# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 05:58:19 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxido)phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl] hexanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[PH](O)=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
 PM4  PM4  'S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxido)phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl] hexanethioate'  ligand  61  28  .  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_PM4
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
 PM4  O23   O  OH1   0  -0.734    8.1003   3.7564  -0.5704
 PM4  P24   P  P     0   1.131    7.8135   2.5699   0.4638
 PM4  O26   O  O     0  -0.709    7.3647   2.9599   1.8200
 PM4  O27   O  O2    0  -0.584    6.7689   1.7636  -0.4398
 PM4  C28   C  CH2   0  -0.150    6.3357   0.4715   0.0017
 PM4  C29   C  CT    0  -0.164    5.7309  -0.2794  -1.1842
 PM4  C30   C  CH3   0  -0.666    4.5148   0.4722  -1.7303
 PM4  C31   C  CH3   0  -0.647    6.7678  -0.4272  -2.3015
 PM4  C32   C  CH1   0  -0.033    5.3145  -1.7095  -0.7363
 PM4  O33   O  OH1   0  -0.661    6.4028  -2.4724  -0.2910
 PM4  C34   C  C     0   0.520    4.2428  -1.7112   0.3549
 PM4  O35   O  O     0  -0.499    4.5705  -1.6854   1.5366
 PM4  N36   N  NH1   0  -0.638    2.9741  -1.7460  -0.0531
 PM4  C37   C  CH2   0  -0.235    1.8517  -1.7214   0.8650
 PM4  C38   C  CH2   0  -0.637    0.5656  -1.5342   0.0816
 PM4  C39   C  C     0   0.574   -0.6561  -1.5009   0.9769
 PM4  O40   O  O     0  -0.496   -0.6119  -1.7582   2.1709
 PM4  N41   N  NH1   0  -0.648   -1.7974  -1.1705   0.3523
 PM4  C42   C  CH2   0  -0.238   -3.0683  -1.1174   1.0413
 PM4  C43   C  CH2   0  -0.602   -4.1462  -0.6694   0.0660
 PM4  S1    S  S2    0   0.007   -5.7223  -0.6031   0.9577
 PM4  C1    C  C     0   0.260   -6.8236  -0.0607  -0.3266
 PM4  O1    O  O     0  -0.384   -6.4463   0.1581  -1.4473
 PM4  C2    C  CH2   0  -0.537   -8.2435   0.0849   0.1540
 PM4  C3    C  CH2   0  -0.416   -9.2105   0.5847  -0.9085
 PM4  C4    C  CH2   0  -0.411  -10.6248   0.7258  -0.3586
 PM4  C5    C  CH2   0  -0.420  -11.6172   1.2294  -1.3990
 PM4  C6    C  CH3   0  -0.662  -13.0287   1.3769  -0.8480
 PM4  H23   H  HOH1  0   0.500    8.5495   4.5144  -0.1737
 PM4  H24   H  H     0   0.071    8.9626   1.7641   0.4717
 PM4  H281  H  HCH2  0   0.237    7.1873  -0.0896   0.4023
 PM4  H282  H  HCH2  0   0.251    5.6054   0.5999   0.8030
 PM4  H301  H  HCH3  0   0.248    4.8136   1.4280  -2.1594
 PM4  H302  H  HCH3  0   0.235    4.0335  -0.1002  -2.5267
 PM4  H303  H  HCH3  0   0.235    3.7659   0.6736  -0.9632
 PM4  H311  H  HCH3  0   0.235    7.6709  -0.9315  -1.9579
 PM4  H312  H  HCH3  0   0.231    6.3550  -1.0081  -3.1291
 PM4  H313  H  HCH3  0   0.240    7.0563   0.5447  -2.6997
 PM4  H32   H  HCH1  0   0.257    4.9162  -2.2044  -1.6301
 PM4  H33   H  HOH1  0   0.446    6.4708  -2.3597   0.6658
 PM4  H36   H  HNH1  0   0.408    2.7878  -1.8586  -1.0368
 PM4  H371  H  HCH2  0   0.249    1.8174  -2.6483   1.4412
 PM4  H372  H  HCH2  0   0.250    1.9858  -0.9036   1.5742
 PM4  H381  H  HCH2  0   0.281    0.6072  -0.6102  -0.5024
 PM4  H382  H  HCH2  0   0.287    0.4410  -2.3480  -0.6401
 PM4  H41   H  HNH1  0   0.408   -1.7762  -0.9887  -0.6387
 PM4  H421  H  HCH2  0   0.250   -3.3197  -2.0988   1.4522
 PM4  H422  H  HCH2  0   0.251   -3.0091  -0.4192   1.8795
 PM4  H431  H  HCH2  0   0.292   -3.9171   0.3195  -0.3317
 PM4  H432  H  HCH2  0   0.292   -4.2321  -1.3725  -0.7629
 PM4  H21   H  HCH2  0   0.281   -8.5650  -0.8871   0.5429
 PM4  H22   H  HCH2  0   0.278   -8.2370   0.7577   1.0179
 PM4  H31   H  HCH2  0   0.228   -8.8717   1.5507  -1.2921
 PM4  H32A  H  HCH2  0   0.228   -9.2160  -0.1037  -1.7577
 PM4  H41A  H  HCH2  0   0.213  -10.9643  -0.2407   0.0296
 PM4  H42   H  HCH2  0   0.213  -10.6165   1.4112   0.4959
 PM4  H51   H  HCH2  0   0.213  -11.2743   2.1930  -1.7883
 PM4  H52   H  HCH2  0   0.213  -11.6283   0.5437  -2.2518
 PM4  H61   H  HCH3  0   0.227  -13.7171   1.7442  -1.6102
 PM4  H62   H  HCH3  0   0.217  -13.4147   0.4215  -0.4879
 PM4  H63   H  HCH3  0   0.216  -13.0562   2.0783  -0.0121

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
 PM4  O23  P24   single  1.600  0.020  1.600
 PM4  O23  H23   single  0.832  0.020  0.971
 PM4  P24  O26   double  1.481  0.020  1.481
 PM4  P24  O27   single  1.599  0.020  1.599
 PM4  P24  H24   single  1.209  0.020  1.412
 PM4  O27  C28   single  1.433  0.020  1.433
 PM4  C28  C29   single  1.528  0.020  1.528
 PM4  C28  H281  single  0.970  0.020  1.090
 PM4  C28  H282  single  0.970  0.020  1.090
 PM4  C29  C30   single  1.530  0.020  1.530
 PM4  C29  C31   single  1.531  0.020  1.531
 PM4  C29  C32   single  1.555  0.020  1.555
 PM4  C30  H301  single  0.970  0.020  1.090
 PM4  C30  H302  single  0.970  0.020  1.090
 PM4  C30  H303  single  0.970  0.020  1.090
 PM4  C31  H311  single  0.970  0.020  1.090
 PM4  C31  H312  single  0.970  0.020  1.090
 PM4  C31  H313  single  0.970  0.020  1.090
 PM4  C32  O33   single  1.402  0.020  1.402
 PM4  C32  C34   single  1.529  0.020  1.529
 PM4  C32  H32   single  0.970  0.020  1.090
 PM4  O33  H33   single  0.850  0.020  0.980
 PM4  C34  O35   double  1.227  0.020  1.227
 PM4  C34  N36   single  1.333  0.020  1.333
 PM4  N36  C37   single  1.450  0.020  1.450
 PM4  N36  H36   single  0.860  0.020  1.020
 PM4  C37  C38   single  1.517  0.020  1.517
 PM4  C37  H371  single  0.970  0.020  1.090
 PM4  C37  H372  single  0.970  0.020  1.090
 PM4  C38  C39   single  1.515  0.020  1.515
 PM4  C38  H381  single  0.970  0.020  1.090
 PM4  C38  H382  single  0.970  0.020  1.090
 PM4  C39  O40   double  1.222  0.020  1.222
 PM4  C39  N41   single  1.342  0.020  1.342
 PM4  N41  C42   single  1.447  0.020  1.447
 PM4  N41  H41   single  0.860  0.020  1.020
 PM4  C42  C43   single  1.521  0.020  1.521
 PM4  C42  H421  single  0.970  0.020  1.090
 PM4  C42  H422  single  0.970  0.020  1.090
 PM4  C43  S1    single  1.812  0.020  1.812
 PM4  C43  H431  single  0.970  0.020  1.090
 PM4  C43  H432  single  0.970  0.020  1.090
 PM4  S1   C1    single  1.777  0.020  1.777
 PM4  C1   O1    double  1.203  0.020  1.203
 PM4  C1   C2    single  1.506  0.020  1.506
 PM4  C2   C3    single  1.521  0.020  1.521
 PM4  C2   H21   single  0.970  0.020  1.090
 PM4  C2   H22   single  0.970  0.020  1.090
 PM4  C3   C4    single  1.524  0.020  1.524
 PM4  C3   H31   single  0.970  0.020  1.090
 PM4  C3   H32A  single  0.970  0.020  1.090
 PM4  C4   C5    single  1.523  0.020  1.523
 PM4  C4   H41A  single  0.970  0.020  1.090
 PM4  C4   H42   single  0.970  0.020  1.090
 PM4  C5   C6    single  1.522  0.020  1.522
 PM4  C5   H51   single  0.970  0.020  1.090
 PM4  C5   H52   single  0.970  0.020  1.090
 PM4  C6   H61   single  0.970  0.020  1.090
 PM4  C6   H62   single  0.970  0.020  1.090
 PM4  C6   H63   single  0.970  0.020  1.090

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
 PM4  H23   O23  P24   113.56  3.000
 PM4  H24   P24  O27   104.39  3.000
 PM4  H24   P24  O26   113.21  3.000
 PM4  O27   P24  O26   116.89  3.000
 PM4  H24   P24  O23   106.42  3.000
 PM4  O27   P24  O23    97.23  3.000
 PM4  O26   P24  O23   116.81  3.000
 PM4  C28   O27  P24   118.56  3.000
 PM4  H282  C28  H281  108.16  3.000
 PM4  H282  C28  C29   111.26  3.000
 PM4  H281  C28  C29   109.85  3.000
 PM4  H282  C28  O27   108.81  3.000
 PM4  H281  C28  O27   109.85  3.000
 PM4  C29   C28  O27   108.89  3.000
 PM4  C32   C29  C31   107.62  3.000
 PM4  C32   C29  C30   109.97  3.000
 PM4  C31   C29  C30   108.97  3.000
 PM4  C32   C29  C28   109.53  3.000
 PM4  C31   C29  C28   110.22  3.000
 PM4  C30   C29  C28   110.48  3.000
 PM4  H303  C30  H302  107.87  3.000
 PM4  H303  C30  H301  107.66  3.000
 PM4  H302  C30  H301  107.06  3.000
 PM4  H303  C30  C29   112.67  3.000
 PM4  H302  C30  C29   110.66  3.000
 PM4  H301  C30  C29   110.70  3.000
 PM4  H313  C31  H312  107.32  3.000
 PM4  H313  C31  H311  107.97  3.000
 PM4  H312  C31  H311  107.82  3.000
 PM4  H313  C31  C29   111.10  3.000
 PM4  H312  C31  C29   110.39  3.000
 PM4  H311  C31  C29   112.07  3.000
 PM4  H32   C32  C34   109.06  3.000
 PM4  H32   C32  O33   107.18  3.000
 PM4  C34   C32  O33   108.47  3.000
 PM4  H32   C32  C29   106.11  3.000
 PM4  C34   C32  C29   113.21  3.000
 PM4  O33   C32  C29   112.58  3.000
 PM4  H33   O33  C32   107.81  3.000
 PM4  N36   C34  O35   123.34  3.000
 PM4  N36   C34  C32   116.65  3.000
 PM4  O35   C34  C32   120.01  3.000
 PM4  H36   N36  C37   118.48  3.000
 PM4  H36   N36  C34   118.53  3.000
 PM4  C37   N36  C34   122.85  3.000
 PM4  H372  C37  H371  107.28  3.000
 PM4  H372  C37  C38   110.33  3.000
 PM4  H371  C37  C38   110.52  3.000
 PM4  H372  C37  N36   109.22  3.000
 PM4  H371  C37  N36   110.11  3.000
 PM4  C38   C37  N36   109.34  3.000
 PM4  H382  C38  H381  106.27  3.000
 PM4  H382  C38  C39   108.31  3.000
 PM4  H381  C38  C39   109.12  3.000
 PM4  H382  C38  C37   110.19  3.000
 PM4  H381  C38  C37   110.34  3.000
 PM4  C39   C38  C37   112.40  3.000
 PM4  N41   C39  O40   122.49  3.000
 PM4  N41   C39  C38   114.59  3.000
 PM4  O40   C39  C38   122.93  3.000
 PM4  H41   N41  C42   118.70  3.000
 PM4  H41   N41  C39   118.95  3.000
 PM4  C42   N41  C39   122.30  3.000
 PM4  H422  C42  H421  107.33  3.000
 PM4  H422  C42  C43   110.00  3.000
 PM4  H421  C42  C43   110.03  3.000
 PM4  H422  C42  N41   109.95  3.000
 PM4  H421  C42  N41   110.37  3.000
 PM4  C43   C42  N41   109.14  3.000
 PM4  H432  C43  H431  108.92  3.000
 PM4  H432  C43  S1    109.22  3.000
 PM4  H431  C43  S1    109.21  3.000
 PM4  H432  C43  C42   110.69  3.000
 PM4  H431  C43  C42   110.62  3.000
 PM4  S1    C43  C42   108.15  3.000
 PM4  C1    S1   C43   101.22  3.000
 PM4  C2    C1   O1    125.14  3.000
 PM4  C2    C1   S1    112.53  3.000
 PM4  O1    C1   S1    122.32  3.000
 PM4  H22   C2   H21   105.48  3.000
 PM4  H22   C2   C3    110.67  3.000
 PM4  H21   C2   C3    110.67  3.000
 PM4  H22   C2   C1    107.79  3.000
 PM4  H21   C2   C1    107.72  3.000
 PM4  C3    C2   C1    114.09  3.000
 PM4  H32A  C3   H31   106.59  3.000
 PM4  H32A  C3   C4    109.51  3.000
 PM4  H31   C3   C4    109.41  3.000
 PM4  H32A  C3   C2    109.81  3.000
 PM4  H31   C3   C2    109.78  3.000
 PM4  C4    C3   C2    111.61  3.000
 PM4  H42   C4   H41A  106.14  3.000
 PM4  H42   C4   C5    109.31  3.000
 PM4  H41A  C4   C5    109.38  3.000
 PM4  H42   C4   C3    109.42  3.000
 PM4  H41A  C4   C3    109.50  3.000
 PM4  C5    C4   C3    112.88  3.000
 PM4  H52   C5   H51   106.12  3.000
 PM4  H52   C5   C6    109.47  3.000
 PM4  H51   C5   C6    109.51  3.000
 PM4  H52   C5   C4    109.36  3.000
 PM4  H51   C5   C4    109.26  3.000
 PM4  C6    C5   C4    112.88  3.000
 PM4  H63   C6   H62   107.51  3.000
 PM4  H63   C6   H61   107.63  3.000
 PM4  H62   C6   H61   107.58  3.000
 PM4  H63   C6   C5    111.27  3.000
 PM4  H62   C6   C5    111.25  3.000
 PM4  H61   C6   C5    111.40  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
 PM4  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 PM4  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 PM4  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 PM4  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 PM4  CONST_05  H36   N36  C34  C32     0.00   0.0  0
 PM4  CONST_06  H41   N41  C39  C38     0.00   0.0  0
 PM4  Var_01    C29   C28  O27  P24  -161.87  30.0  3
 PM4  Var_02    C30   C29  C28  O27   -61.28  30.0  3
 PM4  Var_03    C38   C37  N36  C34   170.42  30.0  3
 PM4  Var_04    C39   C38  C37  N36   179.90  30.0  3
 PM4  Var_05    O40   C39  C38  C37    -8.23  30.0  3
 PM4  Var_06    C43   C42  N41  C39   178.14  30.0  3
 PM4  Var_07    S1    C43  C42  N41  -179.68  30.0  3
 PM4  Var_08    O1    C1   S1   C43     0.07  30.0  3
 PM4  Var_09    C3    C2   C1   S1    178.41  30.0  3
 PM4  Var_10    C4    C3   C2   C1   -179.36  30.0  3
 PM4  Var_11    C5    C4   C3   C2    179.81  30.0  3
 PM4  Var_12    C6    C5   C4   C3   -179.72  30.0  3
 PM4  Var_13    H24   P24  O27  C28    62.65  30.0  1
 PM4  Var_14    H301  C30  C29  C28    65.92  30.0  3
 PM4  Var_15    H311  C31  C29  C28    56.89  30.0  3
 PM4  Var_16    H61   C6   C5   C4    179.65  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
 PM4  chir_02  C32  C29  O33  C34  negativ
 PM4  chir_03  P24  O23  O26  O27  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
 PM4  plan-1  C32  0.020
 PM4  plan-1  C34  0.020
 PM4  plan-1  O35  0.020
 PM4  plan-1  N36  0.020
 PM4  plan-1  C37  0.020
 PM4  plan-1  H36  0.020
 PM4  plan-2  C38  0.020
 PM4  plan-2  C39  0.020
 PM4  plan-2  O40  0.020
 PM4  plan-2  N41  0.020
 PM4  plan-2  C42  0.020
 PM4  plan-2  H41  0.020
 PM4  plan-3  S1   0.020
 PM4  plan-3  C1   0.020
 PM4  plan-3  O1   0.020
 PM4  plan-3  C2   0.020

