# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:23:40 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: N-butylformamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCNC=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
 YIV  YIV  'N-butylformamide         '  ligand  18  7  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YIV
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
 YIV  C    C  C1    0   0.249  -2.6032   0.3711   0.0667
 YIV  N    N  NH1   0  -0.594  -1.3137   0.6888  -0.0547
 YIV  C1   C  CH2   0  -0.238  -0.2379  -0.2828  -0.0483
 YIV  O1   O  O     0  -0.504  -3.0401  -0.7608   0.2084
 YIV  C2   C  CH2   0  -0.465   1.1115   0.4148   0.0088
 YIV  C3   C  CH2   0  -0.423   2.2725  -0.5710   0.0050
 YIV  C4   C  CH3   0  -0.661   3.6234   0.1280   0.0651
 YIV  H1   H  HCH2  0   0.235  -0.3508  -0.9446   0.8141
 YIV  H1A  H  HCH2  0   0.232  -0.2937  -0.9136  -0.9412
 YIV  H2   H  HCH2  0   0.228   1.2088   1.0931  -0.8454
 YIV  H2A  H  HCH2  0   0.229   1.1619   1.0364   0.9084
 YIV  H3   H  HCH2  0   0.219   2.1728  -1.2527   0.8546
 YIV  H3A  H  HCH2  0   0.219   2.2190  -1.1928  -0.8935
 YIV  H4   H  HCH3  0   0.218   3.7600   0.7947  -0.7887
 YIV  H4A  H  HCH3  0   0.218   3.7135   0.7313   0.9706
 YIV  H4B  H  HCH3  0   0.229   4.4453  -0.5882   0.0611
 YIV  H    H  H     0   0.202  -3.2547   1.2573   0.0296
 YIV  HN   H  HNH1  0   0.406  -1.0834   1.6594  -0.1957

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
 YIV  N    C    single  1.334  0.020  1.334
 YIV  O1   C    double  1.222  0.020  1.222
 YIV  C    H    single  0.930  0.020  1.080
 YIV  N    C1   single  1.450  0.020  1.450
 YIV  N    HN   single  0.860  0.020  1.020
 YIV  C2   C1   single  1.520  0.020  1.520
 YIV  H1   C1   single  0.970  0.020  1.090
 YIV  C1   H1A  single  0.970  0.020  1.090
 YIV  H2   C2   single  0.970  0.020  1.090
 YIV  C3   C2   single  1.523  0.020  1.523
 YIV  C2   H2A  single  0.970  0.020  1.090
 YIV  C4   C3   single  1.522  0.020  1.522
 YIV  H3   C3   single  0.970  0.020  1.090
 YIV  C3   H3A  single  0.970  0.020  1.090
 YIV  H4   C4   single  0.970  0.020  1.090
 YIV  H4A  C4   single  0.970  0.020  1.090
 YIV  C4   H4B  single  0.970  0.020  1.090

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
 YIV  H    C   O1   122.56  3.000
 YIV  H    C   N    112.18  3.000
 YIV  O1   C   N    125.25  3.000
 YIV  HN   N   C1   118.47  3.000
 YIV  HN   N   C    117.60  3.000
 YIV  C1   N   C    123.89  3.000
 YIV  H1A  C1  H1   106.82  3.000
 YIV  H1A  C1  C2   109.89  3.000
 YIV  H1   C1  C2   109.87  3.000
 YIV  H1A  C1  N    110.17  3.000
 YIV  H1   C1  N    109.43  3.000
 YIV  C2   C1  N    110.58  3.000
 YIV  H2A  C2  H2   106.57  3.000
 YIV  H2A  C2  C3   109.54  3.000
 YIV  H2   C2  C3   109.34  3.000
 YIV  H2A  C2  C1   109.41  3.000
 YIV  C3   C2  C1   112.31  3.000
 YIV  H2   C2  C1   109.50  3.000
 YIV  H3A  C3  H3   106.22  3.000
 YIV  H3A  C3  C4   109.68  3.000
 YIV  H3   C3  C4   109.66  3.000
 YIV  H3A  C3  C2   109.43  3.000
 YIV  H3   C3  C2   109.39  3.000
 YIV  C4   C3  C2   112.28  3.000
 YIV  H4B  C4  H4A  107.68  3.000
 YIV  H4B  C4  H4   107.70  3.000
 YIV  H4A  C4  H4   107.51  3.000
 YIV  H4B  C4  C3   111.55  3.000
 YIV  H4A  C4  C3   111.08  3.000
 YIV  H4   C4  C3   111.14  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
 YIV  CONST_01  O1  C   N   C1     0.00   0.0  0
 YIV  CONST_02  HN  N   C   O1   180.00   0.0  0
 YIV  Var_01    C2  C1  N   C   -171.33  30.0  3
 YIV  Var_02    C3  C2  C1  N   -179.50  30.0  1
 YIV  Var_03    C4  C3  C2  C1  -179.88  30.0  1
 YIV  Var_04    H4  C4  C3  C2   -59.76  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
 YIV  plan-1  C   0.020
 YIV  plan-1  N   0.020
 YIV  plan-1  C1  0.020
 YIV  plan-1  O1  0.020
 YIV  plan-1  H   0.020
 YIV  plan-1  HN  0.020

