# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:01:04 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: [1-(pyridin-2-yl)cyclopentyl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1(CCCC1)c2ccccn2
#
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
 T5D  T5D  '[1-(pyridin-2-yl)cyclopentyl]methanol'  ligand  28  13  .  2021-08-23  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_T5D
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
 T5D  C4   C  CR16  0  -0.335   3.4221   0.3024   0.0917
 T5D  C5   C  CR16  0  -0.153   2.7625  -0.3284   1.1350
 T5D  C6   C  CR16  0  -0.350   1.3816  -0.4393   1.0886
 T5D  C7   C  CH2   0  -0.444  -1.5488  -0.3242   1.1753
 T5D  C8   C  CH2   0  -0.448  -2.9608   0.2015   0.9462
 T5D  C10  C  CH2   0  -0.430  -1.4601   1.3116  -0.6270
 T5D  N    N  N     0  -0.417   1.3328   0.6884  -1.0018
 T5D  C    C  CH2   0  -0.132  -1.0995  -1.0950  -1.1862
 T5D  O    O  OH1   0  -0.668  -0.5429  -2.3184  -0.7703
 T5D  C1   C  CT    0  -0.154  -0.8107  -0.0139  -0.1392
 T5D  C2   C  CR6   0   0.296   0.6915   0.0914   0.0014
 T5D  C3   C  CR16  0  -0.087   2.6544   0.7900  -0.9544
 T5D  C9   C  CH2   0  -0.442  -2.7193   1.5305   0.2313
 T5D  H4   H  HCR6  0   0.265   4.4977   0.4138   0.0838
 T5D  H5   H  HCR6  0   0.268   3.3142  -0.7319   1.9743
 T5D  H6   H  HCR6  0   0.266   0.8514  -0.9316   1.8914
 T5D  H7   H  HCH2  0   0.228  -1.0936   0.2362   1.9978
 T5D  H8   H  HCH2  0   0.240  -1.5149  -1.3802   1.4466
 T5D  H9   H  HCH2  0   0.220  -3.5309  -0.4818   0.3115
 T5D  H10  H  HCH2  0   0.234  -3.5227   0.3158   1.8744
 T5D  H14  H  HCH2  0   0.239  -0.7668   2.1465  -0.5305
 T5D  H13  H  HCH2  0   0.230  -1.7076   1.2480  -1.6891
 T5D  H2   H  HCH2  0   0.203  -0.6761  -0.7630  -2.1436
 T5D  H1   H  HCH2  0   0.207  -2.1854  -1.1761  -1.3292
 T5D  H    H  HOH1  0   0.454  -0.7788  -2.9895  -1.4169
 T5D  H3   H  HCR6  0   0.256   3.1289   1.2867  -1.7940
 T5D  H11  H  HCH2  0   0.231  -3.5768   1.8561  -0.3591
 T5D  H12  H  HCH2  0   0.223  -2.5334   2.3102   0.9732

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
 T5D  C    O    single    1.407  0.020  1.407
 T5D  C1   C    single    1.532  0.020  1.532
 T5D  C2   C1   single    1.512  0.020  1.512
 T5D  C2   N    aromatic  1.332  0.020  1.332
 T5D  N    C3   aromatic  1.326  0.020  1.326
 T5D  C3   C4   aromatic  1.386  0.020  1.386
 T5D  C4   C5   aromatic  1.386  0.020  1.386
 T5D  C5   C6   aromatic  1.386  0.020  1.386
 T5D  C6   C2   aromatic  1.393  0.020  1.393
 T5D  C1   C7   single    1.539  0.020  1.539
 T5D  C7   C8   single    1.524  0.020  1.524
 T5D  C8   C9   single    1.528  0.020  1.528
 T5D  C9   C10  single    1.540  0.020  1.540
 T5D  C10  C1   single    1.555  0.020  1.555
 T5D  C4   H4   single    0.930  0.020  1.080
 T5D  C5   H5   single    0.930  0.020  1.080
 T5D  C6   H6   single    0.930  0.020  1.080
 T5D  C7   H7   single    0.970  0.020  1.090
 T5D  C7   H8   single    0.970  0.020  1.090
 T5D  C8   H9   single    0.970  0.020  1.090
 T5D  C8   H10  single    0.970  0.020  1.090
 T5D  C10  H14  single    0.970  0.020  1.090
 T5D  C10  H13  single    0.970  0.020  1.090
 T5D  C    H2   single    0.970  0.020  1.090
 T5D  C    H1   single    0.970  0.020  1.090
 T5D  O    H    single    0.850  0.020  0.980
 T5D  C3   H3   single    0.930  0.020  1.080
 T5D  C9   H11  single    0.970  0.020  1.090
 T5D  C9   H12  single    0.970  0.020  1.090

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
 T5D  H4   C4   C3   120.61  3.000
 T5D  H4   C4   C5   121.71  3.000
 T5D  C3   C4   C5   117.67  3.000
 T5D  H5   C5   C6   120.27  3.000
 T5D  H5   C5   C4   120.71  3.000
 T5D  C6   C5   C4   119.03  3.000
 T5D  H6   C6   C2   120.69  3.000
 T5D  H6   C6   C5   120.02  3.000
 T5D  C2   C6   C5   119.30  3.000
 T5D  H8   C7   H7   107.21  3.000
 T5D  H8   C7   C1   113.12  3.000
 T5D  H7   C7   C1   109.82  3.000
 T5D  H8   C7   C8   113.59  3.000
 T5D  H7   C7   C8   108.77  3.000
 T5D  C1   C7   C8   104.27  3.000
 T5D  H10  C8   H9   106.91  3.000
 T5D  H10  C8   C9   112.84  3.000
 T5D  H9   C8   C9   110.76  3.000
 T5D  H10  C8   C7   112.67  3.000
 T5D  H9   C8   C7   110.79  3.000
 T5D  C9   C8   C7   102.94  3.000
 T5D  H13  C10  H14  105.95  3.000
 T5D  H13  C10  C9   111.41  3.000
 T5D  H14  C10  C9   111.24  3.000
 T5D  H13  C10  C1   110.49  3.000
 T5D  H14  C10  C1   111.09  3.000
 T5D  C9   C10  C1   106.74  3.000
 T5D  C3   N    C2   119.16  3.000
 T5D  H1   C    H2   106.86  3.000
 T5D  H1   C    C1   109.11  3.000
 T5D  H2   C    C1   108.04  3.000
 T5D  H1   C    O    111.44  3.000
 T5D  H2   C    O    111.60  3.000
 T5D  C1   C    O    109.68  3.000
 T5D  H    O    C    108.13  3.000
 T5D  C2   C1   C    107.45  3.000
 T5D  C2   C1   C10  112.63  3.000
 T5D  C    C1   C10  107.96  3.000
 T5D  C10  C1   C7   103.86  3.000
 T5D  C2   C1   C7   114.27  3.000
 T5D  C    C1   C7   110.54  3.000
 T5D  C1   C2   N    116.07  3.000
 T5D  N    C2   C6   121.34  3.000
 T5D  C1   C2   C6   122.56  3.000
 T5D  H3   C3   N    116.32  3.000
 T5D  H3   C3   C4   120.18  3.000
 T5D  N    C3   C4   123.50  3.000
 T5D  H12  C9   H11  106.76  3.000
 T5D  H12  C9   C10  109.93  3.000
 T5D  H11  C9   C10  112.56  3.000
 T5D  H12  C9   C8   109.27  3.000
 T5D  H11  C9   C8   112.87  3.000
 T5D  C10  C9   C8   105.45  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
 T5D  CONST_01  C2   N    C3  C4    0.00   0.0  0
 T5D  CONST_02  C2   C6   C5  C4    0.00   0.0  0
 T5D  CONST_03  N    C3   C4  C5    0.00   0.0  0
 T5D  CONST_04  N    C2   C6  C5    0.00   0.0  0
 T5D  CONST_05  C3   C4   C5  C6    0.00   0.0  0
 T5D  CONST_06  C3   N    C2  C6    0.00   0.0  0
 T5D  CONST_07  C1   C2   C6  C5  180.00   0.0  0
 T5D  CONST_08  C3   N    C2  C1  180.00   0.0  0
 T5D  CONST_09  H6   C6   C5  C4  180.00   0.0  0
 T5D  CONST_10  H3   C3   C4  C5  180.00   0.0  0
 T5D  CONST_11  H4   C4   C5  C6  180.00   0.0  0
 T5D  CONST_12  H5   C5   C6  C2  180.00   0.0  0
 T5D  Var_01    C10  C9   C8  C7   33.57  30.0  1
 T5D  Var_02    C1   C10  C9  C8  -13.11  30.0  1
 T5D  Var_03    C9   C8   C7  C1  -41.65  30.0  1

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
 T5D  chir_01  C1  C2  C7  C10  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
 T5D  plan-1  C4  0.020
 T5D  plan-1  C5  0.020
 T5D  plan-1  C6  0.020
 T5D  plan-1  N   0.020
 T5D  plan-1  C1  0.020
 T5D  plan-1  C2  0.020
 T5D  plan-1  C3  0.020
 T5D  plan-1  H4  0.020
 T5D  plan-1  H5  0.020
 T5D  plan-1  H6  0.020
 T5D  plan-1  H3  0.020

