# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 23:50:29 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: N~3~-[(2S)-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
 PN7  PN7  N~3~-[(2S)-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_PN7
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
 PN7  O3   O  OH1   0  -0.660  -2.7376  -2.8669   0.8053
 PN7  O4   O  O     0  -0.497  -0.9242  -1.0755   1.7868
 PN7  C2   C  CT    0  -0.163  -2.7960  -1.0619  -0.8712
 PN7  C1   C  CH2   0  -0.153  -3.4692  -0.1178   0.1237
 PN7  P    P  P     0   1.456  -5.1577   1.8826   0.1820
 PN7  O1P  O  OH1   0  -0.732  -5.7717   2.6097  -1.0966
 PN7  O2P  O  O     0  -0.712  -6.0999   1.3525   1.1852
 PN7  O3P  O  O2    0  -0.587  -4.2685   0.8227  -0.6075
 PN7  CE1  C  CH3   0  -0.651  -3.8520  -1.8119  -1.6893
 PN7  CE2  C  CH3   0  -0.668  -1.8875  -0.2762  -1.8186
 PN7  C3   C  CH1   0  -0.034  -1.9632  -2.1236  -0.0972
 PN7  C4   C  C     0   0.522  -0.7747  -1.5266   0.6562
 PN7  N5   N  NH1   0  -0.638   0.3994  -1.5423   0.0236
 PN7  C6   C  CH2   0  -0.236   1.6077  -0.9902   0.6030
 PN7  C7   C  CH2   0  -0.633   2.7257  -1.0174  -0.4253
 PN7  C8   C  C     0   0.571   4.0065  -0.4265   0.1252
 PN7  O8   O  O     0  -0.496   4.0047   0.4607   0.9664
 PN7  N9   N  NH1   0  -0.633   5.1353  -0.9425  -0.3893
 PN7  C10  C  CH2   0  -0.283   6.4507  -0.4491  -0.0598
 PN7  C11  C  CH2   0  -0.553   6.8330   0.7594  -0.9075
 PN7  S12  S  S2    0  -0.258   8.4940   1.3162  -0.3995
 PN7  H1   H  HOH1  0   0.446  -2.7238  -2.4096   1.6557
 PN7  H2   H  HCH2  0   0.241  -4.1107  -0.6772   0.8099
 PN7  H3   H  HCH2  0   0.248  -2.7253   0.4255   0.7111
 PN7  H4   H  HOH1  0   0.503  -6.5139   3.1955  -0.8964
 PN7  H5   H  HCH3  0   0.241  -4.4566  -1.1231  -2.2779
 PN7  H6   H  HCH3  0   0.231  -3.3717  -2.5007  -2.3874
 PN7  H7   H  HCH3  0   0.236  -4.5223  -2.3898  -1.0534
 PN7  H8   H  HCH3  0   0.248  -2.4760   0.3532  -2.4852
 PN7  H9   H  HCH3  0   0.235  -1.1894   0.3734  -1.2884
 PN7  H10  H  HCH3  0   0.234  -1.3048  -0.9511  -2.4483
 PN7  H11  H  HCH1  0   0.258  -1.5870  -2.8251  -0.8500
 PN7  H12  H  HNH1  0   0.408   0.4620  -2.0032  -0.8704
 PN7  H13  H  HCH2  0   0.250   1.4201   0.0335   0.9265
 PN7  H14  H  HCH2  0   0.249   1.8960  -1.5637   1.4878
 PN7  H15  H  HCH2  0   0.271   2.8969  -2.0384  -0.7751
 PN7  H16  H  HCH2  0   0.289   2.4362  -0.4299  -1.3029
 PN7  H17  H  HNH1  0   0.406   5.0669  -1.6522  -1.1002
 PN7  H18  H  HCH2  0   0.254   6.4851  -0.1939   1.0000
 PN7  H19  H  HCH2  0   0.265   7.1624  -1.2584  -0.2216
 PN7  H20  H  HCH2  0   0.272   6.8460   0.4879  -1.9625
 PN7  H21  H  HCH2  0   0.273   6.1146   1.5653  -0.7624
 PN7  H22  H  HSH1  0   0.229   8.6484   2.2644  -1.3286
 PN7  O4P  O  OH1   0  -0.745  -4.1482   2.9032   0.8878
 PN7  H23  H  HOH1  0   0.495  -3.5271   3.3558   0.3017

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
 PN7  O3   C3   single  1.402  0.020  1.402
 PN7  C3   C4   single  1.529  0.020  1.529
 PN7  C3   C2   single  1.556  0.020  1.556
 PN7  O4   C4   double  1.226  0.020  1.226
 PN7  CE2  C2   single  1.530  0.020  1.530
 PN7  C4   N5   single  1.334  0.020  1.334
 PN7  C1   C2   single  1.528  0.020  1.528
 PN7  C1   O3P  single  1.435  0.020  1.435
 PN7  N5   C6   single  1.449  0.020  1.449
 PN7  C2   CE1  single  1.532  0.020  1.532
 PN7  C6   C7   single  1.519  0.020  1.519
 PN7  O2P  P    double  1.475  0.020  1.475
 PN7  O1P  P    single  1.594  0.020  1.594
 PN7  C7   C8   single  1.514  0.020  1.514
 PN7  P    O3P  single  1.593  0.020  1.593
 PN7  O8   C8   double  1.223  0.020  1.223
 PN7  C8   N9   single  1.344  0.020  1.344
 PN7  N9   C10  single  1.443  0.020  1.443
 PN7  S12  C11  single  1.824  0.020  1.824
 PN7  C10  C11  single  1.525  0.020  1.525
 PN7  O3   H1   single  0.850  0.020  0.980
 PN7  C1   H2   single  0.970  0.020  1.090
 PN7  C1   H3   single  0.970  0.020  1.090
 PN7  O1P  H4   single  0.850  0.020  0.980
 PN7  CE1  H5   single  0.970  0.020  1.090
 PN7  CE1  H6   single  0.970  0.020  1.090
 PN7  CE1  H7   single  0.970  0.020  1.090
 PN7  CE2  H8   single  0.970  0.020  1.090
 PN7  CE2  H9   single  0.970  0.020  1.090
 PN7  CE2  H10  single  0.970  0.020  1.090
 PN7  C3   H11  single  0.970  0.020  1.090
 PN7  N5   H12  single  0.860  0.020  1.020
 PN7  C6   H13  single  0.970  0.020  1.090
 PN7  C6   H14  single  0.970  0.020  1.090
 PN7  C7   H15  single  0.970  0.020  1.090
 PN7  C7   H16  single  0.970  0.020  1.090
 PN7  N9   H17  single  0.860  0.020  1.020
 PN7  C10  H18  single  0.970  0.020  1.090
 PN7  C10  H19  single  0.970  0.020  1.090
 PN7  C11  H20  single  0.970  0.020  1.090
 PN7  C11  H21  single  0.970  0.020  1.090
 PN7  S12  H22  single  1.200  0.020  1.300
 PN7  P    O4P  single  1.600  0.020  1.600
 PN7  O4P  H23  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
 PN7  H1   O3   C3   107.93  3.000
 PN7  C3   C2   CE2  109.93  3.000
 PN7  CE2  C2   CE1  109.27  3.000
 PN7  C3   C2   CE1  107.49  3.000
 PN7  CE1  C2   C1   110.27  3.000
 PN7  CE2  C2   C1   110.34  3.000
 PN7  C3   C2   C1   109.49  3.000
 PN7  H3   C1   H2   108.45  3.000
 PN7  H3   C1   O3P  109.11  3.000
 PN7  H2   C1   O3P  109.17  3.000
 PN7  H3   C1   C2   110.94  3.000
 PN7  H2   C1   C2   110.56  3.000
 PN7  O3P  C1   C2   108.59  3.000
 PN7  O4P  P    O3P  106.92  3.000
 PN7  O4P  P    O2P  109.42  3.000
 PN7  O3P  P    O2P  117.04  3.000
 PN7  O4P  P    O1P  107.82  3.000
 PN7  O3P  P    O1P   96.95  3.000
 PN7  O2P  P    O1P  117.61  3.000
 PN7  H4   O1P  P    113.96  3.000
 PN7  P    O3P  C1   119.65  3.000
 PN7  H7   CE1  H6   108.00  3.000
 PN7  H7   CE1  H5   108.01  3.000
 PN7  H6   CE1  H5   107.31  3.000
 PN7  H7   CE1  C2   111.84  3.000
 PN7  H6   CE1  C2   110.31  3.000
 PN7  H5   CE1  C2   111.20  3.000
 PN7  H10  CE2  H9   107.87  3.000
 PN7  H10  CE2  H8   107.01  3.000
 PN7  H9   CE2  H8   107.40  3.000
 PN7  H10  CE2  C2   110.90  3.000
 PN7  H9   CE2  C2   112.63  3.000
 PN7  H8   CE2  C2   110.79  3.000
 PN7  H11  C3   C4   108.77  3.000
 PN7  H11  C3   C2   106.20  3.000
 PN7  C4   C3   C2   113.26  3.000
 PN7  H11  C3   O3   107.01  3.000
 PN7  C2   C3   O3   112.73  3.000
 PN7  C4   C3   O3   108.62  3.000
 PN7  N5   C4   C3   116.50  3.000
 PN7  N5   C4   O4   123.29  3.000
 PN7  C3   C4   O4   120.21  3.000
 PN7  H12  N5   C6   118.50  3.000
 PN7  H12  N5   C4   118.74  3.000
 PN7  C6   N5   C4   122.67  3.000
 PN7  H14  C6   H13  107.33  3.000
 PN7  H14  C6   C7   110.15  3.000
 PN7  H13  C6   C7   110.14  3.000
 PN7  H14  C6   N5   110.10  3.000
 PN7  H13  C6   N5   109.45  3.000
 PN7  C7   C6   N5   109.64  3.000
 PN7  H16  C7   H15  106.63  3.000
 PN7  H16  C7   C8   107.80  3.000
 PN7  H15  C7   C8   110.39  3.000
 PN7  H16  C7   C6   109.77  3.000
 PN7  H15  C7   C6   110.41  3.000
 PN7  C8   C7   C6   111.68  3.000
 PN7  N9   C8   O8   122.92  3.000
 PN7  N9   C8   C7   114.93  3.000
 PN7  O8   C8   C7   122.15  3.000
 PN7  H17  N9   C10  117.66  3.000
 PN7  H17  N9   C8   118.95  3.000
 PN7  C10  N9   C8   123.17  3.000
 PN7  H19  C10  H18  107.30  3.000
 PN7  H19  C10  C11  110.02  3.000
 PN7  H18  C10  C11  110.29  3.000
 PN7  H19  C10  N9   107.91  3.000
 PN7  H18  C10  N9   109.31  3.000
 PN7  C11  C10  N9   111.88  3.000
 PN7  H21  C11  H20  108.74  3.000
 PN7  H21  C11  S12  109.74  3.000
 PN7  H20  C11  S12  109.57  3.000
 PN7  H21  C11  C10  110.30  3.000
 PN7  H20  C11  C10  110.11  3.000
 PN7  S12  C11  C10  108.39  3.000
 PN7  H22  S12  C11   97.37  3.000
 PN7  H23  O4P  P    115.90  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
 PN7  CONST_01  C6   N5   C4   O4      0.00   0.0  0
 PN7  CONST_02  C6   N5   C4   C3    180.00   0.0  0
 PN7  CONST_03  C10  N9   C8   C7    180.00   0.0  0
 PN7  CONST_04  C10  N9   C8   O8      0.00   0.0  0
 PN7  CONST_05  H12  N5   C4   O4    180.00   0.0  0
 PN7  CONST_06  H17  N9   C8   C7      0.00   0.0  0
 PN7  Var_01    O2P  P    O3P  C1    -54.35  30.0  2
 PN7  Var_02    C3   C2   C1   O3P  -177.99  30.0  3
 PN7  Var_03    C7   C6   N5   C4   -173.43  30.0  3
 PN7  Var_04    C8   C7   C6   N5    178.98  30.0  3
 PN7  Var_05    O8   C8   C7   C6    -30.73  30.0  3
 PN7  Var_06    C11  C10  N9   C8    -83.74  30.0  3
 PN7  Var_07    S12  C11  C10  N9    179.25  30.0  3
 PN7  Var_08    H8   CE2  C2   C1    -68.59  30.0  3
 PN7  Var_09    H5   CE1  C2   C1     62.14  30.0  3
 PN7  Var_10    H2   C1   O3P  P      55.87  30.0  2

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
 PN7  chir_01  C3  O3  C4  C2  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
 PN7  plan-1  O4   0.020
 PN7  plan-1  C3   0.020
 PN7  plan-1  C4   0.020
 PN7  plan-1  N5   0.020
 PN7  plan-1  C6   0.020
 PN7  plan-1  H12  0.020
 PN7  plan-2  C7   0.020
 PN7  plan-2  C8   0.020
 PN7  plan-2  O8   0.020
 PN7  plan-2  N9   0.020
 PN7  plan-2  C10  0.020
 PN7  plan-2  H17  0.020

