# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 16:06:48 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: N-(2-aminoethyl)butane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCNCCN
#
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
 P24  P24  N-(2-aminoethyl)butane-1,4-diamine  ligand  26  9  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P24
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
 P24  N1    N  NH2   0  -0.802  -0.3053   0.0375  -4.8703
 P24  C2    C  CH2   0  -0.299   0.5014   0.0194  -3.6592
 P24  C3    C  CH2   0  -0.262  -0.3904   0.0436  -2.4279
 P24  N4    N  NH1   0  -0.602   0.3973   0.0015  -1.2120
 P24  C5    C  CH2   0  -0.245  -0.4126   0.0159  -0.0088
 P24  C6    C  CH2   0  -0.446   0.4487  -0.0190   1.2439
 P24  C7    C  CH2   0  -0.429  -0.3784   0.0028   2.5224
 P24  C8    C  CH2   0  -0.271   0.4802  -0.0459   3.7771
 P24  N9    N  NH2   0  -0.801  -0.3462  -0.0156   4.9761
 P24  HN11  H  HNH2  0   0.339  -0.7866  -0.8489  -4.9627
 P24  HN12  H  HNH2  0   0.349   0.3000   0.1018  -5.6782
 P24  H21   H  HCH2  0   0.215   1.1349   0.9114  -3.6571
 P24  H22   H  HCH2  0   0.193   1.1774  -0.8434  -3.5851
 P24  H31   H  HCH2  0   0.212  -1.0443  -0.8359  -2.4423
 P24  H32   H  HCH2  0   0.186  -1.0530   0.9221  -2.4829
 P24  HN4   H  HNH1  0   0.335   1.0132   0.8071  -1.1955
 P24  H51   H  HCH2  0   0.212  -1.0626  -0.8653  -0.0236
 P24  H52   H  HCH2  0   0.183  -1.0848   0.8894   0.0367
 P24  H61   H  HCH2  0   0.214   1.1313   0.8383   1.2377
 P24  H62   H  HCH2  0   0.216   1.0768  -0.9152   1.2222
 P24  H71   H  HCH2  0   0.214  -1.0728  -0.8434   2.5316
 P24  H72   H  HCH2  0   0.212  -0.9944   0.9092   2.5421
 P24  H81   H  HCH2  0   0.187   1.2184   0.7683   3.7333
 P24  H82   H  HCH2  0   0.211   1.0535  -0.9774   3.7798
 P24  HN91  H  HNH2  0   0.345   0.2447  -0.0813   5.7951
 P24  HN92  H  HNH2  0   0.336  -0.7986   0.8884   5.0424

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
 P24  N1  C2    single  1.455  0.020  1.455
 P24  N1  HN11  single  0.890  0.020  1.040
 P24  N1  HN12  single  0.890  0.020  1.040
 P24  C2  C3    single  1.521  0.020  1.521
 P24  C2  H21   single  0.970  0.020  1.090
 P24  C2  H22   single  0.970  0.020  1.090
 P24  C3  N4    single  1.449  0.020  1.449
 P24  C3  H31   single  0.970  0.020  1.090
 P24  C3  H32   single  0.970  0.020  1.090
 P24  N4  C5    single  1.450  0.020  1.450
 P24  N4  HN4   single  0.890  0.020  1.040
 P24  C5  C6    single  1.521  0.020  1.521
 P24  C5  H51   single  0.970  0.020  1.090
 P24  C5  H52   single  0.970  0.020  1.090
 P24  C6  C7    single  1.523  0.020  1.523
 P24  C6  H61   single  0.970  0.020  1.090
 P24  C6  H62   single  0.970  0.020  1.090
 P24  C7  C8    single  1.521  0.020  1.521
 P24  C7  H71   single  0.970  0.020  1.090
 P24  C7  H72   single  0.970  0.020  1.090
 P24  C8  N9    single  1.456  0.020  1.456
 P24  C8  H81   single  0.970  0.020  1.090
 P24  C8  H82   single  0.970  0.020  1.090
 P24  N9  HN91  single  0.890  0.020  1.040
 P24  N9  HN92  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
 P24  HN12  N1  HN11  105.49  3.000
 P24  HN12  N1  C2    109.50  3.000
 P24  HN11  N1  C2    109.18  3.000
 P24  H22   C2  H21   106.49  3.000
 P24  H22   C2  C3    108.59  3.000
 P24  H21   C2  C3    108.97  3.000
 P24  H22   C2  N1    114.01  3.000
 P24  H21   C2  N1    108.21  3.000
 P24  C3    C2  N1    110.40  3.000
 P24  H32   C3  H31   106.28  3.000
 P24  H32   C3  N4    113.08  3.000
 P24  H31   C3  N4    108.18  3.000
 P24  H32   C3  C2    108.96  3.000
 P24  H31   C3  C2    109.06  3.000
 P24  N4    C3  C2    111.11  3.000
 P24  HN4   N4  C5    108.52  3.000
 P24  HN4   N4  C3    108.70  3.000
 P24  C5    N4  C3    113.09  3.000
 P24  H52   C5  H51   106.02  3.000
 P24  H52   C5  C6    109.23  3.000
 P24  H51   C5  C6    109.20  3.000
 P24  H52   C5  N4    112.48  3.000
 P24  H51   C5  N4    108.19  3.000
 P24  C6    C5  N4    111.53  3.000
 P24  H62   C6  H61   106.44  3.000
 P24  H62   C6  C7    109.88  3.000
 P24  H61   C6  C7    109.38  3.000
 P24  H62   C6  C5    109.12  3.000
 P24  H61   C6  C5    109.28  3.000
 P24  C7    C6  C5    112.56  3.000
 P24  H72   C7  H71   106.42  3.000
 P24  H72   C7  C8    109.20  3.000
 P24  H71   C7  C8    109.05  3.000
 P24  H72   C7  C6    109.40  3.000
 P24  H71   C7  C6    109.91  3.000
 P24  C8    C7  C6    112.67  3.000
 P24  H82   C8  H81   106.18  3.000
 P24  H82   C8  N9    108.25  3.000
 P24  H81   C8  N9    113.46  3.000
 P24  H82   C8  C7    108.97  3.000
 P24  H81   C8  C7    108.80  3.000
 P24  N9    C8  C7    110.98  3.000
 P24  HN92  N9  HN91  105.41  3.000
 P24  HN92  N9  C8    109.02  3.000
 P24  HN91  N9  C8    109.49  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
 P24  Var_01  N4    C3  C2  N1   178.96  30.0  3
 P24  Var_02  C5    N4  C3  C2  -179.71  30.0  3
 P24  Var_03  C6    C5  N4  C3  -179.59  30.0  3
 P24  Var_04  C7    C6  C5  N4   179.70  30.0  3
 P24  Var_05  C8    C7  C6  C5   179.44  30.0  3
 P24  Var_06  N9    C8  C7  C6   179.67  30.0  3
 P24  Var_07  HN11  N1  C2  C3   -69.81  30.0  3
 P24  Var_08  HN91  N9  C8  C7   178.05  30.0  3

