# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 15:39:33 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-(2-methylphenoxy)-~{N}-pyridin-3-yl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1OCC(=O)Nc2cccnc2
#
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
 JVB  JVB  2-(2-methylphenoxy)-~{N}-pyridin-3-yl-ethanamide  ligand  32  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JVB
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
 JVB  C10  C  C     0   0.512  -0.7351  -0.2066  -0.0078
 JVB  N12  N  NH1   0  -0.744  -1.8218   0.5874   0.1635
 JVB  C13  C  CR6   0   0.290  -3.1700   0.2372   0.1229
 JVB  C15  C  CR16  0  -0.312  -5.0403  -1.2303  -0.0654
 JVB  C02  C  CR6   0  -0.004   3.8688  -0.8988   0.0274
 JVB  C03  C  CR16  0  -0.287   5.1974  -0.5092  -0.0584
 JVB  C04  C  CR16  0  -0.269   5.5646   0.8289  -0.1666
 JVB  C05  C  CR16  0  -0.258   4.5800   1.8000  -0.1881
 JVB  C06  C  CR16  0  -0.376   3.2374   1.4427  -0.1043
 JVB  C07  C  CR6   0   0.357   2.8853   0.1020   0.0004
 JVB  C09  C  CH2   0  -0.306   0.5656   0.5811   0.0153
 JVB  C14  C  CR16  0  -0.211  -3.6650  -1.0537  -0.0485
 JVB  C16  C  CR16  0  -0.085  -5.8750  -0.1367   0.0881
 JVB  C18  C  CR16  0  -0.144  -4.0992   1.2725   0.2694
 JVB  N17  N  N     0  -0.387  -5.4073   1.0961   0.2539
 JVB  O08  O  O2    0  -0.456   1.6110  -0.3424   0.0829
 JVB  O11  O  O     0  -0.439  -0.7730  -1.4044  -0.1846
 JVB  H1   H  HNH1  0   0.423  -1.6435   1.5699   0.3172
 JVB  H2   H  HCR6  0   0.275  -5.4575  -2.2193  -0.1971
 JVB  H3   H  HCH3  0   0.243   3.0005  -2.5501   1.1086
 JVB  H4   H  HCH3  0   0.243   2.7804  -2.6453  -0.6275
 JVB  H5   H  HCH3  0   0.241   4.3599  -2.9824   0.0783
 JVB  H6   H  HCR6  0   0.249   5.9653  -1.2734  -0.0412
 JVB  H7   H  HCR6  0   0.250   6.6096   1.1012  -0.2334
 JVB  H8   H  HCR6  0   0.257   4.8418   2.8468  -0.2709
 JVB  H9   H  HCR6  0   0.280   2.4886   2.2229  -0.1197
 JVB  H10  H  HCH2  0   0.272   0.6121   1.1905  -0.8971
 JVB  H11  H  HCH2  0   0.264   0.5711   1.2715   0.8679
 JVB  H12  H  HCR6  0   0.295  -3.0096  -1.9010  -0.1642
 JVB  H13  H  HCR6  0   0.265  -6.9520  -0.2552   0.0785
 JVB  H14  H  HCR6  0   0.273  -3.7463   2.2912   0.4048
 JVB  C01  C  CH3   0  -0.709   3.4819  -2.3426   0.1510

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
 JVB  C05  C04  aromatic  1.383  0.020  1.383
 JVB  C05  C06  aromatic  1.392  0.020  1.392
 JVB  C04  C03  aromatic  1.392  0.020  1.392
 JVB  C06  C07  aromatic  1.390  0.020  1.390
 JVB  C03  C02  aromatic  1.387  0.020  1.387
 JVB  C07  C02  aromatic  1.403  0.020  1.403
 JVB  C07  O08  single    1.352  0.020  1.352
 JVB  C02  C01  single    1.500  0.020  1.500
 JVB  C09  O08  single    1.396  0.020  1.396
 JVB  C09  C10  single    1.521  0.020  1.521
 JVB  O11  C10  double    1.211  0.020  1.211
 JVB  C10  N12  single    1.357  0.020  1.357
 JVB  N12  C13  single    1.394  0.020  1.394
 JVB  C18  C13  aromatic  1.399  0.020  1.399
 JVB  C18  N17  aromatic  1.320  0.020  1.320
 JVB  C13  C14  aromatic  1.393  0.020  1.393
 JVB  N17  C16  aromatic  1.329  0.020  1.329
 JVB  C14  C15  aromatic  1.387  0.020  1.387
 JVB  C16  C15  aromatic  1.384  0.020  1.384
 JVB  N12  H1   single    0.860  0.020  1.020
 JVB  C15  H2   single    0.930  0.020  1.080
 JVB  C01  H3   single    0.970  0.020  1.090
 JVB  C01  H4   single    0.970  0.020  1.090
 JVB  C01  H5   single    0.970  0.020  1.090
 JVB  C03  H6   single    0.930  0.020  1.080
 JVB  C04  H7   single    0.930  0.020  1.080
 JVB  C05  H8   single    0.930  0.020  1.080
 JVB  C06  H9   single    0.930  0.020  1.080
 JVB  C09  H10  single    0.970  0.020  1.090
 JVB  C09  H11  single    0.970  0.020  1.090
 JVB  C14  H12  single    0.930  0.020  1.080
 JVB  C16  H13  single    0.930  0.020  1.080
 JVB  C18  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
 JVB  O11  C10  C09  122.76  3.000
 JVB  O11  C10  N12  124.89  3.000
 JVB  C09  C10  N12  112.33  3.000
 JVB  H1   N12  C13  114.81  3.000
 JVB  H1   N12  C10  116.55  3.000
 JVB  C13  N12  C10  128.62  3.000
 JVB  C18  C13  C14  117.56  3.000
 JVB  C14  C13  N12  125.47  3.000
 JVB  C18  C13  N12  116.97  3.000
 JVB  H2   C15  C16  120.22  3.000
 JVB  H2   C15  C14  120.04  3.000
 JVB  C16  C15  C14  119.74  3.000
 JVB  C07  C02  C03  118.01  3.000
 JVB  C07  C02  C01  120.49  3.000
 JVB  C03  C02  C01  121.50  3.000
 JVB  H6   C03  C04  119.50  3.000
 JVB  H6   C03  C02  118.67  3.000
 JVB  C04  C03  C02  121.84  3.000
 JVB  H7   C04  C05  120.66  3.000
 JVB  H7   C04  C03  120.10  3.000
 JVB  C05  C04  C03  119.24  3.000
 JVB  H8   C05  C06  119.10  3.000
 JVB  H8   C05  C04  120.53  3.000
 JVB  C06  C05  C04  120.37  3.000
 JVB  H9   C06  C07  121.43  3.000
 JVB  H9   C06  C05  118.81  3.000
 JVB  C07  C06  C05  119.76  3.000
 JVB  O08  C07  C06  124.08  3.000
 JVB  O08  C07  C02  115.14  3.000
 JVB  C06  C07  C02  120.78  3.000
 JVB  H11  C09  H10  107.23  3.000
 JVB  H11  C09  O08  112.01  3.000
 JVB  H10  C09  O08  112.06  3.000
 JVB  H11  C09  C10  110.00  3.000
 JVB  H10  C09  C10  108.12  3.000
 JVB  O08  C09  C10  107.36  3.000
 JVB  H12  C14  C15  120.13  3.000
 JVB  H12  C14  C13  121.71  3.000
 JVB  C15  C14  C13  118.16  3.000
 JVB  H13  C16  N17  116.90  3.000
 JVB  H13  C16  C15  120.79  3.000
 JVB  N17  C16  C15  122.31  3.000
 JVB  H14  C18  N17  116.65  3.000
 JVB  H14  C18  C13  119.42  3.000
 JVB  N17  C18  C13  123.93  3.000
 JVB  C18  N17  C16  118.30  3.000
 JVB  C09  O08  C07  119.02  3.000
 JVB  H5   C01  H4   107.93  3.000
 JVB  H5   C01  H3   107.60  3.000
 JVB  H4   C01  H3   106.84  3.000
 JVB  H5   C01  C02  110.62  3.000
 JVB  H4   C01  C02  111.98  3.000
 JVB  H3   C01  C02  111.65  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
 JVB  CONST_01  C16  N17  C18  C13    0.00   0.0  0
 JVB  CONST_02  C16  C15  C14  C13    0.00   0.0  0
 JVB  CONST_03  C18  C13  C14  C15    0.00   0.0  0
 JVB  CONST_04  C18  N17  C16  C15    0.00   0.0  0
 JVB  CONST_05  C05  C04  C03  C02    0.00   0.0  0
 JVB  CONST_06  C05  C06  C07  C02    0.00   0.0  0
 JVB  CONST_07  C06  C05  C04  C03    0.00   0.0  0
 JVB  CONST_08  C06  C07  C02  C03    0.00   0.0  0
 JVB  CONST_09  C07  C06  C05  C04    0.00   0.0  0
 JVB  CONST_10  C07  C02  C03  C04    0.00   0.0  0
 JVB  CONST_11  N17  C18  C13  C14    0.00   0.0  0
 JVB  CONST_12  N17  C16  C15  C14    0.00   0.0  0
 JVB  CONST_13  N17  C18  C13  N12  180.00   0.0  0
 JVB  CONST_14  C15  C14  C13  N12  180.00   0.0  0
 JVB  CONST_15  C04  C03  C02  C01  180.00   0.0  0
 JVB  CONST_16  C06  C07  C02  C01  180.00   0.0  0
 JVB  CONST_17  O08  C07  C02  C03  180.00   0.0  0
 JVB  CONST_18  O08  C07  C06  C05  180.00   0.0  0
 JVB  CONST_19  H2   C15  C14  C13  180.00   0.0  0
 JVB  CONST_20  H7   C04  C03  C02  180.00   0.0  0
 JVB  CONST_21  H9   C06  C07  C02  180.00   0.0  0
 JVB  CONST_22  H8   C05  C04  C03  180.00   0.0  0
 JVB  CONST_23  H6   C03  C04  C05  180.00   0.0  0
 JVB  CONST_24  H14  C18  C13  C14  180.00   0.0  0
 JVB  CONST_25  H13  C16  C15  C14  180.00   0.0  0
 JVB  CONST_26  H12  C14  C15  C16  180.00   0.0  0
 JVB  CONST_27  C18  C13  N12  C10  180.00   0.0  0
 JVB  CONST_28  C14  C13  N12  C10    0.00   0.0  0
 JVB  CONST_29  H1   N12  C13  C14  180.00   0.0  0
 JVB  CONST_30  C09  C10  N12  C13  180.00   0.0  0
 JVB  CONST_31  O11  C10  N12  C13    0.00   0.0  0
 JVB  Var_01    H3   C01  C02  C03  115.18  30.0  2
 JVB  Var_02    H10  C09  O08  C07   55.83  30.0  1
 JVB  Var_03    O08  C09  C10  N12  169.16  30.0  1

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
 JVB  plan-1  C02  0.020
 JVB  plan-1  C03  0.020
 JVB  plan-1  C04  0.020
 JVB  plan-1  C05  0.020
 JVB  plan-1  C06  0.020
 JVB  plan-1  C07  0.020
 JVB  plan-1  O08  0.020
 JVB  plan-1  H6   0.020
 JVB  plan-1  H7   0.020
 JVB  plan-1  H8   0.020
 JVB  plan-1  H9   0.020
 JVB  plan-1  C01  0.020
 JVB  plan-2  N12  0.020
 JVB  plan-2  C13  0.020
 JVB  plan-2  C15  0.020
 JVB  plan-2  C14  0.020
 JVB  plan-2  C16  0.020
 JVB  plan-2  C18  0.020
 JVB  plan-2  N17  0.020
 JVB  plan-2  H2   0.020
 JVB  plan-2  H12  0.020
 JVB  plan-2  H13  0.020
 JVB  plan-2  H14  0.020
 JVB  plan-3  C10  0.020
 JVB  plan-3  N12  0.020
 JVB  plan-3  C13  0.020
 JVB  plan-3  C09  0.020
 JVB  plan-3  O11  0.020
 JVB  plan-3  H1   0.020

