# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 18:50:38 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N-{7-[4-(dimethylamino)phenyl]-1,6-naphthyridin-5-yl}propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccc(cc1)c2cc3ncccc3c(NCCCN)n2
#
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
 55U  55U  N-{7-[4-(dimethylamino)phenyl]-1,6-naphthyridin-5-yl}propane-1,3-diamine  ligand  47  24  .  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_55U
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
 55U  C10  C  CR6   0   0.256  -0.2110   0.9800  -0.0224
 55U  C15  C  CR16  0  -0.333   4.1323   3.3910   0.0325
 55U  C17  C  CR66  0  -0.080   2.4728   1.6659  -0.0071
 55U  C20  C  CH2   0  -0.236   2.4794  -2.1061  -0.1139
 55U  C21  C  CH2   0  -0.480   3.6786  -3.0167   0.0927
 55U  C22  C  CH2   0  -0.271   3.2945  -4.4849  -0.0011
 55U  C01  C  CH3   0  -0.537  -6.6788   0.0225   0.1285
 55U  C03  C  CH3   0  -0.536  -5.8538  -2.3117  -0.1236
 55U  C04  C  CR6   0   0.387  -4.3002  -0.4427  -0.0655
 55U  C05  C  CR16  0  -0.340  -3.2025  -1.3230  -0.1427
 55U  C06  C  CR16  0  -0.274  -1.9047  -0.8514  -0.1262
 55U  C07  C  CR6   0   0.018  -1.6074   0.5107  -0.0304
 55U  C08  C  CR16  0  -0.327  -2.6973   1.3810   0.0605
 55U  C09  C  CR16  0  -0.335  -4.0015   0.9308   0.0493
 55U  C11  C  CR16  0  -0.463   0.1239   2.3132  -0.0054
 55U  C12  C  CR66  0   0.331   1.4863   2.6775   0.0026
 55U  N13  N  N     0  -0.447   1.8109   3.9912   0.0208
 55U  C14  C  CR16  0  -0.075   3.0791   4.3186   0.0343
 55U  C16  C  CR16  0  -0.181   3.8191   2.0553   0.0124
 55U  C18  C  CR6   0   0.477   2.0048   0.3005  -0.0325
 55U  N19  N  NH1   0  -0.687   2.8828  -0.7202  -0.0301
 55U  N23  N  NH2   0  -0.799   4.4586  -5.3347   0.1990
 55U  N24  N  N     0  -0.517   0.7269   0.0047  -0.0426
 55U  H1   H  HCR6  0   0.274   5.1584   3.7297   0.0478
 55U  H2   H  HCH2  0   0.222   2.0129  -2.3160  -1.0833
 55U  H3   H  HCH2  0   0.232   1.7202  -2.3061   0.6449
 55U  H4   H  HCH2  0   0.229   4.4473  -2.8015  -0.6557
 55U  H5   H  HCH2  0   0.230   4.1199  -2.8138   1.0739
 55U  H6   H  HCH2  0   0.193   2.4764  -4.6861   0.7055
 55U  H7   H  HCH2  0   0.217   2.8940  -4.6860  -0.9984
 55U  H8   H  HCH3  0   0.231  -6.6520   0.4679   1.1282
 55U  H9   H  HCH3  0   0.239  -6.6876   0.8362  -0.6002
 55U  H10  H  HCH3  0   0.257  -7.6195  -0.5118   0.0284
 55U  H11  H  HCH3  0   0.256  -6.9244  -2.4713  -0.2167
 55U  H12  H  HCH3  0   0.239  -5.3779  -2.7979  -0.9780
 55U  H13  H  HCH3  0   0.230  -5.5146  -2.8209   0.7847
 55U  H14  H  HCR6  0   0.263  -3.3546  -2.3909  -0.2137
 55U  H15  H  HCR6  0   0.257  -1.0932  -1.5638  -0.1878
 55U  H16  H  HCR6  0   0.247  -2.5444   2.4488   0.1496
 55U  H17  H  HCR6  0   0.266  -4.7918   1.6629   0.1310
 55U  H18  H  HCR6  0   0.254  -0.6150   3.1011  -0.0014
 55U  H19  H  HCR6  0   0.265   3.3042   5.3800   0.0489
 55U  H20  H  HCR6  0   0.265   4.6204   1.3279   0.0142
 55U  H21  H  HNH1  0   0.403   3.8611  -0.5264  -0.1549
 55U  H22  H  HNH2  0   0.339   4.7752  -5.2494   1.1573
 55U  H23  H  HNH2  0   0.347   4.1893  -6.3039   0.0882
 55U  N02  N  NT    0  -0.501  -5.5858  -0.8927  -0.1030

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
 55U  C20  C21  single    1.520  0.020  1.520
 55U  C20  N19  single    1.446  0.020  1.446
 55U  C21  C22  single    1.521  0.020  1.521
 55U  N19  C18  single    1.346  0.020  1.346
 55U  N23  C22  single    1.455  0.020  1.455
 55U  C18  N24  aromatic  1.312  0.020  1.312
 55U  C18  C17  aromatic  1.444  0.020  1.444
 55U  N24  C10  aromatic  1.353  0.020  1.353
 55U  C16  C17  aromatic  1.402  0.020  1.402
 55U  C16  C15  aromatic  1.372  0.020  1.372
 55U  C06  C05  aromatic  1.381  0.020  1.381
 55U  C06  C07  aromatic  1.398  0.020  1.398
 55U  C17  C12  aromatic  1.413  0.020  1.413
 55U  C05  C04  aromatic  1.409  0.020  1.409
 55U  C01  N02  single    1.444  0.020  1.444
 55U  C10  C07  single    1.473  0.020  1.473
 55U  C10  C11  aromatic  1.375  0.020  1.375
 55U  C15  C14  aromatic  1.403  0.020  1.403
 55U  C07  C08  aromatic  1.398  0.020  1.398
 55U  C04  N02  single    1.363  0.020  1.363
 55U  C04  C09  aromatic  1.410  0.020  1.410
 55U  C12  C11  aromatic  1.410  0.020  1.410
 55U  C12  N13  aromatic  1.353  0.020  1.353
 55U  N02  C03  single    1.444  0.020  1.444
 55U  C08  C09  aromatic  1.380  0.020  1.380
 55U  C14  N13  aromatic  1.310  0.020  1.310
 55U  C15  H1   single    0.930  0.020  1.080
 55U  C20  H2   single    0.970  0.020  1.090
 55U  C20  H3   single    0.970  0.020  1.090
 55U  C21  H4   single    0.970  0.020  1.090
 55U  C21  H5   single    0.970  0.020  1.090
 55U  C22  H6   single    0.970  0.020  1.090
 55U  C22  H7   single    0.970  0.020  1.090
 55U  C01  H8   single    0.970  0.020  1.090
 55U  C01  H9   single    0.970  0.020  1.090
 55U  C01  H10  single    0.970  0.020  1.090
 55U  C03  H11  single    0.970  0.020  1.090
 55U  C03  H12  single    0.970  0.020  1.090
 55U  C03  H13  single    0.970  0.020  1.090
 55U  C05  H14  single    0.930  0.020  1.080
 55U  C06  H15  single    0.930  0.020  1.080
 55U  C08  H16  single    0.930  0.020  1.080
 55U  C09  H17  single    0.930  0.020  1.080
 55U  C11  H18  single    0.930  0.020  1.080
 55U  C14  H19  single    0.930  0.020  1.080
 55U  C16  H20  single    0.930  0.020  1.080
 55U  N19  H21  single    0.860  0.020  1.020
 55U  N23  H22  single    0.890  0.020  1.040
 55U  N23  H23  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
 55U  N24  C10  C11  122.02  3.000
 55U  C11  C10  C07  122.68  3.000
 55U  N24  C10  C07  115.29  3.000
 55U  H1   C15  C16  121.47  3.000
 55U  H1   C15  C14  120.36  3.000
 55U  C16  C15  C14  118.17  3.000
 55U  C18  C17  C16  125.06  3.000
 55U  C16  C17  C12  118.14  3.000
 55U  C18  C17  C12  116.80  3.000
 55U  H3   C20  H2   106.48  3.000
 55U  H3   C20  N19  109.22  3.000
 55U  H2   C20  N19  110.71  3.000
 55U  H3   C20  C21  110.14  3.000
 55U  H2   C20  C21  109.96  3.000
 55U  N19  C20  C21  110.26  3.000
 55U  H5   C21  H4   107.06  3.000
 55U  H5   C21  C22  109.64  3.000
 55U  H4   C21  C22  108.97  3.000
 55U  H5   C21  C20  109.20  3.000
 55U  H4   C21  C20  110.09  3.000
 55U  C22  C21  C20  111.76  3.000
 55U  H7   C22  H6   106.26  3.000
 55U  H7   C22  N23  108.13  3.000
 55U  H6   C22  N23  113.57  3.000
 55U  H7   C22  C21  109.05  3.000
 55U  H6   C22  C21  108.96  3.000
 55U  N23  C22  C21  110.69  3.000
 55U  H10  C01  H9   107.33  3.000
 55U  H10  C01  H8   107.78  3.000
 55U  H9   C01  H8   107.83  3.000
 55U  H10  C01  N02  109.20  3.000
 55U  H9   C01  N02  111.79  3.000
 55U  H8   C01  N02  112.68  3.000
 55U  H13  C03  H12  107.87  3.000
 55U  H13  C03  H11  107.93  3.000
 55U  H12  C03  H11  107.28  3.000
 55U  H13  C03  N02  112.80  3.000
 55U  H12  C03  N02  111.57  3.000
 55U  H11  C03  N02  109.17  3.000
 55U  C09  C04  C05  116.60  3.000
 55U  C09  C04  N02  121.58  3.000
 55U  C05  C04  N02  121.81  3.000
 55U  H14  C05  C06  118.06  3.000
 55U  H14  C05  C04  120.74  3.000
 55U  C06  C05  C04  121.20  3.000
 55U  H15  C06  C07  119.09  3.000
 55U  H15  C06  C05  118.65  3.000
 55U  C07  C06  C05  122.25  3.000
 55U  C08  C07  C06  116.45  3.000
 55U  C08  C07  C10  122.71  3.000
 55U  C06  C07  C10  120.83  3.000
 55U  H16  C08  C09  117.14  3.000
 55U  H16  C08  C07  120.63  3.000
 55U  C09  C08  C07  122.23  3.000
 55U  H17  C09  C08  118.01  3.000
 55U  H17  C09  C04  120.74  3.000
 55U  C08  C09  C04  121.25  3.000
 55U  H18  C11  C12  118.19  3.000
 55U  H18  C11  C10  122.74  3.000
 55U  C12  C11  C10  119.07  3.000
 55U  N13  C12  C11  118.85  3.000
 55U  N13  C12  C17  121.84  3.000
 55U  C11  C12  C17  119.31  3.000
 55U  C14  N13  C12  118.36  3.000
 55U  H19  C14  N13  116.45  3.000
 55U  H19  C14  C15  119.40  3.000
 55U  N13  C14  C15  124.15  3.000
 55U  H20  C16  C17  121.63  3.000
 55U  H20  C16  C15  119.03  3.000
 55U  C17  C16  C15  119.34  3.000
 55U  N24  C18  N19  117.67  3.000
 55U  N24  C18  C17  121.96  3.000
 55U  N19  C18  C17  120.37  3.000
 55U  H21  N19  C18  119.23  3.000
 55U  H21  N19  C20  116.69  3.000
 55U  C18  N19  C20  123.00  3.000
 55U  H23  N23  H22  105.52  3.000
 55U  H23  N23  C22  109.36  3.000
 55U  H22  N23  C22  109.33  3.000
 55U  C18  N24  C10  120.83  3.000
 55U  C04  N02  C03  120.00  3.000
 55U  C03  N02  C01  118.98  3.000
 55U  C04  N02  C01  120.02  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
 55U  CONST_01  C17  C18  N24  C10     0.00   0.0  0
 55U  CONST_02  C05  C06  C07  C10   180.00   0.0  0
 55U  CONST_03  C09  C08  C07  C10   180.00   0.0  0
 55U  CONST_04  C17  C12  C11  C10     0.00   0.0  0
 55U  CONST_05  N13  C12  C11  C10   180.00   0.0  0
 55U  CONST_06  C18  C17  C16  C15   180.00   0.0  0
 55U  CONST_07  C12  C17  C16  C15     0.00   0.0  0
 55U  CONST_08  C12  N13  C14  C15     0.00   0.0  0
 55U  CONST_09  C14  C15  C16  C17     0.00   0.0  0
 55U  CONST_10  C14  N13  C12  C17     0.00   0.0  0
 55U  CONST_11  C07  C06  C05  C04     0.00   0.0  0
 55U  CONST_12  C07  C08  C09  C04     0.00   0.0  0
 55U  CONST_13  C08  C07  C06  C05     0.00   0.0  0
 55U  CONST_14  C08  C09  C04  C05     0.00   0.0  0
 55U  CONST_15  C09  C04  C05  C06     0.00   0.0  0
 55U  CONST_16  N24  C10  C07  C06     0.00   0.0  0
 55U  CONST_17  C11  C10  C07  C06   180.00   0.0  0
 55U  CONST_18  C09  C08  C07  C06     0.00   0.0  0
 55U  CONST_19  C18  N24  C10  C07   180.00   0.0  0
 55U  CONST_20  C12  C11  C10  C07   180.00   0.0  0
 55U  CONST_21  N24  C10  C07  C08   180.00   0.0  0
 55U  CONST_22  C11  C10  C07  C08     0.00   0.0  0
 55U  CONST_23  C18  N24  C10  C11     0.00   0.0  0
 55U  CONST_24  C18  C17  C12  C11     0.00   0.0  0
 55U  CONST_25  C16  C17  C12  C11   180.00   0.0  0
 55U  CONST_26  C14  N13  C12  C11   180.00   0.0  0
 55U  CONST_27  N24  C18  C17  C12     0.00   0.0  0
 55U  CONST_28  N24  C10  C11  C12     0.00   0.0  0
 55U  CONST_29  C18  C17  C12  N13   180.00   0.0  0
 55U  CONST_30  C16  C17  C12  N13     0.00   0.0  0
 55U  CONST_31  C16  C15  C14  N13     0.00   0.0  0
 55U  CONST_32  N24  C18  C17  C16   180.00   0.0  0
 55U  CONST_33  N19  C18  N24  C10   180.00   0.0  0
 55U  CONST_34  C06  C05  C04  N02   180.00   0.0  0
 55U  CONST_35  C08  C09  C04  N02   180.00   0.0  0
 55U  CONST_36  N19  C18  C17  C12   180.00   0.0  0
 55U  CONST_37  N19  C18  C17  C16     0.00   0.0  0
 55U  CONST_38  H15  C06  C07  C10     0.00   0.0  0
 55U  CONST_39  H16  C08  C07  C10     0.00   0.0  0
 55U  CONST_40  H1   C15  C16  C17   180.00   0.0  0
 55U  CONST_41  H18  C11  C12  C17   180.00   0.0  0
 55U  CONST_42  H17  C09  C04  C05   180.00   0.0  0
 55U  CONST_43  H14  C05  C06  C07   180.00   0.0  0
 55U  CONST_44  H20  C16  C17  C12   180.00   0.0  0
 55U  CONST_45  H19  C14  N13  C12   180.00   0.0  0
 55U  CONST_46  C20  N19  C18  C17   180.00   0.0  0
 55U  CONST_47  N24  C18  N19  C20     0.00   0.0  0
 55U  CONST_48  C05  C04  N02  C01   180.00   0.0  0
 55U  CONST_49  C09  C04  N02  C01     0.00   0.0  0
 55U  CONST_50  C05  C04  N02  C03     0.00   0.0  0
 55U  CONST_51  C09  C04  N02  C03   180.00   0.0  0
 55U  CONST_52  H21  N19  C18  C17     0.00   0.0  0
 55U  Var_01    C18  N19  C20  C21  -172.69  30.0  3
 55U  Var_02    H8   C01  N02  C04   -61.96  30.0  3
 55U  Var_03    H11  C03  N02  C04  -176.43  30.0  3
 55U  Var_04    N23  C22  C21  C20   179.96  30.0  3
 55U  Var_05    N19  C20  C21  C22  -179.49  30.0  1
 55U  Var_06    H22  N23  C22  C21    67.64  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
 55U  plan-1  C10  0.020
 55U  plan-1  C04  0.020
 55U  plan-1  C05  0.020
 55U  plan-1  C06  0.020
 55U  plan-1  C07  0.020
 55U  plan-1  C08  0.020
 55U  plan-1  C09  0.020
 55U  plan-1  H14  0.020
 55U  plan-1  H15  0.020
 55U  plan-1  H16  0.020
 55U  plan-1  H17  0.020
 55U  plan-1  N02  0.020
 55U  plan-2  C10  0.020
 55U  plan-2  C15  0.020
 55U  plan-2  C17  0.020
 55U  plan-2  C07  0.020
 55U  plan-2  C11  0.020
 55U  plan-2  C12  0.020
 55U  plan-2  N13  0.020
 55U  plan-2  C14  0.020
 55U  plan-2  C16  0.020
 55U  plan-2  C18  0.020
 55U  plan-2  N19  0.020
 55U  plan-2  N24  0.020
 55U  plan-2  H1   0.020
 55U  plan-2  H18  0.020
 55U  plan-2  H19  0.020
 55U  plan-2  H20  0.020
 55U  plan-3  C20  0.020
 55U  plan-3  C18  0.020
 55U  plan-3  N19  0.020
 55U  plan-3  H21  0.020
 55U  plan-4  C01  0.020
 55U  plan-4  C03  0.020
 55U  plan-4  C04  0.020
 55U  plan-4  N02  0.020

