# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 03:21:37 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: N-(2,4-difluorophenyl)pyrrolidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(NC(=O)N2CCCC2)c(F)c1
#
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
 5VU  5VU  N-(2,4-difluorophenyl)pyrrolidine-1-carboxamide  ligand  28  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5VU
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
 5VU  O01   O  O     0  -0.532  -1.0156  -1.7698   0.5703
 5VU  C02   C  C     0   0.728  -1.3391  -0.6792   0.1169
 5VU  N03   N  NH1   0  -0.787  -0.4067   0.2341  -0.3305
 5VU  C04   C  CR6   0   0.189   0.9703   0.0295  -0.2175
 5VU  C05   C  CR16  0  -0.266   1.6006  -1.1447  -0.6224
 5VU  C06   C  CR16  0  -0.425   2.9731  -1.3031  -0.5042
 5VU  C07   C  CR6   0   0.531   3.7240  -0.2622   0.0044
 5VU  F08   F  F     0  -0.312   5.0526  -0.4018   0.1153
 5VU  C09   C  CR16  0  -0.561   3.1492   0.9296   0.3996
 5VU  C10   C  CR6   0   0.504   1.7786   1.0423   0.2890
 5VU  F11   F  F     0  -0.306   1.1970   2.1866   0.6761
 5VU  N12   N  NT    0  -0.510  -2.6224  -0.2853   0.0056
 5VU  C13   C  CH2   0  -0.252  -3.7113  -1.1254   0.4906
 5VU  C14   C  CH2   0  -0.482  -4.8993  -0.1714   0.5062
 5VU  C15   C  CH2   0  -0.475  -4.6001   0.7757  -0.6513
 5VU  C16   C  CH2   0  -0.301  -3.0913   0.9763  -0.5553
 5VU  H03   H  HNH1  0   0.416  -0.7041   1.1783  -0.5180
 5VU  H05   H  HCR6  0   0.283   1.0151  -1.9479  -1.0435
 5VU  H06   H  HCR6  0   0.286   3.4473  -2.2223  -0.8199
 5VU  H09   H  HCR6  0   0.305   3.7424   1.7435   0.7957
 5VU  H131  H  HCH2  0   0.233  -3.8861  -1.9655  -0.1883
 5VU  H132  H  HCH2  0   0.246  -3.4878  -1.5343   1.4758
 5VU  H161  H  HCH2  0   0.244  -2.8502   1.8159   0.1059
 5VU  H162  H  HCH2  0   0.255  -2.6448   1.1751  -1.5322
 5VU  H141  H  HCH2  0   0.252  -5.8488  -0.6943   0.4000
 5VU  H142  H  HCH2  0   0.239  -4.9249   0.3805   1.4485
 5VU  H151  H  HCH2  0   0.242  -4.8537   0.3034  -1.6024
 5VU  H152  H  HCH2  0   0.254  -5.1429   1.7181  -0.5921

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
 5VU  O01  C02   double    1.225  0.020  1.225
 5VU  C02  N03   single    1.380  0.020  1.380
 5VU  C02  N12   single    1.347  0.020  1.347
 5VU  N03  C04   single    1.397  0.020  1.397
 5VU  C04  C05   aromatic  1.393  0.020  1.393
 5VU  C04  C10   aromatic  1.391  0.020  1.391
 5VU  C05  C06   aromatic  1.387  0.020  1.387
 5VU  C06  C07   aromatic  1.381  0.020  1.381
 5VU  C07  F08   single    1.341  0.020  1.341
 5VU  C07  C09   aromatic  1.381  0.020  1.381
 5VU  C09  C10   aromatic  1.380  0.020  1.380
 5VU  C10  F11   single    1.341  0.020  1.341
 5VU  N12  C13   single    1.458  0.020  1.458
 5VU  N12  C16   single    1.458  0.020  1.458
 5VU  C13  C14   single    1.524  0.020  1.524
 5VU  C14  C15   single    1.525  0.020  1.525
 5VU  C15  C16   single    1.525  0.020  1.525
 5VU  N03  H03   single    0.860  0.020  1.020
 5VU  C05  H05   single    0.930  0.020  1.080
 5VU  C06  H06   single    0.930  0.020  1.080
 5VU  C09  H09   single    0.930  0.020  1.080
 5VU  C13  H131  single    0.970  0.020  1.090
 5VU  C13  H132  single    0.970  0.020  1.090
 5VU  C16  H161  single    0.970  0.020  1.090
 5VU  C16  H162  single    0.970  0.020  1.090
 5VU  C14  H141  single    0.970  0.020  1.090
 5VU  C14  H142  single    0.970  0.020  1.090
 5VU  C15  H151  single    0.970  0.020  1.090
 5VU  C15  H152  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
 5VU  N12   C02  N03   115.05  3.000
 5VU  N12   C02  O01   122.87  3.000
 5VU  N03   C02  O01   122.08  3.000
 5VU  H03   N03  C04   116.31  3.000
 5VU  H03   N03  C02   118.77  3.000
 5VU  C04   N03  C02   122.89  3.000
 5VU  C10   C04  C05   117.17  3.000
 5VU  C10   C04  N03   119.71  3.000
 5VU  C05   C04  N03   123.10  3.000
 5VU  H05   C05  C06   119.02  3.000
 5VU  H05   C05  C04   119.68  3.000
 5VU  C06   C05  C04   121.30  3.000
 5VU  H06   C06  C07   120.66  3.000
 5VU  H06   C06  C05   120.42  3.000
 5VU  C07   C06  C05   118.92  3.000
 5VU  C09   C07  F08   118.60  3.000
 5VU  C09   C07  C06   121.99  3.000
 5VU  F08   C07  C06   119.41  3.000
 5VU  H09   C09  C10   120.83  3.000
 5VU  H09   C09  C07   121.71  3.000
 5VU  C10   C09  C07   117.45  3.000
 5VU  F11   C10  C09   118.52  3.000
 5VU  F11   C10  C04   118.32  3.000
 5VU  C09   C10  C04   123.15  3.000
 5VU  C16   N12  C13   112.72  3.000
 5VU  C16   N12  C02   126.24  3.000
 5VU  C13   N12  C02   121.02  3.000
 5VU  H132  C13  H131  107.79  3.000
 5VU  H132  C13  C14   112.68  3.000
 5VU  H131  C13  C14   111.25  3.000
 5VU  H132  C13  N12   111.33  3.000
 5VU  H131  C13  N12   110.81  3.000
 5VU  C14   C13  N12   102.99  3.000
 5VU  H142  C14  H141  107.83  3.000
 5VU  H142  C14  C15   110.21  3.000
 5VU  H141  C14  C15   113.28  3.000
 5VU  H142  C14  C13   110.09  3.000
 5VU  H141  C14  C13   112.22  3.000
 5VU  C15   C14  C13   103.19  3.000
 5VU  H152  C15  H151  107.81  3.000
 5VU  H152  C15  C16   112.07  3.000
 5VU  H151  C15  C16   109.97  3.000
 5VU  H152  C15  C14   113.47  3.000
 5VU  H151  C15  C14   110.30  3.000
 5VU  C16   C15  C14   103.18  3.000
 5VU  H162  C16  H161  108.08  3.000
 5VU  H162  C16  C15   111.84  3.000
 5VU  H161  C16  C15   110.88  3.000
 5VU  H162  C16  N12   111.71  3.000
 5VU  H161  C16  N12   111.11  3.000
 5VU  C15   C16  N12   103.21  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
 5VU  CONST_01  C07  C06  C05  C04    0.00   0.0  0
 5VU  CONST_02  C07  C09  C10  C04    0.00   0.0  0
 5VU  CONST_03  C09  C10  C04  C05    0.00   0.0  0
 5VU  CONST_04  C09  C07  C06  C05    0.00   0.0  0
 5VU  CONST_05  C10  C04  C05  C06    0.00   0.0  0
 5VU  CONST_06  C10  C09  C07  C06    0.00   0.0  0
 5VU  CONST_07  C06  C05  C04  N03  180.00   0.0  0
 5VU  CONST_08  C09  C10  C04  N03  180.00   0.0  0
 5VU  CONST_09  F11  C10  C04  C05  180.00   0.0  0
 5VU  CONST_10  F08  C07  C06  C05  180.00   0.0  0
 5VU  CONST_11  F11  C10  C09  C07  180.00   0.0  0
 5VU  CONST_12  C10  C09  C07  F08  180.00   0.0  0
 5VU  CONST_13  H06  C06  C05  C04  180.00   0.0  0
 5VU  CONST_14  H09  C09  C10  C04  180.00   0.0  0
 5VU  CONST_15  H05  C05  C06  C07  180.00   0.0  0
 5VU  CONST_16  C13  N12  C02  O01    0.00   0.0  0
 5VU  CONST_17  C16  N12  C02  O01  180.00   0.0  0
 5VU  CONST_20  N12  C02  N03  C04  180.00   0.0  0
 5VU  CONST_21  C13  N12  C02  N03  180.00   0.0  0
 5VU  CONST_22  C16  N12  C02  N03    0.00   0.0  0
 5VU  CONST_24  C04  N03  C02  O01    0.00   0.0  0
 5VU  Var_01    C15  C14  C13  N12   31.62  30.0  1
 5VU  Var_02    C14  C15  C16  N12   30.32  30.0  1
 5VU  Var_03    C15  C16  N12  C13  -10.89  30.0  1
 5VU  Var_04    C16  C15  C14  C13  -38.65  30.0  1
 5VU  Var_05    C16  N12  C13  C14  -13.10  30.0  1

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
 5VU  plan-1  N03  0.020
 5VU  plan-1  C04  0.020
 5VU  plan-1  C05  0.020
 5VU  plan-1  C06  0.020
 5VU  plan-1  C07  0.020
 5VU  plan-1  F08  0.020
 5VU  plan-1  C09  0.020
 5VU  plan-1  C10  0.020
 5VU  plan-1  F11  0.020
 5VU  plan-1  H05  0.020
 5VU  plan-1  H06  0.020
 5VU  plan-1  H09  0.020
 5VU  plan-2  O01  0.020
 5VU  plan-2  C02  0.020
 5VU  plan-2  N03  0.020
 5VU  plan-2  C04  0.020
 5VU  plan-2  N12  0.020
 5VU  plan-2  C13  0.020
 5VU  plan-2  C16  0.020
 5VU  plan-2  H03  0.020

