# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 12:39:19 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 2-(3-methylphenyl)-N-(pyridin-3-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(CC(=O)Nc2cccnc2)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
 H54  H54  2-(3-methylphenyl)-N-(pyridin-3-yl)acetamide  ligand  31  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H54
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
 H54  N1   N  NH1   0  -0.695  -1.5129   0.7134   0.4438
 H54  C4   C  CR16  0  -0.349   3.9308   0.8625  -1.5272
 H54  C5   C  CR16  0  -0.266   2.6923   1.2642  -1.0471
 H54  C6   C  CR6   0   0.101   2.1902   0.7204   0.1305
 H54  C7   C  CH2   0  -0.672   0.8436   1.1322   0.6417
 H54  C8   C  C     0   0.576  -0.2771   0.2511   0.1126
 H54  C10  C  CR16  0  -0.157  -2.9793  -1.0599  -0.4733
 H54  C13  C  CR16  0  -0.075  -3.8807   0.8477   0.6439
 H54  C2   C  CR6   0  -0.078   4.1937  -0.6385   0.3476
 H54  C3   C  CR16  0  -0.143   4.6752  -0.0830  -0.8362
 H54  C9   C  CR6   0   0.133  -2.7582   0.1463   0.1888
 H54  C11  C  CR16  0  -0.291  -4.2884  -1.4870  -0.6374
 H54  C12  C  CR16  0  -0.099  -5.3291  -0.7169  -0.1476
 H54  N2   N  N     0  -0.419  -5.1240   0.4344   0.4837
 H54  O1   O  O     0  -0.449  -0.0811  -0.7658  -0.5209
 H54  C14  C  CR16  0  -0.237   2.9475  -0.2258   0.8124
 H54  H1   H  HNH1  0   0.429  -1.5377   1.5797   0.9620
 H54  H2   H  HCR6  0   0.217   4.3167   1.2876  -2.4449
 H54  H3   H  HCR6  0   0.260   2.1132   2.0018  -1.5901
 H54  H4   H  HCH2  0   0.302   0.8064   1.0824   1.7329
 H54  H5   H  HCH2  0   0.294   0.6346   2.1732   0.3810
 H54  H6   H  HCR6  0   0.292  -2.1646  -1.6551  -0.8515
 H54  H7   H  HCR6  0   0.281  -3.7444   1.7909   1.1670
 H54  H8   H  HCH3  0   0.251   5.6940  -1.1377   1.8042
 H54  H9   H  HCH3  0   0.264   4.3774  -2.2978   1.7108
 H54  H10  H  HCH3  0   0.214   5.6127  -2.2558   0.4527
 H54  H11  H  HCR6  0   0.254   5.6414  -0.3906  -1.2192
 H54  H12  H  HCR6  0   0.243  -4.4947  -2.4188  -1.1460
 H54  H13  H  HCR6  0   0.281  -6.3581  -1.0353  -0.2657
 H54  H14  H  HCR6  0   0.243   2.5597  -0.6521   1.7318
 H54  C1   C  CH3   0  -0.705   5.0087  -1.6381   1.1165

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
 H54  C11  C10  aromatic  1.387  0.020  1.387
 H54  C11  C12  aromatic  1.384  0.020  1.384
 H54  C10  C9   aromatic  1.394  0.020  1.394
 H54  O1   C8   double    1.214  0.020  1.214
 H54  C12  N2   aromatic  1.329  0.020  1.329
 H54  C8   C7   single    1.521  0.020  1.521
 H54  C8   N1   single    1.360  0.020  1.360
 H54  C9   N1   single    1.392  0.020  1.392
 H54  C9   C13  aromatic  1.400  0.020  1.400
 H54  C7   C6   single    1.498  0.020  1.498
 H54  C5   C6   aromatic  1.391  0.020  1.391
 H54  C5   C4   aromatic  1.388  0.020  1.388
 H54  N2   C13  aromatic  1.320  0.020  1.320
 H54  C6   C14  aromatic  1.391  0.020  1.391
 H54  C4   C3   aromatic  1.388  0.020  1.388
 H54  C14  C2   aromatic  1.393  0.020  1.393
 H54  C3   C2   aromatic  1.394  0.020  1.394
 H54  C2   C1   single    1.502  0.020  1.502
 H54  N1   H1   single    0.860  0.020  1.020
 H54  C4   H2   single    0.930  0.020  1.080
 H54  C5   H3   single    0.930  0.020  1.080
 H54  C7   H4   single    0.970  0.020  1.090
 H54  C7   H5   single    0.970  0.020  1.090
 H54  C10  H6   single    0.930  0.020  1.080
 H54  C13  H7   single    0.930  0.020  1.080
 H54  C1   H8   single    0.970  0.020  1.090
 H54  C1   H9   single    0.970  0.020  1.090
 H54  C1   H10  single    0.970  0.020  1.090
 H54  C3   H11  single    0.930  0.020  1.080
 H54  C11  H12  single    0.930  0.020  1.080
 H54  C12  H13  single    0.930  0.020  1.080
 H54  C14  H14  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
 H54  H1   N1   C9   114.93  3.000
 H54  H1   N1   C8   116.03  3.000
 H54  C9   N1   C8   129.03  3.000
 H54  H2   C4   C3   119.89  3.000
 H54  H2   C4   C5   119.86  3.000
 H54  C3   C4   C5   120.25  3.000
 H54  H3   C5   C6   119.83  3.000
 H54  H3   C5   C4   120.04  3.000
 H54  C6   C5   C4   120.13  3.000
 H54  C14  C6   C7   120.61  3.000
 H54  C14  C6   C5   118.99  3.000
 H54  C7   C6   C5   120.40  3.000
 H54  H5   C7   H4   105.96  3.000
 H54  H5   C7   C8   109.14  3.000
 H54  H4   C7   C8   107.22  3.000
 H54  H5   C7   C6   110.61  3.000
 H54  H4   C7   C6   111.02  3.000
 H54  C8   C7   C6   112.61  3.000
 H54  O1   C8   C7   123.23  3.000
 H54  C7   C8   N1   112.82  3.000
 H54  O1   C8   N1   123.94  3.000
 H54  H6   C10  C11  120.14  3.000
 H54  H6   C10  C9   121.66  3.000
 H54  C11  C10  C9   118.20  3.000
 H54  H7   C13  N2   116.62  3.000
 H54  H7   C13  C9   119.39  3.000
 H54  N2   C13  C9   123.99  3.000
 H54  C14  C2   C3   118.34  3.000
 H54  C3   C2   C1   120.85  3.000
 H54  C14  C2   C1   120.80  3.000
 H54  H11  C3   C2   119.67  3.000
 H54  H11  C3   C4   119.71  3.000
 H54  C2   C3   C4   120.61  3.000
 H54  C13  C9   C10  117.45  3.000
 H54  C13  C9   N1   116.99  3.000
 H54  C10  C9   N1   125.56  3.000
 H54  H12  C11  C12  120.16  3.000
 H54  H12  C11  C10  120.07  3.000
 H54  C12  C11  C10  119.77  3.000
 H54  H13  C12  N2   116.93  3.000
 H54  H13  C12  C11  120.79  3.000
 H54  N2   C12  C11  122.28  3.000
 H54  C12  N2   C13  118.31  3.000
 H54  H14  C14  C2   119.09  3.000
 H54  H14  C14  C6   119.22  3.000
 H54  C2   C14  C6   121.69  3.000
 H54  H10  C1   H9   108.07  3.000
 H54  H10  C1   H8   107.19  3.000
 H54  H9   C1   H8   107.31  3.000
 H54  H10  C1   C2   111.49  3.000
 H54  H9   C1   C2   111.58  3.000
 H54  H8   C1   C2   110.98  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
 H54  CONST_01  C14  C6   C5   C4      0.00   0.0  0
 H54  CONST_02  C14  C2   C3   C4      0.00   0.0  0
 H54  CONST_03  C2   C14  C6   C5      0.00   0.0  0
 H54  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 H54  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 H54  CONST_06  C3   C2   C14  C6      0.00   0.0  0
 H54  CONST_07  N2   C12  C11  C10     0.00   0.0  0
 H54  CONST_08  N2   C13  C9   C10     0.00   0.0  0
 H54  CONST_09  C11  C10  C9   C13     0.00   0.0  0
 H54  CONST_10  C11  C12  N2   C13     0.00   0.0  0
 H54  CONST_11  C12  C11  C10  C9      0.00   0.0  0
 H54  CONST_12  C12  N2   C13  C9      0.00   0.0  0
 H54  CONST_13  C11  C10  C9   N1    180.00   0.0  0
 H54  CONST_14  N2   C13  C9   N1    180.00   0.0  0
 H54  CONST_15  C7   C6   C5   C4    180.00   0.0  0
 H54  CONST_16  C1   C2   C3   C4    180.00   0.0  0
 H54  CONST_17  C1   C2   C14  C6    180.00   0.0  0
 H54  CONST_18  C2   C14  C6   C7    180.00   0.0  0
 H54  CONST_19  H14  C14  C6   C5    180.00   0.0  0
 H54  CONST_20  H11  C3   C4   C5    180.00   0.0  0
 H54  CONST_21  H2   C4   C5   C6    180.00   0.0  0
 H54  CONST_22  H13  C12  C11  C10   180.00   0.0  0
 H54  CONST_23  H7   C13  C9   C10   180.00   0.0  0
 H54  CONST_24  H6   C10  C9   C13   180.00   0.0  0
 H54  CONST_25  H3   C5   C4   C3    180.00   0.0  0
 H54  CONST_26  H12  C11  C10  C9    180.00   0.0  0
 H54  CONST_27  C10  C9   N1   C8      0.00   0.0  0
 H54  CONST_28  C13  C9   N1   C8    180.00   0.0  0
 H54  CONST_29  H1   N1   C9   C10   180.00   0.0  0
 H54  CONST_30  C9   N1   C8   C7    180.00   0.0  0
 H54  CONST_31  O1   C8   N1   C9      0.00   0.0  0
 H54  Var_01    C8   C7   C6   C5     90.24  30.0  2
 H54  Var_02    H8   C1   C2   C3     86.56  30.0  2
 H54  Var_03    C6   C7   C8   N1   -172.68  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
 H54  plan-1  C4   0.020
 H54  plan-1  C5   0.020
 H54  plan-1  C6   0.020
 H54  plan-1  C7   0.020
 H54  plan-1  C2   0.020
 H54  plan-1  C3   0.020
 H54  plan-1  C14  0.020
 H54  plan-1  H2   0.020
 H54  plan-1  H3   0.020
 H54  plan-1  H11  0.020
 H54  plan-1  H14  0.020
 H54  plan-1  C1   0.020
 H54  plan-2  N1   0.020
 H54  plan-2  C10  0.020
 H54  plan-2  C13  0.020
 H54  plan-2  C9   0.020
 H54  plan-2  C11  0.020
 H54  plan-2  C12  0.020
 H54  plan-2  N2   0.020
 H54  plan-2  H6   0.020
 H54  plan-2  H7   0.020
 H54  plan-2  H12  0.020
 H54  plan-2  H13  0.020
 H54  plan-3  N1   0.020
 H54  plan-3  C7   0.020
 H54  plan-3  C8   0.020
 H54  plan-3  C9   0.020
 H54  plan-3  O1   0.020
 H54  plan-3  H1   0.020

