# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 05:35:09 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: N-(2-chloro-6-methylphenyl)-8-[(3S)-3-methylpiperazin-1-yl]imidazo[1,5-a]quinoxalin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CN(CCN1)c2ccc3nc(Nc4c(C)cccc4Cl)c5cncn5c3c2
#
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
 KSM  KSM  N-(2-chloro-6-methylphenyl)-8-[(3S)-3-methylpiperazin-1-yl]imidazo[1,5-a]quinoxalin-4-amine  ligand  52  29  .  2022-07-25  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_KSM
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
 KSM  CL24  CL  CL    0  -0.117   4.8300  -0.1345  -2.2693
 KSM  C12   C   CR6   0  -0.086   4.8893   0.7619  -0.7876
 KSM  C13   C   CR16  0  -0.249   5.6838   1.8940  -0.7189
 KSM  C14   C   CR16  0  -0.250   5.7084   2.6178   0.4620
 KSM  C15   C   CR16  0  -0.310   4.9628   2.1978   1.5531
 KSM  C16   C   CR6   0   0.094   4.1778   1.0502   1.4979
 KSM  C20   C   CH3   0  -0.737   3.4066   0.6012   2.6999
 KSM  C11   C   CR6   0   0.340   4.1359   0.3249   0.3013
 KSM  N10   N   NH1   0  -0.779   3.3716  -0.8499   0.2030
 KSM  C9    C   CR6   0   0.434   2.0103  -0.8349   0.1406
 KSM  C4    C   CR56  0   0.247   1.3480  -2.1037  -0.0098
 KSM  C5    C   CR15  0  -0.245   1.7274  -3.4193  -0.1217
 KSM  N1    N   N     0  -0.429   0.6302  -4.2031  -0.2533
 KSM  N8    N   N     0  -0.466   1.3560   0.2726   0.2341
 KSM  C7    C   CR66  0   0.163  -0.0195   0.2384   0.1964
 KSM  C27   C   CR16  0  -0.323  -0.7429   1.4260   0.3163
 KSM  C28   C   CR16  0  -0.361  -2.1215   1.4467   0.2835
 KSM  C29   C   CR6   0   0.388  -2.8666   0.2656   0.1041
 KSM  C26   C   CR16  0  -0.440  -2.1543  -0.9308  -0.0215
 KSM  C6    C   CR66  0   0.427  -0.7704  -0.9356   0.0342
 KSM  N3    N   N     0  -0.592  -0.0283  -2.1118  -0.0746
 KSM  C2    C   CR15  0   0.097  -0.4069  -3.4007  -0.2210
 KSM  N30   N   NT    0  -0.530  -4.2538   0.2696   0.0218
 KSM  C35   C   CH2   0  -0.298  -4.9837  -0.7702   0.7375
 KSM  C34   C   CH2   0  -0.299  -6.4077  -0.8669   0.2292
 KSM  N33   N   NH1   0  -0.598  -7.0566   0.4215   0.3568
 KSM  C32   C   CH1   0  -0.090  -6.3726   1.4241  -0.4395
 KSM  C43   C   CH3   0  -0.672  -7.0861   2.7600  -0.3290
 KSM  C31   C   CH2   0  -0.270  -4.9360   1.5491   0.0523
 KSM  H13   H   HCR6  0   0.280   6.2639   2.2081  -1.5756
 KSM  H14   H   HCR6  0   0.267   6.3187   3.5083   0.5306
 KSM  H15   H   HCR6  0   0.257   5.0008   2.7635   2.4758
 KSM  H20   H   HCH3  0   0.258   2.3523   0.8641   2.6043
 KSM  H20A  H   HCH3  0   0.246   3.4585  -0.4799   2.8278
 KSM  H20B  H   HCH3  0   0.251   3.7909   1.0723   3.6030
 KSM  HN10  H   HNH1  0   0.403   3.8392  -1.6703  -0.1506
 KSM  H5    H   HCR5  0   0.272   2.7255  -3.8299  -0.1104
 KSM  H27   H   HCR6  0   0.261  -0.1947   2.3488   0.4577
 KSM  H28   H   HCR6  0   0.273  -2.6184   2.3969   0.4157
 KSM  H26   H   HCR6  0   0.283  -2.6810  -1.8600  -0.1874
 KSM  H2    H   HCR5  0   0.298  -1.4377  -3.7066  -0.2981
 KSM  H35   H   HCH2  0   0.253  -4.5040  -1.7363   0.5999
 KSM  H35A  H   HCH2  0   0.218  -4.9927  -0.5580   1.8165
 KSM  H34   H   HCH2  0   0.197  -6.3886  -1.2350  -0.8084
 KSM  H34A  H   HCH2  0   0.240  -6.9430  -1.6059   0.8279
 KSM  HN33  H   HNH1  0   0.352  -8.0206   0.3492   0.0557
 KSM  H32   H   HCH1  0   0.199  -6.3293   1.1328  -1.5032
 KSM  H43   H   HCH3  0   0.223  -7.1183   3.0987   0.7079
 KSM  H43A  H   HCH3  0   0.230  -6.5827   3.5233  -0.9232
 KSM  H43B  H   HCH3  0   0.236  -8.1124   2.6830  -0.6916
 KSM  H31   H   HCH2  0   0.207  -4.9420   1.9826   1.0652
 KSM  H31A  H   HCH2  0   0.248  -4.4193   2.2498  -0.6047

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
 KSM  CL24  C12   single    1.733  0.020  1.733
 KSM  C12   C13   aromatic  1.385  0.020  1.385
 KSM  C12   C11   aromatic  1.394  0.020  1.394
 KSM  C13   C14   aromatic  1.385  0.020  1.385
 KSM  C14   C15   aromatic  1.387  0.020  1.387
 KSM  C15   C16   aromatic  1.392  0.020  1.392
 KSM  C16   C20   single    1.497  0.020  1.497
 KSM  C16   C11   aromatic  1.400  0.020  1.400
 KSM  C11   N10   single    1.405  0.020  1.405
 KSM  N10   C9    single    1.363  0.020  1.363
 KSM  C9    C4    aromatic  1.439  0.020  1.439
 KSM  C9    N8    aromatic  1.290  0.020  1.290
 KSM  C4    C5    aromatic  1.374  0.020  1.374
 KSM  C4    N3    aromatic  1.378  0.020  1.378
 KSM  C5    N1    aromatic  1.355  0.020  1.355
 KSM  N1    C2    aromatic  1.312  0.020  1.312
 KSM  N8    C7    aromatic  1.376  0.020  1.376
 KSM  C7    C27   aromatic  1.396  0.020  1.396
 KSM  C7    C6    aromatic  1.403  0.020  1.403
 KSM  C27   C28   aromatic  1.379  0.020  1.379
 KSM  C28   C29   aromatic  1.408  0.020  1.408
 KSM  C29   C26   aromatic  1.398  0.020  1.398
 KSM  C29   N30   single    1.390  0.020  1.390
 KSM  C26   C6    aromatic  1.385  0.020  1.385
 KSM  C6    N3    aromatic  1.395  0.020  1.395
 KSM  N3    C2    aromatic  1.351  0.020  1.351
 KSM  N30   C35   single    1.458  0.020  1.458
 KSM  N30   C31   single    1.450  0.020  1.450
 KSM  C35   C34   single    1.515  0.020  1.515
 KSM  C34   N33   single    1.448  0.020  1.448
 KSM  N33   C32   single    1.452  0.020  1.452
 KSM  C32   C43   single    1.518  0.020  1.518
 KSM  C32   C31   single    1.524  0.020  1.524
 KSM  C13   H13   single    0.930  0.020  1.080
 KSM  C14   H14   single    0.930  0.020  1.080
 KSM  C15   H15   single    0.930  0.020  1.080
 KSM  C20   H20   single    0.970  0.020  1.090
 KSM  C20   H20A  single    0.970  0.020  1.090
 KSM  C20   H20B  single    0.970  0.020  1.090
 KSM  N10   HN10  single    0.890  0.020  1.040
 KSM  C5    H5    single    0.930  0.020  1.080
 KSM  C27   H27   single    0.930  0.020  1.080
 KSM  C28   H28   single    0.930  0.020  1.080
 KSM  C26   H26   single    0.930  0.020  1.080
 KSM  C2    H2    single    0.930  0.020  1.080
 KSM  C35   H35   single    0.970  0.020  1.090
 KSM  C35   H35A  single    0.970  0.020  1.090
 KSM  C34   H34   single    0.970  0.020  1.090
 KSM  C34   H34A  single    0.970  0.020  1.090
 KSM  N33   HN33  single    0.890  0.020  1.040
 KSM  C32   H32   single    0.970  0.020  1.090
 KSM  C43   H43   single    0.970  0.020  1.090
 KSM  C43   H43A  single    0.970  0.020  1.090
 KSM  C43   H43B  single    0.970  0.020  1.090
 KSM  C31   H31   single    0.970  0.020  1.090
 KSM  C31   H31A  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
 KSM  C11   C12  C13   121.84  3.000
 KSM  C11   C12  CL24  119.15  3.000
 KSM  C13   C12  CL24  119.01  3.000
 KSM  H13   C13  C14   120.95  3.000
 KSM  H13   C13  C12   120.39  3.000
 KSM  C14   C13  C12   118.66  3.000
 KSM  H14   C14  C15   120.19  3.000
 KSM  H14   C14  C13   119.61  3.000
 KSM  C15   C14  C13   120.20  3.000
 KSM  H15   C15  C16   118.97  3.000
 KSM  H15   C15  C14   119.56  3.000
 KSM  C16   C15  C14   121.46  3.000
 KSM  C11   C16  C20   121.03  3.000
 KSM  C11   C16  C15   118.56  3.000
 KSM  C20   C16  C15   120.41  3.000
 KSM  H20B  C20  H20A  108.37  3.000
 KSM  H20B  C20  H20   108.03  3.000
 KSM  H20A  C20  H20   107.18  3.000
 KSM  H20B  C20  C16   110.76  3.000
 KSM  H20A  C20  C16   111.55  3.000
 KSM  H20   C20  C16   110.81  3.000
 KSM  N10   C11  C16   120.62  3.000
 KSM  N10   C11  C12   120.09  3.000
 KSM  C16   C11  C12   119.27  3.000
 KSM  HN10  N10  C9    117.13  3.000
 KSM  HN10  N10  C11   116.92  3.000
 KSM  C9    N10  C11   122.50  3.000
 KSM  N8    C9   C4    122.09  3.000
 KSM  N8    C9   N10   120.85  3.000
 KSM  C4    C9   N10   117.05  3.000
 KSM  N3    C4   C5    105.45  3.000
 KSM  N3    C4   C9    118.02  3.000
 KSM  C5    C4   C9    136.53  3.000
 KSM  H5    C5   N1    122.00  3.000
 KSM  H5    C5   C4    128.23  3.000
 KSM  N1    C5   C4    109.77  3.000
 KSM  C2    N1   C5    106.50  3.000
 KSM  C7    N8   C9    118.92  3.000
 KSM  C6    C7   C27   116.39  3.000
 KSM  C6    C7   N8    123.97  3.000
 KSM  C27   C7   N8    119.63  3.000
 KSM  H27   C27  C28   119.77  3.000
 KSM  H27   C27  C7    118.29  3.000
 KSM  C28   C27  C7    121.93  3.000
 KSM  H28   C28  C29   120.66  3.000
 KSM  H28   C28  C27   118.03  3.000
 KSM  C29   C28  C27   121.29  3.000
 KSM  N30   C29  C26   120.39  3.000
 KSM  N30   C29  C28   122.23  3.000
 KSM  C26   C29  C28   117.36  3.000
 KSM  H26   C26  C6    119.35  3.000
 KSM  H26   C26  C29   120.07  3.000
 KSM  C6    C26  C29   120.56  3.000
 KSM  N3    C6   C26   122.09  3.000
 KSM  N3    C6   C7    115.46  3.000
 KSM  C26   C6   C7    122.45  3.000
 KSM  C2    N3   C6    131.58  3.000
 KSM  C2    N3   C4    106.89  3.000
 KSM  C6    N3   C4    121.52  3.000
 KSM  H2    C2   N3    123.11  3.000
 KSM  H2    C2   N1    125.51  3.000
 KSM  N3    C2   N1    111.38  3.000
 KSM  C31   N30  C35   112.55  3.000
 KSM  C31   N30  C29   118.09  3.000
 KSM  C35   N30  C29   117.94  3.000
 KSM  H35A  C35  H35   107.41  3.000
 KSM  H35A  C35  C34   109.50  3.000
 KSM  H35   C35  C34   108.39  3.000
 KSM  H35A  C35  N30   110.37  3.000
 KSM  H35   C35  N30   110.53  3.000
 KSM  C34   C35  N30   110.57  3.000
 KSM  H34A  C34  H34   107.40  3.000
 KSM  H34A  C34  N33   109.53  3.000
 KSM  H34   C34  N33   112.84  3.000
 KSM  H34A  C34  C35   108.68  3.000
 KSM  H34   C34  C35   108.73  3.000
 KSM  N33   C34  C35   109.56  3.000
 KSM  HN33  N33  C32   109.56  3.000
 KSM  HN33  N33  C34   109.69  3.000
 KSM  C32   N33  C34   110.80  3.000
 KSM  H32   C32  C31   107.20  3.000
 KSM  H32   C32  C43   108.71  3.000
 KSM  C31   C32  C43   110.32  3.000
 KSM  H32   C32  N33   111.40  3.000
 KSM  C31   C32  N33   108.90  3.000
 KSM  C43   C32  N33   110.26  3.000
 KSM  H43B  C43  H43A  107.61  3.000
 KSM  H43B  C43  H43   108.05  3.000
 KSM  H43A  C43  H43   108.31  3.000
 KSM  H43B  C43  C32   110.83  3.000
 KSM  H43A  C43  C32   111.05  3.000
 KSM  H43   C43  C32   110.86  3.000
 KSM  H31A  C31  H31   107.68  3.000
 KSM  H31A  C31  C32   107.75  3.000
 KSM  H31   C31  C32   108.90  3.000
 KSM  H31A  C31  N30   109.35  3.000
 KSM  H31   C31  N30   111.65  3.000
 KSM  C32   C31  N30   111.37  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
 KSM  CONST_01  C15  C14  C13  C12      0.00   0.0  0
 KSM  CONST_02  C15  C16  C11  C12      0.00   0.0  0
 KSM  CONST_03  C16  C11  C12  C13      0.00   0.0  0
 KSM  CONST_04  C16  C15  C14  C13      0.00   0.0  0
 KSM  CONST_05  C11  C12  C13  C14      0.00   0.0  0
 KSM  CONST_06  C11  C16  C15  C14      0.00   0.0  0
 KSM  CONST_07  N1   C5   C4   C9     180.00   0.0  0
 KSM  CONST_08  C6   N3   C4   C9       0.00   0.0  0
 KSM  CONST_09  C2   N3   C4   C9     180.00   0.0  0
 KSM  CONST_10  C27  C7   N8   C9     180.00   0.0  0
 KSM  CONST_11  C6   C7   N8   C9       0.00   0.0  0
 KSM  CONST_12  C7   N8   C9   C4       0.00   0.0  0
 KSM  CONST_13  C2   N1   C5   C4       0.00   0.0  0
 KSM  CONST_14  C7   C6   N3   C4       0.00   0.0  0
 KSM  CONST_15  C26  C6   N3   C4     180.00   0.0  0
 KSM  CONST_16  N1   C2   N3   C4       0.00   0.0  0
 KSM  CONST_17  N8   C9   C4   C5     180.00   0.0  0
 KSM  CONST_18  C6   N3   C4   C5     180.00   0.0  0
 KSM  CONST_19  C2   N3   C4   C5       0.00   0.0  0
 KSM  CONST_20  N3   C2   N1   C5       0.00   0.0  0
 KSM  CONST_21  N3   C4   C5   N1       0.00   0.0  0
 KSM  CONST_22  C6   N3   C2   N1     180.00   0.0  0
 KSM  CONST_23  N3   C4   C9   N8       0.00   0.0  0
 KSM  CONST_24  C28  C27  C7   N8     180.00   0.0  0
 KSM  CONST_25  C26  C6   C7   N8     180.00   0.0  0
 KSM  CONST_26  N3   C6   C7   N8       0.00   0.0  0
 KSM  CONST_27  C29  C28  C27  C7       0.00   0.0  0
 KSM  CONST_28  C29  C26  C6   C7       0.00   0.0  0
 KSM  CONST_29  C2   N3   C6   C7     180.00   0.0  0
 KSM  CONST_30  C26  C6   C7   C27      0.00   0.0  0
 KSM  CONST_31  N3   C6   C7   C27    180.00   0.0  0
 KSM  CONST_32  C26  C29  C28  C27      0.00   0.0  0
 KSM  CONST_33  C6   C7   C27  C28      0.00   0.0  0
 KSM  CONST_34  C6   C26  C29  C28      0.00   0.0  0
 KSM  CONST_35  N3   C6   C26  C29    180.00   0.0  0
 KSM  CONST_36  C2   N3   C6   C26      0.00   0.0  0
 KSM  CONST_37  N30  C29  C28  C27    180.00   0.0  0
 KSM  CONST_38  N30  C29  C26  C6     180.00   0.0  0
 KSM  CONST_39  C14  C13  C12  CL24   180.00   0.0  0
 KSM  CONST_40  C16  C11  C12  CL24   180.00   0.0  0
 KSM  CONST_41  C20  C16  C11  C12    180.00   0.0  0
 KSM  CONST_42  N10  C11  C12  C13    180.00   0.0  0
 KSM  CONST_43  C20  C16  C15  C14    180.00   0.0  0
 KSM  CONST_44  N10  C11  C16  C15    180.00   0.0  0
 KSM  CONST_45  C5   C4   C9   N10      0.00   0.0  0
 KSM  CONST_46  N3   C4   C9   N10    180.00   0.0  0
 KSM  CONST_47  C7   N8   C9   N10    180.00   0.0  0
 KSM  CONST_48  H14  C14  C13  C12    180.00   0.0  0
 KSM  CONST_49  H15  C15  C14  C13    180.00   0.0  0
 KSM  CONST_50  H13  C13  C14  C15    180.00   0.0  0
 KSM  CONST_51  H5   C5   C4   C9       0.00   0.0  0
 KSM  CONST_52  H2   C2   N3   C4     180.00   0.0  0
 KSM  CONST_53  H27  C27  C7   N8       0.00   0.0  0
 KSM  CONST_54  H28  C28  C27  C7     180.00   0.0  0
 KSM  CONST_55  H26  C26  C6   C7     180.00   0.0  0
 KSM  Var_01    C35  N30  C29  C28   -137.47  30.0  2
 KSM  Var_02    C34  C35  N30  C29   -163.56  30.0  1
 KSM  Var_03    C32  C31  N30  C29    163.70  30.0  1
 KSM  Var_04    N33  C34  C35  N30    -56.68  30.0  1
 KSM  Var_05    C32  N33  C34  C35     61.39  30.0  1
 KSM  Var_06    C9   N10  C11  C12   -108.46  30.0  2
 KSM  Var_07    C4   C9   N10  C11    177.69  30.0  2
 KSM  Var_08    H20  C20  C16  C15    102.19  30.0  2

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
 KSM  chir_01  C32  N33  C43  C31  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
 KSM  plan-1  CL24  0.020
 KSM  plan-1  C12   0.020
 KSM  plan-1  C13   0.020
 KSM  plan-1  C14   0.020
 KSM  plan-1  C15   0.020
 KSM  plan-1  C16   0.020
 KSM  plan-1  C20   0.020
 KSM  plan-1  C11   0.020
 KSM  plan-1  N10   0.020
 KSM  plan-1  H13   0.020
 KSM  plan-1  H14   0.020
 KSM  plan-1  H15   0.020
 KSM  plan-2  N10   0.020
 KSM  plan-2  C9    0.020
 KSM  plan-2  C4    0.020
 KSM  plan-2  C5    0.020
 KSM  plan-2  N1    0.020
 KSM  plan-2  N8    0.020
 KSM  plan-2  C7    0.020
 KSM  plan-2  C27   0.020
 KSM  plan-2  C28   0.020
 KSM  plan-2  C29   0.020
 KSM  plan-2  C26   0.020
 KSM  plan-2  C6    0.020
 KSM  plan-2  N3    0.020
 KSM  plan-2  C2    0.020
 KSM  plan-2  N30   0.020
 KSM  plan-2  H5    0.020
 KSM  plan-2  H27   0.020
 KSM  plan-2  H28   0.020
 KSM  plan-2  H26   0.020
 KSM  plan-2  H2    0.020

