# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 09:16:04 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: pent-4-ynoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC#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
 54L  54L  'pent-4-ynoic acid        '  ligand  13  7  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_54L
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
 54L  C38  C  C     0   0.557   1.4741   0.0172  -0.0483
 54L  O39  O  O     0  -0.442   1.7695   1.1857  -0.0549
 54L  C40  C  CH2   0  -0.579   0.0682  -0.5171  -0.0337
 54L  C41  C  CH2   0  -0.580  -0.9783   0.5931  -0.0185
 54L  C42  C  CSP   0   0.280  -2.3301   0.0493  -0.0108
 54L  C43  C  CSP1  0  -0.551  -3.4403  -0.4121  -0.0069
 54L  H2   H  HCH2  0   0.293  -0.0677  -1.1603  -0.9070
 54L  H3   H  HCH2  0   0.293  -0.0491  -1.1671   0.8371
 54L  H4   H  HCH2  0   0.281  -0.8451   1.2281   0.8600
 54L  H5   H  HCH2  0   0.281  -0.8581   1.2396  -0.8904
 54L  H6   H  H     0   0.279  -4.4249  -0.8200  -0.0008
 54L  O1   O  OH1   0  -0.594   2.3699  -0.9628  -0.0541
 54L  H1   H  HOH1  0   0.481   3.2663  -0.5950  -0.0657

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
 54L  C41  C40  single  1.526  0.020  1.526
 54L  C41  C42  single  1.457  0.020  1.457
 54L  C38  C40  single  1.504  0.020  1.504
 54L  C38  O39  double  1.205  0.020  1.205
 54L  C42  C43  triple  1.202  0.020  1.202
 54L  C40  H2   single  0.939  0.020  1.096
 54L  C40  H3   single  0.939  0.020  1.096
 54L  C41  H4   single  0.939  0.020  1.096
 54L  C41  H5   single  0.939  0.020  1.096
 54L  C43  H6   single  0.913  0.020  1.066
 54L  C38  O1   single  1.328  0.020  1.328
 54L  O1   H1   single  0.832  0.020  0.971

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
 54L  O1   C38  C40  111.63  3.000
 54L  O1   C38  O39  123.38  3.000
 54L  C40  C38  O39  125.00  3.000
 54L  H3   C40  H2   105.86  3.000
 54L  H3   C40  C41  110.56  3.000
 54L  H2   C40  C41  110.54  3.000
 54L  H3   C40  C38  108.62  3.000
 54L  H2   C40  C38  108.51  3.000
 54L  C41  C40  C38  112.50  3.000
 54L  H5   C41  H4   106.53  3.000
 54L  H5   C41  C42  109.10  3.000
 54L  H4   C41  C42  109.02  3.000
 54L  H5   C41  C40  110.32  3.000
 54L  H4   C41  C40  110.33  3.000
 54L  C42  C41  C40  111.40  3.000
 54L  C43  C42  C41  180.00  3.000
 54L  H6   C43  C42  180.00  3.000
 54L  H1   O1   C38  110.13  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
 54L  CONST_01  H1   O1   C38  O39    0.00   0.0  0
 54L  Var_01    C42  C41  C40  C38  179.74  30.0  1
 54L  Var_02    C41  C40  C38  O39   -0.38  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
 54L  plan-1  C38  0.020
 54L  plan-1  O39  0.020
 54L  plan-1  C40  0.020
 54L  plan-1  O1   0.020
 54L  plan-1  H1   0.020

