# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 09:31:40 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (6-phenylpyridin-3-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(nc1)c2ccccc2
#
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
 JAH  JAH  (6-phenylpyridin-3-yl)methanamine  ligand  26  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JAH
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
 JAH  C10  C  CR16  0  -0.287  -2.2758   1.1704   0.1006
 JAH  C13  C  CR16  0  -0.238  -3.7016  -1.2033  -0.0298
 JAH  N01  N  NH2   0  -0.791   4.8145  -0.3415   0.7661
 JAH  C03  C  CR6   0   0.019   2.6424   0.0727  -0.2667
 JAH  C04  C  CR16  0  -0.169   2.0289  -1.0933   0.1798
 JAH  C05  C  CR16  0  -0.327   0.6502  -1.1527   0.2638
 JAH  C06  C  CR6   0   0.218  -0.1055  -0.0367  -0.1013
 JAH  N07  N  N     0  -0.425   0.4796   1.0867  -0.5088
 JAH  C08  C  CR16  0  -0.122   1.8019   1.1324  -0.5833
 JAH  C09  C  CR6   0   0.077  -1.5835  -0.0351  -0.0309
 JAH  C11  C  CR16  0  -0.240  -3.6598   1.1873   0.1761
 JAH  C12  C  CR16  0  -0.263  -4.3790   0.0004   0.1111
 JAH  C14  C  CR16  0  -0.322  -2.3161  -1.2211  -0.0993
 JAH  H1   H  HCR6  0   0.251  -1.7215   2.0979   0.1529
 JAH  H2   H  HCR6  0   0.259  -4.2532  -2.1323  -0.0934
 JAH  H3   H  HNH2  0   0.355   5.8118  -0.3533   0.5958
 JAH  H4   H  HNH2  0   0.345   4.6714   0.2811   1.5513
 JAH  H6   H  HCH2  0   0.219   4.3846   1.2341  -0.6341
 JAH  H7   H  HCH2  0   0.244   4.4550  -0.3940  -1.2704
 JAH  H8   H  HCR6  0   0.263   2.6271  -1.9467   0.4725
 JAH  H9   H  HCR6  0   0.266   0.1722  -2.0513   0.6286
 JAH  H10  H  HCR6  0   0.253   2.2285   2.0745  -0.9161
 JAH  H11  H  HCR6  0   0.257  -4.1788   2.1305   0.2898
 JAH  H12  H  HCR6  0   0.259  -5.4597   0.0134   0.1670
 JAH  H13  H  HCR6  0   0.253  -1.8097  -2.1692  -0.2288
 JAH  C02  C  CH2   0  -0.353   4.1346   0.1901  -0.4030

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
 JAH  N01  C02  single    1.453  0.020  1.453
 JAH  C02  C03  single    1.503  0.020  1.503
 JAH  C03  C08  aromatic  1.389  0.020  1.389
 JAH  C03  C04  aromatic  1.391  0.020  1.391
 JAH  C08  N07  aromatic  1.325  0.020  1.325
 JAH  C04  C05  aromatic  1.382  0.020  1.382
 JAH  N07  C06  aromatic  1.331  0.020  1.331
 JAH  C05  C06  aromatic  1.396  0.020  1.396
 JAH  C06  C09  single    1.480  0.020  1.480
 JAH  C09  C10  aromatic  1.396  0.020  1.396
 JAH  C09  C14  aromatic  1.396  0.020  1.396
 JAH  C10  C11  aromatic  1.386  0.020  1.386
 JAH  C14  C13  aromatic  1.387  0.020  1.387
 JAH  C11  C12  aromatic  1.389  0.020  1.389
 JAH  C13  C12  aromatic  1.388  0.020  1.388
 JAH  C10  H1   single    0.930  0.020  1.080
 JAH  C13  H2   single    0.930  0.020  1.080
 JAH  N01  H3   single    0.890  0.020  1.040
 JAH  N01  H4   single    0.890  0.020  1.040
 JAH  C02  H6   single    0.970  0.020  1.090
 JAH  C02  H7   single    0.970  0.020  1.090
 JAH  C04  H8   single    0.930  0.020  1.080
 JAH  C05  H9   single    0.930  0.020  1.080
 JAH  C08  H10  single    0.930  0.020  1.080
 JAH  C11  H11  single    0.930  0.020  1.080
 JAH  C12  H12  single    0.930  0.020  1.080
 JAH  C14  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
 JAH  H1   C10  C11  119.90  3.000
 JAH  H1   C10  C09  119.39  3.000
 JAH  C11  C10  C09  120.71  3.000
 JAH  H2   C13  C14  119.67  3.000
 JAH  H2   C13  C12  120.10  3.000
 JAH  C14  C13  C12  120.23  3.000
 JAH  H4   N01  H3   106.09  3.000
 JAH  H4   N01  C02  109.45  3.000
 JAH  H3   N01  C02  109.27  3.000
 JAH  C08  C03  C04  116.47  3.000
 JAH  C04  C03  C02  122.17  3.000
 JAH  C08  C03  C02  121.36  3.000
 JAH  H8   C04  C05  120.05  3.000
 JAH  H8   C04  C03  120.25  3.000
 JAH  C05  C04  C03  119.69  3.000
 JAH  H9   C05  C06  120.88  3.000
 JAH  H9   C05  C04  119.81  3.000
 JAH  C06  C05  C04  119.30  3.000
 JAH  C09  C06  N07  116.93  3.000
 JAH  C09  C06  C05  121.94  3.000
 JAH  N07  C06  C05  121.12  3.000
 JAH  C08  N07  C06  119.02  3.000
 JAH  H10  C08  N07  116.03  3.000
 JAH  H10  C08  C03  119.59  3.000
 JAH  N07  C08  C03  124.37  3.000
 JAH  C14  C09  C06  121.40  3.000
 JAH  C14  C09  C10  118.55  3.000
 JAH  C06  C09  C10  120.04  3.000
 JAH  H11  C11  C12  120.07  3.000
 JAH  H11  C11  C10  119.68  3.000
 JAH  C12  C11  C10  120.25  3.000
 JAH  H12  C12  C11  120.28  3.000
 JAH  H12  C12  C13  120.19  3.000
 JAH  C11  C12  C13  119.53  3.000
 JAH  H13  C14  C09  120.30  3.000
 JAH  H13  C14  C13  118.97  3.000
 JAH  C09  C14  C13  120.72  3.000
 JAH  H7   C02  H6   105.91  3.000
 JAH  H7   C02  C03  108.73  3.000
 JAH  H6   C02  C03  108.62  3.000
 JAH  H7   C02  N01  107.79  3.000
 JAH  H6   C02  N01  114.24  3.000
 JAH  C03  C02  N01  111.28  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
 JAH  CONST_03  C13  C14  C09  C10    0.00   0.0  0
 JAH  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 JAH  CONST_05  C06  C09  C14  C13  180.00   0.0  0
 JAH  CONST_06  C06  N07  C08  C03    0.00   0.0  0
 JAH  CONST_07  C06  C05  C04  C03    0.00   0.0  0
 JAH  CONST_08  N07  C08  C03  C04    0.00   0.0  0
 JAH  CONST_09  N07  C06  C05  C04    0.00   0.0  0
 JAH  CONST_10  C09  C06  C05  C04  180.00   0.0  0
 JAH  CONST_11  C08  C03  C04  C05    0.00   0.0  0
 JAH  CONST_12  C08  N07  C06  C05    0.00   0.0  0
 JAH  CONST_14  C11  C10  C09  C06  180.00   0.0  0
 JAH  CONST_16  C09  C06  N07  C08  180.00   0.0  0
 JAH  CONST_17  C12  C11  C10  C09    0.00   0.0  0
 JAH  CONST_18  C12  C13  C14  C09    0.00   0.0  0
 JAH  CONST_19  C14  C09  C10  C11    0.00   0.0  0
 JAH  CONST_20  C14  C13  C12  C11    0.00   0.0  0
 JAH  CONST_21  N07  C08  C03  C02  180.00   0.0  0
 JAH  CONST_22  C05  C04  C03  C02  180.00   0.0  0
 JAH  CONST_23  H13  C14  C09  C10  180.00   0.0  0
 JAH  CONST_24  H12  C12  C11  C10  180.00   0.0  0
 JAH  CONST_25  H11  C11  C12  C13  180.00   0.0  0
 JAH  CONST_26  H9   C05  C04  C03  180.00   0.0  0
 JAH  CONST_27  H10  C08  C03  C04  180.00   0.0  0
 JAH  CONST_28  H8   C04  C05  C06  180.00   0.0  0
 JAH  CONST_29  H1   C10  C09  C06    0.00   0.0  0
 JAH  CONST_30  H2   C13  C14  C09  180.00   0.0  0
 JAH  Var_01    C08  C03  C02  N01  134.39  30.0  2
 JAH  Var_02    H3   N01  C02  C03  173.06  30.0  3

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
 JAH  plan-1  C03  0.020
 JAH  plan-1  C04  0.020
 JAH  plan-1  C05  0.020
 JAH  plan-1  C06  0.020
 JAH  plan-1  N07  0.020
 JAH  plan-1  C08  0.020
 JAH  plan-1  C09  0.020
 JAH  plan-1  H8   0.020
 JAH  plan-1  H9   0.020
 JAH  plan-1  H10  0.020
 JAH  plan-1  C02  0.020
 JAH  plan-2  C10  0.020
 JAH  plan-2  C13  0.020
 JAH  plan-2  C06  0.020
 JAH  plan-2  C09  0.020
 JAH  plan-2  C11  0.020
 JAH  plan-2  C12  0.020
 JAH  plan-2  C14  0.020
 JAH  plan-2  H1   0.020
 JAH  plan-2  H2   0.020
 JAH  plan-2  H11  0.020
 JAH  plan-2  H12  0.020
 JAH  plan-2  H13  0.020

