# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 12:24:52 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-ethyl-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]-D-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1CCC[C@@H]1C(=O)NC2C3CC4CC(C3)CC2C4
#
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
 A0D  A0D  1-ethyl-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]-D-prolinamide  ligand  48  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A0D
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
 A0D  N1    N  NH1   0  -0.653   0.0148   0.5825  -0.0064
 A0D  C2    C  C     0   0.542  -1.1660   0.2703  -0.5638
 A0D  C3    C  CH1   0  -0.187  -2.3794   0.7851   0.2020
 A0D  O4    O  O     0  -0.496  -1.2721  -0.3222  -1.6274
 A0D  N5    N  NT    0  -0.416  -3.4847  -0.1463   0.1038
 A0D  C6    C  CH2   0  -0.271  -4.7064   0.6038  -0.1127
 A0D  C7    C  CH2   0  -0.445  -4.2463   1.7274  -1.0241
 A0D  C8    C  CH2   0  -0.481  -2.8973   2.1060  -0.4160
 A0D  C9    C  CR16  0  -0.270   2.3669   1.2816  -0.1459
 A0D  C10   C  CR16  0  -0.024   1.2958   0.2906  -0.6180
 A0D  C11   C  C     0  -0.445   2.6727   1.0920   1.3440
 A0D  C12   C  C     0  -0.240   3.1481  -0.3412   1.5946
 A0D  C13   C  C     0  -0.422   4.4233  -0.5977   0.7866
 A0D  C14   C  CR16  0  -0.243   4.1368  -0.4042  -0.7043
 A0D  C15   C  C     0  -0.428   3.0523  -1.3908  -1.1433
 A0D  C16   C  C     0  -0.247   1.7737  -1.1429  -0.3388
 A0D  C17   C  C     0  -0.430   2.0611  -1.3243   1.1524
 A0D  C18   C  CH2   0  -0.425   3.6435   1.0237  -0.9517
 A0D  C19   C  CH2   0  -0.270  -3.5131  -1.1442   1.1475
 A0D  C20   C  CH3   0  -0.679  -4.5210  -2.2492   0.8799
 A0D  HN1   H  HNH1  0   0.394   0.0043   1.0521   0.8849
 A0D  H3    H  HCH1  0   0.235  -2.0931   0.9672   1.2503
 A0D  H6    H  HCH2  0   0.234  -5.4783  -0.0188  -0.5693
 A0D  H6A   H  HCH2  0   0.187  -5.1258   1.0136   0.8225
 A0D  H7    H  HCH2  0   0.231  -4.1141   1.3556  -2.0408
 A0D  H7A   H  HCH2  0   0.237  -4.9456   2.5622  -1.0568
 A0D  H8    H  HCH2  0   0.245  -3.0307   2.8445   0.3750
 A0D  H8A   H  HCH2  0   0.251  -2.2096   2.5394  -1.1428
 A0D  H9    H  HCR6  0   0.238   2.0163   2.3021  -0.3302
 A0D  H10   H  HCR6  0   0.242   1.1696   0.4101  -1.6987
 A0D  H11   H  H     0   0.233   3.4481   1.8040   1.6433
 A0D  H11A  H  H     0   0.227   1.8032   1.3228   1.9690
 A0D  H12   H  H     0   0.225   3.3546  -0.4778   2.6603
 A0D  H13   H  H     0   0.222   5.2185   0.0811   1.1119
 A0D  H13A  H  H     0   0.222   4.7837  -1.6157   0.9690
 A0D  H14   H  HCR6  0   0.225   5.0489  -0.5814  -1.2817
 A0D  H15   H  H     0   0.225   2.8512  -1.2780  -2.2143
 A0D  H15A  H  H     0   0.226   3.3923  -2.4206  -0.9943
 A0D  H16   H  H     0   0.233   0.9964  -1.8425  -0.6584
 A0D  H17   H  H     0   0.227   2.3878  -2.3520   1.3396
 A0D  H17A  H  H     0   0.224   1.1505  -1.1796   1.7423
 A0D  H18   H  HCH2  0   0.227   3.4510   1.1734  -2.0190
 A0D  H18A  H  HCH2  0   0.228   4.4131   1.7479  -0.6670
 A0D  H19   H  HCH2  0   0.225  -2.5167  -1.5900   1.2183
 A0D  H19A  H  HCH2  0   0.188  -3.7186  -0.6931   2.1340
 A0D  H20   H  HCH3  0   0.227  -5.5460  -1.8766   0.8774
 A0D  H20A  H  HCH3  0   0.223  -4.3312  -2.7213  -0.0846
 A0D  H20B  H  HCH3  0   0.231  -4.4530  -3.0146   1.6527

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
 A0D  C10  N1    single  1.449  0.020  1.449
 A0D  N1   C2    single  1.343  0.020  1.343
 A0D  N1   HN1   single  0.860  0.020  1.020
 A0D  C2   O4    double  1.222  0.020  1.222
 A0D  C2   C3    single  1.524  0.020  1.524
 A0D  N5   C3    single  1.449  0.020  1.449
 A0D  C3   C8    single  1.548  0.020  1.548
 A0D  C3   H3    single  0.970  0.020  1.090
 A0D  N5   C19   single  1.444  0.020  1.444
 A0D  N5   C6    single  1.450  0.020  1.450
 A0D  C7   C6    single  1.518  0.020  1.518
 A0D  C6   H6    single  0.970  0.020  1.090
 A0D  C6   H6A   single  0.970  0.020  1.090
 A0D  C7   C8    single  1.527  0.020  1.527
 A0D  C7   H7    single  0.970  0.020  1.090
 A0D  C7   H7A   single  0.970  0.020  1.090
 A0D  C8   H8    single  0.970  0.020  1.090
 A0D  C8   H8A   single  0.970  0.020  1.090
 A0D  C11  C9    single  1.533  0.020  1.533
 A0D  C18  C9    single  1.532  0.020  1.532
 A0D  C9   C10   single  1.534  0.020  1.534
 A0D  C9   H9    single  0.970  0.020  1.090
 A0D  C16  C10   single  1.537  0.020  1.537
 A0D  C10  H10   single  0.970  0.020  1.090
 A0D  C12  C11   single  1.531  0.020  1.531
 A0D  C11  H11   single  0.970  0.020  1.090
 A0D  C11  H11A  single  0.970  0.020  1.090
 A0D  C13  C12   single  1.531  0.020  1.531
 A0D  C12  C17   single  1.531  0.020  1.531
 A0D  C12  H12   single  0.970  0.020  1.090
 A0D  C13  C14   single  1.530  0.020  1.530
 A0D  C13  H13   single  0.970  0.020  1.090
 A0D  C13  H13A  single  0.970  0.020  1.090
 A0D  C14  C18   single  1.531  0.020  1.531
 A0D  C14  C15   single  1.530  0.020  1.530
 A0D  C14  H14   single  0.970  0.020  1.090
 A0D  C15  C16   single  1.531  0.020  1.531
 A0D  C15  H15   single  0.970  0.020  1.090
 A0D  C15  H15A  single  0.970  0.020  1.090
 A0D  C17  C16   single  1.529  0.020  1.529
 A0D  C16  H16   single  0.970  0.020  1.090
 A0D  C17  H17   single  0.970  0.020  1.090
 A0D  C17  H17A  single  0.970  0.020  1.090
 A0D  C18  H18   single  0.970  0.020  1.090
 A0D  C18  H18A  single  0.970  0.020  1.090
 A0D  C20  C19   single  1.519  0.020  1.519
 A0D  C19  H19   single  0.970  0.020  1.090
 A0D  C19  H19A  single  0.970  0.020  1.090
 A0D  C20  H20   single  0.970  0.020  1.090
 A0D  C20  H20A  single  0.970  0.020  1.090
 A0D  C20  H20B  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
 A0D  HN1   N1   C10   118.45  3.000
 A0D  HN1   N1   C2    117.82  3.000
 A0D  C10   N1   C2    123.73  3.000
 A0D  O4    C2   C3    122.13  3.000
 A0D  C3    C2   N1    114.39  3.000
 A0D  O4    C2   N1    123.40  3.000
 A0D  H3    C3   C8    109.02  3.000
 A0D  H3    C3   N5    111.65  3.000
 A0D  C8    C3   N5    105.45  3.000
 A0D  H3    C3   C2    109.08  3.000
 A0D  C8    C3   C2    110.73  3.000
 A0D  N5    C3   C2    110.86  3.000
 A0D  C19   N5   C6    116.67  3.000
 A0D  C6    N5   C3    108.68  3.000
 A0D  C19   N5   C3    114.22  3.000
 A0D  H6A   C6   H6    107.30  3.000
 A0D  H6A   C6   C7    110.43  3.000
 A0D  H6    C6   C7    112.66  3.000
 A0D  H6A   C6   N5    112.69  3.000
 A0D  H6    C6   N5    111.29  3.000
 A0D  C7    C6   N5    102.55  3.000
 A0D  H7A   C7   H7    108.12  3.000
 A0D  H7A   C7   C8    112.89  3.000
 A0D  H7    C7   C8    110.40  3.000
 A0D  H7A   C7   C6    112.99  3.000
 A0D  H7    C7   C6    110.13  3.000
 A0D  C8    C7   C6    102.25  3.000
 A0D  H8A   C8   H8    106.95  3.000
 A0D  H8A   C8   C7    112.97  3.000
 A0D  H8    C8   C7    110.40  3.000
 A0D  H8A   C8   C3    113.23  3.000
 A0D  H8    C8   C3    109.23  3.000
 A0D  C7    C8   C3    104.06  3.000
 A0D  H9    C9   C18   109.60  3.000
 A0D  H9    C9   C11   110.05  3.000
 A0D  C18   C9   C11   108.92  3.000
 A0D  H9    C9   C10   109.08  3.000
 A0D  C18   C9   C10   108.14  3.000
 A0D  C11   C9   C10   111.02  3.000
 A0D  H10   C10  C16   108.49  3.000
 A0D  H10   C10  C9    108.30  3.000
 A0D  C16   C10  C9    109.25  3.000
 A0D  H10   C10  N1    107.03  3.000
 A0D  C16   C10  N1    112.71  3.000
 A0D  C9    C10  N1    110.93  3.000
 A0D  H11A  C11  H11   105.62  3.000
 A0D  H11A  C11  C12   110.51  3.000
 A0D  H11   C11  C12   110.14  3.000
 A0D  H11A  C11  C9    111.73  3.000
 A0D  H11   C11  C9    109.08  3.000
 A0D  C12   C11  C9    109.69  3.000
 A0D  H12   C12  C17   109.58  3.000
 A0D  H12   C12  C13   109.63  3.000
 A0D  C17   C12  C13   109.35  3.000
 A0D  H12   C12  C11   109.58  3.000
 A0D  C17   C12  C11   109.48  3.000
 A0D  C13   C12  C11   109.21  3.000
 A0D  H13A  C13  H13   106.72  3.000
 A0D  H13A  C13  C14   109.96  3.000
 A0D  H13   C13  C14   110.30  3.000
 A0D  H13A  C13  C12   109.99  3.000
 A0D  H13   C13  C12   110.13  3.000
 A0D  C14   C13  C12   109.69  3.000
 A0D  H14   C14  C18   109.54  3.000
 A0D  H14   C14  C15   109.57  3.000
 A0D  C18   C14  C15   109.06  3.000
 A0D  H14   C14  C13   109.73  3.000
 A0D  C15   C14  C13   109.31  3.000
 A0D  C18   C14  C13   109.62  3.000
 A0D  H15A  C15  H15   106.68  3.000
 A0D  H15A  C15  C16   109.89  3.000
 A0D  H15   C15  C16   110.10  3.000
 A0D  H15A  C15  C14   110.32  3.000
 A0D  H15   C15  C14   110.13  3.000
 A0D  C16   C15  C14   109.68  3.000
 A0D  H16   C16  C17   110.04  3.000
 A0D  H16   C16  C15   109.67  3.000
 A0D  C17   C16  C15   109.65  3.000
 A0D  H16   C16  C10   108.83  3.000
 A0D  C17   C16  C10   110.25  3.000
 A0D  C15   C16  C10   108.38  3.000
 A0D  H17A  C17  H17   106.27  3.000
 A0D  H17A  C17  C16   110.70  3.000
 A0D  H17   C17  C16   109.53  3.000
 A0D  H17A  C17  C12   110.50  3.000
 A0D  H17   C17  C12   109.97  3.000
 A0D  C16   C17  C12   109.81  3.000
 A0D  H18A  C18  H18   106.66  3.000
 A0D  H18A  C18  C14   110.40  3.000
 A0D  H18   C18  C14   109.99  3.000
 A0D  H18A  C18  C9    109.74  3.000
 A0D  H18   C18  C9    110.08  3.000
 A0D  C14   C18  C9    109.92  3.000
 A0D  H19A  C19  H19   106.16  3.000
 A0D  H19A  C19  C20   109.34  3.000
 A0D  H19   C19  C20   108.62  3.000
 A0D  H19A  C19  N5    111.53  3.000
 A0D  H19   C19  N5    108.08  3.000
 A0D  C20   C19  N5    112.85  3.000
 A0D  H20B  C20  H20A  108.20  3.000
 A0D  H20B  C20  H20   107.47  3.000
 A0D  H20A  C20  H20   108.02  3.000
 A0D  H20B  C20  C19   110.15  3.000
 A0D  H20A  C20  C19   110.81  3.000
 A0D  H20   C20  C19   112.05  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
 A0D  CONST_01  C10  N1   C2   C3   180.00   0.0  0
 A0D  CONST_02  C10  N1   C2   O4     0.00   0.0  0
 A0D  CONST_03  HN1  N1   C2   C3     0.00   0.0  0
 A0D  Var_01    C7   C6   N5   C3    37.26  30.0  1
 A0D  Var_02    C6   C7   C8   C3    29.92  30.0  1
 A0D  Var_03    C8   C7   C6   N5   -40.86  30.0  1
 A0D  Var_04    C20  C19  N5   C3  -169.49  30.0  3
 A0D  Var_05    H20  C20  C19  N5   -64.70  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
 A0D  chir_01  C3   C2   N5   C8   positiv
 A0D  chir_02  C9   C11  C18  C10  negativ
 A0D  chir_03  C10  N1   C9   C16  negativ
 A0D  chir_04  C12  C17  C13  C11  negativ
 A0D  chir_05  C14  C15  C18  C13  negativ
 A0D  chir_06  C16  C17  C15  C10  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
 A0D  plan-1  N1   0.020
 A0D  plan-1  C2   0.020
 A0D  plan-1  C3   0.020
 A0D  plan-1  O4   0.020
 A0D  plan-1  C10  0.020
 A0D  plan-1  HN1  0.020

