# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 07:24:37 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-[2-(3-methoxyphenyl)ethynyl]-6-methyl-pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)C#Cc2cccc(C)n2
#
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
 D8B  D8B  2-[2-(3-methoxyphenyl)ethynyl]-6-methyl-pyridine  ligand  30  17  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D8B
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
 D8B  C1   C  CR16  0  -0.315  -2.8846  -1.6548  -0.0271
 D8B  N1   N  N     0  -0.433  -3.3040   0.7057   0.0123
 D8B  C11  C  CR16  0  -0.210   3.3102   2.0854   0.0106
 D8B  C12  C  CR16  0  -0.367   4.2411   1.0524   0.0249
 D8B  C13  C  CR6   0   0.406   3.8022  -0.2704   0.0315
 D8B  C14  C  CR16  0  -0.385   2.4345  -0.5412   0.0235
 D8B  C15  C  CH3   0  -0.409   6.0072  -1.1359   0.0397
 D8B  C2   C  CR6   0   0.036  -2.4607  -0.3272  -0.0022
 D8B  C3   C  CR6   0   0.231  -4.6108   0.4668   0.0025
 D8B  C4   C  CR16  0  -0.311  -5.1227  -0.8297  -0.0234
 D8B  C5   C  CR16  0  -0.133  -4.2457  -1.9011  -0.0380
 D8B  C6   C  CH3   0  -0.690  -5.5149   1.6607   0.0243
 D8B  C7   C  CSP   0   0.121  -1.0649  -0.0252   0.0077
 D8B  C8   C  CSP   0   0.145   0.1181   0.2117   0.0020
 D8B  C9   C  CR6   0  -0.079   1.5113   0.5000   0.0093
 D8B  C10  C  CR16  0  -0.296   1.9535   1.8281   0.0024
 D8B  H1   H  HCR6  0   0.254  -2.1635  -2.4593  -0.0375
 D8B  H2   H  HCR6  0   0.245   3.6617   3.1084   0.0040
 D8B  H3   H  HCR6  0   0.263   5.2942   1.2973   0.0315
 D8B  H4   H  HCR6  0   0.249   2.0947  -1.5689   0.0298
 D8B  H5   H  HCH3  0   0.215   6.3397  -0.5986  -0.8527
 D8B  H6   H  HCH3  0   0.216   6.3474  -0.5913   0.9247
 D8B  H7   H  HCH3  0   0.251   6.4647  -2.1216   0.0418
 D8B  H8   H  HCR6  0   0.243  -6.1917  -0.9912  -0.0309
 D8B  H9   H  HCR6  0   0.253  -4.6175  -2.9165  -0.0571
 D8B  H10  H  HCH3  0   0.246  -5.3662   2.2411   0.9353
 D8B  H11  H  HCH3  0   0.245  -5.3048   2.3216  -0.8166
 D8B  H12  H  HCH3  0   0.231  -6.5633   1.3743  -0.0238
 D8B  H13  H  HCR6  0   0.234   1.2364   2.6364  -0.0099
 D8B  O1   O  O2    0  -0.456   4.6120  -1.3413   0.0458

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
 D8B  C6   C3   single    1.498  0.020  1.498
 D8B  C3   C4   aromatic  1.394  0.020  1.394
 D8B  C3   N1   aromatic  1.328  0.020  1.328
 D8B  C4   C5   aromatic  1.385  0.020  1.385
 D8B  N1   C2   aromatic  1.333  0.020  1.333
 D8B  C5   C1   aromatic  1.383  0.020  1.383
 D8B  C2   C1   aromatic  1.394  0.020  1.394
 D8B  C2   C7   single    1.428  0.020  1.428
 D8B  C7   C8   triple    1.207  0.020  1.207
 D8B  C8   C9   single    1.423  0.020  1.423
 D8B  C15  O1   single    1.410  0.020  1.410
 D8B  C9   C14  aromatic  1.392  0.020  1.392
 D8B  C9   C10  aromatic  1.400  0.020  1.400
 D8B  C14  C13  aromatic  1.394  0.020  1.394
 D8B  C10  C11  aromatic  1.381  0.020  1.381
 D8B  C13  O1   single    1.343  0.020  1.343
 D8B  C13  C12  aromatic  1.394  0.020  1.394
 D8B  C11  C12  aromatic  1.391  0.020  1.391
 D8B  C1   H1   single    0.930  0.020  1.080
 D8B  C11  H2   single    0.930  0.020  1.080
 D8B  C12  H3   single    0.930  0.020  1.080
 D8B  C14  H4   single    0.930  0.020  1.080
 D8B  C15  H5   single    0.970  0.020  1.090
 D8B  C15  H6   single    0.970  0.020  1.090
 D8B  C15  H7   single    0.970  0.020  1.090
 D8B  C4   H8   single    0.930  0.020  1.080
 D8B  C5   H9   single    0.930  0.020  1.080
 D8B  C6   H10  single    0.970  0.020  1.090
 D8B  C6   H11  single    0.970  0.020  1.090
 D8B  C6   H12  single    0.970  0.020  1.090
 D8B  C10  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
 D8B  H1   C1   C5   121.61  3.000
 D8B  H1   C1   C2   120.43  3.000
 D8B  C5   C1   C2   117.97  3.000
 D8B  C3   N1   C2   118.86  3.000
 D8B  H2   C11  C10  119.70  3.000
 D8B  H2   C11  C12  119.01  3.000
 D8B  C10  C11  C12  121.29  3.000
 D8B  H3   C12  C13  121.45  3.000
 D8B  H3   C12  C11  118.93  3.000
 D8B  C13  C12  C11  119.62  3.000
 D8B  O1   C13  C14  115.90  3.000
 D8B  O1   C13  C12  124.55  3.000
 D8B  C14  C13  C12  119.55  3.000
 D8B  H4   C14  C9   120.14  3.000
 D8B  H4   C14  C13  119.49  3.000
 D8B  C9   C14  C13  120.36  3.000
 D8B  H7   C15  H6   108.62  3.000
 D8B  H7   C15  H5   108.62  3.000
 D8B  H6   C15  H5   108.73  3.000
 D8B  H7   C15  O1   106.52  3.000
 D8B  H6   C15  O1   112.14  3.000
 D8B  H5   C15  O1   112.08  3.000
 D8B  C7   C2   N1   117.02  3.000
 D8B  C7   C2   C1   119.91  3.000
 D8B  N1   C2   C1   123.07  3.000
 D8B  C6   C3   C4   121.33  3.000
 D8B  C4   C3   N1   121.91  3.000
 D8B  C6   C3   N1   116.76  3.000
 D8B  H8   C4   C5   120.70  3.000
 D8B  H8   C4   C3   120.14  3.000
 D8B  C5   C4   C3   119.16  3.000
 D8B  H9   C5   C4   120.59  3.000
 D8B  H9   C5   C1   120.37  3.000
 D8B  C4   C5   C1   119.03  3.000
 D8B  H12  C6   H11  108.14  3.000
 D8B  H12  C6   H10  107.97  3.000
 D8B  H11  C6   H10  107.19  3.000
 D8B  H12  C6   C3   111.79  3.000
 D8B  H11  C6   C3   110.84  3.000
 D8B  H10  C6   C3   110.74  3.000
 D8B  C8   C7   C2   180.00  3.000
 D8B  C9   C8   C7   180.00  3.000
 D8B  C10  C9   C8   120.11  3.000
 D8B  C10  C9   C14  120.03  3.000
 D8B  C8   C9   C14  119.87  3.000
 D8B  H13  C10  C9   120.01  3.000
 D8B  H13  C10  C11  120.84  3.000
 D8B  C9   C10  C11  119.15  3.000
 D8B  C15  O1   C13  118.72  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
 D8B  CONST_01  C3   C4   C5   C1     0.00   0.0  0
 D8B  CONST_02  C3   N1   C2   C1     0.00   0.0  0
 D8B  CONST_03  C5   C4   C3   N1     0.00   0.0  0
 D8B  CONST_04  C5   C1   C2   N1     0.00   0.0  0
 D8B  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 D8B  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 D8B  CONST_07  C9   C14  C13  C12    0.00   0.0  0
 D8B  CONST_08  C9   C10  C11  C12    0.00   0.0  0
 D8B  CONST_09  C10  C9   C14  C13    0.00   0.0  0
 D8B  CONST_10  C10  C11  C12  C13    0.00   0.0  0
 D8B  CONST_11  C4   C3   N1   C2     0.00   0.0  0
 D8B  CONST_12  C4   C5   C1   C2     0.00   0.0  0
 D8B  CONST_13  C8   C9   C10  C11  180.00   0.0  0
 D8B  CONST_14  O1   C13  C12  C11  180.00   0.0  0
 D8B  CONST_15  C8   C9   C14  C13  180.00   0.0  0
 D8B  CONST_16  C6   C3   N1   C2   180.00   0.0  0
 D8B  CONST_17  C7   C2   N1   C3   180.00   0.0  0
 D8B  CONST_18  C6   C3   C4   C5   180.00   0.0  0
 D8B  CONST_19  C7   C2   C1   C5   180.00   0.0  0
 D8B  CONST_20  O1   C13  C14  C9   180.00   0.0  0
 D8B  CONST_21  H8   C4   C5   C1   180.00   0.0  0
 D8B  CONST_22  H1   C1   C2   N1   180.00   0.0  0
 D8B  CONST_23  H4   C14  C13  C12  180.00   0.0  0
 D8B  CONST_24  H13  C10  C11  C12  180.00   0.0  0
 D8B  CONST_25  H2   C11  C12  C13  180.00   0.0  0
 D8B  CONST_26  H3   C12  C13  C14  180.00   0.0  0
 D8B  CONST_27  H9   C5   C1   C2   180.00   0.0  0
 D8B  Var_01    H10  C6   C3   N1   -61.73  30.0  2
 D8B  Var_02    H5   C15  O1   C13  -60.69  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
 D8B  plan-1  C1   0.020
 D8B  plan-1  N1   0.020
 D8B  plan-1  C2   0.020
 D8B  plan-1  C3   0.020
 D8B  plan-1  C4   0.020
 D8B  plan-1  C5   0.020
 D8B  plan-1  C6   0.020
 D8B  plan-1  C7   0.020
 D8B  plan-1  C8   0.020
 D8B  plan-1  H1   0.020
 D8B  plan-1  H8   0.020
 D8B  plan-1  H9   0.020
 D8B  plan-2  C11  0.020
 D8B  plan-2  C12  0.020
 D8B  plan-2  C13  0.020
 D8B  plan-2  C14  0.020
 D8B  plan-2  C7   0.020
 D8B  plan-2  C8   0.020
 D8B  plan-2  C9   0.020
 D8B  plan-2  C10  0.020
 D8B  plan-2  H2   0.020
 D8B  plan-2  H3   0.020
 D8B  plan-2  H4   0.020
 D8B  plan-2  H13  0.020
 D8B  plan-2  O1   0.020

