# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 01:28:58 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
#   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)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
 PNS  PNS  N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide  ligand  45  22  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PNS
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
 PNS  O23   O  OH1   0  -0.731   2.3307  -0.3011   6.1212
 PNS  P24   P  P     0   1.453   1.7390   0.6972   5.0283
 PNS  O25   O  OH1   0  -0.742   2.8190   0.8314   3.8556
 PNS  O26   O  O     0  -0.712   1.3274   2.0421   5.4721
 PNS  O27   O  O2    0  -0.588   0.5903  -0.2658   4.4894
 PNS  C28   C  CH2   0  -0.156  -0.3553   0.2381   3.5351
 PNS  C29   C  CT    0  -0.160  -1.0687  -0.9446   2.8835
 PNS  C30   C  CH3   0  -0.670  -0.0726  -1.8022   2.1003
 PNS  C31   C  CH3   0  -0.645  -1.7476  -1.8129   3.9479
 PNS  C32   C  CH1   0  -0.035  -2.1819  -0.4213   1.9314
 PNS  O33   O  OH1   0  -0.661  -3.1621   0.3203   2.6058
 PNS  C34   C  C     0   0.522  -1.6450   0.4223   0.7747
 PNS  O35   O  O     0  -0.499  -1.4834   1.6298   0.9171
 PNS  N36   N  NH1   0  -0.640  -1.3920  -0.2219  -0.3647
 PNS  C37   C  CH2   0  -0.235  -0.8422   0.4332  -1.5355
 PNS  C38   C  CH2   0  -0.638  -0.7921  -0.5541  -2.6883
 PNS  C39   C  C     0   0.571  -0.2705   0.0805  -3.9602
 PNS  O40   O  O     0  -0.494  -0.3617   1.2800  -4.1763
 PNS  N41   N  NH1   0  -0.633   0.2782  -0.7809  -4.8345
 PNS  C42   C  CH2   0  -0.283   0.7211  -0.3945  -6.1525
 PNS  C43   C  CH2   0  -0.553  -0.4228  -0.4018  -7.1600
 PNS  S44   S  S2    0  -0.258   0.2348   0.0914  -8.7884
 PNS  HOP1  H  HOH1  0   0.504   2.9960   0.0989   6.6969
 PNS  HOP2  H  HOH1  0   0.494   3.1929   0.0010   3.5319
 PNS  H282  H  HCH2  0   0.246   0.1607   0.8393   2.7818
 PNS  H281  H  HCH2  0   0.246  -1.0667   0.8824   4.0567
 PNS  H303  H  HCH3  0   0.235   0.5320  -1.2182   1.4049
 PNS  H302  H  HCH3  0   0.249   0.6100  -2.3121   2.7790
 PNS  H301  H  HCH3  0   0.235  -0.5891  -2.5771   1.5296
 PNS  H313  H  HCH3  0   0.236  -2.4127  -1.2338   4.5882
 PNS  H312  H  HCH3  0   0.230  -2.3402  -2.5978   3.4730
 PNS  H311  H  HCH3  0   0.239  -1.0126  -2.3051   4.5839
 PNS  H32   H  HCH1  0   0.258  -2.6759  -1.3111   1.5239
 PNS  H33   H  HOH1  0   0.446  -2.8998   1.2494   2.5852
 PNS  H36   H  HNH1  0   0.408  -1.5824  -1.2101  -0.4120
 PNS  H372  H  HCH2  0   0.251  -1.4603   1.2913  -1.8001
 PNS  H371  H  HCH2  0   0.249   0.1600   0.8091  -1.3154
 PNS  H382  H  HCH2  0   0.273  -0.1854  -1.4225  -2.4195
 PNS  H381  H  HCH2  0   0.291  -1.7988  -0.9316  -2.8975
 PNS  H41   H  HNH1  0   0.406   0.2882  -1.7621  -4.6076
 PNS  H422  H  HCH2  0   0.254   1.1745   0.5958  -6.1038
 PNS  H421  H  HCH2  0   0.265   1.4994  -1.0921  -6.4623
 PNS  H431  H  HCH2  0   0.271  -0.8598  -1.3978  -7.2275
 PNS  H432  H  HCH2  0   0.274  -1.1987   0.2991  -6.8546
 PNS  H44   H  HSH1  0   0.229  -0.9240   0.0627  -9.4541

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
 PNS  O23  P24   single  1.594  0.020  1.594
 PNS  O23  HOP1  single  0.850  0.020  0.980
 PNS  P24  O25   single  1.600  0.020  1.600
 PNS  P24  O26   double  1.475  0.020  1.475
 PNS  P24  O27   single  1.593  0.020  1.593
 PNS  O25  HOP2  single  0.850  0.020  0.980
 PNS  O27  C28   single  1.435  0.020  1.435
 PNS  C28  C29   single  1.527  0.020  1.527
 PNS  C28  H282  single  0.970  0.020  1.090
 PNS  C28  H281  single  0.970  0.020  1.090
 PNS  C29  C30   single  1.530  0.020  1.530
 PNS  C29  C31   single  1.532  0.020  1.532
 PNS  C29  C32   single  1.555  0.020  1.555
 PNS  C30  H303  single  0.970  0.020  1.090
 PNS  C30  H302  single  0.970  0.020  1.090
 PNS  C30  H301  single  0.970  0.020  1.090
 PNS  C31  H313  single  0.970  0.020  1.090
 PNS  C31  H312  single  0.970  0.020  1.090
 PNS  C31  H311  single  0.970  0.020  1.090
 PNS  C32  O33   single  1.402  0.020  1.402
 PNS  C32  C34   single  1.529  0.020  1.529
 PNS  C32  H32   single  0.970  0.020  1.090
 PNS  O33  H33   single  0.850  0.020  0.980
 PNS  C34  O35   double  1.227  0.020  1.227
 PNS  C34  N36   single  1.333  0.020  1.333
 PNS  N36  C37   single  1.450  0.020  1.450
 PNS  N36  H36   single  0.860  0.020  1.020
 PNS  C37  C38   single  1.519  0.020  1.519
 PNS  C37  H372  single  0.970  0.020  1.090
 PNS  C37  H371  single  0.970  0.020  1.090
 PNS  C38  C39   single  1.514  0.020  1.514
 PNS  C38  H382  single  0.970  0.020  1.090
 PNS  C38  H381  single  0.970  0.020  1.090
 PNS  C39  O40   double  1.222  0.020  1.222
 PNS  C39  N41   single  1.344  0.020  1.344
 PNS  N41  C42   single  1.443  0.020  1.443
 PNS  N41  H41   single  0.860  0.020  1.020
 PNS  C42  C43   single  1.524  0.020  1.524
 PNS  C42  H422  single  0.970  0.020  1.090
 PNS  C42  H421  single  0.970  0.020  1.090
 PNS  C43  S44   single  1.824  0.020  1.824
 PNS  C43  H431  single  0.970  0.020  1.090
 PNS  C43  H432  single  0.970  0.020  1.090
 PNS  S44  H44   single  1.200  0.020  1.300

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
 PNS  HOP1  O23  P24   113.87  3.000
 PNS  O27   P24  O26   116.86  3.000
 PNS  O27   P24  O25   106.83  3.000
 PNS  O26   P24  O25   109.42  3.000
 PNS  O27   P24  O23    96.95  3.000
 PNS  O26   P24  O23   117.93  3.000
 PNS  O25   P24  O23   107.73  3.000
 PNS  HOP2  O25  P24   115.76  3.000
 PNS  C28   O27  P24   119.21  3.000
 PNS  H281  C28  H282  108.18  3.000
 PNS  H281  C28  C29   110.88  3.000
 PNS  H282  C28  C29   110.64  3.000
 PNS  H281  C28  O27   108.58  3.000
 PNS  H282  C28  O27   109.89  3.000
 PNS  C29   C28  O27   108.64  3.000
 PNS  C32   C29  C31   107.38  3.000
 PNS  C32   C29  C30   109.95  3.000
 PNS  C31   C29  C30   109.05  3.000
 PNS  C32   C29  C28   109.57  3.000
 PNS  C31   C29  C28   110.45  3.000
 PNS  C30   C29  C28   110.38  3.000
 PNS  H301  C30  H302  106.84  3.000
 PNS  H301  C30  H303  107.98  3.000
 PNS  H302  C30  H303  107.49  3.000
 PNS  H301  C30  C29   110.93  3.000
 PNS  H302  C30  C29   110.58  3.000
 PNS  H303  C30  C29   112.77  3.000
 PNS  H311  C31  H312  107.17  3.000
 PNS  H311  C31  H313  107.99  3.000
 PNS  H312  C31  H313  107.84  3.000
 PNS  H311  C31  C29   111.26  3.000
 PNS  H312  C31  C29   110.22  3.000
 PNS  H313  C31  C29   112.17  3.000
 PNS  H32   C32  C34   108.96  3.000
 PNS  H32   C32  O33   107.04  3.000
 PNS  C34   C32  O33   108.52  3.000
 PNS  H32   C32  C29   106.07  3.000
 PNS  C34   C32  C29   113.42  3.000
 PNS  O33   C32  C29   112.57  3.000
 PNS  H33   O33  C32   107.99  3.000
 PNS  N36   C34  O35   123.37  3.000
 PNS  N36   C34  C32   116.53  3.000
 PNS  O35   C34  C32   120.10  3.000
 PNS  H36   N36  C37   118.48  3.000
 PNS  H36   N36  C34   118.58  3.000
 PNS  C37   N36  C34   122.94  3.000
 PNS  H371  C37  H372  107.34  3.000
 PNS  H371  C37  C38   110.26  3.000
 PNS  H372  C37  C38   110.26  3.000
 PNS  H371  C37  N36   109.90  3.000
 PNS  H372  C37  N36   109.67  3.000
 PNS  C38   C37  N36   109.38  3.000
 PNS  H381  C38  H382  106.46  3.000
 PNS  H381  C38  C39   107.50  3.000
 PNS  H382  C38  C39   110.39  3.000
 PNS  H381  C38  C37   109.80  3.000
 PNS  H382  C38  C37   110.38  3.000
 PNS  C39   C38  C37   112.12  3.000
 PNS  N41   C39  O40   122.97  3.000
 PNS  N41   C39  C38   114.73  3.000
 PNS  O40   C39  C38   122.28  3.000
 PNS  H41   N41  C42   117.62  3.000
 PNS  H41   N41  C39   118.80  3.000
 PNS  C42   N41  C39   123.21  3.000
 PNS  H421  C42  H422  107.28  3.000
 PNS  H421  C42  C43   110.17  3.000
 PNS  H422  C42  C43   110.24  3.000
 PNS  H421  C42  N41   107.90  3.000
 PNS  H422  C42  N41   109.27  3.000
 PNS  C43   C42  N41   111.84  3.000
 PNS  H432  C43  H431  108.65  3.000
 PNS  H432  C43  S44   109.46  3.000
 PNS  H431  C43  S44   109.66  3.000
 PNS  H432  C43  C42   110.25  3.000
 PNS  H431  C43  C42   110.25  3.000
 PNS  S44   C43  C42   108.56  3.000
 PNS  H44   S44  C43    97.25  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
 PNS  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 PNS  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 PNS  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 PNS  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 PNS  CONST_05  H36   N36  C34  C32     0.00   0.0  0
 PNS  CONST_06  H41   N41  C39  C38     0.00   0.0  0
 PNS  Var_01    C29   C28  O27  P24   163.60  30.0  3
 PNS  Var_02    C30   C29  C28  O27   -63.46  30.0  3
 PNS  Var_03    C38   C37  N36  C34  -175.11  30.0  3
 PNS  Var_04    C39   C38  C37  N36   178.03  30.0  3
 PNS  Var_05    O40   C39  C38  C37   -25.40  30.0  3
 PNS  Var_06    C43   C42  N41  C39   -84.30  30.0  3
 PNS  Var_07    S44   C43  C42  N41  -179.79  30.0  3
 PNS  Var_08    H303  C30  C29  C28   -51.65  30.0  3
 PNS  Var_09    H313  C31  C29  C28    54.08  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
 PNS  chir_01  C32  C29  O33  C34  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
 PNS  plan-1  C32  0.020
 PNS  plan-1  C34  0.020
 PNS  plan-1  O35  0.020
 PNS  plan-1  N36  0.020
 PNS  plan-1  C37  0.020
 PNS  plan-1  H36  0.020
 PNS  plan-2  C38  0.020
 PNS  plan-2  C39  0.020
 PNS  plan-2  O40  0.020
 PNS  plan-2  N41  0.020
 PNS  plan-2  C42  0.020
 PNS  plan-2  H41  0.020

