# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 01:09:03 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: N-[5-(2,3-dimethylphenyl)-1,6-naphthyridin-7-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cc2ncccc2c(n1)c3cccc(C)c3C
#
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
 8JF  8JF  N-[5-(2,3-dimethylphenyl)-1,6-naphthyridin-7-yl]acetamide  ligand  39  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8JF
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
 8JF  C01  C  CR16  0  -0.331  -0.2718  -3.9935  -0.5614
 8JF  C02  C  CR16  0  -0.068  -1.6821  -4.0313  -0.5828
 8JF  N03  N  N     0  -0.440  -2.4503  -2.9925  -0.3913
 8JF  C04  C  CR66  0   0.321  -1.8528  -1.8013  -0.1467
 8JF  C05  C  CR66  0  -0.008  -0.4460  -1.6581  -0.0785
 8JF  C06  C  CR16  0  -0.188   0.3470  -2.8024  -0.3096
 8JF  C07  C  CR16  0  -0.441  -2.6502  -0.6581   0.0190
 8JF  C08  C  CR6   0   0.497  -2.0304   0.5465   0.2528
 8JF  N09  N  N     0  -0.403  -0.6999   0.6807   0.3626
 8JF  C10  C  CR6   0   0.140   0.0702  -0.3646   0.2001
 8JF  C11  C  CR6   0   0.017   1.5299  -0.1386   0.3476
 8JF  N12  N  NH1   0  -0.729  -2.8114   1.6856   0.4389
 8JF  C13  C  CR6   0   0.035   2.2113   0.7088  -0.5338
 8JF  C14  C  CR6   0   0.077   3.5743   0.9590  -0.3138
 8JF  C15  C  CR16  0  -0.302   4.2193   0.3466   0.7573
 8JF  C16  C  CR16  0  -0.249   3.5422  -0.5077   1.6140
 8JF  C17  C  CR16  0  -0.294   2.1952  -0.7491   1.4082
 8JF  C18  C  CH3   0  -0.743   4.3470   1.8793  -1.2153
 8JF  C19  C  CH3   0  -0.742   1.5068   1.3423  -1.7004
 8JF  C20  C  C     0   0.505  -2.4975   2.9775   0.1174
 8JF  C21  C  CH3   0  -0.789  -3.6066   3.9607   0.3984
 8JF  O22  O  O     0  -0.446  -1.4402   3.3211  -0.3686
 8JF  H1   H  HCR6  0   0.278   0.2929  -4.8957  -0.7485
 8JF  H2   H  HCR6  0   0.273  -2.1825  -4.9744  -0.7764
 8JF  H3   H  HCR6  0   0.279   1.4262  -2.7306  -0.2943
 8JF  H4   H  HCR6  0   0.280  -3.7268  -0.7420  -0.0535
 8JF  H5   H  HNH1  0   0.420  -3.7704   1.5103   0.6951
 8JF  H6   H  HCR6  0   0.248   5.2718   0.5448   0.9219
 8JF  H7   H  HCR6  0   0.255   4.0603  -0.9757   2.4407
 8JF  H8   H  HCR6  0   0.256   1.6507  -1.3993   2.0823
 8JF  H9   H  HCH3  0   0.246   3.8836   2.8652  -1.2822
 8JF  H10  H  HCH3  0   0.251   5.3642   2.0154  -0.8512
 8JF  H11  H  HCH3  0   0.248   4.4119   1.4906  -2.2340
 8JF  H12  H  HCH3  0   0.258   1.1059   2.3229  -1.4385
 8JF  H13  H  HCH3  0   0.244   2.1795   1.4746  -2.5460
 8JF  H14  H  HCH3  0   0.244   0.6670   0.7425  -2.0453
 8JF  H15  H  HCH3  0   0.254  -4.4433   3.5392   0.9520
 8JF  H16  H  HCH3  0   0.272  -3.2077   4.8021   0.9636
 8JF  H17  H  HCH3  0   0.274  -3.9828   4.3533  -0.5469

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
 8JF  C01  C02  aromatic  1.411  0.020  1.411
 8JF  C01  C06  aromatic  1.366  0.020  1.366
 8JF  C02  N03  aromatic  1.306  0.020  1.306
 8JF  C06  C05  aromatic  1.411  0.020  1.411
 8JF  C16  C15  aromatic  1.386  0.020  1.386
 8JF  C16  C17  aromatic  1.384  0.020  1.384
 8JF  C15  C14  aromatic  1.392  0.020  1.392
 8JF  C17  C11  aromatic  1.393  0.020  1.393
 8JF  N03  C04  aromatic  1.355  0.020  1.355
 8JF  C05  C04  aromatic  1.416  0.020  1.416
 8JF  C05  C10  aromatic  1.420  0.020  1.420
 8JF  C14  C18  single    1.502  0.020  1.502
 8JF  C14  C13  aromatic  1.403  0.020  1.403
 8JF  C11  C13  aromatic  1.400  0.020  1.400
 8JF  C11  C10  single    1.484  0.020  1.484
 8JF  C04  C07  aromatic  1.404  0.020  1.404
 8JF  C13  C19  single    1.503  0.020  1.503
 8JF  C10  N09  aromatic  1.308  0.020  1.308
 8JF  C07  C08  aromatic  1.375  0.020  1.375
 8JF  N09  C08  aromatic  1.342  0.020  1.342
 8JF  C08  N12  single    1.394  0.020  1.394
 8JF  N12  C20  single    1.368  0.020  1.368
 8JF  C20  O22  double    1.213  0.020  1.213
 8JF  C20  C21  single    1.509  0.020  1.509
 8JF  C01  H1   single    0.930  0.020  1.080
 8JF  C02  H2   single    0.930  0.020  1.080
 8JF  C06  H3   single    0.930  0.020  1.080
 8JF  C07  H4   single    0.930  0.020  1.080
 8JF  N12  H5   single    0.860  0.020  1.020
 8JF  C15  H6   single    0.930  0.020  1.080
 8JF  C16  H7   single    0.930  0.020  1.080
 8JF  C17  H8   single    0.930  0.020  1.080
 8JF  C18  H9   single    0.970  0.020  1.090
 8JF  C18  H10  single    0.970  0.020  1.090
 8JF  C18  H11  single    0.970  0.020  1.090
 8JF  C19  H12  single    0.970  0.020  1.090
 8JF  C19  H13  single    0.970  0.020  1.090
 8JF  C19  H14  single    0.970  0.020  1.090
 8JF  C21  H15  single    0.970  0.020  1.090
 8JF  C21  H16  single    0.970  0.020  1.090
 8JF  C21  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
 8JF  H1   C01  C06  121.56  3.000
 8JF  H1   C01  C02  119.82  3.000
 8JF  C06  C01  C02  118.62  3.000
 8JF  H2   C02  N03  116.50  3.000
 8JF  H2   C02  C01  119.14  3.000
 8JF  N03  C02  C01  124.36  3.000
 8JF  C04  N03  C02  117.80  3.000
 8JF  C07  C04  C05  118.46  3.000
 8JF  C07  C04  N03  119.13  3.000
 8JF  C05  C04  N03  122.40  3.000
 8JF  C10  C05  C06  124.49  3.000
 8JF  C10  C05  C04  117.56  3.000
 8JF  C06  C05  C04  117.94  3.000
 8JF  H3   C06  C05  120.30  3.000
 8JF  H3   C06  C01  120.83  3.000
 8JF  C05  C06  C01  118.87  3.000
 8JF  H4   C07  C08  121.86  3.000
 8JF  H4   C07  C04  119.61  3.000
 8JF  C08  C07  C04  118.53  3.000
 8JF  N12  C08  N09  117.58  3.000
 8JF  N12  C08  C07  119.10  3.000
 8JF  N09  C08  C07  123.27  3.000
 8JF  C10  N09  C08  119.58  3.000
 8JF  C11  C10  N09  116.41  3.000
 8JF  N09  C10  C05  122.55  3.000
 8JF  C11  C10  C05  121.03  3.000
 8JF  C17  C11  C13  120.81  3.000
 8JF  C13  C11  C10  120.55  3.000
 8JF  C17  C11  C10  118.60  3.000
 8JF  H5   N12  C20  116.25  3.000
 8JF  H5   N12  C08  115.15  3.000
 8JF  C20  N12  C08  127.74  3.000
 8JF  C19  C13  C14  120.13  3.000
 8JF  C19  C13  C11  121.05  3.000
 8JF  C14  C13  C11  118.83  3.000
 8JF  C18  C14  C15  119.53  3.000
 8JF  C18  C14  C13  120.99  3.000
 8JF  C15  C14  C13  119.49  3.000
 8JF  H6   C15  C16  119.55  3.000
 8JF  H6   C15  C14  119.11  3.000
 8JF  C16  C15  C14  121.35  3.000
 8JF  H7   C16  C17  120.28  3.000
 8JF  H7   C16  C15  120.32  3.000
 8JF  C17  C16  C15  119.40  3.000
 8JF  H8   C17  C16  120.09  3.000
 8JF  H8   C17  C11  119.78  3.000
 8JF  C16  C17  C11  120.11  3.000
 8JF  H11  C18  H10  107.51  3.000
 8JF  H11  C18  H9   106.83  3.000
 8JF  H10  C18  H9   107.71  3.000
 8JF  H11  C18  C14  111.85  3.000
 8JF  H10  C18  C14  110.88  3.000
 8JF  H9   C18  C14  111.82  3.000
 8JF  H14  C19  H13  107.32  3.000
 8JF  H14  C19  H12  106.73  3.000
 8JF  H13  C19  H12  107.71  3.000
 8JF  H14  C19  C13  112.06  3.000
 8JF  H13  C19  C13  111.38  3.000
 8JF  H12  C19  C13  111.39  3.000
 8JF  O22  C20  C21  122.06  3.000
 8JF  C21  C20  N12  113.77  3.000
 8JF  O22  C20  N12  124.16  3.000
 8JF  H17  C21  H16  107.33  3.000
 8JF  H17  C21  H15  108.37  3.000
 8JF  H16  C21  H15  108.47  3.000
 8JF  H17  C21  C20  109.08  3.000
 8JF  H16  C21  C20  109.32  3.000
 8JF  H15  C21  C20  114.06  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
 8JF  CONST_01  C04  N03  C02  C01    0.00   0.0  0
 8JF  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 8JF  CONST_03  C10  C05  C06  C01  180.00   0.0  0
 8JF  CONST_04  C05  C06  C01  C02    0.00   0.0  0
 8JF  CONST_05  C05  C04  N03  C02    0.00   0.0  0
 8JF  CONST_06  C07  C04  N03  C02  180.00   0.0  0
 8JF  CONST_07  C06  C01  C02  N03    0.00   0.0  0
 8JF  CONST_08  C06  C05  C04  N03    0.00   0.0  0
 8JF  CONST_09  C10  C05  C04  N03  180.00   0.0  0
 8JF  CONST_10  C08  C07  C04  N03  180.00   0.0  0
 8JF  CONST_11  C11  C10  C05  C04  180.00   0.0  0
 8JF  CONST_12  N09  C10  C05  C04    0.00   0.0  0
 8JF  CONST_13  N09  C08  C07  C04    0.00   0.0  0
 8JF  CONST_14  C08  C07  C04  C05    0.00   0.0  0
 8JF  CONST_17  C08  N09  C10  C05    0.00   0.0  0
 8JF  CONST_18  C07  C04  C05  C06  180.00   0.0  0
 8JF  CONST_19  C11  C10  C05  C06    0.00   0.0  0
 8JF  CONST_20  N09  C10  C05  C06  180.00   0.0  0
 8JF  CONST_21  C10  C05  C04  C07    0.00   0.0  0
 8JF  CONST_22  C10  N09  C08  C07    0.00   0.0  0
 8JF  CONST_23  C11  C10  N09  C08  180.00   0.0  0
 8JF  CONST_26  C16  C17  C11  C10  180.00   0.0  0
 8JF  CONST_27  C14  C13  C11  C10  180.00   0.0  0
 8JF  CONST_28  C15  C16  C17  C11    0.00   0.0  0
 8JF  CONST_29  C15  C14  C13  C11    0.00   0.0  0
 8JF  CONST_30  C16  C15  C14  C13    0.00   0.0  0
 8JF  CONST_31  C16  C17  C11  C13    0.00   0.0  0
 8JF  CONST_32  C17  C16  C15  C14    0.00   0.0  0
 8JF  CONST_33  C17  C11  C13  C14    0.00   0.0  0
 8JF  CONST_34  N12  C08  C07  C04  180.00   0.0  0
 8JF  CONST_35  C19  C13  C11  C10    0.00   0.0  0
 8JF  CONST_36  N12  C08  N09  C10  180.00   0.0  0
 8JF  CONST_37  C18  C14  C13  C11  180.00   0.0  0
 8JF  CONST_38  C19  C13  C14  C15  180.00   0.0  0
 8JF  CONST_39  C18  C14  C15  C16  180.00   0.0  0
 8JF  CONST_40  C19  C13  C11  C17  180.00   0.0  0
 8JF  CONST_41  H3   C06  C01  C02  180.00   0.0  0
 8JF  CONST_42  H1   C01  C02  N03  180.00   0.0  0
 8JF  CONST_43  H4   C07  C04  N03    0.00   0.0  0
 8JF  CONST_44  H2   C02  N03  C04  180.00   0.0  0
 8JF  CONST_45  H8   C17  C11  C10    0.00   0.0  0
 8JF  CONST_46  H7   C16  C17  C11  180.00   0.0  0
 8JF  CONST_47  H6   C15  C14  C13  180.00   0.0  0
 8JF  CONST_51  O22  C20  N12  C08    0.00   0.0  0
 8JF  CONST_52  C21  C20  N12  C08  180.00   0.0  0
 8JF  Var_01    H12  C19  C13  C11   91.86  30.0  2
 8JF  Var_02    H9   C18  C14  C13   55.36  30.0  2
 8JF  Var_03    H15  C21  C20  N12    8.66  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
 8JF  plan-1  C10  0.020
 8JF  plan-1  C11  0.020
 8JF  plan-1  C13  0.020
 8JF  plan-1  C14  0.020
 8JF  plan-1  C15  0.020
 8JF  plan-1  C16  0.020
 8JF  plan-1  C17  0.020
 8JF  plan-1  C18  0.020
 8JF  plan-1  C19  0.020
 8JF  plan-1  H6   0.020
 8JF  plan-1  H7   0.020
 8JF  plan-1  H8   0.020
 8JF  plan-2  C01  0.020
 8JF  plan-2  C02  0.020
 8JF  plan-2  N03  0.020
 8JF  plan-2  C04  0.020
 8JF  plan-2  C05  0.020
 8JF  plan-2  C06  0.020
 8JF  plan-2  C07  0.020
 8JF  plan-2  C08  0.020
 8JF  plan-2  N09  0.020
 8JF  plan-2  C10  0.020
 8JF  plan-2  C11  0.020
 8JF  plan-2  N12  0.020
 8JF  plan-2  H1   0.020
 8JF  plan-2  H2   0.020
 8JF  plan-2  H3   0.020
 8JF  plan-2  H4   0.020
 8JF  plan-3  C08  0.020
 8JF  plan-3  N12  0.020
 8JF  plan-3  C20  0.020
 8JF  plan-3  C21  0.020
 8JF  plan-3  O22  0.020
 8JF  plan-3  H5   0.020

