# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:05:27 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 2-propylpentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(CCC)C(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
 VPR  VPR  '2-propylpentanamide      '  ligand  27  10  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VPR
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
 VPR  C5    C  CH3   0  -0.661   2.3150   0.0097   2.7554
 VPR  C4    C  CH2   0  -0.427   1.0199   0.3718   2.0415
 VPR  C3    C  CH2   0  -0.406   0.9764  -0.1652   0.6150
 VPR  C2    C  CH1   0  -0.364  -0.2509   0.2824  -0.1816
 VPR  C3A   C  CH2   0  -0.400  -0.2709  -0.2716  -1.6122
 VPR  C4A   C  CH2   0  -0.429   0.8615   0.2388  -2.4964
 VPR  C5A   C  CH3   0  -0.660   0.7216  -0.2372  -3.9362
 VPR  C1    C  C     0   0.527  -1.5192  -0.1583   0.5289
 VPR  N     N  NH2   0  -0.800  -2.3534   0.8273   0.8916
 VPR  O     O  O     0  -0.501  -1.7596  -1.3401   0.7424
 VPR  H51   H  HCH3  0   0.228   2.3211   0.3769   3.7821
 VPR  H52   H  HCH3  0   0.217   2.4565  -1.0721   2.7914
 VPR  H53   H  HCH3  0   0.217   3.1797   0.4377   2.2453
 VPR  H41   H  HCH2  0   0.219   0.1737  -0.0156   2.6162
 VPR  H42   H  HCH2  0   0.214   0.9038   1.4599   2.0250
 VPR  H31   H  HCH2  0   0.230   1.8740   0.1705   0.0894
 VPR  H32   H  HCH2  0   0.216   1.0194  -1.2589   0.6290
 VPR  H2    H  HCH1  0   0.237  -0.2357   1.3764  -0.2423
 VPR  H3A1  H  HCH2  0   0.220  -0.2479  -1.3649  -1.5798
 VPR  H3A2  H  HCH2  0   0.226  -1.2225   0.0021  -2.0804
 VPR  H4A1  H  HCH2  0   0.214   0.8774   1.3327  -2.4706
 VPR  H4A2  H  HCH2  0   0.221   1.8271  -0.0900  -2.1054
 VPR  H5A1  H  HCH3  0   0.227   1.5375   0.1319  -4.5588
 VPR  H5A2  H  HCH3  0   0.217   0.7310  -1.3272  -3.9940
 VPR  H5A3  H  HCH3  0   0.217  -0.2146   0.1073  -4.3794
 VPR  HN1   H  HNH2  0   0.396  -3.2191   0.6206   1.3637
 VPR  HN2   H  HNH2  0   0.405  -2.1411   1.7935   0.7159

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
 VPR  C5   C4    single  1.522  0.020  1.522
 VPR  C5   H51   single  0.970  0.020  1.090
 VPR  C5   H52   single  0.970  0.020  1.090
 VPR  C5   H53   single  0.970  0.020  1.090
 VPR  C4   C3    single  1.525  0.020  1.525
 VPR  C4   H41   single  0.970  0.020  1.090
 VPR  C4   H42   single  0.970  0.020  1.090
 VPR  C3   C2    single  1.530  0.020  1.530
 VPR  C3   H31   single  0.970  0.020  1.090
 VPR  C3   H32   single  0.970  0.020  1.090
 VPR  C2   C3A   single  1.534  0.020  1.534
 VPR  C2   C1    single  1.519  0.020  1.519
 VPR  C2   H2    single  0.970  0.020  1.090
 VPR  C3A  C4A   single  1.525  0.020  1.525
 VPR  C3A  H3A1  single  0.970  0.020  1.090
 VPR  C3A  H3A2  single  0.970  0.020  1.090
 VPR  C4A  C5A   single  1.523  0.020  1.523
 VPR  C4A  H4A1  single  0.970  0.020  1.090
 VPR  C4A  H4A2  single  0.970  0.020  1.090
 VPR  C5A  H5A1  single  0.970  0.020  1.090
 VPR  C5A  H5A2  single  0.970  0.020  1.090
 VPR  C5A  H5A3  single  0.970  0.020  1.090
 VPR  C1   N     single  1.341  0.020  1.341
 VPR  C1   O     double  1.225  0.020  1.225
 VPR  N    HN1   single  0.860  0.020  1.020
 VPR  N    HN2   single  0.860  0.020  1.020

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
 VPR  H53   C5   H52   107.54  3.000
 VPR  H53   C5   H51   107.67  3.000
 VPR  H52   C5   H51   107.58  3.000
 VPR  H53   C5   C4    111.19  3.000
 VPR  H52   C5   C4    111.18  3.000
 VPR  H51   C5   C4    111.48  3.000
 VPR  H42   C4   H41   106.14  3.000
 VPR  H42   C4   C3    109.45  3.000
 VPR  H41   C4   C3    110.16  3.000
 VPR  H42   C4   C5    109.50  3.000
 VPR  H41   C4   C5    109.12  3.000
 VPR  C3    C4   C5    112.29  3.000
 VPR  H32   C3   H31   106.30  3.000
 VPR  H32   C3   C2    109.30  3.000
 VPR  H31   C3   C2    108.57  3.000
 VPR  H32   C3   C4    109.80  3.000
 VPR  H31   C3   C4    108.56  3.000
 VPR  C2    C3   C4    114.01  3.000
 VPR  H2    C2   C1    109.10  3.000
 VPR  H2    C2   C3A   108.00  3.000
 VPR  C1    C2   C3A   108.69  3.000
 VPR  H2    C2   C3    108.05  3.000
 VPR  C1    C2   C3    109.96  3.000
 VPR  C3A   C2   C3    112.97  3.000
 VPR  H3A2  C3A  H3A1  106.30  3.000
 VPR  H3A2  C3A  C4A   108.28  3.000
 VPR  H3A1  C3A  C4A   109.64  3.000
 VPR  H3A2  C3A  C2    108.64  3.000
 VPR  H3A1  C3A  C2    109.45  3.000
 VPR  C4A   C3A  C2    114.22  3.000
 VPR  H4A2  C4A  H4A1  106.23  3.000
 VPR  H4A2  C4A  C5A   109.00  3.000
 VPR  H4A1  C4A  C5A   109.64  3.000
 VPR  H4A2  C4A  C3A   110.37  3.000
 VPR  H4A1  C4A  C3A   109.37  3.000
 VPR  C5A   C4A  C3A   112.05  3.000
 VPR  H5A3  C5A  H5A2  107.52  3.000
 VPR  H5A3  C5A  H5A1  107.64  3.000
 VPR  H5A2  C5A  H5A1  107.54  3.000
 VPR  H5A3  C5A  C4A   111.34  3.000
 VPR  H5A2  C5A  C4A   111.18  3.000
 VPR  H5A1  C5A  C4A   111.42  3.000
 VPR  O     C1   N     122.67  3.000
 VPR  O     C1   C2    121.69  3.000
 VPR  N     C1   C2    115.63  3.000
 VPR  HN2   N    HN1   117.43  3.000
 VPR  HN2   N    C1    121.87  3.000
 VPR  HN1   N    C1    120.69  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
 VPR  CONST_01  HN1   N    C1   C2    180.00   0.0  0
 VPR  CONST_02  HN2   N    C1   C2      0.00   0.0  0
 VPR  Var_01    C2    C3   C4   C5   -174.74  30.0  3
 VPR  Var_02    C3A   C2   C3   C4   -179.98  30.0  3
 VPR  Var_03    C4A   C3A  C2   C3    -64.92  30.0  3
 VPR  Var_04    N     C1   C2   C3    120.13  30.0  3
 VPR  Var_05    C5A   C4A  C3A  C2   -174.67  30.0  3
 VPR  Var_06    H51   C5   C4   C3   -178.48  30.0  3
 VPR  Var_07    H5A1  C5A  C4A  C3A  -179.88  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
 VPR  plan-1  C2   0.020
 VPR  plan-1  C1   0.020
 VPR  plan-1  N    0.020
 VPR  plan-1  O    0.020
 VPR  plan-1  HN1  0.020
 VPR  plan-1  HN2  0.020

