# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:45:41 2021
#   Inital geometry file: a 98 line input string
#   Ligand name: N-(3,4-dihydroxyphenyl)-N'-[2-(3,4-dihydroxyphenyl)ethyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(CCNC(=O)Nc2ccc(O)c(O)c2)cc1O
#
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
 SNZ  SNZ  N-(3,4-dihydroxyphenyl)-N'-[2-(3,4-dihydroxyphenyl)ethyl]urea  ligand  38  22  .  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_SNZ
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
 SNZ  N    N  NH1   0  -0.786  -28.7321   7.6916  24.5818
 SNZ  C    C  CR6   0   0.272  -29.9227  10.4599  27.5167
 SNZ  O    O  OH1   0  -0.640  -30.3110  11.3590  28.4517
 SNZ  C1   C  CR16  0  -0.338  -29.2860  10.8999  26.3700
 SNZ  C10  C  CR6   0   0.274  -23.8700   6.9582  17.6437
 SNZ  C11  C  CR16  0  -0.329  -23.8507   7.9480  18.6134
 SNZ  C12  C  CR16  0  -0.320  -24.8660   8.0342  19.5576
 SNZ  C13  C  CR16  0  -0.470  -29.7237   8.2002  26.6944
 SNZ  C14  C  CR6   0   0.279  -30.1494   9.0870  27.6683
 SNZ  C2   C  CR16  0  -0.321  -28.8717  10.0174  25.3785
 SNZ  C3   C  CR6   0   0.362  -29.0812   8.6516  25.5388
 SNZ  C4   C  C     0   0.723  -27.6627   7.7466  23.7233
 SNZ  C5   C  CH2   0  -0.277  -26.5270   6.5569  21.9148
 SNZ  C6   C  CH2   0  -0.519  -26.9946   7.1990  20.6038
 SNZ  C7   C  CR6   0   0.113  -25.9231   7.1317  19.5525
 SNZ  C8   C  CR16  0  -0.431  -25.9357   6.1339  18.5790
 SNZ  C9   C  CR6   0   0.273  -24.9282   6.0415  17.6311
 SNZ  N1   N  NH1   0  -0.677  -27.5062   6.6280  22.9726
 SNZ  O1   O  O     0  -0.524  -26.9091   8.7072  23.6473
 SNZ  O2   O  OH1   0  -0.647  -24.8912   5.0986  16.6602
 SNZ  O4   O  OH1   0  -0.646  -30.7818   8.7048  28.8005
 SNZ  H1   H  HNH1  0   0.404  -29.2006   6.8034  24.6747
 SNZ  H2   H  HOH1  0   0.470  -30.7473  10.9134  29.1867
 SNZ  H3   H  HCR6  0   0.264  -29.1162  11.9618  26.2396
 SNZ  H4   H  HCR6  0   0.261  -23.0332   8.6586  18.6223
 SNZ  H5   H  HCR6  0   0.245  -24.8291   8.8213  20.3014
 SNZ  H6   H  HCR6  0   0.280  -29.8932   7.1375  26.8362
 SNZ  H7   H  HCR6  0   0.264  -28.4002  10.4102  24.4927
 SNZ  H8   H  HCH2  0   0.253  -26.2969   5.5042  21.7462
 SNZ  H9   H  HCH2  0   0.244  -25.6048   7.0319  22.2493
 SNZ  H10  H  HCH2  0   0.248  -27.2635   8.2403  20.7960
 SNZ  H11  H  HCH2  0   0.243  -27.8995   6.6931  20.2598
 SNZ  H12  H  HCR6  0   0.265  -26.7489   5.4150  18.5571
 SNZ  H13  H  HNH1  0   0.395  -28.2228   5.9204  22.9826
 SNZ  H14  H  HOH1  0   0.481  -25.6757   4.5403  16.6944
 SNZ  H15  H  HOH1  0   0.471  -23.0216   6.1902  16.1064
 SNZ  H16  H  HOH1  0   0.482  -30.8760   7.7466  28.8361
 SNZ  O3   O  OH1   0  -0.638  -22.8707   6.9060  16.7345

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
 SNZ  O3   C10  single    1.352  0.020  1.352
 SNZ  C10  C11  aromatic  1.386  0.020  1.386
 SNZ  C10  C9   aromatic  1.400  0.020  1.400
 SNZ  C11  C12  aromatic  1.389  0.020  1.389
 SNZ  O2   C9   single    1.354  0.020  1.354
 SNZ  C9   C8   aromatic  1.386  0.020  1.386
 SNZ  C12  C7   aromatic  1.390  0.020  1.390
 SNZ  C8   C7   aromatic  1.394  0.020  1.394
 SNZ  C7   C6   single    1.503  0.020  1.503
 SNZ  C6   C5   single    1.533  0.020  1.533
 SNZ  C5   N1   single    1.443  0.020  1.443
 SNZ  N1   C4   single    1.356  0.020  1.356
 SNZ  C1   C2   aromatic  1.391  0.020  1.391
 SNZ  C1   C    aromatic  1.383  0.020  1.383
 SNZ  C2   C3   aromatic  1.391  0.020  1.391
 SNZ  C4   O1   double    1.223  0.020  1.223
 SNZ  C4   N    single    1.372  0.020  1.372
 SNZ  O    C    single    1.354  0.020  1.354
 SNZ  C    C14  aromatic  1.400  0.020  1.400
 SNZ  N    C3   single    1.400  0.020  1.400
 SNZ  C3   C13  aromatic  1.397  0.020  1.397
 SNZ  C14  C13  aromatic  1.384  0.020  1.384
 SNZ  C14  O4   single    1.352  0.020  1.352
 SNZ  N    H1   single    0.860  0.020  1.020
 SNZ  O    H2   single    0.850  0.020  0.980
 SNZ  C1   H3   single    0.930  0.020  1.080
 SNZ  C11  H4   single    0.930  0.020  1.080
 SNZ  C12  H5   single    0.930  0.020  1.080
 SNZ  C13  H6   single    0.930  0.020  1.080
 SNZ  C2   H7   single    0.930  0.020  1.080
 SNZ  C5   H8   single    0.970  0.020  1.090
 SNZ  C5   H9   single    0.970  0.020  1.090
 SNZ  C6   H10  single    0.970  0.020  1.090
 SNZ  C6   H11  single    0.970  0.020  1.090
 SNZ  C8   H12  single    0.930  0.020  1.080
 SNZ  N1   H13  single    0.860  0.020  1.020
 SNZ  O2   H14  single    0.850  0.020  0.980
 SNZ  O3   H15  single    0.850  0.020  0.980
 SNZ  O4   H16  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
 SNZ  H1   N    C4   117.06  3.000
 SNZ  H1   N    C3   115.16  3.000
 SNZ  C4   N    C3   126.48  3.000
 SNZ  C14  C    C1   118.44  3.000
 SNZ  C14  C    O    122.01  3.000
 SNZ  C1   C    O    119.55  3.000
 SNZ  H2   O    C    110.45  3.000
 SNZ  H3   C1   C2   119.31  3.000
 SNZ  H3   C1   C    118.93  3.000
 SNZ  C2   C1   C    121.76  3.000
 SNZ  O3   C10  C9   121.82  3.000
 SNZ  C9   C10  C11  118.98  3.000
 SNZ  O3   C10  C11  119.19  3.000
 SNZ  H4   C11  C12  120.36  3.000
 SNZ  H4   C11  C10  119.00  3.000
 SNZ  C12  C11  C10  120.64  3.000
 SNZ  H5   C12  C7   120.01  3.000
 SNZ  H5   C12  C11  119.12  3.000
 SNZ  C7   C12  C11  120.87  3.000
 SNZ  H6   C13  C3   119.75  3.000
 SNZ  H6   C13  C14  119.16  3.000
 SNZ  C3   C13  C14  121.09  3.000
 SNZ  O4   C14  C13  123.50  3.000
 SNZ  O4   C14  C    116.34  3.000
 SNZ  C13  C14  C    120.16  3.000
 SNZ  H7   C2   C3   121.23  3.000
 SNZ  H7   C2   C1   119.03  3.000
 SNZ  C3   C2   C1   119.74  3.000
 SNZ  C2   C3   C13  118.80  3.000
 SNZ  C13  C3   N    117.30  3.000
 SNZ  C2   C3   N    123.85  3.000
 SNZ  O1   C4   N1   122.83  3.000
 SNZ  O1   C4   N    123.39  3.000
 SNZ  N1   C4   N    113.77  3.000
 SNZ  H9   C5   H8   106.83  3.000
 SNZ  H9   C5   N1   109.13  3.000
 SNZ  H8   C5   N1   107.70  3.000
 SNZ  H9   C5   C6   109.76  3.000
 SNZ  H8   C5   C6   109.66  3.000
 SNZ  N1   C5   C6   113.53  3.000
 SNZ  H11  C6   H10  107.03  3.000
 SNZ  H11  C6   C7   110.46  3.000
 SNZ  H10  C6   C7   109.96  3.000
 SNZ  H11  C6   C5   109.15  3.000
 SNZ  H10  C6   C5   108.90  3.000
 SNZ  C7   C6   C5   111.23  3.000
 SNZ  C8   C7   C6   120.94  3.000
 SNZ  C6   C7   C12  120.70  3.000
 SNZ  C8   C7   C12  118.31  3.000
 SNZ  H12  C8   C9   119.11  3.000
 SNZ  H12  C8   C7   119.66  3.000
 SNZ  C9   C8   C7   121.23  3.000
 SNZ  O2   C9   C8   123.82  3.000
 SNZ  C8   C9   C10  119.97  3.000
 SNZ  O2   C9   C10  116.22  3.000
 SNZ  H13  N1   C5   117.09  3.000
 SNZ  H13  N1   C4   119.47  3.000
 SNZ  C5   N1   C4   121.65  3.000
 SNZ  H14  O2   C9   110.85  3.000
 SNZ  H16  O4   C14  110.97  3.000
 SNZ  H15  O3   C10  110.55  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
 SNZ  CONST_01  C3   C2   C1   C      0.00   0.0  0
 SNZ  CONST_02  C3   C13  C14  C      0.00   0.0  0
 SNZ  CONST_03  C13  C3   C2   C1     0.00   0.0  0
 SNZ  CONST_04  C13  C14  C    C1     0.00   0.0  0
 SNZ  CONST_05  C7   C12  C11  C10    0.00   0.0  0
 SNZ  CONST_06  C7   C8   C9   C10    0.00   0.0  0
 SNZ  CONST_07  C8   C9   C10  C11    0.00   0.0  0
 SNZ  CONST_08  C8   C7   C12  C11    0.00   0.0  0
 SNZ  CONST_09  C9   C10  C11  C12    0.00   0.0  0
 SNZ  CONST_10  C9   C8   C7   C12    0.00   0.0  0
 SNZ  CONST_11  C2   C1   C    C14    0.00   0.0  0
 SNZ  CONST_12  C2   C3   C13  C14    0.00   0.0  0
 SNZ  CONST_13  C1   C2   C3   N    180.00   0.0  0
 SNZ  CONST_14  C14  C13  C3   N    180.00   0.0  0
 SNZ  CONST_15  C2   C1   C    O    180.00   0.0  0
 SNZ  CONST_16  C13  C14  C    O    180.00   0.0  0
 SNZ  CONST_17  O4   C14  C    C1   180.00   0.0  0
 SNZ  CONST_18  O2   C9   C10  C11  180.00   0.0  0
 SNZ  CONST_19  C6   C7   C12  C11  180.00   0.0  0
 SNZ  CONST_20  O3   C10  C11  C12  180.00   0.0  0
 SNZ  CONST_21  O4   C14  C13  C3   180.00   0.0  0
 SNZ  CONST_22  C9   C8   C7   C6   180.00   0.0  0
 SNZ  CONST_23  O2   C9   C8   C7   180.00   0.0  0
 SNZ  CONST_24  O3   C10  C9   C8   180.00   0.0  0
 SNZ  CONST_25  H7   C2   C1   C    180.00   0.0  0
 SNZ  CONST_26  H6   C13  C14  C    180.00   0.0  0
 SNZ  CONST_27  H5   C12  C11  C10  180.00   0.0  0
 SNZ  CONST_28  H12  C8   C9   C10  180.00   0.0  0
 SNZ  CONST_29  H3   C1   C    C14  180.00   0.0  0
 SNZ  CONST_30  H4   C11  C12  C7   180.00   0.0  0
 SNZ  CONST_34  O1   C4   N    C3     0.00   0.0  0
 SNZ  CONST_35  N1   C4   N    C3   180.00   0.0  0
 SNZ  CONST_36  O1   C4   N1   C5     0.00   0.0  0
 SNZ  CONST_37  C5   N1   C4   N    180.00   0.0  0
 SNZ  CONST_38  H13  N1   C4   O1   180.00   0.0  0
 SNZ  Var_01    C5   C6   C7   C12  -79.36  30.0  2
 SNZ  Var_02    N1   C5   C6   C7   178.35  30.0  3
 SNZ  Var_03    C6   C5   N1   C4   -81.40  30.0  1

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
 SNZ  plan-1  N    0.020
 SNZ  plan-1  C    0.020
 SNZ  plan-1  O    0.020
 SNZ  plan-1  C1   0.020
 SNZ  plan-1  C13  0.020
 SNZ  plan-1  C14  0.020
 SNZ  plan-1  C2   0.020
 SNZ  plan-1  C3   0.020
 SNZ  plan-1  O4   0.020
 SNZ  plan-1  H3   0.020
 SNZ  plan-1  H6   0.020
 SNZ  plan-1  H7   0.020
 SNZ  plan-2  C10  0.020
 SNZ  plan-2  C11  0.020
 SNZ  plan-2  C12  0.020
 SNZ  plan-2  C6   0.020
 SNZ  plan-2  C7   0.020
 SNZ  plan-2  C8   0.020
 SNZ  plan-2  C9   0.020
 SNZ  plan-2  O2   0.020
 SNZ  plan-2  H4   0.020
 SNZ  plan-2  H5   0.020
 SNZ  plan-2  H12  0.020
 SNZ  plan-2  O3   0.020
 SNZ  plan-3  N    0.020
 SNZ  plan-3  C3   0.020
 SNZ  plan-3  C4   0.020
 SNZ  plan-3  C5   0.020
 SNZ  plan-3  N1   0.020
 SNZ  plan-3  O1   0.020
 SNZ  plan-3  H1   0.020
 SNZ  plan-3  H13  0.020

