# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 02:23:18 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 6-{[(1R,3R)-3-hydroxycyclopentyl]amino}pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(N[C@@H]2CC[C@@H](O)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
 EFW  EFW  6-{[(1R,3R)-3-hydroxycyclopentyl]amino}pyridine-3-carboxamide  ligand  31  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EFW
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
 EFW  C5   C  CR16  0  -0.152   2.1055   1.0696  -0.3065
 EFW  C6   C  CR16  0  -0.393   0.7575   0.8168  -0.3346
 EFW  C16  C  CR16  0  -0.073   2.4639  -1.1812   0.3338
 EFW  C4   C  CR6   0  -0.166   3.0145   0.0564   0.0185
 EFW  C7   C  CR6   0   0.512   0.3105  -0.4863  -0.0282
 EFW  C2   C  C     0   0.486   4.4658   0.3617   0.0472
 EFW  C10  C  CH2   0  -0.461  -2.5161   0.8310   1.0083
 EFW  C11  C  CH2   0  -0.488  -3.9774   1.1580   0.7377
 EFW  C14  C  CH2   0  -0.489  -3.3783  -0.6906  -0.7030
 EFW  C9   C  CR15  0  -0.062  -2.1012   0.0523  -0.2524
 EFW  C12  C  CR15  0   0.073  -4.5102  -0.1666   0.1902
 EFW  N15  N  N     0  -0.466   1.1721  -1.4533   0.3150
 EFW  N1   N  NH2   0  -0.824   5.3081  -0.6847   0.1150
 EFW  N8   N  NH1   0  -0.665  -0.9871  -0.8463  -0.0767
 EFW  O3   O  O     0  -0.492   4.8690   1.5189   0.0164
 EFW  O13  O  OH1   0  -0.675  -5.7098  -0.0787  -0.5411
 EFW  H1   H  HCR6  0   0.268   2.4648   2.0626  -0.5422
 EFW  H2   H  HCR6  0   0.273   0.0629   1.6059  -0.5835
 EFW  H3   H  HCR6  0   0.250   3.0938  -2.0106   0.6414
 EFW  H5   H  HCH2  0   0.231  -2.4317   0.1795   1.8831
 EFW  H6   H  HCH2  0   0.241  -4.5171   1.5034   1.6212
 EFW  H7   H  HCH2  0   0.226  -4.0599   1.9336  -0.0309
 EFW  H8   H  HCH2  0   0.250  -3.5952  -0.4718  -1.7498
 EFW  H9   H  HCH2  0   0.249  -3.2683  -1.7736  -0.6203
 EFW  H10  H  HCR5  0   0.256  -1.8386   0.7734  -1.0297
 EFW  H11  H  HCR5  0   0.203  -4.6295  -0.8538   1.0393
 EFW  H12  H  HNH2  0   0.408   5.0094  -1.6366   0.0003
 EFW  H13  H  HNH2  0   0.403   6.3011  -0.5193   0.1050
 EFW  H14  H  HNH1  0   0.382  -1.1893  -1.7694   0.2767
 EFW  H15  H  HOH1  0   0.449  -6.4182   0.1396   0.0719
 EFW  H4   H  HCH2  0   0.247  -1.8933   1.7077   1.1885

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
 EFW  O13  C12  single    1.408  0.020  1.408
 EFW  C12  C11  single    1.529  0.020  1.529
 EFW  C12  C14  single    1.534  0.020  1.534
 EFW  C11  C10  single    1.522  0.020  1.522
 EFW  C14  C9   single    1.545  0.020  1.545
 EFW  C10  C9   single    1.539  0.020  1.539
 EFW  C9   N8   single    1.442  0.020  1.442
 EFW  N8   C7   single    1.348  0.020  1.348
 EFW  C6   C7   aromatic  1.411  0.020  1.411
 EFW  C6   C5   aromatic  1.372  0.020  1.372
 EFW  C7   N15  aromatic  1.340  0.020  1.340
 EFW  C5   C4   aromatic  1.400  0.020  1.400
 EFW  N15  C16  aromatic  1.320  0.020  1.320
 EFW  C4   C16  aromatic  1.391  0.020  1.391
 EFW  C4   C2   single    1.483  0.020  1.483
 EFW  C2   O3   double    1.226  0.020  1.226
 EFW  C2   N1   single    1.345  0.020  1.345
 EFW  C5   H1   single    0.930  0.020  1.080
 EFW  C6   H2   single    0.930  0.020  1.080
 EFW  C16  H3   single    0.930  0.020  1.080
 EFW  C10  H4   single    0.970  0.020  1.090
 EFW  C10  H5   single    0.970  0.020  1.090
 EFW  C11  H6   single    0.970  0.020  1.090
 EFW  C11  H7   single    0.970  0.020  1.090
 EFW  C14  H8   single    0.970  0.020  1.090
 EFW  C14  H9   single    0.970  0.020  1.090
 EFW  C9   H10  single    0.970  0.020  1.090
 EFW  C12  H11  single    0.970  0.020  1.090
 EFW  N1   H12  single    0.860  0.020  1.020
 EFW  N1   H13  single    0.860  0.020  1.020
 EFW  N8   H14  single    0.860  0.020  1.020
 EFW  O13  H15  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
 EFW  H1   C5   C4   119.95  3.000
 EFW  H1   C5   C6   119.41  3.000
 EFW  C4   C5   C6   120.64  3.000
 EFW  H2   C6   C7   121.39  3.000
 EFW  H2   C6   C5   120.12  3.000
 EFW  C7   C6   C5   118.49  3.000
 EFW  H3   C16  N15  114.47  3.000
 EFW  H3   C16  C4   120.95  3.000
 EFW  N15  C16  C4   124.58  3.000
 EFW  C2   C4   C16  124.48  3.000
 EFW  C2   C4   C5   119.41  3.000
 EFW  C16  C4   C5   116.09  3.000
 EFW  N8   C7   N15  115.83  3.000
 EFW  N15  C7   C6   121.22  3.000
 EFW  N8   C7   C6   122.95  3.000
 EFW  O3   C2   N1   121.98  3.000
 EFW  N1   C2   C4   116.98  3.000
 EFW  O3   C2   C4   121.04  3.000
 EFW  H5   C10  H4   107.61  3.000
 EFW  H5   C10  C9   109.45  3.000
 EFW  H4   C10  C9   112.85  3.000
 EFW  H5   C10  C11  110.14  3.000
 EFW  H4   C10  C11  113.90  3.000
 EFW  C9   C10  C11  102.82  3.000
 EFW  H7   C11  H6   107.87  3.000
 EFW  H7   C11  C12  109.63  3.000
 EFW  H6   C11  C12  113.05  3.000
 EFW  H7   C11  C10  110.45  3.000
 EFW  H6   C11  C10  113.51  3.000
 EFW  C12  C11  C10  102.25  3.000
 EFW  H9   C14  H8   106.96  3.000
 EFW  H9   C14  C12  111.66  3.000
 EFW  H8   C14  C12  110.08  3.000
 EFW  H9   C14  C9   111.82  3.000
 EFW  H8   C14  C9   110.35  3.000
 EFW  C12  C14  C9   106.01  3.000
 EFW  H10  C9   N8   108.20  3.000
 EFW  H10  C9   C14  107.98  3.000
 EFW  N8   C9   C14  112.00  3.000
 EFW  H10  C9   C10  108.29  3.000
 EFW  N8   C9   C10  115.07  3.000
 EFW  C14  C9   C10  105.04  3.000
 EFW  H11  C12  O13  110.36  3.000
 EFW  H11  C12  C14  108.44  3.000
 EFW  O13  C12  C14  110.34  3.000
 EFW  H11  C12  C11  107.64  3.000
 EFW  C14  C12  C11  104.32  3.000
 EFW  O13  C12  C11  115.40  3.000
 EFW  C7   N15  C16  118.95  3.000
 EFW  H13  N1   H12  116.61  3.000
 EFW  H13  N1   C2   119.30  3.000
 EFW  H12  N1   C2   123.05  3.000
 EFW  H14  N8   C9   117.26  3.000
 EFW  H14  N8   C7   115.14  3.000
 EFW  C9   N8   C7   125.58  3.000
 EFW  H15  O13  C12  108.10  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
 EFW  CONST_01  N15  C7   C6   C5     0.00   0.0  0
 EFW  CONST_02  N15  C16  C4   C5     0.00   0.0  0
 EFW  CONST_03  C16  N15  C7   C6     0.00   0.0  0
 EFW  CONST_04  C16  C4   C5   C6     0.00   0.0  0
 EFW  CONST_05  C7   C6   C5   C4     0.00   0.0  0
 EFW  CONST_06  C7   N15  C16  C4     0.00   0.0  0
 EFW  CONST_07  N8   C7   C6   C5   180.00   0.0  0
 EFW  CONST_08  C2   C4   C5   C6   180.00   0.0  0
 EFW  CONST_09  N8   C7   N15  C16  180.00   0.0  0
 EFW  CONST_10  N15  C16  C4   C2   180.00   0.0  0
 EFW  CONST_11  C9   N8   C7   C6     0.00   0.0  0
 EFW  CONST_12  N15  C7   N8   C9   180.00   0.0  0
 EFW  CONST_13  H3   C16  C4   C5   180.00   0.0  0
 EFW  CONST_14  H1   C5   C4   C16  180.00   0.0  0
 EFW  CONST_15  H2   C6   C5   C4   180.00   0.0  0
 EFW  CONST_16  H14  N8   C7   C6   180.00   0.0  0
 EFW  CONST_17  H12  N1   C2   C4     0.00   0.0  0
 EFW  CONST_18  H13  N1   C2   C4   180.00   0.0  0
 EFW  Var_01    C12  C11  C10  C9    44.05  30.0  1
 EFW  Var_02    O3   C2   C4   C5    12.47  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
 EFW  chir_01  C9   C14  C10  N8   negativ
 EFW  chir_02  C12  O13  C11  C14  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
 EFW  plan-1  C5   0.020
 EFW  plan-1  C6   0.020
 EFW  plan-1  C16  0.020
 EFW  plan-1  C4   0.020
 EFW  plan-1  C7   0.020
 EFW  plan-1  C2   0.020
 EFW  plan-1  N15  0.020
 EFW  plan-1  N8   0.020
 EFW  plan-1  H1   0.020
 EFW  plan-1  H2   0.020
 EFW  plan-1  H3   0.020
 EFW  plan-2  C7   0.020
 EFW  plan-2  C9   0.020
 EFW  plan-2  N8   0.020
 EFW  plan-2  H14  0.020
 EFW  plan-3  C4   0.020
 EFW  plan-3  C2   0.020
 EFW  plan-3  N1   0.020
 EFW  plan-3  O3   0.020
 EFW  plan-3  H12  0.020
 EFW  plan-3  H13  0.020

