# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 06:54:03 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: [(3~{R})-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(2-sulfanylethylamino)propyl]amino]butoxy]phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[PH](O)=O)[C@@H](O)C(=O)NCCC(=O)NCCS
#
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
 5PD  5PD  '[(3~{R})-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(2-sulfanylethylamino)propyl]amino]butoxy]phosphinic acid'  ligand  44  21  .  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_5PD
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
 5PD  C10  C  C     0   0.522   1.0142  -1.3882   0.4891
 5PD  C15  C  CH3   0  -0.647   4.1913  -1.5966  -1.7272
 5PD  C17  C  CH2   0  -0.155   3.8082  -0.1048   0.2557
 5PD  O21  O  O     0  -0.708   5.8794   1.9111   1.7922
 5PD  P19  P  P     0   1.128   5.1164   2.1343   0.5430
 5PD  O20  O  OH1   0  -0.733   5.8635   2.9285  -0.6272
 5PD  O18  O  O2    0  -0.584   4.7277   0.8381  -0.3094
 5PD  C14  C  CT    0  -0.156   3.1370  -0.8795  -0.8774
 5PD  C16  C  CH3   0  -0.671   2.3366   0.0715  -1.7696
 5PD  C12  C  CH1   0  -0.035   2.1969  -1.9683  -0.2861
 5PD  O13  O  OH1   0  -0.660   2.8731  -2.8795   0.5378
 5PD  O11  O  O     0  -0.498   1.1355  -1.0915   1.6728
 5PD  N09  N  NH1   0  -0.639  -0.1267  -1.2489  -0.1875
 5PD  C08  C  CH2   0  -0.237  -1.3235  -0.6751   0.3944
 5PD  C07  C  CH2   0  -0.625  -2.4718  -0.7773  -0.5988
 5PD  C02  C  C     0   0.560  -3.7327  -0.1495  -0.0432
 5PD  O01  O  O     0  -0.496  -3.7236   0.9537   0.4841
 5PD  N03  N  NH1   0  -0.630  -4.8444  -0.8912  -0.1747
 5PD  C04  C  CH2   0  -0.283  -6.1533  -0.4491   0.2412
 5PD  C05  C  CH2   0  -0.553  -6.8672   0.3243  -0.8609
 5PD  S06  S  S2    0  -0.258  -8.5129   0.8148  -0.2458
 5PD  H1   H  HCH3  0   0.236   4.8257  -2.2489  -1.1273
 5PD  H2   H  HCH3  0   0.231   3.7079  -2.2093  -2.4913
 5PD  H3   H  HCH3  0   0.240   4.8333  -0.8844  -2.2445
 5PD  H4   H  HCH2  0   0.246   4.3610  -0.7789   0.9140
 5PD  H5   H  HCH2  0   0.242   3.0595   0.4189   0.8593
 5PD  H6   H  HOH1  0   0.500   6.4031   3.6641  -0.3095
 5PD  H7   H  HCH3  0   0.235   1.7508  -0.4822  -2.5063
 5PD  H8   H  HCH3  0   0.235   1.6515   0.7054  -1.2047
 5PD  H9   H  HCH3  0   0.249   3.0052   0.7273  -2.3254
 5PD  H10  H  HCH1  0   0.258   1.8157  -2.5350  -1.1429
 5PD  H11  H  HOH1  0   0.447   2.8575  -2.5386   1.4409
 5PD  H12  H  HNH1  0   0.408  -0.1584  -1.5479  -1.1491
 5PD  H13  H  HCH2  0   0.253  -1.5769  -1.2092   1.3128
 5PD  H14  H  HCH2  0   0.250  -1.1477   0.3684   0.6605
 5PD  H15  H  HCH2  0   0.283  -2.2137  -0.2417  -1.5179
 5PD  H16  H  HCH2  0   0.269  -2.6366  -1.8213  -0.8728
 5PD  H17  H  HNH1  0   0.407  -4.7810  -1.7815  -0.6407
 5PD  H18  H  HCH2  0   0.264  -6.7330  -1.3311   0.5140
 5PD  H19  H  HCH2  0   0.256  -6.0576   0.1660   1.1362
 5PD  H20  H  HCH2  0   0.273  -6.2963   1.2116  -1.1327
 5PD  H21  H  HCH2  0   0.273  -6.9808  -0.3020  -1.7448
 5PD  H22  H  HSH1  0   0.229  -8.9809   1.3228  -1.3900
 5PD  H23  H  H     0   0.070   3.8931   2.7910   0.7509

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
 5PD  S06  C05  single  1.824  0.020  1.824
 5PD  C05  C04  single  1.524  0.020  1.524
 5PD  C04  N03  single  1.443  0.020  1.443
 5PD  N03  C02  single  1.343  0.020  1.343
 5PD  C02  O01  double  1.223  0.020  1.223
 5PD  C02  C07  single  1.514  0.020  1.514
 5PD  C07  C08  single  1.522  0.020  1.522
 5PD  C08  N09  single  1.449  0.020  1.449
 5PD  N09  C10  single  1.334  0.020  1.334
 5PD  C10  O11  double  1.226  0.020  1.226
 5PD  C10  C12  single  1.529  0.020  1.529
 5PD  C12  O13  single  1.402  0.020  1.402
 5PD  C12  C14  single  1.555  0.020  1.555
 5PD  C14  C15  single  1.532  0.020  1.532
 5PD  C14  C17  single  1.528  0.020  1.528
 5PD  C14  C16  single  1.530  0.020  1.530
 5PD  O21  P19  double  1.481  0.020  1.481
 5PD  O18  P19  single  1.599  0.020  1.599
 5PD  O18  C17  single  1.433  0.020  1.433
 5PD  P19  O20  single  1.599  0.020  1.599
 5PD  C15  H1   single  0.939  0.020  1.096
 5PD  C15  H2   single  0.939  0.020  1.096
 5PD  C15  H3   single  0.939  0.020  1.096
 5PD  C17  H4   single  0.939  0.020  1.096
 5PD  C17  H5   single  0.939  0.020  1.096
 5PD  O20  H6   single  0.832  0.020  0.971
 5PD  C16  H7   single  0.939  0.020  1.096
 5PD  C16  H8   single  0.939  0.020  1.096
 5PD  C16  H9   single  0.939  0.020  1.096
 5PD  C12  H10  single  0.939  0.020  1.096
 5PD  O13  H11  single  0.832  0.020  0.971
 5PD  N09  H12  single  0.868  0.020  1.013
 5PD  C08  H13  single  0.939  0.020  1.096
 5PD  C08  H14  single  0.939  0.020  1.096
 5PD  C07  H15  single  0.939  0.020  1.096
 5PD  C07  H16  single  0.939  0.020  1.096
 5PD  N03  H17  single  0.868  0.020  1.013
 5PD  C04  H18  single  0.939  0.020  1.096
 5PD  C04  H19  single  0.939  0.020  1.096
 5PD  C05  H20  single  0.939  0.020  1.096
 5PD  C05  H21  single  0.939  0.020  1.096
 5PD  S06  H22  single  1.156  0.020  1.350
 5PD  P19  H23  single  1.209  0.020  1.412

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
 5PD  N09  C10  O11  123.30  3.000
 5PD  O11  C10  C12  120.32  3.000
 5PD  N09  C10  C12  116.37  3.000
 5PD  H3   C15  H2   107.19  3.000
 5PD  H3   C15  H1   108.03  3.000
 5PD  H2   C15  H1   107.87  3.000
 5PD  H3   C15  C14  111.27  3.000
 5PD  H2   C15  C14  110.24  3.000
 5PD  H1   C15  C14  112.05  3.000
 5PD  H5   C17  H4   107.99  3.000
 5PD  H5   C17  C14  110.54  3.000
 5PD  H4   C17  C14  110.87  3.000
 5PD  H5   C17  O18  109.96  3.000
 5PD  H4   C17  O18  108.60  3.000
 5PD  C14  C17  O18  108.85  3.000
 5PD  H23  P19  O18  104.26  3.000
 5PD  H23  P19  O20  106.45  3.000
 5PD  O18  P19  O20   97.24  3.000
 5PD  H23  P19  O21  113.24  3.000
 5PD  O20  P19  O21  116.83  3.000
 5PD  O18  P19  O21  116.92  3.000
 5PD  H6   O20  P19  113.48  3.000
 5PD  P19  O18  C17  118.62  3.000
 5PD  C12  C14  C16  109.92  3.000
 5PD  C16  C14  C17  110.31  3.000
 5PD  C12  C14  C17  109.79  3.000
 5PD  C16  C14  C15  109.11  3.000
 5PD  C17  C14  C15  110.26  3.000
 5PD  C12  C14  C15  107.40  3.000
 5PD  H9   C16  H8   107.45  3.000
 5PD  H9   C16  H7   106.88  3.000
 5PD  H8   C16  H7   107.88  3.000
 5PD  H9   C16  C14  110.53  3.000
 5PD  H8   C16  C14  112.81  3.000
 5PD  H7   C16  C14  111.03  3.000
 5PD  H10  C12  O13  106.92  3.000
 5PD  H10  C12  C14  105.97  3.000
 5PD  O13  C12  C14  112.76  3.000
 5PD  H10  C12  C10  108.89  3.000
 5PD  C14  C12  C10  113.25  3.000
 5PD  O13  C12  C10  108.77  3.000
 5PD  H11  O13  C12  108.20  3.000
 5PD  H12  N09  C08  118.35  3.000
 5PD  H12  N09  C10  118.70  3.000
 5PD  C08  N09  C10  122.96  3.000
 5PD  H14  C08  H13  107.46  3.000
 5PD  H14  C08  C07  110.18  3.000
 5PD  H13  C08  C07  109.94  3.000
 5PD  H14  C08  N09  110.09  3.000
 5PD  H13  C08  N09  109.61  3.000
 5PD  C07  C08  N09  109.54  3.000
 5PD  H16  C07  H15  107.02  3.000
 5PD  H16  C07  C02  111.27  3.000
 5PD  H15  C07  C02  107.56  3.000
 5PD  H16  C07  C08  109.99  3.000
 5PD  H15  C07  C08  109.71  3.000
 5PD  C02  C07  C08  111.16  3.000
 5PD  N03  C02  O01  123.14  3.000
 5PD  O01  C02  C07  121.74  3.000
 5PD  N03  C02  C07  115.12  3.000
 5PD  H17  N03  C04  117.48  3.000
 5PD  H17  N03  C02  118.79  3.000
 5PD  C04  N03  C02  123.61  3.000
 5PD  H19  C04  H18  107.33  3.000
 5PD  H19  C04  C05  110.40  3.000
 5PD  H18  C04  C05  110.03  3.000
 5PD  H19  C04  N03  109.26  3.000
 5PD  H18  C04  N03  107.85  3.000
 5PD  C05  C04  N03  111.84  3.000
 5PD  H21  C05  H20  108.69  3.000
 5PD  H21  C05  S06  109.52  3.000
 5PD  H20  C05  S06  109.75  3.000
 5PD  H21  C05  C04  110.11  3.000
 5PD  H20  C05  C04  110.38  3.000
 5PD  S06  C05  C04  108.37  3.000
 5PD  H22  S06  C05   97.43  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
 5PD  CONST_01  C08  N09  C10  C12   180.00   0.0  0
 5PD  CONST_02  C08  N09  C10  O11     0.00   0.0  0
 5PD  CONST_03  C04  N03  C02  C07   180.00   0.0  0
 5PD  CONST_04  C04  N03  C02  O01     0.00   0.0  0
 5PD  CONST_05  H12  N09  C10  C12     0.00   0.0  0
 5PD  CONST_06  H17  N03  C02  C07     0.00   0.0  0
 5PD  Var_01    C07  C08  N09  C10  -174.95  30.0  2
 5PD  Var_02    O18  C17  C14  C15    58.48  30.0  3
 5PD  Var_03    O21  P19  O18  C17    66.02  30.0  3
 5PD  Var_04    C14  C17  O18  P19   155.88  30.0  3
 5PD  Var_05    C02  C07  C08  N09  -178.28  30.0  1
 5PD  Var_06    N03  C02  C07  C08  -132.69  30.0  2
 5PD  Var_07    C05  C04  N03  C02    87.95  30.0  2
 5PD  Var_08    S06  C05  C04  N03   179.20  30.0  1
 5PD  Var_09    H7   C16  C14  C15    65.92  30.0  3
 5PD  Var_10    H1   C15  C14  C17    55.67  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
 5PD  chir_02  C12  C10  O13  C14  positiv
 5PD  chir_03  P19  O21  O18  O20  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
 5PD  plan-1  C10  0.020
 5PD  plan-1  C12  0.020
 5PD  plan-1  O11  0.020
 5PD  plan-1  N09  0.020
 5PD  plan-1  C08  0.020
 5PD  plan-1  H12  0.020
 5PD  plan-2  C07  0.020
 5PD  plan-2  C02  0.020
 5PD  plan-2  O01  0.020
 5PD  plan-2  N03  0.020
 5PD  plan-2  C04  0.020
 5PD  plan-2  H17  0.020

