# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 00:45:22 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 4-(4-methoxyphenyl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2ccnc(N)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
 RJ5  RJ5  4-(4-methoxyphenyl)pyridin-2-amine  ligand  27  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RJ5
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
 RJ5  C1   C  CH3   0  -0.437  44.7826  4.1583  18.0452
 RJ5  O1   O  O2    0  -0.464  44.1609  5.3201  17.5331
 RJ5  C2   C  CR6   0   0.377  43.7524  5.3236  16.2538
 RJ5  C3   C  CR16  0  -0.325  43.1344  6.4929  15.8031
 RJ5  C4   C  CR16  0  -0.290  42.6884  6.5877  14.5007
 RJ5  C5   C  CR6   0   0.066  42.8324  5.5259  13.6018
 RJ5  C6   C  CR16  0  -0.293  43.4484  4.3674  14.0668
 RJ5  C7   C  CR16  0  -0.365  43.9079  4.2563  15.3718
 RJ5  C8   C  CR6   0   0.199  42.3489  5.6361  12.2134
 RJ5  C9   C  CR16  0  -0.458  41.8509  4.5350  11.5378
 RJ5  C10  C  CR6   0   0.462  41.4073  4.6763  10.2127
 RJ5  N1   N  NH2   0  -0.836  40.8680  3.6158   9.5443
 RJ5  N2   N  N     0  -0.460  41.4418  5.8433   9.5720
 RJ5  C11  C  CR16  0  -0.059  41.9157  6.8957  10.2320
 RJ5  C12  C  CR16  0  -0.421  42.3773  6.8605  11.5311
 RJ5  H1   H  HCH3  0   0.260  45.0292  4.3721  19.0822
 RJ5  H2   H  HCH3  0   0.229  44.1178  3.2911  18.0135
 RJ5  H3   H  HCH3  0   0.229  45.7033  3.9162  17.5080
 RJ5  H4   H  HCR6  0   0.263  43.0021  7.3231  16.4858
 RJ5  H5   H  HCR6  0   0.255  42.1988  7.5011  14.1867
 RJ5  H6   H  HCR6  0   0.257  43.5997  3.5294  13.3977
 RJ5  H7   H  HCR6  0   0.280  44.3886  3.3368  15.6766
 RJ5  H8   H  HCR6  0   0.260  41.7770  3.5693  12.0224
 RJ5  H9   H  HNH2  0   0.380  40.8162  3.7023   8.5424
 RJ5  H10  H  HNH2  0   0.388  41.1061  2.6922   9.8653
 RJ5  H11  H  HCR6  0   0.253  41.9350  7.8302   9.6807
 RJ5  H12  H  HCR6  0   0.252  42.7724  7.7570  11.9883

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
 RJ5  N1   C10  single    1.365  0.020  1.365
 RJ5  N2   C10  aromatic  1.332  0.020  1.332
 RJ5  N2   C11  aromatic  1.330  0.020  1.330
 RJ5  C10  C9   aromatic  1.405  0.020  1.405
 RJ5  C11  C12  aromatic  1.379  0.020  1.379
 RJ5  C9   C8   aromatic  1.385  0.020  1.385
 RJ5  C12  C8   aromatic  1.402  0.020  1.402
 RJ5  C8   C5   single    1.474  0.020  1.474
 RJ5  C5   C6   aromatic  1.392  0.020  1.392
 RJ5  C5   C4   aromatic  1.399  0.020  1.399
 RJ5  C6   C7   aromatic  1.388  0.020  1.388
 RJ5  C4   C3   aromatic  1.380  0.020  1.380
 RJ5  C7   C2   aromatic  1.393  0.020  1.393
 RJ5  C3   C2   aromatic  1.397  0.020  1.397
 RJ5  C2   O1   single    1.343  0.020  1.343
 RJ5  O1   C1   single    1.414  0.020  1.414
 RJ5  C1   H1   single    0.970  0.020  1.090
 RJ5  C1   H2   single    0.970  0.020  1.090
 RJ5  C1   H3   single    0.970  0.020  1.090
 RJ5  C3   H4   single    0.930  0.020  1.080
 RJ5  C4   H5   single    0.930  0.020  1.080
 RJ5  C6   H6   single    0.930  0.020  1.080
 RJ5  C7   H7   single    0.930  0.020  1.080
 RJ5  C9   H8   single    0.930  0.020  1.080
 RJ5  N1   H9   single    0.890  0.020  1.040
 RJ5  N1   H10  single    0.890  0.020  1.040
 RJ5  C11  H11  single    0.930  0.020  1.080
 RJ5  C12  H12  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
 RJ5  H3   C1   H2   108.80  3.000
 RJ5  H3   C1   H1   108.74  3.000
 RJ5  H2   C1   H1   108.76  3.000
 RJ5  H3   C1   O1   111.99  3.000
 RJ5  H2   C1   O1   111.96  3.000
 RJ5  H1   C1   O1   106.48  3.000
 RJ5  C2   O1   C1   118.75  3.000
 RJ5  C7   C2   C3   119.10  3.000
 RJ5  C3   C2   O1   116.36  3.000
 RJ5  C7   C2   O1   124.55  3.000
 RJ5  H4   C3   C4   120.19  3.000
 RJ5  H4   C3   C2   119.49  3.000
 RJ5  C4   C3   C2   120.32  3.000
 RJ5  H5   C4   C5   120.04  3.000
 RJ5  H5   C4   C3   118.53  3.000
 RJ5  C5   C4   C3   121.41  3.000
 RJ5  C8   C5   C6   121.46  3.000
 RJ5  C6   C5   C4   117.56  3.000
 RJ5  C8   C5   C4   120.98  3.000
 RJ5  H6   C6   C7   118.21  3.000
 RJ5  H6   C6   C5   119.96  3.000
 RJ5  C7   C6   C5   121.81  3.000
 RJ5  H7   C7   C6   118.70  3.000
 RJ5  H7   C7   C2   121.50  3.000
 RJ5  C6   C7   C2   119.80  3.000
 RJ5  C12  C8   C9   117.67  3.000
 RJ5  C12  C8   C5   121.13  3.000
 RJ5  C9   C8   C5   121.21  3.000
 RJ5  H8   C9   C10  119.36  3.000
 RJ5  H8   C9   C8   121.02  3.000
 RJ5  C10  C9   C8   119.60  3.000
 RJ5  N2   C10  N1   117.10  3.000
 RJ5  N2   C10  C9   122.27  3.000
 RJ5  N1   C10  C9   120.58  3.000
 RJ5  H10  N1   H9   114.11  3.000
 RJ5  H10  N1   C10  117.61  3.000
 RJ5  H9   N1   C10  116.16  3.000
 RJ5  C11  N2   C10  117.64  3.000
 RJ5  H11  C11  C12  119.64  3.000
 RJ5  H11  C11  N2   115.83  3.000
 RJ5  C12  C11  N2   124.52  3.000
 RJ5  H12  C12  C11  119.97  3.000
 RJ5  H12  C12  C8   121.72  3.000
 RJ5  C11  C12  C8   118.29  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
 RJ5  CONST_01  C5   C6   C7   C2     0.00   0.0  0
 RJ5  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 RJ5  CONST_03  C8   C5   C4   C3   180.00   0.0  0
 RJ5  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 RJ5  CONST_05  C6   C7   C2   C3     0.00   0.0  0
 RJ5  CONST_08  C7   C6   C5   C4     0.00   0.0  0
 RJ5  CONST_09  C7   C2   C3   C4     0.00   0.0  0
 RJ5  CONST_10  C10  C9   C8   C5   180.00   0.0  0
 RJ5  CONST_11  C11  C12  C8   C5   180.00   0.0  0
 RJ5  CONST_14  C8   C5   C6   C7   180.00   0.0  0
 RJ5  CONST_15  N2   C10  C9   C8     0.00   0.0  0
 RJ5  CONST_16  N2   C11  C12  C8     0.00   0.0  0
 RJ5  CONST_17  C11  N2   C10  C9     0.00   0.0  0
 RJ5  CONST_18  C11  C12  C8   C9     0.00   0.0  0
 RJ5  CONST_19  C12  C11  N2   C10    0.00   0.0  0
 RJ5  CONST_20  C12  C8   C9   C10    0.00   0.0  0
 RJ5  CONST_21  C6   C7   C2   O1   180.00   0.0  0
 RJ5  CONST_22  C4   C3   C2   O1   180.00   0.0  0
 RJ5  CONST_23  N1   C10  C9   C8   180.00   0.0  0
 RJ5  CONST_24  C11  N2   C10  N1   180.00   0.0  0
 RJ5  CONST_25  H6   C6   C7   C2   180.00   0.0  0
 RJ5  CONST_26  H5   C4   C3   C2   180.00   0.0  0
 RJ5  CONST_27  H7   C7   C2   C3   180.00   0.0  0
 RJ5  CONST_28  H8   C9   C8   C5     0.00   0.0  0
 RJ5  CONST_29  H12  C12  C8   C5     0.00   0.0  0
 RJ5  CONST_30  H4   C3   C4   C5   180.00   0.0  0
 RJ5  CONST_31  H11  C11  C12  C8   180.00   0.0  0
 RJ5  Var_01    C7   C2   O1   C1    -0.66  30.0  2
 RJ5  Var_02    H1   C1   O1   C2   179.95  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
 RJ5  plan-1  O1   0.020
 RJ5  plan-1  C2   0.020
 RJ5  plan-1  C3   0.020
 RJ5  plan-1  C4   0.020
 RJ5  plan-1  C5   0.020
 RJ5  plan-1  C6   0.020
 RJ5  plan-1  C7   0.020
 RJ5  plan-1  C8   0.020
 RJ5  plan-1  H4   0.020
 RJ5  plan-1  H5   0.020
 RJ5  plan-1  H6   0.020
 RJ5  plan-1  H7   0.020
 RJ5  plan-2  C5   0.020
 RJ5  plan-2  C8   0.020
 RJ5  plan-2  C9   0.020
 RJ5  plan-2  C10  0.020
 RJ5  plan-2  N1   0.020
 RJ5  plan-2  N2   0.020
 RJ5  plan-2  C11  0.020
 RJ5  plan-2  C12  0.020
 RJ5  plan-2  H8   0.020
 RJ5  plan-2  H11  0.020
 RJ5  plan-2  H12  0.020
 RJ5  plan-3  C10  0.020
 RJ5  plan-3  N1   0.020
 RJ5  plan-3  H9   0.020
 RJ5  plan-3  H10  0.020

