# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 11:47:07 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxido)phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl] heptanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC(=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
 PM5  PM5  'S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxido)phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl] heptanethioate'  ligand  64  29  .  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_PM5
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
 PM5  O23   O  OH1   0  -0.734    8.5148   3.9328  -0.5126
 PM5  P24   P  P     0   1.131    8.2068   2.7356   0.5028
 PM5  O26   O  O     0  -0.708    7.7667   3.1109   1.8657
 PM5  O27   O  O2    0  -0.584    7.1470   1.9637  -0.4128
 PM5  C28   C  CH2   0  -0.150    6.6848   0.6746   0.0066
 PM5  C29   C  CT    0  -0.163    6.0971  -0.0556  -1.2012
 PM5  C30   C  CH3   0  -0.669    4.9181   0.7300  -1.7800
 PM5  C31   C  CH3   0  -0.649    7.1640  -0.2234  -2.2864
 PM5  C32   C  CH1   0  -0.033    5.6302  -1.4764  -0.7751
 PM5  O33   O  OH1   0  -0.661    6.6800  -2.2605  -0.2775
 PM5  C34   C  C     0   0.519    4.5071  -1.4530   0.2635
 PM5  O35   O  O     0  -0.498    4.7786  -1.4406   1.4594
 PM5  N36   N  NH1   0  -0.639    3.2587  -1.4602  -0.2053
 PM5  C37   C  CH2   0  -0.237    2.0938  -1.3661   0.6525
 PM5  C38   C  CH2   0  -0.629    0.8358  -1.6040  -0.1668
 PM5  C39   C  C     0   0.566   -0.4147  -1.4189   0.6660
 PM5  O40   O  O     0  -0.494   -0.5165  -0.5203   1.4883
 PM5  N41   N  NH1   0  -0.632   -1.3961  -2.3042   0.4234
 PM5  C42   C  CH2   0  -0.292   -2.6951  -2.2361   1.0470
 PM5  C43   C  CH2   0  -0.557   -3.6407  -1.3332   0.2595
 PM5  S1    S  S2    0  -0.006   -5.2522  -1.3189   1.0940
 PM5  C1    C  C     0   0.261   -6.2229  -0.3419  -0.0250
 PM5  O1    O  O     0  -0.386   -5.7794   0.0931  -1.0553
 PM5  C2    C  CH2   0  -0.538   -7.6255  -0.1140   0.4744
 PM5  C3    C  CH2   0  -0.416   -8.5868   0.3969  -0.5891
 PM5  C4    C  CH2   0  -0.416   -9.9845   0.6158  -0.0227
 PM5  C5    C  CH2   0  -0.408  -10.9754   1.1193  -1.0642
 PM5  C6    C  CH2   0  -0.418  -12.3735   1.3438  -0.5012
 PM5  C7    C  CH3   0  -0.663  -13.3611   1.8439  -1.5463
 PM5  H23   H  HOH1  0   0.501    8.9795   4.6750  -0.1040
 PM5  H24   H  H     0   0.070    9.3410   1.9089   0.4944
 PM5  H281  H  HCH2  0   0.236    7.5171   0.0950   0.4215
 PM5  H282  H  HCH2  0   0.252    5.9390   0.8079   0.7928
 PM5  H301  H  HCH3  0   0.249    5.2545   1.6774  -2.1997
 PM5  H302  H  HCH3  0   0.235    4.4434   0.1719  -2.5907
 PM5  H303  H  HCH3  0   0.236    4.1546   0.9521  -1.0333
 PM5  H311  H  HCH3  0   0.236    8.0421  -0.7550  -1.9192
 PM5  H312  H  HCH3  0   0.231    6.7626  -0.7870  -3.1314
 PM5  H313  H  HCH3  0   0.241    7.4911   0.7433  -2.6674
 PM5  H32   H  HCH1  0   0.258    5.2644  -1.9635  -1.6868
 PM5  H33   H  HOH1  0   0.446    6.6918  -2.1614   0.6832
 PM5  H36   H  HNH1  0   0.408    3.1188  -1.4839  -1.2028
 PM5  H371  H  HCH2  0   0.254    2.1680  -2.1106   1.4473
 PM5  H372  H  HCH2  0   0.251    2.0557  -0.3842   1.1274
 PM5  H381  H  HCH2  0   0.285    0.7860  -0.8821  -0.9890
 PM5  H382  H  HCH2  0   0.272    0.8634  -2.5970  -0.6201
 PM5  H41   H  HNH1  0   0.407   -1.2563  -3.0040  -0.2869
 PM5  H421  H  HCH2  0   0.270   -3.0957  -3.2482   1.1009
 PM5  H422  H  HCH2  0   0.261   -2.5824  -1.8756   2.0692
 PM5  H431  H  HCH2  0   0.286   -3.2502  -0.3172   0.2119
 PM5  H432  H  HCH2  0   0.285   -3.7697  -1.7089  -0.7550
 PM5  H21   H  HCH2  0   0.269   -7.9977  -1.0411   0.9207
 PM5  H22   H  HCH2  0   0.285   -7.5553   0.6021   1.3011
 PM5  H31   H  HCH2  0   0.228   -8.2134   1.3343  -1.0081
 PM5  H32A  H  HCH2  0   0.228   -8.6354  -0.3175  -1.4155
 PM5  H41A  H  HCH2  0   0.213  -10.3541  -0.3217   0.4067
 PM5  H42   H  HCH2  0   0.214   -9.9325   1.3304   0.8058
 PM5  H51   H  HCH2  0   0.208  -10.6052   2.0554  -1.4967
 PM5  H52   H  HCH2  0   0.209  -11.0295   0.4031  -1.8916
 PM5  H61   H  HCH2  0   0.211  -12.7425   0.4091  -0.0679
 PM5  H62   H  HCH2  0   0.211  -12.3195   2.0598   0.3245
 PM5  H71   H  HCH3  0   0.226  -14.3547   1.9885  -1.1205
 PM5  H72   H  HCH3  0   0.216  -13.0413   2.7986  -1.9688
 PM5  H73   H  HCH3  0   0.216  -13.4557   1.1354  -2.3714

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
 PM5  O23  P24   single  1.600  0.020  1.600
 PM5  O23  H23   single  0.832  0.020  0.971
 PM5  P24  O26   double  1.481  0.020  1.481
 PM5  P24  O27   single  1.599  0.020  1.599
 PM5  P24  H24   single  1.209  0.020  1.412
 PM5  O27  C28   single  1.432  0.020  1.432
 PM5  C28  C29   single  1.529  0.020  1.529
 PM5  C28  H281  single  0.970  0.020  1.090
 PM5  C28  H282  single  0.970  0.020  1.090
 PM5  C29  C30   single  1.530  0.020  1.530
 PM5  C29  C31   single  1.531  0.020  1.531
 PM5  C29  C32   single  1.555  0.020  1.555
 PM5  C30  H301  single  0.970  0.020  1.090
 PM5  C30  H302  single  0.970  0.020  1.090
 PM5  C30  H303  single  0.970  0.020  1.090
 PM5  C31  H311  single  0.970  0.020  1.090
 PM5  C31  H312  single  0.970  0.020  1.090
 PM5  C31  H313  single  0.970  0.020  1.090
 PM5  C32  O33   single  1.402  0.020  1.402
 PM5  C32  C34   single  1.530  0.020  1.530
 PM5  C32  H32   single  0.970  0.020  1.090
 PM5  O33  H33   single  0.850  0.020  0.980
 PM5  C34  O35   double  1.226  0.020  1.226
 PM5  C34  N36   single  1.333  0.020  1.333
 PM5  N36  C37   single  1.450  0.020  1.450
 PM5  N36  H36   single  0.860  0.020  1.020
 PM5  C37  C38   single  1.520  0.020  1.520
 PM5  C37  H371  single  0.970  0.020  1.090
 PM5  C37  H372  single  0.970  0.020  1.090
 PM5  C38  C39   single  1.514  0.020  1.514
 PM5  C38  H381  single  0.970  0.020  1.090
 PM5  C38  H382  single  0.970  0.020  1.090
 PM5  C39  O40   double  1.222  0.020  1.222
 PM5  C39  N41   single  1.344  0.020  1.344
 PM5  N41  C42   single  1.443  0.020  1.443
 PM5  N41  H41   single  0.860  0.020  1.020
 PM5  C42  C43   single  1.526  0.020  1.526
 PM5  C42  H421  single  0.970  0.020  1.090
 PM5  C42  H422  single  0.970  0.020  1.090
 PM5  C43  S1    single  1.815  0.020  1.815
 PM5  C43  H431  single  0.970  0.020  1.090
 PM5  C43  H432  single  0.970  0.020  1.090
 PM5  S1   C1    single  1.775  0.020  1.775
 PM5  C1   O1    double  1.203  0.020  1.203
 PM5  C1   C2    single  1.506  0.020  1.506
 PM5  C2   C3    single  1.522  0.020  1.522
 PM5  C2   H21   single  0.970  0.020  1.090
 PM5  C2   H22   single  0.970  0.020  1.090
 PM5  C3   C4    single  1.524  0.020  1.524
 PM5  C3   H31   single  0.970  0.020  1.090
 PM5  C3   H32A  single  0.970  0.020  1.090
 PM5  C4   C5    single  1.523  0.020  1.523
 PM5  C4   H41A  single  0.970  0.020  1.090
 PM5  C4   H42   single  0.970  0.020  1.090
 PM5  C5   C6    single  1.524  0.020  1.524
 PM5  C5   H51   single  0.970  0.020  1.090
 PM5  C5   H52   single  0.970  0.020  1.090
 PM5  C6   C7    single  1.522  0.020  1.522
 PM5  C6   H61   single  0.970  0.020  1.090
 PM5  C6   H62   single  0.970  0.020  1.090
 PM5  C7   H71   single  0.970  0.020  1.090
 PM5  C7   H72   single  0.970  0.020  1.090
 PM5  C7   H73   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
 PM5  H23   O23  P24   113.52  3.000
 PM5  H24   P24  O27   104.35  3.000
 PM5  H24   P24  O26   113.27  3.000
 PM5  O27   P24  O26   116.90  3.000
 PM5  H24   P24  O23   106.34  3.000
 PM5  O27   P24  O23    97.21  3.000
 PM5  O26   P24  O23   116.86  3.000
 PM5  C28   O27  P24   118.73  3.000
 PM5  H282  C28  H281  108.11  3.000
 PM5  H282  C28  C29   111.38  3.000
 PM5  H281  C28  C29   109.78  3.000
 PM5  H282  C28  O27   108.75  3.000
 PM5  H281  C28  O27   109.99  3.000
 PM5  C29   C28  O27   108.82  3.000
 PM5  C32   C29  C31   107.66  3.000
 PM5  C32   C29  C30   109.96  3.000
 PM5  C31   C29  C30   108.97  3.000
 PM5  C32   C29  C28   109.59  3.000
 PM5  C31   C29  C28   110.14  3.000
 PM5  C30   C29  C28   110.47  3.000
 PM5  H303  C30  H302  107.93  3.000
 PM5  H303  C30  H301  107.62  3.000
 PM5  H302  C30  H301  107.00  3.000
 PM5  H303  C30  C29   112.63  3.000
 PM5  H302  C30  C29   110.68  3.000
 PM5  H301  C30  C29   110.75  3.000
 PM5  H313  C31  H312  107.32  3.000
 PM5  H313  C31  H311  107.98  3.000
 PM5  H312  C31  H311  107.76  3.000
 PM5  H313  C31  C29   111.09  3.000
 PM5  H312  C31  C29   110.41  3.000
 PM5  H311  C31  C29   112.08  3.000
 PM5  H32   C32  C34   109.05  3.000
 PM5  H32   C32  O33   107.25  3.000
 PM5  C34   C32  O33   108.50  3.000
 PM5  H32   C32  C29   106.15  3.000
 PM5  C34   C32  C29   113.11  3.000
 PM5  O33   C32  C29   112.55  3.000
 PM5  H33   O33  C32   107.76  3.000
 PM5  N36   C34  O35   123.37  3.000
 PM5  N36   C34  C32   116.65  3.000
 PM5  O35   C34  C32   119.97  3.000
 PM5  H36   N36  C37   118.41  3.000
 PM5  H36   N36  C34   118.56  3.000
 PM5  C37   N36  C34   122.95  3.000
 PM5  H372  C37  H371  107.41  3.000
 PM5  H372  C37  C38   110.27  3.000
 PM5  H371  C37  C38   110.00  3.000
 PM5  H372  C37  N36   110.12  3.000
 PM5  H371  C37  N36   109.39  3.000
 PM5  C38   C37  N36   109.63  3.000
 PM5  H382  C38  H381  106.79  3.000
 PM5  H382  C38  C39   111.13  3.000
 PM5  H381  C38  C39   107.14  3.000
 PM5  H382  C38  C37   110.19  3.000
 PM5  H381  C38  C37   109.82  3.000
 PM5  C39   C38  C37   111.59  3.000
 PM5  N41   C39  O40   123.02  3.000
 PM5  N41   C39  C38   115.05  3.000
 PM5  O40   C39  C38   121.92  3.000
 PM5  H41   N41  C42   117.56  3.000
 PM5  H41   N41  C39   118.94  3.000
 PM5  C42   N41  C39   123.26  3.000
 PM5  H422  C42  H421  107.38  3.000
 PM5  H422  C42  C43   110.63  3.000
 PM5  H421  C42  C43   110.32  3.000
 PM5  H422  C42  N41   109.14  3.000
 PM5  H421  C42  N41   107.97  3.000
 PM5  C43   C42  N41   111.28  3.000
 PM5  H432  C43  H431  108.87  3.000
 PM5  H432  C43  S1    109.01  3.000
 PM5  H431  C43  S1    109.33  3.000
 PM5  H432  C43  C42   110.47  3.000
 PM5  H431  C43  C42   110.62  3.000
 PM5  S1    C43  C42   108.51  3.000
 PM5  C1    S1   C43   101.54  3.000
 PM5  C2    C1   O1    124.93  3.000
 PM5  C2    C1   S1    112.56  3.000
 PM5  O1    C1   S1    122.51  3.000
 PM5  H22   C2   H21   105.53  3.000
 PM5  H22   C2   C3    110.38  3.000
 PM5  H21   C2   C3    110.77  3.000
 PM5  H22   C2   C1    106.82  3.000
 PM5  H21   C2   C1    108.89  3.000
 PM5  C3    C2   C1    114.03  3.000
 PM5  H32A  C3   H31   106.61  3.000
 PM5  H32A  C3   C4    109.51  3.000
 PM5  H31   C3   C4    109.44  3.000
 PM5  H32A  C3   C2    109.68  3.000
 PM5  H31   C3   C2    109.88  3.000
 PM5  C4    C3   C2    111.58  3.000
 PM5  H42   C4   H41A  106.13  3.000
 PM5  H42   C4   C5    109.41  3.000
 PM5  H41A  C4   C5    109.36  3.000
 PM5  H42   C4   C3    109.35  3.000
 PM5  H41A  C4   C3    109.41  3.000
 PM5  C5    C4   C3    112.95  3.000
 PM5  H52   C5   H51   106.09  3.000
 PM5  H52   C5   C6    109.27  3.000
 PM5  H51   C5   C6    109.27  3.000
 PM5  H52   C5   C4    109.41  3.000
 PM5  H51   C5   C4    109.42  3.000
 PM5  C6    C5   C4    113.14  3.000
 PM5  H62   C6   H61   106.07  3.000
 PM5  H62   C6   C7    109.57  3.000
 PM5  H61   C6   C7    109.49  3.000
 PM5  H62   C6   C5    109.26  3.000
 PM5  H61   C6   C5    109.26  3.000
 PM5  C7    C6   C5    112.95  3.000
 PM5  H73   C7   H72   107.48  3.000
 PM5  H73   C7   H71   107.58  3.000
 PM5  H72   C7   H71   107.58  3.000
 PM5  H73   C7   C6    111.22  3.000
 PM5  H72   C7   C6    111.28  3.000
 PM5  H71   C7   C6    111.50  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
 PM5  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 PM5  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 PM5  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 PM5  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 PM5  CONST_05  H36   N36  C34  C32     0.00   0.0  0
 PM5  CONST_06  H41   N41  C39  C38     0.00   0.0  0
 PM5  Var_01    C29   C28  O27  P24  -160.53  30.0  3
 PM5  Var_02    C30   C29  C28  O27   -60.47  30.0  3
 PM5  Var_03    C38   C37  N36  C34  -171.85  30.0  3
 PM5  Var_04    C39   C38  C37  N36  -175.96  30.0  3
 PM5  Var_05    O40   C39  C38  C37    40.13  30.0  3
 PM5  Var_06    C43   C42  N41  C39    86.82  30.0  3
 PM5  Var_07    S1    C43  C42  N41   179.26  30.0  3
 PM5  Var_08    O1    C1   S1   C43     1.83  30.0  3
 PM5  Var_09    C3    C2   C1   S1   -165.02  30.0  3
 PM5  Var_10    C4    C3   C2   C1   -179.65  30.0  3
 PM5  Var_11    C5    C4   C3   C2   -179.63  30.0  3
 PM5  Var_12    C6    C5   C4   C3   -179.82  30.0  3
 PM5  Var_13    C7    C6   C5   C4   -179.87  30.0  3
 PM5  Var_14    H24   P24  O27  C28    62.92  30.0  1
 PM5  Var_15    H301  C30  C29  C28    66.20  30.0  3
 PM5  Var_16    H311  C31  C29  C28    57.12  30.0  3
 PM5  Var_17    H71   C7   C6   C5    179.52  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
 PM5  chir_02  C32  C29  O33  C34  negativ
 PM5  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
 PM5  plan-1  C32  0.020
 PM5  plan-1  C34  0.020
 PM5  plan-1  O35  0.020
 PM5  plan-1  N36  0.020
 PM5  plan-1  C37  0.020
 PM5  plan-1  H36  0.020
 PM5  plan-2  C38  0.020
 PM5  plan-2  C39  0.020
 PM5  plan-2  O40  0.020
 PM5  plan-2  N41  0.020
 PM5  plan-2  C42  0.020
 PM5  plan-2  H41  0.020
 PM5  plan-3  S1   0.020
 PM5  plan-3  C1   0.020
 PM5  plan-3  O1   0.020
 PM5  plan-3  C2   0.020

