# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:15:42 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 1-methyl-3-[3-(2-methylpyrimidin-4-yl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)Nc1cccc(c1)c2ccnc(C)n2
#
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
 GUV  GUV  1-methyl-3-[3-(2-methylpyrimidin-4-yl)phenyl]urea  ligand  32  18  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GUV
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
 GUV  N1   N  N     0  -0.416   4.3930  -1.0276   0.1155
 GUV  N3   N  NH1   0  -0.786  -2.8249   0.4443  -0.3109
 GUV  C4   C  CR16  0  -0.359   3.2810   1.0527   0.4222
 GUV  C5   C  CR6   0   0.278   2.0929   0.4446   0.0240
 GUV  C6   C  CR6   0   0.071   0.8094   1.1764  -0.0516
 GUV  C7   C  CR16  0  -0.347   0.7760   2.5699  -0.0515
 GUV  C8   C  CR16  0  -0.227  -0.4434   3.2227  -0.1366
 GUV  C10  C  CR6   0   0.404  -1.6059   1.1090  -0.1973
 GUV  C13  C  CH3   0  -0.508  -4.8870  -2.4815   0.3584
 GUV  C2   C  CR6   0   0.349   3.2148  -1.5310  -0.2411
 GUV  C3   C  CR16  0  -0.033   4.4097   0.2579   0.4456
 GUV  N2   N  N     0  -0.443   2.0798  -0.8466  -0.2992
 GUV  C9   C  CR16  0  -0.344  -1.6254   2.5060  -0.1995
 GUV  C11  C  CR16  0  -0.345  -0.3788   0.4519  -0.1378
 GUV  C12  C  C     0   0.721  -3.1301  -0.8063   0.1813
 GUV  O1   O  O     0  -0.520  -2.3310  -1.5071   0.7850
 GUV  N4   N  NH1   0  -0.669  -4.4038  -1.1864  -0.0542
 GUV  H1   H  HNH1  0   0.406  -3.6006   1.0226  -0.5963
 GUV  H2   H  HCR6  0   0.277   3.3389   2.0902   0.7141
 GUV  H3   H  HCR6  0   0.255   1.6840   3.1555  -0.0079
 GUV  H4   H  HCR6  0   0.264  -0.4762   4.3039  -0.1476
 GUV  H5   H  HCH3  0   0.238  -4.7652  -2.6295   1.4309
 GUV  H6   H  HCH3  0   0.249  -5.9479  -2.5351   0.1307
 GUV  H7   H  HCH3  0   0.232  -4.3848  -3.3007  -0.1598
 GUV  H8   H  HCH3  0   0.261   2.8199  -3.5569   0.2889
 GUV  H9   H  HCH3  0   0.253   2.4396  -3.1700  -1.3822
 GUV  H10  H  HCH3  0   0.250   4.1301  -3.3639  -0.8713
 GUV  H11  H  HCR6  0   0.278   5.3657   0.6734   0.7443
 GUV  H12  H  HCR6  0   0.271  -2.5710   3.0324  -0.2533
 GUV  H13  H  HCR6  0   0.269  -0.3282  -0.6242  -0.1643
 GUV  H14  H  HNH1  0   0.402  -4.9829  -0.6453  -0.6738
 GUV  C1   C  CH3   0  -0.731   3.1527  -2.9859  -0.5809

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
 GUV  C13  N4   single    1.443  0.020  1.443
 GUV  C3   N1   aromatic  1.327  0.020  1.327
 GUV  C3   C4   aromatic  1.381  0.020  1.381
 GUV  N1   C2   aromatic  1.330  0.020  1.330
 GUV  C4   C5   aromatic  1.393  0.020  1.393
 GUV  O1   C12  double    1.222  0.020  1.222
 GUV  N4   C12  single    1.350  0.020  1.350
 GUV  C2   C1   single    1.495  0.020  1.495
 GUV  C2   N2   aromatic  1.327  0.020  1.327
 GUV  C12  N3   single    1.378  0.020  1.378
 GUV  C5   N2   aromatic  1.331  0.020  1.331
 GUV  C5   C6   single    1.479  0.020  1.479
 GUV  C11  C6   aromatic  1.394  0.020  1.394
 GUV  C11  C10  aromatic  1.393  0.020  1.393
 GUV  N3   C10  single    1.393  0.020  1.393
 GUV  C6   C7   aromatic  1.394  0.020  1.394
 GUV  C10  C9   aromatic  1.397  0.020  1.397
 GUV  C7   C8   aromatic  1.386  0.020  1.386
 GUV  C9   C8   aromatic  1.384  0.020  1.384
 GUV  N3   H1   single    0.860  0.020  1.020
 GUV  C4   H2   single    0.930  0.020  1.080
 GUV  C7   H3   single    0.930  0.020  1.080
 GUV  C8   H4   single    0.930  0.020  1.080
 GUV  C13  H5   single    0.970  0.020  1.090
 GUV  C13  H6   single    0.970  0.020  1.090
 GUV  C13  H7   single    0.970  0.020  1.090
 GUV  C1   H8   single    0.970  0.020  1.090
 GUV  C1   H9   single    0.970  0.020  1.090
 GUV  C1   H10  single    0.970  0.020  1.090
 GUV  C3   H11  single    0.930  0.020  1.080
 GUV  C9   H12  single    0.930  0.020  1.080
 GUV  C11  H13  single    0.930  0.020  1.080
 GUV  N4   H14  single    0.860  0.020  1.020

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
 GUV  C3   N1   C2   116.39  3.000
 GUV  H1   N3   C12  116.80  3.000
 GUV  H1   N3   C10  114.99  3.000
 GUV  C12  N3   C10  126.70  3.000
 GUV  H2   C4   C3   120.32  3.000
 GUV  H2   C4   C5   122.87  3.000
 GUV  C3   C4   C5   116.80  3.000
 GUV  N2   C5   C6   117.32  3.000
 GUV  C6   C5   C4   122.59  3.000
 GUV  N2   C5   C4   120.09  3.000
 GUV  C11  C6   C7   119.94  3.000
 GUV  C7   C6   C5   121.02  3.000
 GUV  C11  C6   C5   119.04  3.000
 GUV  H3   C7   C8   119.09  3.000
 GUV  H3   C7   C6   121.41  3.000
 GUV  C8   C7   C6   119.48  3.000
 GUV  H4   C8   C9   119.43  3.000
 GUV  H4   C8   C7   119.88  3.000
 GUV  C9   C8   C7   120.69  3.000
 GUV  C11  C10  C9   118.95  3.000
 GUV  C9   C10  N3   117.69  3.000
 GUV  C11  C10  N3   123.31  3.000
 GUV  H7   C13  H6   108.22  3.000
 GUV  H7   C13  H5   108.30  3.000
 GUV  H6   C13  H5   107.99  3.000
 GUV  H7   C13  N4   112.57  3.000
 GUV  H6   C13  N4   108.14  3.000
 GUV  H5   C13  N4   111.47  3.000
 GUV  N2   C2   C1   117.16  3.000
 GUV  N2   C2   N1   125.06  3.000
 GUV  C1   C2   N1   117.78  3.000
 GUV  H11  C3   C4   120.32  3.000
 GUV  H11  C3   N1   116.79  3.000
 GUV  C4   C3   N1   122.89  3.000
 GUV  C2   N2   C5   118.78  3.000
 GUV  H12  C9   C10  119.87  3.000
 GUV  H12  C9   C8   119.74  3.000
 GUV  C10  C9   C8   120.39  3.000
 GUV  H13  C11  C10  120.75  3.000
 GUV  H13  C11  C6   118.71  3.000
 GUV  C10  C11  C6   120.53  3.000
 GUV  N4   C12  O1   122.79  3.000
 GUV  N4   C12  N3   113.71  3.000
 GUV  O1   C12  N3   123.49  3.000
 GUV  H14  N4   C12  119.94  3.000
 GUV  H14  N4   C13  117.79  3.000
 GUV  C12  N4   C13  121.26  3.000
 GUV  H10  C1   H9   109.48  3.000
 GUV  H10  C1   H8   107.74  3.000
 GUV  H9   C1   H8   107.34  3.000
 GUV  H10  C1   C2   111.19  3.000
 GUV  H9   C1   C2   111.05  3.000
 GUV  H8   C1   C2   109.90  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
 GUV  CONST_01  C5   C4   C3   N1     0.00   0.0  0
 GUV  CONST_02  C5   N2   C2   N1     0.00   0.0  0
 GUV  CONST_03  C2   N1   C3   C4     0.00   0.0  0
 GUV  CONST_04  C2   N2   C5   C4     0.00   0.0  0
 GUV  CONST_07  C10  C11  C6   C5   180.00   0.0  0
 GUV  CONST_08  C8   C7   C6   C5   180.00   0.0  0
 GUV  CONST_09  C3   C4   C5   C6   180.00   0.0  0
 GUV  CONST_10  C2   N2   C5   C6   180.00   0.0  0
 GUV  CONST_11  C9   C10  C11  C6     0.00   0.0  0
 GUV  CONST_12  C9   C8   C7   C6     0.00   0.0  0
 GUV  CONST_14  C10  C11  C6   C7     0.00   0.0  0
 GUV  CONST_15  C10  C9   C8   C7     0.00   0.0  0
 GUV  CONST_16  C11  C6   C7   C8     0.00   0.0  0
 GUV  CONST_17  C11  C10  C9   C8     0.00   0.0  0
 GUV  CONST_18  N2   C2   N1   C3     0.00   0.0  0
 GUV  CONST_19  N2   C5   C4   C3     0.00   0.0  0
 GUV  CONST_21  C6   C11  C10  N3   180.00   0.0  0
 GUV  CONST_22  C8   C9   C10  N3   180.00   0.0  0
 GUV  CONST_23  C1   C2   N2   C5   180.00   0.0  0
 GUV  CONST_24  C3   N1   C2   C1   180.00   0.0  0
 GUV  CONST_25  H2   C4   C3   N1   180.00   0.0  0
 GUV  CONST_26  H11  C3   C4   C5   180.00   0.0  0
 GUV  CONST_27  H13  C11  C6   C5     0.00   0.0  0
 GUV  CONST_28  H3   C7   C6   C5     0.00   0.0  0
 GUV  CONST_29  H4   C8   C7   C6   180.00   0.0  0
 GUV  CONST_30  H12  C9   C8   C7   180.00   0.0  0
 GUV  CONST_33  H1   N3   C10  C9     0.00   0.0  0
 GUV  CONST_34  O1   C12  N3   C10    0.00   0.0  0
 GUV  CONST_35  N4   C12  N3   C10  180.00   0.0  0
 GUV  CONST_36  O1   C12  N4   C13    0.00   0.0  0
 GUV  CONST_37  C13  N4   C12  N3   180.00   0.0  0
 GUV  CONST_38  H14  N4   C12  O1   180.00   0.0  0
 GUV  Var_01    H8   C1   C2   N1    96.60  30.0  2
 GUV  Var_02    H5   C13  N4   C12   57.37  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
 GUV  plan-1  N1   0.020
 GUV  plan-1  C4   0.020
 GUV  plan-1  C5   0.020
 GUV  plan-1  C6   0.020
 GUV  plan-1  C2   0.020
 GUV  plan-1  C3   0.020
 GUV  plan-1  N2   0.020
 GUV  plan-1  H2   0.020
 GUV  plan-1  H11  0.020
 GUV  plan-1  C1   0.020
 GUV  plan-2  N3   0.020
 GUV  plan-2  C5   0.020
 GUV  plan-2  C6   0.020
 GUV  plan-2  C7   0.020
 GUV  plan-2  C8   0.020
 GUV  plan-2  C10  0.020
 GUV  plan-2  C9   0.020
 GUV  plan-2  C11  0.020
 GUV  plan-2  H3   0.020
 GUV  plan-2  H4   0.020
 GUV  plan-2  H12  0.020
 GUV  plan-2  H13  0.020
 GUV  plan-3  N3   0.020
 GUV  plan-3  C10  0.020
 GUV  plan-3  C13  0.020
 GUV  plan-3  C12  0.020
 GUV  plan-3  O1   0.020
 GUV  plan-3  N4   0.020
 GUV  plan-3  H1   0.020
 GUV  plan-3  H14  0.020

