# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:11:27 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 3-(piperazin-1-yl)propan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCN1CCNCC1
#
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
 026  026  3-(piperazin-1-yl)propan-1-amine  ligand  27  10  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_026
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
 026  N26   N  NH1   0  -0.579  -3.2768   0.4322  -0.0717
 026  C27   C  CH2   0  -0.324  -2.8133  -0.8399   0.4575
 026  C28   C  CH2   0  -0.286  -1.4658  -1.2745  -0.1033
 026  N29   N  NT    0  -0.421  -0.4649  -0.2452   0.1159
 026  C30   C  CH2   0  -0.292  -0.8902   1.0053  -0.4895
 026  C31   C  CH2   0  -0.321  -2.2401   1.4415   0.0640
 026  C32   C  CH2   0  -0.253   0.8477  -0.6650  -0.3402
 026  C33   C  CH2   0  -0.450   1.9829   0.1598   0.2501
 026  C8    C  CH2   0  -0.272   3.3445  -0.3286  -0.2199
 026  N9    N  NH2   0  -0.800   4.4120   0.4671   0.3695
 026  H271  H  HCH2  0   0.217  -2.7322  -0.7490   1.5455
 026  H272  H  HCH2  0   0.235  -3.5620  -1.6084   0.2557
 026  H281  H  HCH2  0   0.231  -1.1438  -2.1953   0.3907
 026  H282  H  HCH2  0   0.182  -1.5819  -1.5100  -1.1773
 026  H301  H  HCH2  0   0.234  -0.1515   1.7844  -0.2887
 026  H302  H  HCH2  0   0.182  -0.9646   0.9112  -1.5891
 026  H311  H  HCH2  0   0.235  -2.5619   2.3560  -0.4378
 026  H312  H  HCH2  0   0.217  -2.1293   1.6803   1.1265
 026  H321  H  HCH2  0   0.223   0.9873  -1.7077  -0.0397
 026  H322  H  HCH2  0   0.184   0.9152  -0.6528  -1.4428
 026  H331  H  HCH2  0   0.222   1.8808   1.2152  -0.0148
 026  H332  H  HCH2  0   0.215   1.9268   0.1022   1.3419
 026  H8C1  H  HCH2  0   0.188   3.4314  -1.4046  -0.0078
 026  H8C2  H  HCH2  0   0.213   3.4054  -0.2278  -1.3072
 026  H9N1  H  HNH2  0   0.337   4.4413   0.2959   1.3673
 026  H9N2  H  HNH2  0   0.345   5.3049   0.1500   0.0142
 026  H2    H  HNH1  0   0.338  -3.4932   0.3171  -1.0559

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
 026  N26  C27   single  1.454  0.020  1.454
 026  N26  C31   single  1.453  0.020  1.453
 026  C27  C28   single  1.523  0.020  1.523
 026  C27  H271  single  0.970  0.020  1.090
 026  C27  H272  single  0.970  0.020  1.090
 026  C28  N29   single  1.452  0.020  1.452
 026  C28  H281  single  0.970  0.020  1.090
 026  C28  H282  single  0.970  0.020  1.090
 026  N29  C30   single  1.453  0.020  1.453
 026  N29  C32   single  1.452  0.020  1.452
 026  C30  C31   single  1.523  0.020  1.523
 026  C30  H301  single  0.970  0.020  1.090
 026  C30  H302  single  0.970  0.020  1.090
 026  C31  H311  single  0.970  0.020  1.090
 026  C31  H312  single  0.970  0.020  1.090
 026  C32  C33   single  1.522  0.020  1.522
 026  C32  H321  single  0.970  0.020  1.090
 026  C32  H322  single  0.970  0.020  1.090
 026  C33  C8    single  1.521  0.020  1.521
 026  C33  H331  single  0.970  0.020  1.090
 026  C33  H332  single  0.970  0.020  1.090
 026  C8   N9    single  1.456  0.020  1.456
 026  C8   H8C1  single  0.970  0.020  1.090
 026  C8   H8C2  single  0.970  0.020  1.090
 026  N9   H9N1  single  0.890  0.020  1.040
 026  N9   H9N2  single  0.890  0.020  1.040
 026  N26  H2    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
 026  H2    N26  C31   108.76  3.000
 026  H2    N26  C27   108.78  3.000
 026  C31   N26  C27   110.27  3.000
 026  H272  C27  H271  107.04  3.000
 026  H272  C27  C28   109.74  3.000
 026  H271  C27  C28   108.91  3.000
 026  H272  C27  N26   109.27  3.000
 026  H271  C27  N26   108.23  3.000
 026  C28   C27  N26   113.44  3.000
 026  H282  C28  H281  106.88  3.000
 026  H282  C28  N29   111.71  3.000
 026  H281  C28  N29   109.00  3.000
 026  H282  C28  C27   109.00  3.000
 026  H281  C28  C27   109.54  3.000
 026  N29   C28  C27   110.61  3.000
 026  C32   N29  C30   112.50  3.000
 026  C32   N29  C28   111.76  3.000
 026  C30   N29  C28   110.20  3.000
 026  H302  C30  H301  106.79  3.000
 026  H302  C30  C31   109.03  3.000
 026  H301  C30  C31   109.17  3.000
 026  H302  C30  N29   111.14  3.000
 026  H301  C30  N29   109.84  3.000
 026  C31   C30  N29   110.77  3.000
 026  H312  C31  H311  107.06  3.000
 026  H312  C31  C30   109.00  3.000
 026  H311  C31  C30   109.52  3.000
 026  H312  C31  N26   108.32  3.000
 026  H311  C31  N26   109.18  3.000
 026  C30   C31  N26   113.55  3.000
 026  H322  C32  H321  106.07  3.000
 026  H322  C32  C33   109.60  3.000
 026  H321  C32  C33   108.34  3.000
 026  H322  C32  N29   111.45  3.000
 026  H321  C32  N29   107.74  3.000
 026  C33   C32  N29   113.31  3.000
 026  H332  C33  H331  106.72  3.000
 026  H332  C33  C8    109.70  3.000
 026  H331  C33  C8    108.59  3.000
 026  H332  C33  C32   108.66  3.000
 026  H331  C33  C32   111.08  3.000
 026  C8    C33  C32   111.95  3.000
 026  H8C2  C8   H8C1  106.10  3.000
 026  H8C2  C8   N9    108.13  3.000
 026  H8C1  C8   N9    113.49  3.000
 026  H8C2  C8   C33   109.11  3.000
 026  H8C1  C8   C33   108.98  3.000
 026  N9    C8   C33   110.84  3.000
 026  H9N2  N9   H9N1  105.50  3.000
 026  H9N2  N9   C8    109.49  3.000
 026  H9N1  N9   C8    109.13  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
 026  Var_01  N29   C28  C27  N26    55.57  30.0  1
 026  Var_02  N29   C30  C31  N26   -55.00  30.0  1
 026  Var_03  C30   C31  N26  C27    51.16  30.0  1
 026  Var_04  C31   N26  C27  C28   -51.45  30.0  1
 026  Var_05  C31   C30  N29  C28    57.19  30.0  1
 026  Var_06  C33   C32  N29  C28  -161.69  30.0  3
 026  Var_07  C8    C33  C32  N29   178.53  30.0  3
 026  Var_08  N9    C8   C33  C32  -179.40  30.0  3
 026  Var_09  H9N1  N9   C8   C33    67.30  30.0  3

