# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 16:23:33 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-[(2-methoxy-5-methylphenoxy)methyl]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C)cc1OCc2ccccn2
#
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
 B77  B77  2-[(2-methoxy-5-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_B77
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
 B77  C1    C  CH3   0  -0.724  -3.6143   3.1191   0.0258
 B77  C2    C  CR6   0   0.091  -3.0889   1.7129   0.0196
 B77  C3    C  CR16  0  -0.422  -1.7066   1.4855   0.0120
 B77  C4    C  CR6   0   0.352  -1.1899   0.2031   0.0055
 B77  C5    C  CR6   0   0.279  -2.0608  -0.9066   0.0064
 B77  C6    C  CR16  0  -0.372  -3.4254  -0.6826   0.0142
 B77  C7    C  CR16  0  -0.320  -3.9324   0.6186   0.0208
 B77  O8    O  O2    0  -0.463  -1.4670  -2.1166  -0.0008
 B77  C9    C  CH3   0  -0.435  -2.2966  -3.2592   0.0097
 B77  O10   O  O2    0  -0.473   0.1245  -0.0990  -0.0021
 B77  C11   C  CH2   0  -0.204   1.0606   0.9475  -0.0017
 B77  C12   C  CR6   0   0.190   2.4489   0.3707  -0.0168
 B77  N13   N  N     0  -0.427   3.4161   1.2835  -0.0228
 B77  C14   C  CR16  0  -0.077   4.6760   0.8720  -0.0359
 B77  C15   C  CR16  0  -0.326   5.0408  -0.4665  -0.0438
 B77  C16   C  CR16  0  -0.147   4.0301  -1.4140  -0.0374
 B77  C17   C  CR16  0  -0.337   2.7074  -0.9945  -0.0236
 B77  H1    H  HCH3  0   0.242  -3.2802   3.6732  -0.8531
 B77  H1A   H  HCH3  0   0.243  -4.7036   3.1367   0.0345
 B77  H1B   H  HCH3  0   0.242  -3.2662   3.6706   0.9010
 B77  H3    H  HCR6  0   0.278  -1.0426   2.3408   0.0116
 B77  H6    H  HCR6  0   0.280  -4.1218  -1.5100   0.0153
 B77  H7    H  HCR6  0   0.246  -5.0060   0.7608   0.0268
 B77  H9    H  HCH3  0   0.258  -1.6357  -4.1225   0.0070
 B77  H9A   H  HCH3  0   0.226  -2.9246  -3.3013   0.9037
 B77  H9B   H  HCH3  0   0.226  -2.9393  -3.3074  -0.8735
 B77  H11   H  HCH2  0   0.249   0.9337   1.5961  -0.8774
 B77  H11A  H  HCH2  0   0.249   0.9471   1.5828   0.8856
 B77  H14   H  HCR6  0   0.264   5.4358   1.6455  -0.0406
 B77  H15   H  HCR6  0   0.269   6.0842  -0.7494  -0.0547
 B77  H16   H  HCR6  0   0.274   4.2637  -2.4706  -0.0435
 B77  H17   H  HCR6  0   0.271   1.9034  -1.7159  -0.0188

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
 B77  C1   C2    single    1.501  0.020  1.501
 B77  C2   C3    aromatic  1.401  0.020  1.401
 B77  C2   C7    aromatic  1.382  0.020  1.382
 B77  C3   C4    aromatic  1.383  0.020  1.383
 B77  C4   C5    aromatic  1.411  0.020  1.411
 B77  C4   O10   single    1.349  0.020  1.349
 B77  C5   C6    aromatic  1.383  0.020  1.383
 B77  C5   O8    single    1.348  0.020  1.348
 B77  C6   C7    aromatic  1.397  0.020  1.397
 B77  O8   C9    single    1.412  0.020  1.412
 B77  O10  C11   single    1.404  0.020  1.404
 B77  C11  C12   single    1.503  0.020  1.503
 B77  C12  N13   aromatic  1.330  0.020  1.330
 B77  C12  C17   aromatic  1.389  0.020  1.389
 B77  N13  C14   aromatic  1.325  0.020  1.325
 B77  C14  C15   aromatic  1.387  0.020  1.387
 B77  C15  C16   aromatic  1.385  0.020  1.385
 B77  C16  C17   aromatic  1.388  0.020  1.388
 B77  C1   H1    single    0.970  0.020  1.090
 B77  C1   H1A   single    0.970  0.020  1.090
 B77  C1   H1B   single    0.970  0.020  1.090
 B77  C3   H3    single    0.930  0.020  1.080
 B77  C6   H6    single    0.930  0.020  1.080
 B77  C7   H7    single    0.930  0.020  1.080
 B77  C9   H9    single    0.970  0.020  1.090
 B77  C9   H9A   single    0.970  0.020  1.090
 B77  C9   H9B   single    0.970  0.020  1.090
 B77  C11  H11   single    0.970  0.020  1.090
 B77  C11  H11A  single    0.970  0.020  1.090
 B77  C14  H14   single    0.930  0.020  1.080
 B77  C15  H15   single    0.930  0.020  1.080
 B77  C16  H16   single    0.930  0.020  1.080
 B77  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
 B77  H1B   C1   H1A  107.72  3.000
 B77  H1B   C1   H1   106.96  3.000
 B77  H1A   C1   H1   107.71  3.000
 B77  H1B   C1   C2   111.41  3.000
 B77  H1A   C1   C2   111.41  3.000
 B77  H1    C1   C2   111.41  3.000
 B77  C7    C2   C3   118.28  3.000
 B77  C7    C2   C1   121.88  3.000
 B77  C3    C2   C1   119.83  3.000
 B77  H3    C3   C4   120.23  3.000
 B77  H3    C3   C2   118.48  3.000
 B77  C4    C3   C2   121.29  3.000
 B77  O10   C4   C5   115.18  3.000
 B77  O10   C4   C3   124.89  3.000
 B77  C5    C4   C3   119.93  3.000
 B77  O8    C5   C6   125.46  3.000
 B77  O8    C5   C4   115.73  3.000
 B77  C6    C5   C4   118.80  3.000
 B77  H6    C6   C7   118.62  3.000
 B77  H6    C6   C5   120.77  3.000
 B77  C7    C6   C5   120.61  3.000
 B77  H7    C7   C6   118.83  3.000
 B77  H7    C7   C2   120.09  3.000
 B77  C6    C7   C2   121.08  3.000
 B77  C9    O8   C5   117.88  3.000
 B77  H9B   C9   H9A  108.73  3.000
 B77  H9B   C9   H9   108.68  3.000
 B77  H9A   C9   H9   108.70  3.000
 B77  H9B   C9   O8   112.03  3.000
 B77  H9A   C9   O8   112.01  3.000
 B77  H9    C9   O8   106.58  3.000
 B77  C11   O10  C4   118.87  3.000
 B77  H11A  C11  H11  106.93  3.000
 B77  H11A  C11  C12  109.01  3.000
 B77  H11   C11  C12  109.01  3.000
 B77  H11A  C11  O10  111.28  3.000
 B77  H11   C11  O10  111.30  3.000
 B77  C12   C11  O10  109.25  3.000
 B77  C17   C12  N13  122.62  3.000
 B77  C17   C12  C11  123.29  3.000
 B77  N13   C12  C11  114.10  3.000
 B77  C14   N13  C12  118.57  3.000
 B77  H14   C14  C15  120.26  3.000
 B77  H14   C14  N13  116.40  3.000
 B77  C15   C14  N13  123.33  3.000
 B77  H15   C15  C16  121.68  3.000
 B77  H15   C15  C14  120.42  3.000
 B77  C16   C15  C14  117.90  3.000
 B77  H16   C16  C17  120.06  3.000
 B77  H16   C16  C15  120.68  3.000
 B77  C17   C16  C15  119.25  3.000
 B77  H17   C17  C16  120.51  3.000
 B77  H17   C17  C12  121.17  3.000
 B77  C16   C17  C12  118.32  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
 B77  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 B77  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 B77  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 B77  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 B77  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 B77  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 B77  CONST_07  C15  C14  N13  C12     0.00   0.0  0
 B77  CONST_08  C15  C16  C17  C12     0.00   0.0  0
 B77  CONST_09  C16  C17  C12  N13     0.00   0.0  0
 B77  CONST_10  C16  C15  C14  N13     0.00   0.0  0
 B77  CONST_11  C17  C12  N13  C14     0.00   0.0  0
 B77  CONST_12  C17  C16  C15  C14     0.00   0.0  0
 B77  CONST_13  C4   C3   C2   C1    180.00   0.0  0
 B77  CONST_14  C6   C7   C2   C1    180.00   0.0  0
 B77  CONST_15  O10  C4   C3   C2    180.00   0.0  0
 B77  CONST_16  O8   C5   C4   C3    180.00   0.0  0
 B77  CONST_17  O10  C4   C5   C6    180.00   0.0  0
 B77  CONST_18  O8   C5   C6   C7    180.00   0.0  0
 B77  CONST_19  C14  N13  C12  C11   180.00   0.0  0
 B77  CONST_20  C16  C17  C12  C11   180.00   0.0  0
 B77  CONST_21  H6   C6   C7   C2    180.00   0.0  0
 B77  CONST_22  H7   C7   C2   C3    180.00   0.0  0
 B77  CONST_23  H3   C3   C4   C5    180.00   0.0  0
 B77  CONST_24  H14  C14  N13  C12   180.00   0.0  0
 B77  CONST_25  H16  C16  C17  C12   180.00   0.0  0
 B77  CONST_26  H17  C17  C12  N13   180.00   0.0  0
 B77  CONST_27  H15  C15  C14  N13   180.00   0.0  0
 B77  Var_01    C12  C11  O10  C4   -179.76  30.0  3
 B77  Var_02    N13  C12  C11  O10   179.76  30.0  2
 B77  Var_03    H1   C1   C2   C3     59.85  30.0  2
 B77  Var_04    H9   C9   O8   C5   -179.70  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
 B77  plan-1  C1   0.020
 B77  plan-1  C2   0.020
 B77  plan-1  C3   0.020
 B77  plan-1  C4   0.020
 B77  plan-1  C5   0.020
 B77  plan-1  C6   0.020
 B77  plan-1  C7   0.020
 B77  plan-1  O8   0.020
 B77  plan-1  O10  0.020
 B77  plan-1  H3   0.020
 B77  plan-1  H6   0.020
 B77  plan-1  H7   0.020
 B77  plan-2  C11  0.020
 B77  plan-2  C12  0.020
 B77  plan-2  N13  0.020
 B77  plan-2  C14  0.020
 B77  plan-2  C15  0.020
 B77  plan-2  C16  0.020
 B77  plan-2  C17  0.020
 B77  plan-2  H14  0.020
 B77  plan-2  H15  0.020
 B77  plan-2  H16  0.020
 B77  plan-2  H17  0.020

