# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:46:51 2021
#   Inital geometry file: a 141 line input string
#   Ligand name: N-{[5-(methoxymethyl)-2-(trifluoromethoxy)phenyl]methyl}-N'-(8-methyl-2-phenylimidazo[1,2-a]pyrazin-3-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCc1ccc(OC(F)(F)F)c(CNC(=O)Nc2n3ccnc(C)c3nc2c4ccccc4)c1
#
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
 OO7  OO7  N-{[5-(methoxymethyl)-2-(trifluoromethoxy)phenyl]methyl}-N'-(8-methyl-2-phenylimidazo[1,2-a]pyrazin-3-yl)urea  ligand  57  35  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OO7
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
 OO7  C2   C  CT    0   1.082  16.6918  -20.3839  -25.0351
 OO7  C6   C  CR6   0   0.251  17.8573  -22.1834  -24.0854
 OO7  C7   C  CR16  0  -0.277  19.1901  -21.8811  -23.8694
 OO7  C8   C  CR16  0  -0.321  19.8555  -22.4791  -22.8123
 OO7  C12  C  CH3   0  -0.404  19.7932  -24.6395  -18.6085
 OO7  C17  C  C     0   0.730  15.8027  -25.8190  -23.9685
 OO7  C21  C  CR5   0   0.148  17.0868  -28.8874  -23.8516
 OO7  N22  N  N     0  -0.479  17.2279  -29.9288  -24.7027
 OO7  C23  C  CR56  0   0.463  16.1602  -29.9090  -25.4766
 OO7  C24  C  CR6   0   0.165  15.7739  -30.7657  -26.5404
 OO7  C27  C  CR16  0  -0.174  13.8703  -29.5114  -26.8340
 OO7  C30  C  CR6   0   0.038  18.1083  -28.5712  -22.8525
 OO7  C31  C  CR16  0  -0.300  19.4302  -28.9638  -23.0712
 OO7  C32  C  CR16  0  -0.241  20.4147  -28.6769  -22.1385
 OO7  C33  C  CR16  0  -0.268  20.0949  -27.9995  -20.9685
 OO7  C34  C  CR16  0  -0.233  18.7814  -27.6132  -20.7390
 OO7  C35  C  CR16  0  -0.311  17.7960  -27.8951  -21.6720
 OO7  F1   F  F     0  -0.302  15.8180  -20.3059  -24.0280
 OO7  F3   F  F     0  -0.276  16.0620  -20.0793  -26.1586
 OO7  F4   F  F     0  -0.298  17.6179  -19.4496  -24.8097
 OO7  O5   O  O2    0  -0.523  17.2095  -21.6087  -25.1778
 OO7  C9   C  CR6   0   0.081  19.1989  -23.3836  -21.9865
 OO7  C10  C  CH2   0  -0.182  19.9407  -24.0457  -20.8605
 OO7  O11  O  O2    0  -0.481  19.1245  -24.0996  -19.7198
 OO7  C13  C  CR16  0  -0.334  17.8661  -23.6866  -22.2449
 OO7  C14  C  CR6   0   0.078  17.1691  -23.0964  -23.2941
 OO7  N16  N  NH1   0  -0.680  15.3694  -24.7888  -23.2114
 OO7  O18  O  O     0  -0.498  16.5213  -25.6796  -24.9423
 OO7  N19  N  NH1   0  -0.798  15.3586  -27.0611  -23.5608
 OO7  C20  C  CR5   0   0.451  15.9096  -28.2043  -24.1064
 OO7  N26  N  N     0  -0.398  14.6622  -30.5589  -27.1893
 OO7  C28  C  CR16  0  -0.038  14.1652  -28.6516  -25.8294
 OO7  N29  N  N     0  -0.483  15.3270  -28.8684  -25.1490
 OO7  H1   H  HCR6  0   0.277  19.7116  -21.1938  -24.5220
 OO7  H2   H  HCR6  0   0.262  20.8944  -22.2331  -22.6322
 OO7  H3   H  HCH3  0   0.238  19.0947  -24.6597  -17.7733
 OO7  H4   H  HCH3  0   0.202  20.1435  -25.6632  -18.7884
 OO7  H5   H  HCH3  0   0.212  20.6635  -24.0373  -18.3217
 OO7  H6   H  HCH2  0   0.262  15.4570  -23.2394  -24.5899
 OO7  H7   H  HCH2  0   0.285  15.0799  -22.7854  -22.9451
 OO7  H8   H  HCR6  0   0.278  12.9573  -29.3787  -27.3979
 OO7  H9   H  HCR6  0   0.253  19.6871  -29.4915  -23.9804
 OO7  H10  H  HCR6  0   0.259  21.4355  -28.9835  -22.3263
 OO7  H11  H  HCR6  0   0.258  20.8646  -27.7821  -20.2391
 OO7  H12  H  HCR6  0   0.260  18.5123  -27.1013  -19.8248
 OO7  H13  H  HCR6  0   0.240  16.7766  -27.6046  -21.4589
 OO7  H14  H  HCH2  0   0.225  20.2428  -25.0584  -21.1664
 OO7  H15  H  HCH2  0   0.223  20.8677  -23.4924  -20.6546
 OO7  H16  H  HCR6  0   0.247  17.3531  -24.4064  -21.6190
 OO7  H17  H  HNH1  0   0.407  14.8149  -24.9539  -22.3885
 OO7  H18  H  HNH1  0   0.411  14.7386  -27.1445  -22.7683
 OO7  H19  H  HCH3  0   0.257  16.2689  -32.4279  -27.7753
 OO7  H20  H  HCH3  0   0.257  17.6717  -31.5625  -27.1222
 OO7  H21  H  HCH3  0   0.259  16.7370  -32.6161  -26.0780
 OO7  H22  H  HCR6  0   0.312  13.5467  -27.8194  -25.5305
 OO7  C15  C  CH2   0  -0.345  15.7154  -23.4335  -23.5491
 OO7  C25  C  CH3   0  -0.727  16.6604  -31.9077  -26.9045

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
 OO7  N26  C27  aromatic  1.360  0.020  1.360
 OO7  N26  C24  aromatic  1.304  0.020  1.304
 OO7  C25  C24  single    1.491  0.020  1.491
 OO7  C27  C28  aromatic  1.355  0.020  1.355
 OO7  C24  C23  aromatic  1.419  0.020  1.419
 OO7  F3   C2   single    1.323  0.020  1.323
 OO7  C28  N29  aromatic  1.364  0.020  1.364
 OO7  O18  C17  double    1.218  0.020  1.218
 OO7  C23  N29  aromatic  1.373  0.020  1.373
 OO7  C23  N22  aromatic  1.319  0.020  1.319
 OO7  N29  C20  aromatic  1.367  0.020  1.367
 OO7  O5   C2   single    1.337  0.020  1.337
 OO7  O5   C6   single    1.394  0.020  1.394
 OO7  N22  C21  aromatic  1.352  0.020  1.352
 OO7  C2   F4   single    1.335  0.020  1.335
 OO7  C2   F1   single    1.336  0.020  1.336
 OO7  C17  N19  single    1.381  0.020  1.381
 OO7  C17  N16  single    1.350  0.020  1.350
 OO7  C20  C21  aromatic  1.385  0.020  1.385
 OO7  C20  N19  single    1.381  0.020  1.381
 OO7  C15  N16  single    1.439  0.020  1.439
 OO7  C15  C14  single    1.514  0.020  1.514
 OO7  C21  C30  single    1.463  0.020  1.463
 OO7  C31  C30  aromatic  1.396  0.020  1.396
 OO7  C31  C32  aromatic  1.386  0.020  1.386
 OO7  C6   C14  aromatic  1.390  0.020  1.390
 OO7  C6   C7   aromatic  1.384  0.020  1.384
 OO7  C30  C35  aromatic  1.396  0.020  1.396
 OO7  C14  C13  aromatic  1.391  0.020  1.391
 OO7  C32  C33  aromatic  1.389  0.020  1.389
 OO7  C7   C8   aromatic  1.385  0.020  1.385
 OO7  C35  C34  aromatic  1.386  0.020  1.386
 OO7  C13  C9   aromatic  1.391  0.020  1.391
 OO7  C33  C34  aromatic  1.388  0.020  1.388
 OO7  C8   C9   aromatic  1.390  0.020  1.390
 OO7  C9   C10  single    1.502  0.020  1.502
 OO7  C10  O11  single    1.404  0.020  1.404
 OO7  O11  C12  single    1.405  0.020  1.405
 OO7  C7   H1   single    0.930  0.020  1.080
 OO7  C8   H2   single    0.930  0.020  1.080
 OO7  C12  H3   single    0.970  0.020  1.090
 OO7  C12  H4   single    0.970  0.020  1.090
 OO7  C12  H5   single    0.970  0.020  1.090
 OO7  C15  H6   single    0.970  0.020  1.090
 OO7  C15  H7   single    0.970  0.020  1.090
 OO7  C27  H8   single    0.930  0.020  1.080
 OO7  C31  H9   single    0.930  0.020  1.080
 OO7  C32  H10  single    0.930  0.020  1.080
 OO7  C33  H11  single    0.930  0.020  1.080
 OO7  C34  H12  single    0.930  0.020  1.080
 OO7  C35  H13  single    0.930  0.020  1.080
 OO7  C10  H14  single    0.970  0.020  1.090
 OO7  C10  H15  single    0.970  0.020  1.090
 OO7  C13  H16  single    0.930  0.020  1.080
 OO7  N16  H17  single    0.860  0.020  1.020
 OO7  N19  H18  single    0.860  0.020  1.020
 OO7  C25  H19  single    0.970  0.020  1.090
 OO7  C25  H20  single    0.970  0.020  1.090
 OO7  C25  H21  single    0.970  0.020  1.090
 OO7  C28  H22  single    0.930  0.020  1.080

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
 OO7  O5   C2   F4   112.99  3.000
 OO7  F4   C2   F3   108.21  3.000
 OO7  O5   C2   F3   107.72  3.000
 OO7  F4   C2   F1   106.60  3.000
 OO7  O5   C2   F1   112.78  3.000
 OO7  F3   C2   F1   108.39  3.000
 OO7  C14  C6   O5   119.12  3.000
 OO7  C14  C6   C7   122.10  3.000
 OO7  O5   C6   C7   118.68  3.000
 OO7  H1   C7   C8   120.22  3.000
 OO7  H1   C7   C6   120.60  3.000
 OO7  C8   C7   C6   119.18  3.000
 OO7  H2   C8   C9   120.15  3.000
 OO7  H2   C8   C7   119.33  3.000
 OO7  C9   C8   C7   120.51  3.000
 OO7  H5   C12  H4   107.58  3.000
 OO7  H5   C12  H3   108.58  3.000
 OO7  H4   C12  H3   108.26  3.000
 OO7  H5   C12  O11  111.94  3.000
 OO7  H4   C12  O11  112.39  3.000
 OO7  H3   C12  O11  107.97  3.000
 OO7  N19  C17  O18  121.91  3.000
 OO7  N19  C17  N16  114.69  3.000
 OO7  O18  C17  N16  123.39  3.000
 OO7  C20  C21  C30  127.77  3.000
 OO7  C30  C21  N22  121.55  3.000
 OO7  C20  C21  N22  110.66  3.000
 OO7  C23  N22  C21  105.86  3.000
 OO7  N29  C23  C24  118.11  3.000
 OO7  N29  C23  N22  111.27  3.000
 OO7  C24  C23  N22  130.62  3.000
 OO7  N26  C24  C25  120.46  3.000
 OO7  C25  C24  C23  118.92  3.000
 OO7  N26  C24  C23  120.62  3.000
 OO7  H8   C27  C28  119.51  3.000
 OO7  H8   C27  N26  116.73  3.000
 OO7  C28  C27  N26  123.76  3.000
 OO7  C35  C30  C31  118.72  3.000
 OO7  C35  C30  C21  121.73  3.000
 OO7  C31  C30  C21  119.55  3.000
 OO7  H9   C31  C32  119.85  3.000
 OO7  H9   C31  C30  119.56  3.000
 OO7  C32  C31  C30  120.59  3.000
 OO7  H10  C32  C33  120.09  3.000
 OO7  H10  C32  C31  119.64  3.000
 OO7  C33  C32  C31  120.27  3.000
 OO7  H11  C33  C34  120.36  3.000
 OO7  H11  C33  C32  120.12  3.000
 OO7  C34  C33  C32  119.52  3.000
 OO7  H12  C34  C35  119.23  3.000
 OO7  H12  C34  C33  120.45  3.000
 OO7  C35  C34  C33  120.32  3.000
 OO7  H13  C35  C34  118.88  3.000
 OO7  H13  C35  C30  120.52  3.000
 OO7  C34  C35  C30  120.58  3.000
 OO7  C6   O5   C2   118.28  3.000
 OO7  C13  C9   C10  121.09  3.000
 OO7  C10  C9   C8   119.94  3.000
 OO7  C13  C9   C8   118.95  3.000
 OO7  H15  C10  H14  106.49  3.000
 OO7  H15  C10  O11  110.95  3.000
 OO7  H14  C10  O11  110.51  3.000
 OO7  H15  C10  C9   109.57  3.000
 OO7  H14  C10  C9   109.44  3.000
 OO7  O11  C10  C9   109.81  3.000
 OO7  C10  O11  C12  112.38  3.000
 OO7  H16  C13  C14  118.72  3.000
 OO7  H16  C13  C9   119.42  3.000
 OO7  C14  C13  C9   121.86  3.000
 OO7  C13  C14  C15  120.91  3.000
 OO7  C13  C14  C6   117.38  3.000
 OO7  C15  C14  C6   121.71  3.000
 OO7  H17  N16  C17  120.69  3.000
 OO7  H17  N16  C15  118.63  3.000
 OO7  C17  N16  C15  120.66  3.000
 OO7  H18  N19  C20  119.11  3.000
 OO7  H18  N19  C17  120.24  3.000
 OO7  C20  N19  C17  119.98  3.000
 OO7  N29  C20  N19  122.24  3.000
 OO7  N19  C20  C21  132.43  3.000
 OO7  N29  C20  C21  105.25  3.000
 OO7  C27  N26  C24  119.24  3.000
 OO7  H22  C28  N29  118.21  3.000
 OO7  H22  C28  C27  124.76  3.000
 OO7  N29  C28  C27  117.03  3.000
 OO7  C28  N29  C20  131.81  3.000
 OO7  C20  N29  C23  106.96  3.000
 OO7  C28  N29  C23  121.23  3.000
 OO7  H7   C15  H6   106.55  3.000
 OO7  H7   C15  N16  106.84  3.000
 OO7  H6   C15  N16  109.56  3.000
 OO7  H7   C15  C14  109.52  3.000
 OO7  H6   C15  C14  110.42  3.000
 OO7  N16  C15  C14  113.65  3.000
 OO7  H21  C25  H20  106.95  3.000
 OO7  H21  C25  H19  108.73  3.000
 OO7  H20  C25  H19  109.00  3.000
 OO7  H21  C25  C24  110.74  3.000
 OO7  H20  C25  C24  110.96  3.000
 OO7  H19  C25  C24  110.37  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
 OO7  CONST_01  C9   C13  C14  C6      0.00   0.0  0
 OO7  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 OO7  CONST_03  C13  C14  C6   C7      0.00   0.0  0
 OO7  CONST_04  C13  C9   C8   C7      0.00   0.0  0
 OO7  CONST_05  C14  C6   C7   C8      0.00   0.0  0
 OO7  CONST_06  C14  C13  C9   C8      0.00   0.0  0
 OO7  CONST_07  C24  C23  N22  C21   180.00   0.0  0
 OO7  CONST_08  N29  C23  N22  C21     0.00   0.0  0
 OO7  CONST_09  C28  N29  C20  C21   180.00   0.0  0
 OO7  CONST_10  C23  N29  C20  C21     0.00   0.0  0
 OO7  CONST_11  C32  C31  C30  C21   180.00   0.0  0
 OO7  CONST_12  C34  C35  C30  C21   180.00   0.0  0
 OO7  CONST_13  N26  C24  C23  N22   180.00   0.0  0
 OO7  CONST_14  C28  N29  C23  N22   180.00   0.0  0
 OO7  CONST_15  C20  N29  C23  N22     0.00   0.0  0
 OO7  CONST_16  N29  C20  C21  N22     0.00   0.0  0
 OO7  CONST_19  C27  N26  C24  C23     0.00   0.0  0
 OO7  CONST_20  C27  C28  N29  C23     0.00   0.0  0
 OO7  CONST_21  C20  C21  N22  C23     0.00   0.0  0
 OO7  CONST_22  C30  C21  N22  C23   180.00   0.0  0
 OO7  CONST_23  C28  C27  N26  C24     0.00   0.0  0
 OO7  CONST_24  C28  N29  C23  C24     0.00   0.0  0
 OO7  CONST_25  C20  N29  C23  C24   180.00   0.0  0
 OO7  CONST_26  C20  N29  C28  C27   180.00   0.0  0
 OO7  CONST_27  N29  C20  C21  C30   180.00   0.0  0
 OO7  CONST_28  C33  C32  C31  C30     0.00   0.0  0
 OO7  CONST_29  C33  C34  C35  C30     0.00   0.0  0
 OO7  CONST_31  C34  C35  C30  C31     0.00   0.0  0
 OO7  CONST_32  C34  C33  C32  C31     0.00   0.0  0
 OO7  CONST_33  C35  C30  C31  C32     0.00   0.0  0
 OO7  CONST_34  C35  C34  C33  C32     0.00   0.0  0
 OO7  CONST_36  N29  C28  C27  N26     0.00   0.0  0
 OO7  CONST_37  N29  C23  C24  N26     0.00   0.0  0
 OO7  CONST_38  C15  C14  C6   C7    180.00   0.0  0
 OO7  CONST_39  C10  C9   C8   C7    180.00   0.0  0
 OO7  CONST_40  O5   C6   C7   C8    180.00   0.0  0
 OO7  CONST_41  C9   C13  C14  C15   180.00   0.0  0
 OO7  CONST_42  C25  C24  C23  N22     0.00   0.0  0
 OO7  CONST_43  N19  C20  C21  N22   180.00   0.0  0
 OO7  CONST_44  N19  C20  N29  C23   180.00   0.0  0
 OO7  CONST_45  C25  C24  N26  C27   180.00   0.0  0
 OO7  CONST_46  N19  C20  C21  C30     0.00   0.0  0
 OO7  CONST_47  C13  C14  C6   O5    180.00   0.0  0
 OO7  CONST_48  C14  C13  C9   C10   180.00   0.0  0
 OO7  CONST_49  C28  N29  C20  N19     0.00   0.0  0
 OO7  CONST_50  N29  C23  C24  C25   180.00   0.0  0
 OO7  CONST_51  H16  C13  C14  C6    180.00   0.0  0
 OO7  CONST_52  H2   C8   C7   C6    180.00   0.0  0
 OO7  CONST_53  H9   C31  C30  C21     0.00   0.0  0
 OO7  CONST_54  H13  C35  C30  C21     0.00   0.0  0
 OO7  CONST_55  H22  C28  N29  C23   180.00   0.0  0
 OO7  CONST_56  H8   C27  N26  C24   180.00   0.0  0
 OO7  CONST_57  H10  C32  C31  C30   180.00   0.0  0
 OO7  CONST_58  H12  C34  C35  C30   180.00   0.0  0
 OO7  CONST_59  H11  C33  C32  C31   180.00   0.0  0
 OO7  CONST_60  H1   C7   C8   C9    180.00   0.0  0
 OO7  CONST_64  C20  N19  C17  O18     0.00   0.0  0
 OO7  CONST_65  C20  N19  C17  N16   180.00   0.0  0
 OO7  CONST_66  O18  C17  N16  C15     0.00   0.0  0
 OO7  CONST_67  N19  C17  N16  C15   180.00   0.0  0
 OO7  CONST_68  H17  N16  C17  O18   180.00   0.0  0
 OO7  Var_01    C14  C6   O5   C2     98.86  30.0  2
 OO7  Var_02    N16  C15  C14  C6    147.91  30.0  1
 OO7  Var_03    O11  C10  C9   C8    138.81  30.0  2
 OO7  Var_04    H19  C25  C24  C23  -176.11  30.0  2
 OO7  Var_05    F3   C2   O5   C6   -176.21  30.0  3
 OO7  Var_06    C9   C10  O11  C12  -176.52  30.0  1
 OO7  Var_07    C14  C15  N16  C17   -71.62  30.0  1
 OO7  Var_08    H3   C12  O11  C10  -179.27  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
 OO7  plan-1  C6   0.020
 OO7  plan-1  C7   0.020
 OO7  plan-1  C8   0.020
 OO7  plan-1  O5   0.020
 OO7  plan-1  C9   0.020
 OO7  plan-1  C10  0.020
 OO7  plan-1  C13  0.020
 OO7  plan-1  C14  0.020
 OO7  plan-1  H1   0.020
 OO7  plan-1  H2   0.020
 OO7  plan-1  H16  0.020
 OO7  plan-1  C15  0.020
 OO7  plan-2  C21  0.020
 OO7  plan-2  C30  0.020
 OO7  plan-2  C31  0.020
 OO7  plan-2  C32  0.020
 OO7  plan-2  C33  0.020
 OO7  plan-2  C34  0.020
 OO7  plan-2  C35  0.020
 OO7  plan-2  H9   0.020
 OO7  plan-2  H10  0.020
 OO7  plan-2  H11  0.020
 OO7  plan-2  H12  0.020
 OO7  plan-2  H13  0.020
 OO7  plan-3  C21  0.020
 OO7  plan-3  N22  0.020
 OO7  plan-3  C23  0.020
 OO7  plan-3  C24  0.020
 OO7  plan-3  C27  0.020
 OO7  plan-3  C30  0.020
 OO7  plan-3  N19  0.020
 OO7  plan-3  C20  0.020
 OO7  plan-3  N26  0.020
 OO7  plan-3  C28  0.020
 OO7  plan-3  N29  0.020
 OO7  plan-3  H8   0.020
 OO7  plan-3  H22  0.020
 OO7  plan-3  C25  0.020
 OO7  plan-4  C17  0.020
 OO7  plan-4  N16  0.020
 OO7  plan-4  O18  0.020
 OO7  plan-4  N19  0.020
 OO7  plan-4  C20  0.020
 OO7  plan-4  H17  0.020
 OO7  plan-4  H18  0.020
 OO7  plan-4  C15  0.020

