# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:17:43 2021
#   Inital geometry file: a 60 line input string
#   Ligand name: 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)CNC(N)=O
#
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
 UCV  UCV  1-[(2~{S})-2-azanyl-3-methyl-butyl]urea  ligand  25  10  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UCV
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
 UCV  CG2  C  CH3   0  -0.642  -6.2163  12.6218  -28.2881
 UCV  CB   C  CH1   0  -0.232  -6.8042  13.4677  -27.1624
 UCV  CG1  C  CH3   0  -0.669  -7.8442  14.4293  -27.7345
 UCV  CA   C  CH1   0  -0.072  -5.7030  14.1990  -26.3819
 UCV  N1   N  NH2   0  -0.787  -4.7166  13.2428  -25.8992
 UCV  C2   C  CH2   0  -0.280  -6.2883  15.0680  -25.2566
 UCV  N2   N  NH1   0  -0.659  -5.2770  15.7057  -24.4458
 UCV  C    C  C     0   0.659  -4.6737  16.8643  -24.8068
 UCV  O    O  O     0  -0.543  -4.9766  17.4831  -25.8223
 UCV  N3   N  NH2   0  -0.843  -3.7363  17.3270  -23.9265
 UCV  H1   H  HCH3  0   0.229  -5.5202  11.8736  -27.9146
 UCV  H2   H  HCH3  0   0.218  -7.0069  12.1075  -28.8372
 UCV  H3   H  HCH3  0   0.208  -5.6776  13.2511  -29.0013
 UCV  H4   H  HCH1  0   0.208  -7.3163  12.7956  -26.4599
 UCV  H5   H  HCH3  0   0.230  -8.4076  14.9585  -26.9667
 UCV  H6   H  HCH3  0   0.216  -7.3723  15.1778  -28.3761
 UCV  H7   H  HCH3  0   0.230  -8.5684  13.8863  -28.3439
 UCV  H8   H  HCH1  0   0.212  -5.1881  14.8685  -27.0822
 UCV  H9   H  HNH2  0   0.340  -4.0085  13.7312  -25.3644
 UCV  H10  H  HNH2  0   0.330  -5.1578  12.5999  -25.2497
 UCV  H12  H  HCH2  0   0.238  -6.9481  15.8348  -25.6607
 UCV  H13  H  HCH2  0   0.236  -6.8918  14.4435  -24.5931
 UCV  H14  H  HNH1  0   0.392  -4.9783  15.2355  -23.6083
 UCV  H15  H  HNH2  0   0.391  -3.1160  18.0378  -24.2765
 UCV  H16  H  HNH2  0   0.390  -3.3129  16.6958  -23.2660

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
 UCV  CG2  CB   single  1.526  0.020  1.526
 UCV  CG1  CB   single  1.528  0.020  1.528
 UCV  CB   CA   single  1.535  0.020  1.535
 UCV  CA   N1   single  1.456  0.020  1.456
 UCV  CA   C2   single  1.538  0.020  1.538
 UCV  O    C    double  1.227  0.020  1.227
 UCV  C2   N2   single  1.445  0.020  1.445
 UCV  C    N2   single  1.355  0.020  1.355
 UCV  C    N3   single  1.367  0.020  1.367
 UCV  CG2  H1   single  0.970  0.020  1.090
 UCV  CG2  H2   single  0.970  0.020  1.090
 UCV  CG2  H3   single  0.970  0.020  1.090
 UCV  CB   H4   single  0.970  0.020  1.090
 UCV  CG1  H5   single  0.970  0.020  1.090
 UCV  CG1  H6   single  0.970  0.020  1.090
 UCV  CG1  H7   single  0.970  0.020  1.090
 UCV  CA   H8   single  0.970  0.020  1.090
 UCV  N1   H9   single  0.890  0.020  1.040
 UCV  N1   H10  single  0.890  0.020  1.040
 UCV  C2   H12  single  0.970  0.020  1.090
 UCV  C2   H13  single  0.970  0.020  1.090
 UCV  N2   H14  single  0.860  0.020  1.020
 UCV  N3   H15  single  0.890  0.020  1.040
 UCV  N3   H16  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
 UCV  H3   CG2  H2   107.46  3.000
 UCV  H3   CG2  H1   107.73  3.000
 UCV  H2   CG2  H1   108.19  3.000
 UCV  H3   CG2  CB   110.61  3.000
 UCV  H2   CG2  CB   110.69  3.000
 UCV  H1   CG2  CB   111.99  3.000
 UCV  H4   CB   CA   107.49  3.000
 UCV  H4   CB   CG1  107.89  3.000
 UCV  CA   CB   CG1  112.26  3.000
 UCV  H4   CB   CG2  108.19  3.000
 UCV  CA   CB   CG2  111.27  3.000
 UCV  CG1  CB   CG2  109.57  3.000
 UCV  H7   CG1  H6   107.43  3.000
 UCV  H7   CG1  H5   106.98  3.000
 UCV  H6   CG1  H5   107.72  3.000
 UCV  H7   CG1  CB   110.35  3.000
 UCV  H6   CG1  CB   110.92  3.000
 UCV  H5   CG1  CB   113.20  3.000
 UCV  H8   CA   C2   107.51  3.000
 UCV  H8   CA   N1   107.12  3.000
 UCV  C2   CA   N1   112.73  3.000
 UCV  H8   CA   CB   107.63  3.000
 UCV  C2   CA   CB   111.61  3.000
 UCV  N1   CA   CB   109.97  3.000
 UCV  H10  N1   H9   105.75  3.000
 UCV  H10  N1   CA   109.49  3.000
 UCV  H9   N1   CA   109.39  3.000
 UCV  H13  C2   H12  107.03  3.000
 UCV  H13  C2   N2   107.35  3.000
 UCV  H12  C2   N2   108.75  3.000
 UCV  H13  C2   CA   109.36  3.000
 UCV  H12  C2   CA   110.91  3.000
 UCV  N2   C2   CA   113.19  3.000
 UCV  H14  N2   C    119.29  3.000
 UCV  H14  N2   C2   117.96  3.000
 UCV  C    N2   C2   122.65  3.000
 UCV  N3   C    O    122.11  3.000
 UCV  N3   C    N2   115.04  3.000
 UCV  O    C    N2   122.79  3.000
 UCV  H16  N3   H15  114.32  3.000
 UCV  H16  N3   C    119.91  3.000
 UCV  H15  N3   C    115.97  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
 UCV  CONST_01  O    C    N2  C2      0.00   0.0  0
 UCV  CONST_02  N3   C    N2  C2    180.00   0.0  0
 UCV  CONST_03  H14  N2   C   O     180.00   0.0  0
 UCV  Var_01    C    N2   C2  CA     83.05  30.0  3
 UCV  Var_02    H5   CG1  CB  CG2   171.47  30.0  3
 UCV  Var_03    H1   CG2  CB  CG1  -176.00  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
 UCV  chir_01  CA  CB  N1  C2  positiv

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
 UCV  plan-1  C2   0.020
 UCV  plan-1  N2   0.020
 UCV  plan-1  C    0.020
 UCV  plan-1  O    0.020
 UCV  plan-1  N3   0.020
 UCV  plan-1  H14  0.020
 UCV  plan-1  H15  0.020
 UCV  plan-1  H16  0.020

