# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 07:03:55 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 8-(3-bromopropoxy)-7-methoxynaphthalene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2ccc(cc2c1OCCCBr)C(N)=N
#
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
 8UP  8UP  8-(3-bromopropoxy)-7-methoxynaphthalene-2-carboximidamide  ligand  37  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8UP
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
 8UP  BR   BR  BR    0  -0.138  -4.8950  -0.9044  -0.2052
 8UP  C14  C   CH2   0  -0.514  -3.2630  -0.0505  -0.8960
 8UP  C13  C   CH2   0  -0.462  -2.2081   0.0655   0.1840
 8UP  C12  C   CH2   0  -0.152  -0.9621   0.7242  -0.3839
 8UP  O2   O   O2    0  -0.488  -0.0211   0.8528   0.6802
 8UP  C11  C   CR6   0   0.218   1.2219   1.2563   0.3046
 8UP  C2   C   CR6   0   0.323   1.4914   2.5999   0.1184
 8UP  O1   O   O2    0  -0.462   0.4691   3.4504   0.3073
 8UP  C1   C   CH3   0  -0.440   0.6827   4.8339   0.1002
 8UP  C10  C   CR66  0   0.060   2.2350   0.2869   0.1312
 8UP  C5   C   CR66  0   0.088   3.5420   0.7042  -0.2334
 8UP  C4   C   CR16  0  -0.318   3.7890   2.0786  -0.4179
 8UP  C3   C   CR16  0  -0.382   2.7954   3.0039  -0.2448
 8UP  C9   C   CR16  0  -0.361   1.9883  -1.0920   0.3281
 8UP  C8   C   CR6   0   0.011   2.9828  -2.0202   0.1538
 8UP  C15  C   C     0   0.329   2.6886  -3.4640   0.3833
 8UP  N2   N   NH2   0  -0.803   3.3524  -4.3195  -0.4441
 8UP  N1   N   N     0  -0.640   1.9150  -3.9117   1.2971
 8UP  C7   C   CR16  0  -0.287   4.2820  -1.5994  -0.2249
 8UP  C6   C   CR16  0  -0.296   4.5498  -0.2729  -0.4046
 8UP  H14  H   HCH2  0   0.291  -2.9284  -0.6648  -1.7312
 8UP  H13  H   HCH2  0   0.291  -3.5670   0.9240  -1.2757
 8UP  H12  H   HCH2  0   0.255  -2.5857   0.6638   1.0159
 8UP  H11  H   HCH2  0   0.252  -1.9527  -0.9234   0.5703
 8UP  H9   H   HCH2  0   0.224  -0.5407   0.1127  -1.1895
 8UP  H10  H   HCH2  0   0.233  -1.2041   1.7066  -0.8009
 8UP  H2   H   HCH3  0   0.232   1.4296   5.2402   0.7863
 8UP  H3   H   HCH3  0   0.232   0.9872   5.0512  -0.9263
 8UP  H1   H   HCH3  0   0.263  -0.2692   5.3219   0.2936
 8UP  H5   H   HCR6  0   0.264   4.7818   2.4066  -0.6985
 8UP  H4   H   HCR6  0   0.290   3.0238   4.0507  -0.3915
 8UP  H8   H   HCR6  0   0.255   0.9936  -1.4161   0.6050
 8UP  H17  H   HNH2  0   0.393   3.5975  -3.9980  -1.3658
 8UP  H15  H   HNH2  0   0.385   3.0703  -5.2863  -0.4052
 8UP  H16  H   H     0   0.332   1.5898  -3.1571   1.8897
 8UP  H7   H   HCR6  0   0.262   5.0707  -2.3295  -0.3489
 8UP  H6   H   HCR6  0   0.260   5.5475   0.0482  -0.6779

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
 8UP  BR   C14  single    1.967  0.020  1.967
 8UP  C14  C13  single    1.514  0.020  1.514
 8UP  C13  C12  single    1.519  0.020  1.519
 8UP  O2   C12  single    1.426  0.020  1.426
 8UP  O2   C11  single    1.360  0.020  1.360
 8UP  N1   C15  double    1.278  0.020  1.278
 8UP  O1   C1   single    1.415  0.020  1.415
 8UP  O1   C2   single    1.343  0.020  1.343
 8UP  C11  C2   aromatic  1.383  0.020  1.383
 8UP  C11  C10  aromatic  1.413  0.020  1.413
 8UP  C9   C10  aromatic  1.415  0.020  1.415
 8UP  C9   C8   aromatic  1.371  0.020  1.371
 8UP  C15  N2   single    1.363  0.020  1.363
 8UP  C15  C8   single    1.491  0.020  1.491
 8UP  C2   C3   aromatic  1.413  0.020  1.413
 8UP  C10  C5   aromatic  1.420  0.020  1.420
 8UP  C8   C7   aromatic  1.417  0.020  1.417
 8UP  C3   C4   aromatic  1.369  0.020  1.369
 8UP  C5   C4   aromatic  1.409  0.020  1.409
 8UP  C5   C6   aromatic  1.414  0.020  1.414
 8UP  C7   C6   aromatic  1.365  0.020  1.365
 8UP  C14  H14  single    0.970  0.020  1.090
 8UP  C14  H13  single    0.970  0.020  1.090
 8UP  C13  H12  single    0.970  0.020  1.090
 8UP  C13  H11  single    0.970  0.020  1.090
 8UP  C12  H9   single    0.970  0.020  1.090
 8UP  C12  H10  single    0.970  0.020  1.090
 8UP  C1   H2   single    0.970  0.020  1.090
 8UP  C1   H3   single    0.970  0.020  1.090
 8UP  C1   H1   single    0.970  0.020  1.090
 8UP  C4   H5   single    0.930  0.020  1.080
 8UP  C3   H4   single    0.930  0.020  1.080
 8UP  C9   H8   single    0.930  0.020  1.080
 8UP  N2   H17  single    0.890  0.020  1.040
 8UP  N2   H15  single    0.890  0.020  1.040
 8UP  N1   H16  single    0.890  0.020  1.040
 8UP  C7   H7   single    0.930  0.020  1.080
 8UP  C6   H6   single    0.930  0.020  1.080

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
 8UP  H13  C14  H14  108.84  3.000
 8UP  H13  C14  C13  112.00  3.000
 8UP  H14  C14  C13  112.09  3.000
 8UP  H13  C14  BR   106.22  3.000
 8UP  H14  C14  BR   106.21  3.000
 8UP  C13  C14  BR   111.15  3.000
 8UP  H11  C13  H12  107.91  3.000
 8UP  H11  C13  C12  109.45  3.000
 8UP  H12  C13  C12  109.31  3.000
 8UP  H11  C13  C14  110.24  3.000
 8UP  H12  C13  C14  110.14  3.000
 8UP  C12  C13  C14  109.75  3.000
 8UP  H10  C12  H9   107.81  3.000
 8UP  H10  C12  O2   110.44  3.000
 8UP  H9   C12  O2   110.19  3.000
 8UP  H10  C12  C13  110.50  3.000
 8UP  H9   C12  C13  110.38  3.000
 8UP  O2   C12  C13  107.53  3.000
 8UP  C11  O2   C12  115.08  3.000
 8UP  C10  C11  C2   120.68  3.000
 8UP  C10  C11  O2   119.06  3.000
 8UP  C2   C11  O2   120.25  3.000
 8UP  C3   C2   O1   123.89  3.000
 8UP  C3   C2   C11  119.50  3.000
 8UP  O1   C2   C11  116.61  3.000
 8UP  C1   O1   C2   118.92  3.000
 8UP  H1   C1   H3   108.78  3.000
 8UP  H1   C1   H2   108.66  3.000
 8UP  H3   C1   H2   109.00  3.000
 8UP  H1   C1   O1   106.30  3.000
 8UP  H3   C1   O1   111.96  3.000
 8UP  H2   C1   O1   112.02  3.000
 8UP  C9   C10  C5   118.87  3.000
 8UP  C5   C10  C11  119.34  3.000
 8UP  C9   C10  C11  121.78  3.000
 8UP  C6   C5   C4   122.24  3.000
 8UP  C6   C5   C10  118.96  3.000
 8UP  C4   C5   C10  118.81  3.000
 8UP  H5   C4   C3   119.58  3.000
 8UP  H5   C4   C5   119.37  3.000
 8UP  C3   C4   C5   121.05  3.000
 8UP  H4   C3   C4   118.94  3.000
 8UP  H4   C3   C2   120.45  3.000
 8UP  C4   C3   C2   120.61  3.000
 8UP  H8   C9   C8   119.76  3.000
 8UP  H8   C9   C10  119.20  3.000
 8UP  C8   C9   C10  121.03  3.000
 8UP  C7   C8   C15  120.62  3.000
 8UP  C7   C8   C9   119.86  3.000
 8UP  C15  C8   C9   119.52  3.000
 8UP  N1   C15  N2   120.59  3.000
 8UP  N2   C15  C8   114.73  3.000
 8UP  N1   C15  C8   124.65  3.000
 8UP  H15  N2   H17  114.21  3.000
 8UP  H15  N2   C15  116.26  3.000
 8UP  H17  N2   C15  118.30  3.000
 8UP  H16  N1   C15  110.58  3.000
 8UP  H7   C7   C6   119.84  3.000
 8UP  H7   C7   C8   119.91  3.000
 8UP  C6   C7   C8   120.23  3.000
 8UP  H6   C6   C7   120.13  3.000
 8UP  H6   C6   C5   118.83  3.000
 8UP  C7   C6   C5   121.04  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
 8UP  CONST_01  C4   C3   C2   C11    0.00   0.0  0
 8UP  CONST_02  C8   C9   C10  C11  180.00   0.0  0
 8UP  CONST_03  C4   C5   C10  C11    0.00   0.0  0
 8UP  CONST_04  C6   C5   C10  C11  180.00   0.0  0
 8UP  CONST_05  C9   C10  C11  C2   180.00   0.0  0
 8UP  CONST_06  C5   C10  C11  C2     0.00   0.0  0
 8UP  CONST_07  C5   C4   C3   C2     0.00   0.0  0
 8UP  CONST_08  C3   C2   C11  C10    0.00   0.0  0
 8UP  CONST_09  C7   C8   C9   C10    0.00   0.0  0
 8UP  CONST_10  C3   C4   C5   C10    0.00   0.0  0
 8UP  CONST_11  C7   C6   C5   C10    0.00   0.0  0
 8UP  CONST_12  C8   C9   C10  C5     0.00   0.0  0
 8UP  CONST_13  C8   C7   C6   C5     0.00   0.0  0
 8UP  CONST_14  C9   C10  C5   C4   180.00   0.0  0
 8UP  CONST_15  C7   C6   C5   C4   180.00   0.0  0
 8UP  CONST_16  C6   C5   C4   C3   180.00   0.0  0
 8UP  CONST_17  C6   C5   C10  C9     0.00   0.0  0
 8UP  CONST_18  C6   C7   C8   C9     0.00   0.0  0
 8UP  CONST_19  C3   C2   C11  O2   180.00   0.0  0
 8UP  CONST_20  C9   C10  C11  O2     0.00   0.0  0
 8UP  CONST_21  C5   C10  C11  O2   180.00   0.0  0
 8UP  CONST_22  C10  C11  C2   O1   180.00   0.0  0
 8UP  CONST_23  C4   C3   C2   O1   180.00   0.0  0
 8UP  CONST_24  C15  C8   C9   C10  180.00   0.0  0
 8UP  CONST_25  C6   C7   C8   C15  180.00   0.0  0
 8UP  CONST_26  H4   C3   C2   C11  180.00   0.0  0
 8UP  CONST_27  H8   C9   C10  C11    0.00   0.0  0
 8UP  CONST_28  H5   C4   C3   C2   180.00   0.0  0
 8UP  CONST_29  H6   C6   C5   C10  180.00   0.0  0
 8UP  CONST_30  H7   C7   C6   C5   180.00   0.0  0
 8UP  CONST_31  H16  N1   C15  C8     0.00   0.0  0
 8UP  CONST_33  H15  N2   C15  C8   180.00   0.0  0
 8UP  Var_01    C2   C11  O2   C12   82.83  30.0  2
 8UP  Var_02    C3   C2   O1   C1     1.76  30.0  2
 8UP  Var_03    N1   C15  C8   C9   -36.87  30.0  2
 8UP  Var_04    H9   C12  O2   C11   50.98  30.0  3
 8UP  Var_05    H2   C1   O1   C2   -62.25  30.0  3
 8UP  Var_06    C12  C13  C14  BR   179.82  30.0  3
 8UP  Var_07    O2   C12  C13  C14  177.97  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
 8UP  plan-1  O2   0.020
 8UP  plan-1  C11  0.020
 8UP  plan-1  C2   0.020
 8UP  plan-1  O1   0.020
 8UP  plan-1  C10  0.020
 8UP  plan-1  C5   0.020
 8UP  plan-1  C4   0.020
 8UP  plan-1  C3   0.020
 8UP  plan-1  C9   0.020
 8UP  plan-1  C8   0.020
 8UP  plan-1  C15  0.020
 8UP  plan-1  C7   0.020
 8UP  plan-1  C6   0.020
 8UP  plan-1  H5   0.020
 8UP  plan-1  H4   0.020
 8UP  plan-1  H8   0.020
 8UP  plan-1  H7   0.020
 8UP  plan-1  H6   0.020
 8UP  plan-2  C8   0.020
 8UP  plan-2  C15  0.020
 8UP  plan-2  N2   0.020
 8UP  plan-2  N1   0.020
 8UP  plan-2  H17  0.020
 8UP  plan-2  H15  0.020
 8UP  plan-2  H16  0.020

