# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 00:40:46 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 6-{[(1R,3S)-3-phenylcyclopentyl]amino}pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(N[C@@H]2CC[C@@H](C2)c3ccccc3)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
 58G  58G  6-{[(1R,3S)-3-phenylcyclopentyl]amino}pyridine-3-carboxamide  ligand  40  21  .  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_58G
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
 58G  C17  C  CR16  0  -0.276   6.8712   0.8239  -0.0538
 58G  C16  C  CR16  0  -0.237   5.8153   1.5838   0.4360
 58G  C18  C  CR16  0  -0.237   6.6218  -0.4437  -0.5596
 58G  C5   C  CR16  0  -0.151  -3.7684  -1.0681  -0.0308
 58G  C15  C  CR16  0  -0.328   4.5238   1.0776   0.4202
 58G  C19  C  CR16  0  -0.339   5.3256  -0.9452  -0.5740
 58G  C6   C  CR16  0  -0.390  -2.4076  -0.9490  -0.1527
 58G  C21  C  CR16  0  -0.071  -3.9327   1.2923  -0.1075
 58G  C4   C  CR6   0  -0.168  -4.5862   0.0677  -0.0063
 58G  C14  C  CR6   0   0.202   4.2587  -0.1959  -0.0849
 58G  C7   C  CR6   0   0.510  -1.8526   0.3444  -0.2582
 58G  C11  C  CH2   0  -0.420   2.2212  -0.9089   1.2919
 58G  C10  C  CH2   0  -0.462   0.7375  -1.1376   0.9909
 58G  C13  C  CH2   0  -0.452   1.8306   0.0943  -0.8334
 58G  C12  C  CR15  0  -0.353   2.8629  -0.7561  -0.0919
 58G  C9   C  CR15  0  -0.068   0.4782  -0.4764  -0.3924
 58G  N20  N  N     0  -0.466  -2.6265   1.4383  -0.2287
 58G  N1   N  NH2   0  -0.830  -6.8102   1.0036   0.1564
 58G  N8   N  NH1   0  -0.661  -0.5322   0.5546  -0.4004
 58G  O3   O  O     0  -0.494  -6.5479  -1.2263   0.2103
 58G  H1   H  HCR6  0   0.253   7.8793   1.2177  -0.0392
 58G  H2   H  HCR6  0   0.253   6.0004   2.5738   0.8331
 58G  H3   H  HCR6  0   0.252   7.4358  -1.0457  -0.9434
 58G  H4   H  HCR6  0   0.268  -4.2103  -2.0521   0.0526
 58G  H5   H  HCR6  0   0.246   3.7142   1.6859   0.8080
 58G  H6   H  HCR6  0   0.246   5.1399  -1.9364  -0.9719
 58G  H7   H  HCR6  0   0.273  -1.7815  -1.8298  -0.1586
 58G  H8   H  HCR6  0   0.247  -4.4844   2.2279  -0.0900
 58G  H9   H  HCH2  0   0.229   2.3548   0.0123   1.8658
 58G  H10  H  HCH2  0   0.244   2.6679  -1.7173   1.8722
 58G  H11  H  HCH2  0   0.238   0.5197  -2.2054   0.9359
 58G  H12  H  HCH2  0   0.245   0.0902  -0.7179   1.7620
 58G  H13  H  HCH2  0   0.236   1.9195   1.1364  -0.5080
 58G  H14  H  HCH2  0   0.261   1.9586   0.0790  -1.9160
 58G  H15  H  HCR5  0   0.252   2.8955  -1.7445  -0.5633
 58G  H16  H  HCR5  0   0.257   0.1806  -1.2525  -1.1038
 58G  H17  H  HNH2  0   0.410  -6.4413   1.9331   0.0722
 58G  H18  H  HNH2  0   0.403  -7.8108   0.9181   0.2215
 58G  H19  H  HNH1  0   0.385  -0.2348   1.5179  -0.3898
 58G  C2   C  C     0   0.493  -6.0538  -0.1064   0.1276

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
 58G  C19  C18  aromatic  1.390  0.020  1.390
 58G  C19  C14  aromatic  1.392  0.020  1.392
 58G  C18  C17  aromatic  1.387  0.020  1.387
 58G  C12  C14  single    1.504  0.020  1.504
 58G  C12  C11  single    1.533  0.020  1.533
 58G  C12  C13  single    1.529  0.020  1.529
 58G  C14  C15  aromatic  1.395  0.020  1.395
 58G  C17  C16  aromatic  1.390  0.020  1.390
 58G  C11  C10  single    1.531  0.020  1.531
 58G  C15  C16  aromatic  1.387  0.020  1.387
 58G  C13  C9   single    1.533  0.020  1.533
 58G  C10  C9   single    1.555  0.020  1.555
 58G  C9   N8   single    1.444  0.020  1.444
 58G  N8   C7   single    1.345  0.020  1.345
 58G  N20  C7   aromatic  1.340  0.020  1.340
 58G  N20  C21  aromatic  1.320  0.020  1.320
 58G  C7   C6   aromatic  1.411  0.020  1.411
 58G  C21  C4   aromatic  1.392  0.020  1.392
 58G  C6   C5   aromatic  1.371  0.020  1.371
 58G  C4   C5   aromatic  1.400  0.020  1.400
 58G  C4   C2   single    1.484  0.020  1.484
 58G  O3   C2   double    1.227  0.020  1.227
 58G  C2   N1   single    1.344  0.020  1.344
 58G  C17  H1   single    0.930  0.020  1.080
 58G  C16  H2   single    0.930  0.020  1.080
 58G  C18  H3   single    0.930  0.020  1.080
 58G  C5   H4   single    0.930  0.020  1.080
 58G  C15  H5   single    0.930  0.020  1.080
 58G  C19  H6   single    0.930  0.020  1.080
 58G  C6   H7   single    0.930  0.020  1.080
 58G  C21  H8   single    0.930  0.020  1.080
 58G  C11  H9   single    0.970  0.020  1.090
 58G  C11  H10  single    0.970  0.020  1.090
 58G  C10  H11  single    0.970  0.020  1.090
 58G  C10  H12  single    0.970  0.020  1.090
 58G  C13  H13  single    0.970  0.020  1.090
 58G  C13  H14  single    0.970  0.020  1.090
 58G  C12  H15  single    0.970  0.020  1.090
 58G  C9   H16  single    0.970  0.020  1.090
 58G  N1   H17  single    0.860  0.020  1.020
 58G  N1   H18  single    0.860  0.020  1.020
 58G  N8   H19  single    0.860  0.020  1.020

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
 58G  H1   C17  C18  120.32  3.000
 58G  H1   C17  C16  120.25  3.000
 58G  C18  C17  C16  119.43  3.000
 58G  H2   C16  C15  119.80  3.000
 58G  H2   C16  C17  119.95  3.000
 58G  C15  C16  C17  120.25  3.000
 58G  H3   C18  C19  119.79  3.000
 58G  H3   C18  C17  120.13  3.000
 58G  C19  C18  C17  120.07  3.000
 58G  H4   C5   C4   119.87  3.000
 58G  H4   C5   C6   119.42  3.000
 58G  C4   C5   C6   120.71  3.000
 58G  H5   C15  C14  119.97  3.000
 58G  H5   C15  C16  119.10  3.000
 58G  C14  C15  C16  120.93  3.000
 58G  H6   C19  C14  119.32  3.000
 58G  H6   C19  C18  119.57  3.000
 58G  C14  C19  C18  121.11  3.000
 58G  H7   C6   C7   121.25  3.000
 58G  H7   C6   C5   120.30  3.000
 58G  C7   C6   C5   118.45  3.000
 58G  H8   C21  N20  114.13  3.000
 58G  H8   C21  C4   121.21  3.000
 58G  N20  C21  C4   124.66  3.000
 58G  C2   C4   C21  125.04  3.000
 58G  C2   C4   C5   118.96  3.000
 58G  C21  C4   C5   116.00  3.000
 58G  C12  C14  C19  120.59  3.000
 58G  C12  C14  C15  121.19  3.000
 58G  C19  C14  C15  118.21  3.000
 58G  N8   C7   N20  116.22  3.000
 58G  N20  C7   C6   121.28  3.000
 58G  N8   C7   C6   122.50  3.000
 58G  H10  C11  H9   107.17  3.000
 58G  H10  C11  C12  112.50  3.000
 58G  H9   C11  C12  109.80  3.000
 58G  H10  C11  C10  113.00  3.000
 58G  H9   C11  C10  110.33  3.000
 58G  C12  C11  C10  104.06  3.000
 58G  H12  C10  H11  107.08  3.000
 58G  H12  C10  C9   111.49  3.000
 58G  H11  C10  C9   109.76  3.000
 58G  H12  C10  C11  112.25  3.000
 58G  H11  C10  C11  110.45  3.000
 58G  C9   C10  C11  105.84  3.000
 58G  H14  C13  H13  107.39  3.000
 58G  H14  C13  C9   112.59  3.000
 58G  H13  C13  C9   109.90  3.000
 58G  H14  C13  C12  113.23  3.000
 58G  H13  C13  C12  109.28  3.000
 58G  C9   C13  C12  104.42  3.000
 58G  H15  C12  C13  108.25  3.000
 58G  H15  C12  C11  108.11  3.000
 58G  C13  C12  C11  102.16  3.000
 58G  H15  C12  C14  108.09  3.000
 58G  C13  C12  C14  114.93  3.000
 58G  C11  C12  C14  114.92  3.000
 58G  H16  C9   N8   108.21  3.000
 58G  H16  C9   C13  108.48  3.000
 58G  N8   C9   C13  110.49  3.000
 58G  H16  C9   C10  108.79  3.000
 58G  N8   C9   C10  115.17  3.000
 58G  C13  C9   C10  105.50  3.000
 58G  C7   N20  C21  118.89  3.000
 58G  H18  N1   H17  116.72  3.000
 58G  H18  N1   C2   119.40  3.000
 58G  H17  N1   C2   123.81  3.000
 58G  H19  N8   C9   118.41  3.000
 58G  H19  N8   C7   115.97  3.000
 58G  C9   N8   C7   125.11  3.000
 58G  O3   C2   N1   121.73  3.000
 58G  N1   C2   C4   117.50  3.000
 58G  O3   C2   C4   120.76  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
 58G  CONST_01  C14  C19  C18  C17    0.00   0.0  0
 58G  CONST_02  C14  C15  C16  C17    0.00   0.0  0
 58G  CONST_03  C19  C18  C17  C16    0.00   0.0  0
 58G  CONST_04  C19  C14  C15  C16    0.00   0.0  0
 58G  CONST_05  C15  C14  C19  C18    0.00   0.0  0
 58G  CONST_06  C15  C16  C17  C18    0.00   0.0  0
 58G  CONST_07  N20  C7   C6   C5     0.00   0.0  0
 58G  CONST_08  N20  C21  C4   C5     0.00   0.0  0
 58G  CONST_09  C21  N20  C7   C6     0.00   0.0  0
 58G  CONST_10  C21  C4   C5   C6     0.00   0.0  0
 58G  CONST_11  C7   N20  C21  C4     0.00   0.0  0
 58G  CONST_12  C7   C6   C5   C4     0.00   0.0  0
 58G  CONST_13  C12  C14  C15  C16  180.00   0.0  0
 58G  CONST_14  C12  C14  C19  C18  180.00   0.0  0
 58G  CONST_15  N8   C7   C6   C5   180.00   0.0  0
 58G  CONST_16  C2   C4   C5   C6   180.00   0.0  0
 58G  CONST_17  N8   C7   N20  C21  180.00   0.0  0
 58G  CONST_18  N20  C21  C4   C2   180.00   0.0  0
 58G  CONST_19  C9   N8   C7   C6     0.00   0.0  0
 58G  CONST_20  N20  C7   N8   C9   180.00   0.0  0
 58G  CONST_21  H6   C19  C18  C17  180.00   0.0  0
 58G  CONST_22  H5   C15  C16  C17  180.00   0.0  0
 58G  CONST_23  H3   C18  C17  C16  180.00   0.0  0
 58G  CONST_24  H2   C16  C17  C18  180.00   0.0  0
 58G  CONST_25  H8   C21  C4   C5   180.00   0.0  0
 58G  CONST_26  H1   C17  C16  C15  180.00   0.0  0
 58G  CONST_27  H4   C5   C4   C21  180.00   0.0  0
 58G  CONST_28  H7   C6   C5   C4   180.00   0.0  0
 58G  CONST_29  H19  N8   C7   C6   180.00   0.0  0
 58G  CONST_30  H17  N1   C2   C4     0.00   0.0  0
 58G  CONST_31  H18  N1   C2   C4   180.00   0.0  0
 58G  Var_01    C9   C10  C11  C12  -25.55  30.0  1
 58G  Var_02    O3   C2   C4   C5    -0.30  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
 58G  chir_01  C12  C14  C11  C13  negativ
 58G  chir_02  C9   N8   C10  C13  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
 58G  plan-1  C17  0.020
 58G  plan-1  C16  0.020
 58G  plan-1  C18  0.020
 58G  plan-1  C15  0.020
 58G  plan-1  C19  0.020
 58G  plan-1  C14  0.020
 58G  plan-1  C12  0.020
 58G  plan-1  H1   0.020
 58G  plan-1  H2   0.020
 58G  plan-1  H3   0.020
 58G  plan-1  H5   0.020
 58G  plan-1  H6   0.020
 58G  plan-2  C5   0.020
 58G  plan-2  C6   0.020
 58G  plan-2  C21  0.020
 58G  plan-2  C4   0.020
 58G  plan-2  C7   0.020
 58G  plan-2  N20  0.020
 58G  plan-2  N8   0.020
 58G  plan-2  H4   0.020
 58G  plan-2  H7   0.020
 58G  plan-2  H8   0.020
 58G  plan-2  C2   0.020
 58G  plan-3  C7   0.020
 58G  plan-3  C9   0.020
 58G  plan-3  N8   0.020
 58G  plan-3  H19  0.020
 58G  plan-4  C4   0.020
 58G  plan-4  N1   0.020
 58G  plan-4  O3   0.020
 58G  plan-4  H17  0.020
 58G  plan-4  H18  0.020
 58G  plan-4  C2   0.020

