# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 03:15:59 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (3-exo)-8,8-dimethyl-3-[4-(pyridin-4-yl)-1H-1,2,3-triazol-1-yl]-8-azoniabicyclo[3.2.1]octane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+]1(C)[C@@H]2CC[C@H]1CC(C2)n3cc(nn3)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
 MD4  MD4  (3-exo)-8,8-dimethyl-3-[4-(pyridin-4-yl)-1H-1,2,3-triazol-1-yl]-8-azoniabicyclo[3.2.1]octane  ligand  43  21  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MD4
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
 MD4  C21   C  CH3   0  -0.551   5.0800  -1.5237   0.1884
 MD4  N16   N  NT    1  -0.387   3.6534  -1.0882   0.1171
 MD4  C20   C  CH3   0  -0.547   2.8432  -2.3169   0.3206
 MD4  C15   C  CH1   0  -0.121   3.3846  -0.3556  -1.1837
 MD4  C14   C  CH2   0  -0.503   4.1664   0.9496  -0.9929
 MD4  C13   C  CH2   0  -0.501   4.1761   1.1899   0.5336
 MD4  C17   C  CH2   0  -0.490   1.8916  -0.0967  -1.3337
 MD4  C19   C  CH1   0  -0.082   1.3800   0.7827  -0.1885
 MD4  C18   C  CH2   0  -0.495   1.8934   0.3198   1.1787
 MD4  C12   C  CH1   0  -0.122   3.3853   0.0176   1.1213
 MD4  N10   N  NR5   0  -0.283  -0.0676   0.8770  -0.2045
 MD4  N9    N  N     0  -0.078  -0.6575   2.0281  -0.4935
 MD4  N8    N  N     0  -0.311  -1.9255   1.8445  -0.4572
 MD4  C11   C  CR15  0  -0.073  -0.9769  -0.0815   0.0243
 MD4  C7    C  CR5   0   0.165  -2.1846   0.5543  -0.1403
 MD4  C5    C  CR6   0   0.154  -3.5385   0.0302  -0.0176
 MD4  C6    C  CR16  0  -0.408  -3.7792  -1.2868   0.3681
 MD4  C1    C  CR16  0  -0.056  -5.0878  -1.7284   0.4700
 MD4  C4    C  CR16  0  -0.355  -4.6469   0.8324  -0.2810
 MD4  C3    C  CR16  0  -0.059  -5.9139   0.2894  -0.1494
 MD4  N2    N  N     0  -0.408  -6.1460  -0.9657   0.2189
 MD4  H212  H  HCH3  0   0.298   5.2459  -2.2873  -0.5664
 MD4  H213  H  HCH3  0   0.305   5.7610  -0.6990   0.0153
 MD4  H211  H  HCH3  0   0.297   5.2652  -1.9381   1.1759
 MD4  H201  H  HCH3  0   0.303   3.1073  -2.7453   1.2836
 MD4  H202  H  HCH3  0   0.281   1.7808  -2.1159   0.3072
 MD4  H203  H  HCH3  0   0.303   3.0779  -3.0225  -0.4717
 MD4  H15   H  HCH1  0   0.325   3.7520  -0.9684  -2.0058
 MD4  H141  H  HCH2  0   0.294   5.1762   0.8677  -1.3904
 MD4  H142  H  HCH2  0   0.292   3.6841   1.7579  -1.5408
 MD4  H132  H  HCH2  0   0.294   5.1905   1.2156   0.9271
 MD4  H131  H  HCH2  0   0.293   3.7103   2.1344   0.8107
 MD4  H172  H  HCH2  0   0.311   1.7423   0.4161  -2.2847
 MD4  H171  H  HCH2  0   0.286   1.3342  -1.0315  -1.4035
 MD4  H19   H  HCH1  0   0.310   1.7170   1.8060  -0.3586
 MD4  H182  H  HCH2  0   0.313   1.7505   1.1158   1.9105
 MD4  H181  H  HCH2  0   0.284   1.3352  -0.5376   1.5567
 MD4  H12   H  HCH1  0   0.326   3.7421  -0.3121   2.0961
 MD4  H11   H  HCR5  0   0.325  -0.7184  -1.0965   0.2742
 MD4  H6    H  HCR6  0   0.263  -2.9709  -1.9708   0.5913
 MD4  H1    H  HCR6  0   0.268  -5.2870  -2.7510   0.7701
 MD4  H4    H  HCR6  0   0.270  -4.5312   1.8637  -0.5841
 MD4  H3    H  HCR6  0   0.266  -6.7838   0.9038  -0.3528

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
 MD4  C1   N2    aromatic  1.328  0.020  1.328
 MD4  C1   C6    aromatic  1.385  0.020  1.385
 MD4  N2   C3    aromatic  1.328  0.020  1.328
 MD4  C6   C5    aromatic  1.393  0.020  1.393
 MD4  C3   C4    aromatic  1.385  0.020  1.385
 MD4  C5   C4    aromatic  1.393  0.020  1.393
 MD4  C5   C7    single    1.457  0.020  1.457
 MD4  C7   C11   aromatic  1.375  0.020  1.375
 MD4  C7   N8    aromatic  1.354  0.020  1.354
 MD4  C11  N10   aromatic  1.341  0.020  1.341
 MD4  N8   N9    aromatic  1.282  0.020  1.282
 MD4  N10  N9    aromatic  1.325  0.020  1.325
 MD4  N10  C19   single    1.451  0.020  1.451
 MD4  C19  C18   single    1.532  0.020  1.532
 MD4  C19  C17   single    1.532  0.020  1.532
 MD4  C18  C12   single    1.523  0.020  1.523
 MD4  C13  C12   single    1.531  0.020  1.531
 MD4  C13  C14   single    1.545  0.020  1.545
 MD4  C17  C15   single    1.523  0.020  1.523
 MD4  C12  N16   single    1.518  0.020  1.518
 MD4  C14  C15   single    1.533  0.020  1.533
 MD4  C15  N16   single    1.517  0.020  1.517
 MD4  N16  C20   single    1.486  0.020  1.486
 MD4  N16  C21   single    1.493  0.020  1.493
 MD4  C21  H212  single    0.970  0.020  1.090
 MD4  C21  H213  single    0.970  0.020  1.090
 MD4  C21  H211  single    0.970  0.020  1.090
 MD4  C20  H201  single    0.970  0.020  1.090
 MD4  C20  H202  single    0.970  0.020  1.090
 MD4  C20  H203  single    0.970  0.020  1.090
 MD4  C15  H15   single    0.970  0.020  1.090
 MD4  C14  H141  single    0.970  0.020  1.090
 MD4  C14  H142  single    0.970  0.020  1.090
 MD4  C13  H132  single    0.970  0.020  1.090
 MD4  C13  H131  single    0.970  0.020  1.090
 MD4  C17  H172  single    0.970  0.020  1.090
 MD4  C17  H171  single    0.970  0.020  1.090
 MD4  C19  H19   single    0.970  0.020  1.090
 MD4  C18  H182  single    0.970  0.020  1.090
 MD4  C18  H181  single    0.970  0.020  1.090
 MD4  C12  H12   single    0.970  0.020  1.090
 MD4  C11  H11   single    0.930  0.020  1.080
 MD4  C6   H6    single    0.930  0.020  1.080
 MD4  C1   H1    single    0.930  0.020  1.080
 MD4  C4   H4    single    0.930  0.020  1.080
 MD4  C3   H3    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
 MD4  H211  C21  H213  109.16  3.000
 MD4  H211  C21  H212  109.71  3.000
 MD4  H213  C21  H212  109.15  3.000
 MD4  H211  C21  N16   108.50  3.000
 MD4  H213  C21  N16   111.77  3.000
 MD4  H212  C21  N16   108.53  3.000
 MD4  C12   N16  C15   100.61  3.000
 MD4  C15   N16  C20   114.85  3.000
 MD4  C12   N16  C20   114.56  3.000
 MD4  C20   N16  C21   105.86  3.000
 MD4  C15   N16  C21   110.55  3.000
 MD4  C12   N16  C21   110.47  3.000
 MD4  H203  C20  H202  108.89  3.000
 MD4  H203  C20  H201  109.74  3.000
 MD4  H202  C20  H201  108.85  3.000
 MD4  H203  C20  N16   108.62  3.000
 MD4  H202  C20  N16   112.35  3.000
 MD4  H201  C20  N16   108.36  3.000
 MD4  H15   C15  C17   110.61  3.000
 MD4  H15   C15  C14   113.63  3.000
 MD4  C17   C15  C14   111.55  3.000
 MD4  H15   C15  N16   108.41  3.000
 MD4  C14   C15  N16   102.36  3.000
 MD4  C17   C15  N16   109.90  3.000
 MD4  H142  C14  H141  106.44  3.000
 MD4  H142  C14  C13   112.60  3.000
 MD4  H141  C14  C13   111.51  3.000
 MD4  H142  C14  C15   110.09  3.000
 MD4  H141  C14  C15   111.32  3.000
 MD4  C13   C14  C15   104.98  3.000
 MD4  H131  C13  H132  106.64  3.000
 MD4  H131  C13  C12   110.21  3.000
 MD4  H132  C13  C12   111.14  3.000
 MD4  H131  C13  C14   112.55  3.000
 MD4  H132  C13  C14   111.51  3.000
 MD4  C12   C13  C14   104.88  3.000
 MD4  H171  C17  H172  106.09  3.000
 MD4  H171  C17  C19   111.67  3.000
 MD4  H172  C17  C19   109.65  3.000
 MD4  H171  C17  C15   111.20  3.000
 MD4  H172  C17  C15   107.47  3.000
 MD4  C19   C17  C15   110.58  3.000
 MD4  H19   C19  N10   104.22  3.000
 MD4  H19   C19  C18   108.61  3.000
 MD4  N10   C19  C18   111.34  3.000
 MD4  H19   C19  C17   108.59  3.000
 MD4  C18   C19  C17   112.44  3.000
 MD4  N10   C19  C17   111.24  3.000
 MD4  H181  C18  H182  105.91  3.000
 MD4  H181  C18  C12   111.00  3.000
 MD4  H182  C18  C12   107.36  3.000
 MD4  H181  C18  C19   112.04  3.000
 MD4  H182  C18  C19   109.53  3.000
 MD4  C12   C18  C19   110.77  3.000
 MD4  H12   C12  C18   110.32  3.000
 MD4  H12   C12  C13   113.96  3.000
 MD4  C18   C12  C13   111.61  3.000
 MD4  H12   C12  N16   108.28  3.000
 MD4  C13   C12  N16   102.28  3.000
 MD4  C18   C12  N16   110.03  3.000
 MD4  C11   N10  N9    110.87  3.000
 MD4  N9    N10  C19   120.20  3.000
 MD4  C11   N10  C19   128.93  3.000
 MD4  N8    N9   N10   108.04  3.000
 MD4  C7    N8   N9    109.42  3.000
 MD4  H11   C11  C7    132.43  3.000
 MD4  H11   C11  N10   123.41  3.000
 MD4  C7    C11  N10   104.16  3.000
 MD4  C5    C7   C11   129.78  3.000
 MD4  C11   C7   N8    107.50  3.000
 MD4  C5    C7   N8    122.72  3.000
 MD4  C4    C5   C6    117.33  3.000
 MD4  C4    C5   C7    121.07  3.000
 MD4  C6    C5   C7    121.60  3.000
 MD4  H6    C6   C1    119.28  3.000
 MD4  H6    C6   C5    121.70  3.000
 MD4  C1    C6   C5    119.02  3.000
 MD4  H1    C1   N2    116.58  3.000
 MD4  H1    C1   C6    119.66  3.000
 MD4  N2    C1   C6    123.76  3.000
 MD4  H4    C4   C3    119.91  3.000
 MD4  H4    C4   C5    121.14  3.000
 MD4  C3    C4   C5    118.95  3.000
 MD4  H3    C3   N2    116.57  3.000
 MD4  H3    C3   C4    119.61  3.000
 MD4  N2    C3   C4    123.83  3.000
 MD4  C3    N2   C1    117.11  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
 MD4  CONST_01  C5    C7   C11  N10   180.00   0.0  0
 MD4  CONST_02  N8    C7   C11  N10     0.00   0.0  0
 MD4  CONST_03  C7    N8   N9   N10     0.00   0.0  0
 MD4  CONST_04  C5    C7   N8   N9    180.00   0.0  0
 MD4  CONST_05  C11   C7   N8   N9      0.00   0.0  0
 MD4  CONST_06  C7    C11  N10  N9      0.00   0.0  0
 MD4  CONST_07  C6    C5   C7   N8    180.00   0.0  0
 MD4  CONST_08  C4    C5   C7   N8      0.00   0.0  0
 MD4  CONST_09  C11   N10  N9   N8      0.00   0.0  0
 MD4  CONST_10  C6    C5   C7   C11     0.00   0.0  0
 MD4  CONST_11  C4    C5   C7   C11   180.00   0.0  0
 MD4  CONST_12  C1    C6   C5   C7    180.00   0.0  0
 MD4  CONST_13  C3    C4   C5   C7    180.00   0.0  0
 MD4  CONST_14  N2    C1   C6   C5      0.00   0.0  0
 MD4  CONST_15  N2    C3   C4   C5      0.00   0.0  0
 MD4  CONST_16  C3    N2   C1   C6      0.00   0.0  0
 MD4  CONST_17  C3    C4   C5   C6      0.00   0.0  0
 MD4  CONST_18  C4    C3   N2   C1      0.00   0.0  0
 MD4  CONST_19  C4    C5   C6   C1      0.00   0.0  0
 MD4  CONST_20  C7    C11  N10  C19   180.00   0.0  0
 MD4  CONST_21  N8    N9   N10  C19   180.00   0.0  0
 MD4  CONST_22  H11   C11  N10  C19     0.00   0.0  0
 MD4  CONST_23  H6    C6   C5   C7      0.00   0.0  0
 MD4  CONST_24  H4    C4   C5   C7      0.00   0.0  0
 MD4  CONST_25  H1    C1   C6   C5    180.00   0.0  0
 MD4  CONST_26  H3    C3   C4   C5    180.00   0.0  0
 MD4  Var_01    C12   C13  C14  C15    -0.67  30.0  3
 MD4  Var_02    H201  C20  N16  C15  -179.13  30.0  3
 MD4  Var_03    H212  C21  N16  C15   -67.43  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
 MD4  chir_01  C15  C17  C14  N16  negativ
 MD4  chir_02  C19  N10  C18  C17  negativ
 MD4  chir_03  C12  N16  C18  C13  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
 MD4  plan-1  C19  0.020
 MD4  plan-1  N10  0.020
 MD4  plan-1  N9   0.020
 MD4  plan-1  N8   0.020
 MD4  plan-1  C11  0.020
 MD4  plan-1  C7   0.020
 MD4  plan-1  C5   0.020
 MD4  plan-1  H11  0.020
 MD4  plan-2  C7   0.020
 MD4  plan-2  C5   0.020
 MD4  plan-2  C6   0.020
 MD4  plan-2  C1   0.020
 MD4  plan-2  C4   0.020
 MD4  plan-2  C3   0.020
 MD4  plan-2  N2   0.020
 MD4  plan-2  H6   0.020
 MD4  plan-2  H1   0.020
 MD4  plan-2  H4   0.020
 MD4  plan-2  H3   0.020

