# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 18:14:56 2021
#   Inital geometry file: a 50 line input string
#   Ligand name: ~{N}-methyl-1-pyridin-4-yl-methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1ccncc1
#
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
 RYP  RYP  ~{N}-methyl-1-pyridin-4-yl-methanamine  ligand  19  9  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RYP
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
 RYP  C01  C  CH3   0  -0.513  15.2478  19.7235   6.8496
 RYP  C03  C  CH2   0  -0.367  13.8679  19.1957   8.7567
 RYP  C04  C  CR6   0   0.210  14.4184  20.2271   9.7043
 RYP  C05  C  CR16  0  -0.321  15.5942  19.9898  10.4116
 RYP  C06  C  CR16  0  -0.063  16.0600  20.9576  11.2848
 RYP  C08  C  CR16  0  -0.102  14.3262  22.3443  10.8208
 RYP  C09  C  CR16  0  -0.343  13.7808  21.4407   9.9185
 RYP  N02  N  NH1   0  -0.562  14.8787  18.7247   7.8334
 RYP  N07  N  N     0  -0.391  15.4451  22.1189  11.4960
 RYP  H1   H  HCH3  0   0.239  15.9214  19.2847   6.1140
 RYP  H2   H  HCH3  0   0.204  14.3919  20.1570   6.3125
 RYP  H3   H  HCH3  0   0.202  15.7805  20.5466   7.3292
 RYP  H4   H  HCH2  0   0.197  12.9830  19.6142   8.2521
 RYP  H5   H  HCH2  0   0.270  13.5151  18.3406   9.3402
 RYP  H6   H  HCR6  0   0.230  16.1410  19.0649  10.2847
 RYP  H7   H  HCR6  0   0.236  16.9756  20.7902  11.8419
 RYP  H8   H  HCR6  0   0.275  13.8351  23.2953  10.9980
 RYP  H9   H  HCR6  0   0.260  12.8667  21.6869   9.3925
 RYP  H10  H  HNH1  0   0.341  14.5208  17.9079   7.3568

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
 RYP  C01  N02  single    1.450  0.020  1.450
 RYP  N02  C03  single    1.448  0.020  1.448
 RYP  C03  C04  single    1.505  0.020  1.505
 RYP  C04  C09  aromatic  1.388  0.020  1.388
 RYP  C04  C05  aromatic  1.393  0.020  1.393
 RYP  C09  C08  aromatic  1.389  0.020  1.389
 RYP  C05  C06  aromatic  1.384  0.020  1.384
 RYP  C08  N07  aromatic  1.326  0.020  1.326
 RYP  C06  N07  aromatic  1.331  0.020  1.331
 RYP  C01  H1   single    0.970  0.020  1.090
 RYP  C01  H2   single    0.970  0.020  1.090
 RYP  C01  H3   single    0.970  0.020  1.090
 RYP  C03  H4   single    0.970  0.020  1.090
 RYP  C03  H5   single    0.970  0.020  1.090
 RYP  C05  H6   single    0.930  0.020  1.080
 RYP  C06  H7   single    0.930  0.020  1.080
 RYP  C08  H8   single    0.930  0.020  1.080
 RYP  C09  H9   single    0.930  0.020  1.080
 RYP  N02  H10  single    0.890  0.020  1.040

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
 RYP  H3   C01  H2   107.29  3.000
 RYP  H3   C01  H1   107.37  3.000
 RYP  H2   C01  H1   108.08  3.000
 RYP  H3   C01  N02  110.22  3.000
 RYP  H2   C01  N02  113.88  3.000
 RYP  H1   C01  N02  109.76  3.000
 RYP  H5   C03  H4   106.41  3.000
 RYP  H5   C03  N02  108.13  3.000
 RYP  H4   C03  N02  113.11  3.000
 RYP  H5   C03  C04  108.53  3.000
 RYP  H4   C03  C04  108.78  3.000
 RYP  N02  C03  C04  111.66  3.000
 RYP  C09  C04  C05  117.30  3.000
 RYP  C05  C04  C03  120.79  3.000
 RYP  C09  C04  C03  121.91  3.000
 RYP  H6   C05  C06  120.11  3.000
 RYP  H6   C05  C04  120.85  3.000
 RYP  C06  C05  C04  119.04  3.000
 RYP  H7   C06  N07  116.30  3.000
 RYP  H7   C06  C05  120.01  3.000
 RYP  N07  C06  C05  123.69  3.000
 RYP  H8   C08  N07  116.60  3.000
 RYP  H8   C08  C09  119.92  3.000
 RYP  N07  C08  C09  123.48  3.000
 RYP  H9   C09  C08  119.95  3.000
 RYP  H9   C09  C04  120.78  3.000
 RYP  C08  C09  C04  119.27  3.000
 RYP  H10  N02  C03  108.44  3.000
 RYP  H10  N02  C01  109.07  3.000
 RYP  C03  N02  C01  112.73  3.000
 RYP  C08  N07  C06  117.21  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
 RYP  CONST_01  N07  C08  C09  C04     0.00   0.0  0
 RYP  CONST_02  N07  C06  C05  C04     0.00   0.0  0
 RYP  CONST_03  C08  C09  C04  C05     0.00   0.0  0
 RYP  CONST_04  C08  N07  C06  C05     0.00   0.0  0
 RYP  CONST_05  C09  C04  C05  C06     0.00   0.0  0
 RYP  CONST_06  C09  C08  N07  C06     0.00   0.0  0
 RYP  CONST_07  C08  C09  C04  C03   180.00   0.0  0
 RYP  CONST_08  C06  C05  C04  C03   180.00   0.0  0
 RYP  CONST_09  H8   C08  C09  C04   180.00   0.0  0
 RYP  CONST_10  H7   C06  C05  C04   180.00   0.0  0
 RYP  CONST_11  H9   C09  C04  C05   180.00   0.0  0
 RYP  CONST_12  H6   C05  C04  C09   180.00   0.0  0
 RYP  Var_01    N02  C03  C04  C05   -50.30  30.0  2
 RYP  Var_02    C04  C03  N02  C01   -70.89  30.0  3
 RYP  Var_03    H1   C01  N02  C03  -173.52  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
 RYP  plan-1  C03  0.020
 RYP  plan-1  C04  0.020
 RYP  plan-1  C05  0.020
 RYP  plan-1  C06  0.020
 RYP  plan-1  C08  0.020
 RYP  plan-1  C09  0.020
 RYP  plan-1  N07  0.020
 RYP  plan-1  H6   0.020
 RYP  plan-1  H7   0.020
 RYP  plan-1  H8   0.020
 RYP  plan-1  H9   0.020

