# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 11:58:59 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: N-(4-methoxybenzyl)quinoxaline-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CNC(=O)c2ccc3nccnc3c2)cc1
#
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
 RQQ  RQQ  N-(4-methoxybenzyl)quinoxaline-6-carboxamide  ligand  37  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RQQ
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
 RQQ  O1    O  O     0  -0.485   0.8175  -2.7067  -0.4440
 RQQ  C6    C  C     0   0.546   0.6714  -1.5410  -0.1048
 RQQ  C4    C  CR6   0  -0.037   1.8163  -0.5755  -0.1480
 RQQ  C3    C  CR16  0  -0.283   1.6236   0.8113  -0.3575
 RQQ  C2    C  CR16  0  -0.289   2.6873   1.6686  -0.4041
 RQQ  C5    C  CR16  0  -0.333   3.0862  -1.0743  -0.0039
 RQQ  C     C  CR66  0   0.255   4.1961  -0.2084  -0.0319
 RQQ  N2    N  N     0  -0.377   5.4409  -0.7168   0.1342
 RQQ  C16   C  CR16  0  -0.111   6.4304   0.1274   0.0962
 RQQ  C15   C  CR16  0  -0.109   6.2312   1.5165  -0.1111
 RQQ  N1    N  N     0  -0.377   5.0472   2.0323  -0.2732
 RQQ  C1    C  CR66  0   0.231   3.9978   1.1772  -0.2348
 RQQ  N     N  NH1   0  -0.643  -0.4949  -1.0374   0.3279
 RQQ  C7    C  CH2   0  -0.333  -1.7093  -1.8209   0.4418
 RQQ  C8    C  CR6   0   0.052  -2.9200  -0.9534   0.2393
 RQQ  C14   C  CR16  0  -0.268  -3.1614  -0.3444  -0.9939
 RQQ  C13   C  CR16  0  -0.328  -4.2677   0.4573  -1.1903
 RQQ  C11   C  CR6   0   0.372  -5.1734   0.6753  -0.1468
 RQQ  O     O  O2    0  -0.470  -6.2242   1.4681  -0.4283
 RQQ  C12   C  CH3   0  -0.436  -7.1505   1.7535   0.6007
 RQQ  C10   C  CR16  0  -0.371  -4.9450   0.0771   1.0880
 RQQ  C9    C  CR16  0  -0.288  -3.8226  -0.7270   1.2658
 RQQ  H     H  HNH1  0   0.409  -0.5082  -0.1218   0.7491
 RQQ  H3    H  HCR6  0   0.269   0.6277   1.2057  -0.5130
 RQQ  H5    H  HCR6  0   0.274   3.2584  -2.1324   0.1449
 RQQ  H2    H  HCR6  0   0.277   2.5436   2.7272  -0.5756
 RQQ  H16   H  HCR6  0   0.282   7.4348  -0.2576   0.2286
 RQQ  H15   H  HCR6  0   0.283   7.0850   2.1834  -0.1383
 RQQ  H71C  H  HCH2  0   0.264  -1.6745  -2.6112  -0.3083
 RQQ  H72C  H  HCH2  0   0.258  -1.7592  -2.3123   1.4181
 RQQ  H14   H  HCR6  0   0.254  -2.4725  -0.5007  -1.8159
 RQQ  H9    H  HCR6  0   0.256  -3.6589  -1.1834   2.2350
 RQQ  H13   H  HCR6  0   0.263  -4.4436   0.9210  -2.1532
 RQQ  H10   H  HCR6  0   0.278  -5.6199   0.2214   1.9205
 RQQ  H121  H  HCH3  0   0.260  -7.9028   2.4075   0.1665
 RQQ  H122  H  HCH3  0   0.228  -7.6433   0.8507   0.9707
 RQQ  H123  H  HCH3  0   0.228  -6.6804   2.2692   1.4422

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
 RQQ  O1   C6    double    1.223  0.020  1.223
 RQQ  C6   C4    single    1.498  0.020  1.498
 RQQ  C6   N     single    1.342  0.020  1.342
 RQQ  C4   C3    aromatic  1.416  0.020  1.416
 RQQ  C4   C5    aromatic  1.372  0.020  1.372
 RQQ  C3   C2    aromatic  1.367  0.020  1.367
 RQQ  C2   C1    aromatic  1.410  0.020  1.410
 RQQ  C5   C     aromatic  1.408  0.020  1.408
 RQQ  C    N2    aromatic  1.355  0.020  1.355
 RQQ  C    C1    aromatic  1.414  0.020  1.414
 RQQ  N2   C16   aromatic  1.301  0.020  1.301
 RQQ  C16  C15   aromatic  1.419  0.020  1.419
 RQQ  C15  N1    aromatic  1.302  0.020  1.302
 RQQ  N1   C1    aromatic  1.354  0.020  1.354
 RQQ  N    C7    single    1.450  0.020  1.450
 RQQ  C7   C8    single    1.503  0.020  1.503
 RQQ  C8   C14   aromatic  1.396  0.020  1.396
 RQQ  C8   C9    aromatic  1.385  0.020  1.385
 RQQ  C14  C13   aromatic  1.380  0.020  1.380
 RQQ  C13  C11   aromatic  1.399  0.020  1.399
 RQQ  C11  O     single    1.346  0.020  1.346
 RQQ  C11  C10   aromatic  1.391  0.020  1.391
 RQQ  O    C12   single    1.414  0.020  1.414
 RQQ  C10  C9    aromatic  1.392  0.020  1.392
 RQQ  N    H     single    0.860  0.020  1.020
 RQQ  C3   H3    single    0.930  0.020  1.080
 RQQ  C5   H5    single    0.930  0.020  1.080
 RQQ  C2   H2    single    0.930  0.020  1.080
 RQQ  C16  H16   single    0.930  0.020  1.080
 RQQ  C15  H15   single    0.930  0.020  1.080
 RQQ  C7   H71C  single    0.970  0.020  1.090
 RQQ  C7   H72C  single    0.970  0.020  1.090
 RQQ  C14  H14   single    0.930  0.020  1.080
 RQQ  C9   H9    single    0.930  0.020  1.080
 RQQ  C13  H13   single    0.930  0.020  1.080
 RQQ  C10  H10   single    0.930  0.020  1.080
 RQQ  C12  H121  single    0.970  0.020  1.090
 RQQ  C12  H122  single    0.970  0.020  1.090
 RQQ  C12  H123  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
 RQQ  N     C6   C4    115.56  3.000
 RQQ  N     C6   O1    123.44  3.000
 RQQ  C4    C6   O1    121.00  3.000
 RQQ  C5    C4   C3    119.85  3.000
 RQQ  C5    C4   C6    118.03  3.000
 RQQ  C3    C4   C6    122.11  3.000
 RQQ  H3    C3   C2    118.85  3.000
 RQQ  H3    C3   C4    120.23  3.000
 RQQ  C2    C3   C4    120.89  3.000
 RQQ  H2    C2   C1    118.92  3.000
 RQQ  H2    C2   C3    121.04  3.000
 RQQ  C1    C2   C3    120.04  3.000
 RQQ  H5    C5   C     118.59  3.000
 RQQ  H5    C5   C4    121.14  3.000
 RQQ  C     C5   C4    120.26  3.000
 RQQ  C1    C    N2    120.93  3.000
 RQQ  C1    C    C5    119.66  3.000
 RQQ  N2    C    C5    119.41  3.000
 RQQ  C16   N2   C     116.85  3.000
 RQQ  H16   C16  C15   119.72  3.000
 RQQ  H16   C16  N2    118.08  3.000
 RQQ  C15   C16  N2    122.20  3.000
 RQQ  H15   C15  N1    118.01  3.000
 RQQ  H15   C15  C16   119.71  3.000
 RQQ  N1    C15  C16   122.28  3.000
 RQQ  C1    N1   C15   116.81  3.000
 RQQ  N1    C1   C     120.93  3.000
 RQQ  N1    C1   C2    119.79  3.000
 RQQ  C     C1   C2    119.28  3.000
 RQQ  H     N    C7    116.55  3.000
 RQQ  H     N    C6    119.16  3.000
 RQQ  C7    N    C6    123.40  3.000
 RQQ  H72C  C7   H71C  106.85  3.000
 RQQ  H72C  C7   C8    110.04  3.000
 RQQ  H71C  C7   C8    110.57  3.000
 RQQ  H72C  C7   N     110.55  3.000
 RQQ  H71C  C7   N     108.12  3.000
 RQQ  C8    C7   N     110.62  3.000
 RQQ  C9    C8   C14   118.07  3.000
 RQQ  C9    C8   C7    121.28  3.000
 RQQ  C14   C8   C7    120.66  3.000
 RQQ  H14   C14  C13   119.04  3.000
 RQQ  H14   C14  C8    119.80  3.000
 RQQ  C13   C14  C8    121.16  3.000
 RQQ  H13   C13  C11   119.42  3.000
 RQQ  H13   C13  C14   120.35  3.000
 RQQ  C11   C13  C14   120.22  3.000
 RQQ  C10   C11  O     124.55  3.000
 RQQ  C10   C11  C13   119.27  3.000
 RQQ  O     C11  C13   116.18  3.000
 RQQ  C12   O    C11   118.57  3.000
 RQQ  H123  C12  H122  108.84  3.000
 RQQ  H123  C12  H121  108.74  3.000
 RQQ  H122  C12  H121  108.67  3.000
 RQQ  H123  C12  O     111.95  3.000
 RQQ  H122  C12  O     112.03  3.000
 RQQ  H121  C12  O     106.51  3.000
 RQQ  H10   C10  C9    118.81  3.000
 RQQ  H10   C10  C11   121.57  3.000
 RQQ  C9    C10  C11   119.62  3.000
 RQQ  H9    C9   C10   118.64  3.000
 RQQ  H9    C9   C8    119.70  3.000
 RQQ  C10   C9   C8    121.66  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
 RQQ  CONST_01  C1    C2   C3   C4      0.00   0.0  0
 RQQ  CONST_02  N2    C    C5   C4    180.00   0.0  0
 RQQ  CONST_03  C1    C    C5   C4      0.00   0.0  0
 RQQ  CONST_04  C     C5   C4   C3      0.00   0.0  0
 RQQ  CONST_05  C     C1   C2   C3      0.00   0.0  0
 RQQ  CONST_06  N1    C1   C2   C3    180.00   0.0  0
 RQQ  CONST_07  C5    C4   C3   C2      0.00   0.0  0
 RQQ  CONST_08  C5    C    C1   C2      0.00   0.0  0
 RQQ  CONST_09  N2    C    C1   C2    180.00   0.0  0
 RQQ  CONST_10  C15   N1   C1   C2    180.00   0.0  0
 RQQ  CONST_11  C16   N2   C    C5    180.00   0.0  0
 RQQ  CONST_12  N1    C1   C    C5    180.00   0.0  0
 RQQ  CONST_13  C15   C16  N2   C       0.00   0.0  0
 RQQ  CONST_14  C15   N1   C1   C       0.00   0.0  0
 RQQ  CONST_15  N1    C1   C    N2      0.00   0.0  0
 RQQ  CONST_16  N1    C15  C16  N2      0.00   0.0  0
 RQQ  CONST_17  C1    C    N2   C16     0.00   0.0  0
 RQQ  CONST_18  C1    N1   C15  C16     0.00   0.0  0
 RQQ  CONST_19  C11   C13  C14  C8      0.00   0.0  0
 RQQ  CONST_20  C11   C10  C9   C8      0.00   0.0  0
 RQQ  CONST_21  C10   C9   C8   C14     0.00   0.0  0
 RQQ  CONST_22  C10   C11  C13  C14     0.00   0.0  0
 RQQ  CONST_23  C9    C8   C14  C13     0.00   0.0  0
 RQQ  CONST_24  C9    C10  C11  C13     0.00   0.0  0
 RQQ  CONST_25  C2    C3   C4   C6    180.00   0.0  0
 RQQ  CONST_26  C     C5   C4   C6    180.00   0.0  0
 RQQ  CONST_27  C13   C14  C8   C7    180.00   0.0  0
 RQQ  CONST_28  C10   C9   C8   C7    180.00   0.0  0
 RQQ  CONST_29  O     C11  C13  C14   180.00   0.0  0
 RQQ  CONST_30  C9    C10  C11  O     180.00   0.0  0
 RQQ  CONST_31  H2    C2   C3   C4    180.00   0.0  0
 RQQ  CONST_32  H5    C5   C4   C3    180.00   0.0  0
 RQQ  CONST_33  H3    C3   C4   C5    180.00   0.0  0
 RQQ  CONST_34  H16   C16  N2   C     180.00   0.0  0
 RQQ  CONST_35  H15   C15  C16  N2    180.00   0.0  0
 RQQ  CONST_36  H13   C13  C14  C8    180.00   0.0  0
 RQQ  CONST_37  H10   C10  C9   C8    180.00   0.0  0
 RQQ  CONST_38  H9    C9   C8   C14   180.00   0.0  0
 RQQ  CONST_39  H14   C14  C13  C11   180.00   0.0  0
 RQQ  CONST_40  C7    N    C6   C4    180.00   0.0  0
 RQQ  CONST_41  H     N    C6   C4      0.00   0.0  0
 RQQ  CONST_42  C7    N    C6   O1      0.00   0.0  0
 RQQ  Var_01    C3    C4   C6   O1    151.04  30.0  2
 RQQ  Var_02    C14   C8   C7   N      65.03  30.0  2
 RQQ  Var_03    C10   C11  O    C12     1.85  30.0  3
 RQQ  Var_04    C8    C7   N    C6   -150.38  30.0  3
 RQQ  Var_05    H121  C12  O    C11   179.51  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
 RQQ  plan-1  C7   0.020
 RQQ  plan-1  C8   0.020
 RQQ  plan-1  C14  0.020
 RQQ  plan-1  C13  0.020
 RQQ  plan-1  C11  0.020
 RQQ  plan-1  O    0.020
 RQQ  plan-1  C10  0.020
 RQQ  plan-1  C9   0.020
 RQQ  plan-1  H14  0.020
 RQQ  plan-1  H9   0.020
 RQQ  plan-1  H13  0.020
 RQQ  plan-1  H10  0.020
 RQQ  plan-2  C6   0.020
 RQQ  plan-2  C4   0.020
 RQQ  plan-2  C3   0.020
 RQQ  plan-2  C2   0.020
 RQQ  plan-2  C5   0.020
 RQQ  plan-2  C    0.020
 RQQ  plan-2  N2   0.020
 RQQ  plan-2  C16  0.020
 RQQ  plan-2  C15  0.020
 RQQ  plan-2  N1   0.020
 RQQ  plan-2  C1   0.020
 RQQ  plan-2  H3   0.020
 RQQ  plan-2  H5   0.020
 RQQ  plan-2  H2   0.020
 RQQ  plan-2  H16  0.020
 RQQ  plan-2  H15  0.020
 RQQ  plan-3  O1   0.020
 RQQ  plan-3  C6   0.020
 RQQ  plan-3  C4   0.020
 RQQ  plan-3  N    0.020
 RQQ  plan-3  C7   0.020
 RQQ  plan-3  H    0.020

