# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 00:04:18 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-(3,5-dichloropyridin-4-yl)-3-[(3-ethyl-1,2-oxazol-5-yl)methoxy]-4-methoxybenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cc(COc2cc(ccc2OC)C(=O)Nc3c(Cl)cncc3Cl)on1
#
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
 3GJ  3GJ  N-(3,5-dichloropyridin-4-yl)-3-[(3-ethyl-1,2-oxazol-5-yl)methoxy]-4-methoxybenzamide  ligand  45  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3GJ
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
 3GJ  O11  O   O     0  -0.438   1.9114  -1.2311   0.5924
 3GJ  C10  C   C     0   0.535   2.0068  -0.0816   0.2122
 3GJ  N9   N   NH1   0  -0.760   3.2138   0.4565  -0.1564
 3GJ  C1   C   CR6   0   0.603   4.3966  -0.2687  -0.0876
 3GJ  C6   C   CR6   0  -0.168   4.9168  -0.7369   1.1179
 3GJ  CL7  CL  CL    0  -0.079   4.1359  -0.3902   2.6060
 3GJ  C5   C   CR16  0  -0.034   6.1064  -1.4495   1.1251
 3GJ  N4   N   N     0  -0.397   6.7999  -1.6939   0.0251
 3GJ  C3   C   CR16  0  -0.032   6.3403  -1.2413  -1.1297
 3GJ  C2   C   CR6   0  -0.194   5.1500  -0.5387  -1.2286
 3GJ  CL8  CL  CL    0  -0.078   4.5965  -0.0086  -2.7686
 3GJ  C12  C   CR6   0  -0.051   0.8442   0.8302   0.1032
 3GJ  C17  C   CR16  0  -0.406  -0.4310   0.2532   0.0399
 3GJ  C16  C   CR6   0   0.343  -1.5553   1.0450  -0.0513
 3GJ  C15  C   CR6   0   0.322  -1.4247   2.4523  -0.0688
 3GJ  O18  O   O2    0  -0.453  -2.5684   3.1368  -0.1620
 3GJ  C19  C   CH3   0  -0.441  -2.5089   4.5520  -0.1777
 3GJ  C14  C   CR16  0  -0.373  -0.1614   3.0163   0.0128
 3GJ  C13  C   CR16  0  -0.298   0.9676   2.2095   0.0977
 3GJ  O20  O   O2    0  -0.465  -2.8209   0.5891  -0.1300
 3GJ  C21  C   CH2   0  -0.282  -3.0328  -0.8056  -0.0322
 3GJ  C22  C   CR5   0   0.434  -4.4977  -1.0369  -0.0533
 3GJ  C26  C   CR15  0  -0.505  -5.2994  -1.7294  -0.8886
 3GJ  C25  C   CR5   0   0.265  -6.5957  -1.5730  -0.3223
 3GJ  N24  N   N     0  -0.178  -6.5386  -0.8422   0.7529
 3GJ  O23  O   O     0  -0.342  -5.2288  -0.5071   0.9311
 3GJ  C27  C   CH2   0  -0.503  -7.8798  -2.1343  -0.8322
 3GJ  C28  C   CH3   0  -0.668  -9.1059  -1.7619  -0.0130
 3GJ  H1   H   HNH1  0   0.421   3.2139   1.2731  -0.7503
 3GJ  H2   H   HCR6  0   0.297   6.5091  -1.8165   2.0616
 3GJ  H3   H   HCR6  0   0.298   6.9250  -1.4460  -2.0185
 3GJ  H4   H   HCR6  0   0.294  -0.5133  -0.8250   0.0535
 3GJ  H5   H   HCH3  0   0.265  -3.5348   4.9002  -0.2603
 3GJ  H6   H   HCH3  0   0.235  -2.0722   4.9491   0.7418
 3GJ  H7   H   HCH3  0   0.235  -1.9382   4.9239  -1.0320
 3GJ  H8   H   HCR6  0   0.294  -0.0354   4.0897   0.0186
 3GJ  H9   H   HCR6  0   0.267   1.9320   2.6918   0.1880
 3GJ  H10  H   HCH2  0   0.268  -2.5815  -1.3443  -0.8710
 3GJ  H11  H   HCH2  0   0.266  -2.5996  -1.2021   0.8935
 3GJ  H12  H   HCR5  0   0.283  -5.0233  -2.2686  -1.7791
 3GJ  H13  H   HCH2  0   0.259  -8.0049  -1.8076  -1.8678
 3GJ  H14  H   HCH2  0   0.259  -7.7760  -3.2214  -0.8801
 3GJ  H15  H   HCH3  0   0.229  -9.0215  -2.1088   1.0163
 3GJ  H16  H   HCH3  0   0.230  -9.2616  -0.6836   0.0095
 3GJ  H17  H   HCH3  0   0.239  -9.9941  -2.2187  -0.4471

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
 3GJ  C19  O18  single    1.417  0.020  1.417
 3GJ  O18  C15  single    1.336  0.020  1.336
 3GJ  C15  C14  aromatic  1.386  0.020  1.386
 3GJ  C15  C16  aromatic  1.413  0.020  1.413
 3GJ  O20  C21  single    1.414  0.020  1.414
 3GJ  O20  C16  single    1.347  0.020  1.347
 3GJ  C21  C22  single    1.483  0.020  1.483
 3GJ  C14  C13  aromatic  1.390  0.020  1.390
 3GJ  C16  C17  aromatic  1.378  0.020  1.378
 3GJ  C26  C22  aromatic  1.349  0.020  1.349
 3GJ  C26  C25  aromatic  1.423  0.020  1.423
 3GJ  C22  O23  aromatic  1.336  0.020  1.336
 3GJ  C13  C12  aromatic  1.385  0.020  1.385
 3GJ  C17  C12  aromatic  1.401  0.020  1.401
 3GJ  C25  C27  single    1.491  0.020  1.491
 3GJ  C25  N24  aromatic  1.301  0.020  1.301
 3GJ  C12  C10  single    1.482  0.020  1.482
 3GJ  C27  C28  single    1.521  0.020  1.521
 3GJ  O23  N24  aromatic  1.364  0.020  1.364
 3GJ  C10  N9   single    1.372  0.020  1.372
 3GJ  C10  O11  double    1.215  0.020  1.215
 3GJ  N9   C1   single    1.389  0.020  1.389
 3GJ  CL8  C2   single    1.720  0.020  1.720
 3GJ  C1   C2   aromatic  1.394  0.020  1.394
 3GJ  C1   C6   aromatic  1.394  0.020  1.394
 3GJ  CL7  C6   single    1.716  0.020  1.716
 3GJ  C2   C3   aromatic  1.386  0.020  1.386
 3GJ  C6   C5   aromatic  1.387  0.020  1.387
 3GJ  C3   N4   aromatic  1.323  0.020  1.323
 3GJ  C5   N4   aromatic  1.323  0.020  1.323
 3GJ  N9   H1   single    0.860  0.020  1.020
 3GJ  C5   H2   single    0.930  0.020  1.080
 3GJ  C3   H3   single    0.930  0.020  1.080
 3GJ  C17  H4   single    0.930  0.020  1.080
 3GJ  C19  H5   single    0.970  0.020  1.090
 3GJ  C19  H6   single    0.970  0.020  1.090
 3GJ  C19  H7   single    0.970  0.020  1.090
 3GJ  C14  H8   single    0.930  0.020  1.080
 3GJ  C13  H9   single    0.930  0.020  1.080
 3GJ  C21  H10  single    0.970  0.020  1.090
 3GJ  C21  H11  single    0.970  0.020  1.090
 3GJ  C26  H12  single    0.930  0.020  1.080
 3GJ  C27  H13  single    0.970  0.020  1.090
 3GJ  C27  H14  single    0.970  0.020  1.090
 3GJ  C28  H15  single    0.970  0.020  1.090
 3GJ  C28  H16  single    0.970  0.020  1.090
 3GJ  C28  H17  single    0.970  0.020  1.090

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
 3GJ  C12  C10  N9   115.42  3.000
 3GJ  N9   C10  O11  121.63  3.000
 3GJ  C12  C10  O11  122.95  3.000
 3GJ  H1   N9   C1   116.82  3.000
 3GJ  H1   N9   C10  118.38  3.000
 3GJ  C1   N9   C10  122.08  3.000
 3GJ  C2   C1   C6   116.18  3.000
 3GJ  C6   C1   N9   122.41  3.000
 3GJ  C2   C1   N9   121.39  3.000
 3GJ  C5   C6   CL7  119.32  3.000
 3GJ  C5   C6   C1   119.82  3.000
 3GJ  CL7  C6   C1   120.82  3.000
 3GJ  H2   C5   N4   117.47  3.000
 3GJ  H2   C5   C6   119.83  3.000
 3GJ  N4   C5   C6   122.70  3.000
 3GJ  C3   N4   C5   118.72  3.000
 3GJ  H3   C3   C2   120.06  3.000
 3GJ  H3   C3   N4   117.65  3.000
 3GJ  C2   C3   N4   122.29  3.000
 3GJ  CL8  C2   C3   119.77  3.000
 3GJ  C3   C2   C1   120.27  3.000
 3GJ  CL8  C2   C1   119.95  3.000
 3GJ  C13  C12  C17  119.42  3.000
 3GJ  C17  C12  C10  117.65  3.000
 3GJ  C13  C12  C10  122.91  3.000
 3GJ  H4   C17  C16  120.77  3.000
 3GJ  H4   C17  C12  118.64  3.000
 3GJ  C16  C17  C12  120.59  3.000
 3GJ  O20  C16  C15  115.02  3.000
 3GJ  O20  C16  C17  125.15  3.000
 3GJ  C15  C16  C17  119.84  3.000
 3GJ  C14  C15  O18  125.16  3.000
 3GJ  C14  C15  C16  119.25  3.000
 3GJ  O18  C15  C16  115.59  3.000
 3GJ  C19  O18  C15  118.47  3.000
 3GJ  H7   C19  H6   109.00  3.000
 3GJ  H7   C19  H5   108.94  3.000
 3GJ  H6   C19  H5   108.96  3.000
 3GJ  H7   C19  O18  111.75  3.000
 3GJ  H6   C19  O18  111.75  3.000
 3GJ  H5   C19  O18  106.34  3.000
 3GJ  H8   C14  C13  118.77  3.000
 3GJ  H8   C14  C15  120.71  3.000
 3GJ  C13  C14  C15  120.52  3.000
 3GJ  H9   C13  C14  118.05  3.000
 3GJ  H9   C13  C12  121.54  3.000
 3GJ  C14  C13  C12  120.38  3.000
 3GJ  C21  O20  C16  118.06  3.000
 3GJ  H11  C21  H10  107.83  3.000
 3GJ  H11  C21  C22  110.24  3.000
 3GJ  H10  C21  C22  108.65  3.000
 3GJ  H11  C21  O20  110.85  3.000
 3GJ  H10  C21  O20  111.76  3.000
 3GJ  C22  C21  O20  107.51  3.000
 3GJ  O23  C22  C26  109.55  3.000
 3GJ  O23  C22  C21  117.92  3.000
 3GJ  C26  C22  C21  132.51  3.000
 3GJ  H12  C26  C25  128.14  3.000
 3GJ  H12  C26  C22  128.06  3.000
 3GJ  C25  C26  C22  103.80  3.000
 3GJ  C27  C25  N24  122.12  3.000
 3GJ  N24  C25  C26  110.52  3.000
 3GJ  C27  C25  C26  127.36  3.000
 3GJ  O23  N24  C25  106.75  3.000
 3GJ  N24  O23  C22  109.38  3.000
 3GJ  H14  C27  H13  105.46  3.000
 3GJ  H14  C27  C28  110.10  3.000
 3GJ  H13  C27  C28  110.17  3.000
 3GJ  H14  C27  C25  107.91  3.000
 3GJ  H13  C27  C25  108.06  3.000
 3GJ  C28  C27  C25  114.70  3.000
 3GJ  H17  C28  H16  107.86  3.000
 3GJ  H17  C28  H15  107.83  3.000
 3GJ  H16  C28  H15  107.85  3.000
 3GJ  H17  C28  C27  109.88  3.000
 3GJ  H16  C28  C27  111.63  3.000
 3GJ  H15  C28  C27  111.62  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
 3GJ  CONST_01  N4   C3   C2   C1      0.00   0.0  0
 3GJ  CONST_02  N4   C5   C6   C1      0.00   0.0  0
 3GJ  CONST_03  C3   C2   C1   C6      0.00   0.0  0
 3GJ  CONST_04  C3   N4   C5   C6      0.00   0.0  0
 3GJ  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 3GJ  CONST_06  C2   C3   N4   C5      0.00   0.0  0
 3GJ  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 3GJ  CONST_08  C15  C16  C17  C12     0.00   0.0  0
 3GJ  CONST_09  C14  C15  C16  C17     0.00   0.0  0
 3GJ  CONST_10  C14  C13  C12  C17     0.00   0.0  0
 3GJ  CONST_11  C13  C14  C15  C16     0.00   0.0  0
 3GJ  CONST_12  C13  C12  C17  C16     0.00   0.0  0
 3GJ  CONST_13  N24  C25  C26  C22     0.00   0.0  0
 3GJ  CONST_14  C25  N24  O23  C22     0.00   0.0  0
 3GJ  CONST_15  N24  O23  C22  C26     0.00   0.0  0
 3GJ  CONST_16  O23  N24  C25  C26     0.00   0.0  0
 3GJ  CONST_17  O23  C22  C26  C25     0.00   0.0  0
 3GJ  CONST_18  C14  C13  C12  C10   180.00   0.0  0
 3GJ  CONST_19  C16  C17  C12  C10   180.00   0.0  0
 3GJ  CONST_20  C3   C2   C1   N9    180.00   0.0  0
 3GJ  CONST_21  C5   C6   C1   N9    180.00   0.0  0
 3GJ  CONST_22  CL8  C2   C1   C6    180.00   0.0  0
 3GJ  CONST_23  C2   C1   C6   CL7   180.00   0.0  0
 3GJ  CONST_24  N4   C5   C6   CL7   180.00   0.0  0
 3GJ  CONST_25  CL8  C2   C3   N4    180.00   0.0  0
 3GJ  CONST_26  O20  C16  C17  C12   180.00   0.0  0
 3GJ  CONST_27  O18  C15  C16  C17   180.00   0.0  0
 3GJ  CONST_28  C13  C14  C15  O18   180.00   0.0  0
 3GJ  CONST_29  O20  C16  C15  C14   180.00   0.0  0
 3GJ  CONST_30  C25  C26  C22  C21   180.00   0.0  0
 3GJ  CONST_31  N24  O23  C22  C21   180.00   0.0  0
 3GJ  CONST_32  C27  C25  C26  C22   180.00   0.0  0
 3GJ  CONST_33  C27  C25  N24  O23   180.00   0.0  0
 3GJ  CONST_34  H3   C3   C2   C1    180.00   0.0  0
 3GJ  CONST_35  H2   C5   C6   C1    180.00   0.0  0
 3GJ  CONST_36  H8   C14  C13  C12   180.00   0.0  0
 3GJ  CONST_37  H9   C13  C12  C17   180.00   0.0  0
 3GJ  CONST_38  H4   C17  C16  C15   180.00   0.0  0
 3GJ  CONST_39  H12  C26  C25  N24   180.00   0.0  0
 3GJ  CONST_40  C12  C10  N9   C1    180.00   0.0  0
 3GJ  CONST_44  C1   N9   C10  O11     0.00   0.0  0
 3GJ  Var_01    C13  C12  C10  O11   158.49  30.0  2
 3GJ  Var_02    C22  C21  O20  C16   176.18  30.0  3
 3GJ  Var_03    C14  C15  O18  C19    -0.14  30.0  2
 3GJ  Var_04    C26  C22  C21  O20   119.79  30.0  2
 3GJ  Var_05    C28  C27  C25  C26  -178.81  30.0  2
 3GJ  Var_06    H5   C19  O18  C15   179.85  30.0  3
 3GJ  Var_07    H15  C28  C27  C25   -59.88  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
 3GJ  plan-1  C21  0.020
 3GJ  plan-1  C22  0.020
 3GJ  plan-1  C26  0.020
 3GJ  plan-1  C25  0.020
 3GJ  plan-1  N24  0.020
 3GJ  plan-1  O23  0.020
 3GJ  plan-1  C27  0.020
 3GJ  plan-1  H12  0.020
 3GJ  plan-2  N9   0.020
 3GJ  plan-2  C1   0.020
 3GJ  plan-2  C6   0.020
 3GJ  plan-2  CL7  0.020
 3GJ  plan-2  C5   0.020
 3GJ  plan-2  N4   0.020
 3GJ  plan-2  C3   0.020
 3GJ  plan-2  C2   0.020
 3GJ  plan-2  CL8  0.020
 3GJ  plan-2  H2   0.020
 3GJ  plan-2  H3   0.020
 3GJ  plan-3  C10  0.020
 3GJ  plan-3  C12  0.020
 3GJ  plan-3  C17  0.020
 3GJ  plan-3  C16  0.020
 3GJ  plan-3  C15  0.020
 3GJ  plan-3  O18  0.020
 3GJ  plan-3  C14  0.020
 3GJ  plan-3  C13  0.020
 3GJ  plan-3  O20  0.020
 3GJ  plan-3  H4   0.020
 3GJ  plan-3  H8   0.020
 3GJ  plan-3  H9   0.020
 3GJ  plan-4  O11  0.020
 3GJ  plan-4  C10  0.020
 3GJ  plan-4  N9   0.020
 3GJ  plan-4  C1   0.020
 3GJ  plan-4  C12  0.020
 3GJ  plan-4  H1   0.020

