# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 23:05:05 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 3-(2-chlorobenzyl)-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)NCc2ccccc2Cl)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
 LIC  LIC  3-(2-chlorobenzyl)-1-(2-{[(1S)-2-hydroxy-1,2-dimethylpropyl]amino}pyrimidin-4-yl)-1-(4-methoxyphenyl)urea  ligand  61  33  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LIC
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
 LIC  N1    N   NT    0  -0.663  -0.0469   0.3473   0.0917
 LIC  C7    C   CH2   0  -0.361  -2.0549  -2.6210  -0.7282
 LIC  C13   C   CR16  0  -0.315  -4.4481  -2.7453  -1.4769
 LIC  C15   C   CR16  0  -0.198  -5.4011  -2.0852   1.0364
 LIC  C21   C   CR6   0   0.391  -3.0089   3.2667  -0.5917
 LIC  C22   C   CR16  0  -0.222  -2.1163   1.4737   0.7478
 LIC  C24   C   CR16  0  -0.384  -1.9448   3.1248  -1.4806
 LIC  C12   C   CR6   0  -0.100  -4.0400  -2.1964   0.8025
 LIC  C11   C   CR16  0  -0.276  -6.2912  -2.3080  -0.0048
 LIC  C14   C   CR16  0  -0.231  -5.8153  -2.6411  -1.2639
 LIC  C9    C   CR6   0   0.184  -3.5322  -2.5261  -0.4524
 LIC  C1    C   C     0   0.706  -0.3682  -1.0230   0.0781
 LIC  O4    O   O     0  -0.483   0.2525  -1.8421   0.7238
 LIC  C2    C   CR6   0   0.158  -1.0553   1.3251  -0.1421
 LIC  C25   C   CR16  0  -0.344  -3.0889   2.4260   0.5226
 LIC  C31   C   CH3   0  -0.440  -3.9455   5.0698  -1.8158
 LIC  C23   C   CR16  0  -0.229  -0.9824   2.1500  -1.2537
 LIC  C3    C   CR6   0   0.517   1.2417   0.7808   0.3934
 LIC  C35   C   CR16  0  -0.429   1.4432   2.0322   0.9902
 LIC  C37   C   CR16  0  -0.018   2.7586   2.3744   1.2176
 LIC  N39   N   N     0  -0.480   3.7905   1.5976   0.9164
 LIC  C41   C   CR6   0   0.598   3.4850   0.4264   0.3497
 LIC  N42   N   N     0  -0.484   2.2479  -0.0018   0.0645
 LIC  N36   N   NH1   0  -0.661   4.4878  -0.3996   0.0042
 LIC  C43   C   CH1   0  -0.040   5.8837  -0.1786   0.3193
 LIC  C45   C   CH3   0  -0.672   6.1932  -0.5997   1.7550
 LIC  C47   C   CT    0   0.186   6.7521  -0.8814  -0.7428
 LIC  C53   C   CH3   0  -0.670   6.4675  -0.3001  -2.1271
 LIC  O52   O   OH1   0  -0.680   6.3876  -2.2545  -0.7009
 LIC  C51   C   CH3   0  -0.679   8.2351  -0.7132  -0.4190
 LIC  H71   H   HCH2  0   0.271  -1.9056  -3.0801  -1.7077
 LIC  H72   H   HCH2  0   0.274  -1.5585  -3.2607  -0.0001
 LIC  H15   H   HCR6  0   0.280  -5.7642  -1.8286   2.0222
 LIC  H22   H   HCR6  0   0.261  -2.1824   0.8346   1.6186
 LIC  H24   H   HCR6  0   0.286  -1.8496   3.7557  -2.3533
 LIC  H11   H   HCR6  0   0.269  -7.3544  -2.2224   0.1760
 LIC  H14   H   HCR6  0   0.264  -6.5043  -2.8180  -2.0788
 LIC  H25   H   HCR6  0   0.270  -3.9143   2.5339   1.2147
 LIC  H311  H   HCH3  0   0.231  -3.9913   4.5476  -2.7745
 LIC  H312  H   HCH3  0   0.263  -4.8180   5.7115  -1.7251
 LIC  H313  H   HCH3  0   0.232  -3.0460   5.6898  -1.7943
 LIC  H23   H   HCR6  0   0.275  -0.1636   2.0405  -1.9537
 LIC  H35   H   HCR6  0   0.274   0.6347   2.6903   1.2680
 LIC  H37   H   HCR6  0   0.265   2.9948   3.3263   1.6812
 LIC  HN36  H   HNH1  0   0.383   4.2200  -1.3139  -0.3245
 LIC  H43   H   HCH1  0   0.244   6.0770   0.8921   0.2264
 LIC  H451  H   HCH3  0   0.226   6.1064  -1.6787   1.8832
 LIC  H452  H   HCH3  0   0.230   7.1964  -0.2992   2.0553
 LIC  H453  H   HCH3  0   0.237   5.4931  -0.1182   2.4377
 LIC  H531  H   HCH3  0   0.227   6.7144   0.7618  -2.1647
 LIC  H532  H   HCH3  0   0.230   7.0751  -0.8020  -2.8838
 LIC  H533  H   HCH3  0   0.238   5.4207  -0.4132  -2.4089
 LIC  HO52  H   HOH1  0   0.449   6.8225  -2.7085  -1.4302
 LIC  H511  H   HCH3  0   0.241   8.5107  -1.2282   0.5008
 LIC  H512  H   HCH3  0   0.234   8.8478  -1.1225  -1.2252
 LIC  H513  H   HCH3  0   0.226   8.4990   0.3404  -0.3107
 LIC  O30   O   O2    0  -0.467  -3.9916   4.1724  -0.7227
 LIC  N5    N   NH1   0  -0.650  -1.4318  -1.3194  -0.6955
 LIC  H13   H   HCR6  0   0.265  -4.0762  -3.0045  -2.4608
 LIC  CL16  CL  CL    0  -0.119  -2.9539  -1.9348   2.1308
 LIC  HN5   H   HNH1  0   0.409  -1.8467  -0.6029  -1.2701

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
 LIC  N1    C1    single    1.407  0.020  1.407
 LIC  N1    C2    single    1.424  0.020  1.424
 LIC  N1    C3    single    1.393  0.020  1.393
 LIC  C7    C9    single    1.506  0.020  1.506
 LIC  C7    N5    single    1.443  0.020  1.443
 LIC  C7    H71   single    0.970  0.020  1.090
 LIC  C7    H72   single    0.970  0.020  1.090
 LIC  C13   C14   aromatic  1.388  0.020  1.388
 LIC  C13   C9    aromatic  1.392  0.020  1.392
 LIC  C13   H13   single    0.930  0.020  1.080
 LIC  C15   C12   aromatic  1.385  0.020  1.385
 LIC  C15   C11   aromatic  1.388  0.020  1.388
 LIC  C15   H15   single    0.930  0.020  1.080
 LIC  C21   C24   aromatic  1.394  0.020  1.394
 LIC  C21   C25   aromatic  1.398  0.020  1.398
 LIC  C21   O30   single    1.343  0.020  1.343
 LIC  C22   C2    aromatic  1.393  0.020  1.393
 LIC  C22   C25   aromatic  1.380  0.020  1.380
 LIC  C22   H22   single    0.930  0.020  1.080
 LIC  C24   C23   aromatic  1.388  0.020  1.388
 LIC  C24   H24   single    0.930  0.020  1.080
 LIC  CL16  C12   single    1.736  0.020  1.736
 LIC  C12   C9    aromatic  1.393  0.020  1.393
 LIC  C11   C14   aromatic  1.387  0.020  1.387
 LIC  C11   H11   single    0.930  0.020  1.080
 LIC  C14   H14   single    0.930  0.020  1.080
 LIC  N5    C1    single    1.348  0.020  1.348
 LIC  N5    HN5   single    0.860  0.020  1.020
 LIC  C1    O4    double    1.214  0.020  1.214
 LIC  C2    C23   aromatic  1.386  0.020  1.386
 LIC  C25   H25   single    0.930  0.020  1.080
 LIC  O30   C31   single    1.415  0.020  1.415
 LIC  C31   H311  single    0.970  0.020  1.090
 LIC  C31   H312  single    0.970  0.020  1.090
 LIC  C31   H313  single    0.970  0.020  1.090
 LIC  C23   H23   single    0.930  0.020  1.080
 LIC  C3    C35   aromatic  1.401  0.020  1.401
 LIC  C3    N42   aromatic  1.316  0.020  1.316
 LIC  C35   C37   aromatic  1.378  0.020  1.378
 LIC  C35   H35   single    0.930  0.020  1.080
 LIC  C37   N39   aromatic  1.326  0.020  1.326
 LIC  C37   H37   single    0.930  0.020  1.080
 LIC  N39   C41   aromatic  1.336  0.020  1.336
 LIC  C41   N42   aromatic  1.340  0.020  1.340
 LIC  C41   N36   single    1.344  0.020  1.344
 LIC  N36   C43   single    1.448  0.020  1.448
 LIC  N36   HN36  single    0.860  0.020  1.020
 LIC  C43   C45   single    1.528  0.020  1.528
 LIC  C43   C47   single    1.541  0.020  1.541
 LIC  C43   H43   single    0.970  0.020  1.090
 LIC  C45   H451  single    0.970  0.020  1.090
 LIC  C45   H452  single    0.970  0.020  1.090
 LIC  C45   H453  single    0.970  0.020  1.090
 LIC  C47   C53   single    1.528  0.020  1.528
 LIC  C47   O52   single    1.421  0.020  1.421
 LIC  C47   C51   single    1.527  0.020  1.527
 LIC  C53   H531  single    0.970  0.020  1.090
 LIC  C53   H532  single    0.970  0.020  1.090
 LIC  C53   H533  single    0.970  0.020  1.090
 LIC  O52   HO52  single    0.850  0.020  0.980
 LIC  C51   H511  single    0.970  0.020  1.090
 LIC  C51   H512  single    0.970  0.020  1.090
 LIC  C51   H513  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
 LIC  C3    N1   C2    118.49  3.000
 LIC  C3    N1   C1    121.09  3.000
 LIC  C2    N1   C1    120.35  3.000
 LIC  H72   C7   H71   106.88  3.000
 LIC  H72   C7   N5    108.53  3.000
 LIC  H71   C7   N5    109.90  3.000
 LIC  H72   C7   C9    111.22  3.000
 LIC  H71   C7   C9    108.96  3.000
 LIC  N5    C7   C9    111.26  3.000
 LIC  H13   C13  C9    118.71  3.000
 LIC  H13   C13  C14   119.71  3.000
 LIC  C9    C13  C14   121.58  3.000
 LIC  H15   C15  C11   120.44  3.000
 LIC  H15   C15  C12   120.18  3.000
 LIC  C11   C15  C12   119.38  3.000
 LIC  O30   C21  C25   116.20  3.000
 LIC  O30   C21  C24   124.41  3.000
 LIC  C25   C21  C24   119.39  3.000
 LIC  H22   C22  C25   119.73  3.000
 LIC  H22   C22  C2    119.84  3.000
 LIC  C25   C22  C2    120.42  3.000
 LIC  H24   C24  C23   118.72  3.000
 LIC  H24   C24  C21   121.51  3.000
 LIC  C23   C24  C21   119.77  3.000
 LIC  C9    C12  CL16  119.79  3.000
 LIC  C9    C12  C15   121.94  3.000
 LIC  CL16  C12  C15   118.26  3.000
 LIC  H11   C11  C14   120.53  3.000
 LIC  H11   C11  C15   119.49  3.000
 LIC  C14   C11  C15   119.98  3.000
 LIC  H14   C14  C11   120.32  3.000
 LIC  H14   C14  C13   119.98  3.000
 LIC  C11   C14  C13   119.71  3.000
 LIC  C12   C9   C13   117.42  3.000
 LIC  C12   C9   C7    122.51  3.000
 LIC  C13   C9   C7    120.06  3.000
 LIC  O4    C1   N5    124.08  3.000
 LIC  O4    C1   N1    122.35  3.000
 LIC  N5    C1   N1    113.56  3.000
 LIC  C23   C2   C22   119.27  3.000
 LIC  C23   C2   N1    120.20  3.000
 LIC  C22   C2   N1    120.52  3.000
 LIC  H25   C25  C22   120.13  3.000
 LIC  H25   C25  C21   119.56  3.000
 LIC  C22   C25  C21   120.32  3.000
 LIC  H313  C31  H312  108.91  3.000
 LIC  H313  C31  H311  108.84  3.000
 LIC  H312  C31  H311  108.77  3.000
 LIC  H313  C31  O30   111.80  3.000
 LIC  H312  C31  O30   106.49  3.000
 LIC  H311  C31  O30   111.92  3.000
 LIC  H23   C23  C2    119.87  3.000
 LIC  H23   C23  C24   119.31  3.000
 LIC  C2    C23  C24   120.82  3.000
 LIC  N42   C3   C35   121.84  3.000
 LIC  N42   C3   N1    117.91  3.000
 LIC  C35   C3   N1    120.22  3.000
 LIC  H35   C35  C37   121.43  3.000
 LIC  H35   C35  C3    123.14  3.000
 LIC  C37   C35  C3    115.43  3.000
 LIC  H37   C37  N39   116.21  3.000
 LIC  H37   C37  C35   119.75  3.000
 LIC  N39   C37  C35   124.04  3.000
 LIC  C41   N39  C37   115.58  3.000
 LIC  N36   C41  N42   115.95  3.000
 LIC  N36   C41  N39   118.49  3.000
 LIC  N42   C41  N39   125.55  3.000
 LIC  C41   N42  C3    117.55  3.000
 LIC  HN36  N36  C43   117.75  3.000
 LIC  HN36  N36  C41   116.30  3.000
 LIC  C43   N36  C41   124.70  3.000
 LIC  H43   C43  C47   106.78  3.000
 LIC  H43   C43  C45   108.32  3.000
 LIC  C47   C43  C45   114.06  3.000
 LIC  H43   C43  N36   107.57  3.000
 LIC  C47   C43  N36   108.88  3.000
 LIC  C45   C43  N36   110.96  3.000
 LIC  H453  C45  H452  107.27  3.000
 LIC  H453  C45  H451  108.21  3.000
 LIC  H452  C45  H451  108.29  3.000
 LIC  H453  C45  C43   109.68  3.000
 LIC  H452  C45  C43   111.69  3.000
 LIC  H451  C45  C43   111.54  3.000
 LIC  C51   C47  O52   110.44  3.000
 LIC  C51   C47  C53   109.33  3.000
 LIC  O52   C47  C53   110.27  3.000
 LIC  C51   C47  C43   110.54  3.000
 LIC  O52   C47  C43   106.00  3.000
 LIC  C53   C47  C43   110.23  3.000
 LIC  H533  C53  H532  107.90  3.000
 LIC  H533  C53  H531  108.02  3.000
 LIC  H532  C53  H531  107.31  3.000
 LIC  H533  C53  C47   111.94  3.000
 LIC  H532  C53  C47   110.43  3.000
 LIC  H531  C53  C47   111.06  3.000
 LIC  HO52  O52  C47   108.50  3.000
 LIC  H513  C51  H512  107.42  3.000
 LIC  H513  C51  H511  108.14  3.000
 LIC  H512  C51  H511  107.71  3.000
 LIC  H513  C51  C47   111.23  3.000
 LIC  H512  C51  C47   110.30  3.000
 LIC  H511  C51  C47   111.87  3.000
 LIC  C31   O30  C21   118.64  3.000
 LIC  HN5   N5   C1    119.71  3.000
 LIC  HN5   N5   C7    116.77  3.000
 LIC  C1    N5   C7    123.49  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
 LIC  CONST_01  C15   C11  C14  C13      0.00   0.0  0
 LIC  CONST_02  C15   C12  C9   C13      0.00   0.0  0
 LIC  CONST_03  C2    C23  C24  C21      0.00   0.0  0
 LIC  CONST_04  C2    C22  C25  C21      0.00   0.0  0
 LIC  CONST_05  C24   C23  C2   C22      0.00   0.0  0
 LIC  CONST_06  C24   C21  C25  C22      0.00   0.0  0
 LIC  CONST_07  C14   C11  C15  C12      0.00   0.0  0
 LIC  CONST_08  C14   C13  C9   C12      0.00   0.0  0
 LIC  CONST_09  C9    C12  C15  C11      0.00   0.0  0
 LIC  CONST_10  C9    C13  C14  C11      0.00   0.0  0
 LIC  CONST_11  C23   C24  C21  C25      0.00   0.0  0
 LIC  CONST_12  C23   C2   C22  C25      0.00   0.0  0
 LIC  CONST_13  N39   C37  C35  C3       0.00   0.0  0
 LIC  CONST_14  N39   C41  N42  C3       0.00   0.0  0
 LIC  CONST_15  C41   N42  C3   C35      0.00   0.0  0
 LIC  CONST_16  C41   N39  C37  C35      0.00   0.0  0
 LIC  CONST_17  N42   C3   C35  C37      0.00   0.0  0
 LIC  CONST_18  N42   C41  N39  C37      0.00   0.0  0
 LIC  CONST_19  C25   C22  C2   N1     180.00   0.0  0
 LIC  CONST_20  C24   C23  C2   N1     180.00   0.0  0
 LIC  CONST_21  C37   C35  C3   N1     180.00   0.0  0
 LIC  CONST_22  C41   N42  C3   N1     180.00   0.0  0
 LIC  CONST_23  C14   C13  C9   C7     180.00   0.0  0
 LIC  CONST_24  C15   C12  C9   C7     180.00   0.0  0
 LIC  CONST_25  CL16  C12  C9   C13    180.00   0.0  0
 LIC  CONST_26  O30   C21  C25  C22    180.00   0.0  0
 LIC  CONST_27  C11   C15  C12  CL16   180.00   0.0  0
 LIC  CONST_28  C23   C24  C21  O30    180.00   0.0  0
 LIC  CONST_29  N36   C41  N42  C3     180.00   0.0  0
 LIC  CONST_30  N36   C41  N39  C37    180.00   0.0  0
 LIC  CONST_31  H11   C11  C14  C13    180.00   0.0  0
 LIC  CONST_32  H14   C14  C11  C15    180.00   0.0  0
 LIC  CONST_33  H23   C23  C24  C21    180.00   0.0  0
 LIC  CONST_34  H22   C22  C25  C21    180.00   0.0  0
 LIC  CONST_35  H25   C25  C21  C24    180.00   0.0  0
 LIC  CONST_36  H13   C13  C9   C12    180.00   0.0  0
 LIC  CONST_37  H15   C15  C11  C14    180.00   0.0  0
 LIC  CONST_38  H24   C24  C23  C2     180.00   0.0  0
 LIC  CONST_39  H37   C37  C35  C3     180.00   0.0  0
 LIC  CONST_40  H35   C35  C37  N39    180.00   0.0  0
 LIC  CONST_41  C43   N36  C41  N39      0.00   0.0  0
 LIC  CONST_42  C43   N36  C41  N42    180.00   0.0  0
 LIC  CONST_43  HN36  N36  C41  N39    180.00   0.0  0
 LIC  CONST_48  O4    C1   N5   C7       0.00   0.0  0
 LIC  CONST_49  C7    N5   C1   N1     180.00   0.0  0
 LIC  CONST_50  HN5   N5   C1   O4     180.00   0.0  0
 LIC  Var_01    C3    N1   C2   C22   -112.61  30.0  2
 LIC  Var_02    C35   C3   N1   C2      26.14  30.0  2
 LIC  Var_03    N5    C7   C9   C13    108.90  30.0  2
 LIC  Var_04    C1    N5   C7   C9     125.83  30.0  3
 LIC  Var_05    H311  C31  O30  C21     61.77  30.0  3
 LIC  Var_06    H531  C53  C47  C43     61.57  30.0  3
 LIC  Var_07    H511  C51  C47  C43     65.94  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
 LIC  chir_01  C43  N36  C45  C47  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
 LIC  plan-1  C7    0.020
 LIC  plan-1  C13   0.020
 LIC  plan-1  C15   0.020
 LIC  plan-1  C12   0.020
 LIC  plan-1  C11   0.020
 LIC  plan-1  C14   0.020
 LIC  plan-1  C9    0.020
 LIC  plan-1  H15   0.020
 LIC  plan-1  H11   0.020
 LIC  plan-1  H14   0.020
 LIC  plan-1  H13   0.020
 LIC  plan-1  CL16  0.020
 LIC  plan-2  N1    0.020
 LIC  plan-2  C21   0.020
 LIC  plan-2  C22   0.020
 LIC  plan-2  C24   0.020
 LIC  plan-2  C2    0.020
 LIC  plan-2  C25   0.020
 LIC  plan-2  C23   0.020
 LIC  plan-2  H22   0.020
 LIC  plan-2  H24   0.020
 LIC  plan-2  H25   0.020
 LIC  plan-2  H23   0.020
 LIC  plan-2  O30   0.020
 LIC  plan-3  N1    0.020
 LIC  plan-3  C3    0.020
 LIC  plan-3  C35   0.020
 LIC  plan-3  C37   0.020
 LIC  plan-3  N39   0.020
 LIC  plan-3  C41   0.020
 LIC  plan-3  N42   0.020
 LIC  plan-3  N36   0.020
 LIC  plan-3  H35   0.020
 LIC  plan-3  H37   0.020
 LIC  plan-4  N1    0.020
 LIC  plan-4  C7    0.020
 LIC  plan-4  C1    0.020
 LIC  plan-4  O4    0.020
 LIC  plan-4  C2    0.020
 LIC  plan-4  C3    0.020
 LIC  plan-4  N5    0.020
 LIC  plan-4  HN5   0.020
 LIC  plan-5  C41   0.020
 LIC  plan-5  N36   0.020
 LIC  plan-5  C43   0.020
 LIC  plan-5  HN36  0.020

