# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:42:02 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: cyclohexylmethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]CC1CCCCC1
#
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
 AMC  AMC  'cyclohexylmethanaminium  '  ligand  24  8  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AMC
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
 AMC  C1   C  CH1   0  -0.267   0.5130   0.2366   0.2395
 AMC  C2   C  CH2   0  -0.434   0.0381  -1.1173  -0.2905
 AMC  C3   C  CH2   0  -0.430  -1.3788  -1.4364   0.1776
 AMC  C4   C  CH2   0  -0.432  -2.3561  -0.3321  -0.2071
 AMC  C5   C  CH2   0  -0.434  -1.8882   1.0202   0.3176
 AMC  C6   C  CH2   0  -0.421  -0.4722   1.3402  -0.1494
 AMC  CM   C  CH2   0  -0.296   1.8953   0.6110  -0.2668
 AMC  N    N  NT3   1  -0.784   2.9414  -0.3301   0.2184
 AMC  H1   H  HCH1  0   0.244   0.5523   0.1917   1.3360
 AMC  H21  H  HCH2  0   0.223   0.0657  -1.0995  -1.3865
 AMC  H22  H  HCH2  0   0.230   0.7060  -1.9246   0.0255
 AMC  H31  H  HCH2  0   0.215  -1.3805  -1.5618   1.2655
 AMC  H32  H  HCH2  0   0.234  -1.6986  -2.3915  -0.2443
 AMC  H41  H  HCH2  0   0.231  -3.3537  -0.5613   0.1745
 AMC  H42  H  HCH2  0   0.212  -2.4429  -0.2888  -1.2982
 AMC  H51  H  HCH2  0   0.214  -1.9142   1.0136   1.4126
 AMC  H52  H  HCH2  0   0.233  -2.5692   1.8112  -0.0046
 AMC  H61  H  HCH2  0   0.239  -0.1439   2.2942   0.2714
 AMC  H62  H  HCH2  0   0.219  -0.4653   1.4598  -1.2389
 AMC  HM1  H  HCH2  0   0.298   2.1906   1.5986   0.0820
 AMC  HM2  H  HCH2  0   0.287   1.9439   0.5983  -1.3548
 AMC  HN1  H  HNT3  0   0.469   2.9969  -0.3401   1.2365
 AMC  HN2  H  HNT3  0   0.479   3.8651  -0.0725  -0.1268
 AMC  HN3  H  HNT3  0   0.469   2.7733  -1.2890  -0.0831

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
 AMC  C1  C2   single  1.530  0.020  1.530
 AMC  C1  C6   single  1.530  0.020  1.530
 AMC  C1  CM   single  1.519  0.020  1.519
 AMC  C1  H1   single  0.970  0.020  1.090
 AMC  C2  C3   single  1.526  0.020  1.526
 AMC  C2  H21  single  0.970  0.020  1.090
 AMC  C2  H22  single  0.970  0.020  1.090
 AMC  C3  C4   single  1.524  0.020  1.524
 AMC  C3  H31  single  0.970  0.020  1.090
 AMC  C3  H32  single  0.970  0.020  1.090
 AMC  C4  C5   single  1.524  0.020  1.524
 AMC  C4  H41  single  0.970  0.020  1.090
 AMC  C4  H42  single  0.970  0.020  1.090
 AMC  C5  C6   single  1.525  0.020  1.525
 AMC  C5  H51  single  0.970  0.020  1.090
 AMC  C5  H52  single  0.970  0.020  1.090
 AMC  C6  H61  single  0.970  0.020  1.090
 AMC  C6  H62  single  0.970  0.020  1.090
 AMC  CM  N    single  1.488  0.020  1.488
 AMC  CM  HM1  single  0.970  0.020  1.090
 AMC  CM  HM2  single  0.970  0.020  1.090
 AMC  N   HN1  single  0.890  0.020  1.040
 AMC  N   HN2  single  0.890  0.020  1.040
 AMC  N   HN3  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
 AMC  H1   C1  CM   108.09  3.000
 AMC  H1   C1  C6   107.84  3.000
 AMC  CM   C1  C6   108.88  3.000
 AMC  H1   C1  C2   108.72  3.000
 AMC  CM   C1  C2   112.66  3.000
 AMC  C6   C1  C2   110.52  3.000
 AMC  H22  C2  H21  106.57  3.000
 AMC  H22  C2  C3   108.90  3.000
 AMC  H21  C2  C3   109.48  3.000
 AMC  H22  C2  C1   111.30  3.000
 AMC  H21  C2  C1   108.92  3.000
 AMC  C3   C2  C1   111.54  3.000
 AMC  H32  C3  H31  106.45  3.000
 AMC  H32  C3  C4   110.40  3.000
 AMC  H31  C3  C4   109.44  3.000
 AMC  H32  C3  C2   109.65  3.000
 AMC  H31  C3  C2   109.28  3.000
 AMC  C4   C3  C2   111.50  3.000
 AMC  H42  C4  H41  106.49  3.000
 AMC  H42  C4  C5   109.40  3.000
 AMC  H41  C4  C5   110.26  3.000
 AMC  H42  C4  C3   109.32  3.000
 AMC  H41  C4  C3   110.20  3.000
 AMC  C5   C4  C3   111.05  3.000
 AMC  H52  C5  H51  106.52  3.000
 AMC  H52  C5  C6   109.67  3.000
 AMC  H51  C5  C6   109.23  3.000
 AMC  H52  C5  C4   110.46  3.000
 AMC  H51  C5  C4   109.37  3.000
 AMC  C6   C5  C4   111.46  3.000
 AMC  H62  C6  H61  106.59  3.000
 AMC  H62  C6  C5   109.46  3.000
 AMC  H61  C6  C5   110.13  3.000
 AMC  H62  C6  C1   109.11  3.000
 AMC  H61  C6  C1   109.77  3.000
 AMC  C5   C6  C1   111.64  3.000
 AMC  HM2  CM  HM1  108.58  3.000
 AMC  HM2  CM  N    106.68  3.000
 AMC  HM1  CM  N    106.18  3.000
 AMC  HM2  CM  C1   111.76  3.000
 AMC  HM1  CM  C1   111.33  3.000
 AMC  N    CM  C1   112.03  3.000
 AMC  HN3  N   HN2  106.69  3.000
 AMC  HN3  N   HN1  107.16  3.000
 AMC  HN2  N   HN1  106.94  3.000
 AMC  HN3  N   CM   112.49  3.000
 AMC  HN2  N   CM   111.52  3.000
 AMC  HN1  N   CM   111.71  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
 AMC  Var_01  C4   C3  C2  C1   55.57  30.0  1
 AMC  Var_02  C4   C5  C6  C1  -55.51  30.0  1
 AMC  Var_03  C5   C4  C3  C2  -55.12  30.0  1
 AMC  Var_04  C6   C5  C4  C3   55.06  30.0  1
 AMC  Var_05  HN1  N   CM  C1  -60.46  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
 AMC  chir_01  C1  C2  C6  CM  positiv

