# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:59:51 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: 3-(2-chlorophenyl)-1-(2-{[(1S)-2-hydroxy-1,2-dimethylpropyl]amino}pyrimidin-4-yl)-1-(4-methoxyphenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)N(C(=O)Nc2ccccc2Cl)c3ccnc(N[C@@H](C)C(C)(C)O)n3
#
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
 LIB  LIB  3-(2-chlorophenyl)-1-(2-{[(1S)-2-hydroxy-1,2-dimethylpropyl]amino}pyrimidin-4-yl)-1-(4-methoxyphenyl)urea  ligand  58  32  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LIB
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
 LIB  N1    N   NT    0  -0.666   0.4760   0.4770  -0.6622
 LIB  C4    C   CR6   0   0.395   3.7622   2.9118   0.3514
 LIB  C5    C   CR16  0  -0.227   2.5506   1.6188  -1.2827
 LIB  C6    C   CR16  0  -0.225   1.7241   1.7892   0.9637
 LIB  C7    C   CR16  0  -0.382   2.7983   2.5981   1.3081
 LIB  C8    C   CR16  0  -0.343   3.6284   2.4126  -0.9483
 LIB  C20   C   CR6   0   0.428   2.2295  -2.7064  -0.7158
 LIB  C22   C   CR16  0  -0.271   3.1461  -5.3243  -1.0963
 LIB  C24   C   CR6   0  -0.130   2.7786  -3.4414   0.3366
 LIB  C26   C   CR16  0  -0.250   2.6031  -4.6085  -2.1546
 LIB  CL28  CL  CL    0  -0.093   2.8904  -2.7221   1.9107
 LIB  C25   C   CR16  0  -0.203   3.2422  -4.7344   0.1536
 LIB  C23   C   CR16  0  -0.293   2.1588  -3.3099  -1.9705
 LIB  C1    C   C     0   0.696   0.6411  -0.8723  -0.9703
 LIB  O18   O   O     0  -0.463  -0.1660  -1.5092  -1.6088
 LIB  C2    C   CR6   0   0.149   1.5911   1.2972  -0.3254
 LIB  C14   C   CH3   0  -0.439   5.0244   4.2132   1.8804
 LIB  C3    C   CR6   0   0.511  -0.7915   1.0715  -0.7021
 LIB  C32   C   CR16  0  -0.421  -0.9266   2.3991  -1.1162
 LIB  C37   C   CR16  0  -0.015  -2.2151   2.8926  -1.0992
 LIB  N38   N   N     0  -0.477  -3.2720   2.1868  -0.7236
 LIB  C34   C   CR6   0   0.602  -3.0254   0.9325  -0.3329
 LIB  N33   N   N     0  -0.477  -1.8165   0.3528  -0.3022
 LIB  N35   N   NH1   0  -0.659  -4.0490   0.1747   0.0927
 LIB  C40   C   CH1   0  -0.051  -5.4449   0.5558   0.0510
 LIB  C43   C   CH3   0  -0.667  -6.0545   0.2043  -1.3043
 LIB  C42   C   CT    0   0.191  -6.1721  -0.0735   1.2554
 LIB  C47   C   CH3   0  -0.671  -5.5656   0.4357   2.5624
 LIB  C46   C   CH3   0  -0.678  -7.6603   0.2696   1.2269
 LIB  O45   O   OH1   0  -0.681  -5.9838  -1.4771   1.1356
 LIB  H5    H   HCR6  0   0.274   2.4516   1.2479  -2.2950
 LIB  H6    H   HCR6  0   0.276   0.9836   1.5432   1.7147
 LIB  H7    H   HCR6  0   0.288   2.8671   2.9629   2.3234
 LIB  H8    H   HCR6  0   0.273   4.3737   2.6596  -1.6937
 LIB  H22   H   HCR6  0   0.265   3.5009  -6.3354  -1.2415
 LIB  H26   H   HCR6  0   0.265   2.5379  -5.0560  -3.1372
 LIB  H25   H   HCR6  0   0.286   3.6682  -5.2763   0.9871
 LIB  H23   H   HCR6  0   0.274   1.7664  -2.7548  -2.8101
 LIB  HN19  H   HNH1  0   0.407   2.3361  -0.8567   0.1779
 LIB  H141  H   HCH3  0   0.263   5.9424   4.7939   1.8449
 LIB  H142  H   HCH3  0   0.232   4.2016   4.8718   2.1696
 LIB  H143  H   HCH3  0   0.232   5.1337   3.4293   2.6341
 LIB  H32   H   HCR6  0   0.276  -0.0931   3.0013  -1.4434
 LIB  H37   H   HCR6  0   0.268  -2.4075   3.9114  -1.4180
 LIB  HN35  H   HNH1  0   0.384  -3.8353  -0.7893   0.2948
 LIB  H40   H   HCH1  0   0.248  -5.4953   1.6381   0.1817
 LIB  H431  H   HCH3  0   0.226  -6.0657  -0.8731  -1.4707
 LIB  H432  H   HCH3  0   0.231  -7.0742   0.5753  -1.4024
 LIB  H433  H   HCH3  0   0.236  -5.4665   0.6632  -2.0994
 LIB  H471  H   HCH3  0   0.227  -5.6930   1.5151   2.6565
 LIB  H472  H   HCH3  0   0.230  -6.0646  -0.0263   3.4175
 LIB  H473  H   HCH3  0   0.238  -4.5006   0.2149   2.6322
 LIB  H461  H   HCH3  0   0.240  -8.1655  -0.1744   0.3696
 LIB  H462  H   HCH3  0   0.234  -8.1492  -0.1005   2.1308
 LIB  H463  H   HCH3  0   0.226  -7.8149   1.3491   1.1903
 LIB  HO45  H   HOH1  0   0.449  -6.3207  -1.9004   1.9321
 LIB  O13   O   O2    0  -0.465   4.8398   3.6762   0.5841
 LIB  N19   N   NH1   0  -0.773   1.8146  -1.3909  -0.5010

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
 LIB  N1   C1    single    1.394  0.020  1.394
 LIB  N1   C2    single    1.425  0.020  1.425
 LIB  N1   C3    single    1.401  0.020  1.401
 LIB  C4   C7    aromatic  1.394  0.020  1.394
 LIB  C4   C8    aromatic  1.399  0.020  1.399
 LIB  C4   O13   single    1.341  0.020  1.341
 LIB  C5   C8    aromatic  1.380  0.020  1.380
 LIB  C5   C2    aromatic  1.393  0.020  1.393
 LIB  C5   H5    single    0.930  0.020  1.080
 LIB  C6   C7    aromatic  1.388  0.020  1.388
 LIB  C6   C2    aromatic  1.386  0.020  1.386
 LIB  C6   H6    single    0.930  0.020  1.080
 LIB  C7   H7    single    0.930  0.020  1.080
 LIB  C8   H8    single    0.930  0.020  1.080
 LIB  C20  C24   aromatic  1.396  0.020  1.396
 LIB  C20  C23   aromatic  1.394  0.020  1.394
 LIB  C20  N19   single    1.396  0.020  1.396
 LIB  C22  C26   aromatic  1.388  0.020  1.388
 LIB  C22  C25   aromatic  1.385  0.020  1.385
 LIB  C22  H22   single    0.930  0.020  1.080
 LIB  C24  CL28  single    1.734  0.020  1.734
 LIB  C24  C25   aromatic  1.386  0.020  1.386
 LIB  C26  C23   aromatic  1.385  0.020  1.385
 LIB  C26  H26   single    0.930  0.020  1.080
 LIB  C25  H25   single    0.930  0.020  1.080
 LIB  C23  H23   single    0.930  0.020  1.080
 LIB  N19  C1    single    1.366  0.020  1.366
 LIB  N19  HN19  single    0.860  0.020  1.020
 LIB  C1   O18   double    1.210  0.020  1.210
 LIB  O13  C14   single    1.415  0.020  1.415
 LIB  C14  H141  single    0.970  0.020  1.090
 LIB  C14  H142  single    0.970  0.020  1.090
 LIB  C14  H143  single    0.970  0.020  1.090
 LIB  C3   C32   aromatic  1.397  0.020  1.397
 LIB  C3   N33   aromatic  1.314  0.020  1.314
 LIB  C32  C37   aromatic  1.380  0.020  1.380
 LIB  C32  H32   single    0.930  0.020  1.080
 LIB  C37  N38   aromatic  1.325  0.020  1.325
 LIB  C37  H37   single    0.930  0.020  1.080
 LIB  N38  C34   aromatic  1.337  0.020  1.337
 LIB  C34  N33   aromatic  1.341  0.020  1.341
 LIB  C34  N35   single    1.343  0.020  1.343
 LIB  N35  C40   single    1.448  0.020  1.448
 LIB  N35  HN35  single    0.860  0.020  1.020
 LIB  C40  C43   single    1.527  0.020  1.527
 LIB  C40  C42   single    1.541  0.020  1.541
 LIB  C40  H40   single    0.970  0.020  1.090
 LIB  C43  H431  single    0.970  0.020  1.090
 LIB  C43  H432  single    0.970  0.020  1.090
 LIB  C43  H433  single    0.970  0.020  1.090
 LIB  C42  C47   single    1.528  0.020  1.528
 LIB  C42  C46   single    1.527  0.020  1.527
 LIB  C42  O45   single    1.421  0.020  1.421
 LIB  C47  H471  single    0.970  0.020  1.090
 LIB  C47  H472  single    0.970  0.020  1.090
 LIB  C47  H473  single    0.970  0.020  1.090
 LIB  C46  H461  single    0.970  0.020  1.090
 LIB  C46  H462  single    0.970  0.020  1.090
 LIB  C46  H463  single    0.970  0.020  1.090
 LIB  O45  HO45  single    0.850  0.020  0.980

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
 LIB  C3    N1   C2    118.08  3.000
 LIB  C3    N1   C1    120.78  3.000
 LIB  C2    N1   C1    121.12  3.000
 LIB  O13   C4   C8    116.20  3.000
 LIB  O13   C4   C7    124.38  3.000
 LIB  C8    C4   C7    119.43  3.000
 LIB  H5    C5   C2    120.03  3.000
 LIB  H5    C5   C8    119.68  3.000
 LIB  C2    C5   C8    120.29  3.000
 LIB  H6    C6   C2    119.91  3.000
 LIB  H6    C6   C7    119.31  3.000
 LIB  C2    C6   C7    120.78  3.000
 LIB  H7    C7   C6    118.61  3.000
 LIB  H7    C7   C4    121.65  3.000
 LIB  C6    C7   C4    119.74  3.000
 LIB  H8    C8   C5    120.14  3.000
 LIB  H8    C8   C4    119.51  3.000
 LIB  C5    C8   C4    120.35  3.000
 LIB  N19   C20  C23   122.10  3.000
 LIB  N19   C20  C24   119.80  3.000
 LIB  C23   C20  C24   118.07  3.000
 LIB  H22   C22  C25   119.77  3.000
 LIB  H22   C22  C26   120.54  3.000
 LIB  C25   C22  C26   119.69  3.000
 LIB  C25   C24  CL28  119.03  3.000
 LIB  C25   C24  C20   121.55  3.000
 LIB  CL28  C24  C20   119.42  3.000
 LIB  H26   C26  C23   119.30  3.000
 LIB  H26   C26  C22   120.18  3.000
 LIB  C23   C26  C22   120.51  3.000
 LIB  H25   C25  C24   119.83  3.000
 LIB  H25   C25  C22   120.61  3.000
 LIB  C24   C25  C22   119.55  3.000
 LIB  H23   C23  C26   119.68  3.000
 LIB  H23   C23  C20   119.70  3.000
 LIB  C26   C23  C20   120.62  3.000
 LIB  O18   C1   N19   123.66  3.000
 LIB  O18   C1   N1    123.17  3.000
 LIB  N19   C1   N1    113.16  3.000
 LIB  C6    C2   C5    119.41  3.000
 LIB  C6    C2   N1    119.95  3.000
 LIB  C5    C2   N1    120.64  3.000
 LIB  H143  C14  H142  108.97  3.000
 LIB  H143  C14  H141  108.74  3.000
 LIB  H142  C14  H141  108.82  3.000
 LIB  H143  C14  O13   111.88  3.000
 LIB  H142  C14  O13   111.89  3.000
 LIB  H141  C14  O13   106.44  3.000
 LIB  N33   C3   C32   122.30  3.000
 LIB  N33   C3   N1    117.72  3.000
 LIB  C32   C3   N1    119.95  3.000
 LIB  H32   C32  C37   121.69  3.000
 LIB  H32   C32  C3    123.05  3.000
 LIB  C37   C32  C3    115.25  3.000
 LIB  H37   C37  N38   116.24  3.000
 LIB  H37   C37  C32   119.86  3.000
 LIB  N38   C37  C32   123.90  3.000
 LIB  C34   N38  C37   115.81  3.000
 LIB  N35   C34  N33   115.85  3.000
 LIB  N35   C34  N38   118.79  3.000
 LIB  N33   C34  N38   125.35  3.000
 LIB  C34   N33  C3    117.37  3.000
 LIB  HN35  N35  C40   117.51  3.000
 LIB  HN35  N35  C34   116.22  3.000
 LIB  C40   N35  C34   125.27  3.000
 LIB  H40   C40  C42   106.84  3.000
 LIB  H40   C40  C43   108.43  3.000
 LIB  C42   C40  C43   114.28  3.000
 LIB  H40   C40  N35   107.58  3.000
 LIB  C42   C40  N35   108.97  3.000
 LIB  C43   C40  N35   110.48  3.000
 LIB  H433  C43  H432  107.20  3.000
 LIB  H433  C43  H431  108.07  3.000
 LIB  H432  C43  H431  108.25  3.000
 LIB  H433  C43  C40   109.58  3.000
 LIB  H432  C43  C40   112.03  3.000
 LIB  H431  C43  C40   111.53  3.000
 LIB  O45   C42  C46   110.45  3.000
 LIB  O45   C42  C47   110.39  3.000
 LIB  C46   C42  C47   109.13  3.000
 LIB  O45   C42  C40   105.96  3.000
 LIB  C46   C42  C40   110.70  3.000
 LIB  C47   C42  C40   110.18  3.000
 LIB  H473  C47  H472  108.10  3.000
 LIB  H473  C47  H471  108.00  3.000
 LIB  H472  C47  H471  107.31  3.000
 LIB  H473  C47  C42   112.03  3.000
 LIB  H472  C47  C42   110.31  3.000
 LIB  H471  C47  C42   110.92  3.000
 LIB  H463  C46  H462  107.43  3.000
 LIB  H463  C46  H461  108.12  3.000
 LIB  H462  C46  H461  107.80  3.000
 LIB  H463  C46  C42   111.15  3.000
 LIB  H462  C46  C42   110.16  3.000
 LIB  H461  C46  C42   112.01  3.000
 LIB  HO45  O45  C42   108.55  3.000
 LIB  C14   O13  C4    118.68  3.000
 LIB  HN19  N19  C1    118.30  3.000
 LIB  HN19  N19  C20   116.66  3.000
 LIB  C1    N19  C20   124.07  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
 LIB  CONST_01  C2    C6   C7   C4       0.00   0.0  0
 LIB  CONST_02  C2    C5   C8   C4       0.00   0.0  0
 LIB  CONST_03  C7    C4   C8   C5       0.00   0.0  0
 LIB  CONST_04  C7    C6   C2   C5       0.00   0.0  0
 LIB  CONST_05  C8    C4   C7   C6       0.00   0.0  0
 LIB  CONST_06  C8    C5   C2   C6       0.00   0.0  0
 LIB  CONST_07  C22   C25  C24  C20      0.00   0.0  0
 LIB  CONST_08  C22   C26  C23  C20      0.00   0.0  0
 LIB  CONST_09  C26   C23  C20  C24      0.00   0.0  0
 LIB  CONST_10  C26   C22  C25  C24      0.00   0.0  0
 LIB  CONST_11  C23   C26  C22  C25      0.00   0.0  0
 LIB  CONST_12  C23   C20  C24  C25      0.00   0.0  0
 LIB  CONST_13  N38   C37  C32  C3       0.00   0.0  0
 LIB  CONST_14  N38   C34  N33  C3       0.00   0.0  0
 LIB  CONST_15  C34   N33  C3   C32      0.00   0.0  0
 LIB  CONST_16  C34   N38  C37  C32      0.00   0.0  0
 LIB  CONST_17  N33   C3   C32  C37      0.00   0.0  0
 LIB  CONST_18  N33   C34  N38  C37      0.00   0.0  0
 LIB  CONST_19  C8    C5   C2   N1     180.00   0.0  0
 LIB  CONST_20  C7    C6   C2   N1     180.00   0.0  0
 LIB  CONST_21  C37   C32  C3   N1     180.00   0.0  0
 LIB  CONST_22  C34   N33  C3   N1     180.00   0.0  0
 LIB  CONST_23  O13   C4   C8   C5     180.00   0.0  0
 LIB  CONST_24  O13   C4   C7   C6     180.00   0.0  0
 LIB  CONST_25  CL28  C24  C25  C22    180.00   0.0  0
 LIB  CONST_26  N19   C20  C23  C26    180.00   0.0  0
 LIB  CONST_27  C23   C20  C24  CL28   180.00   0.0  0
 LIB  CONST_28  N19   C20  C24  C25    180.00   0.0  0
 LIB  CONST_29  N35   C34  N33  C3     180.00   0.0  0
 LIB  CONST_30  N35   C34  N38  C37    180.00   0.0  0
 LIB  CONST_31  H6    C6   C7   C4     180.00   0.0  0
 LIB  CONST_32  H5    C5   C8   C4     180.00   0.0  0
 LIB  CONST_33  H8    C8   C4   C7     180.00   0.0  0
 LIB  CONST_34  H7    C7   C4   C8     180.00   0.0  0
 LIB  CONST_35  H25   C25  C24  C20    180.00   0.0  0
 LIB  CONST_36  H26   C26  C23  C20    180.00   0.0  0
 LIB  CONST_37  H23   C23  C26  C22    180.00   0.0  0
 LIB  CONST_38  H22   C22  C25  C24    180.00   0.0  0
 LIB  CONST_39  H37   C37  C32  C3     180.00   0.0  0
 LIB  CONST_40  H32   C32  C37  N38    180.00   0.0  0
 LIB  CONST_43  C40   N35  C34  N38      0.00   0.0  0
 LIB  CONST_44  C40   N35  C34  N33    180.00   0.0  0
 LIB  CONST_46  HN35  N35  C34  N38    180.00   0.0  0
 LIB  CONST_47  O18   C1   N19  C20      0.00   0.0  0
 LIB  CONST_50  C20   N19  C1   N1     180.00   0.0  0
 LIB  Var_01    C3    N1   C2   C5    -110.51  30.0  2
 LIB  Var_02    C32   C3   N1   C2      33.66  30.0  2
 LIB  Var_03    H141  C14  O13  C4    -179.78  30.0  3
 LIB  Var_04    H471  C47  C42  C40     62.51  30.0  3
 LIB  Var_05    H461  C46  C42  C40     65.31  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
 LIB  chir_01  C40  N35  C43  C42  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
 LIB  plan-1  N1    0.020
 LIB  plan-1  C4    0.020
 LIB  plan-1  C5    0.020
 LIB  plan-1  C6    0.020
 LIB  plan-1  C7    0.020
 LIB  plan-1  C8    0.020
 LIB  plan-1  C2    0.020
 LIB  plan-1  H5    0.020
 LIB  plan-1  H6    0.020
 LIB  plan-1  H7    0.020
 LIB  plan-1  H8    0.020
 LIB  plan-1  O13   0.020
 LIB  plan-2  C20   0.020
 LIB  plan-2  C22   0.020
 LIB  plan-2  C24   0.020
 LIB  plan-2  C26   0.020
 LIB  plan-2  CL28  0.020
 LIB  plan-2  C25   0.020
 LIB  plan-2  C23   0.020
 LIB  plan-2  H22   0.020
 LIB  plan-2  H26   0.020
 LIB  plan-2  H25   0.020
 LIB  plan-2  H23   0.020
 LIB  plan-2  N19   0.020
 LIB  plan-3  N1    0.020
 LIB  plan-3  C3    0.020
 LIB  plan-3  C32   0.020
 LIB  plan-3  C37   0.020
 LIB  plan-3  N38   0.020
 LIB  plan-3  C34   0.020
 LIB  plan-3  N33   0.020
 LIB  plan-3  N35   0.020
 LIB  plan-3  H32   0.020
 LIB  plan-3  H37   0.020
 LIB  plan-4  N1    0.020
 LIB  plan-4  C20   0.020
 LIB  plan-4  C1    0.020
 LIB  plan-4  O18   0.020
 LIB  plan-4  C2    0.020
 LIB  plan-4  C3    0.020
 LIB  plan-4  HN19  0.020
 LIB  plan-4  N19   0.020
 LIB  plan-5  C34   0.020
 LIB  plan-5  N35   0.020
 LIB  plan-5  C40   0.020
 LIB  plan-5  HN35  0.020

