# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 22:51:59 2021
#   Inital geometry file: a 135 line input string
#   Ligand name: (2~{S})-2-[[[(3~{R})-3-acetamido-4-(ethylamino)-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)[C@@H](CC[P@@](=O)(C[C@@H](CCC(O)=O)C(O)=O)O[P](O)(O)=O)NC(C)=O
#
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
 2TI  2TI  '(2~{S})-2-[[[(3~{R})-3-acetamido-4-(ethylamino)-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid'  ligand  55  29  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2TI
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
 2TI  C02  C  CH1   0  -0.229  11.5758  16.2216  72.8503
 2TI  C03  C  C     0   0.550  12.2943  16.6241  71.5634
 2TI  C06  C  CH2   0  -0.299  14.5249  16.8905  70.5714
 2TI  C07  C  CH3   0  -0.660  14.9642  18.3297  70.7965
 2TI  C08  C  CH2   0  -0.424  11.7532  17.3367  73.8883
 2TI  C09  C  CH2   0  -0.742  11.3121  16.8848  75.2831
 2TI  C17  C  CH2   0  -0.716  11.5853  17.2103  78.1669
 2TI  C18  C  CH1   0  -0.374  12.4521  17.6335  79.3600
 2TI  C19  C  C     0   0.554  12.0799  16.7724  80.5496
 2TI  C22  C  CH2   0  -0.429  12.2523  19.1117  79.7239
 2TI  C23  C  CH2   0  -0.592  13.1570  19.5607  80.8604
 2TI  C24  C  C     0   0.556  13.0879  21.0418  81.1148
 2TI  C28  C  CH3   0  -0.775   8.0837  14.7809  72.6287
 2TI  N01  N  NH1   0  -0.620  10.1916  15.9453  72.5792
 2TI  N05  N  NH1   0  -0.631  13.6160  16.4141  71.5941
 2TI  O04  O  O     0  -0.490  11.6977  17.1225  70.6199
 2TI  O11  O  O     0  -0.685  12.0160  19.3373  76.3821
 2TI  O12  O  O2    0  -0.713  13.7146  17.4384  76.4735
 2TI  O14  O  OH1   0  -0.715  15.9588  16.4038  76.6634
 2TI  O15  O  O     0  -0.680  14.4319  15.6768  74.6879
 2TI  O16  O  OH1   0  -0.732  13.8918  15.0988  77.1784
 2TI  O20  O  O     0  -0.436  10.9467  16.6045  80.9255
 2TI  O21  O  OH1   0  -0.582  13.1366  16.2435  81.1483
 2TI  O25  O  OH1   0  -0.596  13.8839  21.4039  82.1150
 2TI  O26  O  O     0  -0.442  12.4032  21.8216  80.5013
 2TI  O29  O  O     0  -0.504  10.0490  14.0193  73.7556
 2TI  P10  P  P     0   1.260  12.1178  17.8655  76.5651
 2TI  P13  P  P     0   1.483  14.5071  16.0922  76.1024
 2TI  H1   H  HCH1  0   0.282  12.0318  15.3082  73.2369
 2TI  H2   H  HCH2  0   0.243  14.0447  16.7854  69.5993
 2TI  H3   H  HCH2  0   0.249  15.3896  16.2274  70.5708
 2TI  H4   H  HCH3  0   0.232  15.6663  18.6382  70.0215
 2TI  H5   H  HCH3  0   0.230  14.1123  19.0092  70.7703
 2TI  H6   H  HCH3  0   0.226  15.4601  18.4411  71.7614
 2TI  H7   H  HCH2  0   0.253  12.8030  17.6308  73.8886
 2TI  H8   H  HCH2  0   0.269  11.1877  18.2185  73.5822
 2TI  H9   H  HCH2  0   0.312  10.2331  16.9968  75.4123
 2TI  H10  H  HCH2  0   0.285  11.5303  15.8267  75.4490
 2TI  H11  H  HCH2  0   0.306  10.5502  17.5343  78.3048
 2TI  H12  H  HCH2  0   0.306  11.5619  16.1223  78.0716
 2TI  H13  H  HCH1  0   0.283  13.5067  17.4657  79.1308
 2TI  H14  H  HCH2  0   0.268  12.4556  19.7136  78.8392
 2TI  H15  H  HCH2  0   0.248  11.2033  19.2779  79.9802
 2TI  H16  H  HCH2  0   0.285  12.9154  19.0548  81.8011
 2TI  H17  H  HCH2  0   0.287  14.1987  19.3003  80.6477
 2TI  H18  H  HCH3  0   0.266   7.8905  13.8024  72.1904
 2TI  H19  H  HCH3  0   0.268   7.4516  14.8707  73.5125
 2TI  H20  H  HCH3  0   0.249   7.7856  15.5468  71.9153
 2TI  H21  H  HNH1  0   0.398   9.7040  16.5967  71.9843
 2TI  H22  H  HNH1  0   0.406  14.0212  16.0520  72.4458
 2TI  H23  H  HOH1  0   0.508  16.5949  16.6878  75.9924
 2TI  H24  H  HOH1  0   0.510  14.0596  14.1604  77.0117
 2TI  H25  H  HOH1  0   0.483  12.8595  15.7347  81.9263
 2TI  H26  H  HOH1  0   0.480  13.8194  22.3595  82.2612
 2TI  C27  C  C     0   0.530   9.5309  14.8680  73.0425

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
 2TI  C06  C07  single  1.521  0.020  1.521
 2TI  C06  N05  single  1.449  0.020  1.449
 2TI  N05  C03  single  1.339  0.020  1.339
 2TI  O04  C03  double  1.223  0.020  1.223
 2TI  C03  C02  single  1.528  0.020  1.528
 2TI  C02  N01  single  1.437  0.020  1.437
 2TI  C02  C08  single  1.534  0.020  1.534
 2TI  N01  C27  single  1.346  0.020  1.346
 2TI  C28  C27  single  1.508  0.020  1.508
 2TI  C27  O29  double  1.224  0.020  1.224
 2TI  C08  C09  single  1.531  0.020  1.531
 2TI  C09  P10  single  1.804  0.020  1.804
 2TI  O15  P13  double  1.476  0.020  1.476
 2TI  O12  P10  single  1.656  0.020  1.656
 2TI  O12  P13  single  1.606  0.020  1.606
 2TI  O11  P10  double  1.487  0.020  1.487
 2TI  P10  C17  single  1.811  0.020  1.811
 2TI  P13  O14  single  1.587  0.020  1.587
 2TI  P13  O16  single  1.588  0.020  1.588
 2TI  C17  C18  single  1.534  0.020  1.534
 2TI  C18  C22  single  1.535  0.020  1.535
 2TI  C18  C19  single  1.515  0.020  1.515
 2TI  C22  C23  single  1.521  0.020  1.521
 2TI  C19  O20  double  1.206  0.020  1.206
 2TI  C19  O21  single  1.325  0.020  1.325
 2TI  O26  C24  double  1.205  0.020  1.205
 2TI  C23  C24  single  1.504  0.020  1.504
 2TI  C24  O25  single  1.329  0.020  1.329
 2TI  C02  H1   single  0.970  0.020  1.090
 2TI  C06  H2   single  0.970  0.020  1.090
 2TI  C06  H3   single  0.970  0.020  1.090
 2TI  C07  H4   single  0.970  0.020  1.090
 2TI  C07  H5   single  0.970  0.020  1.090
 2TI  C07  H6   single  0.970  0.020  1.090
 2TI  C08  H7   single  0.970  0.020  1.090
 2TI  C08  H8   single  0.970  0.020  1.090
 2TI  C09  H9   single  0.970  0.020  1.090
 2TI  C09  H10  single  0.970  0.020  1.090
 2TI  C17  H11  single  0.970  0.020  1.090
 2TI  C17  H12  single  0.970  0.020  1.090
 2TI  C18  H13  single  0.970  0.020  1.090
 2TI  C22  H14  single  0.970  0.020  1.090
 2TI  C22  H15  single  0.970  0.020  1.090
 2TI  C23  H16  single  0.970  0.020  1.090
 2TI  C23  H17  single  0.970  0.020  1.090
 2TI  C28  H18  single  0.970  0.020  1.090
 2TI  C28  H19  single  0.970  0.020  1.090
 2TI  C28  H20  single  0.970  0.020  1.090
 2TI  N01  H21  single  0.860  0.020  1.020
 2TI  N05  H22  single  0.860  0.020  1.020
 2TI  O14  H23  single  0.850  0.020  0.980
 2TI  O16  H24  single  0.850  0.020  0.980
 2TI  O21  H25  single  0.850  0.020  0.980
 2TI  O25  H26  single  0.850  0.020  0.980

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
 2TI  H1   C02  N01  107.95  3.000
 2TI  H1   C02  C08  108.69  3.000
 2TI  N01  C02  C08  112.26  3.000
 2TI  H1   C02  C03  108.80  3.000
 2TI  C08  C02  C03  108.91  3.000
 2TI  N01  C02  C03  110.16  3.000
 2TI  O04  C03  N05  124.29  3.000
 2TI  O04  C03  C02  121.87  3.000
 2TI  N05  C03  C02  113.81  3.000
 2TI  H3   C06  H2   106.89  3.000
 2TI  H3   C06  N05  107.35  3.000
 2TI  H2   C06  N05  108.76  3.000
 2TI  H3   C06  C07  110.28  3.000
 2TI  H2   C06  C07  110.52  3.000
 2TI  N05  C06  C07  112.81  3.000
 2TI  H6   C07  H5   108.24  3.000
 2TI  H6   C07  H4   107.89  3.000
 2TI  H5   C07  H4   108.05  3.000
 2TI  H6   C07  C06  111.02  3.000
 2TI  H5   C07  C06  111.13  3.000
 2TI  H4   C07  C06  110.39  3.000
 2TI  H8   C08  H7   106.33  3.000
 2TI  H8   C08  C09  110.16  3.000
 2TI  H7   C08  C09  110.90  3.000
 2TI  H8   C08  C02  109.74  3.000
 2TI  H7   C08  C02  107.92  3.000
 2TI  C09  C08  C02  111.63  3.000
 2TI  H10  C09  H9   106.17  3.000
 2TI  H10  C09  P10  109.22  3.000
 2TI  H9   C09  P10  107.54  3.000
 2TI  H10  C09  C08  111.50  3.000
 2TI  H9   C09  C08  111.22  3.000
 2TI  P10  C09  C08  111.00  3.000
 2TI  H12  C17  H11  106.61  3.000
 2TI  H12  C17  P10  106.83  3.000
 2TI  H11  C17  P10  106.43  3.000
 2TI  H12  C17  C18  110.77  3.000
 2TI  H11  C17  C18  110.79  3.000
 2TI  P10  C17  C18  114.96  3.000
 2TI  H13  C18  C22  108.87  3.000
 2TI  H13  C18  C19  108.34  3.000
 2TI  C22  C18  C19  109.22  3.000
 2TI  H13  C18  C17  109.87  3.000
 2TI  C19  C18  C17  108.36  3.000
 2TI  C22  C18  C17  112.11  3.000
 2TI  O21  C19  O20  123.59  3.000
 2TI  O21  C19  C18  112.70  3.000
 2TI  O20  C19  C18  123.70  3.000
 2TI  H15  C22  H14  106.60  3.000
 2TI  H15  C22  C23  110.55  3.000
 2TI  H14  C22  C23  109.44  3.000
 2TI  H15  C22  C18  109.09  3.000
 2TI  H14  C22  C18  108.38  3.000
 2TI  C23  C22  C18  112.58  3.000
 2TI  H17  C23  H16  105.49  3.000
 2TI  H17  C23  C24  108.11  3.000
 2TI  H16  C23  C24  107.42  3.000
 2TI  H17  C23  C22  110.53  3.000
 2TI  H16  C23  C22  111.98  3.000
 2TI  C24  C23  C22  112.94  3.000
 2TI  O26  C24  O25  123.17  3.000
 2TI  O25  C24  C23  111.59  3.000
 2TI  O26  C24  C23  125.23  3.000
 2TI  H20  C28  H19  108.34  3.000
 2TI  H20  C28  H18  108.66  3.000
 2TI  H19  C28  H18  107.30  3.000
 2TI  H20  C28  C27  113.71  3.000
 2TI  H19  C28  C27  109.22  3.000
 2TI  H18  C28  C27  109.42  3.000
 2TI  H21  N01  C27  118.87  3.000
 2TI  H21  N01  C02  116.94  3.000
 2TI  C27  N01  C02  124.17  3.000
 2TI  H22  N05  C06  117.47  3.000
 2TI  H22  N05  C03  118.13  3.000
 2TI  C06  N05  C03  123.49  3.000
 2TI  P13  O12  P10  134.84  3.000
 2TI  H23  O14  P13  114.45  3.000
 2TI  H24  O16  P13  114.99  3.000
 2TI  H25  O21  C19  110.12  3.000
 2TI  H26  O25  C24  110.02  3.000
 2TI  O12  P10  O11  108.34  3.000
 2TI  O11  P10  C17  116.55  3.000
 2TI  O12  P10  C17  103.84  3.000
 2TI  C17  P10  C09  107.50  3.000
 2TI  O11  P10  C09  114.84  3.000
 2TI  O12  P10  C09  104.55  3.000
 2TI  O16  P13  O15  116.96  3.000
 2TI  O16  P13  O14  103.75  3.000
 2TI  O15  P13  O14  116.14  3.000
 2TI  O16  P13  O12  100.17  3.000
 2TI  O14  P13  O12  101.84  3.000
 2TI  O15  P13  O12  115.61  3.000
 2TI  O29  C27  N01  123.22  3.000
 2TI  O29  C27  C28  121.76  3.000
 2TI  N01  C27  C28  115.02  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
 2TI  CONST_01  C06  N05  C03  C02  180.00   0.0  0
 2TI  CONST_02  C28  C27  N01  C02  180.00   0.0  0
 2TI  CONST_03  O29  C27  N01  C02    0.00   0.0  0
 2TI  CONST_04  O04  C03  N05  C06    0.00   0.0  0
 2TI  CONST_05  H22  N05  C03  C02    0.00   0.0  0
 2TI  CONST_06  H21  N01  C27  C28    0.00   0.0  0
 2TI  CONST_07  H25  O21  C19  C18  180.00   0.0  0
 2TI  CONST_08  H26  O25  C24  C23  180.00   0.0  0
 2TI  Var_01    P10  C09  C08  C02  156.48  30.0  3
 2TI  Var_02    C07  C06  N05  C03   84.49  30.0  2
 2TI  Var_03    O12  P10  C09  C08  -67.75  30.0  3
 2TI  Var_04    C18  C17  P10  C09  163.26  30.0  3
 2TI  Var_05    C24  C23  C22  C18  173.15  30.0  3
 2TI  Var_06    O26  C24  C23  C22   -0.21  30.0  3
 2TI  Var_07    H18  C28  C27  N01  128.06  30.0  3
 2TI  Var_08    H4   C07  C06  N05  178.47  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
 2TI  chir_01  C02  C03  N01  C08  positiv
 2TI  chir_02  C18  C17  C22  C19  negativ
 2TI  chir_03  P10  O12  O11  C17  both

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
 2TI  plan-1  C02  0.020
 2TI  plan-1  C03  0.020
 2TI  plan-1  C06  0.020
 2TI  plan-1  N05  0.020
 2TI  plan-1  O04  0.020
 2TI  plan-1  H22  0.020
 2TI  plan-2  C02  0.020
 2TI  plan-2  C28  0.020
 2TI  plan-2  N01  0.020
 2TI  plan-2  O29  0.020
 2TI  plan-2  H21  0.020
 2TI  plan-2  C27  0.020
 2TI  plan-3  C18  0.020
 2TI  plan-3  C19  0.020
 2TI  plan-3  O20  0.020
 2TI  plan-3  O21  0.020
 2TI  plan-3  H25  0.020
 2TI  plan-4  C23  0.020
 2TI  plan-4  C24  0.020
 2TI  plan-4  O25  0.020
 2TI  plan-4  O26  0.020
 2TI  plan-4  H26  0.020

