# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 17:15:28 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: N-(3,5-dichloro-4-{[6-(methylamino)pyrimidin-4-yl]oxy}phenyl)-N'-[3-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(Oc2c(Cl)cc(NC(=O)Nc3cccc(c3)C(F)(F)F)cc2Cl)ncn1
#
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
 ZGD  ZGD  "N-(3,5-dichloro-4-{[6-(methylamino)pyrimidin-4-yl]oxy}phenyl)-N'-[3-(trifluoromethyl)phenyl]urea"
  ligand  45  31  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZGD
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
 ZGD  C01   C   CH3   0  -0.531    0.1249  39.0691  -12.9930
 ZGD  N05   N   NH1   0  -0.637   -0.8030  39.1469  -11.8952
 ZGD  C07   C   CR6   0   0.532   -1.8794  38.3670  -11.7598
 ZGD  C08   C   CR16  0  -0.485   -2.2241  37.3829  -12.6987
 ZGD  C10   C   CR6   0   0.545   -3.3599  36.6598  -12.4070
 ZGD  O11   O   O2    0  -0.488   -3.7253  35.7026  -13.2898
 ZGD  C12   C   CR6   0   0.479   -4.7931  34.9149  -12.9892
 ZGD  C13   C   CR6   0  -0.113   -6.0730  35.2511  -13.4049
 ZGD  CL14  CL  CL    0  -0.084   -6.3075  36.7393  -14.2370
 ZGD  C15   C   CR16  0  -0.332   -7.1475  34.4194  -13.1650
 ZGD  C17   C   CR6   0   0.388   -6.9664  33.2158  -12.4776
 ZGD  N18   N   NH1   0  -0.800   -8.1029  32.4400  -12.2845
 ZGD  C20   C   C     0   0.748   -8.2277  31.2899  -11.5466
 ZGD  O21   O   O     0  -0.482   -7.3098  30.7708  -10.9414
 ZGD  N22   N   NH1   0  -0.793   -9.5045  30.7942  -11.5655
 ZGD  C24   C   CR6   0   0.399   -9.9587  29.6341  -10.9353
 ZGD  C25   C   CR16  0  -0.328  -11.0743  29.0023  -11.4855
 ZGD  C27   C   CR16  0  -0.230  -11.6101  27.8744  -10.8911
 ZGD  C29   C   CR16  0  -0.293  -11.0415  27.3436   -9.7447
 ZGD  C31   C   CR6   0  -0.183   -9.9347  27.9761   -9.1930
 ZGD  C32   C   CR16  0  -0.340   -9.3898  29.1150   -9.7719
 ZGD  C34   C   CT    0   1.050   -9.2922  27.3779   -7.9786
 ZGD  F35   F   F     0  -0.310  -10.1977  26.8899   -7.1210
 ZGD  F36   F   F     0  -0.303   -8.5446  28.2526   -7.2992
 ZGD  F37   F   F     0  -0.314   -8.4834  26.3585   -8.3065
 ZGD  C38   C   CR16  0  -0.296   -5.6868  32.8650  -12.0459
 ZGD  C40   C   CR6   0  -0.110   -4.6303  33.7224  -12.3036
 ZGD  CL41  CL  CL    0  -0.085   -3.0495  33.2971  -11.7661
 ZGD  N42   N   N     0  -0.467   -4.1082  36.8420  -11.3350
 ZGD  C43   C   CR16  0   0.067   -3.6899  37.8021  -10.5183
 ZGD  N45   N   N     0  -0.464   -2.6346  38.5676  -10.6610
 ZGD  H1    H   HCH3  0   0.269    0.9046  39.8086  -12.8369
 ZGD  H2    H   HCH3  0   0.241    0.5976  38.0867  -13.0582
 ZGD  H3    H   HCH3  0   0.241   -0.3566  39.2809  -13.9501
 ZGD  H4    H   HNH1  0   0.397   -0.6396  39.8207  -11.1655
 ZGD  H5    H   HCR6  0   0.289   -1.6448  37.1913  -13.5903
 ZGD  H6    H   HCR6  0   0.302   -8.1333  34.7111  -13.5043
 ZGD  H7    H   HNH1  0   0.424   -8.9383  32.8147  -12.7087
 ZGD  H8    H   HNH1  0   0.419  -10.1592  31.2028  -12.2168
 ZGD  H9    H   HCR6  0   0.280  -11.5277  29.3981  -12.3866
 ZGD  H10   H   HCR6  0   0.271  -12.4760  27.4000  -11.3327
 ZGD  H11   H   HCR6  0   0.273  -11.4654  26.4556   -9.2957
 ZGD  H12   H   HCR6  0   0.286   -8.5423  29.6049   -9.3202
 ZGD  H13   H   HCR6  0   0.311   -5.5050  31.9475  -11.5127
 ZGD  H14   H   HCR6  0   0.259   -4.2935  37.9705   -9.6322

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
 ZGD  CL14  C13   single    1.721  0.020  1.721
 ZGD  C13   C15   aromatic  1.380  0.020  1.380
 ZGD  C13   C12   aromatic  1.387  0.020  1.387
 ZGD  O11   C12   single    1.361  0.020  1.361
 ZGD  O11   C10   single    1.352  0.020  1.352
 ZGD  C15   C17   aromatic  1.398  0.020  1.398
 ZGD  C12   C40   aromatic  1.385  0.020  1.385
 ZGD  C17   N18   single    1.390  0.020  1.390
 ZGD  C17   C38   aromatic  1.395  0.020  1.395
 ZGD  C40   C38   aromatic  1.385  0.020  1.385
 ZGD  C40   CL41  single    1.723  0.020  1.723
 ZGD  C01   N05   single    1.440  0.020  1.440
 ZGD  C08   C10   aromatic  1.378  0.020  1.378
 ZGD  C08   C07   aromatic  1.403  0.020  1.403
 ZGD  C10   N42   aromatic  1.320  0.020  1.320
 ZGD  N18   C20   single    1.372  0.020  1.372
 ZGD  C20   N22   single    1.370  0.020  1.370
 ZGD  C20   O21   double    1.216  0.020  1.216
 ZGD  N22   C24   single    1.396  0.020  1.396
 ZGD  C25   C24   aromatic  1.395  0.020  1.395
 ZGD  C25   C27   aromatic  1.383  0.020  1.383
 ZGD  C07   N05   single    1.336  0.020  1.336
 ZGD  C07   N45   aromatic  1.348  0.020  1.348
 ZGD  N42   C43   aromatic  1.328  0.020  1.328
 ZGD  C24   C32   aromatic  1.395  0.020  1.395
 ZGD  C27   C29   aromatic  1.385  0.020  1.385
 ZGD  N45   C43   aromatic  1.311  0.020  1.311
 ZGD  C32   C31   aromatic  1.389  0.020  1.389
 ZGD  C29   C31   aromatic  1.389  0.020  1.389
 ZGD  C31   C34   single    1.498  0.020  1.498
 ZGD  F37   C34   single    1.342  0.020  1.342
 ZGD  C34   F36   single    1.336  0.020  1.336
 ZGD  C34   F35   single    1.339  0.020  1.339
 ZGD  C01   H1    single    0.970  0.020  1.090
 ZGD  C01   H2    single    0.970  0.020  1.090
 ZGD  C01   H3    single    0.970  0.020  1.090
 ZGD  N05   H4    single    0.860  0.020  1.020
 ZGD  C08   H5    single    0.930  0.020  1.080
 ZGD  C15   H6    single    0.930  0.020  1.080
 ZGD  N18   H7    single    0.860  0.020  1.020
 ZGD  N22   H8    single    0.860  0.020  1.020
 ZGD  C25   H9    single    0.930  0.020  1.080
 ZGD  C27   H10   single    0.930  0.020  1.080
 ZGD  C29   H11   single    0.930  0.020  1.080
 ZGD  C32   H12   single    0.930  0.020  1.080
 ZGD  C38   H13   single    0.930  0.020  1.080
 ZGD  C43   H14   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
 ZGD  H3    C01  H2    108.24  3.000
 ZGD  H3    C01  H1    108.09  3.000
 ZGD  H2    C01  H1    108.09  3.000
 ZGD  H3    C01  N05   111.94  3.000
 ZGD  H2    C01  N05   111.91  3.000
 ZGD  H1    C01  N05   108.44  3.000
 ZGD  H4    N05  C07   116.62  3.000
 ZGD  H4    N05  C01   118.97  3.000
 ZGD  C07   N05  C01   124.40  3.000
 ZGD  N45   C07  C08   120.80  3.000
 ZGD  N45   C07  N05   116.55  3.000
 ZGD  C08   C07  N05   122.65  3.000
 ZGD  H5    C08  C10   121.58  3.000
 ZGD  H5    C08  C07   123.02  3.000
 ZGD  C10   C08  C07   115.40  3.000
 ZGD  N42   C10  O11   118.34  3.000
 ZGD  N42   C10  C08   124.54  3.000
 ZGD  O11   C10  C08   117.12  3.000
 ZGD  C12   O11  C10   118.52  3.000
 ZGD  C40   C12  C13   117.74  3.000
 ZGD  C40   C12  O11   121.03  3.000
 ZGD  C13   C12  O11   121.18  3.000
 ZGD  C15   C13  CL14  119.94  3.000
 ZGD  C15   C13  C12   121.36  3.000
 ZGD  CL14  C13  C12   118.70  3.000
 ZGD  H6    C15  C17   120.27  3.000
 ZGD  H6    C15  C13   119.49  3.000
 ZGD  C17   C15  C13   120.24  3.000
 ZGD  C38   C17  N18   124.53  3.000
 ZGD  C38   C17  C15   119.17  3.000
 ZGD  N18   C17  C15   116.30  3.000
 ZGD  H7    N18  C20   117.52  3.000
 ZGD  H7    N18  C17   114.30  3.000
 ZGD  C20   N18  C17   128.10  3.000
 ZGD  N22   C20  O21   123.78  3.000
 ZGD  O21   C20  N18   123.84  3.000
 ZGD  N22   C20  N18   112.38  3.000
 ZGD  H8    N22  C24   114.61  3.000
 ZGD  H8    N22  C20   117.82  3.000
 ZGD  C24   N22  C20   126.71  3.000
 ZGD  C32   C24  C25   119.10  3.000
 ZGD  C32   C24  N22   123.57  3.000
 ZGD  C25   C24  N22   117.29  3.000
 ZGD  H9    C25  C27   119.55  3.000
 ZGD  H9    C25  C24   119.81  3.000
 ZGD  C27   C25  C24   120.64  3.000
 ZGD  H10   C27  C29   119.90  3.000
 ZGD  H10   C27  C25   119.50  3.000
 ZGD  C29   C27  C25   120.61  3.000
 ZGD  H11   C29  C31   121.42  3.000
 ZGD  H11   C29  C27   119.82  3.000
 ZGD  C31   C29  C27   118.77  3.000
 ZGD  C34   C31  C32   119.80  3.000
 ZGD  C34   C31  C29   118.80  3.000
 ZGD  C32   C31  C29   121.36  3.000
 ZGD  H12   C32  C31   120.43  3.000
 ZGD  H12   C32  C24   120.05  3.000
 ZGD  C31   C32  C24   119.52  3.000
 ZGD  F37   C34  F36   106.51  3.000
 ZGD  F36   C34  F35   106.93  3.000
 ZGD  F37   C34  F35   106.68  3.000
 ZGD  F35   C34  C31   112.00  3.000
 ZGD  F36   C34  C31   112.99  3.000
 ZGD  F37   C34  C31   111.33  3.000
 ZGD  H13   C38  C40   119.40  3.000
 ZGD  H13   C38  C17   121.49  3.000
 ZGD  C40   C38  C17   119.11  3.000
 ZGD  CL41  C40  C38   119.28  3.000
 ZGD  CL41  C40  C12   118.35  3.000
 ZGD  C38   C40  C12   122.38  3.000
 ZGD  C43   N42  C10   114.88  3.000
 ZGD  H14   C43  N45   116.47  3.000
 ZGD  H14   C43  N42   116.05  3.000
 ZGD  N45   C43  N42   127.48  3.000
 ZGD  C43   N45  C07   116.91  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
 ZGD  CONST_01  N42   C10  C08  C07      0.00   0.0  0
 ZGD  CONST_02  N42   C43  N45  C07      0.00   0.0  0
 ZGD  CONST_03  C43   N42  C10  C08      0.00   0.0  0
 ZGD  CONST_04  C43   N45  C07  C08      0.00   0.0  0
 ZGD  CONST_05  N45   C07  C08  C10      0.00   0.0  0
 ZGD  CONST_06  N45   C43  N42  C10      0.00   0.0  0
 ZGD  CONST_07  C17   C15  C13  C12      0.00   0.0  0
 ZGD  CONST_08  C17   C38  C40  C12      0.00   0.0  0
 ZGD  CONST_09  C38   C17  C15  C13      0.00   0.0  0
 ZGD  CONST_10  C38   C40  C12  C13      0.00   0.0  0
 ZGD  CONST_11  C40   C12  C13  C15      0.00   0.0  0
 ZGD  CONST_12  C40   C38  C17  C15      0.00   0.0  0
 ZGD  CONST_13  C29   C27  C25  C24      0.00   0.0  0
 ZGD  CONST_14  C29   C31  C32  C24      0.00   0.0  0
 ZGD  CONST_15  C31   C32  C24  C25      0.00   0.0  0
 ZGD  CONST_16  C31   C29  C27  C25      0.00   0.0  0
 ZGD  CONST_17  C32   C24  C25  C27      0.00   0.0  0
 ZGD  CONST_18  C32   C31  C29  C27      0.00   0.0  0
 ZGD  CONST_19  C10   C08  C07  N05    180.00   0.0  0
 ZGD  CONST_20  C43   N45  C07  N05    180.00   0.0  0
 ZGD  CONST_21  O11   C10  C08  C07    180.00   0.0  0
 ZGD  CONST_22  C15   C13  C12  O11    180.00   0.0  0
 ZGD  CONST_23  C38   C40  C12  O11    180.00   0.0  0
 ZGD  CONST_24  C43   N42  C10  O11    180.00   0.0  0
 ZGD  CONST_25  N18   C17  C15  C13    180.00   0.0  0
 ZGD  CONST_26  CL41  C40  C12  C13    180.00   0.0  0
 ZGD  CONST_27  C17   C15  C13  CL14   180.00   0.0  0
 ZGD  CONST_28  C40   C12  C13  CL14   180.00   0.0  0
 ZGD  CONST_29  CL41  C40  C38  C17    180.00   0.0  0
 ZGD  CONST_30  C40   C38  C17  N18    180.00   0.0  0
 ZGD  CONST_31  C27   C25  C24  N22    180.00   0.0  0
 ZGD  CONST_32  C31   C32  C24  N22    180.00   0.0  0
 ZGD  CONST_33  C34   C31  C32  C24    180.00   0.0  0
 ZGD  CONST_34  C34   C31  C29  C27    180.00   0.0  0
 ZGD  CONST_35  H14   C43  N45  C07    180.00   0.0  0
 ZGD  CONST_36  H14   C43  N42  C10    180.00   0.0  0
 ZGD  CONST_37  H6    C15  C13  C12    180.00   0.0  0
 ZGD  CONST_38  H13   C38  C40  C12    180.00   0.0  0
 ZGD  CONST_39  H13   C38  C17  C15    180.00   0.0  0
 ZGD  CONST_40  H10   C27  C25  C24    180.00   0.0  0
 ZGD  CONST_41  H12   C32  C24  C25    180.00   0.0  0
 ZGD  CONST_42  H11   C29  C27  C25    180.00   0.0  0
 ZGD  CONST_43  H9    C25  C27  C29    180.00   0.0  0
 ZGD  CONST_44  H12   C32  C31  C29    180.00   0.0  0
 ZGD  CONST_45  H10   C27  C29  C31    180.00   0.0  0
 ZGD  CONST_46  H9    C25  C24  C32    180.00   0.0  0
 ZGD  CONST_47  H11   C29  C31  C32    180.00   0.0  0
 ZGD  CONST_48  H6    C15  C17  C38    180.00   0.0  0
 ZGD  CONST_49  H5    C08  C10  N42    180.00   0.0  0
 ZGD  CONST_50  H5    C08  C07  N45    180.00   0.0  0
 ZGD  CONST_51  C08   C07  N05  C01      0.00   0.0  0
 ZGD  CONST_52  N45   C07  N05  C01    180.00   0.0  0
 ZGD  CONST_53  C20   N18  C17  C15    180.00   0.0  0
 ZGD  CONST_54  C38   C17  N18  C20      0.00   0.0  0
 ZGD  CONST_57  H4    N05  C07  C08    180.00   0.0  0
 ZGD  CONST_58  H7    N18  C17  C15      0.00   0.0  0
 ZGD  CONST_61  H7    N18  C17  C38    180.00   0.0  0
 ZGD  CONST_62  H4    N05  C07  N45      0.00   0.0  0
 ZGD  CONST_63  O21   C20  N18  C17      0.00   0.0  0
 ZGD  CONST_64  C24   N22  C20  O21      0.00   0.0  0
 ZGD  CONST_65  N22   C20  N18  C17    180.00   0.0  0
 ZGD  CONST_66  C24   N22  C20  N18    180.00   0.0  0
 ZGD  CONST_67  H7    N18  C20  O21    180.00   0.0  0
 ZGD  CONST_68  H8    N22  C20  O21    180.00   0.0  0
 ZGD  CONST_69  H8    N22  C20  N18      0.00   0.0  0
 ZGD  CONST_70  H7    N18  C20  N22      0.00   0.0  0
 ZGD  Var_01    C12   O11  C10  C08    175.91  30.0  1
 ZGD  Var_02    C13   C12  O11  C10     91.99  30.0  2
 ZGD  Var_03    C40   C12  O11  C10    -90.63  30.0  2
 ZGD  Var_04    N42   C10  O11  C12     -4.28  30.0  2
 ZGD  Var_05    F37   C34  C31  C29     80.28  30.0  2
 ZGD  Var_06    F36   C34  C31  C29   -159.91  30.0  2
 ZGD  Var_07    F35   C34  C31  C29    -39.07  30.0  2
 ZGD  Var_08    F37   C34  C31  C32    -97.38  30.0  2
 ZGD  Var_09    F36   C34  C31  C32     22.43  30.0  2
 ZGD  Var_10    F35   C34  C31  C32    143.26  30.0  2
 ZGD  Var_11    H1    C01  N05  C07   -179.27  30.0  3
 ZGD  Var_12    H2    C01  N05  C07    -60.13  30.0  3
 ZGD  Var_13    H3    C01  N05  C07     61.57  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
 ZGD  plan-1  N05   0.020
 ZGD  plan-1  C07   0.020
 ZGD  plan-1  C08   0.020
 ZGD  plan-1  C10   0.020
 ZGD  plan-1  O11   0.020
 ZGD  plan-1  N42   0.020
 ZGD  plan-1  C43   0.020
 ZGD  plan-1  N45   0.020
 ZGD  plan-1  H5    0.020
 ZGD  plan-1  H14   0.020
 ZGD  plan-2  O11   0.020
 ZGD  plan-2  C12   0.020
 ZGD  plan-2  C13   0.020
 ZGD  plan-2  CL14  0.020
 ZGD  plan-2  C15   0.020
 ZGD  plan-2  C17   0.020
 ZGD  plan-2  N18   0.020
 ZGD  plan-2  C38   0.020
 ZGD  plan-2  C40   0.020
 ZGD  plan-2  CL41  0.020
 ZGD  plan-2  H6    0.020
 ZGD  plan-2  H13   0.020
 ZGD  plan-3  N22   0.020
 ZGD  plan-3  C24   0.020
 ZGD  plan-3  C25   0.020
 ZGD  plan-3  C27   0.020
 ZGD  plan-3  C29   0.020
 ZGD  plan-3  C31   0.020
 ZGD  plan-3  C32   0.020
 ZGD  plan-3  C34   0.020
 ZGD  plan-3  H9    0.020
 ZGD  plan-3  H10   0.020
 ZGD  plan-3  H11   0.020
 ZGD  plan-3  H12   0.020
 ZGD  plan-4  C17   0.020
 ZGD  plan-4  N18   0.020
 ZGD  plan-4  C20   0.020
 ZGD  plan-4  O21   0.020
 ZGD  plan-4  N22   0.020
 ZGD  plan-4  C24   0.020
 ZGD  plan-4  H7    0.020
 ZGD  plan-4  H8    0.020
 ZGD  plan-5  C01   0.020
 ZGD  plan-5  N05   0.020
 ZGD  plan-5  C07   0.020
 ZGD  plan-5  H4    0.020

