# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 19:17:02 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N'-[3-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]phenyl]-N,N'-dimethyl-ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCN(C)c1cccc(CCc2cc(C)cc(N)n2)c1
#
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
 4V4  4V4  N'-[3-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]phenyl]-N,N'-dimethyl-ethane-1,2-diamine  ligand  48  22  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4V4
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
 4V4  N01   N  N     0  -0.487  -3.6409  -1.1059   0.0649
 4V4  C02   C  CR6   0   0.440  -4.8888  -1.4998   0.2913
 4V4  N02   N  NH2   0  -0.839  -5.0669  -2.7828   0.7236
 4V4  C03   C  CR16  0  -0.450  -5.9886  -0.6361   0.1400
 4V4  C04   C  CR6   0   0.206  -5.7677   0.6684  -0.2486
 4V4  C05   C  CR16  0  -0.437  -4.4464   1.0751  -0.4715
 4V4  C06   C  CR6   0   0.283  -3.4243   0.1585  -0.3060
 4V4  C07   C  CH3   0  -0.726  -6.9005   1.6331  -0.4219
 4V4  C08   C  CH2   0  -0.487  -1.9895   0.5467  -0.5232
 4V4  C09   C  CH2   0  -0.512  -1.1548   0.4265   0.7591
 4V4  C11   C  CR6   0   0.157   0.2759   0.8265   0.5275
 4V4  C12   C  CR16  0  -0.364   0.6881   2.1386   0.7386
 4V4  C13   C  CR16  0  -0.228   2.0080   2.4800   0.4760
 4V4  C14   C  CR16  0  -0.371   2.9164   1.5496   0.0018
 4V4  C15   C  CR6   0   0.414   2.5193   0.2194  -0.2387
 4V4  C16   C  CR16  0  -0.429   1.1829  -0.1130   0.0513
 4V4  C17   C  CH3   0  -0.544   2.9777  -2.1054  -0.8066
 4V4  N17   N  NT    0  -0.509   3.3801  -0.7203  -0.7453
 4V4  C18   C  CH2   0  -0.349   4.7639  -0.4100  -1.0149
 4V4  C19   C  CH2   0  -0.264   5.6697  -0.5307   0.2074
 4V4  N20   N  NH1   0  -0.594   7.0310  -0.1827  -0.1389
 4V4  C21   C  CH3   0  -0.515   7.9337  -0.2431   0.9920
 4V4  HN02  H  HNH2  0   0.379  -4.3093  -3.4205   0.5422
 4V4  HN0A  H  HNH2  0   0.387  -5.9808  -3.1889   0.6133
 4V4  H03   H  HCR6  0   0.255  -6.9928  -0.9970   0.3271
 4V4  H05   H  HCR6  0   0.243  -4.2248   2.0909  -0.7742
 4V4  H07   H  HCH3  0   0.252  -6.8306   2.4439   0.3048
 4V4  H07A  H  HCH3  0   0.250  -6.8772   2.0901  -1.4121
 4V4  H07B  H  HCH3  0   0.246  -7.8675   1.1492  -0.2942
 4V4  H08   H  HCH2  0   0.246  -1.5525  -0.0976  -1.2917
 4V4  H08A  H  HCH2  0   0.245  -1.9345   1.5698  -0.9001
 4V4  H09   H  HCH2  0   0.244  -1.5968   1.0566   1.5351
 4V4  H09A  H  HCH2  0   0.244  -1.2083  -0.6036   1.1170
 4V4  H12   H  HCR6  0   0.233  -0.0101   2.8792   1.1097
 4V4  H13   H  HCR6  0   0.245   2.3456   3.4942   0.6516
 4V4  H14   H  HCR6  0   0.255   3.9352   1.8692  -0.1683
 4V4  H16   H  HCR6  0   0.254   0.8268  -1.1238  -0.1031
 4V4  H17   H  HCH3  0   0.235   2.1358  -2.2604  -1.4872
 4V4  H17A  H  HCH3  0   0.256   3.8087  -2.7007  -1.1774
 4V4  H17B  H  HCH3  0   0.231   2.6947  -2.5072   0.1711
 4V4  H18   H  HCH2  0   0.252   5.1166  -1.0913  -1.7939
 4V4  H18A  H  HCH2  0   0.245   4.8526   0.5908  -1.4417
 4V4  H19   H  HCH2  0   0.221   5.3235   0.1539   0.9880
 4V4  H19A  H  HCH2  0   0.197   5.5772  -1.5461   0.6271
 4V4  HN20  H  HNH1  0   0.343   7.3607  -0.8202  -0.8536
 4V4  H21   H  HCH3  0   0.231   8.9542  -0.0502   0.6610
 4V4  H21A  H  HCH3  0   0.221   7.6733   0.5283   1.7194
 4V4  H21B  H  HCH3  0   0.193   7.9283  -1.2065   1.5212

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
 4V4  N01  C02   aromatic  1.328  0.020  1.328
 4V4  N01  C06   aromatic  1.335  0.020  1.335
 4V4  C02  N02   single    1.366  0.020  1.366
 4V4  C02  C03   aromatic  1.407  0.020  1.407
 4V4  C03  C04   aromatic  1.379  0.020  1.379
 4V4  C04  C05   aromatic  1.400  0.020  1.400
 4V4  C04  C07   single    1.498  0.020  1.498
 4V4  C05  C06   aromatic  1.383  0.020  1.383
 4V4  C06  C08   single    1.502  0.020  1.502
 4V4  C08  C09   single    1.535  0.020  1.535
 4V4  C09  C11   single    1.504  0.020  1.504
 4V4  C11  C12   aromatic  1.391  0.020  1.391
 4V4  C11  C16   aromatic  1.390  0.020  1.390
 4V4  C12  C13   aromatic  1.388  0.020  1.388
 4V4  C13  C14   aromatic  1.384  0.020  1.384
 4V4  C14  C15   aromatic  1.409  0.020  1.409
 4V4  C15  C16   aromatic  1.407  0.020  1.407
 4V4  C15  N17   single    1.371  0.020  1.371
 4V4  C17  N17   single    1.444  0.020  1.444
 4V4  N17  C18   single    1.444  0.020  1.444
 4V4  C18  C19   single    1.526  0.020  1.526
 4V4  C19  N20   single    1.447  0.020  1.447
 4V4  N20  C21   single    1.448  0.020  1.448
 4V4  N02  HN02  single    0.890  0.020  1.040
 4V4  N02  HN0A  single    0.890  0.020  1.040
 4V4  C03  H03   single    0.930  0.020  1.080
 4V4  C05  H05   single    0.930  0.020  1.080
 4V4  C07  H07   single    0.970  0.020  1.090
 4V4  C07  H07A  single    0.970  0.020  1.090
 4V4  C07  H07B  single    0.970  0.020  1.090
 4V4  C08  H08   single    0.970  0.020  1.090
 4V4  C08  H08A  single    0.970  0.020  1.090
 4V4  C09  H09   single    0.970  0.020  1.090
 4V4  C09  H09A  single    0.970  0.020  1.090
 4V4  C12  H12   single    0.930  0.020  1.080
 4V4  C13  H13   single    0.930  0.020  1.080
 4V4  C14  H14   single    0.930  0.020  1.080
 4V4  C16  H16   single    0.930  0.020  1.080
 4V4  C17  H17   single    0.970  0.020  1.090
 4V4  C17  H17A  single    0.970  0.020  1.090
 4V4  C17  H17B  single    0.970  0.020  1.090
 4V4  C18  H18   single    0.970  0.020  1.090
 4V4  C18  H18A  single    0.970  0.020  1.090
 4V4  C19  H19   single    0.970  0.020  1.090
 4V4  C19  H19A  single    0.970  0.020  1.090
 4V4  N20  HN20  single    0.890  0.020  1.040
 4V4  C21  H21   single    0.970  0.020  1.090
 4V4  C21  H21A  single    0.970  0.020  1.090
 4V4  C21  H21B  single    0.970  0.020  1.090

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
 4V4  C06   N01  C02   118.73  3.000
 4V4  C03   C02  N02   120.59  3.000
 4V4  C03   C02  N01   122.30  3.000
 4V4  N02   C02  N01   117.08  3.000
 4V4  HN0A  N02  HN02  114.08  3.000
 4V4  HN0A  N02  C02   117.59  3.000
 4V4  HN02  N02  C02   116.10  3.000
 4V4  H03   C03  C04   120.81  3.000
 4V4  H03   C03  C02   120.12  3.000
 4V4  C04   C03  C02   119.07  3.000
 4V4  C07   C04  C05   120.54  3.000
 4V4  C07   C04  C03   121.38  3.000
 4V4  C05   C04  C03   118.08  3.000
 4V4  H05   C05  C06   120.27  3.000
 4V4  H05   C05  C04   120.66  3.000
 4V4  C06   C05  C04   119.07  3.000
 4V4  C08   C06  C05   121.16  3.000
 4V4  C08   C06  N01   116.09  3.000
 4V4  C05   C06  N01   122.75  3.000
 4V4  H07B  C07  H07A  108.15  3.000
 4V4  H07B  C07  H07   108.00  3.000
 4V4  H07A  C07  H07   106.97  3.000
 4V4  H07B  C07  C04   111.83  3.000
 4V4  H07A  C07  C04   111.02  3.000
 4V4  H07   C07  C04   110.68  3.000
 4V4  H08A  C08  H08   106.82  3.000
 4V4  H08A  C08  C09   109.54  3.000
 4V4  H08   C08  C09   108.88  3.000
 4V4  H08A  C08  C06   109.89  3.000
 4V4  H08   C08  C06   109.32  3.000
 4V4  C09   C08  C06   112.24  3.000
 4V4  H09A  C09  H09   106.94  3.000
 4V4  H09A  C09  C11   110.37  3.000
 4V4  H09   C09  C11   109.92  3.000
 4V4  H09A  C09  C08   108.73  3.000
 4V4  H09   C09  C08   109.16  3.000
 4V4  C11   C09  C08   111.59  3.000
 4V4  C16   C11  C12   119.74  3.000
 4V4  C16   C11  C09   119.60  3.000
 4V4  C12   C11  C09   120.62  3.000
 4V4  H12   C12  C13   120.62  3.000
 4V4  H12   C12  C11   120.38  3.000
 4V4  C13   C12  C11   119.00  3.000
 4V4  H13   C13  C14   118.70  3.000
 4V4  H13   C13  C12   119.73  3.000
 4V4  C14   C13  C12   121.56  3.000
 4V4  H14   C14  C15   121.19  3.000
 4V4  H14   C14  C13   118.27  3.000
 4V4  C15   C14  C13   120.54  3.000
 4V4  N17   C15  C16   120.69  3.000
 4V4  N17   C15  C14   122.21  3.000
 4V4  C16   C15  C14   117.10  3.000
 4V4  H16   C16  C15   120.23  3.000
 4V4  H16   C16  C11   117.72  3.000
 4V4  C15   C16  C11   122.04  3.000
 4V4  H17B  C17  H17A  107.53  3.000
 4V4  H17B  C17  H17   107.76  3.000
 4V4  H17A  C17  H17   107.37  3.000
 4V4  H17B  C17  N17   112.73  3.000
 4V4  H17A  C17  N17   109.07  3.000
 4V4  H17   C17  N17   112.15  3.000
 4V4  C18   N17  C17   117.75  3.000
 4V4  C18   N17  C15   121.56  3.000
 4V4  C17   N17  C15   119.88  3.000
 4V4  H18A  C18  H18   105.46  3.000
 4V4  H18A  C18  C19   109.72  3.000
 4V4  H18   C18  C19   109.26  3.000
 4V4  H18A  C18  N17   110.37  3.000
 4V4  H18   C18  N17   107.96  3.000
 4V4  C19   C18  N17   113.73  3.000
 4V4  H19A  C19  H19   106.14  3.000
 4V4  H19A  C19  N20   113.05  3.000
 4V4  H19   C19  N20   108.53  3.000
 4V4  H19A  C19  C18   109.14  3.000
 4V4  H19   C19  C18   109.51  3.000
 4V4  N20   C19  C18   110.34  3.000
 4V4  HN20  N20  C21   108.77  3.000
 4V4  HN20  N20  C19   108.89  3.000
 4V4  C21   N20  C19   112.92  3.000
 4V4  H21B  C21  H21A  107.29  3.000
 4V4  H21B  C21  H21   107.81  3.000
 4V4  H21A  C21  H21   107.49  3.000
 4V4  H21B  C21  N20   114.17  3.000
 4V4  H21A  C21  N20   110.01  3.000
 4V4  H21   C21  N20   109.82  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
 4V4  CONST_01  C04  C03  C02  N01     0.00   0.0  0
 4V4  CONST_02  C04  C05  C06  N01     0.00   0.0  0
 4V4  CONST_03  C05  C06  N01  C02     0.00   0.0  0
 4V4  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 4V4  CONST_05  C06  N01  C02  C03     0.00   0.0  0
 4V4  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 4V4  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 4V4  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 4V4  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 4V4  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 4V4  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 4V4  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 4V4  CONST_13  C08  C06  N01  C02   180.00   0.0  0
 4V4  CONST_14  C07  C04  C03  C02   180.00   0.0  0
 4V4  CONST_15  C06  N01  C02  N02   180.00   0.0  0
 4V4  CONST_16  C04  C03  C02  N02   180.00   0.0  0
 4V4  CONST_17  C08  C06  C05  C04   180.00   0.0  0
 4V4  CONST_18  C07  C04  C05  C06   180.00   0.0  0
 4V4  CONST_19  C13  C12  C11  C09   180.00   0.0  0
 4V4  CONST_20  C15  C16  C11  C09   180.00   0.0  0
 4V4  CONST_21  N17  C15  C16  C11   180.00   0.0  0
 4V4  CONST_22  N17  C15  C14  C13   180.00   0.0  0
 4V4  CONST_23  H03  C03  C02  N01   180.00   0.0  0
 4V4  CONST_24  H05  C05  C06  N01   180.00   0.0  0
 4V4  CONST_25  H13  C13  C12  C11   180.00   0.0  0
 4V4  CONST_26  H16  C16  C11  C12   180.00   0.0  0
 4V4  CONST_27  H14  C14  C13  C12   180.00   0.0  0
 4V4  CONST_28  H12  C12  C13  C14   180.00   0.0  0
 4V4  CONST_29  C17  N17  C15  C14   180.00   0.0  0
 4V4  CONST_30  C18  N17  C15  C14     0.00   0.0  0
 4V4  CONST_31  C17  N17  C15  C16     0.00   0.0  0
 4V4  CONST_32  C18  N17  C15  C16   180.00   0.0  0
 4V4  Var_01    C09  C08  C06  N01   -62.45  30.0  2
 4V4  Var_02    C11  C09  C08  C06  -179.64  30.0  3
 4V4  Var_03    C12  C11  C09  C08    91.90  30.0  2
 4V4  Var_04    H07  C07  C04  C03   115.33  30.0  2
 4V4  Var_05    C19  C18  N17  C15    84.14  30.0  3
 4V4  Var_06    H17  C17  N17  C15    64.64  30.0  3
 4V4  Var_07    N20  C19  C18  N17  -179.03  30.0  3
 4V4  Var_08    C21  N20  C19  C18   178.41  30.0  3
 4V4  Var_09    H21  C21  N20  C19   175.53  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
 4V4  plan-1  N01   0.020
 4V4  plan-1  C02   0.020
 4V4  plan-1  N02   0.020
 4V4  plan-1  C03   0.020
 4V4  plan-1  C04   0.020
 4V4  plan-1  C05   0.020
 4V4  plan-1  C06   0.020
 4V4  plan-1  C07   0.020
 4V4  plan-1  C08   0.020
 4V4  plan-1  H03   0.020
 4V4  plan-1  H05   0.020
 4V4  plan-2  C09   0.020
 4V4  plan-2  C11   0.020
 4V4  plan-2  C12   0.020
 4V4  plan-2  C13   0.020
 4V4  plan-2  C14   0.020
 4V4  plan-2  C15   0.020
 4V4  plan-2  C16   0.020
 4V4  plan-2  N17   0.020
 4V4  plan-2  H12   0.020
 4V4  plan-2  H13   0.020
 4V4  plan-2  H14   0.020
 4V4  plan-2  H16   0.020
 4V4  plan-3  C02   0.020
 4V4  plan-3  N02   0.020
 4V4  plan-3  HN02  0.020
 4V4  plan-3  HN0A  0.020
 4V4  plan-4  C15   0.020
 4V4  plan-4  C17   0.020
 4V4  plan-4  N17   0.020
 4V4  plan-4  C18   0.020

