# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 21 14:42:49 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: N-[2,6-di(propan-2-yl)phenyl]-N'-(N-ethylcarbamimidoyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=N)NC(=O)Nc1c(cccc1C(C)C)C(C)C
#
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
 0UD  0UD  N-[2,6-di(propan-2-yl)phenyl]-N'-(N-ethylcarbamimidoyl)urea  ligand  47  21  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0UD
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
 0UD  C01  C  CH3   0  -0.641  12.9587  30.9341  13.1015
 0UD  C02  C  CH1   0  -0.332  12.2940  29.8310  12.2764
 0UD  C03  C  CH3   0  -0.643  12.4546  30.0956  10.7788
 0UD  C04  C  CR6   0   0.208  12.8283  28.4663  12.6534
 0UD  C05  C  CR16  0  -0.362  14.1921  28.2145  12.5168
 0UD  C06  C  CR16  0  -0.208  14.7284  26.9915  12.8752
 0UD  C07  C  CR16  0  -0.372  13.9037  25.9992  13.3809
 0UD  C08  C  CR6   0   0.179  12.5334  26.1988  13.5241
 0UD  C09  C  CH1   0  -0.310  11.7158  25.0610  14.1074
 0UD  C10  C  CH3   0  -0.653  10.6252  24.5180  13.1831
 0UD  C11  C  CH3   0  -0.647  11.1580  25.3804  15.4954
 0UD  C12  C  CR6   0   0.138  12.0078  27.4425  13.1444
 0UD  C14  C  C     0   0.739   9.7771  27.6504  12.2188
 0UD  C16  C  C     0   0.617   7.3959  28.0235  11.6418
 0UD  C18  C  CH2   0  -0.253   5.0811  28.7695  11.4721
 0UD  C19  C  CH3   0  -0.686   3.9516  29.2264  12.3769
 0UD  N13  N  NH1   0  -0.778  10.6149  27.6804  13.2863
 0UD  N15  N  NH1   0  -0.770   8.4736  27.9601  12.5352
 0UD  N17  N  NH1   0  -0.665   6.2814  28.5370  12.2470
 0UD  N20  N  N     0  -0.693   7.3727  27.6344  10.4305
 0UD  O21  O  O     0  -0.494  10.1519  27.3641  11.0934
 0UD  H1   H  HCH3  0   0.230  12.8328  30.7624  14.1711
 0UD  H2   H  HCH3  0   0.220  14.0278  31.0081  12.8964
 0UD  H3   H  HCH3  0   0.229  12.5124  31.9011  12.8638
 0UD  H4   H  HCH1  0   0.240  11.2281  29.8673  12.5049
 0UD  H5   H  HCH3  0   0.227  12.0128  31.0575  10.5137
 0UD  H6   H  HCH3  0   0.218  13.5061  30.1248  10.4869
 0UD  H7   H  HCH3  0   0.233  11.9613  29.3251  10.1870
 0UD  H8   H  HCR6  0   0.249  14.8453  28.9881  12.1310
 0UD  H9   H  HCR6  0   0.250  15.7902  26.8108  12.7658
 0UD  H10  H  HCR6  0   0.246  14.3301  25.0460  13.6700
 0UD  H11  H  HCH1  0   0.242  12.4300  24.2442  14.2474
 0UD  H12  H  HCH3  0   0.232  10.2884  23.5473  13.5507
 0UD  H13  H  HCH3  0   0.225   9.7510  25.1656  13.1456
 0UD  H14  H  HCH3  0   0.228  10.9913  24.3763  12.1660
 0UD  H15  H  HCH3  0   0.230  11.9391  25.7415  16.1652
 0UD  H16  H  HCH3  0   0.217  10.3680  26.1303  15.4604
 0UD  H17  H  HCH3  0   0.231  10.7292  24.4807  15.9398
 0UD  H18  H  HCH2  0   0.214   5.2510  29.5098  10.6819
 0UD  H19  H  HCH2  0   0.230   4.8045  27.8411  10.9719
 0UD  H20  H  HCH3  0   0.237   3.0478  29.3943  11.7927
 0UD  H21  H  HCH3  0   0.229   3.7285  28.4790  13.1385
 0UD  H22  H  HCH3  0   0.227   4.1972  30.1626  12.8809
 0UD  H23  H  HNH1  0   0.406  10.2775  27.9961  14.1833
 0UD  H24  H  HNH1  0   0.410   8.2576  28.1298  13.5066
 0UD  H25  H  HNH1  0   0.383   6.4378  29.2036  12.9887
 0UD  H26  H  H     0   0.343   8.2518  27.2114  10.1674

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
 0UD  N20  C16  double    1.273  0.020  1.273
 0UD  C03  C02  single    1.529  0.020  1.529
 0UD  O21  C14  double    1.220  0.020  1.220
 0UD  C18  N17  single    1.447  0.020  1.447
 0UD  C18  C19  single    1.518  0.020  1.518
 0UD  C16  N17  single    1.368  0.020  1.368
 0UD  C16  N15  single    1.401  0.020  1.401
 0UD  C02  C04  single    1.513  0.020  1.513
 0UD  C02  C01  single    1.529  0.020  1.529
 0UD  C14  N15  single    1.377  0.020  1.377
 0UD  C14  N13  single    1.357  0.020  1.357
 0UD  C05  C04  aromatic  1.394  0.020  1.394
 0UD  C05  C06  aromatic  1.383  0.020  1.383
 0UD  C04  C12  aromatic  1.401  0.020  1.401
 0UD  C06  C07  aromatic  1.386  0.020  1.386
 0UD  C12  N13  single    1.420  0.020  1.420
 0UD  C12  C08  aromatic  1.403  0.020  1.403
 0UD  C10  C09  single    1.529  0.020  1.529
 0UD  C07  C08  aromatic  1.392  0.020  1.392
 0UD  C08  C09  single    1.518  0.020  1.518
 0UD  C09  C11  single    1.530  0.020  1.530
 0UD  C01  H1   single    0.970  0.020  1.090
 0UD  C01  H2   single    0.970  0.020  1.090
 0UD  C01  H3   single    0.970  0.020  1.090
 0UD  C02  H4   single    0.970  0.020  1.090
 0UD  C03  H5   single    0.970  0.020  1.090
 0UD  C03  H6   single    0.970  0.020  1.090
 0UD  C03  H7   single    0.970  0.020  1.090
 0UD  C05  H8   single    0.930  0.020  1.080
 0UD  C06  H9   single    0.930  0.020  1.080
 0UD  C07  H10  single    0.930  0.020  1.080
 0UD  C09  H11  single    0.970  0.020  1.090
 0UD  C10  H12  single    0.970  0.020  1.090
 0UD  C10  H13  single    0.970  0.020  1.090
 0UD  C10  H14  single    0.970  0.020  1.090
 0UD  C11  H15  single    0.970  0.020  1.090
 0UD  C11  H16  single    0.970  0.020  1.090
 0UD  C11  H17  single    0.970  0.020  1.090
 0UD  C18  H18  single    0.970  0.020  1.090
 0UD  C18  H19  single    0.970  0.020  1.090
 0UD  C19  H20  single    0.970  0.020  1.090
 0UD  C19  H21  single    0.970  0.020  1.090
 0UD  C19  H22  single    0.970  0.020  1.090
 0UD  N13  H23  single    0.860  0.020  1.020
 0UD  N15  H24  single    0.860  0.020  1.020
 0UD  N17  H25  single    0.890  0.020  1.040
 0UD  N20  H26  single    0.890  0.020  1.040

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
 0UD  H3   C01  H2   107.44  3.000
 0UD  H3   C01  H1   107.82  3.000
 0UD  H2   C01  H1   107.95  3.000
 0UD  H3   C01  C02  110.12  3.000
 0UD  H2   C01  C02  111.92  3.000
 0UD  H1   C01  C02  111.43  3.000
 0UD  H4   C02  C04  108.84  3.000
 0UD  H4   C02  C03  107.58  3.000
 0UD  C04  C02  C03  111.28  3.000
 0UD  H4   C02  C01  106.72  3.000
 0UD  C04  C02  C01  111.26  3.000
 0UD  C03  C02  C01  110.97  3.000
 0UD  H7   C03  H6   108.04  3.000
 0UD  H7   C03  H5   107.94  3.000
 0UD  H6   C03  H5   107.54  3.000
 0UD  H7   C03  C02  111.23  3.000
 0UD  H6   C03  C02  111.57  3.000
 0UD  H5   C03  C02  110.36  3.000
 0UD  C12  C04  C05  118.39  3.000
 0UD  C12  C04  C02  122.66  3.000
 0UD  C05  C04  C02  118.95  3.000
 0UD  H8   C05  C06  119.34  3.000
 0UD  H8   C05  C04  119.73  3.000
 0UD  C06  C05  C04  120.93  3.000
 0UD  H9   C06  C07  120.07  3.000
 0UD  H9   C06  C05  120.13  3.000
 0UD  C07  C06  C05  119.81  3.000
 0UD  H10  C07  C08  119.08  3.000
 0UD  H10  C07  C06  119.55  3.000
 0UD  C08  C07  C06  121.38  3.000
 0UD  C12  C08  C09  124.54  3.000
 0UD  C09  C08  C07  117.54  3.000
 0UD  C12  C08  C07  117.91  3.000
 0UD  H11  C09  C11  106.13  3.000
 0UD  H11  C09  C10  106.13  3.000
 0UD  C11  C09  C10  111.26  3.000
 0UD  H11  C09  C08  104.91  3.000
 0UD  C11  C09  C08  112.88  3.000
 0UD  C10  C09  C08  114.72  3.000
 0UD  H14  C10  H13  108.35  3.000
 0UD  H14  C10  H12  107.60  3.000
 0UD  H13  C10  H12  107.04  3.000
 0UD  H14  C10  C09  111.74  3.000
 0UD  H13  C10  C09  112.47  3.000
 0UD  H12  C10  C09  109.42  3.000
 0UD  H17  C11  H16  107.18  3.000
 0UD  H17  C11  H15  107.72  3.000
 0UD  H16  C11  H15  108.12  3.000
 0UD  H17  C11  C09  109.92  3.000
 0UD  H16  C11  C09  112.26  3.000
 0UD  H15  C11  C09  111.43  3.000
 0UD  N13  C12  C08  119.28  3.000
 0UD  C08  C12  C04  121.56  3.000
 0UD  N13  C12  C04  119.15  3.000
 0UD  O21  C14  N15  123.75  3.000
 0UD  N15  C14  N13  113.50  3.000
 0UD  O21  C14  N13  122.75  3.000
 0UD  N20  C16  N17  121.40  3.000
 0UD  N17  C16  N15  111.19  3.000
 0UD  N20  C16  N15  127.37  3.000
 0UD  H19  C18  H18  106.48  3.000
 0UD  H19  C18  N17  108.62  3.000
 0UD  H18  C18  N17  111.46  3.000
 0UD  H19  C18  C19  109.94  3.000
 0UD  H18  C18  C19  109.99  3.000
 0UD  N17  C18  C19  110.26  3.000
 0UD  H22  C19  H21  108.16  3.000
 0UD  H22  C19  H20  107.59  3.000
 0UD  H21  C19  H20  108.09  3.000
 0UD  H22  C19  C18  111.48  3.000
 0UD  H21  C19  C18  111.25  3.000
 0UD  H20  C19  C18  110.13  3.000
 0UD  H23  N13  C14  119.98  3.000
 0UD  H23  N13  C12  117.99  3.000
 0UD  C14  N13  C12  121.54  3.000
 0UD  H24  N15  C16  116.19  3.000
 0UD  H24  N15  C14  117.49  3.000
 0UD  C16  N15  C14  126.29  3.000
 0UD  H25  N17  C18  114.57  3.000
 0UD  H25  N17  C16  116.53  3.000
 0UD  C18  N17  C16  119.93  3.000
 0UD  H26  N20  C16  111.11  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
 0UD  CONST_01  C07  C06  C05  C04     0.00   0.0  0
 0UD  CONST_02  C07  C08  C12  C04     0.00   0.0  0
 0UD  CONST_03  C08  C12  C04  C05     0.00   0.0  0
 0UD  CONST_04  C08  C07  C06  C05     0.00   0.0  0
 0UD  CONST_05  C12  C04  C05  C06     0.00   0.0  0
 0UD  CONST_06  C12  C08  C07  C06     0.00   0.0  0
 0UD  CONST_07  C06  C05  C04  C02   180.00   0.0  0
 0UD  CONST_08  C08  C12  C04  C02   180.00   0.0  0
 0UD  CONST_09  C09  C08  C12  C04   180.00   0.0  0
 0UD  CONST_10  N13  C12  C04  C05   180.00   0.0  0
 0UD  CONST_11  C09  C08  C07  C06   180.00   0.0  0
 0UD  CONST_12  N13  C12  C08  C07   180.00   0.0  0
 0UD  CONST_13  H9   C06  C05  C04   180.00   0.0  0
 0UD  CONST_14  H10  C07  C06  C05   180.00   0.0  0
 0UD  CONST_15  H8   C05  C06  C07   180.00   0.0  0
 0UD  CONST_19  O21  C14  N13  C12     0.00   0.0  0
 0UD  CONST_20  N15  C14  N13  C12   180.00   0.0  0
 0UD  CONST_21  O21  C14  N15  C16     0.00   0.0  0
 0UD  CONST_22  N20  C16  N15  C14     0.00   0.0  0
 0UD  CONST_23  N17  C16  N15  C14   180.00   0.0  0
 0UD  CONST_24  N13  C14  N15  C16   180.00   0.0  0
 0UD  CONST_25  N20  C16  N17  C18     0.00   0.0  0
 0UD  CONST_26  N15  C16  N17  C18   180.00   0.0  0
 0UD  CONST_27  H24  N15  C14  O21   180.00   0.0  0
 0UD  CONST_28  H26  N20  C16  N15     0.00   0.0  0
 0UD  Var_01    C05  C04  C02  C01   -59.19  30.0  2
 0UD  Var_02    C10  C09  C08  C07  -119.41  30.0  2
 0UD  Var_03    H5   C03  C02  C04   176.71  30.0  3
 0UD  Var_04    H1   C01  C02  C04   -56.56  30.0  3
 0UD  Var_05    H12  C10  C09  C08   164.02  30.0  3
 0UD  Var_06    H15  C11  C09  C08   -50.97  30.0  3
 0UD  Var_07    C19  C18  N17  C16   175.18  30.0  1
 0UD  Var_08    H20  C19  C18  N17  -179.62  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
 0UD  plan-1  C02  0.020
 0UD  plan-1  C04  0.020
 0UD  plan-1  C05  0.020
 0UD  plan-1  C06  0.020
 0UD  plan-1  C07  0.020
 0UD  plan-1  C08  0.020
 0UD  plan-1  C09  0.020
 0UD  plan-1  C12  0.020
 0UD  plan-1  N13  0.020
 0UD  plan-1  H8   0.020
 0UD  plan-1  H9   0.020
 0UD  plan-1  H10  0.020
 0UD  plan-2  C12  0.020
 0UD  plan-2  C14  0.020
 0UD  plan-2  C16  0.020
 0UD  plan-2  C18  0.020
 0UD  plan-2  N13  0.020
 0UD  plan-2  N15  0.020
 0UD  plan-2  N17  0.020
 0UD  plan-2  N20  0.020
 0UD  plan-2  O21  0.020
 0UD  plan-2  H23  0.020
 0UD  plan-2  H24  0.020
 0UD  plan-2  H25  0.020
 0UD  plan-2  H26  0.020

