# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:16:13 2021
#   Inital geometry file: a 84 line input string
#   Ligand name: 3-cyclopentyl-1-(piperazin-1-yl)propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCC1CCCC1)N2CCNCC2
#
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
 RDV  RDV  3-cyclopentyl-1-(piperazin-1-yl)propan-1-one  ligand  37  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RDV
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
 RDV  C4   C  CH2   0  -0.443  32.2304  8.3878  63.6042
 RDV  C5   C  CH2   0  -0.433  29.9468  7.7669  62.5893
 RDV  C6   C  CH2   0  -0.585  30.0309  8.7538  61.4195
 RDV  N1   N  NH1   0  -0.602  29.4590  4.7175  58.6256
 RDV  C7   C  C     0   0.533  29.0577  8.3899  60.3175
 RDV  C8   C  CH2   0  -0.306  28.4655  6.9243  58.4561
 RDV  C9   C  CH2   0  -0.291  28.2027  5.4426  58.6691
 RDV  C10  C  CH2   0  -0.288  30.3709  5.1797  59.6544
 RDV  C11  C  CH2   0  -0.310  30.6491  6.6622  59.4591
 RDV  O    O  O     0  -0.512  27.9701  8.9551  60.2521
 RDV  C3   C  CH1   0  -0.226  30.7149  8.2364  63.8146
 RDV  C2   C  CH2   0  -0.422  30.6214  7.2845  65.0066
 RDV  C1   C  CH2   0  -0.449  31.7238  7.7836  65.9347
 RDV  C    C  CH2   0  -0.443  32.8803  8.1445  64.9862
 RDV  N    N  NT    0  -0.451  29.4035  7.4086  59.4558
 RDV  H1   H  HCH2  0   0.218  32.5773  7.6386  62.8856
 RDV  H2   H  HCH2  0   0.232  32.4923  9.3620  63.1888
 RDV  H3   H  HCH2  0   0.238  28.8954  7.6257  62.8574
 RDV  H4   H  HCH2  0   0.223  30.3202  6.7823  62.2870
 RDV  H5   H  HCH2  0   0.259  31.0570  8.8357  61.0559
 RDV  H6   H  HCH2  0   0.261  29.7472  9.7470  61.7712
 RDV  H9   H  HCH2  0   0.237  28.8929  7.0830  57.4607
 RDV  H10  H  HCH2  0   0.262  27.5417  7.4915  58.5174
 RDV  H11  H  HCH2  0   0.240  27.5480  5.0774  57.8756
 RDV  H12  H  HCH2  0   0.199  27.6652  5.3155  59.6223
 RDV  H13  H  HCH2  0   0.199  29.9820  5.0263  60.6741
 RDV  H14  H  HCH2  0   0.242  31.3096  4.6277  59.5791
 RDV  H15  H  HCH2  0   0.259  31.3201  7.0193  60.2346
 RDV  H16  H  HCH2  0   0.249  31.1539  6.8133  58.4993
 RDV  H17  H  HCH1  0   0.221  30.3052  9.2068  64.1248
 RDV  H18  H  HCH2  0   0.228  29.6326  7.2777  65.4699
 RDV  H19  H  HCH2  0   0.210  30.8370  6.2620  64.6764
 RDV  H20  H  HCH2  0   0.227  32.0107  7.0562  66.6956
 RDV  H21  H  HCH2  0   0.217  31.3751  8.6760  66.4611
 RDV  H22  H  HCH2  0   0.224  33.5953  7.3227  64.9275
 RDV  H23  H  HCH2  0   0.227  33.4351  9.0141  65.3403
 RDV  H7   H  HNH1  0   0.358  29.2874  3.7278  58.7424

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
 RDV  N1   C9   single  1.451  0.020  1.451
 RDV  N1   C10  single  1.450  0.020  1.450
 RDV  C9   C8   single  1.520  0.020  1.520
 RDV  C8   N    single  1.454  0.020  1.454
 RDV  C11  C10  single  1.521  0.020  1.521
 RDV  C11  N    single  1.452  0.020  1.452
 RDV  N    C7   single  1.351  0.020  1.351
 RDV  C7   O    double  1.227  0.020  1.227
 RDV  C7   C6   single  1.515  0.020  1.515
 RDV  C6   C5   single  1.533  0.020  1.533
 RDV  C5   C3   single  1.520  0.020  1.520
 RDV  C4   C3   single  1.538  0.020  1.538
 RDV  C4   C    single  1.546  0.020  1.546
 RDV  C3   C2   single  1.528  0.020  1.528
 RDV  C    C1   single  1.539  0.020  1.539
 RDV  C2   C1   single  1.525  0.020  1.525
 RDV  C4   H1   single  0.970  0.020  1.090
 RDV  C4   H2   single  0.970  0.020  1.090
 RDV  C5   H3   single  0.970  0.020  1.090
 RDV  C5   H4   single  0.970  0.020  1.090
 RDV  C6   H5   single  0.970  0.020  1.090
 RDV  C6   H6   single  0.970  0.020  1.090
 RDV  N1   H7   single  0.890  0.020  1.040
 RDV  C8   H9   single  0.970  0.020  1.090
 RDV  C8   H10  single  0.970  0.020  1.090
 RDV  C9   H11  single  0.970  0.020  1.090
 RDV  C9   H12  single  0.970  0.020  1.090
 RDV  C10  H13  single  0.970  0.020  1.090
 RDV  C10  H14  single  0.970  0.020  1.090
 RDV  C11  H15  single  0.970  0.020  1.090
 RDV  C11  H16  single  0.970  0.020  1.090
 RDV  C3   H17  single  0.970  0.020  1.090
 RDV  C2   H18  single  0.970  0.020  1.090
 RDV  C2   H19  single  0.970  0.020  1.090
 RDV  C1   H20  single  0.970  0.020  1.090
 RDV  C1   H21  single  0.970  0.020  1.090
 RDV  C    H22  single  0.970  0.020  1.090
 RDV  C    H23  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
 RDV  H2   C4   H1   106.57  3.000
 RDV  H2   C4   C    112.33  3.000
 RDV  H1   C4   C    110.23  3.000
 RDV  H2   C4   C3   112.13  3.000
 RDV  H1   C4   C3   109.56  3.000
 RDV  C    C4   C3   106.05  3.000
 RDV  H4   C5   H3   106.21  3.000
 RDV  H4   C5   C3   109.13  3.000
 RDV  H3   C5   C3   109.13  3.000
 RDV  H4   C5   C6   110.45  3.000
 RDV  H3   C5   C6   108.83  3.000
 RDV  C3   C5   C6   112.86  3.000
 RDV  H6   C6   H5   106.47  3.000
 RDV  H6   C6   C7   106.63  3.000
 RDV  H5   C6   C7   112.31  3.000
 RDV  H6   C6   C5   109.02  3.000
 RDV  H5   C6   C5   110.73  3.000
 RDV  C7   C6   C5   111.43  3.000
 RDV  H7   N1   C10  109.67  3.000
 RDV  H7   N1   C9   109.79  3.000
 RDV  C10  N1   C9   111.34  3.000
 RDV  N    C7   O    121.82  3.000
 RDV  O    C7   C6   119.84  3.000
 RDV  N    C7   C6   118.30  3.000
 RDV  H10  C8   H9   107.92  3.000
 RDV  H10  C8   N    109.64  3.000
 RDV  H9   C8   N    108.97  3.000
 RDV  H10  C8   C9   110.75  3.000
 RDV  H9   C8   C9   109.64  3.000
 RDV  N    C8   C9   109.88  3.000
 RDV  H12  C9   H11  107.32  3.000
 RDV  H12  C9   C8   108.55  3.000
 RDV  H11  C9   C8   109.15  3.000
 RDV  H12  C9   N1   112.99  3.000
 RDV  H11  C9   N1   109.29  3.000
 RDV  C8   C9   N1   109.46  3.000
 RDV  H14  C10  H13  107.27  3.000
 RDV  H14  C10  C11  109.07  3.000
 RDV  H13  C10  C11  108.60  3.000
 RDV  H14  C10  N1   109.31  3.000
 RDV  H13  C10  N1   112.96  3.000
 RDV  C11  C10  N1   109.54  3.000
 RDV  H16  C11  H15  107.20  3.000
 RDV  H16  C11  N    108.82  3.000
 RDV  H15  C11  N    111.26  3.000
 RDV  H16  C11  C10  109.35  3.000
 RDV  H15  C11  C10  109.99  3.000
 RDV  N    C11  C10  110.15  3.000
 RDV  H17  C3   C2   107.89  3.000
 RDV  H17  C3   C5   108.19  3.000
 RDV  C2   C3   C5   113.91  3.000
 RDV  H17  C3   C4   108.63  3.000
 RDV  C2   C3   C4   103.20  3.000
 RDV  C5   C3   C4   114.71  3.000
 RDV  H19  C2   H18  107.46  3.000
 RDV  H19  C2   C1   110.27  3.000
 RDV  H18  C2   C1   113.47  3.000
 RDV  H19  C2   C3   109.52  3.000
 RDV  H18  C2   C3   112.97  3.000
 RDV  C1   C2   C3   103.10  3.000
 RDV  H21  C1   H20  107.00  3.000
 RDV  H21  C1   C    110.19  3.000
 RDV  H20  C1   C    112.87  3.000
 RDV  H21  C1   C2   109.24  3.000
 RDV  H20  C1   C2   113.35  3.000
 RDV  C    C1   C2   104.17  3.000
 RDV  H23  C    H22  106.54  3.000
 RDV  H23  C    C1   111.67  3.000
 RDV  H22  C    C1   110.43  3.000
 RDV  H23  C    C4   112.24  3.000
 RDV  H22  C    C4   110.24  3.000
 RDV  C1   C    C4   105.78  3.000
 RDV  C11  N    C8   112.57  3.000
 RDV  C11  N    C7   126.26  3.000
 RDV  C8   N    C7   121.03  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
 RDV  CONST_01  C8   N    C7   C6    180.00   0.0  0
 RDV  CONST_02  C11  N    C7   C6      0.00   0.0  0
 RDV  CONST_03  O    C7   N    C8      0.00   0.0  0
 RDV  CONST_04  O    C7   N    C11   180.00   0.0  0
 RDV  Var_01    C2   C1   C    C4     22.37  30.0  1
 RDV  Var_02    N    C8   C9   N1    -56.85  30.0  1
 RDV  Var_03    N    C11  C10  N1     56.19  30.0  1
 RDV  Var_04    C10  N1   C9   C8     59.84  30.0  1
 RDV  Var_05    C10  C11  N    C8    -55.86  30.0  1
 RDV  Var_06    C11  C10  N1   C9    -59.42  30.0  1
 RDV  Var_07    C11  N    C8   C9     56.16  30.0  1
 RDV  Var_08    C1   C    C4   C3      3.04  30.0  1
 RDV  Var_09    C    C1   C2   C3    -39.52  30.0  1
 RDV  Var_10    N    C7   C6   C5    -80.16  30.0  1
 RDV  Var_11    C3   C5   C6   C7   -169.44  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
 RDV  chir_01  C3  C5  C4  C2  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
 RDV  plan-1  C6   0.020
 RDV  plan-1  C7   0.020
 RDV  plan-1  C8   0.020
 RDV  plan-1  C11  0.020
 RDV  plan-1  O    0.020
 RDV  plan-1  N    0.020

