# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:24:58 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2,4-diiodo-6-{[methyl(1-methylpiperidin-4-yl)amino]methyl}phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC(CC1)N(C)Cc2cc(I)cc(I)c2O
#
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
 P84  P84  2,4-diiodo-6-{[methyl(1-methylpiperidin-4-yl)amino]methyl}phenol  ligand  39  19  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P84
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
 P84  C1    C  CR6   0   0.035   0.4963   0.2417   0.6722
 P84  C2    C  CR6   0   0.388   0.0879  -1.0936   0.5185
 P84  C3    C  CR6   0  -0.346  -1.2601  -1.3551   0.2688
 P84  C4    C  CH2   0  -0.347   1.9470   0.5581   0.9239
 P84  N5    N  NT    0  -0.406   2.7564   0.3119  -0.2545
 P84  C6    C  CR16  0  -0.211  -2.1964  -0.3319   0.1691
 P84  C8    C  CR16  0  -0.261  -0.4378   1.2584   0.5761
 P84  C9    C  CH3   0  -0.538   2.5716   1.3492  -1.2465
 P84  C10   C  CR6   0  -0.233  -1.7742   0.9744   0.3263
 P84  I15   I  I     0   0.085  -1.9328  -3.3364   0.0251
 P84  O16   O  OH1   0  -0.591   1.0330  -2.0298   0.6372
 P84  I17   I  I     0   0.059  -3.1672   2.5416   0.1775
 P84  C11   C  CH2   0  -0.272   6.3769   0.6763   0.9805
 P84  C12   C  CH2   0  -0.278   6.2991  -1.0074  -0.7173
 P84  C13   C  CH2   0  -0.443   4.8865  -0.6094  -1.1209
 P84  C14   C  CH1   0  -0.073   4.1414  -0.0108   0.0661
 P84  N6    N  NT    0  -0.407   7.0354   0.1248  -0.1878
 P84  C15   C  CH2   0  -0.454   4.9654   1.1394   0.6516
 P84  C16   C  CH3   0  -0.517   8.4079  -0.2244   0.0956
 P84  H41C  H  HCH2  0   0.226   2.0181   1.5988   1.2758
 P84  H42C  H  HCH2  0   0.254   2.3166  -0.0657   1.7413
 P84  H8    H  HCR6  0   0.281  -0.1029   2.2801   0.7034
 P84  H16   H  HOH1  0   0.472   0.6699  -2.9240   0.6070
 P84  H6    H  HCR6  0   0.298  -3.2339  -0.5628  -0.0276
 P84  H91C  H  HCH3  0   0.196   2.8746   2.3514  -0.9097
 P84  H92C  H  HCH3  0   0.239   3.1241   1.1199  -2.1566
 P84  H93C  H  HCH3  0   0.239   1.5185   1.4086  -1.5257
 P84  H141  H  HCH1  0   0.220   4.0895  -0.7995   0.8288
 P84  H111  H  HCH2  0   0.182   6.3351  -0.0621   1.8034
 P84  H112  H  HCH2  0   0.232   6.9666   1.5196   1.3493
 P84  H131  H  HCH2  0   0.219   4.9505   0.1081  -1.9432
 P84  H132  H  HCH2  0   0.232   4.3487  -1.4849  -1.4916
 P84  H121  H  HCH2  0   0.183   6.2515  -1.8337   0.0165
 P84  H122  H  HCH2  0   0.234   6.8339  -1.3948  -1.5881
 P84  H151  H  HCH2  0   0.235   4.4969   1.5255   1.5608
 P84  H152  H  HCH2  0   0.220   5.0173   1.9675  -0.0616
 P84  H161  H  HCH3  0   0.188   8.5096  -1.0071   0.8645
 P84  H162  H  HCH3  0   0.230   8.8991  -0.5844  -0.8098
 P84  H163  H  HCH3  0   0.230   8.9546   0.6536   0.4437

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
 P84  C1   C2    aromatic  1.405  0.020  1.405
 P84  C1   C4    single    1.506  0.020  1.506
 P84  C1   C8    aromatic  1.384  0.020  1.384
 P84  C2   C3    aromatic  1.396  0.020  1.396
 P84  C2   O16   single    1.336  0.020  1.336
 P84  C3   C6    aromatic  1.390  0.020  1.390
 P84  C3   I15   single    2.107  0.020  2.107
 P84  C4   N5    single    1.451  0.020  1.451
 P84  N5   C9    single    1.447  0.020  1.447
 P84  N5   C14   single    1.458  0.020  1.458
 P84  C6   C10   aromatic  1.382  0.020  1.382
 P84  C8   C10   aromatic  1.389  0.020  1.389
 P84  C10  I17   single    2.102  0.020  2.102
 P84  C12  N6    single    1.451  0.020  1.451
 P84  C11  N6    single    1.450  0.020  1.450
 P84  C16  N6    single    1.444  0.020  1.444
 P84  C13  C12   single    1.522  0.020  1.522
 P84  C13  C14   single    1.524  0.020  1.524
 P84  C15  C14   single    1.531  0.020  1.531
 P84  C11  C15   single    1.522  0.020  1.522
 P84  C4   H41C  single    0.970  0.020  1.090
 P84  C4   H42C  single    0.970  0.020  1.090
 P84  C8   H8    single    0.930  0.020  1.080
 P84  O16  H16   single    0.850  0.020  0.980
 P84  C6   H6    single    0.930  0.020  1.080
 P84  C11  H111  single    0.970  0.020  1.090
 P84  C11  H112  single    0.970  0.020  1.090
 P84  C9   H91C  single    0.970  0.020  1.090
 P84  C9   H92C  single    0.970  0.020  1.090
 P84  C9   H93C  single    0.970  0.020  1.090
 P84  C14  H141  single    0.970  0.020  1.090
 P84  C13  H131  single    0.970  0.020  1.090
 P84  C13  H132  single    0.970  0.020  1.090
 P84  C12  H121  single    0.970  0.020  1.090
 P84  C12  H122  single    0.970  0.020  1.090
 P84  C15  H151  single    0.970  0.020  1.090
 P84  C15  H152  single    0.970  0.020  1.090
 P84  C16  H161  single    0.970  0.020  1.090
 P84  C16  H162  single    0.970  0.020  1.090
 P84  C16  H163  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
 P84  C8    C1   C4    120.49  3.000
 P84  C8    C1   C2    119.63  3.000
 P84  C4    C1   C2    119.87  3.000
 P84  O16   C2   C3    124.62  3.000
 P84  O16   C2   C1    116.79  3.000
 P84  C3    C2   C1    118.58  3.000
 P84  I15   C3   C6    117.96  3.000
 P84  I15   C3   C2    120.35  3.000
 P84  C6    C3   C2    121.69  3.000
 P84  H42C  C4   H41C  106.19  3.000
 P84  H42C  C4   N5    108.78  3.000
 P84  H41C  C4   N5    112.59  3.000
 P84  H42C  C4   C1    109.32  3.000
 P84  H41C  C4   C1    108.32  3.000
 P84  N5    C4   C1    111.47  3.000
 P84  C14   N5   C9    115.51  3.000
 P84  C14   N5   C4    112.89  3.000
 P84  C9    N5   C4    111.34  3.000
 P84  H6    C6   C10   121.06  3.000
 P84  H6    C6   C3    120.14  3.000
 P84  C10   C6   C3    118.80  3.000
 P84  H8    C8   C10   120.78  3.000
 P84  H8    C8   C1    118.44  3.000
 P84  C10   C8   C1    120.77  3.000
 P84  H93C  C9   H92C  106.70  3.000
 P84  H93C  C9   H91C  107.14  3.000
 P84  H92C  C9   H91C  107.94  3.000
 P84  H93C  C9   N5    109.73  3.000
 P84  H92C  C9   N5    110.92  3.000
 P84  H91C  C9   N5    114.08  3.000
 P84  I17   C10  C8    119.86  3.000
 P84  I17   C10  C6    119.62  3.000
 P84  C8    C10  C6    120.52  3.000
 P84  H16   O16  C2    112.35  3.000
 P84  H112  C11  H111  106.52  3.000
 P84  H112  C11  C15   109.79  3.000
 P84  H111  C11  C15   109.20  3.000
 P84  H112  C11  N6    108.68  3.000
 P84  H111  C11  N6    111.26  3.000
 P84  C15   C11  N6    111.27  3.000
 P84  H122  C12  H121  106.55  3.000
 P84  H122  C12  N6    108.61  3.000
 P84  H121  C12  N6    111.27  3.000
 P84  H122  C12  C13   109.60  3.000
 P84  H121  C12  C13   109.35  3.000
 P84  N6    C12  C13   111.33  3.000
 P84  H132  C13  H131  107.44  3.000
 P84  H132  C13  C14   109.78  3.000
 P84  H131  C13  C14   110.89  3.000
 P84  H132  C13  C12   109.71  3.000
 P84  H131  C13  C12   108.47  3.000
 P84  C14   C13  C12   110.48  3.000
 P84  H141  C14  C15   107.42  3.000
 P84  H141  C14  C13   106.37  3.000
 P84  C15   C14  C13   109.25  3.000
 P84  H141  C14  N5    105.47  3.000
 P84  C15   C14  N5    115.41  3.000
 P84  C13   C14  N5    112.34  3.000
 P84  C16   N6   C12   111.42  3.000
 P84  C16   N6   C11   111.43  3.000
 P84  C12   N6   C11   111.13  3.000
 P84  H152  C15  H151  107.16  3.000
 P84  H152  C15  C14   110.18  3.000
 P84  H151  C15  C14   110.65  3.000
 P84  H152  C15  C11   109.10  3.000
 P84  H151  C15  C11   108.98  3.000
 P84  C14   C15  C11   110.69  3.000
 P84  H163  C16  H162  107.73  3.000
 P84  H163  C16  H161  107.62  3.000
 P84  H162  C16  H161  107.64  3.000
 P84  H163  C16  N6    110.13  3.000
 P84  H162  C16  N6    110.17  3.000
 P84  H161  C16  N6    113.35  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
 P84  CONST_01  C6    C3   C2   C1      0.00   0.0  0
 P84  CONST_02  C6    C10  C8   C1      0.00   0.0  0
 P84  CONST_03  C10   C8   C1   C2      0.00   0.0  0
 P84  CONST_04  C10   C6   C3   C2      0.00   0.0  0
 P84  CONST_05  C8    C1   C2   C3      0.00   0.0  0
 P84  CONST_06  C8    C10  C6   C3      0.00   0.0  0
 P84  CONST_07  I15   C3   C2   C1    180.00   0.0  0
 P84  CONST_08  I17   C10  C8   C1    180.00   0.0  0
 P84  CONST_09  C4    C1   C2   C3    180.00   0.0  0
 P84  CONST_10  I17   C10  C6   C3    180.00   0.0  0
 P84  CONST_11  C10   C8   C1   C4    180.00   0.0  0
 P84  CONST_12  O16   C2   C3   C6    180.00   0.0  0
 P84  CONST_13  O16   C2   C1   C8    180.00   0.0  0
 P84  CONST_14  I15   C3   C6   C10   180.00   0.0  0
 P84  CONST_15  H8    C8   C1   C2    180.00   0.0  0
 P84  CONST_16  H6    C6   C3   C2    180.00   0.0  0
 P84  Var_01    C13   C12  N6   C11    59.70  30.0  1
 P84  Var_02    C15   C11  N6   C12   -59.36  30.0  1
 P84  Var_03    N6    C12  C13  C14   -57.41  30.0  1
 P84  Var_04    N6    C11  C15  C14    56.78  30.0  1
 P84  Var_05    C14   N5   C4   C1   -152.88  30.0  3
 P84  Var_06    N5    C4   C1   C2     70.43  30.0  2
 P84  Var_07    H161  C16  N6   C11    62.48  30.0  3
 P84  Var_08    H91C  C9   N5   C14   -68.41  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 P84  chir_01  C14  N5  C13  C15  negativ

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
 P84  plan-1  C1   0.020
 P84  plan-1  C2   0.020
 P84  plan-1  C3   0.020
 P84  plan-1  C4   0.020
 P84  plan-1  C6   0.020
 P84  plan-1  C8   0.020
 P84  plan-1  C10  0.020
 P84  plan-1  I15  0.020
 P84  plan-1  O16  0.020
 P84  plan-1  I17  0.020
 P84  plan-1  H8   0.020
 P84  plan-1  H6   0.020

