# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:15:43 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: 3,6,9,12-tetrazacyclododecane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CNCCNCCNCCN1
#
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
 YCN  YCN  3,6,9,12-tetrazacyclododecane  ligand  32  12  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YCN
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
 YCN  C1   C  CH2   0  -0.302   1.6459  -2.4058  -0.0339
 YCN  N1   N  NH1   0  -0.607   0.2700  -2.4310   0.4363
 YCN  C2   C  CH2   0  -0.241   2.3931  -1.1347   0.3632
 YCN  N2   N  NH1   0  -0.607   1.8749   0.0285  -0.3212
 YCN  C3   C  CH2   0  -0.295   2.1031   1.3416   0.2460
 YCN  N3   N  NH1   0  -0.625  -0.2886   1.6273   0.3894
 YCN  C4   C  CH2   0  -0.264   0.9235   2.2460  -0.1091
 YCN  N4   N  NH1   0  -0.611  -2.6361  -0.2107  -0.3728
 YCN  C5   C  CH2   0  -0.260  -1.5080   2.0234  -0.2847
 YCN  C6   C  CH2   0  -0.309  -2.6981   1.1592   0.1178
 YCN  C7   C  CH2   0  -0.315  -1.8438  -1.1551   0.4098
 YCN  C8   C  CH2   0  -0.280  -0.7225  -1.7916  -0.4144
 YCN  H1   H  HCH2  0   0.225   2.1697  -3.2472   0.4258
 YCN  H1A  H  HCH2  0   0.191   1.7331  -2.5545  -1.1219
 YCN  HN1  H  HNH1  0   0.344  -0.0022  -3.3857   0.6187
 YCN  H2   H  HCH2  0   0.212   2.2587  -0.9876   1.4378
 YCN  H2A  H  HCH2  0   0.188   3.4702  -1.2936   0.1988
 YCN  HN2  H  HNH1  0   0.344   2.1199   0.0105  -1.3019
 YCN  H3   H  HCH2  0   0.220   2.1554   1.2418   1.3336
 YCN  H3A  H  HCH2  0   0.212   3.0431   1.8095  -0.0735
 YCN  HN3  H  HNH1  0   0.383  -0.1427   0.6387   0.2272
 YCN  H4   H  HCH2  0   0.211   1.0685   3.2384   0.3297
 YCN  H4A  H  HCH2  0   0.181   0.9024   2.3888  -1.2030
 YCN  HN4  H  HNH1  0   0.351  -3.5747  -0.5602  -0.4849
 YCN  H5   H  HCH2  0   0.205  -1.7404   3.0615  -0.0247
 YCN  H5A  H  HCH2  0   0.176  -1.4094   1.9917  -1.3825
 YCN  H6   H  HCH2  0   0.229  -3.5905   1.6179  -0.3132
 YCN  H6A  H  HCH2  0   0.190  -2.8165   1.2127   1.2110
 YCN  H7   H  HCH2  0   0.207  -1.3915  -0.6551   1.2720
 YCN  H7A  H  HCH2  0   0.223  -2.4814  -1.9408   0.8288
 YCN  H8   H  HCH2  0   0.223  -0.2316  -1.0081  -0.9889
 YCN  H8A  H  HCH2  0   0.200  -1.1582  -2.4819  -1.1508

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
 YCN  C1  N1   single  1.454  0.020  1.454
 YCN  C1  C2   single  1.527  0.020  1.527
 YCN  N1  C8   single  1.455  0.020  1.455
 YCN  C2  N2   single  1.446  0.020  1.446
 YCN  N2  C3   single  1.449  0.020  1.449
 YCN  C3  C4   single  1.528  0.020  1.528
 YCN  N3  C4   single  1.449  0.020  1.449
 YCN  N3  C5   single  1.449  0.020  1.449
 YCN  N4  C6   single  1.456  0.020  1.456
 YCN  N4  C7   single  1.460  0.020  1.460
 YCN  C5  C6   single  1.525  0.020  1.525
 YCN  C7  C8   single  1.530  0.020  1.530
 YCN  C1  H1   single  0.970  0.020  1.090
 YCN  C1  H1A  single  0.970  0.020  1.090
 YCN  N1  HN1  single  0.890  0.020  1.040
 YCN  C2  H2   single  0.970  0.020  1.090
 YCN  C2  H2A  single  0.970  0.020  1.090
 YCN  N2  HN2  single  0.890  0.020  1.040
 YCN  C3  H3   single  0.970  0.020  1.090
 YCN  C3  H3A  single  0.970  0.020  1.090
 YCN  N3  HN3  single  0.890  0.020  1.040
 YCN  C4  H4   single  0.970  0.020  1.090
 YCN  C4  H4A  single  0.970  0.020  1.090
 YCN  N4  HN4  single  0.890  0.020  1.040
 YCN  C5  H5   single  0.970  0.020  1.090
 YCN  C5  H5A  single  0.970  0.020  1.090
 YCN  C6  H6   single  0.970  0.020  1.090
 YCN  C6  H6A  single  0.970  0.020  1.090
 YCN  C7  H7   single  0.970  0.020  1.090
 YCN  C7  H7A  single  0.970  0.020  1.090
 YCN  C8  H8   single  0.970  0.020  1.090
 YCN  C8  H8A  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
 YCN  H1A  C1  H1  105.88  3.000
 YCN  H1A  C1  C2  109.30  3.000
 YCN  H1   C1  C2  107.28  3.000
 YCN  H1A  C1  N1  113.08  3.000
 YCN  H1   C1  N1  107.71  3.000
 YCN  C2   C1  N1  113.17  3.000
 YCN  HN1  N1  C8  109.71  3.000
 YCN  HN1  N1  C1  109.27  3.000
 YCN  C8   N1  C1  116.66  3.000
 YCN  H2A  C2  H2  106.65  3.000
 YCN  H2A  C2  N2  113.34  3.000
 YCN  H2   C2  N2  108.24  3.000
 YCN  H2A  C2  C1  108.65  3.000
 YCN  H2   C2  C1  107.91  3.000
 YCN  N2   C2  C1  111.79  3.000
 YCN  HN2  N2  C3  110.96  3.000
 YCN  HN2  N2  C2  110.98  3.000
 YCN  C3   N2  C2  119.18  3.000
 YCN  H3A  C3  H3  106.71  3.000
 YCN  H3A  C3  C4  109.95  3.000
 YCN  H3   C3  C4  108.79  3.000
 YCN  H3A  C3  N2  114.04  3.000
 YCN  H3   C3  N2  108.32  3.000
 YCN  C4   C3  N2  108.90  3.000
 YCN  HN3  N3  C5  108.28  3.000
 YCN  HN3  N3  C4  103.96  3.000
 YCN  C5   N3  C4  115.29  3.000
 YCN  H4A  C4  H4  106.42  3.000
 YCN  H4A  C4  N3  112.35  3.000
 YCN  H4   C4  N3  111.09  3.000
 YCN  H4A  C4  C3  108.77  3.000
 YCN  H4   C4  C3  109.94  3.000
 YCN  N3   C4  C3  108.24  3.000
 YCN  HN4  N4  C7  109.92  3.000
 YCN  HN4  N4  C6  108.90  3.000
 YCN  C7   N4  C6  116.80  3.000
 YCN  H5A  C5  H5  106.41  3.000
 YCN  H5A  C5  C6  108.44  3.000
 YCN  H5   C5  C6  108.00  3.000
 YCN  H5A  C5  N3  112.35  3.000
 YCN  H5   C5  N3  109.10  3.000
 YCN  C6   C5  N3  112.28  3.000
 YCN  H6A  C6  H6  106.48  3.000
 YCN  H6A  C6  C5  108.58  3.000
 YCN  H6   C6  C5  107.19  3.000
 YCN  H6A  C6  N4  112.63  3.000
 YCN  H6   C6  N4  107.27  3.000
 YCN  C5   C6  N4  114.26  3.000
 YCN  H7A  C7  H7  105.48  3.000
 YCN  H7A  C7  C8  109.53  3.000
 YCN  H7   C7  C8  108.15  3.000
 YCN  H7A  C7  N4  110.68  3.000
 YCN  H7   C7  N4  110.55  3.000
 YCN  C8   C7  N4  112.21  3.000
 YCN  H8A  C8  H8  106.09  3.000
 YCN  H8A  C8  C7  109.36  3.000
 YCN  H8   C8  C7  108.38  3.000
 YCN  H8A  C8  N1  112.71  3.000
 YCN  H8   C8  N1  108.50  3.000
 YCN  C7   C8  N1  111.57  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
 YCN  Var_01  C7  C8  N1  C1  -146.77  30.0  1
 YCN  Var_02  C3  N2  C2  C1   158.17  30.0  1
 YCN  Var_03  N2  C2  C1  N1   -68.12  30.0  1
 YCN  Var_04  N4  C7  C8  N1   164.25  30.0  1
 YCN  Var_05  C8  N1  C1  C2    86.06  30.0  1
 YCN  Var_06  C4  C3  N2  C2  -148.59  30.0  1
 YCN  Var_07  N3  C4  C3  N2    57.30  30.0  1
 YCN  Var_08  C5  N3  C4  C3  -156.25  30.0  1
 YCN  Var_09  N4  C6  C5  N3   -69.75  30.0  1
 YCN  Var_10  C6  C5  N3  C4   169.83  30.0  1
 YCN  Var_11  C7  N4  C6  C5    82.89  30.0  1
 YCN  Var_12  C8  C7  N4  C6  -121.64  30.0  1

