# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 18:35:29 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (3~{R})-4-cyclopentyl-~{N}-(2,4-dimethylphenyl)-1,3-dimethyl-2-oxidanylidene-3~{H}-quinoxaline-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N(C2CCCC2)c3cc(ccc3N(C)C1=O)C(=O)Nc4ccc(C)cc4C
#
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
 8XR  8XR  (3~{R})-4-cyclopentyl-~{N}-(2,4-dimethylphenyl)-1,3-dimethyl-2-oxidanylidene-3~{H}-quinoxaline-6-carboxamide  ligand  58  29  .  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_8XR
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
 8XR  C13  C  CH3   0  -0.692   5.2752   1.1716   1.5951
 8XR  C17  C  CR6   0   0.279  -4.2165  -0.3401   0.2671
 8XR  C20  C  CR16  0  -0.356  -6.3106  -0.1314  -0.8770
 8XR  C21  C  CR6   0   0.107  -6.9467   0.2951   0.2846
 8XR  C22  C  CR16  0  -0.322  -6.1842   0.3954   1.4447
 8XR  C24  C  CH2   0  -0.468   3.9101   0.8575  -1.7214
 8XR  C26  C  CH2   0  -0.449   2.7749   2.9151  -2.4582
 8XR  C01  C  CR16  0  -0.301  -0.2196  -1.8427   0.5231
 8XR  C02  C  CR6   0  -0.063  -0.4816  -0.4800   0.6451
 8XR  C03  C  CR16  0  -0.328   0.5913   0.4033   0.7130
 8XR  C04  C  CR66  0   0.281   1.8985  -0.0387   0.5968
 8XR  C05  C  CR66  0   0.352   2.1504  -1.4125   0.4611
 8XR  C06  C  CR16  0  -0.327   1.0818  -2.3070   0.4458
 8XR  N07  N  NR6   0  -0.496   2.9818   0.8544   0.6688
 8XR  C08  C  CR16  0  -0.255   4.0913   0.2443   1.3899
 8XR  C09  C  CR6   0   0.563   4.5107  -1.0814   0.7647
 8XR  N10  N  NR6   0  -0.569   3.4692  -1.8472   0.3171
 8XR  O11  O  O     0  -0.460   5.6671  -1.4498   0.6923
 8XR  C12  C  CH3   0  -0.559   3.7288  -3.1708  -0.2209
 8XR  C14  C  CR15  0  -0.096   3.3101   1.6211  -0.5324
 8XR  N16  N  NH1   0  -0.764  -2.8501  -0.6820   0.2526
 8XR  O18  O  O     0  -0.466  -2.0549   1.1660   1.2935
 8XR  C19  C  CR6   0   0.082  -4.9555  -0.4458  -0.9156
 8XR  C23  C  CR16  0  -0.261  -4.8369   0.0739   1.4411
 8XR  C25  C  CH2   0  -0.439   3.7885   1.8350  -2.9041
 8XR  C27  C  CH2   0  -0.452   2.1461   2.3708  -1.1767
 8XR  C29  C  CH3   0  -0.723  -8.4154   0.6053   0.2907
 8XR  H1   H  HCH3  0   0.249   4.9350   2.1197   2.0108
 8XR  H2   H  HCH3  0   0.256   5.9710   0.7293   2.3049
 8XR  H3   H  HCH3  0   0.236   5.8245   1.3720   0.6758
 8XR  H4   H  HCR6  0   0.242  -6.8861  -0.2109  -1.7932
 8XR  H5   H  HCR6  0   0.248  -6.6470   0.7212   2.3685
 8XR  H6   H  HCH2  0   0.236   4.9404   0.5414  -1.5469
 8XR  H7   H  HCH2  0   0.229   3.3214  -0.0441  -1.9136
 8XR  H8   H  HCH2  0   0.228   3.2903   3.8543  -2.2480
 8XR  H9   H  HCH2  0   0.235   2.0277   3.1278  -3.2228
 8XR  H10  H  HCH3  0   0.249  -3.9477  -1.9138  -2.1426
 8XR  H11  H  HCH3  0   0.257  -5.0180  -0.8361  -3.0226
 8XR  H12  H  HCH3  0   0.251  -3.4538  -0.2584  -2.4549
 8XR  H13  H  HCR6  0   0.263  -1.0195  -2.5719   0.5219
 8XR  H14  H  HCR6  0   0.265   0.4141   1.4612   0.8527
 8XR  H15  H  HCR6  0   0.286   1.2514  -3.3724   0.3744
 8XR  H19  H  HCH3  0   0.258   3.0807  -3.3565  -1.0749
 8XR  H20  H  HCH3  0   0.275   4.7598  -3.2290  -0.5516
 8XR  H21  H  HCH3  0   0.255   3.5594  -3.9481   0.5255
 8XR  H22  H  HCR5  0   0.249   4.0285   2.3841  -0.2194
 8XR  H23  H  HNH1  0   0.415  -2.5881  -1.4725  -0.3156
 8XR  H24  H  HCR6  0   0.260  -4.2717   0.1357   2.3607
 8XR  H25  H  HCH2  0   0.231   4.7516   2.2844  -3.1473
 8XR  H26  H  HCH2  0   0.232   3.4518   1.3180  -3.8029
 8XR  H27  H  HCH2  0   0.240   1.7317   3.1490  -0.5335
 8XR  H28  H  HCH2  0   0.231   1.3377   1.6787  -1.4258
 8XR  H29  H  HCH3  0   0.248  -8.9991  -0.2719   0.5785
 8XR  H30  H  HCH3  0   0.243  -8.6547   1.3973   0.9999
 8XR  H31  H  HCH3  0   0.243  -8.7632   0.9159  -0.6941
 8XR  H16  H  HCR6  0   0.293   3.7034  -0.0090   2.3865
 8XR  C15  C  C     0   0.530  -1.8556   0.0825   0.7697
 8XR  C28  C  CH3   0  -0.746  -4.3100  -0.8843  -2.1973

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
 8XR  C13  C08  single    1.518  0.020  1.518
 8XR  C15  C02  single    1.490  0.020  1.490
 8XR  C15  N16  single    1.357  0.020  1.357
 8XR  C15  O18  double    1.220  0.020  1.220
 8XR  C17  N16  single    1.409  0.020  1.409
 8XR  C17  C19  aromatic  1.399  0.020  1.399
 8XR  C17  C23  aromatic  1.391  0.020  1.391
 8XR  C20  C21  aromatic  1.391  0.020  1.391
 8XR  C20  C19  aromatic  1.392  0.020  1.392
 8XR  C21  C22  aromatic  1.392  0.020  1.392
 8XR  C21  C29  single    1.501  0.020  1.501
 8XR  C22  C23  aromatic  1.385  0.020  1.385
 8XR  C24  C14  single    1.535  0.020  1.535
 8XR  C24  C25  single    1.539  0.020  1.539
 8XR  C26  C25  single    1.547  0.020  1.547
 8XR  C26  C27  single    1.528  0.020  1.528
 8XR  C28  C19  single    1.501  0.020  1.501
 8XR  C01  C02  aromatic  1.393  0.020  1.393
 8XR  C01  C06  aromatic  1.384  0.020  1.384
 8XR  C02  C03  aromatic  1.391  0.020  1.391
 8XR  C03  C04  aromatic  1.385  0.020  1.385
 8XR  C04  C05  aromatic  1.403  0.020  1.403
 8XR  C04  N07  single    1.406  0.020  1.406
 8XR  C05  C06  aromatic  1.394  0.020  1.394
 8XR  C05  N10  single    1.396  0.020  1.396
 8XR  N07  C08  single    1.457  0.020  1.457
 8XR  N07  C14  single    1.462  0.020  1.462
 8XR  C09  N10  single    1.368  0.020  1.368
 8XR  C09  O11  double    1.216  0.020  1.216
 8XR  N10  C12  single    1.452  0.020  1.452
 8XR  C14  C27  single    1.527  0.020  1.527
 8XR  C13  H1   single    0.970  0.020  1.090
 8XR  C13  H2   single    0.970  0.020  1.090
 8XR  C13  H3   single    0.970  0.020  1.090
 8XR  C20  H4   single    0.930  0.020  1.080
 8XR  C22  H5   single    0.930  0.020  1.080
 8XR  C24  H6   single    0.970  0.020  1.090
 8XR  C24  H7   single    0.970  0.020  1.090
 8XR  C26  H8   single    0.970  0.020  1.090
 8XR  C26  H9   single    0.970  0.020  1.090
 8XR  C28  H10  single    0.970  0.020  1.090
 8XR  C28  H11  single    0.970  0.020  1.090
 8XR  C28  H12  single    0.970  0.020  1.090
 8XR  C01  H13  single    0.930  0.020  1.080
 8XR  C03  H14  single    0.930  0.020  1.080
 8XR  C06  H15  single    0.930  0.020  1.080
 8XR  C12  H19  single    0.970  0.020  1.090
 8XR  C12  H20  single    0.970  0.020  1.090
 8XR  C12  H21  single    0.970  0.020  1.090
 8XR  C14  H22  single    0.970  0.020  1.090
 8XR  N16  H23  single    0.860  0.020  1.020
 8XR  C23  H24  single    0.930  0.020  1.080
 8XR  C25  H25  single    0.970  0.020  1.090
 8XR  C25  H26  single    0.970  0.020  1.090
 8XR  C27  H27  single    0.970  0.020  1.090
 8XR  C27  H28  single    0.970  0.020  1.090
 8XR  C29  H29  single    0.970  0.020  1.090
 8XR  C29  H30  single    0.970  0.020  1.090
 8XR  C29  H31  single    0.970  0.020  1.090
 8XR  C08  C09  single    1.525  0.020  1.525
 8XR  C08  H16  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
 8XR  H3   C13  H2   107.63  3.000
 8XR  H3   C13  H1   108.62  3.000
 8XR  H2   C13  H1   107.74  3.000
 8XR  H3   C13  C08  113.05  3.000
 8XR  H2   C13  C08  109.79  3.000
 8XR  H1   C13  C08  109.85  3.000
 8XR  C23  C17  C19  120.04  3.000
 8XR  C23  C17  N16  120.91  3.000
 8XR  C19  C17  N16  119.04  3.000
 8XR  H4   C20  C19  118.47  3.000
 8XR  H4   C20  C21  119.01  3.000
 8XR  C19  C20  C21  122.52  3.000
 8XR  C29  C21  C22  121.18  3.000
 8XR  C29  C21  C20  120.94  3.000
 8XR  C22  C21  C20  117.87  3.000
 8XR  H5   C22  C23  119.18  3.000
 8XR  H5   C22  C21  119.89  3.000
 8XR  C23  C22  C21  120.93  3.000
 8XR  H7   C24  H6   107.30  3.000
 8XR  H7   C24  C25  110.23  3.000
 8XR  H6   C24  C25  112.42  3.000
 8XR  H7   C24  C14  109.61  3.000
 8XR  H6   C24  C14  112.90  3.000
 8XR  C25  C24  C14  104.38  3.000
 8XR  H9   C26  H8   106.90  3.000
 8XR  H9   C26  C27  112.07  3.000
 8XR  H8   C26  C27  109.84  3.000
 8XR  H9   C26  C25  112.53  3.000
 8XR  H8   C26  C25  110.30  3.000
 8XR  C27  C26  C25  105.23  3.000
 8XR  H13  C01  C06  117.96  3.000
 8XR  H13  C01  C02  121.34  3.000
 8XR  C06  C01  C02  120.66  3.000
 8XR  C03  C02  C01  118.70  3.000
 8XR  C03  C02  C15  117.86  3.000
 8XR  C01  C02  C15  123.38  3.000
 8XR  H14  C03  C04  118.53  3.000
 8XR  H14  C03  C02  120.05  3.000
 8XR  C04  C03  C02  121.41  3.000
 8XR  N07  C04  C05  119.25  3.000
 8XR  N07  C04  C03  121.35  3.000
 8XR  C05  C04  C03  119.34  3.000
 8XR  N10  C05  C06  121.56  3.000
 8XR  N10  C05  C04  118.97  3.000
 8XR  C06  C05  C04  119.46  3.000
 8XR  H15  C06  C05  120.86  3.000
 8XR  H15  C06  C01  118.80  3.000
 8XR  C05  C06  C01  120.34  3.000
 8XR  C14  N07  C08  117.07  3.000
 8XR  C14  N07  C04  117.64  3.000
 8XR  C08  N07  C04  110.25  3.000
 8XR  H16  C08  C09  105.58  3.000
 8XR  H16  C08  N07  106.05  3.000
 8XR  C09  C08  N07  111.75  3.000
 8XR  H16  C08  C13  107.07  3.000
 8XR  C09  C08  C13  111.85  3.000
 8XR  N07  C08  C13  113.89  3.000
 8XR  O11  C09  N10  122.35  3.000
 8XR  O11  C09  C08  123.33  3.000
 8XR  N10  C09  C08  114.30  3.000
 8XR  C12  N10  C09  119.69  3.000
 8XR  C12  N10  C05  119.40  3.000
 8XR  C09  N10  C05  120.74  3.000
 8XR  H21  C12  H20  108.55  3.000
 8XR  H21  C12  H19  108.85  3.000
 8XR  H20  C12  H19  108.53  3.000
 8XR  H21  C12  N10  111.61  3.000
 8XR  H20  C12  N10  109.38  3.000
 8XR  H19  C12  N10  109.87  3.000
 8XR  H22  C14  C27  106.20  3.000
 8XR  H22  C14  N07  106.15  3.000
 8XR  C27  C14  N07  115.65  3.000
 8XR  H22  C14  C24  108.17  3.000
 8XR  C27  C14  C24  102.43  3.000
 8XR  N07  C14  C24  117.59  3.000
 8XR  H23  N16  C17  116.63  3.000
 8XR  H23  N16  C15  117.79  3.000
 8XR  C17  N16  C15  124.77  3.000
 8XR  C28  C19  C20  120.57  3.000
 8XR  C28  C19  C17  121.14  3.000
 8XR  C20  C19  C17  118.29  3.000
 8XR  H24  C23  C22  119.54  3.000
 8XR  H24  C23  C17  120.12  3.000
 8XR  C22  C23  C17  120.34  3.000
 8XR  H26  C25  H25  106.53  3.000
 8XR  H26  C25  C26  111.49  3.000
 8XR  H25  C25  C26  110.81  3.000
 8XR  H26  C25  C24  110.91  3.000
 8XR  H25  C25  C24  111.31  3.000
 8XR  C26  C25  C24  105.88  3.000
 8XR  H28  C27  H27  107.76  3.000
 8XR  H28  C27  C14  110.43  3.000
 8XR  H27  C27  C14  113.00  3.000
 8XR  H28  C27  C26  109.81  3.000
 8XR  H27  C27  C26  113.37  3.000
 8XR  C14  C27  C26  102.42  3.000
 8XR  H31  C29  H30  108.11  3.000
 8XR  H31  C29  H29  107.25  3.000
 8XR  H30  C29  H29  107.15  3.000
 8XR  H31  C29  C21  111.57  3.000
 8XR  H30  C29  C21  111.57  3.000
 8XR  H29  C29  C21  110.98  3.000
 8XR  O18  C15  N16  122.98  3.000
 8XR  O18  C15  C02  121.46  3.000
 8XR  N16  C15  C02  115.55  3.000
 8XR  H12  C28  H11  107.81  3.000
 8XR  H12  C28  H10  106.97  3.000
 8XR  H11  C28  H10  107.18  3.000
 8XR  H12  C28  C19  111.80  3.000
 8XR  H11  C28  C19  110.79  3.000
 8XR  H10  C28  C19  112.04  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
 8XR  CONST_01  C21  C20  C19  C17    0.00   0.0  0
 8XR  CONST_02  C21  C22  C23  C17    0.00   0.0  0
 8XR  CONST_03  C23  C22  C21  C20    0.00   0.0  0
 8XR  CONST_04  C23  C17  C19  C20    0.00   0.0  0
 8XR  CONST_05  C19  C20  C21  C22    0.00   0.0  0
 8XR  CONST_06  C19  C17  C23  C22    0.00   0.0  0
 8XR  CONST_07  C04  C03  C02  C01    0.00   0.0  0
 8XR  CONST_08  C04  C05  C06  C01    0.00   0.0  0
 8XR  CONST_09  C05  C06  C01  C02    0.00   0.0  0
 8XR  CONST_10  C05  C04  C03  C02    0.00   0.0  0
 8XR  CONST_11  C06  C01  C02  C03    0.00   0.0  0
 8XR  CONST_12  C06  C05  C04  C03    0.00   0.0  0
 8XR  CONST_13  C08  C09  N10  C05    0.00   0.0  0
 8XR  CONST_14  C06  C01  C02  C15  180.00   0.0  0
 8XR  CONST_15  C04  C03  C02  C15  180.00   0.0  0
 8XR  CONST_16  N16  C17  C19  C20  180.00   0.0  0
 8XR  CONST_17  C28  C19  C20  C21  180.00   0.0  0
 8XR  CONST_18  N16  C17  C23  C22  180.00   0.0  0
 8XR  CONST_19  C23  C17  C19  C28  180.00   0.0  0
 8XR  CONST_20  C29  C21  C20  C19  180.00   0.0  0
 8XR  CONST_21  C29  C21  C22  C23  180.00   0.0  0
 8XR  CONST_22  O11  C09  N10  C05  180.00   0.0  0
 8XR  CONST_23  C12  N10  C09  C08  180.00   0.0  0
 8XR  CONST_24  H4   C20  C19  C17  180.00   0.0  0
 8XR  CONST_25  H5   C22  C23  C17  180.00   0.0  0
 8XR  CONST_26  H24  C23  C22  C21  180.00   0.0  0
 8XR  CONST_27  H14  C03  C02  C01  180.00   0.0  0
 8XR  CONST_28  H15  C06  C01  C02  180.00   0.0  0
 8XR  CONST_29  H13  C01  C02  C03  180.00   0.0  0
 8XR  CONST_30  C02  C15  N16  C17  180.00   0.0  0
 8XR  CONST_33  C12  N10  C09  O11    0.00   0.0  0
 8XR  CONST_35  O18  C15  N16  C17    0.00   0.0  0
 8XR  Var_01    C27  C26  C25  C24  -11.25  30.0  1
 8XR  Var_02    C14  C24  C25  C26  -16.20  30.0  1
 8XR  Var_03    C08  N07  C04  C03  141.94  30.0  1
 8XR  Var_04    C09  N10  C05  C04   23.31  30.0  1
 8XR  Var_05    C25  C26  C27  C14   34.44  30.0  1
 8XR  Var_06    N16  C15  C02  C01  -24.78  30.0  2
 8XR  Var_07    H10  C28  C19  C17   64.60  30.0  2
 8XR  Var_08    H29  C29  C21  C20   92.44  30.0  2
 8XR  Var_09    H19  C12  N10  C05   43.40  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
 8XR  chir_01  C08  C13  N07  C09  negativ
 8XR  chir_02  C14  N07  C24  C27  negativ

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
 8XR  plan-1  C17  0.020
 8XR  plan-1  C20  0.020
 8XR  plan-1  C21  0.020
 8XR  plan-1  C22  0.020
 8XR  plan-1  N16  0.020
 8XR  plan-1  C19  0.020
 8XR  plan-1  C23  0.020
 8XR  plan-1  C29  0.020
 8XR  plan-1  H4   0.020
 8XR  plan-1  H5   0.020
 8XR  plan-1  H24  0.020
 8XR  plan-1  C28  0.020
 8XR  plan-2  C01  0.020
 8XR  plan-2  C02  0.020
 8XR  plan-2  C03  0.020
 8XR  plan-2  C04  0.020
 8XR  plan-2  C05  0.020
 8XR  plan-2  C06  0.020
 8XR  plan-2  N07  0.020
 8XR  plan-2  N10  0.020
 8XR  plan-2  H13  0.020
 8XR  plan-2  H14  0.020
 8XR  plan-2  H15  0.020
 8XR  plan-2  C15  0.020
 8XR  plan-3  C17  0.020
 8XR  plan-3  C02  0.020
 8XR  plan-3  N16  0.020
 8XR  plan-3  O18  0.020
 8XR  plan-3  H23  0.020
 8XR  plan-3  C15  0.020
 8XR  plan-4  C05  0.020
 8XR  plan-4  C08  0.020
 8XR  plan-4  C09  0.020
 8XR  plan-4  N10  0.020
 8XR  plan-4  O11  0.020
 8XR  plan-4  C12  0.020

