# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 16:38:37 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 4-[(5-methoxy-2-methylphenoxy)methyl]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C)c(OCc2ccncc2)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
 B78  B78  4-[(5-methoxy-2-methylphenoxy)methyl]pyridine  ligand  32  17  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B78
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
 B78  C1    C  CH3   0  -0.709  -0.7491   2.8777   0.5236
 B78  C2    C  CR6   0  -0.023  -1.5854   1.6504   0.3135
 B78  C3    C  CR6   0   0.380  -0.9893   0.4167  -0.0000
 B78  C4    C  CR16  0  -0.481  -1.7543  -0.7213  -0.1988
 B78  C5    C  CR6   0   0.393  -3.1472  -0.6566  -0.0863
 B78  C6    C  CR16  0  -0.403  -3.7600   0.5487   0.2228
 B78  C7    C  CR16  0  -0.274  -2.9641   1.6767   0.4154
 B78  O8    O  O2    0  -0.474  -3.8010  -1.8163  -0.2973
 B78  C9    C  CH3   0  -0.435  -5.2112  -1.8170  -0.2099
 B78  O10   O  O2    0  -0.467   0.3571   0.4346  -0.0912
 B78  C11   C  CH2   0  -0.226   1.0504  -0.7698  -0.3263
 B78  C12   C  CR6   0   0.163   2.5217  -0.4933  -0.2354
 B78  C13   C  CR16  0  -0.362   3.0463   0.3756   0.7159
 B78  C14   C  CR16  0  -0.057   4.4198   0.5492   0.7760
 B78  N15   N  N     0  -0.408   5.2785  -0.0717  -0.0260
 B78  C16   C  CR16  0  -0.058   4.7739  -0.9001  -0.9315
 B78  C17   C  CR16  0  -0.368   3.4155  -1.1408  -1.0772
 B78  H1    H  HCH3  0   0.239  -0.2034   3.1588  -0.3794
 B78  H1A   H  HCH3  0   0.240  -1.3756   3.7230   0.8058
 B78  H1B   H  HCH3  0   0.239  -0.0073   2.7360   1.3114
 B78  H4    H  HCR6  0   0.284  -1.3043  -1.6735  -0.4490
 B78  H6    H  HCR6  0   0.273  -4.8330   0.6392   0.3157
 B78  H7    H  HCR6  0   0.251  -3.4493   2.6142   0.6605
 B78  H9    H  HCH3  0   0.227  -5.5610  -1.5405   0.7883
 B78  H9A   H  HCH3  0   0.227  -5.6672  -1.1439  -0.9406
 B78  H9B   H  HCH3  0   0.258  -5.5337  -2.8331  -0.4230
 B78  H11   H  HCH2  0   0.254   0.7848  -1.5253   0.4237
 B78  H11A  H  HCH2  0   0.249   0.8016  -1.1846  -1.3089
 B78  H13   H  HCR6  0   0.267   2.4093   0.9140   1.4043
 B78  H14   H  HCR6  0   0.265   4.8454   1.2239   1.5107
 B78  H16   H  HCR6  0   0.266   5.4825  -1.3975  -1.5846
 B78  H17   H  HCR6  0   0.270   3.0683  -1.8204  -1.8451

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
 B78  C1   C2    single    1.500  0.020  1.500
 B78  C2   C3    aromatic  1.406  0.020  1.406
 B78  C2   C7    aromatic  1.383  0.020  1.383
 B78  C3   C4    aromatic  1.386  0.020  1.386
 B78  C3   O10   single    1.350  0.020  1.350
 B78  C4   C5    aromatic  1.399  0.020  1.399
 B78  C5   C6    aromatic  1.387  0.020  1.387
 B78  C5   O8    single    1.348  0.020  1.348
 B78  C6   C7    aromatic  1.394  0.020  1.394
 B78  O8   C9    single    1.413  0.020  1.413
 B78  O10  C11   single    1.409  0.020  1.409
 B78  C11  C12   single    1.500  0.020  1.500
 B78  C12  C13   aromatic  1.391  0.020  1.391
 B78  C12  C17   aromatic  1.388  0.020  1.388
 B78  C13  C14   aromatic  1.386  0.020  1.386
 B78  C14  N15   aromatic  1.329  0.020  1.329
 B78  N15  C16   aromatic  1.327  0.020  1.327
 B78  C16  C17   aromatic  1.387  0.020  1.387
 B78  C1   H1    single    0.970  0.020  1.090
 B78  C1   H1A   single    0.970  0.020  1.090
 B78  C1   H1B   single    0.970  0.020  1.090
 B78  C4   H4    single    0.930  0.020  1.080
 B78  C6   H6    single    0.930  0.020  1.080
 B78  C7   H7    single    0.930  0.020  1.080
 B78  C9   H9    single    0.970  0.020  1.090
 B78  C9   H9A   single    0.970  0.020  1.090
 B78  C9   H9B   single    0.970  0.020  1.090
 B78  C11  H11   single    0.970  0.020  1.090
 B78  C11  H11A  single    0.970  0.020  1.090
 B78  C13  H13   single    0.930  0.020  1.080
 B78  C14  H14   single    0.930  0.020  1.080
 B78  C16  H16   single    0.930  0.020  1.080
 B78  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
 B78  H1B   C1   H1A  107.74  3.000
 B78  H1B   C1   H1   106.90  3.000
 B78  H1A   C1   H1   107.57  3.000
 B78  H1B   C1   C2   111.96  3.000
 B78  H1A   C1   C2   110.52  3.000
 B78  H1    C1   C2   111.93  3.000
 B78  C7    C2   C3   117.13  3.000
 B78  C7    C2   C1   122.01  3.000
 B78  C3    C2   C1   120.86  3.000
 B78  O10   C3   C4   123.50  3.000
 B78  O10   C3   C2   115.25  3.000
 B78  C4    C3   C2   121.25  3.000
 B78  H4    C4   C5   118.24  3.000
 B78  H4    C4   C3   121.75  3.000
 B78  C5    C4   C3   120.01  3.000
 B78  O8    C5   C6   124.63  3.000
 B78  O8    C5   C4   115.50  3.000
 B78  C6    C5   C4   119.87  3.000
 B78  H6    C6   C7   119.16  3.000
 B78  H6    C6   C5   122.04  3.000
 B78  C7    C6   C5   118.80  3.000
 B78  H7    C7   C6   118.40  3.000
 B78  H7    C7   C2   118.66  3.000
 B78  C6    C7   C2   122.94  3.000
 B78  C9    O8   C5   118.35  3.000
 B78  H9B   C9   H9A  108.71  3.000
 B78  H9B   C9   H9   108.69  3.000
 B78  H9A   C9   H9   108.74  3.000
 B78  H9B   C9   O8   106.52  3.000
 B78  H9A   C9   O8   112.00  3.000
 B78  H9    C9   O8   112.06  3.000
 B78  C11   O10  C3   119.38  3.000
 B78  H11A  C11  H11  107.31  3.000
 B78  H11A  C11  C12  110.31  3.000
 B78  H11   C11  C12  108.85  3.000
 B78  H11A  C11  O10  111.19  3.000
 B78  H11   C11  O10  110.82  3.000
 B78  C12   C11  O10  108.35  3.000
 B78  C17   C12  C13  117.60  3.000
 B78  C17   C12  C11  120.59  3.000
 B78  C13   C12  C11  121.77  3.000
 B78  H13   C13  C14  119.60  3.000
 B78  H13   C13  C12  121.61  3.000
 B78  C14   C13  C12  118.80  3.000
 B78  H14   C14  N15  116.48  3.000
 B78  H14   C14  C13  119.76  3.000
 B78  N15   C14  C13  123.76  3.000
 B78  C16   N15  C14  117.24  3.000
 B78  H16   C16  C17  119.80  3.000
 B78  H16   C16  N15  116.67  3.000
 B78  C17   C16  N15  123.53  3.000
 B78  H17   C17  C16  119.83  3.000
 B78  H17   C17  C12  121.10  3.000
 B78  C16   C17  C12  119.06  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
 B78  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 B78  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 B78  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 B78  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 B78  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 B78  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 B78  CONST_07  N15  C14  C13  C12     0.00   0.0  0
 B78  CONST_08  N15  C16  C17  C12     0.00   0.0  0
 B78  CONST_09  C16  C17  C12  C13     0.00   0.0  0
 B78  CONST_10  C16  N15  C14  C13     0.00   0.0  0
 B78  CONST_11  C17  C12  C13  C14     0.00   0.0  0
 B78  CONST_12  C17  C16  N15  C14     0.00   0.0  0
 B78  CONST_13  C4   C3   C2   C1    180.00   0.0  0
 B78  CONST_14  C6   C7   C2   C1    180.00   0.0  0
 B78  CONST_15  O8   C5   C4   C3    180.00   0.0  0
 B78  CONST_16  O10  C3   C4   C5    180.00   0.0  0
 B78  CONST_17  O10  C3   C2   C7    180.00   0.0  0
 B78  CONST_18  O8   C5   C6   C7    180.00   0.0  0
 B78  CONST_19  C14  C13  C12  C11   180.00   0.0  0
 B78  CONST_20  C16  C17  C12  C11   180.00   0.0  0
 B78  CONST_21  H4   C4   C3   C2    180.00   0.0  0
 B78  CONST_22  H6   C6   C7   C2    180.00   0.0  0
 B78  CONST_23  H7   C7   C2   C3    180.00   0.0  0
 B78  CONST_24  H14  C14  C13  C12   180.00   0.0  0
 B78  CONST_25  H16  C16  C17  C12   180.00   0.0  0
 B78  CONST_26  H17  C17  C12  C13   180.00   0.0  0
 B78  CONST_27  H13  C13  C14  N15   180.00   0.0  0
 B78  Var_01    C12  C11  O10  C3   -174.01  30.0  3
 B78  Var_02    C13  C12  C11  O10    38.88  30.0  2
 B78  Var_03    H1   C1   C2   C3     62.96  30.0  2
 B78  Var_04    H9   C9   O8   C5    -61.94  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
 B78  plan-1  C1   0.020
 B78  plan-1  C2   0.020
 B78  plan-1  C3   0.020
 B78  plan-1  C4   0.020
 B78  plan-1  C5   0.020
 B78  plan-1  C6   0.020
 B78  plan-1  C7   0.020
 B78  plan-1  O8   0.020
 B78  plan-1  O10  0.020
 B78  plan-1  H4   0.020
 B78  plan-1  H6   0.020
 B78  plan-1  H7   0.020
 B78  plan-2  C11  0.020
 B78  plan-2  C12  0.020
 B78  plan-2  C13  0.020
 B78  plan-2  C14  0.020
 B78  plan-2  N15  0.020
 B78  plan-2  C16  0.020
 B78  plan-2  C17  0.020
 B78  plan-2  H13  0.020
 B78  plan-2  H14  0.020
 B78  plan-2  H16  0.020
 B78  plan-2  H17  0.020

