# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:57:09 2021
#   Inital geometry file: a 134 line input string
#   Ligand name: (3~{R})-1,3-dimethyl-6-[(4-phenylpyrimidin-2-yl)amino]-4-propan-2-yl-3~{H}-quinoxalin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N1[C@H](C)C(=O)N(C)c2ccc(Nc3nccc(n3)c4ccccc4)cc12
#
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
 EDF  EDF  (3~{R})-1,3-dimethyl-6-[(4-phenylpyrimidin-2-yl)amino]-4-propan-2-yl-3~{H}-quinoxalin-2-one  ligand  54  29  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EDF
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
 EDF  C10   C  CH3   0  -0.667  -14.6333   -8.7464   2.9649
 EDF  C13   C  CR16  0  -0.464  -11.9491   -7.4137   1.2436
 EDF  C20   C  CR6   0   0.323   -9.7058   -9.3079   4.1953
 EDF  C21   C  CR6   0   0.064  -10.6972   -9.3709   5.2879
 EDF  C22   C  CR16  0  -0.315  -10.6225  -10.3463   6.2826
 EDF  C24   C  CR16  0  -0.258  -12.5978   -9.4612   7.3339
 EDF  C26   C  CR16  0  -0.284  -11.7372   -8.4421   5.3333
 EDF  C28   C  C     0   0.544  -15.4040   -5.5884  -0.3437
 EDF  C03   C  CR6   0   0.284  -13.0358   -6.0223  -0.4146
 EDF  C04   C  CR16  0  -0.327  -11.8425   -5.9730  -1.1193
 EDF  C05   C  CR16  0  -0.386  -10.7059   -6.6103  -0.6505
 EDF  C06   C  CR6   0   0.415  -13.0929   -6.7661   0.7775
 EDF  C08   C  CH1   0  -0.133  -14.4133   -7.2420   2.8137
 EDF  C09   C  CH3   0  -0.663  -15.4768   -6.4552   3.5727
 EDF  C11   C  CH1   0  -0.260  -15.4605   -6.8025   0.5635
 EDF  C12   C  CH3   0  -0.658  -15.6193   -8.0675  -0.2875
 EDF  C14   C  CR6   0   0.379  -10.7446   -7.3276   0.5457
 EDF  C16   C  CR6   0   0.597   -9.2179   -8.5901   2.0899
 EDF  C18   C  CR16  0  -0.018   -7.6046   -9.7047   3.2012
 EDF  C19   C  CR16  0  -0.405   -8.4322   -9.8537   4.3042
 EDF  C23   C  CR16  0  -0.237  -11.5682  -10.3923   7.2961
 EDF  C25   C  CR16  0  -0.242  -12.6776   -8.4839   6.3498
 EDF  N02   N  NT    0  -0.549  -14.1671   -5.2888  -0.8161
 EDF  N07   N  NT    0  -0.513  -14.3028   -6.7924   1.4326
 EDF  N17   N  N     0  -0.461   -7.9729   -9.0851   2.0959
 EDF  N27   N  N     0  -0.503  -10.0867   -8.6782   3.0864
 EDF  O29   O  O     0  -0.480  -16.4085   -4.9651  -0.6454
 EDF  H103  H  HCH3  0   0.236  -14.5656   -9.0333   4.0153
 EDF  H101  H  HCH3  0   0.230  -15.6221   -9.0394   2.6086
 EDF  H102  H  HCH3  0   0.237  -13.8907   -9.3241   2.4137
 EDF  H131  H  HCR6  0   0.299  -11.9930   -7.9978   2.1469
 EDF  H221  H  HCR6  0   0.258   -9.8375  -11.0908   6.2614
 EDF  H241  H  HCR6  0   0.264  -13.3343   -9.4974   8.1257
 EDF  H261  H  HCR6  0   0.260  -11.7978   -7.6748   4.5735
 EDF  H011  H  HCH3  0   0.274  -14.9147   -3.6274  -1.8178
 EDF  H013  H  HCH3  0   0.253  -13.1916   -3.5429  -1.4334
 EDF  H012  H  HCH3  0   0.250  -13.7581   -4.5732  -2.7578
 EDF  H041  H  HCR6  0   0.275  -11.7732   -5.4112  -2.0406
 EDF  H051  H  HCR6  0   0.263   -9.7855   -6.5401  -1.2169
 EDF  H081  H  HCH1  0   0.244  -13.4581   -6.9838   3.2772
 EDF  H092  H  HCH3  0   0.242  -15.3907   -6.6661   4.6391
 EDF  H091  H  HCH3  0   0.241  -15.3502   -5.3820   3.4302
 EDF  H093  H  HCH3  0   0.228  -16.4911   -6.7264   3.2774
 EDF  H111  H  HCH1  0   0.281  -16.3513   -6.6826   1.1785
 EDF  H123  H  HCH3  0   0.253  -15.7100   -8.9490   0.3444
 EDF  H121  H  HCH3  0   0.245  -16.5213   -7.9997  -0.8965
 EDF  H122  H  HCH3  0   0.235  -14.7715   -8.2175  -0.9576
 EDF  H181  H  HCR6  0   0.277   -6.5958  -10.1023   3.2191
 EDF  H191  H  HCR6  0   0.273   -8.0796  -10.3507   5.1948
 EDF  H231  H  HCR6  0   0.263  -11.5027  -11.1610   8.0546
 EDF  H251  H  HCR6  0   0.262  -13.4745   -7.7518   6.3756
 EDF  H151  H  HNH1  0   0.407   -8.8108   -7.9111   0.2688
 EDF  N15   N  NH1   0  -0.778   -9.5633   -7.9526   0.9394
 EDF  C01   C  CH3   0  -0.555  -13.9961   -4.2004  -1.7608

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
 EDF  C01  N02   single    1.451  0.020  1.451
 EDF  C04  C05   aromatic  1.385  0.020  1.385
 EDF  C04  C03   aromatic  1.387  0.020  1.387
 EDF  C05  C14   aromatic  1.395  0.020  1.395
 EDF  N02  C03   single    1.407  0.020  1.407
 EDF  N02  C28   single    1.358  0.020  1.358
 EDF  C12  C11   single    1.533  0.020  1.533
 EDF  O29  C28   double    1.220  0.020  1.220
 EDF  C03  C06   aromatic  1.406  0.020  1.406
 EDF  C28  C11   single    1.517  0.020  1.517
 EDF  C14  N15   single    1.393  0.020  1.393
 EDF  C14  C13   aromatic  1.395  0.020  1.395
 EDF  C11  N07   single    1.448  0.020  1.448
 EDF  N15  C16   single    1.360  0.020  1.360
 EDF  C06  C13   aromatic  1.395  0.020  1.395
 EDF  C06  N07   single    1.376  0.020  1.376
 EDF  N07  C08   single    1.457  0.020  1.457
 EDF  C16  N17   aromatic  1.340  0.020  1.340
 EDF  C16  N27   aromatic  1.325  0.020  1.325
 EDF  N17  C18   aromatic  1.320  0.020  1.320
 EDF  C10  C08   single    1.528  0.020  1.528
 EDF  C08  C09   single    1.525  0.020  1.525
 EDF  N27  C20   aromatic  1.331  0.020  1.331
 EDF  C18  C19   aromatic  1.387  0.020  1.387
 EDF  C20  C19   aromatic  1.390  0.020  1.390
 EDF  C20  C21   single    1.477  0.020  1.477
 EDF  C21  C26   aromatic  1.395  0.020  1.395
 EDF  C21  C22   aromatic  1.395  0.020  1.395
 EDF  C26  C25   aromatic  1.385  0.020  1.385
 EDF  C22  C23   aromatic  1.387  0.020  1.387
 EDF  C25  C24   aromatic  1.389  0.020  1.389
 EDF  C23  C24   aromatic  1.389  0.020  1.389
 EDF  C10  H103  single    0.970  0.020  1.090
 EDF  C10  H101  single    0.970  0.020  1.090
 EDF  C10  H102  single    0.970  0.020  1.090
 EDF  C13  H131  single    0.930  0.020  1.080
 EDF  C22  H221  single    0.930  0.020  1.080
 EDF  C24  H241  single    0.930  0.020  1.080
 EDF  C26  H261  single    0.930  0.020  1.080
 EDF  C01  H011  single    0.970  0.020  1.090
 EDF  C01  H013  single    0.970  0.020  1.090
 EDF  C01  H012  single    0.970  0.020  1.090
 EDF  C04  H041  single    0.930  0.020  1.080
 EDF  C05  H051  single    0.930  0.020  1.080
 EDF  C08  H081  single    0.970  0.020  1.090
 EDF  C09  H092  single    0.970  0.020  1.090
 EDF  C09  H091  single    0.970  0.020  1.090
 EDF  C09  H093  single    0.970  0.020  1.090
 EDF  C11  H111  single    0.970  0.020  1.090
 EDF  C12  H123  single    0.970  0.020  1.090
 EDF  C12  H121  single    0.970  0.020  1.090
 EDF  C12  H122  single    0.970  0.020  1.090
 EDF  C18  H181  single    0.930  0.020  1.080
 EDF  C19  H191  single    0.930  0.020  1.080
 EDF  C23  H231  single    0.930  0.020  1.080
 EDF  C25  H251  single    0.930  0.020  1.080
 EDF  N15  H151  single    0.860  0.020  1.020

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
 EDF  H102  C10  H101  108.05  3.000
 EDF  H102  C10  H103  107.76  3.000
 EDF  H101  C10  H103  107.46  3.000
 EDF  H102  C10  C08   111.93  3.000
 EDF  H101  C10  C08   111.26  3.000
 EDF  H103  C10  C08   110.20  3.000
 EDF  H131  C13  C14   119.25  3.000
 EDF  H131  C13  C06   119.93  3.000
 EDF  C14   C13  C06   120.83  3.000
 EDF  N27   C20  C19   120.88  3.000
 EDF  C19   C20  C21   122.72  3.000
 EDF  N27   C20  C21   116.39  3.000
 EDF  C26   C21  C22   118.83  3.000
 EDF  C22   C21  C20   121.43  3.000
 EDF  C26   C21  C20   119.74  3.000
 EDF  H221  C22  C23   119.08  3.000
 EDF  H221  C22  C21   120.39  3.000
 EDF  C23   C22  C21   120.51  3.000
 EDF  H241  C24  C25   120.19  3.000
 EDF  H241  C24  C23   120.14  3.000
 EDF  C25   C24  C23   119.67  3.000
 EDF  H261  C26  C25   119.92  3.000
 EDF  H261  C26  C21   119.43  3.000
 EDF  C25   C26  C21   120.65  3.000
 EDF  O29   C28  N02   123.46  3.000
 EDF  O29   C28  C11   121.75  3.000
 EDF  N02   C28  C11   114.76  3.000
 EDF  N02   C03  C06   119.02  3.000
 EDF  C06   C03  C04   118.98  3.000
 EDF  N02   C03  C04   121.90  3.000
 EDF  H041  C04  C05   118.36  3.000
 EDF  H041  C04  C03   120.43  3.000
 EDF  C05   C04  C03   121.19  3.000
 EDF  H051  C05  C14   120.35  3.000
 EDF  H051  C05  C04   119.38  3.000
 EDF  C14   C05  C04   120.27  3.000
 EDF  N07   C06  C03   116.70  3.000
 EDF  N07   C06  C13   123.58  3.000
 EDF  C03   C06  C13   119.71  3.000
 EDF  H081  C08  N07   105.24  3.000
 EDF  H081  C08  C09   106.06  3.000
 EDF  N07   C08  C09   111.44  3.000
 EDF  H081  C08  C10   108.46  3.000
 EDF  C09   C08  C10   110.99  3.000
 EDF  N07   C08  C10   114.12  3.000
 EDF  H093  C09  H091  108.51  3.000
 EDF  H093  C09  H092  106.87  3.000
 EDF  H091  C09  H092  108.01  3.000
 EDF  H093  C09  C08   112.67  3.000
 EDF  H091  C09  C08   111.21  3.000
 EDF  H092  C09  C08   109.38  3.000
 EDF  H111  C11  N07   108.32  3.000
 EDF  H111  C11  C12   108.64  3.000
 EDF  N07   C11  C12   114.96  3.000
 EDF  H111  C11  C28   106.26  3.000
 EDF  N07   C11  C28   108.89  3.000
 EDF  C12   C11  C28   109.41  3.000
 EDF  H122  C12  H121  107.96  3.000
 EDF  H122  C12  H123  108.06  3.000
 EDF  H121  C12  H123  107.79  3.000
 EDF  H122  C12  C11   111.96  3.000
 EDF  H121  C12  C11   110.15  3.000
 EDF  H123  C12  C11   110.77  3.000
 EDF  N15   C14  C05   116.70  3.000
 EDF  N15   C14  C13   124.27  3.000
 EDF  C05   C14  C13   118.99  3.000
 EDF  N27   C16  N17   125.55  3.000
 EDF  N27   C16  N15   120.06  3.000
 EDF  N17   C16  N15   114.40  3.000
 EDF  H181  C18  N17   116.46  3.000
 EDF  H181  C18  C19   120.17  3.000
 EDF  N17   C18  C19   123.36  3.000
 EDF  H191  C19  C18   120.72  3.000
 EDF  H191  C19  C20   123.02  3.000
 EDF  C18   C19  C20   116.25  3.000
 EDF  H231  C23  C24   120.15  3.000
 EDF  H231  C23  C22   119.64  3.000
 EDF  C24   C23  C22   120.21  3.000
 EDF  H251  C25  C26   119.79  3.000
 EDF  H251  C25  C24   120.08  3.000
 EDF  C26   C25  C24   120.13  3.000
 EDF  C03   N02  C01   118.82  3.000
 EDF  C03   N02  C28   121.22  3.000
 EDF  C01   N02  C28   119.96  3.000
 EDF  C11   N07  C08   120.43  3.000
 EDF  C08   N07  C06   121.60  3.000
 EDF  C11   N07  C06   114.67  3.000
 EDF  C18   N17  C16   115.89  3.000
 EDF  C16   N27  C20   118.06  3.000
 EDF  H151  N15  C16   113.09  3.000
 EDF  H151  N15  C14   115.23  3.000
 EDF  C16   N15  C14   131.66  3.000
 EDF  H012  C01  H013  108.65  3.000
 EDF  H012  C01  H011  108.51  3.000
 EDF  H013  C01  H011  108.82  3.000
 EDF  H012  C01  N02   111.37  3.000
 EDF  H013  C01  N02   110.12  3.000
 EDF  H011  C01  N02   109.32  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
 EDF  CONST_01  C04   C05  C14  C13     0.00   0.0  0
 EDF  CONST_02  C04   C03  C06  C13     0.00   0.0  0
 EDF  CONST_03  N17   C16  N27  C20     0.00   0.0  0
 EDF  CONST_04  N17   C18  C19  C20     0.00   0.0  0
 EDF  CONST_05  C25   C26  C21  C20   180.00   0.0  0
 EDF  CONST_06  C23   C22  C21  C20   180.00   0.0  0
 EDF  CONST_07  C16   N27  C20  C21   180.00   0.0  0
 EDF  CONST_08  C18   C19  C20  C21   180.00   0.0  0
 EDF  CONST_09  C24   C25  C26  C21     0.00   0.0  0
 EDF  CONST_10  C24   C23  C22  C21     0.00   0.0  0
 EDF  CONST_13  C25   C26  C21  C22     0.00   0.0  0
 EDF  CONST_14  C25   C24  C23  C22     0.00   0.0  0
 EDF  CONST_17  C23   C22  C21  C26     0.00   0.0  0
 EDF  CONST_18  C23   C24  C25  C26     0.00   0.0  0
 EDF  CONST_19  C14   C05  C04  C03     0.00   0.0  0
 EDF  CONST_20  C14   C13  C06  C03     0.00   0.0  0
 EDF  CONST_21  C06   C03  C04  C05     0.00   0.0  0
 EDF  CONST_22  C06   C13  C14  C05     0.00   0.0  0
 EDF  CONST_23  C19   C18  N17  C16     0.00   0.0  0
 EDF  CONST_24  C19   C20  N27  C16     0.00   0.0  0
 EDF  CONST_25  N27   C16  N17  C18     0.00   0.0  0
 EDF  CONST_26  N27   C20  C19  C18     0.00   0.0  0
 EDF  CONST_27  C11   C28  N02  C03     0.00   0.0  0
 EDF  CONST_28  N15   C16  N27  C20   180.00   0.0  0
 EDF  CONST_29  N15   C14  C05  C04   180.00   0.0  0
 EDF  CONST_30  N15   C14  C13  C06   180.00   0.0  0
 EDF  CONST_31  N15   C16  N17  C18   180.00   0.0  0
 EDF  CONST_32  C11   C28  N02  C01   180.00   0.0  0
 EDF  CONST_33  O29   C28  N02  C03   180.00   0.0  0
 EDF  CONST_34  H051  C05  C14  C13   180.00   0.0  0
 EDF  CONST_35  H181  C18  C19  C20   180.00   0.0  0
 EDF  CONST_36  H261  C26  C21  C20     0.00   0.0  0
 EDF  CONST_37  H221  C22  C21  C20     0.00   0.0  0
 EDF  CONST_38  H191  C19  C20  C21     0.00   0.0  0
 EDF  CONST_39  H251  C25  C26  C21   180.00   0.0  0
 EDF  CONST_40  H231  C23  C22  C21   180.00   0.0  0
 EDF  CONST_41  H241  C24  C23  C22   180.00   0.0  0
 EDF  CONST_42  H131  C13  C06  C03   180.00   0.0  0
 EDF  CONST_43  H041  C04  C03  C06   180.00   0.0  0
 EDF  CONST_44  O29   C28  N02  C01     0.00   0.0  0
 EDF  Var_01    C11   N07  C06  C13  -145.30  30.0  1
 EDF  Var_02    C04   C03  N02  C28   163.14  30.0  1
 EDF  Var_03    C16   N15  C14  C13   -10.39  30.0  2
 EDF  Var_04    N17   C16  N15  C14   179.35  30.0  2
 EDF  Var_05    H011  C01  N02  C28    11.13  30.0  3
 EDF  Var_06    H103  C10  C08  N07   172.01  30.0  3
 EDF  Var_07    H092  C09  C08  N07  -168.24  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 EDF  chir_01  C11  C12  C28  N07  positiv

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
 EDF  plan-1  C20   0.020
 EDF  plan-1  C21   0.020
 EDF  plan-1  C22   0.020
 EDF  plan-1  C24   0.020
 EDF  plan-1  C26   0.020
 EDF  plan-1  C23   0.020
 EDF  plan-1  C25   0.020
 EDF  plan-1  H221  0.020
 EDF  plan-1  H241  0.020
 EDF  plan-1  H261  0.020
 EDF  plan-1  H231  0.020
 EDF  plan-1  H251  0.020
 EDF  plan-2  C20   0.020
 EDF  plan-2  C21   0.020
 EDF  plan-2  C16   0.020
 EDF  plan-2  C18   0.020
 EDF  plan-2  C19   0.020
 EDF  plan-2  N17   0.020
 EDF  plan-2  N27   0.020
 EDF  plan-2  H181  0.020
 EDF  plan-2  H191  0.020
 EDF  plan-2  N15   0.020
 EDF  plan-3  C13   0.020
 EDF  plan-3  C03   0.020
 EDF  plan-3  C04   0.020
 EDF  plan-3  C05   0.020
 EDF  plan-3  C06   0.020
 EDF  plan-3  C14   0.020
 EDF  plan-3  N02   0.020
 EDF  plan-3  N07   0.020
 EDF  plan-3  H131  0.020
 EDF  plan-3  H041  0.020
 EDF  plan-3  H051  0.020
 EDF  plan-3  N15   0.020
 EDF  plan-4  C28   0.020
 EDF  plan-4  C03   0.020
 EDF  plan-4  C11   0.020
 EDF  plan-4  N02   0.020
 EDF  plan-4  O29   0.020
 EDF  plan-4  C01   0.020

