# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:31:37 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 5-methoxy-2-(pyridin-3-ylmethoxy)benzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OCc2cccnc2)c(C=O)c1
#
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
 3R5  3R5  5-methoxy-2-(pyridin-3-ylmethoxy)benzaldehyde  ligand  31  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3R5
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
 3R5  C1    C  C1    0   0.128  -0.9018  -2.2835  -0.3320
 3R5  C2    C  CR6   0  -0.119  -1.5098  -0.9504  -0.1877
 3R5  C3    C  CR6   0   0.386  -0.7128   0.1968  -0.0245
 3R5  C4    C  CR16  0  -0.366  -1.3357   1.4326   0.0989
 3R5  C5    C  CR16  0  -0.353  -2.7206   1.5344   0.0684
 3R5  C6    C  CR6   0   0.386  -3.5161   0.4014  -0.0849
 3R5  C7    C  CR16  0  -0.359  -2.8952  -0.8331  -0.2147
 3R5  O8    O  O2    0  -0.474  -4.8646   0.4106  -0.1172
 3R5  C9    C  CH3   0  -0.439  -5.5297   1.6450   0.0579
 3R5  O10   O  O2    0  -0.467   0.6197   0.0162   0.0066
 3R5  C11   C  CH2   0  -0.262   1.4650   1.1512   0.1159
 3R5  C12   C  CR6   0   0.001   2.8789   0.6644   0.0664
 3R5  C13   C  CR16  0  -0.098   3.7472   0.8845   1.1273
 3R5  N14   N  N     0  -0.400   5.0146   0.4881   1.1416
 3R5  C15   C  CR16  0  -0.062   5.4706  -0.1639   0.0805
 3R5  C16   C  CR16  0  -0.320   4.6897  -0.4435  -1.0334
 3R5  C17   C  CR16  0  -0.166   3.3726  -0.0195  -1.0401
 3R5  O18   O  O     0  -0.389  -1.5448  -3.2992  -0.4842
 3R5  H1    H  H     0   0.208   0.1962  -2.3241  -0.2963
 3R5  H4    H  HCR6  0   0.297  -0.7623   2.3403   0.2252
 3R5  H5    H  HCR6  0   0.293  -3.1576   2.5186   0.1710
 3R5  H7    H  HCR6  0   0.275  -3.4999  -1.7233  -0.3387
 3R5  H9    H  HCH3  0   0.228  -5.2831   2.1098   1.0163
 3R5  H9A   H  HCH3  0   0.229  -5.3011   2.3521  -0.7442
 3R5  H9B   H  HCH3  0   0.261  -6.5949   1.4284   0.0382
 3R5  H11   H  HCH2  0   0.253   1.2717   1.8474  -0.7074
 3R5  H11A  H  HCH2  0   0.252   1.2787   1.6856   1.0532
 3R5  H13   H  HCR6  0   0.263   3.3972   1.4113   2.0101
 3R5  H15   H  HCR6  0   0.268   6.5070  -0.4807   0.1133
 3R5  H16   H  HCR6  0   0.275   5.1104  -0.9778  -1.8738
 3R5  H17   H  HCR6  0   0.273   2.7384  -0.2151  -1.8962

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
 3R5  C2   C1    single    1.472  0.020  1.472
 3R5  C1   O18   double    1.212  0.020  1.212
 3R5  C1   H1    single    0.930  0.020  1.080
 3R5  C7   C2    aromatic  1.391  0.020  1.391
 3R5  C3   C2    aromatic  1.406  0.020  1.406
 3R5  C4   C3    aromatic  1.389  0.020  1.389
 3R5  C3   O10   single    1.345  0.020  1.345
 3R5  C5   C4    aromatic  1.389  0.020  1.389
 3R5  C4   H4    single    0.930  0.020  1.080
 3R5  C5   C6    aromatic  1.393  0.020  1.393
 3R5  C5   H5    single    0.930  0.020  1.080
 3R5  O8   C6    single    1.349  0.020  1.349
 3R5  C6   C7    aromatic  1.388  0.020  1.388
 3R5  C7   H7    single    0.930  0.020  1.080
 3R5  O8   C9    single    1.413  0.020  1.413
 3R5  C9   H9    single    0.970  0.020  1.090
 3R5  C9   H9A   single    0.970  0.020  1.090
 3R5  C9   H9B   single    0.970  0.020  1.090
 3R5  C11  O10   single    1.419  0.020  1.419
 3R5  C11  C12   single    1.496  0.020  1.496
 3R5  C11  H11   single    0.970  0.020  1.090
 3R5  C11  H11A  single    0.970  0.020  1.090
 3R5  C12  C17   aromatic  1.391  0.020  1.391
 3R5  C12  C13   aromatic  1.388  0.020  1.388
 3R5  C13  N14   aromatic  1.328  0.020  1.328
 3R5  C13  H13   single    0.930  0.020  1.080
 3R5  N14  C15   aromatic  1.326  0.020  1.326
 3R5  C16  C15   aromatic  1.389  0.020  1.389
 3R5  C15  H15   single    0.930  0.020  1.080
 3R5  C17  C16   aromatic  1.384  0.020  1.384
 3R5  C16  H16   single    0.930  0.020  1.080
 3R5  C17  H17   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
 3R5  H1    C1   O18  120.20  3.000
 3R5  H1    C1   C2   116.28  3.000
 3R5  O18   C1   C2   123.52  3.000
 3R5  C7    C2   C3   119.87  3.000
 3R5  C3    C2   C1   121.06  3.000
 3R5  C7    C2   C1   119.07  3.000
 3R5  O10   C3   C4   124.16  3.000
 3R5  O10   C3   C2   117.04  3.000
 3R5  C4    C3   C2   118.80  3.000
 3R5  H4    C4   C5   118.03  3.000
 3R5  H4    C4   C3   121.29  3.000
 3R5  C5    C4   C3   120.68  3.000
 3R5  H5    C5   C6   121.32  3.000
 3R5  H5    C5   C4   117.86  3.000
 3R5  C6    C5   C4   120.82  3.000
 3R5  O8    C6   C7   116.81  3.000
 3R5  C7    C6   C5   118.57  3.000
 3R5  O8    C6   C5   124.61  3.000
 3R5  H7    C7   C6   119.46  3.000
 3R5  H7    C7   C2   119.28  3.000
 3R5  C6    C7   C2   121.26  3.000
 3R5  C9    O8   C6   118.26  3.000
 3R5  H9B   C9   H9A  108.68  3.000
 3R5  H9B   C9   H9   108.75  3.000
 3R5  H9A   C9   H9   108.72  3.000
 3R5  H9B   C9   O8   106.55  3.000
 3R5  H9A   C9   O8   112.06  3.000
 3R5  H9    C9   O8   111.96  3.000
 3R5  C11   O10  C3   118.98  3.000
 3R5  H11A  C11  H11  107.65  3.000
 3R5  H11A  C11  C12  110.36  3.000
 3R5  H11   C11  C12  110.41  3.000
 3R5  H11A  C11  O10  110.79  3.000
 3R5  H11   C11  O10  110.19  3.000
 3R5  C12   C11  O10  107.46  3.000
 3R5  C17   C12  C13  117.62  3.000
 3R5  C13   C12  C11  120.93  3.000
 3R5  C17   C12  C11  121.44  3.000
 3R5  H13   C13  N14  116.33  3.000
 3R5  H13   C13  C12  119.77  3.000
 3R5  N14   C13  C12  123.90  3.000
 3R5  C15   N14  C13  117.79  3.000
 3R5  H15   C15  C16  120.19  3.000
 3R5  H15   C15  N14  116.62  3.000
 3R5  C16   C15  N14  123.19  3.000
 3R5  H16   C16  C17  121.21  3.000
 3R5  H16   C16  C15  120.28  3.000
 3R5  C17   C16  C15  118.52  3.000
 3R5  H17   C17  C16  120.38  3.000
 3R5  H17   C17  C12  120.63  3.000
 3R5  C16   C17  C12  118.98  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
 3R5  CONST_01  C5   C6   C7   C2      0.00   0.0  0
 3R5  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 3R5  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 3R5  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 3R5  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 3R5  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 3R5  CONST_07  C15  C16  C17  C12     0.00   0.0  0
 3R5  CONST_08  C15  N14  C13  C12     0.00   0.0  0
 3R5  CONST_09  C16  C17  C12  C13     0.00   0.0  0
 3R5  CONST_10  C16  C15  N14  C13     0.00   0.0  0
 3R5  CONST_11  C17  C12  C13  N14     0.00   0.0  0
 3R5  CONST_12  C17  C16  C15  N14     0.00   0.0  0
 3R5  CONST_13  C6   C7   C2   C1    180.00   0.0  0
 3R5  CONST_14  C4   C3   C2   C1    180.00   0.0  0
 3R5  CONST_15  O8   C6   C7   C2    180.00   0.0  0
 3R5  CONST_16  O8   C6   C5   C4    180.00   0.0  0
 3R5  CONST_17  O10  C3   C4   C5    180.00   0.0  0
 3R5  CONST_18  O10  C3   C2   C7    180.00   0.0  0
 3R5  CONST_19  C16  C17  C12  C11   180.00   0.0  0
 3R5  CONST_20  N14  C13  C12  C11   180.00   0.0  0
 3R5  CONST_21  H4   C4   C3   C2    180.00   0.0  0
 3R5  CONST_22  H7   C7   C2   C3    180.00   0.0  0
 3R5  CONST_23  H5   C5   C4   C3    180.00   0.0  0
 3R5  CONST_24  H16  C16  C17  C12   180.00   0.0  0
 3R5  CONST_25  H17  C17  C12  C13   180.00   0.0  0
 3R5  CONST_26  H15  C15  N14  C13   180.00   0.0  0
 3R5  CONST_27  H13  C13  N14  C15   180.00   0.0  0
 3R5  Var_01    O18  C1   C2   C3   -179.47  30.0  2
 3R5  Var_02    C12  C11  O10  C3   -177.54  30.0  1
 3R5  Var_03    C17  C12  C11  O10    60.60  30.0  2
 3R5  Var_04    H9   C9   O8   C6    -59.01  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
 3R5  plan-1  C1   0.020
 3R5  plan-1  C2   0.020
 3R5  plan-1  C3   0.020
 3R5  plan-1  C4   0.020
 3R5  plan-1  C5   0.020
 3R5  plan-1  C6   0.020
 3R5  plan-1  C7   0.020
 3R5  plan-1  O8   0.020
 3R5  plan-1  O10  0.020
 3R5  plan-1  H4   0.020
 3R5  plan-1  H5   0.020
 3R5  plan-1  H7   0.020
 3R5  plan-2  C11  0.020
 3R5  plan-2  C12  0.020
 3R5  plan-2  C13  0.020
 3R5  plan-2  N14  0.020
 3R5  plan-2  C15  0.020
 3R5  plan-2  C16  0.020
 3R5  plan-2  C17  0.020
 3R5  plan-2  H13  0.020
 3R5  plan-2  H15  0.020
 3R5  plan-2  H16  0.020
 3R5  plan-2  H17  0.020
 3R5  plan-3  C1   0.020
 3R5  plan-3  C2   0.020
 3R5  plan-3  O18  0.020
 3R5  plan-3  H1   0.020

