# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 06:30:39 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: [({4-[4-(propan-2-yloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Oc1ccc(cc1)c2ccnc(NC([P](O)(O)=O)[P](O)(O)=O)c2
#
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
 YS4  YS4  '[({4-[4-(propan-2-yloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)'  ligand  46  26  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YS4
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
 YS4  O5   O  O     0  -0.688  -5.4779   0.4246   0.8590
 YS4  P2   P  P     0   1.398  -4.3488  -0.4378   1.2638
 YS4  O6   O  OH1   0  -0.729  -3.9530  -0.1415   2.7831
 YS4  O7   O  OH1   0  -0.750  -4.5260  -2.0220   1.1028
 YS4  C13  C  CH1   0  -0.658  -2.8294  -0.2078   0.2697
 YS4  P1   P  P     0   1.376  -2.9093  -1.0754  -1.3544
 YS4  O3   O  OH1   0  -0.727  -1.5384  -0.6827  -2.0769
 YS4  O2   O  OH1   0  -0.736  -2.5559  -2.6093  -1.0726
 YS4  O4   O  O     0  -0.690  -4.1614  -0.7756  -2.0842
 YS4  N1   N  NH1   0  -0.687  -2.6620   1.2072   0.0987
 YS4  C12  C  CR6   0   0.509  -1.4611   1.8510  -0.0603
 YS4  C11  C  CR16  0  -0.456  -0.2278   1.2226   0.1413
 YS4  N2   N  N     0  -0.462  -1.5604   3.1344  -0.3995
 YS4  C14  C  CR16  0  -0.056  -0.4380   3.8270  -0.5460
 YS4  C15  C  CR16  0  -0.421   0.8278   3.2993  -0.3850
 YS4  C10  C  CR6   0   0.202   0.9408   1.9490  -0.0378
 YS4  C9   C  CR6   0   0.061   2.2563   1.3017   0.1029
 YS4  C6   C  CR16  0  -0.294   2.4437  -0.0298  -0.2593
 YS4  C5   C  CR16  0  -0.366   3.6794  -0.6508  -0.1536
 YS4  C8   C  CR16  0  -0.289   3.3649   2.0034   0.5842
 YS4  C7   C  CR16  0  -0.339   4.6006   1.3992   0.6991
 YS4  C4   C  CR6   0   0.394   4.7772   0.0637   0.3248
 YS4  O1   O  O2    0  -0.480   6.0237  -0.4193   0.4431
 YS4  C2   C  CH1   0  -0.004   6.3081  -1.7969   0.1712
 YS4  C1   C  CH3   0  -0.665   7.8027  -1.8828  -0.0638
 YS4  C3   C  CH3   0  -0.680   5.8620  -2.6771   1.3268
 YS4  H1   H  HOH1  0   0.498  -3.2695  -0.7055   3.1692
 YS4  H2   H  HOH1  0   0.509  -5.3604  -2.3875   1.4316
 YS4  H3   H  HCH1  0   0.340  -1.9984  -0.6272   0.8422
 YS4  H4   H  HOH1  0   0.503  -1.5982   0.0825  -2.6635
 YS4  H5   H  HOH1  0   0.499  -3.2642  -3.1032  -0.6376
 YS4  H6   H  HNH1  0   0.395  -3.4641   1.7300  -0.2215
 YS4  H7   H  HCR6  0   0.264  -0.1705   0.1851   0.4368
 YS4  H8   H  HCR6  0   0.261  -0.5571   4.8690  -0.8228
 YS4  H9   H  HCR6  0   0.258   1.6976   3.9168  -0.5597
 YS4  H10  H  HCR6  0   0.255   1.6174  -0.6016  -0.6637
 YS4  H11  H  HCR6  0   0.281   3.7636  -1.6839  -0.4603
 YS4  H12  H  HCR6  0   0.257   3.2620   3.0364   0.8924
 YS4  H13  H  HCR6  0   0.264   5.4456   1.9589   1.0802
 YS4  H14  H  HCH1  0   0.232   5.7935  -2.1001  -0.7472
 YS4  H15  H  HCH3  0   0.231   8.3603  -1.5880   0.8266
 YS4  H16  H  HCH3  0   0.236   8.0768  -2.9090  -0.3068
 YS4  H17  H  HCH3  0   0.241   8.1127  -1.2482  -0.8943
 YS4  H18  H  HCH3  0   0.239   6.1077  -3.7178   1.1142
 YS4  H19  H  HCH3  0   0.233   6.3732  -2.3909   2.2475
 YS4  H20  H  HCH3  0   0.242   4.7872  -2.6225   1.5026

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
 YS4  O4   P1   double    1.480  0.020  1.480
 YS4  O2   P1   single    1.599  0.020  1.599
 YS4  P1   O3   single    1.599  0.020  1.599
 YS4  P1   C13  single    1.843  0.020  1.843
 YS4  C14  N2   aromatic  1.327  0.020  1.327
 YS4  C14  C15  aromatic  1.381  0.020  1.381
 YS4  N2   C12  aromatic  1.331  0.020  1.331
 YS4  C15  C10  aromatic  1.399  0.020  1.399
 YS4  C13  N1   single    1.435  0.020  1.435
 YS4  C13  P2   single    1.830  0.020  1.830
 YS4  O5   P2   double    1.477  0.020  1.477
 YS4  C6   C5   aromatic  1.387  0.020  1.387
 YS4  C6   C9   aromatic  1.392  0.020  1.392
 YS4  C12  N1   single    1.372  0.020  1.372
 YS4  C12  C11  aromatic  1.399  0.020  1.399
 YS4  C10  C11  aromatic  1.388  0.020  1.388
 YS4  C10  C9   single    1.473  0.020  1.473
 YS4  C5   C4   aromatic  1.394  0.020  1.394
 YS4  P2   O6   single    1.598  0.020  1.598
 YS4  P2   O7   single    1.602  0.020  1.602
 YS4  C9   C8   aromatic  1.398  0.020  1.398
 YS4  C4   O1   single    1.342  0.020  1.342
 YS4  C4   C7   aromatic  1.398  0.020  1.398
 YS4  C8   C7   aromatic  1.380  0.020  1.380
 YS4  O1   C2   single    1.433  0.020  1.433
 YS4  C1   C2   single    1.515  0.020  1.515
 YS4  C2   C3   single    1.520  0.020  1.520
 YS4  O6   H1   single    0.850  0.020  0.980
 YS4  O7   H2   single    0.850  0.020  0.980
 YS4  C13  H3   single    0.970  0.020  1.090
 YS4  O3   H4   single    0.850  0.020  0.980
 YS4  O2   H5   single    0.850  0.020  0.980
 YS4  N1   H6   single    0.890  0.020  1.040
 YS4  C11  H7   single    0.930  0.020  1.080
 YS4  C14  H8   single    0.930  0.020  1.080
 YS4  C15  H9   single    0.930  0.020  1.080
 YS4  C6   H10  single    0.930  0.020  1.080
 YS4  C5   H11  single    0.930  0.020  1.080
 YS4  C8   H12  single    0.930  0.020  1.080
 YS4  C7   H13  single    0.930  0.020  1.080
 YS4  C2   H14  single    0.970  0.020  1.090
 YS4  C1   H15  single    0.970  0.020  1.090
 YS4  C1   H16  single    0.970  0.020  1.090
 YS4  C1   H17  single    0.970  0.020  1.090
 YS4  C3   H18  single    0.970  0.020  1.090
 YS4  C3   H19  single    0.970  0.020  1.090
 YS4  C3   H20  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
 YS4  C13  P2   O7    99.30  3.000
 YS4  O7   P2   O6   107.84  3.000
 YS4  C13  P2   O6   106.71  3.000
 YS4  O7   P2   O5   117.72  3.000
 YS4  O6   P2   O5   109.97  3.000
 YS4  C13  P2   O5   114.35  3.000
 YS4  H1   O6   P2   116.54  3.000
 YS4  H2   O7   P2   115.75  3.000
 YS4  H3   C13  N1   110.62  3.000
 YS4  H3   C13  P1   108.30  3.000
 YS4  N1   C13  P1   111.36  3.000
 YS4  H3   C13  P2   107.37  3.000
 YS4  N1   C13  P2   106.59  3.000
 YS4  P1   C13  P2   112.55  3.000
 YS4  O4   P1   O2   117.92  3.000
 YS4  O2   P1   O3    97.22  3.000
 YS4  O4   P1   O3   116.93  3.000
 YS4  O3   P1   C13  104.21  3.000
 YS4  O2   P1   C13  106.66  3.000
 YS4  O4   P1   C13  112.08  3.000
 YS4  H4   O3   P1   114.58  3.000
 YS4  H5   O2   P1   114.04  3.000
 YS4  H6   N1   C12  114.56  3.000
 YS4  H6   N1   C13  117.11  3.000
 YS4  C12  N1   C13  125.36  3.000
 YS4  N2   C12  C11  122.39  3.000
 YS4  C11  C12  N1   122.97  3.000
 YS4  N2   C12  N1   114.63  3.000
 YS4  H7   C11  C10  119.56  3.000
 YS4  H7   C11  C12  121.18  3.000
 YS4  C10  C11  C12  119.26  3.000
 YS4  C14  N2   C12  117.92  3.000
 YS4  H8   C14  C15  119.84  3.000
 YS4  H8   C14  N2   115.89  3.000
 YS4  C15  C14  N2   124.26  3.000
 YS4  H9   C15  C10  121.77  3.000
 YS4  H9   C15  C14  120.03  3.000
 YS4  C10  C15  C14  118.16  3.000
 YS4  C9   C10  C15  121.34  3.000
 YS4  C9   C10  C11  120.65  3.000
 YS4  C15  C10  C11  117.99  3.000
 YS4  C8   C9   C6   117.58  3.000
 YS4  C8   C9   C10  121.38  3.000
 YS4  C6   C9   C10  121.04  3.000
 YS4  H10  C6   C5   118.14  3.000
 YS4  H10  C6   C9   119.95  3.000
 YS4  C5   C6   C9   121.88  3.000
 YS4  H11  C5   C4   121.72  3.000
 YS4  H11  C5   C6   118.40  3.000
 YS4  C4   C5   C6   119.88  3.000
 YS4  H12  C8   C7   118.62  3.000
 YS4  H12  C8   C9   120.11  3.000
 YS4  C7   C8   C9   121.27  3.000
 YS4  H13  C7   C4   119.30  3.000
 YS4  H13  C7   C8   120.11  3.000
 YS4  C4   C7   C8   120.59  3.000
 YS4  O1   C4   C7   115.95  3.000
 YS4  C7   C4   C5   118.80  3.000
 YS4  O1   C4   C5   125.24  3.000
 YS4  C2   O1   C4   120.91  3.000
 YS4  H14  C2   C3   109.83  3.000
 YS4  H14  C2   C1   108.52  3.000
 YS4  C3   C2   C1   112.00  3.000
 YS4  H14  C2   O1   109.39  3.000
 YS4  C3   C2   O1   110.75  3.000
 YS4  C1   C2   O1   106.25  3.000
 YS4  H17  C1   H16  107.87  3.000
 YS4  H17  C1   H15  108.60  3.000
 YS4  H16  C1   H15  107.93  3.000
 YS4  H17  C1   C2   111.44  3.000
 YS4  H16  C1   C2   109.64  3.000
 YS4  H15  C1   C2   111.23  3.000
 YS4  H20  C3   H19  108.21  3.000
 YS4  H20  C3   H18  107.55  3.000
 YS4  H19  C3   H18  108.01  3.000
 YS4  H20  C3   C2   112.52  3.000
 YS4  H19  C3   C2   110.62  3.000
 YS4  H18  C3   C2   109.78  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
 YS4  CONST_01  C15  C14  N2   C12     0.00   0.0  0
 YS4  CONST_02  C15  C10  C11  C12     0.00   0.0  0
 YS4  CONST_03  C9   C10  C11  C12   180.00   0.0  0
 YS4  CONST_04  C14  N2   C12  C11     0.00   0.0  0
 YS4  CONST_05  C14  C15  C10  C11     0.00   0.0  0
 YS4  CONST_08  C10  C15  C14  N2      0.00   0.0  0
 YS4  CONST_09  C10  C11  C12  N2      0.00   0.0  0
 YS4  CONST_10  C9   C10  C15  C14   180.00   0.0  0
 YS4  CONST_13  C5   C6   C9   C10   180.00   0.0  0
 YS4  CONST_14  C7   C8   C9   C10   180.00   0.0  0
 YS4  CONST_15  C4   C5   C6   C9      0.00   0.0  0
 YS4  CONST_16  C4   C7   C8   C9      0.00   0.0  0
 YS4  CONST_17  C7   C4   C5   C6      0.00   0.0  0
 YS4  CONST_18  C7   C8   C9   C6      0.00   0.0  0
 YS4  CONST_19  C8   C9   C6   C5      0.00   0.0  0
 YS4  CONST_20  C8   C7   C4   C5      0.00   0.0  0
 YS4  CONST_21  C14  N2   C12  N1    180.00   0.0  0
 YS4  CONST_22  C10  C11  C12  N1    180.00   0.0  0
 YS4  CONST_23  O1   C4   C5   C6    180.00   0.0  0
 YS4  CONST_24  O1   C4   C7   C8    180.00   0.0  0
 YS4  CONST_25  H8   C14  N2   C12   180.00   0.0  0
 YS4  CONST_26  H9   C15  C10  C11   180.00   0.0  0
 YS4  CONST_27  H7   C11  C12  N2    180.00   0.0  0
 YS4  CONST_28  H10  C6   C9   C10     0.00   0.0  0
 YS4  CONST_29  H12  C8   C9   C10     0.00   0.0  0
 YS4  CONST_30  H11  C5   C6   C9    180.00   0.0  0
 YS4  CONST_31  H13  C7   C8   C9    180.00   0.0  0
 YS4  CONST_32  N2   C12  N1   C13   180.00   0.0  0
 YS4  CONST_33  C11  C12  N1   C13     0.00   0.0  0
 YS4  CONST_34  H6   N1   C12  C11   180.00   0.0  0
 YS4  Var_01    C12  N1   C13  P2    150.98  30.0  3
 YS4  Var_02    C1   C2   O1   C4    161.05  30.0  3
 YS4  Var_03    P1   C13  P2   O5    -79.18  30.0  3
 YS4  Var_04    O4   P1   C13  P2     49.73  30.0  2
 YS4  Var_05    H15  C1   C2   O1     62.40  30.0  3
 YS4  Var_06    H18  C3   C2   O1   -178.62  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
 YS4  plan-1  N1   0.020
 YS4  plan-1  C12  0.020
 YS4  plan-1  C11  0.020
 YS4  plan-1  N2   0.020
 YS4  plan-1  C14  0.020
 YS4  plan-1  C15  0.020
 YS4  plan-1  C10  0.020
 YS4  plan-1  C9   0.020
 YS4  plan-1  H7   0.020
 YS4  plan-1  H8   0.020
 YS4  plan-1  H9   0.020
 YS4  plan-2  C10  0.020
 YS4  plan-2  C9   0.020
 YS4  plan-2  C6   0.020
 YS4  plan-2  C5   0.020
 YS4  plan-2  C8   0.020
 YS4  plan-2  C7   0.020
 YS4  plan-2  C4   0.020
 YS4  plan-2  O1   0.020
 YS4  plan-2  H10  0.020
 YS4  plan-2  H11  0.020
 YS4  plan-2  H12  0.020
 YS4  plan-2  H13  0.020
 YS4  plan-3  C13  0.020
 YS4  plan-3  N1   0.020
 YS4  plan-3  C12  0.020
 YS4  plan-3  H6   0.020

