# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 07:26:39 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N'-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbonyl]pyridine-4-carbohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NNC(=O)C12CC3CC(CC(C3)C1)C2)c4ccncc4
#
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
 D5I  D5I  N'-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbonyl]pyridine-4-carbohydrazide  ligand  43  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D5I
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
 D5I  O1   O  O     0  -0.455   0.1445  -1.6644  -0.5424
 D5I  C2   C  C     0   0.616   0.5977  -0.7163   0.0668
 D5I  C3   C  CT    0  -0.275   2.0656  -0.3146   0.0437
 D5I  C4   C  CH2   0  -0.398   2.8944  -1.4304  -0.6071
 D5I  C5   C  CH1   0  -0.251   4.3675  -1.0235  -0.6765
 D5I  C12  C  CH2   0  -0.418   4.5071   0.2487  -1.5137
 D5I  C10  C  CH1   0  -0.249   3.6968   1.3717  -0.8659
 D5I  C11  C  CH2   0  -0.405   2.2211   0.9688  -0.8001
 D5I  C6   C  CH2   0  -0.418   4.8983  -0.7666   0.7342
 D5I  C7   C  CH1   0  -0.247   4.0870   0.3548   1.3828
 D5I  C9   C  CH2   0  -0.420   4.2179   1.6312   0.5486
 D5I  C8   C  CH2   0  -0.414   2.6135  -0.0514   1.4595
 D5I  N13  N  NH1   0  -0.504  -0.2050   0.0781   0.8309
 D5I  N14  N  NH1   0  -0.505  -1.5552  -0.0686   0.8007
 D5I  C15  C  C     0   0.536  -2.2725   0.3972  -0.2495
 D5I  O16  O  O     0  -0.441  -1.7768   0.9991  -1.1797
 D5I  C17  C  CR6   0   0.053  -3.7416   0.1250  -0.1757
 D5I  C18  C  CR16  0  -0.339  -4.4605   0.0341  -1.3608
 D5I  C19  C  CR16  0  -0.054  -5.8228  -0.2097  -1.2932
 D5I  N20  N  N     0  -0.395  -6.4867  -0.3447  -0.1507
 D5I  C21  C  CR16  0  -0.053  -5.7991  -0.2389   0.9784
 D5I  C22  C  CR16  0  -0.355  -4.4314  -0.0082   1.0234
 D5I  H1   H  HCH2  0   0.230   2.7917  -2.3577  -0.0353
 D5I  H2   H  HCH2  0   0.232   2.5205  -1.6337  -1.6140
 D5I  H3   H  HCH1  0   0.227   4.9360  -1.8340  -1.1421
 D5I  H4   H  HCH2  0   0.225   5.5600   0.5385  -1.5888
 D5I  H5   H  HCH2  0   0.224   4.1543   0.0709  -2.5350
 D5I  H6   H  HCH1  0   0.231   3.7834   2.2825  -1.4654
 D5I  H7   H  HCH2  0   0.239   1.8314   0.7966  -1.8087
 D5I  H8   H  HCH2  0   0.233   1.6342   1.7873  -0.3717
 D5I  H9   H  HCH2  0   0.224   4.8320  -1.6784   1.3366
 D5I  H10  H  HCH2  0   0.225   5.9569  -0.4904   0.6953
 D5I  H11  H  HCH1  0   0.231   4.4528   0.5389   2.3971
 D5I  H12  H  HCH2  0   0.227   5.2637   1.9517   0.5117
 D5I  H13  H  HCH2  0   0.224   3.6541   2.4463   1.0134
 D5I  H14  H  HCH2  0   0.228   2.0577   0.7465   1.9609
 D5I  H15  H  HCH2  0   0.242   2.4998  -0.9486   2.0756
 D5I  H16  H  HNH1  0   0.415   0.1378   0.9275   1.2511
 D5I  H17  H  HNH1  0   0.425  -1.9578  -0.7094   1.4677
 D5I  H18  H  HCR6  0   0.280  -3.9752   0.1419  -2.3207
 D5I  H19  H  HCR6  0   0.274  -6.4021  -0.2991  -2.2049
 D5I  H20  H  HCR6  0   0.275  -6.3587  -0.3400   1.9011
 D5I  H21  H  HCR6  0   0.282  -3.9440   0.0858   1.9848

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
 D5I  O1   C2   double    1.215  0.020  1.215
 D5I  C11  C10  single    1.531  0.020  1.531
 D5I  C11  C3   single    1.544  0.020  1.544
 D5I  C2   C3   single    1.522  0.020  1.522
 D5I  C2   N13  single    1.363  0.020  1.363
 D5I  C9   C10  single    1.530  0.020  1.530
 D5I  C9   C7   single    1.530  0.020  1.530
 D5I  C10  C12  single    1.529  0.020  1.529
 D5I  C8   C3   single    1.541  0.020  1.541
 D5I  C8   C7   single    1.530  0.020  1.530
 D5I  C3   C4   single    1.535  0.020  1.535
 D5I  C22  C21  aromatic  1.388  0.020  1.388
 D5I  C22  C17  aromatic  1.390  0.020  1.390
 D5I  C7   C6   single    1.529  0.020  1.529
 D5I  N13  N14  single    1.358  0.020  1.358
 D5I  N14  C15  single    1.354  0.020  1.354
 D5I  C21  N20  aromatic  1.326  0.020  1.326
 D5I  C15  C17  single    1.496  0.020  1.496
 D5I  C15  O16  double    1.214  0.020  1.214
 D5I  C12  C5   single    1.529  0.020  1.529
 D5I  C17  C18  aromatic  1.389  0.020  1.389
 D5I  C4   C5   single    1.530  0.020  1.530
 D5I  N20  C19  aromatic  1.328  0.020  1.328
 D5I  C6   C5   single    1.529  0.020  1.529
 D5I  C18  C19  aromatic  1.386  0.020  1.386
 D5I  C4   H1   single    0.970  0.020  1.090
 D5I  C4   H2   single    0.970  0.020  1.090
 D5I  C5   H3   single    0.970  0.020  1.090
 D5I  C12  H4   single    0.970  0.020  1.090
 D5I  C12  H5   single    0.970  0.020  1.090
 D5I  C10  H6   single    0.970  0.020  1.090
 D5I  C11  H7   single    0.970  0.020  1.090
 D5I  C11  H8   single    0.970  0.020  1.090
 D5I  C6   H9   single    0.970  0.020  1.090
 D5I  C6   H10  single    0.970  0.020  1.090
 D5I  C7   H11  single    0.970  0.020  1.090
 D5I  C9   H12  single    0.970  0.020  1.090
 D5I  C9   H13  single    0.970  0.020  1.090
 D5I  C8   H14  single    0.970  0.020  1.090
 D5I  C8   H15  single    0.970  0.020  1.090
 D5I  N13  H16  single    0.860  0.020  1.020
 D5I  N14  H17  single    0.860  0.020  1.020
 D5I  C18  H18  single    0.930  0.020  1.080
 D5I  C19  H19  single    0.930  0.020  1.080
 D5I  C21  H20  single    0.930  0.020  1.080
 D5I  C22  H21  single    0.930  0.020  1.080

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
 D5I  N13  C2   C3   115.00  3.000
 D5I  N13  C2   O1   121.07  3.000
 D5I  C3   C2   O1   123.93  3.000
 D5I  C8   C3   C11  108.93  3.000
 D5I  C8   C3   C4   108.77  3.000
 D5I  C11  C3   C4   108.56  3.000
 D5I  C4   C3   C2   109.60  3.000
 D5I  C8   C3   C2   111.96  3.000
 D5I  C11  C3   C2   108.96  3.000
 D5I  H2   C4   H1   106.96  3.000
 D5I  H2   C4   C5   109.70  3.000
 D5I  H1   C4   C5   109.84  3.000
 D5I  H2   C4   C3   109.94  3.000
 D5I  H1   C4   C3   110.11  3.000
 D5I  C5   C4   C3   110.23  3.000
 D5I  H3   C5   C6   109.68  3.000
 D5I  H3   C5   C12  109.63  3.000
 D5I  C6   C5   C12  109.49  3.000
 D5I  H3   C5   C4   108.82  3.000
 D5I  C6   C5   C4   109.70  3.000
 D5I  C12  C5   C4   109.51  3.000
 D5I  H5   C12  H4   106.79  3.000
 D5I  H5   C12  C10  110.10  3.000
 D5I  H4   C12  C10  110.14  3.000
 D5I  H5   C12  C5   110.25  3.000
 D5I  H4   C12  C5   110.22  3.000
 D5I  C10  C12  C5   109.31  3.000
 D5I  H6   C10  C9   109.80  3.000
 D5I  H6   C10  C11  108.60  3.000
 D5I  C9   C10  C11  109.47  3.000
 D5I  H6   C10  C12  109.72  3.000
 D5I  C9   C10  C12  109.63  3.000
 D5I  C11  C10  C12  109.61  3.000
 D5I  H8   C11  H7   106.70  3.000
 D5I  H8   C11  C10  109.68  3.000
 D5I  H7   C11  C10  110.18  3.000
 D5I  H8   C11  C3   110.72  3.000
 D5I  H7   C11  C3   109.68  3.000
 D5I  C10  C11  C3   109.84  3.000
 D5I  H10  C6   H9   106.75  3.000
 D5I  H10  C6   C7   110.07  3.000
 D5I  H9   C6   C7   110.20  3.000
 D5I  H10  C6   C5   110.20  3.000
 D5I  H9   C6   C5   110.29  3.000
 D5I  C7   C6   C5   109.30  3.000
 D5I  H11  C7   C8   108.67  3.000
 D5I  H11  C7   C9   109.66  3.000
 D5I  C8   C7   C9   109.33  3.000
 D5I  H11  C7   C6   109.85  3.000
 D5I  C8   C7   C6   109.73  3.000
 D5I  C9   C7   C6   109.58  3.000
 D5I  H13  C9   H12  106.76  3.000
 D5I  H13  C9   C7   110.22  3.000
 D5I  H12  C9   C7   110.14  3.000
 D5I  H13  C9   C10  110.09  3.000
 D5I  H12  C9   C10  110.12  3.000
 D5I  C7   C9   C10  109.48  3.000
 D5I  H15  C8   H14  106.69  3.000
 D5I  H15  C8   C7   110.23  3.000
 D5I  H14  C8   C7   108.57  3.000
 D5I  H15  C8   C3   109.90  3.000
 D5I  H14  C8   C3   111.41  3.000
 D5I  C7   C8   C3   109.98  3.000
 D5I  H16  N13  N14  116.00  3.000
 D5I  H16  N13  C2   121.63  3.000
 D5I  N14  N13  C2   120.65  3.000
 D5I  H17  N14  C15  121.32  3.000
 D5I  H17  N14  N13  116.78  3.000
 D5I  C15  N14  N13  120.43  3.000
 D5I  C17  C15  O16  121.95  3.000
 D5I  O16  C15  N14  123.26  3.000
 D5I  C17  C15  N14  114.79  3.000
 D5I  C22  C17  C18  118.23  3.000
 D5I  C18  C17  C15  118.56  3.000
 D5I  C22  C17  C15  123.19  3.000
 D5I  H18  C18  C19  120.15  3.000
 D5I  H18  C18  C17  121.24  3.000
 D5I  C19  C18  C17  118.61  3.000
 D5I  H19  C19  N20  116.62  3.000
 D5I  H19  C19  C18  119.93  3.000
 D5I  N20  C19  C18  123.45  3.000
 D5I  C21  N20  C19  117.72  3.000
 D5I  H20  C21  C22  119.79  3.000
 D5I  H20  C21  N20  116.72  3.000
 D5I  C22  C21  N20  123.49  3.000
 D5I  H21  C22  C21  119.16  3.000
 D5I  H21  C22  C17  122.33  3.000
 D5I  C21  C22  C17  118.50  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
 D5I  CONST_01  N20  C21  C22  C17    0.00   0.0  0
 D5I  CONST_02  N20  C19  C18  C17    0.00   0.0  0
 D5I  CONST_03  C21  C22  C17  C18    0.00   0.0  0
 D5I  CONST_04  C21  N20  C19  C18    0.00   0.0  0
 D5I  CONST_05  C22  C21  N20  C19    0.00   0.0  0
 D5I  CONST_06  C22  C17  C18  C19    0.00   0.0  0
 D5I  CONST_07  C21  C22  C17  C15  180.00   0.0  0
 D5I  CONST_08  C19  C18  C17  C15  180.00   0.0  0
 D5I  CONST_09  H20  C21  C22  C17  180.00   0.0  0
 D5I  CONST_10  H19  C19  C18  C17  180.00   0.0  0
 D5I  CONST_11  H21  C22  C17  C18  180.00   0.0  0
 D5I  CONST_12  H18  C18  C19  N20  180.00   0.0  0
 D5I  CONST_13  N14  N13  C2   C3   180.00   0.0  0
 D5I  CONST_14  C17  C15  N14  N13  180.00   0.0  0
 D5I  CONST_15  H16  N13  C2   C3     0.00   0.0  0
 D5I  CONST_16  H17  N14  C15  C17    0.00   0.0  0
 D5I  CONST_17  N14  N13  C2   O1     0.00   0.0  0
 D5I  CONST_18  O16  C15  N14  N13    0.00   0.0  0
 D5I  Var_01    C22  C17  C15  N14   28.34  30.0  2
 D5I  Var_02    C15  N14  N13  C2   -75.91  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
 D5I  chir_01  C3   C11  C8  C4   positiv
 D5I  chir_02  C5   C12  C4  C6   positiv
 D5I  chir_03  C10  C11  C9  C12  negativ
 D5I  chir_04  C7   C6   C8  C9   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
 D5I  plan-1  C15  0.020
 D5I  plan-1  C17  0.020
 D5I  plan-1  C18  0.020
 D5I  plan-1  C19  0.020
 D5I  plan-1  N20  0.020
 D5I  plan-1  C21  0.020
 D5I  plan-1  C22  0.020
 D5I  plan-1  H18  0.020
 D5I  plan-1  H19  0.020
 D5I  plan-1  H20  0.020
 D5I  plan-1  H21  0.020
 D5I  plan-2  O1   0.020
 D5I  plan-2  C2   0.020
 D5I  plan-2  C3   0.020
 D5I  plan-2  N13  0.020
 D5I  plan-2  N14  0.020
 D5I  plan-2  H16  0.020
 D5I  plan-3  N13  0.020
 D5I  plan-3  N14  0.020
 D5I  plan-3  C15  0.020
 D5I  plan-3  O16  0.020
 D5I  plan-3  C17  0.020
 D5I  plan-3  H17  0.020

