# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 01:16:11 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: [(3~{S})-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-[2-(prop-2-enoylamino)ethylamino]propyl]amino]butyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P](O)(O)=O)[C@H](O)C(=O)NCCC(=O)NCCNC(=O)C=C
#
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
 6W5  6W5  '[(3~{S})-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-[2-(prop-2-enoylamino)ethylamino]propyl]amino]butyl] dihydrogen phosphate'  ligand  52  26  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6W5
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
 6W5  C13  C  CT    0  -0.202  -3.5283   0.4041   0.0604
 6W5  C26  C  C2    0  -0.473  11.0215   0.9526   0.2017
 6W5  C01  C  C1    0  -0.328  10.1511  -0.0419   0.3287
 6W5  C02  C  C     0   0.537   8.7343   0.1021  -0.1020
 6W5  N03  N  NH1   0  -0.646   7.9900  -1.0047   0.0724
 6W5  C04  C  CH2   0  -0.293   6.5843  -1.0743  -0.2432
 6W5  C05  C  CH2   0  -0.296   5.7097  -0.5478   0.8974
 6W5  N06  N  NH1   0  -0.636   4.3032  -0.7039   0.6129
 6W5  C07  C  C     0   0.565   3.5806   0.1939  -0.0780
 6W5  C08  C  CH2   0  -0.630   2.1622  -0.2340  -0.3904
 6W5  C09  C  CH2   0  -0.232   1.1934   0.9366  -0.3678
 6W5  N10  N  NH1   0  -0.637  -0.1264   0.4775  -0.7446
 6W5  C11  C  C     0   0.520  -1.2092   1.2567  -0.6527
 6W5  C12  C  CH1   0  -0.033  -2.5298   0.6236  -1.1109
 6W5  C14  C  CH2   0  -0.134  -4.7545  -0.2870  -0.5556
 6W5  O15  O  O2    0  -0.590  -5.7463  -0.5030   0.4548
 6W5  P16  P  P     0   1.449  -7.2731  -0.1416   0.1812
 6W5  O17  O  O     0  -0.708  -7.5741   1.2359  -0.2506
 6W5  C18  C  CH3   0  -0.669  -2.9134  -0.4760   1.1523
 6W5  C19  C  CH3   0  -0.648  -3.9699   1.7427   0.6553
 6W5  O20  O  OH1   0  -0.741  -7.8043  -1.1705  -0.9224
 6W5  O22  O  OH1   0  -0.662  -2.3119  -0.5472  -1.8649
 6W5  O23  O  O     0  -0.494  -1.1640   2.4050  -0.2306
 6W5  O24  O  O     0  -0.496   4.0291   1.2694  -0.4483
 6W5  O25  O  O     0  -0.495   8.2890   1.1365  -0.5816
 6W5  O1   O  OH1   0  -0.731  -7.8299  -0.6082   1.6003
 6W5  H1   H  H     0   0.257  10.7362   1.9072  -0.2212
 6W5  H2   H  H     0   0.260  12.0497   0.8414   0.5167
 6W5  H3   H  H     0   0.269  10.4615  -0.9900   0.7537
 6W5  H4   H  HNH1  0   0.406   8.4120  -1.8106   0.5041
 6W5  H5   H  HCH2  0   0.250   6.3846  -0.5075  -1.1527
 6W5  H6   H  HCH2  0   0.256   6.3373  -2.1167  -0.4448
 6W5  H7   H  HCH2  0   0.255   5.9332  -1.0933   1.8145
 6W5  H8   H  HCH2  0   0.252   5.9293   0.5037   1.0781
 6W5  H9   H  HNH1  0   0.404   3.8728  -1.5795   0.8619
 6W5  H10  H  HCH2  0   0.283   2.1751  -0.6835  -1.3896
 6W5  H11  H  HCH2  0   0.268   1.8284  -1.0141   0.2974
 6W5  H12  H  HCH2  0   0.246   1.1517   1.3692   0.6336
 6W5  H13  H  HCH2  0   0.244   1.5355   1.7229  -1.0439
 6W5  H14  H  HNH1  0   0.398  -0.2042  -0.4009  -1.2313
 6W5  H15  H  HCH1  0   0.271  -2.9823   1.3443  -1.8009
 6W5  H16  H  HCH2  0   0.243  -5.1474   0.3334  -1.3681
 6W5  H17  H  HCH2  0   0.250  -4.5041  -1.2630  -0.9709
 6W5  H18  H  HCH3  0   0.226  -2.6314  -1.4691   0.7923
 6W5  H19  H  HCH3  0   0.246  -2.0242  -0.0132   1.5821
 6W5  H20  H  HCH3  0   0.254  -3.6205  -0.6262   1.9674
 6W5  H21  H  HCH3  0   0.235  -4.7299   1.5819   1.4183
 6W5  H22  H  HCH3  0   0.248  -3.1445   2.2706   1.1237
 6W5  H23  H  HCH3  0   0.227  -4.3970   2.3937  -0.1103
 6W5  H24  H  HOH1  0   0.495  -7.6676  -2.1065  -0.7231
 6W5  H25  H  HOH1  0   0.455  -2.2191  -1.3077  -1.2804
 6W5  H26  H  HOH1  0   0.503  -8.7411  -0.3364   1.7727

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
 6W5  C26  C01  double  1.328  0.020  1.328
 6W5  C01  C02  single  1.488  0.020  1.488
 6W5  C02  O25  double  1.224  0.020  1.224
 6W5  C02  N03  single  1.345  0.020  1.345
 6W5  C18  C13  single  1.531  0.020  1.531
 6W5  N03  C04  single  1.442  0.020  1.442
 6W5  C19  C13  single  1.530  0.020  1.530
 6W5  C13  C14  single  1.536  0.020  1.536
 6W5  C13  C12  single  1.555  0.020  1.555
 6W5  C04  C05  single  1.531  0.020  1.531
 6W5  O22  C12  single  1.410  0.020  1.410
 6W5  C14  O15  single  1.432  0.020  1.432
 6W5  N10  C09  single  1.447  0.020  1.447
 6W5  N10  C11  single  1.337  0.020  1.337
 6W5  C12  C11  single  1.535  0.020  1.535
 6W5  O24  C07  double  1.223  0.020  1.223
 6W5  C05  N06  single  1.443  0.020  1.443
 6W5  C09  C08  single  1.520  0.020  1.520
 6W5  C11  O23  double  1.224  0.020  1.224
 6W5  O15  P16  single  1.593  0.020  1.593
 6W5  C07  N06  single  1.344  0.020  1.344
 6W5  C07  C08  single  1.514  0.020  1.514
 6W5  P16  O17  double  1.475  0.020  1.475
 6W5  P16  O20  single  1.599  0.020  1.599
 6W5  P16  O1   single  1.594  0.020  1.594
 6W5  C26  H1   single  0.930  0.020  1.080
 6W5  C26  H2   single  0.930  0.020  1.080
 6W5  C01  H3   single  0.930  0.020  1.080
 6W5  N03  H4   single  0.860  0.020  1.020
 6W5  C04  H5   single  0.970  0.020  1.090
 6W5  C04  H6   single  0.970  0.020  1.090
 6W5  C05  H7   single  0.970  0.020  1.090
 6W5  C05  H8   single  0.970  0.020  1.090
 6W5  N06  H9   single  0.860  0.020  1.020
 6W5  C08  H10  single  0.970  0.020  1.090
 6W5  C08  H11  single  0.970  0.020  1.090
 6W5  C09  H12  single  0.970  0.020  1.090
 6W5  C09  H13  single  0.970  0.020  1.090
 6W5  N10  H14  single  0.860  0.020  1.020
 6W5  C12  H15  single  0.970  0.020  1.090
 6W5  C14  H16  single  0.970  0.020  1.090
 6W5  C14  H17  single  0.970  0.020  1.090
 6W5  C18  H18  single  0.970  0.020  1.090
 6W5  C18  H19  single  0.970  0.020  1.090
 6W5  C18  H20  single  0.970  0.020  1.090
 6W5  C19  H21  single  0.970  0.020  1.090
 6W5  C19  H22  single  0.970  0.020  1.090
 6W5  C19  H23  single  0.970  0.020  1.090
 6W5  O20  H24  single  0.850  0.020  0.980
 6W5  O22  H25  single  0.850  0.020  0.980
 6W5  O1   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
 6W5  C19  C13  C18  109.97  3.000
 6W5  C19  C13  C14  108.61  3.000
 6W5  C18  C13  C14  110.35  3.000
 6W5  C14  C13  C12  105.91  3.000
 6W5  C19  C13  C12  110.78  3.000
 6W5  C18  C13  C12  111.13  3.000
 6W5  H2   C26  H1   117.08  3.000
 6W5  H2   C26  C01  121.24  3.000
 6W5  H1   C26  C01  121.68  3.000
 6W5  H3   C01  C02  118.08  3.000
 6W5  H3   C01  C26  120.31  3.000
 6W5  C02  C01  C26  121.61  3.000
 6W5  O25  C02  N03  123.01  3.000
 6W5  N03  C02  C01  114.19  3.000
 6W5  O25  C02  C01  122.79  3.000
 6W5  H4   N03  C04  117.62  3.000
 6W5  H4   N03  C02  118.83  3.000
 6W5  C04  N03  C02  123.41  3.000
 6W5  H6   C04  H5   107.54  3.000
 6W5  H6   C04  C05  109.71  3.000
 6W5  H5   C04  C05  109.76  3.000
 6W5  H6   C04  N03  107.91  3.000
 6W5  H5   C04  N03  109.63  3.000
 6W5  C05  C04  N03  112.16  3.000
 6W5  H8   C05  H7   107.59  3.000
 6W5  H8   C05  N06  109.48  3.000
 6W5  H7   C05  N06  108.15  3.000
 6W5  H8   C05  C04  109.91  3.000
 6W5  H7   C05  C04  109.73  3.000
 6W5  N06  C05  C04  111.88  3.000
 6W5  H9   N06  C07  118.57  3.000
 6W5  H9   N06  C05  117.50  3.000
 6W5  C07  N06  C05  123.58  3.000
 6W5  O24  C07  C08  121.99  3.000
 6W5  C08  C07  N06  114.90  3.000
 6W5  O24  C07  N06  123.10  3.000
 6W5  H11  C08  H10  106.55  3.000
 6W5  H11  C08  C09  110.24  3.000
 6W5  H10  C08  C09  109.70  3.000
 6W5  H11  C08  C07  110.99  3.000
 6W5  H10  C08  C07  107.04  3.000
 6W5  C09  C08  C07  112.11  3.000
 6W5  H13  C09  H12  107.13  3.000
 6W5  H13  C09  N10  110.66  3.000
 6W5  H12  C09  N10  109.25  3.000
 6W5  H13  C09  C08  110.23  3.000
 6W5  H12  C09  C08  110.08  3.000
 6W5  N10  C09  C08  109.46  3.000
 6W5  H14  N10  C11  118.61  3.000
 6W5  H14  N10  C09  118.22  3.000
 6W5  C11  N10  C09  122.39  3.000
 6W5  O23  C11  C12  121.45  3.000
 6W5  O23  C11  N10  122.71  3.000
 6W5  C12  C11  N10  115.84  3.000
 6W5  H15  C12  O22  105.86  3.000
 6W5  H15  C12  C11  105.79  3.000
 6W5  O22  C12  C11  111.68  3.000
 6W5  H15  C12  C13  107.58  3.000
 6W5  C11  C12  C13  112.71  3.000
 6W5  O22  C12  C13  112.65  3.000
 6W5  H17  C14  H16  107.88  3.000
 6W5  H17  C14  O15  107.03  3.000
 6W5  H16  C14  O15  111.13  3.000
 6W5  H17  C14  C13  111.85  3.000
 6W5  H16  C14  C13  109.20  3.000
 6W5  O15  C14  C13  109.74  3.000
 6W5  P16  O15  C14  120.56  3.000
 6W5  O1   P16  O20  108.06  3.000
 6W5  O1   P16  O17  117.56  3.000
 6W5  O20  P16  O17  109.33  3.000
 6W5  O1   P16  O15   96.63  3.000
 6W5  O20  P16  O15  106.92  3.000
 6W5  O17  P16  O15  117.25  3.000
 6W5  H20  C18  H19  107.02  3.000
 6W5  H20  C18  H18  106.77  3.000
 6W5  H19  C18  H18  107.75  3.000
 6W5  H20  C18  C13  110.62  3.000
 6W5  H19  C18  C13  111.38  3.000
 6W5  H18  C18  C13  113.01  3.000
 6W5  H23  C19  H22  108.06  3.000
 6W5  H23  C19  H21  107.84  3.000
 6W5  H22  C19  H21  107.46  3.000
 6W5  H23  C19  C13  111.21  3.000
 6W5  H22  C19  C13  111.94  3.000
 6W5  H21  C19  C13  110.16  3.000
 6W5  H24  O20  P16  115.70  3.000
 6W5  H25  O22  C12  110.23  3.000
 6W5  H26  O1   P16  113.94  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
 6W5  CONST_01  C04  N03  C02  C01   180.00   0.0  0
 6W5  CONST_02  O25  C02  N03  C04     0.00   0.0  0
 6W5  CONST_03  O24  C07  N06  C05     0.00   0.0  0
 6W5  CONST_04  C08  C07  N06  C05   180.00   0.0  0
 6W5  CONST_05  C12  C11  N10  C09   180.00   0.0  0
 6W5  CONST_06  O23  C11  N10  C09     0.00   0.0  0
 6W5  CONST_07  H4   N03  C02  C01     0.00   0.0  0
 6W5  CONST_08  H9   N06  C07  C08     0.00   0.0  0
 6W5  CONST_09  H14  N10  C11  C12     0.00   0.0  0
 6W5  Var_01    O25  C02  C01  C26    -0.69  30.0  2
 6W5  Var_02    C05  C04  N03  C02   -84.21  30.0  3
 6W5  Var_03    N06  C05  C04  N03  -176.07  30.0  3
 6W5  Var_04    C07  N06  C05  C04   -86.13  30.0  3
 6W5  Var_05    C09  C08  C07  N06   145.36  30.0  3
 6W5  Var_06    N10  C09  C08  C07   176.88  30.0  1
 6W5  Var_07    C11  N10  C09  C08   171.61  30.0  1
 6W5  Var_08    O15  C14  C13  C12  -178.73  30.0  3
 6W5  Var_09    O17  P16  O15  C14   -55.02  30.0  3
 6W5  Var_10    H1   C26  C01  C02    -0.08   0.0  2
 6W5  Var_11    H18  C18  C13  C12   -60.23  30.0  3
 6W5  Var_12    H21  C19  C13  C12   175.34  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
 6W5  chir_01  C12  C13  O22  C11  positiv

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
 6W5  plan-1  C01  0.020
 6W5  plan-1  C02  0.020
 6W5  plan-1  N03  0.020
 6W5  plan-1  C04  0.020
 6W5  plan-1  O25  0.020
 6W5  plan-1  H4   0.020
 6W5  plan-2  C05  0.020
 6W5  plan-2  N06  0.020
 6W5  plan-2  C07  0.020
 6W5  plan-2  C08  0.020
 6W5  plan-2  O24  0.020
 6W5  plan-2  H9   0.020
 6W5  plan-3  C09  0.020
 6W5  plan-3  N10  0.020
 6W5  plan-3  C11  0.020
 6W5  plan-3  C12  0.020
 6W5  plan-3  O23  0.020
 6W5  plan-3  H14  0.020
 6W5  plan-4  C26  0.020
 6W5  plan-4  C01  0.020
 6W5  plan-4  C02  0.020
 6W5  plan-4  H1   0.020
 6W5  plan-4  H2   0.020
 6W5  plan-4  H3   0.020

