# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:07:45 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: N~1~,N~1~,N~1~-tris(3-azaniumylpropyl)butane-1,4-diaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]CCCC[N+](CCC[NH3+])(CCC[NH3+])CCC[NH3+]
#
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
 B5L  B5L  N~1~,N~1~,N~1~-tris(3-azaniumylpropyl)butane-1,4-diaminium  ligand  56  18  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B5L
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
 B5L  C5   C  CH2   0  -0.345   0.9047   0.0056  -0.7784
 B5L  C4   C  CH2   0  -0.493   2.1926   0.0165   0.0233
 B5L  C3   C  CH2   0  -0.448   3.3882   0.0105  -0.9254
 B5L  C2   C  CH2   0  -0.303   4.6743   0.0481  -0.1235
 B5L  N18  N  NT3   1  -0.779  -0.3530  -4.9657   0.7020
 B5L  C17  C  CH2   0  -0.294  -0.4029  -3.6210   1.3228
 B5L  C16  C  CH2   0  -0.510  -0.3610  -2.5386   0.2582
 B5L  C15  C  CH2   0  -0.353  -0.4161  -1.1925   0.9573
 B5L  N6   N  NT    1  -0.424  -0.3643   0.0056   0.0442
 B5L  C11  C  CH2   0  -0.354  -0.4240   1.2137   0.9430
 B5L  C12  C  CH2   0  -0.510  -0.3785   2.5546   0.2321
 B5L  C13  C  CH2   0  -0.293  -0.4294   3.6414   1.2920
 B5L  N14  N  NT3   1  -0.778  -0.3929   4.9824   0.6637
 B5L  C7   C  CH2   0  -0.354  -1.5059  -0.0026  -0.9370
 B5L  C8   C  CH2   0  -0.511  -2.8908  -0.0049  -0.3141
 B5L  C9   C  CH2   0  -0.294  -3.9073  -0.0111  -1.4422
 B5L  N10  N  NT3   1  -0.778  -5.2873  -0.0185  -0.9046
 B5L  N1   N  NT3   1  -0.777   5.8592   0.0283  -1.0170
 B5L  H1   H  HCH2  0   0.321   0.8507   0.8749  -1.4321
 B5L  H2   H  HCH2  0   0.321   0.8588  -0.8719  -1.4219
 B5L  H3   H  HCH2  0   0.270   2.2540   0.9006   0.6608
 B5L  H4   H  HCH2  0   0.270   2.2599  -0.8547   0.6777
 B5L  H5   H  HCH2  0   0.268   3.3638  -0.8861  -1.5501
 B5L  H6   H  HCH2  0   0.268   3.3406   0.8755  -1.5916
 B5L  H7   H  HCH2  0   0.298   4.7461   0.9527   0.4766
 B5L  H8   H  HCH2  0   0.297   4.7627  -0.8130   0.5356
 B5L  H9   H  HNT3  0   0.485  -0.3846  -5.6982   1.4108
 B5L  H10  H  HNT3  0   0.474  -1.1389  -5.1301   0.0728
 B5L  H11  H  HNT3  0   0.475   0.5022  -5.1106   0.1651
 B5L  H12  H  HCH2  0   0.310  -1.3182  -3.5772   1.9086
 B5L  H13  H  HCH2  0   0.309   0.4469  -3.5529   1.9976
 B5L  H14  H  HCH2  0   0.289   0.5551  -2.6444  -0.3253
 B5L  H15  H  HCH2  0   0.288  -1.2031  -2.6689  -0.4241
 B5L  H16  H  HCH2  0   0.326  -1.3266  -1.1052   1.5489
 B5L  H17  H  HCH2  0   0.329   0.4150  -1.0873   1.6520
 B5L  H18  H  HCH2  0   0.326  -1.3339   1.1259   1.5355
 B5L  H19  H  HCH2  0   0.330   0.4082   1.1210   1.6381
 B5L  H20  H  HCH2  0   0.290   0.5373   2.6654  -0.3512
 B5L  H21  H  HCH2  0   0.289  -1.2220   2.6757  -0.4505
 B5L  H22  H  HCH2  0   0.309  -1.3435   3.5918   1.8791
 B5L  H23  H  HCH2  0   0.309   0.4220   3.5856   1.9661
 B5L  H24  H  HNT3  0   0.475   0.4578   5.1279   0.1202
 B5L  H25  H  HNT3  0   0.475  -1.1830   5.1349   0.0370
 B5L  H26  H  HNT3  0   0.484  -0.4259   5.7197   1.3672
 B5L  H27  H  HCH2  0   0.330  -1.3758   0.8673  -1.5791
 B5L  H28  H  HCH2  0   0.330  -1.3701  -0.8760  -1.5733
 B5L  H29  H  HCH2  0   0.288  -3.0410  -0.8834   0.3166
 B5L  H30  H  HCH2  0   0.289  -3.0462   0.8771   0.3104
 B5L  H31  H  HCH2  0   0.310  -3.8182   0.8727  -2.0697
 B5L  H32  H  HCH2  0   0.310  -3.8089  -0.8942  -2.0694
 B5L  H33  H  HNT3  0   0.475  -5.4732  -0.8448  -0.3363
 B5L  H34  H  HNT3  0   0.475  -5.4783   0.7994  -0.3260
 B5L  H35  H  HNT3  0   0.485  -5.9746  -0.0160  -1.6581
 B5L  H36  H  HNT3  0   0.472   5.8925  -0.8187  -1.5842
 B5L  H37  H  HNT3  0   0.472   5.8671   0.8234  -1.6556
 B5L  H38  H  HNT3  0   0.480   6.7286   0.0640  -0.4859

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
 B5L  N14  C13  single  1.481  0.020  1.481
 B5L  C2   C3   single  1.516  0.020  1.516
 B5L  C2   N1   single  1.484  0.020  1.484
 B5L  C3   C4   single  1.526  0.020  1.526
 B5L  C13  C12  single  1.519  0.020  1.519
 B5L  C12  C11  single  1.518  0.020  1.518
 B5L  C4   C5   single  1.517  0.020  1.517
 B5L  C5   N6   single  1.512  0.020  1.512
 B5L  C8   C7   single  1.518  0.020  1.518
 B5L  C8   C9   single  1.519  0.020  1.519
 B5L  C7   N6   single  1.505  0.020  1.505
 B5L  C9   N10  single  1.481  0.020  1.481
 B5L  C11  N6   single  1.507  0.020  1.507
 B5L  N6   C15  single  1.507  0.020  1.507
 B5L  C15  C16  single  1.518  0.020  1.518
 B5L  C16  C17  single  1.519  0.020  1.519
 B5L  C17  N18  single  1.482  0.020  1.482
 B5L  C5   H1   single  0.970  0.020  1.090
 B5L  C5   H2   single  0.970  0.020  1.090
 B5L  C4   H3   single  0.970  0.020  1.090
 B5L  C4   H4   single  0.970  0.020  1.090
 B5L  C3   H5   single  0.970  0.020  1.090
 B5L  C3   H6   single  0.970  0.020  1.090
 B5L  C2   H7   single  0.970  0.020  1.090
 B5L  C2   H8   single  0.970  0.020  1.090
 B5L  N18  H9   single  0.890  0.020  1.040
 B5L  N18  H10  single  0.890  0.020  1.040
 B5L  N18  H11  single  0.890  0.020  1.040
 B5L  C17  H12  single  0.970  0.020  1.090
 B5L  C17  H13  single  0.970  0.020  1.090
 B5L  C16  H14  single  0.970  0.020  1.090
 B5L  C16  H15  single  0.970  0.020  1.090
 B5L  C15  H16  single  0.970  0.020  1.090
 B5L  C15  H17  single  0.970  0.020  1.090
 B5L  C11  H18  single  0.970  0.020  1.090
 B5L  C11  H19  single  0.970  0.020  1.090
 B5L  C12  H20  single  0.970  0.020  1.090
 B5L  C12  H21  single  0.970  0.020  1.090
 B5L  C13  H22  single  0.970  0.020  1.090
 B5L  C13  H23  single  0.970  0.020  1.090
 B5L  N14  H24  single  0.890  0.020  1.040
 B5L  N14  H25  single  0.890  0.020  1.040
 B5L  N14  H26  single  0.890  0.020  1.040
 B5L  C7   H27  single  0.970  0.020  1.090
 B5L  C7   H28  single  0.970  0.020  1.090
 B5L  C8   H29  single  0.970  0.020  1.090
 B5L  C8   H30  single  0.970  0.020  1.090
 B5L  C9   H31  single  0.970  0.020  1.090
 B5L  C9   H32  single  0.970  0.020  1.090
 B5L  N10  H33  single  0.890  0.020  1.040
 B5L  N10  H34  single  0.890  0.020  1.040
 B5L  N10  H35  single  0.890  0.020  1.040
 B5L  N1   H36  single  0.890  0.020  1.040
 B5L  N1   H37  single  0.890  0.020  1.040
 B5L  N1   H38  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
 B5L  H2   C5   H1   106.64  3.000
 B5L  H2   C5   N6   106.62  3.000
 B5L  H1   C5   N6   106.56  3.000
 B5L  H2   C5   C4   110.72  3.000
 B5L  H1   C5   C4   110.70  3.000
 B5L  N6   C5   C4   115.15  3.000
 B5L  H4   C4   H3   107.02  3.000
 B5L  H4   C4   C3   108.73  3.000
 B5L  H3   C4   C3   108.79  3.000
 B5L  H4   C4   C5   111.31  3.000
 B5L  H3   C4   C5   111.24  3.000
 B5L  C3   C4   C5   109.67  3.000
 B5L  H6   C3   H5   107.45  3.000
 B5L  H6   C3   C2   109.86  3.000
 B5L  H5   C3   C2   109.97  3.000
 B5L  H6   C3   C4   109.98  3.000
 B5L  H5   C3   C4   109.94  3.000
 B5L  C2   C3   C4   109.61  3.000
 B5L  H8   C2   H7   108.58  3.000
 B5L  H8   C2   N1   106.82  3.000
 B5L  H7   C2   N1   106.88  3.000
 B5L  H8   C2   C3   111.70  3.000
 B5L  H7   C2   C3   111.61  3.000
 B5L  N1   C2   C3   111.01  3.000
 B5L  H11  N18  H10  107.36  3.000
 B5L  H11  N18  H9   106.84  3.000
 B5L  H10  N18  H9   106.80  3.000
 B5L  H11  N18  C17  112.19  3.000
 B5L  H10  N18  C17  112.25  3.000
 B5L  H9   N18  C17  111.08  3.000
 B5L  H13  C17  H12  108.72  3.000
 B5L  H13  C17  C16  111.64  3.000
 B5L  H12  C17  C16  111.84  3.000
 B5L  H13  C17  N18  106.89  3.000
 B5L  H12  C17  N18  106.89  3.000
 B5L  C16  C17  N18  110.62  3.000
 B5L  H15  C16  H14  107.57  3.000
 B5L  H15  C16  C15  111.45  3.000
 B5L  H14  C16  C15  111.27  3.000
 B5L  H15  C16  C17  109.38  3.000
 B5L  H14  C16  C17  109.20  3.000
 B5L  C15  C16  C17  107.95  3.000
 B5L  H17  C15  H16  106.49  3.000
 B5L  H17  C15  N6   106.48  3.000
 B5L  H16  C15  N6   107.10  3.000
 B5L  H17  C15  C16  110.61  3.000
 B5L  H16  C15  C16  110.58  3.000
 B5L  N6   C15  C16  115.13  3.000
 B5L  C7   N6   C11  111.30  3.000
 B5L  C11  N6   C15  105.94  3.000
 B5L  C7   N6   C15  111.38  3.000
 B5L  C15  N6   C5   111.00  3.000
 B5L  C11  N6   C5   110.96  3.000
 B5L  C7   N6   C5   106.36  3.000
 B5L  H19  C11  H18  106.53  3.000
 B5L  H19  C11  C12  110.57  3.000
 B5L  H18  C11  C12  110.54  3.000
 B5L  H19  C11  N6   106.40  3.000
 B5L  H18  C11  N6   107.03  3.000
 B5L  C12  C11  N6   115.31  3.000
 B5L  H21  C12  H20  107.63  3.000
 B5L  H21  C12  C13  109.33  3.000
 B5L  H20  C12  C13  109.17  3.000
 B5L  H21  C12  C11  111.56  3.000
 B5L  H20  C12  C11  111.41  3.000
 B5L  C13  C12  C11  107.71  3.000
 B5L  H23  C13  H22  108.73  3.000
 B5L  H23  C13  N14  106.87  3.000
 B5L  H22  C13  N14  106.92  3.000
 B5L  H23  C13  C12  111.69  3.000
 B5L  H22  C13  C12  111.85  3.000
 B5L  N14  C13  C12  110.55  3.000
 B5L  H26  N14  H25  106.90  3.000
 B5L  H26  N14  H24  106.94  3.000
 B5L  H25  N14  H24  107.30  3.000
 B5L  H26  N14  C13  111.17  3.000
 B5L  H25  N14  C13  112.14  3.000
 B5L  H24  N14  C13  112.07  3.000
 B5L  H28  C7   H27  106.34  3.000
 B5L  H28  C7   C8   110.62  3.000
 B5L  H27  C7   C8   110.61  3.000
 B5L  H28  C7   N6   106.90  3.000
 B5L  H27  C7   N6   106.82  3.000
 B5L  C8   C7   N6   115.10  3.000
 B5L  H30  C8   H29  107.46  3.000
 B5L  H30  C8   C9   109.45  3.000
 B5L  H29  C8   C9   109.49  3.000
 B5L  H30  C8   C7   111.30  3.000
 B5L  H29  C8   C7   111.32  3.000
 B5L  C9   C8   C7   107.81  3.000
 B5L  H32  C9   H31  108.64  3.000
 B5L  H32  C9   N10  106.83  3.000
 B5L  H31  C9   N10  106.85  3.000
 B5L  H32  C9   C8   111.79  3.000
 B5L  H31  C9   C8   111.74  3.000
 B5L  N10  C9   C8   110.74  3.000
 B5L  H35  N10  H34  106.91  3.000
 B5L  H35  N10  H33  106.91  3.000
 B5L  H34  N10  H33  107.43  3.000
 B5L  H35  N10  C9   111.08  3.000
 B5L  H34  N10  C9   112.11  3.000
 B5L  H33  N10  C9   112.10  3.000
 B5L  H38  N1   H37  107.00  3.000
 B5L  H38  N1   H36  106.92  3.000
 B5L  H37  N1   H36  107.39  3.000
 B5L  H38  N1   C2   111.51  3.000
 B5L  H37  N1   C2   111.88  3.000
 B5L  H36  N1   C2   111.83  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
 B5L  Var_01  C2   C3   C4   C5    178.93  30.0  1
 B5L  Var_02  C8   C7   N6   C5    179.96  30.0  2
 B5L  Var_03  C12  C11  N6   C5     59.17  30.0  2
 B5L  Var_04  C16  C15  N6   C5    -59.17  30.0  3
 B5L  Var_05  N1   C2   C3   C4    179.38  30.0  1
 B5L  Var_06  C7   N6   C5   C4    179.87  30.0  3
 B5L  Var_07  N6   C5   C4   C3    179.81  30.0  3
 B5L  Var_08  C15  C16  C17  N18   179.96  30.0  1
 B5L  Var_09  N6   C15  C16  C17   179.19  30.0  1
 B5L  Var_10  C9   C8   C7   N6    179.91  30.0  1
 B5L  Var_11  C13  C12  C11  N6   -179.24  30.0  1
 B5L  Var_12  N14  C13  C12  C11  -179.81  30.0  1
 B5L  Var_13  N10  C9   C8   C7    179.79  30.0  3
 B5L  Var_14  H36  N1   C2   C3    -60.98  30.0  3
 B5L  Var_15  H9   N18  C17  C16  -179.77  30.0  3
 B5L  Var_16  H24  N14  C13  C12   -60.34  30.0  3
 B5L  Var_17  H33  N10  C9   C8    -60.88  30.0  3

