# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:12:27 2022
#   Inital geometry file: a 144 line input string
#   Ligand name: (2E)-9,10-dimethoxy-3-methyl-2-[(2,4,6-trimethylphenyl)imino]-2,3,6,7-tetrahydro-4H-pyrimido[6,1-a]isoquinolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2CCN3C(=O)N(C)C(C=C3c2cc1OC)=Nc4c(C)cc(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
 XKG  XKG  (2E)-9,10-dimethoxy-3-methyl-2-[(2,4,6-trimethylphenyl)imino]-2,3,6,7-tetrahydro-4H-pyrimido[6,1-a]isoquinolin-4-one  ligand  57  30  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XKG
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
 XKG  C01  C  CH3   0  -0.722  -30.3895   9.1873  -37.8462
 XKG  C02  C  CR6   0   0.122  -29.1048   8.9916  -38.5994
 XKG  C03  C  CR16  0  -0.385  -28.9864   8.0041  -39.5713
 XKG  C04  C  CR6   0   0.097  -27.7990   7.7895  -40.2623
 XKG  C05  C  CR6   0   0.079  -26.6856   8.5897  -39.9726
 XKG  C06  C  CR6   0   0.107  -26.7815   9.5969  -39.0015
 XKG  C07  C  CR16  0  -0.387  -27.9890   9.7781  -38.3344
 XKG  C08  C  CH3   0  -0.732  -25.6004  10.4693  -38.6921
 XKG  N09  N  N     0  -0.482  -25.5180   8.4259  -40.7214
 XKG  C10  C  CR6   0   0.539  -24.5189   7.7941  -40.2291
 XKG  C11  C  CR16  0  -0.507  -24.4599   7.1832  -38.9331
 XKG  C12  C  CR6   0   0.452  -23.3404   6.5712  -38.4886
 XKG  C13  C  CR6   0   0.058  -23.2480   5.9488  -37.1637
 XKG  C14  C  CR16  0  -0.483  -24.1378   6.3103  -36.1395
 XKG  C15  C  CR6   0   0.337  -24.0949   5.6857  -34.9119
 XKG  C16  C  CR6   0   0.329  -23.1416   4.6643  -34.6842
 XKG  C17  C  CR16  0  -0.454  -22.2567   4.3251  -35.6924
 XKG  C18  C  CR6   0   0.112  -22.2986   4.9649  -36.9291
 XKG  C19  C  CH2   0  -0.534  -21.3363   4.6254  -38.0238
 XKG  C20  C  CH2   0  -0.305  -21.0053   5.8761  -38.8081
 XKG  N21  N  NR6   0  -0.626  -22.2344   6.4941  -39.3047
 XKG  C22  C  CR6   0   0.748  -22.2112   7.0661  -40.5599
 XKG  O23  O  O     0  -0.488  -21.2101   7.0461  -41.2506
 XKG  N24  N  NR6   0  -0.594  -23.3682   7.6583  -41.0017
 XKG  C25  C  CH3   0  -0.531  -23.3278   8.2199  -42.3442
 XKG  O26  O  O2    0  -0.452  -23.1683   4.1099  -33.4671
 XKG  C27  C  CH3   0  -0.440  -22.2438   3.0798  -33.1738
 XKG  O28  O  O2    0  -0.460  -24.8933   5.9720  -33.8694
 XKG  C29  C  CH3   0  -0.440  -25.8606   6.9888  -34.0294
 XKG  C30  C  CH3   0  -0.723  -27.7018   6.7164  -41.3055
 XKG  H1   H  HCH3  0   0.240  -30.4099   8.5860  -36.9344
 XKG  H2   H  HCH3  0   0.238  -30.5260  10.2268  -37.5482
 XKG  H3   H  HCH3  0   0.238  -31.2526   8.8936  -38.4434
 XKG  H4   H  HCR6  0   0.230  -29.8444   7.3813  -39.8040
 XKG  H5   H  HCR6  0   0.231  -28.0584  10.5605  -37.5856
 XKG  H6   H  HCH3  0   0.237  -25.1833  10.9172  -39.5956
 XKG  H7   H  HCH3  0   0.243  -25.8764  11.2748  -38.0124
 XKG  H8   H  HCH3  0   0.241  -24.7929   9.9047  -38.2203
 XKG  H10  H  HCR6  0   0.284  -25.3487   7.2120  -38.3230
 XKG  H12  H  HCR6  0   0.285  -24.8506   7.1054  -36.3092
 XKG  H13  H  HCR6  0   0.285  -21.5090   3.5586  -35.5343
 XKG  H14  H  HCH2  0   0.266  -21.7603   3.8685  -38.6912
 XKG  H15  H  HCH2  0   0.273  -20.4155   4.2082  -37.6146
 XKG  H16  H  HCH2  0   0.283  -20.3736   5.6393  -39.6574
 XKG  H17  H  HCH2  0   0.261  -20.4689   6.5901  -38.1774
 XKG  H18  H  HCH3  0   0.268  -24.3361   8.4930  -42.6289
 XKG  H19  H  HCH3  0   0.249  -22.6979   9.1082  -42.3781
 XKG  H20  H  HCH3  0   0.252  -22.9425   7.4873  -43.0483
 XKG  H21  H  HCH3  0   0.263  -22.4385   2.7755  -32.1487
 XKG  H22  H  HCH3  0   0.233  -22.3760   2.2166  -33.8308
 XKG  H23  H  HCH3  0   0.232  -21.2105   3.4274  -33.2491
 XKG  H24  H  HCH3  0   0.262  -26.3893   7.0634  -33.0824
 XKG  H25  H  HCH3  0   0.229  -25.4032   7.9561  -34.2548
 XKG  H26  H  HCH3  0   0.229  -26.5807   6.7485  -34.8167
 XKG  H27  H  HCH3  0   0.237  -26.9761   5.9484  -41.0294
 XKG  H28  H  HCH3  0   0.239  -28.6628   6.2251  -41.4528
 XKG  H29  H  HCH3  0   0.237  -27.3780   7.1206  -42.2665

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
 XKG  C25  N24  single    1.456  0.020  1.456
 XKG  C30  C04  single    1.500  0.020  1.500
 XKG  O23  C22  double    1.216  0.020  1.216
 XKG  N24  C22  single    1.373  0.020  1.373
 XKG  N24  C10  single    1.393  0.020  1.393
 XKG  N09  C10  double    1.281  0.020  1.281
 XKG  N09  C05  single    1.397  0.020  1.397
 XKG  C22  N21  single    1.380  0.020  1.380
 XKG  C04  C05  aromatic  1.401  0.020  1.401
 XKG  C04  C03  aromatic  1.391  0.020  1.391
 XKG  C10  C11  single    1.434  0.020  1.434
 XKG  C05  C06  aromatic  1.402  0.020  1.402
 XKG  C03  C02  aromatic  1.391  0.020  1.391
 XKG  N21  C20  single    1.463  0.020  1.463
 XKG  N21  C12  single    1.377  0.020  1.377
 XKG  C06  C08  single    1.501  0.020  1.501
 XKG  C06  C07  aromatic  1.391  0.020  1.391
 XKG  C11  C12  double    1.351  0.020  1.351
 XKG  C20  C19  single    1.513  0.020  1.513
 XKG  C02  C07  aromatic  1.391  0.020  1.391
 XKG  C02  C01  single    1.502  0.020  1.502
 XKG  C12  C13  single    1.467  0.020  1.467
 XKG  C19  C18  single    1.497  0.020  1.497
 XKG  C13  C18  aromatic  1.387  0.020  1.387
 XKG  C13  C14  aromatic  1.404  0.020  1.404
 XKG  C18  C17  aromatic  1.393  0.020  1.393
 XKG  C14  C15  aromatic  1.378  0.020  1.378
 XKG  C17  C16  aromatic  1.384  0.020  1.384
 XKG  C15  C16  aromatic  1.416  0.020  1.416
 XKG  C15  O28  single    1.344  0.020  1.344
 XKG  C16  O26  single    1.338  0.020  1.338
 XKG  C29  O28  single    1.412  0.020  1.412
 XKG  O26  C27  single    1.415  0.020  1.415
 XKG  C01  H1   single    0.970  0.020  1.090
 XKG  C01  H2   single    0.970  0.020  1.090
 XKG  C01  H3   single    0.970  0.020  1.090
 XKG  C03  H4   single    0.930  0.020  1.080
 XKG  C07  H5   single    0.930  0.020  1.080
 XKG  C08  H6   single    0.970  0.020  1.090
 XKG  C08  H7   single    0.970  0.020  1.090
 XKG  C08  H8   single    0.970  0.020  1.090
 XKG  C11  H10  single    0.930  0.020  1.080
 XKG  C14  H12  single    0.930  0.020  1.080
 XKG  C17  H13  single    0.930  0.020  1.080
 XKG  C19  H14  single    0.970  0.020  1.090
 XKG  C19  H15  single    0.970  0.020  1.090
 XKG  C20  H16  single    0.970  0.020  1.090
 XKG  C20  H17  single    0.970  0.020  1.090
 XKG  C25  H18  single    0.970  0.020  1.090
 XKG  C25  H19  single    0.970  0.020  1.090
 XKG  C25  H20  single    0.970  0.020  1.090
 XKG  C27  H21  single    0.970  0.020  1.090
 XKG  C27  H22  single    0.970  0.020  1.090
 XKG  C27  H23  single    0.970  0.020  1.090
 XKG  C29  H24  single    0.970  0.020  1.090
 XKG  C29  H25  single    0.970  0.020  1.090
 XKG  C29  H26  single    0.970  0.020  1.090
 XKG  C30  H27  single    0.970  0.020  1.090
 XKG  C30  H28  single    0.970  0.020  1.090
 XKG  C30  H29  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
 XKG  H3   C01  H2   107.91  3.000
 XKG  H3   C01  H1   107.11  3.000
 XKG  H2   C01  H1   107.12  3.000
 XKG  H3   C01  C02  111.56  3.000
 XKG  H2   C01  C02  111.62  3.000
 XKG  H1   C01  C02  111.28  3.000
 XKG  C07  C02  C03  117.81  3.000
 XKG  C07  C02  C01  121.13  3.000
 XKG  C03  C02  C01  121.05  3.000
 XKG  H4   C03  C04  118.68  3.000
 XKG  H4   C03  C02  119.34  3.000
 XKG  C04  C03  C02  121.98  3.000
 XKG  C30  C04  C05  120.06  3.000
 XKG  C05  C04  C03  119.18  3.000
 XKG  C30  C04  C03  120.76  3.000
 XKG  N09  C05  C06  120.84  3.000
 XKG  C06  C05  C04  119.93  3.000
 XKG  N09  C05  C04  119.10  3.000
 XKG  C08  C06  C07  120.56  3.000
 XKG  C07  C06  C05  119.01  3.000
 XKG  C08  C06  C05  120.43  3.000
 XKG  H5   C07  C06  118.70  3.000
 XKG  H5   C07  C02  119.20  3.000
 XKG  C06  C07  C02  122.09  3.000
 XKG  H8   C08  H7   107.45  3.000
 XKG  H8   C08  H6   106.68  3.000
 XKG  H7   C08  H6   108.05  3.000
 XKG  H8   C08  C06  111.74  3.000
 XKG  H7   C08  C06  111.05  3.000
 XKG  H6   C08  C06  111.64  3.000
 XKG  C10  N09  C05  120.26  3.000
 XKG  N24  C10  C11  115.21  3.000
 XKG  C11  C10  N09  126.14  3.000
 XKG  N24  C10  N09  118.65  3.000
 XKG  H10  C11  C12  120.58  3.000
 XKG  H10  C11  C10  117.78  3.000
 XKG  C12  C11  C10  121.62  3.000
 XKG  N21  C12  C13  117.46  3.000
 XKG  C13  C12  C11  122.79  3.000
 XKG  N21  C12  C11  119.74  3.000
 XKG  C18  C13  C14  119.53  3.000
 XKG  C14  C13  C12  120.65  3.000
 XKG  C18  C13  C12  119.79  3.000
 XKG  H12  C14  C15  119.58  3.000
 XKG  H12  C14  C13  119.51  3.000
 XKG  C15  C14  C13  120.89  3.000
 XKG  O28  C15  C16  115.41  3.000
 XKG  O28  C15  C14  125.16  3.000
 XKG  C16  C15  C14  119.43  3.000
 XKG  O26  C16  C17  125.04  3.000
 XKG  O26  C16  C15  115.59  3.000
 XKG  C17  C16  C15  119.37  3.000
 XKG  H13  C17  C18  118.41  3.000
 XKG  H13  C17  C16  120.59  3.000
 XKG  C18  C17  C16  121.00  3.000
 XKG  C19  C18  C17  121.73  3.000
 XKG  C17  C18  C13  119.77  3.000
 XKG  C19  C18  C13  118.51  3.000
 XKG  H15  C19  H14  106.94  3.000
 XKG  H15  C19  C20  109.03  3.000
 XKG  H14  C19  C20  109.90  3.000
 XKG  H15  C19  C18  110.80  3.000
 XKG  H14  C19  C18  110.72  3.000
 XKG  C20  C19  C18  109.41  3.000
 XKG  H17  C20  H16  107.98  3.000
 XKG  H17  C20  N21  109.40  3.000
 XKG  H16  C20  N21  108.41  3.000
 XKG  H17  C20  C19  110.38  3.000
 XKG  H16  C20  C19  110.66  3.000
 XKG  N21  C20  C19  109.96  3.000
 XKG  C22  N21  C20  118.03  3.000
 XKG  C20  N21  C12  119.84  3.000
 XKG  C22  N21  C12  121.98  3.000
 XKG  N24  C22  O23  121.20  3.000
 XKG  N24  C22  N21  117.23  3.000
 XKG  O23  C22  N21  121.57  3.000
 XKG  C25  N24  C22  116.09  3.000
 XKG  C22  N24  C10  124.04  3.000
 XKG  C25  N24  C10  119.80  3.000
 XKG  H20  C25  H19  108.93  3.000
 XKG  H20  C25  H18  109.26  3.000
 XKG  H19  C25  H18  108.94  3.000
 XKG  H20  C25  N24  110.32  3.000
 XKG  H19  C25  N24  111.06  3.000
 XKG  H18  C25  N24  108.30  3.000
 XKG  C27  O26  C16  118.51  3.000
 XKG  H23  C27  H22  108.92  3.000
 XKG  H23  C27  H21  108.87  3.000
 XKG  H22  C27  H21  108.91  3.000
 XKG  H23  C27  O26  111.83  3.000
 XKG  H22  C27  O26  111.80  3.000
 XKG  H21  C27  O26  106.40  3.000
 XKG  C29  O28  C15  118.19  3.000
 XKG  H26  C29  H25  108.75  3.000
 XKG  H26  C29  H24  108.78  3.000
 XKG  H25  C29  H24  108.80  3.000
 XKG  H26  C29  O28  111.98  3.000
 XKG  H25  C29  O28  111.94  3.000
 XKG  H24  C29  O28  106.49  3.000
 XKG  H29  C30  H28  108.04  3.000
 XKG  H29  C30  H27  106.61  3.000
 XKG  H28  C30  H27  107.65  3.000
 XKG  H29  C30  C04  111.51  3.000
 XKG  H28  C30  C04  111.07  3.000
 XKG  H27  C30  C04  111.74  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
 XKG  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 XKG  CONST_02  C05  C06  C07  C02     0.00   0.0  0
 XKG  CONST_03  C06  C05  C04  C03     0.00   0.0  0
 XKG  CONST_04  C06  C07  C02  C03     0.00   0.0  0
 XKG  CONST_05  C07  C06  C05  C04     0.00   0.0  0
 XKG  CONST_06  C07  C02  C03  C04     0.00   0.0  0
 XKG  CONST_07  C16  C17  C18  C13     0.00   0.0  0
 XKG  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 XKG  CONST_09  C17  C18  C13  C14     0.00   0.0  0
 XKG  CONST_10  C17  C16  C15  C14     0.00   0.0  0
 XKG  CONST_11  C18  C13  C14  C15     0.00   0.0  0
 XKG  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 XKG  CONST_13  N21  C22  N24  C10     0.00   0.0  0
 XKG  CONST_14  C22  N24  C10  C11     0.00   0.0  0
 XKG  CONST_15  N24  C22  N21  C12     0.00   0.0  0
 XKG  CONST_16  N24  C22  N21  C20   180.00   0.0  0
 XKG  CONST_17  C04  C03  C02  C01   180.00   0.0  0
 XKG  CONST_18  C06  C07  C02  C01   180.00   0.0  0
 XKG  CONST_19  C30  C04  C03  C02   180.00   0.0  0
 XKG  CONST_20  C08  C06  C07  C02   180.00   0.0  0
 XKG  CONST_21  N09  C05  C04  C03   180.00   0.0  0
 XKG  CONST_22  C08  C06  C05  C04   180.00   0.0  0
 XKG  CONST_23  C30  C04  C05  C06   180.00   0.0  0
 XKG  CONST_24  N09  C05  C06  C07   180.00   0.0  0
 XKG  CONST_25  O28  C15  C14  C13   180.00   0.0  0
 XKG  CONST_26  O26  C16  C15  C14   180.00   0.0  0
 XKG  CONST_27  O28  C15  C16  C17   180.00   0.0  0
 XKG  CONST_28  O26  C16  C17  C18   180.00   0.0  0
 XKG  CONST_29  N24  C10  N09  C05   180.00   0.0  0
 XKG  CONST_30  C11  C10  N09  C05     0.00   0.0  0
 XKG  CONST_31  C22  N24  C10  N09   180.00   0.0  0
 XKG  CONST_32  O23  C22  N24  C10   180.00   0.0  0
 XKG  CONST_33  C25  N24  C10  C11   180.00   0.0  0
 XKG  CONST_34  O23  C22  N21  C12   180.00   0.0  0
 XKG  CONST_35  O23  C22  N21  C20     0.00   0.0  0
 XKG  CONST_36  C25  N24  C22  N21   180.00   0.0  0
 XKG  CONST_37  H5   C07  C02  C03   180.00   0.0  0
 XKG  CONST_38  H4   C03  C04  C05   180.00   0.0  0
 XKG  CONST_39  H12  C14  C13  C12     0.00   0.0  0
 XKG  CONST_40  H13  C17  C18  C13   180.00   0.0  0
 XKG  CONST_41  C25  N24  C10  N09     0.00   0.0  0
 XKG  CONST_42  C25  N24  C22  O23     0.00   0.0  0
 XKG  Var_01    N21  C12  C11  C10    -1.79   0.0  0
 XKG  Var_02    C18  C13  C12  C11   157.68  30.0  1
 XKG  Var_03    C19  C20  N21  C12    41.93  30.0  1
 XKG  Var_04    C20  C19  C18  C13    34.53  30.0  1
 XKG  Var_05    N21  C20  C19  C18   -55.56  30.0  1
 XKG  Var_06    H10  C11  C12  C13    -1.58   0.0  0
 XKG  Var_07    H27  C30  C04  C03  -116.88  30.0  2
 XKG  Var_08    H1   C01  C02  C03    90.49  30.0  2
 XKG  Var_09    H6   C08  C06  C05    52.18  30.0  2
 XKG  Var_10    H18  C25  N24  C10   -12.57  30.0  3
 XKG  Var_11    H24  C29  O28  C15  -179.78  30.0  3
 XKG  Var_12    H21  C27  O26  C16  -179.88  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
 XKG  plan-1  C01  0.020
 XKG  plan-1  C02  0.020
 XKG  plan-1  C03  0.020
 XKG  plan-1  C04  0.020
 XKG  plan-1  C05  0.020
 XKG  plan-1  C06  0.020
 XKG  plan-1  C07  0.020
 XKG  plan-1  C08  0.020
 XKG  plan-1  N09  0.020
 XKG  plan-1  C30  0.020
 XKG  plan-1  H4   0.020
 XKG  plan-1  H5   0.020
 XKG  plan-2  C12  0.020
 XKG  plan-2  C13  0.020
 XKG  plan-2  C14  0.020
 XKG  plan-2  C15  0.020
 XKG  plan-2  C16  0.020
 XKG  plan-2  C17  0.020
 XKG  plan-2  C18  0.020
 XKG  plan-2  C19  0.020
 XKG  plan-2  O26  0.020
 XKG  plan-2  O28  0.020
 XKG  plan-2  H12  0.020
 XKG  plan-2  H13  0.020
 XKG  plan-3  C05  0.020
 XKG  plan-3  N09  0.020
 XKG  plan-3  C10  0.020
 XKG  plan-3  C11  0.020
 XKG  plan-3  C12  0.020
 XKG  plan-3  C13  0.020
 XKG  plan-3  C20  0.020
 XKG  plan-3  N21  0.020
 XKG  plan-3  C22  0.020
 XKG  plan-3  O23  0.020
 XKG  plan-3  N24  0.020
 XKG  plan-3  C25  0.020
 XKG  plan-3  H10  0.020

