# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 19:01:17 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: [4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCCN(CC1)Cc2ccc(CN)cc2
#
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
 5R8  5R8  '[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]methanamine'  ligand  40  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5R8
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
 5R8  C6   C  CH2   0  -0.274  -2.3786  -1.4455  -0.0882
 5R8  C1   C  CH3   0  -0.525  -4.4537  -2.0423   0.9187
 5R8  N2   N  NT    0  -0.414  -3.6715  -0.9573   0.3586
 5R8  C7   C  CH2   0  -0.283  -1.6337  -0.5285  -1.0395
 5R8  N8   N  NT    0  -0.416  -1.3845   0.8081  -0.5302
 5R8  C9   C  CH2   0  -0.276  -2.5883   1.6230  -0.5762
 5R8  C10  C  CH2   0  -0.420  -3.4455   1.5181   0.6821
 5R8  C11  C  CH2   0  -0.277  -3.5255   0.1329   1.3137
 5R8  C22  C  CH2   0  -0.321  -0.2494   1.4262  -1.1872
 5R8  C23  C  CR6   0   0.064   1.0569   0.7701  -0.8172
 5R8  C26  C  CR16  0  -0.299   2.0515   0.5765  -1.7668
 5R8  C27  C  CR16  0  -0.299   3.2736   0.0130  -1.4166
 5R8  C28  C  CR6   0   0.080   3.5301  -0.3838  -0.1097
 5R8  C29  C  CR16  0  -0.273   2.5295  -0.1900   0.8430
 5R8  C30  C  CR16  0  -0.269   1.3128   0.3739   0.4952
 5R8  C35  C  CH2   0  -0.343   4.8395  -1.0336   0.2587
 5R8  N36  N  NH2   0  -0.792   5.3464  -0.5430   1.5298
 5R8  H1   H  HCH2  0   0.185  -1.7262  -1.6715   0.7735
 5R8  H2   H  HCH2  0   0.227  -2.5310  -2.3890  -0.6192
 5R8  H3   H  HCH3  0   0.189  -4.0026  -2.4944   1.8162
 5R8  H4   H  HCH3  0   0.232  -5.4481  -1.6868   1.1915
 5R8  H5   H  HCH3  0   0.230  -4.5778  -2.8346   0.1791
 5R8  H7   H  HCH2  0   0.236  -0.6763  -1.0119  -1.2471
 5R8  H8   H  HCH2  0   0.194  -2.1753  -0.4840  -1.9993
 5R8  H10  H  HCH2  0   0.229  -2.3063   2.6697  -0.7079
 5R8  H11  H  HCH2  0   0.196  -3.1963   1.3664  -1.4566
 5R8  H12  H  HCH2  0   0.215  -3.0651   2.2023   1.4456
 5R8  H13  H  HCH2  0   0.214  -4.4510   1.8657   0.4302
 5R8  H14  H  HCH2  0   0.229  -4.3863   0.1263   1.9856
 5R8  H15  H  HCH2  0   0.196  -2.6440  -0.0323   1.9527
 5R8  H16  H  HCH2  0   0.207  -0.3452   1.4418  -2.2860
 5R8  H17  H  HCH2  0   0.250  -0.2100   2.4745  -0.8762
 5R8  H18  H  HCR6  0   0.243   1.8738   0.8679  -2.7960
 5R8  H19  H  HCR6  0   0.243   4.0339  -0.1213  -2.1777
 5R8  H20  H  HCR6  0   0.241   2.7117  -0.4827   1.8695
 5R8  H21  H  HCR6  0   0.240   0.5388   0.4963   1.2431
 5R8  H22  H  HCH2  0   0.236   4.6811  -2.1117   0.3589
 5R8  H23  H  HCH2  0   0.213   5.5403  -0.9111  -0.5779
 5R8  H24  H  HNH2  0   0.352   6.1731  -1.0673   1.7852
 5R8  H25  H  HNH2  0   0.342   5.6464   0.4181   1.4245

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
 5R8  N36  C35  single    1.454  0.020  1.454
 5R8  C35  C28  single    1.507  0.020  1.507
 5R8  C28  C27  aromatic  1.390  0.020  1.390
 5R8  C28  C29  aromatic  1.395  0.020  1.395
 5R8  C27  C26  aromatic  1.391  0.020  1.391
 5R8  C29  C30  aromatic  1.385  0.020  1.385
 5R8  C26  C23  aromatic  1.389  0.020  1.389
 5R8  C30  C23  aromatic  1.395  0.020  1.395
 5R8  C23  C22  single    1.508  0.020  1.508
 5R8  C7   C6   single    1.517  0.020  1.517
 5R8  C7   N8   single    1.452  0.020  1.452
 5R8  C6   N2   single    1.452  0.020  1.452
 5R8  C1   N2   single    1.450  0.020  1.450
 5R8  C22  N8   single    1.450  0.020  1.450
 5R8  N8   C9   single    1.454  0.020  1.454
 5R8  N2   C11  single    1.457  0.020  1.457
 5R8  C9   C10  single    1.526  0.020  1.526
 5R8  C11  C10  single    1.525  0.020  1.525
 5R8  C6   H1   single    0.970  0.020  1.090
 5R8  C6   H2   single    0.970  0.020  1.090
 5R8  C1   H3   single    0.970  0.020  1.090
 5R8  C1   H4   single    0.970  0.020  1.090
 5R8  C1   H5   single    0.970  0.020  1.090
 5R8  C7   H7   single    0.970  0.020  1.090
 5R8  C7   H8   single    0.970  0.020  1.090
 5R8  C9   H10  single    0.970  0.020  1.090
 5R8  C9   H11  single    0.970  0.020  1.090
 5R8  C10  H12  single    0.970  0.020  1.090
 5R8  C10  H13  single    0.970  0.020  1.090
 5R8  C11  H14  single    0.970  0.020  1.090
 5R8  C11  H15  single    0.970  0.020  1.090
 5R8  C22  H16  single    0.970  0.020  1.090
 5R8  C22  H17  single    0.970  0.020  1.090
 5R8  C26  H18  single    0.930  0.020  1.080
 5R8  C27  H19  single    0.930  0.020  1.080
 5R8  C29  H20  single    0.930  0.020  1.080
 5R8  C30  H21  single    0.930  0.020  1.080
 5R8  C35  H22  single    0.970  0.020  1.090
 5R8  C35  H23  single    0.970  0.020  1.090
 5R8  N36  H24  single    0.890  0.020  1.040
 5R8  N36  H25  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
 5R8  H2   C6   H1   106.54  3.000
 5R8  H2   C6   C7   106.59  3.000
 5R8  H1   C6   C7   108.84  3.000
 5R8  H2   C6   N2   108.39  3.000
 5R8  H1   C6   N2   110.78  3.000
 5R8  C7   C6   N2   115.27  3.000
 5R8  H5   C1   H4   107.62  3.000
 5R8  H5   C1   H3   107.51  3.000
 5R8  H4   C1   H3   107.65  3.000
 5R8  H5   C1   N2   110.06  3.000
 5R8  H4   C1   N2   110.16  3.000
 5R8  H3   C1   N2   113.63  3.000
 5R8  C11  N2   C1   111.15  3.000
 5R8  C11  N2   C6   111.35  3.000
 5R8  C1   N2   C6   110.33  3.000
 5R8  H8   C7   H7   106.43  3.000
 5R8  H8   C7   N8   110.63  3.000
 5R8  H7   C7   N8   108.88  3.000
 5R8  H8   C7   C6   109.21  3.000
 5R8  H7   C7   C6   106.38  3.000
 5R8  N8   C7   C6   114.89  3.000
 5R8  C22  N8   C9   113.25  3.000
 5R8  C9   N8   C7   111.27  3.000
 5R8  C22  N8   C7   111.58  3.000
 5R8  H11  C9   H10  105.65  3.000
 5R8  H11  C9   C10  109.47  3.000
 5R8  H10  C9   C10  108.08  3.000
 5R8  H11  C9   N8   110.61  3.000
 5R8  H10  C9   N8   109.10  3.000
 5R8  C10  C9   N8   113.60  3.000
 5R8  H13  C10  H12  106.37  3.000
 5R8  H13  C10  C11  109.63  3.000
 5R8  H12  C10  C11  107.31  3.000
 5R8  H13  C10  C9   107.75  3.000
 5R8  H12  C10  C9   109.71  3.000
 5R8  C11  C10  C9   115.69  3.000
 5R8  H15  C11  H14  105.85  3.000
 5R8  H15  C11  C10  109.56  3.000
 5R8  H14  C11  C10  107.56  3.000
 5R8  H15  C11  N2   110.39  3.000
 5R8  H14  C11  N2   108.65  3.000
 5R8  C10  C11  N2   114.43  3.000
 5R8  H17  C22  H16  105.82  3.000
 5R8  H17  C22  C23  108.41  3.000
 5R8  H16  C22  C23  109.02  3.000
 5R8  H17  C22  N8   107.93  3.000
 5R8  H16  C22  N8   112.92  3.000
 5R8  C23  C22  N8   112.43  3.000
 5R8  C30  C23  C26  118.20  3.000
 5R8  C30  C23  C22  120.90  3.000
 5R8  C26  C23  C22  120.88  3.000
 5R8  H18  C26  C27  119.47  3.000
 5R8  H18  C26  C23  119.62  3.000
 5R8  C27  C26  C23  120.91  3.000
 5R8  H19  C27  C28  119.69  3.000
 5R8  H19  C27  C26  119.33  3.000
 5R8  C28  C27  C26  120.98  3.000
 5R8  C35  C28  C29  121.06  3.000
 5R8  C29  C28  C27  118.05  3.000
 5R8  C35  C28  C27  120.88  3.000
 5R8  H20  C29  C30  119.72  3.000
 5R8  H20  C29  C28  119.28  3.000
 5R8  C30  C29  C28  120.99  3.000
 5R8  H21  C30  C29  120.01  3.000
 5R8  H21  C30  C23  119.11  3.000
 5R8  C29  C30  C23  120.87  3.000
 5R8  H23  C35  H22  105.78  3.000
 5R8  H23  C35  N36  113.95  3.000
 5R8  H22  C35  N36  107.63  3.000
 5R8  H23  C35  C28  108.66  3.000
 5R8  H22  C35  C28  108.74  3.000
 5R8  N36  C35  C28  111.79  3.000
 5R8  H25  N36  H24  106.03  3.000
 5R8  H25  N36  C35  109.44  3.000
 5R8  H24  N36  C35  109.32  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
 5R8  CONST_01  C28  C27  C26  C23    0.00   0.0  0
 5R8  CONST_02  C28  C29  C30  C23    0.00   0.0  0
 5R8  CONST_03  C29  C28  C27  C26    0.00   0.0  0
 5R8  CONST_04  C29  C30  C23  C26    0.00   0.0  0
 5R8  CONST_05  C30  C29  C28  C27    0.00   0.0  0
 5R8  CONST_06  C30  C23  C26  C27    0.00   0.0  0
 5R8  CONST_07  C27  C26  C23  C22  180.00   0.0  0
 5R8  CONST_08  C29  C30  C23  C22  180.00   0.0  0
 5R8  CONST_09  C35  C28  C27  C26  180.00   0.0  0
 5R8  CONST_10  C35  C28  C29  C30  180.00   0.0  0
 5R8  CONST_11  H19  C27  C26  C23  180.00   0.0  0
 5R8  CONST_12  H20  C29  C30  C23  180.00   0.0  0
 5R8  CONST_13  H21  C30  C23  C26  180.00   0.0  0
 5R8  CONST_14  H18  C26  C27  C28  180.00   0.0  0
 5R8  Var_01    C26  C23  C22  N8   140.87  30.0  2
 5R8  Var_02    N36  C35  C28  C27  138.82  30.0  3
 5R8  Var_03    H24  N36  C35  C28  174.37  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
 5R8  plan-1  C22  0.020
 5R8  plan-1  C23  0.020
 5R8  plan-1  C26  0.020
 5R8  plan-1  C27  0.020
 5R8  plan-1  C28  0.020
 5R8  plan-1  C29  0.020
 5R8  plan-1  C30  0.020
 5R8  plan-1  C35  0.020
 5R8  plan-1  H18  0.020
 5R8  plan-1  H19  0.020
 5R8  plan-1  H20  0.020
 5R8  plan-1  H21  0.020

