# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 14:58:31 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: N-{[(3S)-oxolan-3-yl]methyl}pyrrolidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC[C@@H]1CCOC1)N2CCCC2
#
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
 6C9  6C9  N-{[(3S)-oxolan-3-yl]methyl}pyrrolidine-1-carboxamide  ligand  32  14  .  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_6C9
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
 6C9  O1   O  O     0  -0.559   1.2803  -2.1947   0.0862
 6C9  C5   C  C     0   0.739   1.2226  -0.9668   0.1287
 6C9  N1   N  NT    0  -0.512   2.3307  -0.1932   0.0785
 6C9  C9   C  CH2   0  -0.293   2.3636   1.2553   0.2251
 6C9  C8   C  CH2   0  -0.476   3.8491   1.5548   0.4032
 6C9  C7   C  CH2   0  -0.480   4.5259   0.4381  -0.3855
 6C9  C6   C  CH2   0  -0.250   3.6561  -0.7748  -0.0780
 6C9  N    N  NH1   0  -0.700   0.0349  -0.3054   0.2583
 6C9  C4   C  CH2   0  -0.234  -1.2163  -1.0263   0.1460
 6C9  C1   C  CH1   0  -0.331  -2.3932  -0.1214   0.4558
 6C9  C2   C  CH2   0  -0.145  -2.6365   0.9816  -0.5696
 6C9  O    O  O2    0  -0.500  -3.9779   1.3757  -0.3824
 6C9  C3   C  CH2   0  -0.153  -4.7354   0.2587   0.0689
 6C9  C    C  CH2   0  -0.501  -3.7360  -0.8511   0.4104
 6C9  H1   H  HCH2  0   0.237   1.9698   1.7550  -0.6675
 6C9  H2   H  HCH2  0   0.252   4.1125   2.5545   0.0611
 6C9  H3   H  HCH2  0   0.237   4.5011   0.6590  -1.4549
 6C9  H4   H  HCH2  0   0.226   3.9835  -1.2688   0.8426
 6C9  H5   H  HNH1  0   0.398   0.0070   0.6719   0.0169
 6C9  H6   H  HCH2  0   0.218  -1.3470  -1.4553  -0.8560
 6C9  H7   H  HCH2  0   0.245  -1.2078  -1.8636   0.8452
 6C9  H8   H  HCH1  0   0.253  -2.2510   0.3305   1.4435
 6C9  H9   H  HCH2  0   0.230  -1.9996   1.8599  -0.4382
 6C9  H10  H  HCH2  0   0.196  -2.4665   0.5942  -1.5858
 6C9  H11  H  HCH2  0   0.216  -5.3184   0.5658   0.9411
 6C9  H12  H  HCH2  0   0.239  -3.7208  -1.6146  -0.3718
 6C9  H13  H  HCH2  0   0.248   1.7746   1.5881   1.0830
 6C9  H14  H  HCH2  0   0.239   4.1166   1.4810   1.4595
 6C9  H15  H  HCH2  0   0.249   5.5656   0.2820  -0.1003
 6C9  H16  H  HCH2  0   0.241   3.6712  -1.5166  -0.8766
 6C9  H17  H  HCH2  0   0.213  -5.4423  -0.0615  -0.7031
 6C9  H18  H  HCH2  0   0.258  -3.9706  -1.3479   1.3512

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
 6C9  O   C2   single  1.411  0.020  1.411
 6C9  O   C3   single  1.423  0.020  1.423
 6C9  C2  C1   single  1.526  0.020  1.526
 6C9  C3  C    single  1.532  0.020  1.532
 6C9  C1  C    single  1.529  0.020  1.529
 6C9  C1  C4   single  1.516  0.020  1.516
 6C9  C9  C8   single  1.526  0.020  1.526
 6C9  C9  N1   single  1.456  0.020  1.456
 6C9  C8  C7   single  1.525  0.020  1.525
 6C9  N   C4   single  1.448  0.020  1.448
 6C9  N   C5   single  1.366  0.020  1.366
 6C9  N1  C5   single  1.352  0.020  1.352
 6C9  N1  C6   single  1.456  0.020  1.456
 6C9  C7  C6   single  1.524  0.020  1.524
 6C9  C5  O1   double  1.230  0.020  1.230
 6C9  C9  H1   single  0.970  0.020  1.090
 6C9  C8  H2   single  0.970  0.020  1.090
 6C9  C7  H3   single  0.970  0.020  1.090
 6C9  C6  H4   single  0.970  0.020  1.090
 6C9  N   H5   single  0.890  0.020  1.040
 6C9  C4  H6   single  0.970  0.020  1.090
 6C9  C4  H7   single  0.970  0.020  1.090
 6C9  C1  H8   single  0.970  0.020  1.090
 6C9  C2  H9   single  0.970  0.020  1.090
 6C9  C2  H10  single  0.970  0.020  1.090
 6C9  C3  H11  single  0.970  0.020  1.090
 6C9  C   H12  single  0.970  0.020  1.090
 6C9  C9  H13  single  0.970  0.020  1.090
 6C9  C8  H14  single  0.970  0.020  1.090
 6C9  C7  H15  single  0.970  0.020  1.090
 6C9  C6  H16  single  0.970  0.020  1.090
 6C9  C3  H17  single  0.970  0.020  1.090
 6C9  C   H18  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
 6C9  N    C5  N1   116.05  3.000
 6C9  N1   C5  O1   122.10  3.000
 6C9  N    C5  O1   121.84  3.000
 6C9  C6   N1  C9   112.81  3.000
 6C9  C6   N1  C5   121.43  3.000
 6C9  C9   N1  C5   125.71  3.000
 6C9  H13  C9  H1   107.88  3.000
 6C9  H13  C9  C8   111.93  3.000
 6C9  H1   C9  C8   110.81  3.000
 6C9  H13  C9  N1   111.71  3.000
 6C9  H1   C9  N1   111.30  3.000
 6C9  C8   C9  N1   103.23  3.000
 6C9  H14  C8  H2   107.86  3.000
 6C9  H14  C8  C7   110.00  3.000
 6C9  H2   C8  C7   113.72  3.000
 6C9  H14  C8  C9   109.76  3.000
 6C9  H2   C8  C9   112.27  3.000
 6C9  C7   C8  C9   103.18  3.000
 6C9  H15  C7  H3   107.89  3.000
 6C9  H15  C7  C6   112.20  3.000
 6C9  H3   C7  C6   110.22  3.000
 6C9  H15  C7  C8   113.14  3.000
 6C9  H3   C7  C8   110.37  3.000
 6C9  C6   C7  C8   103.01  3.000
 6C9  H16  C6  H4   107.75  3.000
 6C9  H16  C6  C7   112.70  3.000
 6C9  H4   C6  C7   110.98  3.000
 6C9  H16  C6  N1   111.30  3.000
 6C9  H4   C6  N1   111.22  3.000
 6C9  C7   C6  N1   102.90  3.000
 6C9  H5   N   C4   116.13  3.000
 6C9  H5   N   C5   118.12  3.000
 6C9  C4   N   C5   120.19  3.000
 6C9  H7   C4  H6   106.62  3.000
 6C9  H7   C4  C1   109.45  3.000
 6C9  H6   C4  C1   109.10  3.000
 6C9  H7   C4  N    109.00  3.000
 6C9  H6   C4  N    111.61  3.000
 6C9  C1   C4  N    110.95  3.000
 6C9  H8   C1  C    109.73  3.000
 6C9  H8   C1  C2   109.17  3.000
 6C9  C    C1  C2   100.66  3.000
 6C9  H8   C1  C4   109.24  3.000
 6C9  C    C1  C4   113.00  3.000
 6C9  C2   C1  C4   114.70  3.000
 6C9  H10  C2  H9   107.69  3.000
 6C9  H10  C2  O    111.57  3.000
 6C9  H9   C2  O    108.28  3.000
 6C9  H10  C2  C1   109.96  3.000
 6C9  H9   C2  C1   114.04  3.000
 6C9  O    C2  C1   105.34  3.000
 6C9  C3   O   C2   109.21  3.000
 6C9  H17  C3  H11  107.49  3.000
 6C9  H17  C3  C    111.51  3.000
 6C9  H11  C3  C    111.94  3.000
 6C9  H17  C3  O    110.47  3.000
 6C9  H11  C3  O    108.44  3.000
 6C9  C    C3  O    106.98  3.000
 6C9  H18  C   H12  107.60  3.000
 6C9  H18  C   C3   112.48  3.000
 6C9  H12  C   C3   110.83  3.000
 6C9  H18  C   C1   112.40  3.000
 6C9  H12  C   C1   110.02  3.000
 6C9  C3   C   C1   103.53  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
 6C9  CONST_01  C9  N1  C5  O1   180.00   0.0  0
 6C9  CONST_02  C6  N1  C5  O1     0.00   0.0  0
 6C9  CONST_03  N   C5  N1  C9     0.00   0.0  0
 6C9  CONST_04  N   C5  N1  C6   180.00   0.0  0
 6C9  CONST_05  C4  N   C5  N1   180.00   0.0  0
 6C9  CONST_07  C4  N   C5  O1     0.00   0.0  0
 6C9  Var_01    C7  C8  C9  N1    29.82  30.0  1
 6C9  Var_02    C6  C7  C8  C9   -38.77  30.0  1
 6C9  Var_03    C7  C6  N1  C9   -14.26  30.0  1
 6C9  Var_04    C6  N1  C9  C8    -9.83  30.0  1
 6C9  Var_05    O   C3  C   C1    14.33  30.0  1
 6C9  Var_06    C   C3  O   C2    10.08  30.0  1
 6C9  Var_07    H9  C2  O   C3  -153.11  30.0  1
 6C9  Var_08    C1  C4  N   C5   174.51  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
 6C9  chir_01  C1  C2  C  C4  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
 6C9  plan-1  O1  0.020
 6C9  plan-1  C5  0.020
 6C9  plan-1  N1  0.020
 6C9  plan-1  C9  0.020
 6C9  plan-1  C6  0.020
 6C9  plan-1  N   0.020
 6C9  plan-1  C4  0.020
 6C9  plan-1  H5  0.020

