16  C9   112.40  3.000
 4H3  H5   C16  C13  108.96  3.000
 4H3  H4   C16  C13  113.21  3.000
 4H3  C9   C16  C13  105.30  3.000
 4H3  H7   C10  H6   107.50  3.000
 4H3  H7   C10  C11  112.99  3.000
 4H3  H6   C10  C11  108.69  3.000
 4H3  H7   C10  C9   112.15  3.000
 4H3  H6   C10  C9   109.99  3.000
 4H3  C11  C10  C9   105.48  3.000
 4H3  H8   C13  C14  109.40  3.000
 4H3  H8   C13  C11  108.47  3.000
 4H3  C14  C13  C11  116.59  3.000
 4H3  H8   C13  C16  109.04  3.000
 4H3  C11  C13  C16  101.55  3.000
 4H3  C14  C13  C16  111.38  3.000
 4H3  H9   C9   N8   107.75  3.000
 4H3  H9   C9   C10  109.41  3.000
 4H3  N8   C9   C10  115.00  3.000
 4H3  H9   C9   C16  108.70  3.000
 4H3  N8   C9   C16  110.77  3.000
 4H3  C10  C9   C16  105.08  3.000
 4H3  H10  C11  O12  110.70  3.000
 4H3  H10  C11  C13  107.49  3.000
 4H3  O12  C11  C13  112.33  3.000
 4H3  H10  C11  C10  108.76  3.000
 4H3  C13  C11  C10  103.07  3.000
 4H3  O12  C11  C10  114.05  3.000
 4H3  H12  C14  H11  106.50  3.000
 4H3  H12  C14  O15  111.09  3.000
 4H3  H11  C14  O15  111.57  3.000
 4H3  H12  C14  C13  108.42  3.000
 4H3  H11  C14  C13  108.53  3.000
 4H3  O15  C14  C13  110.58  3.000
 4H3  C7   N17  C18  118.90  3.000
 4H3  H14  N1   H13  116.70  3.000
 4H3  H14  N1   C2   119.38  3.000
 4H3  H13  N1   C2   122.58  3.000
 4H3  H15  N8   C9   117.90  3.000
 4H3  H15  N8   C7   115.34  3.000
 4H3  C9   N8   C7   124.29  3.000
 4H3  H16  O12  C11  107.92  3.000
 4H3  H17  O15  C14  107.74  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
 4H3  CONST_01  N17  C7   C6   C5     0.00   0.0  0
 4H3  CONST_02  N17  C18  C4   C5     0.00   0.0  0
 4H3  CONST_03  C18  N17  C7   C6     0.00   0.0  0
 4H3  CONST_04  C18  C4   C5   C6     0.00   0.0  0
 4H3  CONST_05  C7   C6   C5   C4     0.00   0.0  0
 4H3  CONST_06  C7   N17  C18  C4     0.00   0.0  0
 4H3  CONST_07  N8   C7   C6   C5   180.00   0.0  0
 4H3  CONST_08  C2   C4   C5   C6   180.00   0.0  0
 4H3  CONST_09  N8   C7   N17  C18  180.00   0.0  0
 4H3  CONST_10  N17  C18  C4   C2   180.00   0.0  0
 4H3  CONST_11  C9   N8   C7   C6     0.00   0.0  0
 4H3  CONST_12  N17  C7   N8   C9   180.00   0.0  0
 4H3  CONST_13  H3   C18  C4   C5   180.00   0.0  0
 4H3  CONST_14  H1   C5   C4   C18  180.00   0.0  0
 4H3  CONST_15  H2   C6   C5   C4   180.00   0.0  0
 4H3  CONST_16  H15  N8   C7   C6   180.00   0.0  0
 4H3  CONST_17  H13  N1   C2   C4     0.00   0.0  0
 4H3  CONST_18  H14  N1   C2   C4   180.00   0.0  0
 4H3  Var_01    O3   C2   C4   C5    17.29  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
 4H3  chir_01  C13  C14  C11  C16  positiv
 4H3  chir_02  C9   N8   C10  C16  negativ
 4H3  chir_03  C11  O12  C13  C10  positiv

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
 4H3  plan-1  C5   0.020
 4H3  plan-1  C6   0.020
 4H3  plan-1  C18  0.020
 4H3  plan-1  C4   0.020
 4H3  plan-1  C7   0.020
 4H3  plan-1  C2   0.020
 4H3  plan-1  N17  0.020
 4H3  plan-1  N8   0.020
 4H3  plan-1  H1   0.020
 4H3  plan-1  H2   0.020
 4H3  plan-1  H3   0.020
 4H3  plan-2  C7   0.020
 4H3  plan-2  C9   0.020
 4H3  plan-2  N8   0.020
 4H3  plan-2  H15  0.020
 4H3  plan-3  C4   0.020
 4H3  plan-3  C2   0.020
 4H3  plan-3  N1   0.020
 4H3  plan-3  O3   0.020
 4H3  plan-3  H13  0.020
 4H3  plan-3  H14  0.020

