# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 12:01:54 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: ~{N}',~{N}'-bis(3-azanylpropyl)butane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCN(CCCN)CCCN
#
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
 N4P  N4P  ~{N}',~{N}'-bis(3-azanylpropyl)butane-1,4-diamine  ligand  40  14  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_N4P
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
 N4P  C4   C  CH2   0  -0.436   2.0131  -0.0925  -0.2097
 N4P  C5   C  CH2   0  -0.269   0.8601   0.4535   0.6217
 N4P  N1   N  NH2   0  -0.800   5.7926   0.4241  -0.0705
 N4P  C3   C  CH2   0  -0.429   3.3588   0.4505   0.2538
 N4P  C2   C  CH2   0  -0.271   4.5241  -0.1092  -0.5469
 N4P  N6   N  NT    0  -0.425  -0.4430  -0.0364   0.2003
 N4P  C7   C  CH2   0  -0.279  -0.6833  -1.4041   0.6352
 N4P  C8   C  CH2   0  -0.440  -1.6759  -2.1410  -0.2534
 N4P  C9   C  CH2   0  -0.275  -1.9721  -3.5407   0.2621
 N4P  N10  N  NH2   0  -0.800  -2.9141  -4.2294  -0.6092
 N4P  C11  C  CH2   0  -0.278  -1.5132   0.8531   0.6284
 N4P  C12  C  CH2   0  -0.442  -1.6831   2.0675  -0.2738
 N4P  C13  C  CH2   0  -0.273  -2.7648   3.0057   0.2381
 N4P  N14  N  NH2   0  -0.800  -2.9434   4.1377  -0.6611
 N4P  H1   H  HCH2  0   0.216   2.0380  -1.1854  -0.1629
 N4P  H2   H  HCH2  0   0.214   1.8453   0.1669  -1.2590
 N4P  H3   H  HCH2  0   0.189   1.0395   0.2471   1.6916
 N4P  H4   H  HCH2  0   0.226   0.8680   1.5419   0.5231
 N4P  H5   H  HNH2  0   0.345   6.5502   0.0153  -0.6024
 N4P  H6   H  HNH2  0   0.336   5.8309   1.4169  -0.2677
 N4P  H8   H  HCH2  0   0.212   3.3584   1.5439   0.1755
 N4P  H9   H  HCH2  0   0.213   3.5092   0.2175   1.3125
 N4P  H10  H  HCH2  0   0.186   4.3448   0.0789  -1.6159
 N4P  H11  H  HCH2  0   0.211   4.5449  -1.1965  -0.4299
 N4P  H13  H  HCH2  0   0.228   0.2595  -1.9545   0.6169
 N4P  H14  H  HCH2  0   0.192  -1.0239  -1.4368   1.6849
 N4P  H15  H  HCH2  0   0.218  -2.6159  -1.5871  -0.3294
 N4P  H16  H  HCH2  0   0.215  -1.2642  -2.1982  -1.2662
 N4P  H17  H  HCH2  0   0.188  -1.0235  -4.0818   0.3952
 N4P  H18  H  HCH2  0   0.212  -2.4203  -3.4665   1.2570
 N4P  H19  H  HNH2  0   0.337  -2.4674  -4.4163  -1.4987
 N4P  H20  H  HNH2  0   0.345  -3.1293  -5.1386  -0.2198
 N4P  H22  H  HCH2  0   0.229  -2.4524   0.2946   0.6237
 N4P  H23  H  HCH2  0   0.192  -1.3663   1.1797   1.6724
 N4P  H24  H  HCH2  0   0.217  -0.7407   2.6207  -0.3477
 N4P  H25  H  HCH2  0   0.217  -1.9333   1.7334  -1.2842
 N4P  H26  H  HCH2  0   0.211  -3.7126   2.4624   0.2968
 N4P  H27  H  HCH2  0   0.188  -2.5187   3.3023   1.2683
 N4P  H28  H  HNH2  0   0.344  -3.6601   4.7491  -0.2910
 N4P  H29  H  HNH2  0   0.337  -2.0952   4.6918  -0.6645

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
 N4P  N1   C2   single  1.456  0.020  1.456
 N4P  C2   C3   single  1.521  0.020  1.521
 N4P  C3   C4   single  1.523  0.020  1.523
 N4P  C4   C5   single  1.523  0.020  1.523
 N4P  C5   N6   single  1.455  0.020  1.455
 N4P  C8   C7   single  1.522  0.020  1.522
 N4P  C8   C9   single  1.521  0.020  1.521
 N4P  C7   N6   single  1.455  0.020  1.455
 N4P  N6   C11  single  1.456  0.020  1.456
 N4P  N10  C9   single  1.456  0.020  1.456
 N4P  C11  C12  single  1.522  0.020  1.522
 N4P  C12  C13  single  1.521  0.020  1.521
 N4P  C13  N14  single  1.457  0.020  1.457
 N4P  C4   H1   single  0.970  0.020  1.090
 N4P  C4   H2   single  0.970  0.020  1.090
 N4P  C5   H3   single  0.970  0.020  1.090
 N4P  C5   H4   single  0.970  0.020  1.090
 N4P  N1   H5   single  0.890  0.020  1.040
 N4P  N1   H6   single  0.890  0.020  1.040
 N4P  C3   H8   single  0.970  0.020  1.090
 N4P  C3   H9   single  0.970  0.020  1.090
 N4P  C2   H10  single  0.970  0.020  1.090
 N4P  C2   H11  single  0.970  0.020  1.090
 N4P  C7   H13  single  0.970  0.020  1.090
 N4P  C7   H14  single  0.970  0.020  1.090
 N4P  C8   H15  single  0.970  0.020  1.090
 N4P  C8   H16  single  0.970  0.020  1.090
 N4P  C9   H17  single  0.970  0.020  1.090
 N4P  C9   H18  single  0.970  0.020  1.090
 N4P  N10  H19  single  0.890  0.020  1.040
 N4P  N10  H20  single  0.890  0.020  1.040
 N4P  C11  H22  single  0.970  0.020  1.090
 N4P  C11  H23  single  0.970  0.020  1.090
 N4P  C12  H24  single  0.970  0.020  1.090
 N4P  C12  H25  single  0.970  0.020  1.090
 N4P  C13  H26  single  0.970  0.020  1.090
 N4P  C13  H27  single  0.970  0.020  1.090
 N4P  N14  H28  single  0.890  0.020  1.040
 N4P  N14  H29  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
 N4P  H2   C4   H1   106.34  3.000
 N4P  H2   C4   C3   110.05  3.000
 N4P  H1   C4   C3   108.84  3.000
 N4P  H2   C4   C5   108.82  3.000
 N4P  H1   C4   C5   110.61  3.000
 N4P  C3   C4   C5   112.02  3.000
 N4P  H4   C5   H3   105.81  3.000
 N4P  H4   C5   N6   108.41  3.000
 N4P  H3   C5   N6   111.30  3.000
 N4P  H4   C5   C4   107.60  3.000
 N4P  H3   C5   C4   109.81  3.000
 N4P  N6   C5   C4   113.54  3.000
 N4P  H6   N1   H5   105.38  3.000
 N4P  H6   N1   C2   109.16  3.000
 N4P  H5   N1   C2   109.41  3.000
 N4P  H9   C3   H8   106.35  3.000
 N4P  H9   C3   C2   109.01  3.000
 N4P  H8   C3   C2   109.26  3.000
 N4P  H9   C3   C4   109.86  3.000
 N4P  H8   C3   C4   109.48  3.000
 N4P  C2   C3   C4   112.68  3.000
 N4P  H11  C2   H10  106.08  3.000
 N4P  H11  C2   C3   108.92  3.000
 N4P  H10  C2   C3   108.90  3.000
 N4P  H11  C2   N1   108.21  3.000
 N4P  H10  C2   N1   113.41  3.000
 N4P  C3   C2   N1   111.13  3.000
 N4P  C11  N6   C7   111.40  3.000
 N4P  C11  N6   C5   111.57  3.000
 N4P  C7   N6   C5   112.21  3.000
 N4P  H14  C7   H13  105.51  3.000
 N4P  H14  C7   C8   109.85  3.000
 N4P  H13  C7   C8   108.01  3.000
 N4P  H14  C7   N6   111.28  3.000
 N4P  H13  C7   N6   109.03  3.000
 N4P  C8   C7   N6   112.84  3.000
 N4P  H16  C8   H15  106.58  3.000
 N4P  H16  C8   C9   109.80  3.000
 N4P  H15  C8   C9   108.80  3.000
 N4P  H16  C8   C7   108.67  3.000
 N4P  H15  C8   C7   110.84  3.000
 N4P  C9   C8   C7   112.00  3.000
 N4P  H18  C9   H17  106.06  3.000
 N4P  H18  C9   N10  108.13  3.000
 N4P  H17  C9   N10  113.42  3.000
 N4P  H18  C9   C8   109.01  3.000
 N4P  H17  C9   C8   109.01  3.000
 N4P  N10  C9   C8   111.01  3.000
 N4P  H20  N10  H19  105.42  3.000
 N4P  H20  N10  C9   109.40  3.000
 N4P  H19  N10  C9   109.11  3.000
 N4P  H23  C11  H22  105.65  3.000
 N4P  H23  C11  C12  109.84  3.000
 N4P  H22  C11  C12  108.01  3.000
 N4P  H23  C11  N6   111.17  3.000
 N4P  H22  C11  N6   108.56  3.000
 N4P  C12  C11  N6   113.27  3.000
 N4P  H25  C12  H24  106.79  3.000
 N4P  H25  C12  C13  109.69  3.000
 N4P  H24  C12  C13  108.85  3.000
 N4P  H25  C12  C11  109.24  3.000
 N4P  H24  C12  C11  110.30  3.000
 N4P  C13  C12  C11  111.84  3.000
 N4P  H27  C13  H26  106.11  3.000
 N4P  H27  C13  N14  113.33  3.000
 N4P  H26  C13  N14  108.23  3.000
 N4P  H27  C13  C12  108.81  3.000
 N4P  H26  C13  C12  109.14  3.000
 N4P  N14  C13  C12  111.03  3.000
 N4P  H29  N14  H28  105.29  3.000
 N4P  H29  N14  C13  108.93  3.000
 N4P  H28  N14  C13  109.30  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
 N4P  Var_01  N1   C2   C3   C4   -179.60  30.0  1
 N4P  Var_02  C7   N6   C5   C4     76.39  30.0  3
 N4P  Var_03  C2   C3   C4   C5    178.73  30.0  1
 N4P  Var_04  C8   C7   N6   C5   -154.40  30.0  2
 N4P  Var_05  C12  C11  N6   C5     80.42  30.0  3
 N4P  Var_06  N6   C5   C4   C3    179.56  30.0  3
 N4P  Var_07  C9   C8   C7   N6   -176.81  30.0  1
 N4P  Var_08  C13  C12  C11  N6   -177.37  30.0  3
 N4P  Var_09  N10  C9   C8   C7   -179.52  30.0  3
 N4P  Var_10  N14  C13  C12  C11  -178.10  30.0  3
 N4P  Var_11  H5   N1   C2   C3    178.39  30.0  3
 N4P  Var_12  H19  N10  C9   C8     67.95  30.0  3
 N4P  Var_13  H28  N14  C13  C12  -179.37  30.0  3

