# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 12:47:46 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: [(2~{S})-2-azanyl-3-methyl-butyl]carbamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)CNC(O)=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
 URV  URV  '[(2~{S})-2-azanyl-3-methyl-butyl]carbamic acid'  L-peptide  23  10  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_URV
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
 URV  CA   C  CH1    0  -0.092  -30.5263  35.5388  -15.5057
 URV  C    C  C      0   0.495  -29.5901  37.5759  -13.2126
 URV  O    O  O      0  -0.642  -30.8130  37.7590  -13.0309
 URV  CB   C  CH1    0  -0.215  -31.5568  34.5262  -16.0309
 URV  CG1  C  CH3    0  -0.670  -31.0316  33.0934  -16.1035
 URV  CG2  C  CH3    0  -0.662  -32.8628  34.5759  -15.2419
 URV  C2   C  CH2    0  -0.280  -30.1024  35.2862  -14.0492
 URV  N1   N  NH2    0  -0.796  -29.3987  35.6215  -16.4305
 URV  N2   N  NH1    0  -0.657  -29.1809  36.2620  -13.5207
 URV  OXT  O  OC    -1  -0.652  -28.6755  38.4230  -13.1172
 URV  H1   H  HCH1   0   0.211  -31.0146  36.5193  -15.5281
 URV  H2   H  HCH1   0   0.213  -31.7815  34.8420  -17.0557
 URV  H3   H  HCH3   0   0.226  -31.7763  32.4402  -16.5615
 URV  H4   H  HCH3   0   0.222  -30.1247  33.0137  -16.7050
 URV  H5   H  HCH3   0   0.216  -30.8142  32.6875  -15.1136
 URV  H6   H  HCH3   0   0.222  -33.2353  35.5981  -15.1488
 URV  H7   H  HCH3   0   0.226  -33.6353  33.9873  -15.7394
 URV  H8   H  HCH3   0   0.215  -32.7493  34.1715  -14.2344
 URV  H9   H  HCH2   0   0.212  -30.9803  35.2559  -13.4035
 URV  H10  H  HCH2   0   0.208  -29.6280  34.3019  -13.9767
 URV  H11  H  HNH2   0   0.337  -28.8110  36.4037  -16.1684
 URV  H12  H  HNH2   0   0.331  -28.8097  34.8017  -16.3301
 URV  H14  H  HNH1   0   0.335  -28.2414  36.1966  -13.8791

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
 URV  N1   CA   single  1.461  0.020  1.461
 URV  CB   CG1  single  1.528  0.020  1.528
 URV  CB   CA   single  1.521  0.033  1.521
 URV  CB   CG2  single  1.527  0.020  1.527
 URV  CA   C2   single  1.538  0.020  1.538
 URV  C2   N2   single  1.442  0.020  1.442
 URV  N2   C    single  1.410  0.020  1.410
 URV  C    O    deloc   1.231  0.020  1.231
 URV  C    OXT  deloc   1.250  0.020  1.250
 URV  CA   H1   single  0.970  0.020  1.090
 URV  CB   H2   single  0.970  0.020  1.090
 URV  CG1  H3   single  0.970  0.020  1.090
 URV  CG1  H4   single  0.970  0.020  1.090
 URV  CG1  H5   single  0.970  0.020  1.090
 URV  CG2  H6   single  0.970  0.020  1.090
 URV  CG2  H7   single  0.970  0.020  1.090
 URV  CG2  H8   single  0.970  0.020  1.090
 URV  C2   H9   single  0.970  0.020  1.090
 URV  C2   H10  single  0.970  0.020  1.090
 URV  N1   H11  single  0.890  0.020  1.040
 URV  N1   H12  single  0.890  0.020  1.040
 URV  N2   H14  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
 URV  H1   CA   N1   106.29  3.000
 URV  H1   CA   C2   106.81  3.000
 URV  N1   CA   C2   113.34  3.000
 URV  H1   CA   CB   106.48  3.000
 URV  C2   CA   CB   113.59  3.000
 URV  N1   CA   CB   109.78  3.000
 URV  OXT  C    N2   115.83  3.000
 URV  OXT  C    O    127.26  3.000
 URV  N2   C    O    116.88  3.000
 URV  H2   CB   CG2  107.37  3.000
 URV  H2   CB   CG1  107.24  3.000
 URV  CG2  CB   CG1  110.44  3.000
 URV  H2   CB   CA   105.50  3.000
 URV  CG2  CB   CA   112.05  3.000
 URV  CG1  CB   CA   113.80  3.000
 URV  H5   CG1  H4   107.88  3.000
 URV  H5   CG1  H3   107.09  3.000
 URV  H4   CG1  H3   106.98  3.000
 URV  H5   CG1  CB   111.96  3.000
 URV  H4   CG1  CB   112.36  3.000
 URV  H3   CG1  CB   110.29  3.000
 URV  H8   CG2  H7   107.13  3.000
 URV  H8   CG2  H6   107.67  3.000
 URV  H7   CG2  H6   107.60  3.000
 URV  H8   CG2  CB   112.09  3.000
 URV  H7   CG2  CB   110.64  3.000
 URV  H6   CG2  CB   111.49  3.000
 URV  H10  C2   H9   106.54  3.000
 URV  H10  C2   N2   107.88  3.000
 URV  H9   C2   N2   108.44  3.000
 URV  H10  C2   CA   109.25  3.000
 URV  H9   C2   CA   110.09  3.000
 URV  N2   C2   CA   114.33  3.000
 URV  H12  N1   H11  105.17  3.000
 URV  H12  N1   CA   109.86  3.000
 URV  H11  N1   CA   109.13  3.000
 URV  H14  N2   C2   114.93  3.000
 URV  H14  N2   C    114.13  3.000
 URV  C2   N2   C    121.66  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
 URV  Var_01  C   N2   C2  CA    71.79  30.0  3
 URV  Var_02  C2  N2   C   O     20.71  30.0  3
 URV  Var_03  H3  CG1  CB  CA  -175.18  30.0  3
 URV  Var_04  H6  CG2  CB  CA    49.97  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
 URV  chir_01  CA  N1  CB  C2  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
 URV  plan-1  C    0.020
 URV  plan-1  O    0.020
 URV  plan-1  N2   0.020
 URV  plan-1  OXT  0.020

