# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:13:55 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-[2-(propanoylamino)ethyl]-beta-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)NCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(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
 42X  42X  N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-[2-(propanoylamino)ethyl]-beta-alaninamide  ligand  54  26  .  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_42X
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
 42X  C14  C  CH3   0  -0.669  -3.1074   0.0259   1.8606
 42X  C10  C  CH3   0  -0.647  -5.0166  -1.5715   2.0239
 42X  O01  O  OH1   0  -0.745  -6.8545   1.4690  -1.6300
 42X  P02  P  P     0   1.450  -6.0410   2.0165  -0.3661
 42X  O03  O  O     0  -0.709  -4.9731   2.9224  -0.8293
 42X  O04  O  OH1   0  -0.731  -7.0912   2.5952   0.6846
 42X  O05  O  O2    0  -0.586  -5.5985   0.7491   0.4886
 42X  C06  C  CH2   0  -0.155  -4.6946  -0.2153  -0.0679
 42X  C09  C  CT    0  -0.157  -3.9898  -0.9455   1.0743
 42X  C18  C  CH1   0  -0.036  -3.1275  -2.1030   0.4978
 42X  O20  O  OH1   0  -0.661  -3.8959  -3.0521  -0.1918
 42X  C22  C  C     0   0.524  -2.0067  -1.6274  -0.4271
 42X  O23  O  O     0  -0.500  -2.2227  -1.4764  -1.6251
 42X  N24  N  NH1   0  -0.639  -0.8166  -1.4159   0.1347
 42X  C26  C  CH2   0  -0.235   0.3443  -0.9946  -0.6253
 42X  C29  C  CH2   0  -0.637   1.5347  -0.8395   0.3048
 42X  C32  C  C     0   0.569   2.8137  -0.5528  -0.4550
 42X  O33  O  O     0  -0.498   3.0247  -1.0115  -1.5687
 42X  N34  N  NH1   0  -0.635   3.6983   0.2179   0.1986
 42X  C36  C  CH2   0  -0.299   5.0275   0.4918  -0.2946
 42X  C39  C  CH2   0  -0.295   6.0057  -0.6334   0.0495
 42X  N42  N  NH1   0  -0.635   7.3379  -0.3771  -0.4414
 42X  C44  C  C     0   0.556   8.2289   0.3964   0.2043
 42X  O45  O  O     0  -0.505   7.9875   0.9165   1.2855
 42X  C46  C  CH2   0  -0.570   9.5516   0.5900  -0.5069
 42X  C49  C  CH3   0  -0.660  10.7288   0.6343   0.4559
 42X  H1   H  HCH3  0   0.235  -2.5024  -0.5040   2.5996
 42X  H2   H  HCH3  0   0.236  -2.4333   0.5928   1.2177
 42X  H3   H  HCH3  0   0.248  -3.7205   0.7420   2.4064
 42X  H4   H  HCH3  0   0.240  -5.5937  -0.8074   2.5432
 42X  H5   H  HCH3  0   0.236  -5.7153  -2.2244   1.5008
 42X  H6   H  HCH3  0   0.230  -4.5106  -2.1679   2.7862
 42X  H7   H  HOH1  0   0.495  -7.6071   0.8959  -1.4311
 42X  H8   H  HOH1  0   0.503  -7.3970   3.4891   0.4817
 42X  H9   H  HCH2  0   0.244  -5.2696  -0.9152  -0.6793
 42X  H10  H  HCH2  0   0.244  -3.9678   0.2863  -0.7119
 42X  H11  H  HCH1  0   0.257  -2.6857  -2.6131   1.3613
 42X  H12  H  HOH1  0   0.446  -3.9099  -2.7995  -1.1237
 42X  H13  H  HNH1  0   0.408  -0.6999  -1.6279   1.1130
 42X  H14  H  HCH2  0   0.249   0.5655  -1.7309  -1.3991
 42X  H15  H  HCH2  0   0.251   0.1325  -0.0479  -1.1268
 42X  H16  H  HCH2  0   0.272   1.3427  -0.0610   1.0466
 42X  H17  H  HCH2  0   0.287   1.6929  -1.7698   0.8614
 42X  H18  H  HNH1  0   0.405   3.4674   0.5383   1.1248
 42X  H19  H  HCH2  0   0.247   4.9926   0.6377  -1.3742
 42X  H20  H  HCH2  0   0.258   5.3654   1.4269   0.1504
 42X  H21  H  HCH2  0   0.245   6.0361  -0.7778   1.1301
 42X  H22  H  HCH2  0   0.256   5.6611  -1.5676  -0.3929
 42X  H23  H  HNH1  0   0.402   7.5894  -0.7589  -1.3382
 42X  H24  H  HCH2  0   0.249   9.7015  -0.1895  -1.2565
 42X  H25  H  HCH2  0   0.267   9.4891   1.5330  -1.0590
 42X  H26  H  HCH3  0   0.229  10.6206   1.4415   1.1780
 42X  H27  H  HCH3  0   0.228  10.8251  -0.3012   1.0078
 42X  H28  H  HCH3  0   0.235  11.6582   0.7945  -0.0890

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
 42X  O45  C44  double  1.224  0.020  1.224
 42X  C39  C36  single  1.530  0.020  1.530
 42X  C39  N42  single  1.443  0.020  1.443
 42X  C36  N34  single  1.444  0.020  1.444
 42X  O33  C32  double  1.223  0.020  1.223
 42X  C44  N42  single  1.345  0.020  1.345
 42X  C44  C46  single  1.514  0.020  1.514
 42X  O23  C22  double  1.227  0.020  1.227
 42X  N34  C32  single  1.343  0.020  1.343
 42X  C18  C22  single  1.529  0.020  1.529
 42X  C18  O20  single  1.402  0.020  1.402
 42X  C18  C09  single  1.554  0.020  1.554
 42X  C32  C29  single  1.515  0.020  1.515
 42X  C46  C49  single  1.521  0.020  1.521
 42X  C22  N24  single  1.333  0.020  1.333
 42X  C10  C09  single  1.532  0.020  1.532
 42X  C14  C09  single  1.530  0.020  1.530
 42X  C09  C06  single  1.528  0.020  1.528
 42X  N24  C26  single  1.450  0.020  1.450
 42X  C26  C29  single  1.519  0.020  1.519
 42X  C06  O05  single  1.434  0.020  1.434
 42X  O05  P02  single  1.592  0.020  1.592
 42X  P02  O03  double  1.475  0.020  1.475
 42X  P02  O04  single  1.594  0.020  1.594
 42X  P02  O01  single  1.600  0.020  1.600
 42X  C14  H1   single  0.970  0.020  1.090
 42X  C14  H2   single  0.970  0.020  1.090
 42X  C14  H3   single  0.970  0.020  1.090
 42X  C10  H4   single  0.970  0.020  1.090
 42X  C10  H5   single  0.970  0.020  1.090
 42X  C10  H6   single  0.970  0.020  1.090
 42X  O01  H7   single  0.850  0.020  0.980
 42X  O04  H8   single  0.850  0.020  0.980
 42X  C06  H9   single  0.970  0.020  1.090
 42X  C06  H10  single  0.970  0.020  1.090
 42X  C18  H11  single  0.970  0.020  1.090
 42X  O20  H12  single  0.850  0.020  0.980
 42X  N24  H13  single  0.860  0.020  1.020
 42X  C26  H14  single  0.970  0.020  1.090
 42X  C26  H15  single  0.970  0.020  1.090
 42X  C29  H16  single  0.970  0.020  1.090
 42X  C29  H17  single  0.970  0.020  1.090
 42X  N34  H18  single  0.860  0.020  1.020
 42X  C36  H19  single  0.970  0.020  1.090
 42X  C36  H20  single  0.970  0.020  1.090
 42X  C39  H21  single  0.970  0.020  1.090
 42X  C39  H22  single  0.970  0.020  1.090
 42X  N42  H23  single  0.860  0.020  1.020
 42X  C46  H24  single  0.970  0.020  1.090
 42X  C46  H25  single  0.970  0.020  1.090
 42X  C49  H26  single  0.970  0.020  1.090
 42X  C49  H27  single  0.970  0.020  1.090
 42X  C49  H28  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
 42X  H3   C14  H2   107.55  3.000
 42X  H3   C14  H1   106.96  3.000
 42X  H2   C14  H1   107.98  3.000
 42X  H3   C14  C09  110.51  3.000
 42X  H2   C14  C09  112.56  3.000
 42X  H1   C14  C09  111.05  3.000
 42X  H6   C10  H5   107.75  3.000
 42X  H6   C10  H4   107.20  3.000
 42X  H5   C10  H4   108.02  3.000
 42X  H6   C10  C09  110.19  3.000
 42X  H5   C10  C09  112.14  3.000
 42X  H4   C10  C09  111.34  3.000
 42X  H7   O01  P02  115.87  3.000
 42X  O05  P02  O04   96.79  3.000
 42X  O04  P02  O03  117.45  3.000
 42X  O05  P02  O03  117.16  3.000
 42X  O04  P02  O01  108.06  3.000
 42X  O03  P02  O01  109.28  3.000
 42X  O05  P02  O01  107.05  3.000
 42X  H8   O04  P02  113.94  3.000
 42X  C06  O05  P02  120.16  3.000
 42X  H10  C06  H9   108.31  3.000
 42X  H10  C06  C09  110.68  3.000
 42X  H9   C06  C09  110.79  3.000
 42X  H10  C06  O05  109.82  3.000
 42X  H9   C06  O05  108.43  3.000
 42X  C09  C06  O05  108.78  3.000
 42X  C18  C09  C06  109.54  3.000
 42X  C06  C09  C10  110.45  3.000
 42X  C18  C09  C10  107.30  3.000
 42X  C06  C09  C14  110.29  3.000
 42X  C10  C09  C14  109.11  3.000
 42X  C18  C09  C14  110.09  3.000
 42X  H11  C18  C22  109.01  3.000
 42X  H11  C18  O20  107.06  3.000
 42X  C22  C18  O20  108.35  3.000
 42X  H11  C18  C09  106.14  3.000
 42X  O20  C18  C09  112.48  3.000
 42X  C22  C18  C09  113.54  3.000
 42X  H12  O20  C18  107.78  3.000
 42X  N24  C22  O23  123.32  3.000
 42X  N24  C22  C18  116.67  3.000
 42X  O23  C22  C18  120.00  3.000
 42X  H13  N24  C26  118.50  3.000
 42X  H13  N24  C22  118.63  3.000
 42X  C26  N24  C22  122.68  3.000
 42X  H15  C26  H14  107.38  3.000
 42X  H15  C26  C29  110.17  3.000
 42X  H14  C26  C29  110.15  3.000
 42X  H15  C26  N24  109.71  3.000
 42X  H14  C26  N24  109.75  3.000
 42X  C29  C26  N24  109.65  3.000
 42X  H17  C29  H16  106.60  3.000
 42X  H17  C29  C32  107.07  3.000
 42X  H16  C29  C32  110.74  3.000
 42X  H17  C29  C26  109.73  3.000
 42X  H16  C29  C26  110.54  3.000
 42X  C32  C29  C26  111.96  3.000
 42X  N34  C32  O33  123.01  3.000
 42X  N34  C32  C29  114.87  3.000
 42X  O33  C32  C29  122.10  3.000
 42X  H18  N34  C36  117.71  3.000
 42X  H18  N34  C32  118.63  3.000
 42X  C36  N34  C32  123.30  3.000
 42X  H20  C36  H19  107.44  3.000
 42X  H20  C36  C39  109.94  3.000
 42X  H19  C36  C39  109.98  3.000
 42X  H20  C36  N34  107.98  3.000
 42X  H19  C36  N34  109.52  3.000
 42X  C39  C36  N34  111.85  3.000
 42X  H22  C39  H21  107.32  3.000
 42X  H22  C39  N42  107.83  3.000
 42X  H21  C39  N42  109.57  3.000
 42X  H22  C39  C36  109.69  3.000
 42X  H21  C39  C36  109.76  3.000
 42X  N42  C39  C36  112.53  3.000
 42X  H23  N42  C44  118.71  3.000
 42X  H23  N42  C39  117.81  3.000
 42X  C44  N42  C39  123.40  3.000
 42X  C46  C44  O45  122.20  3.000
 42X  C46  C44  N42  115.26  3.000
 42X  O45  C44  N42  122.54  3.000
 42X  H25  C46  H24  106.06  3.000
 42X  H25  C46  C49  109.77  3.000
 42X  H24  C46  C49  110.43  3.000
 42X  H25  C46  C44  107.29  3.000
 42X  H24  C46  C44  110.55  3.000
 42X  C49  C46  C44  112.48  3.000
 42X  H28  C49  H27  107.70  3.000
 42X  H28  C49  H26  107.91  3.000
 42X  H27  C49  H26  108.02  3.000
 42X  H28  C49  C46  110.36  3.000
 42X  H27  C49  C46  111.33  3.000
 42X  H26  C49  C46  111.38  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
 42X  CONST_01  C26  N24  C22  C18   180.00   0.0  0
 42X  CONST_02  C26  N24  C22  O23     0.00   0.0  0
 42X  CONST_03  C36  N34  C32  C29   180.00   0.0  0
 42X  CONST_04  C36  N34  C32  O33     0.00   0.0  0
 42X  CONST_05  O45  C44  N42  C39     0.00   0.0  0
 42X  CONST_06  C46  C44  N42  C39   180.00   0.0  0
 42X  CONST_07  H13  N24  C22  C18     0.00   0.0  0
 42X  CONST_08  H18  N34  C32  C29     0.00   0.0  0
 42X  CONST_09  H23  N42  C44  O45   180.00   0.0  0
 42X  Var_01    O05  C06  C09  C14   -65.05  30.0  3
 42X  Var_02    C09  C06  O05  P02   156.13  30.0  1
 42X  Var_03    C29  C26  N24  C22   179.85  30.0  3
 42X  Var_04    C32  C29  C26  N24   173.55  30.0  3
 42X  Var_05    O33  C32  C29  C26   -32.90  30.0  2
 42X  Var_06    C39  C36  N34  C32   -82.91  30.0  2
 42X  Var_07    N42  C39  C36  N34   179.77  30.0  1
 42X  Var_08    C44  N42  C39  C36    82.38  30.0  3
 42X  Var_09    C49  C46  C44  N42  -143.29  30.0  3
 42X  Var_10    H4   C10  C09  C14    55.07  30.0  3
 42X  Var_11    H1   C14  C09  C10    65.63  30.0  3
 42X  Var_12    H26  C49  C46  C44   -59.02  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
 42X  chir_01  C18  C22  O20  C09  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
 42X  plan-1  C18  0.020
 42X  plan-1  C22  0.020
 42X  plan-1  O23  0.020
 42X  plan-1  N24  0.020
 42X  plan-1  C26  0.020
 42X  plan-1  H13  0.020
 42X  plan-2  C29  0.020
 42X  plan-2  C32  0.020
 42X  plan-2  O33  0.020
 42X  plan-2  N34  0.020
 42X  plan-2  C36  0.020
 42X  plan-2  H18  0.020
 42X  plan-3  C39  0.020
 42X  plan-3  N42  0.020
 42X  plan-3  C44  0.020
 42X  plan-3  O45  0.020
 42X  plan-3  C46  0.020
 42X  plan-3  H23  0.020

