# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 00:39:36 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 4-methoxy-N-[(pyridin-2-yl)methyl]aniline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NCc2ccccn2)cc1
#
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
 6RN  6RN  4-methoxy-N-[(pyridin-2-yl)methyl]aniline  ligand  30  16  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6RN
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
 6RN  C4   C  CR6   0   0.342   0.9197   0.3496  -0.0407
 6RN  C5   C  CH2   0  -0.316  -1.2785  -0.6763  -0.3499
 6RN  C6   C  CR6   0   0.242  -2.7386  -0.3129  -0.2596
 6RN  N1   N  N     0  -0.449  -3.0508   0.8448   0.3052
 6RN  C7   C  CR16  0  -0.330  -3.7080  -1.1982  -0.7243
 6RN  C8   C  CR16  0  -0.147  -5.0419  -0.8582  -0.5880
 6RN  C9   C  CR16  0  -0.335  -5.3680   0.3564   0.0024
 6RN  C10  C  CR16  0  -0.066  -4.3341   1.1706   0.4297
 6RN  C11  C  CR16  0  -0.333   1.6739   1.4340   0.4344
 6RN  C12  C  CR16  0  -0.326   3.0438   1.3514   0.5699
 6RN  C1   C  CR6   0   0.342   3.7270   0.1797   0.2354
 6RN  C3   C  CR16  0  -0.339   1.6097  -0.8176  -0.3661
 6RN  C2   C  CR16  0  -0.369   2.9952  -0.9017  -0.2339
 6RN  N    N  NH1   0  -0.697  -0.4445   0.4824  -0.2004
 6RN  H1   H  HCH2  0   0.241  -1.0713  -1.4427   0.4144
 6RN  H2   H  HCH2  0   0.248  -1.0952  -1.1619  -1.3136
 6RN  H3   H  HCR6  0   0.268  -3.4153  -2.1337  -1.1836
 6RN  H4   H  HCR6  0   0.275  -5.8166  -1.5270  -0.9397
 6RN  H5   H  HCR6  0   0.272  -6.3961   0.6664   0.1274
 6RN  H6   H  HCR6  0   0.265  -4.5453   2.1274   0.8938
 6RN  H7   H  HCR6  0   0.256   1.1715   2.3559   0.7042
 6RN  H8   H  HCR6  0   0.257   3.5971   2.2051   0.9425
 6RN  H10  H  HCR6  0   0.266   1.0815  -1.6861  -0.7371
 6RN  H11  H  HCR6  0   0.272   3.4754  -1.8320  -0.5071
 6RN  H12  H  HNH1  0   0.376  -0.8776   1.2135   0.3449
 6RN  C13  C  CH3   0  -0.431   5.7895  -0.9808   0.0982
 6RN  H9   H  HCH3  0   0.221   5.4732  -1.8275   0.7146
 6RN  H13  H  HCH3  0   0.221   5.6928  -1.2623  -0.9546
 6RN  H14  H  HCH3  0   0.255   6.8365  -0.7718   0.3066
 6RN  O    O  O2    0  -0.480   5.0725   0.1945   0.4020

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
 6RN  O    C1   single    1.356  0.020  1.356
 6RN  C1   C12  aromatic  1.397  0.020  1.397
 6RN  C1   C2   aromatic  1.387  0.020  1.387
 6RN  C12  C11  aromatic  1.379  0.020  1.379
 6RN  C2   C3   aromatic  1.394  0.020  1.394
 6RN  C11  C4   aromatic  1.404  0.020  1.404
 6RN  C8   C7   aromatic  1.383  0.020  1.383
 6RN  C8   C9   aromatic  1.389  0.020  1.389
 6RN  C3   C4   aromatic  1.394  0.020  1.394
 6RN  C7   C6   aromatic  1.393  0.020  1.393
 6RN  C4   N    single    1.380  0.020  1.380
 6RN  C9   C10  aromatic  1.384  0.020  1.384
 6RN  C6   C5   single    1.507  0.020  1.507
 6RN  C6   N1   aromatic  1.325  0.020  1.325
 6RN  N    C5   single    1.435  0.020  1.435
 6RN  C10  N1   aromatic  1.330  0.020  1.330
 6RN  C5   H1   single    0.970  0.020  1.090
 6RN  C5   H2   single    0.970  0.020  1.090
 6RN  C7   H3   single    0.930  0.020  1.080
 6RN  C8   H4   single    0.930  0.020  1.080
 6RN  C9   H5   single    0.930  0.020  1.080
 6RN  C10  H6   single    0.930  0.020  1.080
 6RN  C11  H7   single    0.930  0.020  1.080
 6RN  C12  H8   single    0.930  0.020  1.080
 6RN  C3   H10  single    0.930  0.020  1.080
 6RN  C2   H11  single    0.930  0.020  1.080
 6RN  N    H12  single    0.890  0.020  1.040
 6RN  O    C13  single    1.410  0.020  1.410
 6RN  C13  H9   single    0.970  0.020  1.090
 6RN  C13  H13  single    0.970  0.020  1.090
 6RN  C13  H14  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
 6RN  N    C4   C3   122.87  3.000
 6RN  N    C4   C11  119.73  3.000
 6RN  C3   C4   C11  117.37  3.000
 6RN  H2   C5   H1   105.70  3.000
 6RN  H2   C5   N    110.64  3.000
 6RN  H1   C5   N    112.33  3.000
 6RN  H2   C5   C6   108.78  3.000
 6RN  H1   C5   C6   107.95  3.000
 6RN  N    C5   C6   111.22  3.000
 6RN  C7   C6   N1   122.24  3.000
 6RN  N1   C6   C5   117.67  3.000
 6RN  C7   C6   C5   120.07  3.000
 6RN  C10  N1   C6   118.76  3.000
 6RN  H3   C7   C8   121.00  3.000
 6RN  H3   C7   C6   120.18  3.000
 6RN  C8   C7   C6   118.83  3.000
 6RN  H4   C8   C9   120.69  3.000
 6RN  H4   C8   C7   120.43  3.000
 6RN  C9   C8   C7   118.89  3.000
 6RN  H5   C9   C10  120.41  3.000
 6RN  H5   C9   C8   121.54  3.000
 6RN  C10  C9   C8   118.05  3.000
 6RN  H6   C10  C9   120.39  3.000
 6RN  H6   C10  N1   116.38  3.000
 6RN  C9   C10  N1   123.23  3.000
 6RN  H7   C11  C12  119.14  3.000
 6RN  H7   C11  C4   119.48  3.000
 6RN  C12  C11  C4   121.38  3.000
 6RN  H8   C12  C1   119.58  3.000
 6RN  H8   C12  C11  119.59  3.000
 6RN  C1   C12  C11  120.83  3.000
 6RN  C2   C1   O    124.99  3.000
 6RN  C2   C1   C12  118.48  3.000
 6RN  O    C1   C12  116.53  3.000
 6RN  H10  C3   C2   117.98  3.000
 6RN  H10  C3   C4   120.68  3.000
 6RN  C2   C3   C4   121.34  3.000
 6RN  H11  C2   C3   117.96  3.000
 6RN  H11  C2   C1   121.43  3.000
 6RN  C3   C2   C1   120.60  3.000
 6RN  H12  N    C5   113.05  3.000
 6RN  H12  N    C4   115.54  3.000
 6RN  C5   N    C4   120.58  3.000
 6RN  H14  C13  H13  108.60  3.000
 6RN  H14  C13  H9   108.61  3.000
 6RN  H13  C13  H9   108.51  3.000
 6RN  H14  C13  O    106.74  3.000
 6RN  H13  C13  O    112.14  3.000
 6RN  H9   C13  O    112.13  3.000
 6RN  C13  O    C1   117.98  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
 6RN  CONST_01  C1   C12  C11  C4     0.00   0.0  0
 6RN  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 6RN  CONST_03  C9   C8   C7   C6     0.00   0.0  0
 6RN  CONST_04  C9   C10  N1   C6     0.00   0.0  0
 6RN  CONST_05  C8   C7   C6   N1     0.00   0.0  0
 6RN  CONST_06  C8   C9   C10  N1     0.00   0.0  0
 6RN  CONST_07  C10  C9   C8   C7     0.00   0.0  0
 6RN  CONST_08  C10  N1   C6   C7     0.00   0.0  0
 6RN  CONST_09  C2   C1   C12  C11    0.00   0.0  0
 6RN  CONST_10  C2   C3   C4   C11    0.00   0.0  0
 6RN  CONST_11  C3   C2   C1   C12    0.00   0.0  0
 6RN  CONST_12  C3   C4   C11  C12    0.00   0.0  0
 6RN  CONST_13  C8   C7   C6   C5   180.00   0.0  0
 6RN  CONST_14  C10  N1   C6   C5   180.00   0.0  0
 6RN  CONST_15  O    C1   C12  C11  180.00   0.0  0
 6RN  CONST_16  N    C4   C11  C12  180.00   0.0  0
 6RN  CONST_17  C3   C2   C1   O    180.00   0.0  0
 6RN  CONST_18  N    C4   C3   C2   180.00   0.0  0
 6RN  CONST_19  H8   C12  C11  C4   180.00   0.0  0
 6RN  CONST_20  H11  C2   C3   C4   180.00   0.0  0
 6RN  CONST_21  H4   C8   C7   C6   180.00   0.0  0
 6RN  CONST_22  H6   C10  N1   C6   180.00   0.0  0
 6RN  CONST_23  H3   C7   C6   N1   180.00   0.0  0
 6RN  CONST_24  H5   C9   C10  N1   180.00   0.0  0
 6RN  CONST_25  H10  C3   C4   C11  180.00   0.0  0
 6RN  CONST_26  H7   C11  C12  C1   180.00   0.0  0
 6RN  Var_01    C6   C5   N    C4   169.75  30.0  3
 6RN  Var_02    N    C5   C6   N1   -19.00  30.0  2
 6RN  Var_03    H9   C13  O    C1   -60.50  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
 6RN  plan-1  C5   0.020
 6RN  plan-1  C6   0.020
 6RN  plan-1  N1   0.020
 6RN  plan-1  C7   0.020
 6RN  plan-1  C8   0.020
 6RN  plan-1  C9   0.020
 6RN  plan-1  C10  0.020
 6RN  plan-1  H3   0.020
 6RN  plan-1  H4   0.020
 6RN  plan-1  H5   0.020
 6RN  plan-1  H6   0.020
 6RN  plan-2  C4   0.020
 6RN  plan-2  C11  0.020
 6RN  plan-2  C12  0.020
 6RN  plan-2  C1   0.020
 6RN  plan-2  C3   0.020
 6RN  plan-2  C2   0.020
 6RN  plan-2  N    0.020
 6RN  plan-2  H7   0.020
 6RN  plan-2  H8   0.020
 6RN  plan-2  H10  0.020
 6RN  plan-2  H11  0.020
 6RN  plan-2  O    0.020
 6RN  plan-3  C4   0.020
 6RN  plan-3  C5   0.020
 6RN  plan-3  N    0.020
 6RN  plan-3  H12  0.020

