# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 18:27:33 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N,N,N-trimethyl-5-({[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]methyl}amino)pentan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)CCCCCNCC12CC3CC(CC(C3)C1)C2
#
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
 GZD  GZD  N,N,N-trimethyl-5-({[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]methyl}amino)pentan-1-aminium  ligand  58  21  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GZD
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
 GZD  C4   C  CH3   0  -0.551  -6.9167   1.1312  -1.1930
 GZD  C5   C  CH2   0  -0.304  -5.6267  -0.5796   0.0308
 GZD  C6   C  CH2   0  -0.477  -4.3036   0.1599  -0.0095
 GZD  C7   C  CH2   0  -0.420  -3.1487  -0.8386  -0.0084
 GZD  C8   C  CH2   0  -0.445  -1.7977  -0.1382  -0.0537
 GZD  C13  C  C     0  -0.418   3.2962   0.3964  -1.2636
 GZD  C15  C  C     0  -0.417   5.7774   0.0977  -1.1763
 GZD  C17  C  C     0  -0.401   4.2735  -1.5082   0.0017
 GZD  C20  C  CH2   0  -0.417   4.6950   1.9918   0.0462
 GZD  C21  C  C     0  -0.392   3.2037   0.3749   1.2307
 GZD  C1   C  CH3   0  -0.550  -6.8815   1.1696   1.2388
 GZD  C11  C  CH2   0  -0.227   1.7935  -1.2618  -0.0820
 GZD  C12  C  C     0  -0.111   3.1170  -0.4984  -0.0279
 GZD  C14  C  CR16  0  -0.242   4.6429   1.1219  -1.2114
 GZD  C16  C  C     0  -0.245   5.6231  -0.7893   0.0611
 GZD  C18  C  C     0  -0.417   5.6837   0.0823   1.3181
 GZD  C19  C  CR16  0  -0.246   4.5474   1.1062   1.2851
 GZD  C3   C  CH3   0  -0.544  -8.0519  -0.5962   0.0672
 GZD  C9   C  CH2   0  -0.247  -0.6263  -1.1084  -0.0469
 GZD  N10  N  NH1   0  -0.605   0.6333  -0.3931  -0.0905
 GZD  N2   N  NT    1  -0.385  -6.8567   0.2930   0.0358
 GZD  H1   H  HCH3  0   0.296  -6.0986   1.8442  -1.1954
 GZD  H2   H  HCH3  0   0.294  -6.8496   0.4878  -2.0665
 GZD  H3   H  HCH3  0   0.297  -7.8611   1.6688  -1.2050
 GZD  H4   H  HCH2  0   0.297  -5.7241  -1.2331  -0.8375
 GZD  H5   H  HCH2  0   0.297  -5.6909  -1.1993   0.9262
 GZD  H6   H  HCH2  0   0.254  -4.2330   0.7823  -0.9041
 GZD  H7   H  HCH2  0   0.254  -4.1996   0.8210   0.8535
 GZD  H8   H  HCH2  0   0.229  -3.2084  -1.4663   0.8864
 GZD  H9   H  HCH2  0   0.229  -3.2456  -1.5115  -0.8661
 GZD  H10  H  HCH2  0   0.219  -1.7448   0.4861  -0.9527
 GZD  H11  H  HCH2  0   0.221  -1.7029   0.5394   0.8001
 GZD  H13  H  H     0   0.220   2.4950   1.1421  -1.3210
 GZD  H14  H  H     0   0.219   5.7600  -0.5134  -2.0850
 GZD  H15  H  H     0   0.219   6.7463   0.6080  -1.1567
 GZD  H16  H  H     0   0.217   4.1622  -2.1691   0.8688
 GZD  H17  H  H     0   0.217   4.2311  -2.1452  -0.8891
 GZD  H18  H  HCH2  0   0.219   5.6385   2.5469   0.0847
 GZD  H19  H  HCH2  0   0.218   3.8931   2.7373   0.0187
 GZD  H20  H  H     0   0.220   2.3783   1.0923   1.2413
 GZD  H21  H  H     0   0.210   3.0874  -0.2551   2.1209
 GZD  H22  H  HCH3  0   0.297  -7.8173   1.7222   1.2499
 GZD  H23  H  HCH3  0   0.294  -6.8097   0.5518   2.1302
 GZD  H24  H  HCH3  0   0.296  -6.0517   1.8674   1.2037
 GZD  H25  H  HCH2  0   0.187   1.8123  -1.9415  -0.9526
 GZD  H26  H  HCH2  0   0.212   1.7256  -1.9049   0.8034
 GZD  H27  H  HCR6  0   0.220   4.7449   1.7546  -2.0987
 GZD  H28  H  H     0   0.220   6.4276  -1.5307   0.0872
 GZD  H29  H  H     0   0.218   5.6013  -0.5416   2.2143
 GZD  H30  H  H     0   0.218   6.6514   0.5921   1.3733
 GZD  H31  H  HCR6  0   0.218   4.5858   1.7273   2.1856
 GZD  H32  H  HCH3  0   0.294  -8.0472  -1.2320  -0.8137
 GZD  H33  H  HCH3  0   0.295  -8.0198  -1.2073   0.9650
 GZD  H34  H  HCH3  0   0.294  -8.9496   0.0159   0.0728
 GZD  H35  H  HCH2  0   0.213  -0.6546  -1.7040   0.8716
 GZD  H36  H  HCH2  0   0.183  -0.7394  -1.8244  -0.8784
 GZD  H37  H  HNH1  0   0.341   0.6482   0.1700  -0.9327
 GZD  H12  H  H     0   0.217   3.2317  -0.2119  -2.1739

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
 GZD  C4   N2   single  1.489  0.020  1.489
 GZD  C1   N2   single  1.489  0.020  1.489
 GZD  N2   C3   single  1.490  0.020  1.490
 GZD  N2   C5   single  1.508  0.020  1.508
 GZD  C5   C6   single  1.516  0.020  1.516
 GZD  C6   C7   single  1.527  0.020  1.527
 GZD  C7   C8   single  1.523  0.020  1.523
 GZD  C8   C9   single  1.521  0.020  1.521
 GZD  C9   N10  single  1.449  0.020  1.449
 GZD  N10  C11  single  1.449  0.020  1.449
 GZD  C11  C12  single  1.529  0.020  1.529
 GZD  C17  C12  single  1.536  0.020  1.536
 GZD  C17  C16  single  1.530  0.020  1.530
 GZD  C12  C13  single  1.536  0.020  1.536
 GZD  C12  C21  single  1.534  0.020  1.534
 GZD  C13  C14  single  1.531  0.020  1.531
 GZD  C21  C19  single  1.531  0.020  1.531
 GZD  C16  C15  single  1.530  0.020  1.530
 GZD  C16  C18  single  1.531  0.020  1.531
 GZD  C15  C14  single  1.529  0.020  1.529
 GZD  C18  C19  single  1.530  0.020  1.530
 GZD  C14  C20  single  1.530  0.020  1.530
 GZD  C19  C20  single  1.530  0.020  1.530
 GZD  C4   H1   single  0.970  0.020  1.090
 GZD  C4   H2   single  0.970  0.020  1.090
 GZD  C4   H3   single  0.970  0.020  1.090
 GZD  C5   H4   single  0.970  0.020  1.090
 GZD  C5   H5   single  0.970  0.020  1.090
 GZD  C6   H6   single  0.970  0.020  1.090
 GZD  C6   H7   single  0.970  0.020  1.090
 GZD  C7   H8   single  0.970  0.020  1.090
 GZD  C7   H9   single  0.970  0.020  1.090
 GZD  C8   H10  single  0.970  0.020  1.090
 GZD  C8   H11  single  0.970  0.020  1.090
 GZD  C13  H12  single  0.970  0.020  1.090
 GZD  C13  H13  single  0.970  0.020  1.090
 GZD  C15  H14  single  0.970  0.020  1.090
 GZD  C15  H15  single  0.970  0.020  1.090
 GZD  C17  H16  single  0.970  0.020  1.090
 GZD  C17  H17  single  0.970  0.020  1.090
 GZD  C20  H18  single  0.970  0.020  1.090
 GZD  C20  H19  single  0.970  0.020  1.090
 GZD  C21  H20  single  0.970  0.020  1.090
 GZD  C21  H21  single  0.970  0.020  1.090
 GZD  C1   H22  single  0.970  0.020  1.090
 GZD  C1   H23  single  0.970  0.020  1.090
 GZD  C1   H24  single  0.970  0.020  1.090
 GZD  C11  H25  single  0.970  0.020  1.090
 GZD  C11  H26  single  0.970  0.020  1.090
 GZD  C14  H27  single  0.970  0.020  1.090
 GZD  C16  H28  single  0.970  0.020  1.090
 GZD  C18  H29  single  0.970  0.020  1.090
 GZD  C18  H30  single  0.970  0.020  1.090
 GZD  C19  H31  single  0.970  0.020  1.090
 GZD  C3   H32  single  0.970  0.020  1.090
 GZD  C3   H33  single  0.970  0.020  1.090
 GZD  C3   H34  single  0.970  0.020  1.090
 GZD  C9   H35  single  0.970  0.020  1.090
 GZD  C9   H36  single  0.970  0.020  1.090
 GZD  N10  H37  single  0.890  0.020  1.040

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
 GZD  H3   C4   H2   109.73  3.000
 GZD  H3   C4   H1   109.27  3.000
 GZD  H2   C4   H1   109.91  3.000
 GZD  H3   C4   N2   108.82  3.000
 GZD  H2   C4   N2   109.12  3.000
 GZD  H1   C4   N2   109.96  3.000
 GZD  H5   C5   H4   107.93  3.000
 GZD  H5   C5   N2   106.14  3.000
 GZD  H4   C5   N2   106.05  3.000
 GZD  H5   C5   C6   110.50  3.000
 GZD  H4   C5   C6   110.41  3.000
 GZD  N2   C5   C6   115.44  3.000
 GZD  H7   C6   H6   107.23  3.000
 GZD  H7   C6   C7   108.87  3.000
 GZD  H6   C6   C7   108.93  3.000
 GZD  H7   C6   C5   110.94  3.000
 GZD  H6   C6   C5   110.86  3.000
 GZD  C7   C6   C5   109.94  3.000
 GZD  H9   C7   H8   106.46  3.000
 GZD  H9   C7   C8   109.76  3.000
 GZD  H8   C7   C8   109.66  3.000
 GZD  H9   C7   C6   109.55  3.000
 GZD  H8   C7   C6   109.54  3.000
 GZD  C8   C7   C6   111.74  3.000
 GZD  H11  C8   H10  106.45  3.000
 GZD  H11  C8   C9   108.96  3.000
 GZD  H10  C8   C9   109.26  3.000
 GZD  H11  C8   C7   109.79  3.000
 GZD  H10  C8   C7   109.23  3.000
 GZD  C9   C8   C7   112.94  3.000
 GZD  H13  C13  H12  106.91  3.000
 GZD  H13  C13  C14  108.81  3.000
 GZD  H12  C13  C14  110.06  3.000
 GZD  H13  C13  C12  110.68  3.000
 GZD  H12  C13  C12  109.74  3.000
 GZD  C14  C13  C12  110.57  3.000
 GZD  H15  C15  H14  106.79  3.000
 GZD  H15  C15  C16  110.17  3.000
 GZD  H14  C15  C16  110.24  3.000
 GZD  H15  C15  C14  110.17  3.000
 GZD  H14  C15  C14  110.05  3.000
 GZD  C16  C15  C14  109.40  3.000
 GZD  H17  C17  H16  106.78  3.000
 GZD  H17  C17  C16  109.80  3.000
 GZD  H16  C17  C16  110.01  3.000
 GZD  H17  C17  C12  109.72  3.000
 GZD  H16  C17  C12  109.59  3.000
 GZD  C16  C17  C12  110.86  3.000
 GZD  H19  C20  H18  106.66  3.000
 GZD  H19  C20  C19  110.10  3.000
 GZD  H18  C20  C19  110.37  3.000
 GZD  H19  C20  C14  109.96  3.000
 GZD  H18  C20  C14  110.26  3.000
 GZD  C19  C20  C14  109.46  3.000
 GZD  H21  C21  H20  106.79  3.000
 GZD  H21  C21  C19  109.79  3.000
 GZD  H20  C21  C19  110.41  3.000
 GZD  H21  C21  C12  109.45  3.000
 GZD  H20  C21  C12  109.80  3.000
 GZD  C19  C21  C12  110.52  3.000
 GZD  H24  C1   H23  109.97  3.000
 GZD  H24  C1   H22  109.38  3.000
 GZD  H23  C1   H22  109.73  3.000
 GZD  H24  C1   N2   109.87  3.000
 GZD  H23  C1   N2   109.08  3.000
 GZD  H22  C1   N2   108.79  3.000
 GZD  H26  C11  H25  106.05  3.000
 GZD  H26  C11  N10  107.86  3.000
 GZD  H25  C11  N10  112.20  3.000
 GZD  H26  C11  C12  108.54  3.000
 GZD  H25  C11  C12  108.69  3.000
 GZD  N10  C11  C12  113.20  3.000
 GZD  C11  C12  C21  111.23  3.000
 GZD  C21  C12  C17  108.42  3.000
 GZD  C11  C12  C17  108.92  3.000
 GZD  C21  C12  C13  108.77  3.000
 GZD  C17  C12  C13  108.10  3.000
 GZD  C11  C12  C13  111.31  3.000
 GZD  H27  C14  C20  109.54  3.000
 GZD  H27  C14  C15  109.68  3.000
 GZD  C20  C14  C15  109.68  3.000
 GZD  H27  C14  C13  109.17  3.000
 GZD  C20  C14  C13  109.12  3.000
 GZD  C15  C14  C13  109.64  3.000
 GZD  H28  C16  C18  109.70  3.000
 GZD  H28  C16  C17  109.33  3.000
 GZD  C18  C16  C17  109.53  3.000
 GZD  H28  C16  C15  109.74  3.000
 GZD  C18  C16  C15  109.26  3.000
 GZD  C17  C16  C15  109.26  3.000
 GZD  H30  C18  H29  106.89  3.000
 GZD  H30  C18  C19  110.24  3.000
 GZD  H29  C18  C19  110.06  3.000
 GZD  H30  C18  C16  109.96  3.000
 GZD  H29  C18  C16  110.16  3.000
 GZD  C19  C18  C16  109.51  3.000
 GZD  H31  C19  C18  109.63  3.000
 GZD  H31  C19  C21  109.33  3.000
 GZD  C18  C19  C21  109.46  3.000
 GZD  H31  C19  C20  109.53  3.000
 GZD  C18  C19  C20  109.46  3.000
 GZD  C21  C19  C20  109.42  3.000
 GZD  H34  C3   H33  109.69  3.000
 GZD  H34  C3   H32  109.72  3.000
 GZD  H33  C3   H32  109.92  3.000
 GZD  H34  C3   N2   109.07  3.000
 GZD  H33  C3   N2   109.23  3.000
 GZD  H32  C3   N2   109.19  3.000
 GZD  H36  C9   H35  106.06  3.000
 GZD  H36  C9   N10  112.76  3.000
 GZD  H35  C9   N10  108.43  3.000
 GZD  H36  C9   C8   109.37  3.000
 GZD  H35  C9   C8   109.31  3.000
 GZD  N10  C9   C8   110.76  3.000
 GZD  H37  N10  C9   108.18  3.000
 GZD  H37  N10  C11  109.04  3.000
 GZD  C9   N10  C11  113.56  3.000
 GZD  C3   N2   C1   108.72  3.000
 GZD  C3   N2   C5   108.00  3.000
 GZD  C1   N2   C5   110.92  3.000
 GZD  C5   N2   C4   110.85  3.000
 GZD  C3   N2   C4   108.73  3.000
 GZD  C1   N2   C4   109.56  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
 GZD  Var_01  C9   N10  C11  C12  -175.91  30.0  2
 GZD  Var_02  C6   C5   N2   C4     60.60  30.0  3
 GZD  Var_03  C8   C7   C6   C5    179.79  30.0  3
 GZD  Var_04  C9   C8   C7   C6    179.72  30.0  3
 GZD  Var_05  N2   C5   C6   C7    179.92  30.0  1
 GZD  Var_06  N10  C9   C8   C7   -179.98  30.0  3
 GZD  Var_07  C11  N10  C9   C8    179.81  30.0  3
 GZD  Var_08  H22  C1   N2   C4     61.88  30.0  3
 GZD  Var_09  H32  C3   N2   C4     60.15  30.0  3
 GZD  Var_10  H1   C4   N2   C5    -66.08  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
 GZD  chir_01  C12  C17  C13  C21  positiv
 GZD  chir_02  C14  C13  C15  C20  positiv
 GZD  chir_03  C16  C17  C15  C18  negativ
 GZD  chir_04  C19  C21  C18  C20  negativ

