# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 07:18:40 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-[2-(3-chlorophenyl)ethyl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncccc1CCc2cccc(Cl)c2
#
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
 D8Y  D8Y  3-[2-(3-chlorophenyl)ethyl]pyridin-2-amine  ligand  29  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_D8Y
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
 D8Y  C1    C   CR16  0  -0.074  -5.0703  -0.8193   0.2954
 D8Y  N1    N   N     0  -0.453  -4.6463   0.4400   0.2584
 D8Y  CL1   CL  CL    0  -0.134   4.6295  -1.5118  -0.0631
 D8Y  C2    C   CR6   0   0.391  -3.3712   0.6803  -0.0333
 D8Y  N2    N   NH2   0  -0.831  -2.9759   1.9909   0.0015
 D8Y  C3    C   CR6   0   0.007  -2.4476  -0.3517  -0.3160
 D8Y  C4    C   CR16  0  -0.204  -2.9266  -1.6465  -0.2746
 D8Y  C5    C   CR16  0  -0.352  -4.2595  -1.9054   0.0357
 D8Y  C6    C   CH2   0  -0.535  -0.9996  -0.0663  -0.5869
 D8Y  C7    C   CH2   0  -0.509  -0.2134   0.2262   0.7025
 D8Y  C8    C   CR6   0   0.130   1.2279   0.5306   0.4112
 D8Y  C9    C   CR16  0  -0.301   1.6457   1.8353   0.1602
 D8Y  C10   C   CR16  0  -0.245   2.9690   2.1072  -0.1548
 D8Y  C11   C   CR16  0  -0.234   3.9025   1.0827  -0.2290
 D8Y  C12   C   CR6   0  -0.021   3.4798  -0.2135   0.0197
 D8Y  C13   C   CR16  0  -0.270   2.1617  -0.4997   0.3369
 D8Y  H1    H   HCR6  0   0.254  -6.1174  -0.9615   0.5416
 D8Y  HN2   H   HNH2  0   0.382  -3.7258   2.6630  -0.0285
 D8Y  HN2A  H   HNH2  0   0.386  -2.1864   2.2579  -0.5626
 D8Y  H4    H   HCR6  0   0.257  -2.2497  -2.4670  -0.4839
 D8Y  H5    H   HCR6  0   0.256  -4.6476  -2.9134   0.0740
 D8Y  H6    H   HCH2  0   0.266  -0.5509  -0.9275  -1.0872
 D8Y  H6A   H   HCH2  0   0.250  -0.8818   0.7704  -1.2831
 D8Y  H7    H   HCH2  0   0.256  -0.6688   1.0664   1.2317
 D8Y  H7A   H   HCH2  0   0.258  -0.2893  -0.6404   1.3624
 D8Y  H9    H   HCR6  0   0.253   0.9300   2.6467   0.2172
 D8Y  H10   H   HCR6  0   0.266   3.2827   3.1255  -0.3440
 D8Y  H11   H   HCR6  0   0.278   4.9354   1.2920  -0.4712
 D8Y  H13   H   HCR6  0   0.271   1.8588  -1.5211   0.5311

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
 D8Y  C5   C1    aromatic  1.380  0.020  1.380
 D8Y  N1   C1    aromatic  1.329  0.020  1.329
 D8Y  C1   H1    single    0.930  0.020  1.080
 D8Y  C2   N1    aromatic  1.330  0.020  1.330
 D8Y  CL1  C12   single    1.736  0.020  1.736
 D8Y  C3   C2    aromatic  1.413  0.020  1.413
 D8Y  N2   C2    single    1.369  0.020  1.369
 D8Y  N2   HN2   single    0.890  0.020  1.040
 D8Y  N2   HN2A  single    0.890  0.020  1.040
 D8Y  C6   C3    single    1.501  0.020  1.501
 D8Y  C3   C4    aromatic  1.381  0.020  1.381
 D8Y  C4   C5    aromatic  1.393  0.020  1.393
 D8Y  C4   H4    single    0.930  0.020  1.080
 D8Y  C5   H5    single    0.930  0.020  1.080
 D8Y  C7   C6    single    1.538  0.020  1.538
 D8Y  C6   H6    single    0.970  0.020  1.090
 D8Y  C6   H6A   single    0.970  0.020  1.090
 D8Y  C8   C7    single    1.502  0.020  1.502
 D8Y  C7   H7    single    0.970  0.020  1.090
 D8Y  C7   H7A   single    0.970  0.020  1.090
 D8Y  C13  C8    aromatic  1.392  0.020  1.392
 D8Y  C8   C9    aromatic  1.393  0.020  1.393
 D8Y  C10  C9    aromatic  1.387  0.020  1.387
 D8Y  C9   H9    single    0.930  0.020  1.080
 D8Y  C11  C10   aromatic  1.388  0.020  1.388
 D8Y  C10  H10   single    0.930  0.020  1.080
 D8Y  C12  C11   aromatic  1.386  0.020  1.386
 D8Y  C11  H11   single    0.930  0.020  1.080
 D8Y  C12  C13   aromatic  1.386  0.020  1.386
 D8Y  C13  H13   single    0.930  0.020  1.080

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
 D8Y  H1    C1   C5   120.43  3.000
 D8Y  H1    C1   N1   116.00  3.000
 D8Y  C5    C1   N1   123.57  3.000
 D8Y  C2    N1   C1   118.89  3.000
 D8Y  C3    C2   N2   121.01  3.000
 D8Y  N2    C2   N1   116.37  3.000
 D8Y  C3    C2   N1   122.57  3.000
 D8Y  HN2A  N2   HN2  112.97  3.000
 D8Y  HN2A  N2   C2   117.79  3.000
 D8Y  HN2   N2   C2   115.01  3.000
 D8Y  C6    C3   C4   121.22  3.000
 D8Y  C4    C3   C2   116.86  3.000
 D8Y  C6    C3   C2   121.86  3.000
 D8Y  H4    C4   C5   120.00  3.000
 D8Y  H4    C4   C3   119.15  3.000
 D8Y  C5    C4   C3   120.85  3.000
 D8Y  H5    C5   C4   121.66  3.000
 D8Y  H5    C5   C1   121.09  3.000
 D8Y  C4    C5   C1   117.25  3.000
 D8Y  H6A   C6   H6   105.49  3.000
 D8Y  H6A   C6   C7   109.43  3.000
 D8Y  H6    C6   C7   108.90  3.000
 D8Y  H6A   C6   C3   111.34  3.000
 D8Y  H6    C6   C3   109.22  3.000
 D8Y  C7    C6   C3   112.21  3.000
 D8Y  H7A   C7   H7   106.78  3.000
 D8Y  H7A   C7   C8   110.17  3.000
 D8Y  H7    C7   C8   109.77  3.000
 D8Y  H7A   C7   C6   108.67  3.000
 D8Y  H7    C7   C6   109.84  3.000
 D8Y  C8    C7   C6   111.50  3.000
 D8Y  C13   C8   C9   118.84  3.000
 D8Y  C9    C8   C7   120.85  3.000
 D8Y  C13   C8   C7   120.27  3.000
 D8Y  H9    C9   C10  119.69  3.000
 D8Y  H9    C9   C8   119.60  3.000
 D8Y  C10   C9   C8   120.71  3.000
 D8Y  H10   C10  C11  119.35  3.000
 D8Y  H10   C10  C9   120.04  3.000
 D8Y  C11   C10  C9   120.60  3.000
 D8Y  H11   C11  C12  120.83  3.000
 D8Y  H11   C11  C10  120.77  3.000
 D8Y  C12   C11  C10  118.40  3.000
 D8Y  C13   C12  C11  121.62  3.000
 D8Y  C13   C12  CL1  119.11  3.000
 D8Y  C11   C12  CL1  119.27  3.000
 D8Y  H13   C13  C12  120.12  3.000
 D8Y  H13   C13  C8   120.05  3.000
 D8Y  C12   C13  C8   119.82  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
 D8Y  CONST_01  C3   C4   C5   C1      0.00   0.0  0
 D8Y  CONST_02  C3   C2   N1   C1      0.00   0.0  0
 D8Y  CONST_03  C4   C5   C1   N1      0.00   0.0  0
 D8Y  CONST_04  C4   C3   C2   N1      0.00   0.0  0
 D8Y  CONST_05  C5   C1   N1   C2      0.00   0.0  0
 D8Y  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 D8Y  CONST_07  C11  C12  C13  C8      0.00   0.0  0
 D8Y  CONST_08  C11  C10  C9   C8      0.00   0.0  0
 D8Y  CONST_09  C12  C13  C8   C9      0.00   0.0  0
 D8Y  CONST_10  C12  C11  C10  C9      0.00   0.0  0
 D8Y  CONST_11  C13  C8   C9   C10     0.00   0.0  0
 D8Y  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 D8Y  CONST_13  N2   C2   N1   C1    180.00   0.0  0
 D8Y  CONST_14  C6   C3   C2   N1    180.00   0.0  0
 D8Y  CONST_15  C10  C11  C12  CL1   180.00   0.0  0
 D8Y  CONST_16  C8   C13  C12  CL1   180.00   0.0  0
 D8Y  CONST_17  C4   C3   C2   N2    180.00   0.0  0
 D8Y  CONST_18  C6   C3   C4   C5    180.00   0.0  0
 D8Y  CONST_19  C12  C13  C8   C7    180.00   0.0  0
 D8Y  CONST_20  C10  C9   C8   C7    180.00   0.0  0
 D8Y  CONST_21  H4   C4   C5   C1    180.00   0.0  0
 D8Y  CONST_22  H5   C5   C1   N1    180.00   0.0  0
 D8Y  CONST_23  H1   C1   N1   C2    180.00   0.0  0
 D8Y  CONST_24  H10  C10  C9   C8    180.00   0.0  0
 D8Y  CONST_25  H13  C13  C8   C9    180.00   0.0  0
 D8Y  CONST_26  H11  C11  C10  C9    180.00   0.0  0
 D8Y  CONST_27  H9   C9   C10  C11   180.00   0.0  0
 D8Y  Var_01    C7   C6   C3   C2     77.36  30.0  2
 D8Y  Var_02    C8   C7   C6   C3   -179.11  30.0  2
 D8Y  Var_03    C13  C8   C7   C6    -88.04  30.0  2

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
 D8Y  plan-1  C1    0.020
 D8Y  plan-1  N1    0.020
 D8Y  plan-1  C2    0.020
 D8Y  plan-1  N2    0.020
 D8Y  plan-1  C3    0.020
 D8Y  plan-1  C4    0.020
 D8Y  plan-1  C5    0.020
 D8Y  plan-1  C6    0.020
 D8Y  plan-1  H1    0.020
 D8Y  plan-1  H4    0.020
 D8Y  plan-1  H5    0.020
 D8Y  plan-2  CL1   0.020
 D8Y  plan-2  C7    0.020
 D8Y  plan-2  C8    0.020
 D8Y  plan-2  C9    0.020
 D8Y  plan-2  C10   0.020
 D8Y  plan-2  C11   0.020
 D8Y  plan-2  C12   0.020
 D8Y  plan-2  C13   0.020
 D8Y  plan-2  H9    0.020
 D8Y  plan-2  H10   0.020
 D8Y  plan-2  H11   0.020
 D8Y  plan-2  H13   0.020
 D8Y  plan-3  C2    0.020
 D8Y  plan-3  N2    0.020
 D8Y  plan-3  HN2   0.020
 D8Y  plan-3  HN2A  0.020

