# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 08:55:21 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: N-(pyridin-4-yl)ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCNc1ccncc1
#
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
 01R  01R  N-(pyridin-4-yl)ethane-1,2-diamine  ligand  21  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 PERFECT
;

data_comp_01R
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
 01R  N19   N  NH2   0  -0.799   4.2618   0.4822  -0.0083
 01R  C20   C  CH2   0  -0.318   3.1663  -0.4704   0.0168
 01R  C30   C  CH2   0  -0.260   1.8413   0.2712  -0.0677
 01R  N27   N  NH1   0  -0.691   0.7401  -0.6588  -0.0150
 01R  C21   C  CR6   0   0.474  -0.5583  -0.2980  -0.0127
 01R  C22   C  CR16  0  -0.416  -1.5819  -1.2648   0.0092
 01R  C23   C  CR16  0  -0.074  -2.8966  -0.8562   0.0206
 01R  N24   N  N     0  -0.443  -3.2962   0.4171   0.0118
 01R  C25   C  CR16  0  -0.076  -2.3272   1.3271  -0.0117
 01R  C26   C  CR16  0  -0.424  -0.9739   1.0442  -0.0260
 01R  H19   H  HNH2  0   0.344   4.2977   0.9766   0.8745
 01R  H201  H  HCH2  0   0.233   3.2599  -1.1297  -0.8498
 01R  H202  H  HCH2  0   0.208   3.1563  -1.1169   0.9054
 01R  H301  H  HCH2  0   0.227   1.7727   0.9811   0.7651
 01R  H302  H  HCH2  0   0.228   1.8190   0.8606  -0.9913
 01R  H27   H  HNH1  0   0.392   0.9490  -1.6432  -0.0537
 01R  H22   H  HCR6  0   0.265  -1.3435  -2.3214   0.0184
 01R  H23   H  HCR6  0   0.253  -3.6803  -1.6065   0.0387
 01R  H25   H  HCR6  0   0.252  -2.6427   2.3658  -0.0208
 01R  H26   H  HCR6  0   0.271  -0.2635   1.8587  -0.0493
 01R  H2    H  HNH2  0   0.354   5.1390  -0.0161  -0.0779

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
 01R  N19  C20   single    1.452  0.020  1.452
 01R  N19  H19   single    0.890  0.020  1.040
 01R  C20  C30   single    1.521  0.020  1.521
 01R  C20  H201  single    0.970  0.020  1.090
 01R  C20  H202  single    0.970  0.020  1.090
 01R  C30  N27   single    1.442  0.020  1.442
 01R  C30  H301  single    0.970  0.020  1.090
 01R  C30  H302  single    0.970  0.020  1.090
 01R  N27  C21   single    1.348  0.020  1.348
 01R  N27  H27   single    0.860  0.020  1.020
 01R  C21  C22   aromatic  1.408  0.020  1.408
 01R  C21  C26   aromatic  1.405  0.020  1.405
 01R  C22  C23   aromatic  1.377  0.020  1.377
 01R  C22  H22   single    0.930  0.020  1.080
 01R  C23  N24   aromatic  1.335  0.020  1.335
 01R  C23  H23   single    0.930  0.020  1.080
 01R  N24  C25   aromatic  1.330  0.020  1.330
 01R  C25  C26   aromatic  1.383  0.020  1.383
 01R  C25  H25   single    0.930  0.020  1.080
 01R  C26  H26   single    0.930  0.020  1.080
 01R  N19  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
 01R  H2    N19  H19   105.65  3.000
 01R  H2    N19  C20   109.41  3.000
 01R  H19   N19  C20   109.40  3.000
 01R  H202  C20  H201  106.68  3.000
 01R  H202  C20  C30   108.90  3.000
 01R  H201  C20  C30   108.95  3.000
 01R  H202  C20  N19   114.00  3.000
 01R  H201  C20  N19   108.51  3.000
 01R  C30   C20  N19   109.66  3.000
 01R  H302  C30  H301  106.90  3.000
 01R  H302  C30  N27   111.23  3.000
 01R  H301  C30  N27   110.00  3.000
 01R  H302  C30  C20   109.08  3.000
 01R  H301  C30  C20   109.15  3.000
 01R  N27   C30  C20   110.41  3.000
 01R  H27   N27  C21   117.49  3.000
 01R  H27   N27  C30   118.07  3.000
 01R  C21   N27  C30   124.26  3.000
 01R  C26   C21  C22   116.16  3.000
 01R  C26   C21  N27   122.73  3.000
 01R  C22   C21  N27   121.10  3.000
 01R  H22   C22  C23   119.97  3.000
 01R  H22   C22  C21   120.65  3.000
 01R  C23   C22  C21   119.38  3.000
 01R  H23   C23  N24   116.33  3.000
 01R  H23   C23  C22   118.99  3.000
 01R  N24   C23  C22   124.68  3.000
 01R  C25   N24  C23   115.78  3.000
 01R  H25   C25  C26   118.69  3.000
 01R  H25   C25  N24   116.31  3.000
 01R  C26   C25  N24   125.00  3.000
 01R  H26   C26  C25   119.30  3.000
 01R  H26   C26  C21   121.70  3.000
 01R  C25   C26  C21   119.00  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
 01R  CONST_01  N24  C23  C22  C21     0.00   0.0  0
 01R  CONST_02  N24  C25  C26  C21     0.00   0.0  0
 01R  CONST_03  C25  C26  C21  C22     0.00   0.0  0
 01R  CONST_04  C25  N24  C23  C22     0.00   0.0  0
 01R  CONST_05  C26  C21  C22  C23     0.00   0.0  0
 01R  CONST_06  C26  C25  N24  C23     0.00   0.0  0
 01R  CONST_07  C23  C22  C21  N27   180.00   0.0  0
 01R  CONST_08  C25  C26  C21  N27   180.00   0.0  0
 01R  CONST_09  H23  C23  C22  C21   180.00   0.0  0
 01R  CONST_10  H25  C25  C26  C21   180.00   0.0  0
 01R  CONST_11  H26  C26  C21  C22   180.00   0.0  0
 01R  CONST_12  H22  C22  C23  N24   180.00   0.0  0
 01R  CONST_13  C22  C21  N27  C30   180.00   0.0  0
 01R  CONST_14  C26  C21  N27  C30     0.00   0.0  0
 01R  CONST_15  H27  N27  C21  C22     0.00   0.0  0
 01R  Var_01    C21  N27  C30  C20   177.13  30.0  3
 01R  Var_02    N27  C30  C20  N19  -178.77  30.0  3
 01R  Var_03    H19  N19  C20  C30    72.27  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 01R  plan-1  N27  0.020
 01R  plan-1  C21  0.020
 01R  plan-1  C22  0.020
 01R  plan-1  C23  0.020
 01R  plan-1  N24  0.020
 01R  plan-1  C25  0.020
 01R  plan-1  C26  0.020
 01R  plan-1  H22  0.020
 01R  plan-1  H23  0.020
 01R  plan-1  H25  0.020
 01R  plan-1  H26  0.020
 01R  plan-2  C30  0.020
 01R  plan-2  N27  0.020
 01R  plan-2  C21  0.020
 01R  plan-2  H27  0.020

