# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:54:24 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 1-{5-[2-fluoro-5-(hydroxymethyl)phenyl]pyridin-2-yl}piperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccc(F)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
 4VL  4VL  '1-{5-[2-fluoro-5-(hydroxymethyl)phenyl]pyridin-2-yl}piperidine-4-carboxylic acid'  ligand  43  24  .  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_4VL
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
 4VL  C1   C  CR16  0  -0.395   5.4329   1.4128  -0.4463
 4VL  C2   C  CR6   0   0.502   4.0533   1.4473  -0.4705
 4VL  C3   C  CR6   0  -0.124   3.2633   0.4052   0.0005
 4VL  C7   C  CR6   0  -0.024   1.7932   0.4472  -0.0460
 4VL  C8   C  CR16  0  -0.177   1.0327   1.5363   0.3918
 4VL  C9   C  CR16  0  -0.406  -0.3409   1.4992   0.3441
 4VL  C10  C  CR6   0   0.547  -0.9818   0.3434  -0.1537
 4VL  C11  C  CR16  0  -0.090   1.0671  -0.6358  -0.5207
 4VL  C12  C  CH2   0  -0.304  -3.2333   1.3410  -0.0238
 4VL  C13  C  CH2   0  -0.418  -4.5413   0.9211   0.6324
 4VL  C14  C  CH1   0  -0.401  -5.2135  -0.1929  -0.1545
 4VL  C15  C  CH2   0  -0.434  -4.2342  -1.3600  -0.3117
 4VL  C16  C  CH2   0  -0.298  -2.9364  -0.8880  -0.9472
 4VL  F    F  F     0  -0.308   3.4525   2.5315  -0.9895
 4VL  C4   C  CR16  0  -0.333   3.9365  -0.7109   0.5000
 4VL  C5   C  CR6   0   0.096   5.3232  -0.7868   0.5390
 4VL  C6   C  CH2   0  -0.230   6.0058  -2.0230   1.0487
 4VL  O    O  OH1   0  -0.668   6.2711  -2.8661  -0.0547
 4VL  C    C  CR16  0  -0.283   6.0657   0.2875   0.0592
 4VL  N    N  N     0  -0.477  -0.2531  -0.6910  -0.5794
 4VL  N1   N  NT    0  -0.502  -2.3419   0.2097  -0.2031
 4VL  H1   H  HCR6  0   0.279   6.0020   2.2516  -0.8257
 4VL  H2   H  HCR6  0   0.260   1.5122   2.4185   0.7949
 4VL  H3   H  HCR6  0   0.271  -0.8918   2.3560   0.6988
 4VL  H4   H  HCR6  0   0.255   1.5898  -1.5111  -0.8955
 4VL  H5   H  HCH2  0   0.229  -3.4414   1.8117  -0.9949
 4VL  H6   H  HCH2  0   0.266  -2.7710   2.0969   0.6041
 4VL  H7   H  HCH2  0   0.234  -4.3376   0.5858   1.6524
 4VL  H8   H  HCH2  0   0.251  -5.1871   1.7978   0.7009
 4VL  H9   H  HCH1  0   0.278  -5.4595   0.1770  -1.1588
 4VL  H10  H  HCH2  0   0.237  -4.0227  -1.7981   0.6683
 4VL  H11  H  HCH2  0   0.256  -4.6550  -2.1466  -0.9387
 4VL  H12  H  HCH2  0   0.273  -2.2299  -1.7102  -0.9917
 4VL  H13  H  HCH2  0   0.223  -3.1324  -0.5714  -1.9813
 4VL  H14  H  HCR6  0   0.259   3.3520  -1.5352   0.8924
 4VL  H15  H  HCH2  0   0.210   6.9303  -1.7407   1.5661
 4VL  H16  H  HCH2  0   0.210   5.3624  -2.5169   1.7866
 4VL  H17  H  HOH1  0   0.456   6.7259  -3.6474   0.2756
 4VL  H18  H  HCR6  0   0.263   7.1479   0.2545   0.0851
 4VL  H19  H  HOH1  0   0.480  -7.9476  -1.8319   0.1967
 4VL  C17  C  C     0   0.570  -6.5088  -0.6334   0.4803
 4VL  O2   O  O     0  -0.439  -6.9533  -0.2080   1.5178
 4VL  O1   O  OH1   0  -0.595  -7.1258  -1.5636  -0.2408

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
 4VL  O    C6   single    1.414  0.020  1.414
 4VL  C6   C5   single    1.501  0.020  1.501
 4VL  C5   C4   aromatic  1.389  0.020  1.389
 4VL  C5   C    aromatic  1.391  0.020  1.391
 4VL  C4   C3   aromatic  1.396  0.020  1.396
 4VL  C    C1   aromatic  1.386  0.020  1.386
 4VL  C11  N    aromatic  1.323  0.020  1.323
 4VL  C11  C7   aromatic  1.388  0.020  1.388
 4VL  N    C10  aromatic  1.335  0.020  1.335
 4VL  C3   C7   single    1.471  0.020  1.471
 4VL  C3   C2   aromatic  1.390  0.020  1.390
 4VL  C16  C15  single    1.520  0.020  1.520
 4VL  C16  N1   single    1.453  0.020  1.453
 4VL  C1   C2   aromatic  1.380  0.020  1.380
 4VL  C7   C8   aromatic  1.399  0.020  1.399
 4VL  C2   F    single    1.344  0.020  1.344
 4VL  C15  C14  single    1.532  0.020  1.532
 4VL  C10  N1   single    1.367  0.020  1.367
 4VL  C10  C9   aromatic  1.412  0.020  1.412
 4VL  N1   C12  single    1.451  0.020  1.451
 4VL  C8   C9   aromatic  1.375  0.020  1.375
 4VL  C14  C17  single    1.508  0.020  1.508
 4VL  C14  C13  single    1.521  0.020  1.521
 4VL  O2   C17  double    1.206  0.020  1.206
 4VL  C17  O1   single    1.329  0.020  1.329
 4VL  C12  C13  single    1.522  0.020  1.522
 4VL  C1   H1   single    0.930  0.020  1.080
 4VL  C8   H2   single    0.930  0.020  1.080
 4VL  C9   H3   single    0.930  0.020  1.080
 4VL  C11  H4   single    0.930  0.020  1.080
 4VL  C12  H5   single    0.970  0.020  1.090
 4VL  C12  H6   single    0.970  0.020  1.090
 4VL  C13  H7   single    0.970  0.020  1.090
 4VL  C13  H8   single    0.970  0.020  1.090
 4VL  C14  H9   single    0.970  0.020  1.090
 4VL  C15  H10  single    0.970  0.020  1.090
 4VL  C15  H11  single    0.970  0.020  1.090
 4VL  C16  H12  single    0.970  0.020  1.090
 4VL  C16  H13  single    0.970  0.020  1.090
 4VL  C4   H14  single    0.930  0.020  1.080
 4VL  C6   H15  single    0.970  0.020  1.090
 4VL  C6   H16  single    0.970  0.020  1.090
 4VL  O    H17  single    0.850  0.020  0.980
 4VL  C    H18  single    0.930  0.020  1.080
 4VL  O1   H19  single    0.850  0.020  0.980

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
 4VL  H1   C1   C    121.12  3.000
 4VL  H1   C1   C2   120.00  3.000
 4VL  C    C1   C2   118.87  3.000
 4VL  F    C2   C3   118.80  3.000
 4VL  F    C2   C1   118.28  3.000
 4VL  C3   C2   C1   122.91  3.000
 4VL  C4   C3   C7   121.07  3.000
 4VL  C7   C3   C2   122.39  3.000
 4VL  C4   C3   C2   116.53  3.000
 4VL  C11  C7   C8   115.48  3.000
 4VL  C8   C7   C3   123.76  3.000
 4VL  C11  C7   C3   120.75  3.000
 4VL  H2   C8   C9   118.54  3.000
 4VL  H2   C8   C7   120.69  3.000
 4VL  C9   C8   C7   120.76  3.000
 4VL  H3   C9   C10  122.29  3.000
 4VL  H3   C9   C8   118.52  3.000
 4VL  C10  C9   C8   119.19  3.000
 4VL  N1   C10  N    117.11  3.000
 4VL  N1   C10  C9   122.96  3.000
 4VL  N    C10  C9   119.92  3.000
 4VL  H4   C11  N    115.56  3.000
 4VL  H4   C11  C7   119.68  3.000
 4VL  N    C11  C7   124.76  3.000
 4VL  H6   C12  H5   107.06  3.000
 4VL  H6   C12  N1   110.64  3.000
 4VL  H5   C12  N1   109.93  3.000
 4VL  H6   C12  C13  107.97  3.000
 4VL  H5   C12  C13  109.65  3.000
 4VL  N1   C12  C13  111.46  3.000
 4VL  H8   C13  H7   107.35  3.000
 4VL  H8   C13  C14  111.07  3.000
 4VL  H7   C13  C14  109.91  3.000
 4VL  H8   C13  C12  108.30  3.000
 4VL  H7   C13  C12  109.08  3.000
 4VL  C14  C13  C12  111.03  3.000
 4VL  H9   C14  C17  106.91  3.000
 4VL  H9   C14  C15  107.82  3.000
 4VL  C17  C14  C15  111.70  3.000
 4VL  H9   C14  C13  109.00  3.000
 4VL  C17  C14  C13  112.08  3.000
 4VL  C15  C14  C13  109.19  3.000
 4VL  H11  C15  H10  107.50  3.000
 4VL  H11  C15  C16  108.24  3.000
 4VL  H10  C15  C16  109.49  3.000
 4VL  H11  C15  C14  111.23  3.000
 4VL  H10  C15  C14  109.68  3.000
 4VL  C16  C15  C14  110.62  3.000
 4VL  H13  C16  H12  107.21  3.000
 4VL  H13  C16  N1   109.70  3.000
 4VL  H12  C16  N1   109.09  3.000
 4VL  H13  C16  C15  109.30  3.000
 4VL  H12  C16  C15  109.74  3.000
 4VL  N1   C16  C15  111.70  3.000
 4VL  H14  C4   C5   119.11  3.000
 4VL  H14  C4   C3   118.52  3.000
 4VL  C5   C4   C3   122.35  3.000
 4VL  C    C5   C6   120.69  3.000
 4VL  C    C5   C4   118.73  3.000
 4VL  C6   C5   C4   120.55  3.000
 4VL  H16  C6   H15  107.05  3.000
 4VL  H16  C6   O    111.52  3.000
 4VL  H15  C6   O    111.32  3.000
 4VL  H16  C6   C5   109.43  3.000
 4VL  H15  C6   C5   109.36  3.000
 4VL  O    C6   C5   108.15  3.000
 4VL  H17  O    C6   107.75  3.000
 4VL  H18  C    C5   120.10  3.000
 4VL  H18  C    C1   119.31  3.000
 4VL  C5   C    C1   120.59  3.000
 4VL  C11  N    C10  119.89  3.000
 4VL  C16  N1   C12  113.62  3.000
 4VL  C12  N1   C10  122.02  3.000
 4VL  C16  N1   C10  119.95  3.000
 4VL  O1   C17  O2   122.86  3.000
 4VL  O1   C17  C14  112.01  3.000
 4VL  O2   C17  C14  125.13  3.000
 4VL  H19  O1   C17  110.03  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
 4VL  CONST_01  C4   C5   C    C1      0.00   0.0  0
 4VL  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 4VL  CONST_03  C7   C3   C2   C1    180.00   0.0  0
 4VL  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 4VL  CONST_07  C5   C    C1   C2      0.00   0.0  0
 4VL  CONST_08  C    C5   C4   C3      0.00   0.0  0
 4VL  CONST_09  N    C11  C7   C3    180.00   0.0  0
 4VL  CONST_10  C9   C8   C7   C3    180.00   0.0  0
 4VL  CONST_11  C    C1   C2   C3      0.00   0.0  0
 4VL  CONST_12  C10  N    C11  C7      0.00   0.0  0
 4VL  CONST_13  C5   C4   C3   C7    180.00   0.0  0
 4VL  CONST_14  C10  C9   C8   C7      0.00   0.0  0
 4VL  CONST_15  N    C11  C7   C8      0.00   0.0  0
 4VL  CONST_17  N    C10  C9   C8      0.00   0.0  0
 4VL  CONST_18  C11  N    C10  C9      0.00   0.0  0
 4VL  CONST_19  C11  C7   C8   C9      0.00   0.0  0
 4VL  CONST_21  N1   C10  C9   C8    180.00   0.0  0
 4VL  CONST_22  N1   C10  N    C11   180.00   0.0  0
 4VL  CONST_23  C6   C5   C    C1    180.00   0.0  0
 4VL  CONST_24  C6   C5   C4   C3    180.00   0.0  0
 4VL  CONST_25  F    C2   C3   C7      0.00   0.0  0
 4VL  CONST_26  C4   C3   C2   F     180.00   0.0  0
 4VL  CONST_27  C    C1   C2   F     180.00   0.0  0
 4VL  CONST_28  H14  C4   C3   C2    180.00   0.0  0
 4VL  CONST_29  H18  C    C1   C2    180.00   0.0  0
 4VL  CONST_30  H4   C11  C7   C3      0.00   0.0  0
 4VL  CONST_31  H2   C8   C7   C3      0.00   0.0  0
 4VL  CONST_32  H1   C1   C2   C3    180.00   0.0  0
 4VL  CONST_33  H3   C9   C8   C7    180.00   0.0  0
 4VL  CONST_34  H19  O1   C17  C14   180.00   0.0  0
 4VL  Var_01    C16  N1   C10  C9    168.60  30.0  2
 4VL  Var_02    C15  C16  N1   C10   147.60  30.0  1
 4VL  Var_03    C13  C12  N1   C10  -148.37  30.0  1
 4VL  Var_04    N1   C16  C15  C14    55.16  30.0  1
 4VL  Var_05    N1   C12  C13  C14   -55.28  30.0  1
 4VL  Var_06    O    C6   C5   C4     92.78  30.0  2

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
 4VL  chir_01  C14  C15  C17  C13  negativ

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
 4VL  plan-1  C3   0.020
 4VL  plan-1  C7   0.020
 4VL  plan-1  C8   0.020
 4VL  plan-1  C9   0.020
 4VL  plan-1  C10  0.020
 4VL  plan-1  C11  0.020
 4VL  plan-1  N    0.020
 4VL  plan-1  N1   0.020
 4VL  plan-1  H2   0.020
 4VL  plan-1  H3   0.020
 4VL  plan-1  H4   0.020
 4VL  plan-2  C1   0.020
 4VL  plan-2  C2   0.020
 4VL  plan-2  C3   0.020
 4VL  plan-2  C7   0.020
 4VL  plan-2  F    0.020
 4VL  plan-2  C4   0.020
 4VL  plan-2  C5   0.020
 4VL  plan-2  C6   0.020
 4VL  plan-2  C    0.020
 4VL  plan-2  H1   0.020
 4VL  plan-2  H14  0.020
 4VL  plan-2  H18  0.020
 4VL  plan-3  C14  0.020
 4VL  plan-3  H19  0.020
 4VL  plan-3  C17  0.020
 4VL  plan-3  O2   0.020
 4VL  plan-3  O1   0.020

