# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 23:48:02 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 1-{5-[2-chloro-5-(hydroxymethyl)phenyl]pyridin-2-yl}piperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccc(Cl)c(c1)c2ccc(nc2)N3CCC(CC3)C(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
 4VN  4VN  '1-{5-[2-chloro-5-(hydroxymethyl)phenyl]pyridin-2-yl}piperidine-4-carboxylic acid'  ligand  42  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4VN
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
 4VN  C1   C   CR16   0  -0.177   5.3046   1.1319  -0.5917
 4VN  C2   C   CR6    0  -0.152   3.9212   1.2249  -0.5635
 4VN  C3   C   CR6    0   0.185   3.1261   0.1451  -0.1811
 4VN  C7   C   CR6    0  -0.053   1.6546   0.1965  -0.1339
 4VN  C8   C   CR16   0  -0.169   0.9400   1.1346   0.6147
 4VN  C9   C   CR16   0  -0.411  -0.4352   1.1061   0.6445
 4VN  C10  C   CR6    0   0.539  -1.1199   0.1105  -0.0873
 4VN  C11  C   CR16   0  -0.089   0.8886  -0.7288  -0.8290
 4VN  C12  C   CH2    0  -0.295  -3.1493  -0.6557  -1.2022
 4VN  C13  C   CH2    0  -0.423  -4.4786  -1.2716  -0.8025
 4VN  C14  C   CH1    0  -0.400  -5.3891  -0.2505  -0.1339
 4VN  C15  C   CH2    0  -0.414  -4.6473   0.3604   1.0444
 4VN  C16  C   CH2    0  -0.297  -3.3020   0.9480   0.6404
 4VN  CL   CL  CL     0  -0.133   3.1944   2.7199  -1.0627
 4VN  C4   C   CR16   0  -0.376   3.7841  -1.0376   0.1628
 4VN  C5   C   CR6    0   0.099   5.1661  -1.1617   0.1290
 4VN  C6   C   CH2    0  -0.202   5.8165  -2.4737   0.4684
 4VN  O    O   OH1    0  -0.666   6.9981  -2.2369   1.1956
 4VN  C    C   CR16   0  -0.314   5.9247  -0.0570  -0.2463
 4VN  N    N   N      0  -0.471  -0.4329  -0.7730  -0.8169
 4VN  N1   N   NT     0  -0.494  -2.4821  -0.0126  -0.0766
 4VN  H1   H   HCR6   0   0.277   5.8974   1.9851  -0.8931
 4VN  H2   H   HCR6   0   0.260   1.4599   1.8941   1.1845
 4VN  H3   H   HCR6   0   0.269  -0.9583   1.8589   1.2137
 4VN  H4   H   HCR6   0   0.252   1.3793  -1.4763  -1.4464
 4VN  H5   H   HCH2   0   0.259  -2.4909  -1.4148  -1.6136
 4VN  H6   H   HCH2   0   0.210  -3.3205   0.0885  -1.9942
 4VN  H7   H   HCH2   0   0.228  -4.9490  -1.6814  -1.6965
 4VN  H8   H   HCH2   0   0.209  -4.2996  -2.1111  -0.1221
 4VN  H9   H   HCH1   0   0.219  -5.5700   0.5533  -0.8653
 4VN  H10  H   HCH2   0   0.230  -5.2356   1.1531   1.5070
 4VN  H11  H   HCH2   0   0.211  -4.4847  -0.4035   1.8116
 4VN  H12  H   HCH2   0   0.215  -3.4585   1.8498   0.0306
 4VN  H13  H   HCH2   0   0.249  -2.7887   1.2601   1.5477
 4VN  H14  H   HCR6   0   0.256   3.1851  -1.8814   0.4861
 4VN  H15  H   HCH2   0   0.214   5.1059  -3.0920   1.0312
 4VN  H16  H   HCH2   0   0.223   6.0260  -3.0122  -0.4652
 4VN  H17  H   HOH1   0   0.460   7.4804  -3.0663   1.2593
 4VN  H18  H   HCR6   0   0.262   7.0045  -0.1142  -0.2770
 4VN  C17  C   C      0   0.433  -6.7725  -0.8250   0.2377
 4VN  O2   O   OC    -1  -0.608  -7.3331  -0.3551   1.2483
 4VN  O1   O   O      0  -0.612  -7.2393  -1.6990  -0.5213

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
 4VN  C6   O    single    1.408  0.020  1.408
 4VN  C6   C5   single    1.503  0.020  1.503
 4VN  C5   C    aromatic  1.392  0.020  1.392
 4VN  C5   C4   aromatic  1.388  0.020  1.388
 4VN  C    C1   aromatic  1.385  0.020  1.385
 4VN  C4   C3   aromatic  1.396  0.020  1.396
 4VN  C1   C2   aromatic  1.387  0.020  1.387
 4VN  C3   C2   aromatic  1.394  0.020  1.394
 4VN  C3   C7   single    1.473  0.020  1.473
 4VN  C8   C7   aromatic  1.397  0.020  1.397
 4VN  C8   C9   aromatic  1.376  0.020  1.376
 4VN  C2   CL   single    1.736  0.020  1.736
 4VN  C7   C11  aromatic  1.388  0.020  1.388
 4VN  C9   C10  aromatic  1.413  0.020  1.413
 4VN  C11  N    aromatic  1.322  0.020  1.322
 4VN  C10  N    aromatic  1.336  0.020  1.336
 4VN  C10  N1   single    1.368  0.020  1.368
 4VN  C12  N1   single    1.458  0.020  1.458
 4VN  C12  C13  single    1.519  0.020  1.519
 4VN  N1   C16  single    1.452  0.020  1.452
 4VN  C16  C15  single    1.523  0.020  1.523
 4VN  C13  C14  single    1.523  0.020  1.523
 4VN  C14  C15  single    1.521  0.020  1.521
 4VN  C14  C17  single    1.543  0.020  1.543
 4VN  O1   C17  deloc     1.248  0.020  1.248
 4VN  C17  O2   deloc     1.248  0.020  1.248
 4VN  C1   H1   single    0.930  0.020  1.080
 4VN  C8   H2   single    0.930  0.020  1.080
 4VN  C9   H3   single    0.930  0.020  1.080
 4VN  C11  H4   single    0.930  0.020  1.080
 4VN  C12  H5   single    0.970  0.020  1.090
 4VN  C12  H6   single    0.970  0.020  1.090
 4VN  C13  H7   single    0.970  0.020  1.090
 4VN  C13  H8   single    0.970  0.020  1.090
 4VN  C14  H9   single    0.970  0.020  1.090
 4VN  C15  H10  single    0.970  0.020  1.090
 4VN  C15  H11  single    0.970  0.020  1.090
 4VN  C16  H12  single    0.970  0.020  1.090
 4VN  C16  H13  single    0.970  0.020  1.090
 4VN  C4   H14  single    0.930  0.020  1.080
 4VN  C6   H15  single    0.970  0.020  1.090
 4VN  C6   H16  single    0.970  0.020  1.090
 4VN  O    H17  single    0.850  0.020  0.980
 4VN  C    H18  single    0.930  0.020  1.080

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
 4VN  H1   C1   C    120.09  3.000
 4VN  H1   C1   C2   119.96  3.000
 4VN  C    C1   C2   119.95  3.000
 4VN  CL   C2   C3   120.47  3.000
 4VN  CL   C2   C1   118.01  3.000
 4VN  C3   C2   C1   121.50  3.000
 4VN  C4   C3   C7   119.49  3.000
 4VN  C7   C3   C2   123.46  3.000
 4VN  C4   C3   C2   117.05  3.000
 4VN  C11  C7   C8   115.71  3.000
 4VN  C11  C7   C3   120.80  3.000
 4VN  C8   C7   C3   123.48  3.000
 4VN  H2   C8   C9   118.89  3.000
 4VN  H2   C8   C7   120.50  3.000
 4VN  C9   C8   C7   120.61  3.000
 4VN  H3   C9   C10  122.00  3.000
 4VN  H3   C9   C8   118.79  3.000
 4VN  C10  C9   C8   119.20  3.000
 4VN  N1   C10  N    117.18  3.000
 4VN  N1   C10  C9   122.83  3.000
 4VN  N    C10  C9   119.98  3.000
 4VN  H4   C11  N    115.69  3.000
 4VN  H4   C11  C7   119.60  3.000
 4VN  N    C11  C7   124.70  3.000
 4VN  H6   C12  H5   107.12  3.000
 4VN  H6   C12  N1   109.18  3.000
 4VN  H5   C12  N1   108.87  3.000
 4VN  H6   C12  C13  109.13  3.000
 4VN  H5   C12  C13  110.31  3.000
 4VN  N1   C12  C13  112.10  3.000
 4VN  H8   C13  H7   106.97  3.000
 4VN  H8   C13  C14  109.81  3.000
 4VN  H7   C13  C14  110.74  3.000
 4VN  H8   C13  C12  109.35  3.000
 4VN  H7   C13  C12  108.32  3.000
 4VN  C14  C13  C12  111.54  3.000
 4VN  H9   C14  C17  106.51  3.000
 4VN  H9   C14  C15  107.54  3.000
 4VN  C17  C14  C15  113.60  3.000
 4VN  H9   C14  C13  107.22  3.000
 4VN  C17  C14  C13  113.09  3.000
 4VN  C15  C14  C13  108.54  3.000
 4VN  H11  C15  H10  106.86  3.000
 4VN  H11  C15  C16  108.91  3.000
 4VN  H10  C15  C16  107.99  3.000
 4VN  H11  C15  C14  109.58  3.000
 4VN  H10  C15  C14  110.96  3.000
 4VN  C16  C15  C14  112.37  3.000
 4VN  H13  C16  H12  107.10  3.000
 4VN  H13  C16  N1   109.57  3.000
 4VN  H12  C16  N1   110.43  3.000
 4VN  H13  C16  C15  107.83  3.000
 4VN  H12  C16  C15  109.75  3.000
 4VN  N1   C16  C15  112.00  3.000
 4VN  H14  C4   C5   119.19  3.000
 4VN  H14  C4   C3   118.19  3.000
 4VN  C5   C4   C3   122.61  3.000
 4VN  C    C5   C6   121.19  3.000
 4VN  C    C5   C4   118.58  3.000
 4VN  C6   C5   C4   120.22  3.000
 4VN  H16  C6   H15  106.46  3.000
 4VN  H16  C6   O    111.20  3.000
 4VN  H15  C6   O    111.93  3.000
 4VN  H16  C6   C5   108.59  3.000
 4VN  H15  C6   C5   109.11  3.000
 4VN  O    C6   C5   109.45  3.000
 4VN  H17  O    C6   108.07  3.000
 4VN  H18  C    C5   120.65  3.000
 4VN  H18  C    C1   119.03  3.000
 4VN  C5   C    C1   120.31  3.000
 4VN  C11  N    C10  119.79  3.000
 4VN  C16  N1   C12  114.49  3.000
 4VN  C16  N1   C10  120.44  3.000
 4VN  C12  N1   C10  119.30  3.000
 4VN  O1   C17  O2   126.04  3.000
 4VN  O2   C17  C14  117.23  3.000
 4VN  O1   C17  C14  116.71  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
 4VN  CONST_01  C4   C5   C    C1      0.00   0.0  0
 4VN  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 4VN  CONST_03  C7   C3   C2   C1    180.00   0.0  0
 4VN  CONST_04  C5   C    C1   C2      0.00   0.0  0
 4VN  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 4VN  CONST_08  C    C5   C4   C3      0.00   0.0  0
 4VN  CONST_09  C    C1   C2   C3      0.00   0.0  0
 4VN  CONST_10  C9   C8   C7   C3    180.00   0.0  0
 4VN  CONST_11  N    C11  C7   C3    180.00   0.0  0
 4VN  CONST_12  C5   C4   C3   C7    180.00   0.0  0
 4VN  CONST_13  C10  C9   C8   C7      0.00   0.0  0
 4VN  CONST_14  C10  N    C11  C7      0.00   0.0  0
 4VN  CONST_16  N    C11  C7   C8      0.00   0.0  0
 4VN  CONST_17  N    C10  C9   C8      0.00   0.0  0
 4VN  CONST_18  C11  C7   C8   C9      0.00   0.0  0
 4VN  CONST_19  C11  N    C10  C9      0.00   0.0  0
 4VN  CONST_21  N1   C10  C9   C8    180.00   0.0  0
 4VN  CONST_22  N1   C10  N    C11   180.00   0.0  0
 4VN  CONST_23  C6   C5   C    C1    180.00   0.0  0
 4VN  CONST_24  C6   C5   C4   C3    180.00   0.0  0
 4VN  CONST_25  CL   C2   C3   C7      0.00   0.0  0
 4VN  CONST_26  C    C1   C2   CL    180.00   0.0  0
 4VN  CONST_27  C4   C3   C2   CL    180.00   0.0  0
 4VN  CONST_28  H18  C    C1   C2    180.00   0.0  0
 4VN  CONST_29  H14  C4   C3   C2    180.00   0.0  0
 4VN  CONST_30  H1   C1   C2   C3    180.00   0.0  0
 4VN  CONST_31  H2   C8   C7   C3      0.00   0.0  0
 4VN  CONST_32  H4   C11  C7   C3      0.00   0.0  0
 4VN  CONST_33  H3   C9   C8   C7    180.00   0.0  0
 4VN  Var_01    C12  N1   C10  C9    155.59  30.0  2
 4VN  Var_02    C13  C12  N1   C10   154.00  30.0  1
 4VN  Var_03    C15  C16  N1   C10  -155.42  30.0  1
 4VN  Var_04    N1   C12  C13  C14    54.61  30.0  1
 4VN  Var_05    N1   C16  C15  C14   -53.05  30.0  1
 4VN  Var_06    O    C6   C5   C4   -141.83  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
 4VN  chir_01  C14  C13  C15  C17  positiv

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
 4VN  plan-1  C3   0.020
 4VN  plan-1  C7   0.020
 4VN  plan-1  C8   0.020
 4VN  plan-1  C9   0.020
 4VN  plan-1  C10  0.020
 4VN  plan-1  C11  0.020
 4VN  plan-1  N    0.020
 4VN  plan-1  N1   0.020
 4VN  plan-1  H2   0.020
 4VN  plan-1  H3   0.020
 4VN  plan-1  H4   0.020
 4VN  plan-2  C1   0.020
 4VN  plan-2  C2   0.020
 4VN  plan-2  C3   0.020
 4VN  plan-2  C7   0.020
 4VN  plan-2  CL   0.020
 4VN  plan-2  C4   0.020
 4VN  plan-2  C5   0.020
 4VN  plan-2  C6   0.020
 4VN  plan-2  C    0.020
 4VN  plan-2  H1   0.020
 4VN  plan-2  H14  0.020
 4VN  plan-2  H18  0.020
 4VN  plan-3  C14  0.020
 4VN  plan-3  C17  0.020
 4VN  plan-3  O2   0.020
 4VN  plan-3  O1   0.020

