# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 04:09:43 2021
#   Inital geometry file: a 96 line input string
#   Ligand name: piperidin-4-ylmethyl 4-(aminomethyl)-4-fluoranyl-piperidine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1(F)CCN(CC1)C(=O)OCC2CCNCC2
#
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
 CVO  CVO  'piperidin-4-ylmethyl 4-(aminomethyl)-4-fluoranyl-piperidine-1-carboxylate'  ligand  43  19  .  2022-03-15  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CVO
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
 CVO  N1   N  NH1   0  -0.595  -0.2744  54.6190  86.3034
 CVO  C2   C  CH2   0  -0.291   0.3386  53.4239  86.8540
 CVO  C3   C  CH2   0  -0.419   0.6706  52.4503  85.7330
 CVO  C4   C  CH1   0  -0.294  -0.5807  52.0988  84.9272
 CVO  C5   C  CH2   0  -0.419  -1.2699  53.3778  84.4527
 CVO  C6   C  CH2   0  -0.292  -1.5221  54.3135  85.6268
 CVO  C7   C  CH2   0  -0.158  -0.1901  51.1717  83.7878
 CVO  O8   O  O2    0  -0.487  -1.2733  50.8425  82.9182
 CVO  C9   C  C     0   0.760  -2.1617  49.9374  83.3363
 CVO  N10  N  NT    0  -0.488  -3.1279  49.7147  82.4183
 CVO  O11  O  O     0  -0.526  -2.0798  49.3631  84.4054
 CVO  C12  C  CH2   0  -0.282  -4.3586  49.0488  82.8210
 CVO  C13  C  CH2   0  -0.524  -5.5818  49.9134  82.4748
 CVO  C14  C  CT    0   0.398  -5.2490  51.3943  82.4966
 CVO  C15  C  CH2   0  -0.489  -4.1726  51.7128  81.4591
 CVO  C16  C  CH2   0  -0.331  -3.2731  50.5026  81.2080
 CVO  C17  C  CH2   0  -0.346  -6.4763  52.2902  82.3695
 CVO  F18  F  F     0  -0.391  -4.7040  51.6786  83.7711
 CVO  N19  N  NH2   0  -0.804  -7.1960  52.0389  81.1335
 CVO  H1   H  HNH1  0   0.350  -0.4493  55.2803  87.0486
 CVO  H3   H  HCH2  0   0.185  -0.3131  52.9145  87.5839
 CVO  H4   H  HCH2  0   0.230   1.2505  53.7059  87.3848
 CVO  H5   H  HCH2  0   0.232   1.1217  51.5473  86.1525
 CVO  H6   H  HCH2  0   0.213   1.4165  52.9080  85.0742
 CVO  H7   H  HCH1  0   0.229  -1.2688  51.5696  85.5961
 CVO  H8   H  HCH2  0   0.209  -0.6406  53.8851  83.7132
 CVO  H9   H  HCH2  0   0.237  -2.2218  53.1459  83.9704
 CVO  H10  H  HCH2  0   0.230  -1.9705  55.2445  85.2735
 CVO  H11  H  HCH2  0   0.183  -2.2577  53.8397  86.2994
 CVO  H12  H  HCH2  0   0.237   0.2766  50.2624  84.1751
 CVO  H13  H  HCH2  0   0.236   0.5353  51.6687  83.1405
 CVO  H14  H  HCH2  0   0.258  -4.3209  48.8552  83.8893
 CVO  H15  H  HCH2  0   0.243  -4.4408  48.0799  82.3217
 CVO  H16  H  HCH2  0   0.258  -6.3892  49.6916  83.1763
 CVO  H17  H  HCH2  0   0.252  -5.9626  49.6713  81.4819
 CVO  H18  H  HCH2  0   0.246  -4.6324  52.0078  80.5136
 CVO  H19  H  HCH2  0   0.257  -3.5937  52.5718  81.8050
 CVO  H20  H  HCH2  0   0.254  -3.7286  49.8517  80.4581
 CVO  H21  H  HCH2  0   0.275  -2.3062  50.7973  80.8112
 CVO  H22  H  HCH2  0   0.218  -6.1539  53.3341  82.4893
 CVO  H23  H  HCH2  0   0.240  -7.1433  52.0691  83.2060
 CVO  H24  H  HNH2  0   0.359  -8.1458  52.3716  81.2240
 CVO  H25  H  HNH2  0   0.349  -6.7905  52.5703  80.3751

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
 CVO  N19  C17  single  1.452  0.020  1.452
 CVO  C17  C14  single  1.525  0.020  1.525
 CVO  C14  C15  single  1.529  0.020  1.529
 CVO  C14  C13  single  1.518  0.020  1.518
 CVO  C14  F18  single  1.415  0.020  1.415
 CVO  C15  C16  single  1.529  0.020  1.529
 CVO  C13  C12  single  1.537  0.020  1.537
 CVO  C16  N10  single  1.451  0.020  1.451
 CVO  C12  N10  single  1.456  0.020  1.456
 CVO  N10  C9   single  1.351  0.020  1.351
 CVO  C9   O8   single  1.335  0.020  1.335
 CVO  C9   O11  double  1.216  0.020  1.216
 CVO  O8   C7   single  1.428  0.020  1.428
 CVO  C7   C4   single  1.520  0.020  1.520
 CVO  C3   C4   single  1.529  0.020  1.529
 CVO  C3   C2   single  1.521  0.020  1.521
 CVO  C4   C5   single  1.528  0.020  1.528
 CVO  C5   C6   single  1.522  0.020  1.522
 CVO  C2   N1   single  1.452  0.020  1.452
 CVO  N1   C6   single  1.452  0.020  1.452
 CVO  N1   H1   single  0.890  0.020  1.040
 CVO  C2   H3   single  0.970  0.020  1.090
 CVO  C2   H4   single  0.970  0.020  1.090
 CVO  C3   H5   single  0.970  0.020  1.090
 CVO  C3   H6   single  0.970  0.020  1.090
 CVO  C4   H7   single  0.970  0.020  1.090
 CVO  C5   H8   single  0.970  0.020  1.090
 CVO  C5   H9   single  0.970  0.020  1.090
 CVO  C6   H10  single  0.970  0.020  1.090
 CVO  C6   H11  single  0.970  0.020  1.090
 CVO  C7   H12  single  0.970  0.020  1.090
 CVO  C7   H13  single  0.970  0.020  1.090
 CVO  C12  H14  single  0.970  0.020  1.090
 CVO  C12  H15  single  0.970  0.020  1.090
 CVO  C13  H16  single  0.970  0.020  1.090
 CVO  C13  H17  single  0.970  0.020  1.090
 CVO  C15  H18  single  0.970  0.020  1.090
 CVO  C15  H19  single  0.970  0.020  1.090
 CVO  C16  H20  single  0.970  0.020  1.090
 CVO  C16  H21  single  0.970  0.020  1.090
 CVO  C17  H22  single  0.970  0.020  1.090
 CVO  C17  H23  single  0.970  0.020  1.090
 CVO  N19  H24  single  0.890  0.020  1.040
 CVO  N19  H25  single  0.890  0.020  1.040

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
 CVO  H1   N1   C6   109.40  3.000
 CVO  H1   N1   C2   109.38  3.000
 CVO  C6   N1   C2   111.50  3.000
 CVO  H4   C2   H3   106.91  3.000
 CVO  H4   C2   C3   109.95  3.000
 CVO  H3   C2   C3   108.72  3.000
 CVO  H4   C2   N1   108.92  3.000
 CVO  H3   C2   N1   112.44  3.000
 CVO  C3   C2   N1   109.85  3.000
 CVO  H6   C3   H5   107.15  3.000
 CVO  H6   C3   C4   109.66  3.000
 CVO  H5   C3   C4   110.49  3.000
 CVO  H6   C3   C2   108.92  3.000
 CVO  H5   C3   C2   109.63  3.000
 CVO  C4   C3   C2   110.90  3.000
 CVO  H7   C4   C7   108.93  3.000
 CVO  H7   C4   C5   108.09  3.000
 CVO  C7   C4   C5   113.17  3.000
 CVO  H7   C4   C3   107.65  3.000
 CVO  C5   C4   C3   109.89  3.000
 CVO  C7   C4   C3   108.96  3.000
 CVO  H9   C5   H8   107.52  3.000
 CVO  H9   C5   C6   109.07  3.000
 CVO  H8   C5   C6   109.34  3.000
 CVO  H9   C5   C4   110.64  3.000
 CVO  H8   C5   C4   109.76  3.000
 CVO  C6   C5   C4   110.46  3.000
 CVO  H11  C6   H10  106.83  3.000
 CVO  H11  C6   C5   108.45  3.000
 CVO  H10  C6   C5   110.02  3.000
 CVO  H11  C6   N1   112.28  3.000
 CVO  H10  C6   N1   108.92  3.000
 CVO  C5   C6   N1   110.26  3.000
 CVO  H13  C7   H12  107.76  3.000
 CVO  H13  C7   O8   104.36  3.000
 CVO  H12  C7   O8   110.36  3.000
 CVO  H13  C7   C4   109.73  3.000
 CVO  H12  C7   C4   110.58  3.000
 CVO  O8   C7   C4   113.72  3.000
 CVO  C9   O8   C7   118.06  3.000
 CVO  O11  C9   N10  124.57  3.000
 CVO  O11  C9   O8   123.39  3.000
 CVO  N10  C9   O8   112.01  3.000
 CVO  C16  N10  C12  113.23  3.000
 CVO  C12  N10  C9   119.46  3.000
 CVO  C16  N10  C9   123.27  3.000
 CVO  H15  C12  H14  107.08  3.000
 CVO  H15  C12  C13  109.63  3.000
 CVO  H14  C12  C13  110.45  3.000
 CVO  H15  C12  N10  110.03  3.000
 CVO  H14  C12  N10  108.91  3.000
 CVO  C13  C12  N10  110.67  3.000
 CVO  H17  C13  H16  106.35  3.000
 CVO  H17  C13  C14  107.83  3.000
 CVO  H16  C13  C14  110.54  3.000
 CVO  H17  C13  C12  110.98  3.000
 CVO  H16  C13  C12  109.22  3.000
 CVO  C14  C13  C12  111.78  3.000
 CVO  F18  C14  C17  105.49  3.000
 CVO  F18  C14  C15  107.35  3.000
 CVO  C17  C14  C15  112.82  3.000
 CVO  F18  C14  C13  107.06  3.000
 CVO  C15  C14  C13  110.36  3.000
 CVO  C17  C14  C13  113.30  3.000
 CVO  H19  C15  H18  106.55  3.000
 CVO  H19  C15  C16  111.27  3.000
 CVO  H18  C15  C16  108.63  3.000
 CVO  H19  C15  C14  108.80  3.000
 CVO  H18  C15  C14  110.33  3.000
 CVO  C16  C15  C14  111.16  3.000
 CVO  H21  C16  H20  106.39  3.000
 CVO  H21  C16  C15  111.67  3.000
 CVO  H20  C16  C15  109.82  3.000
 CVO  H21  C16  N10  111.28  3.000
 CVO  H20  C16  N10  106.90  3.000
 CVO  C15  C16  N10  110.59  3.000
 CVO  H23  C17  H22  106.73  3.000
 CVO  H23  C17  N19  108.30  3.000
 CVO  H22  C17  N19  113.74  3.000
 CVO  H23  C17  C14  107.98  3.000
 CVO  H22  C17  C14  108.23  3.000
 CVO  N19  C17  C14  111.60  3.000
 CVO  H25  N19  H24  105.73  3.000
 CVO  H25  N19  C17  110.41  3.000
 CVO  H24  N19  C17  109.43  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
 CVO  Var_01  C4   C3   C2   N1    -57.11  30.0  1
 CVO  Var_02  C4   C5   C6   N1     57.12  30.0  1
 CVO  Var_03  C5   C6   N1   C2    -61.96  30.0  1
 CVO  Var_04  C6   N1   C2   C3     61.70  30.0  1
 CVO  Var_05  C14  C15  C16  N10   -32.59  30.0  1
 CVO  Var_06  C14  C13  C12  N10   -29.20  30.0  1
 CVO  Var_07  C15  C16  N10  C12    68.20  30.0  1
 CVO  Var_08  C16  N10  C12  C13   -34.12  30.0  1
 CVO  Var_09  N10  C9   O8   C7   -179.70  30.0  1
 CVO  Var_10  H24  N19  C17  C14   159.28  30.0  3
 CVO  Var_11  H12  C7   O8   C9     47.92  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
 CVO  chir_01  C4   C7   C3   C5   negativ
 CVO  chir_02  C14  C15  C13  F18  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
 CVO  plan-1  O8   0.020
 CVO  plan-1  C9   0.020
 CVO  plan-1  N10  0.020
 CVO  plan-1  O11  0.020

