# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 08:12:40 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: N-(1,3-benzodioxol-5-ylmethyl)-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-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)NCc1ccc2OCOc2c1
#
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
 3V9  3V9  N-(1,3-benzodioxol-5-ylmethyl)-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide  ligand  54  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3V9
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
 3V9  O1   O  OH1   0  -0.732  -5.3349  -3.4377  -1.2403
 3V9  O2   O  O     0  -0.712  -6.4892  -2.0756   0.6860
 3V9  O3   O  OH1   0  -0.745  -4.1511  -2.9292   0.9971
 3V9  P    P  P     0   1.455  -5.2446  -2.3932  -0.0390
 3V9  O01  O  O2    0  -0.587  -4.5661  -1.2117  -0.8647
 3V9  C02  C  CH2   0  -0.149  -4.2516   0.0262  -0.2132
 3V9  C03  C  CT    0  -0.162  -3.9218   1.0688  -1.2798
 3V9  C04  C  CH3   0  -0.675  -2.7315   0.6094  -2.1236
 3V9  C25  C  CH3   0  -0.647  -5.1282   1.2888  -2.1966
 3V9  C05  C  CH1   0  -0.030  -3.6009   2.4261  -0.5896
 3V9  O24  O  OH1   0  -0.663  -4.6858   2.9150   0.1494
 3V9  C06  C  C     0   0.508  -2.3821   2.3567   0.3337
 3V9  O23  O  O     0  -0.498  -2.5394   2.1302   1.5293
 3V9  N07  N  NH1   0  -0.624  -1.1899   2.5656  -0.2260
 3V9  C08  C  CH2   0  -0.280   0.0587   2.4585   0.4989
 3V9  C09  C  CH2   0  -0.599   0.5218   1.0124   0.6220
 3V9  C10  C  C     0   0.578   1.8431   0.8882   1.3534
 3V9  O22  O  O     0  -0.505   2.3750   1.8407   1.9074
 3V9  N11  N  NH1   0  -0.623   2.3658  -0.3505   1.3498
 3V9  C12  C  CH2   0  -0.391   3.6228  -0.7062   1.9723
 3V9  C13  C  CR6   0   0.107   4.7565  -0.8136   0.9839
 3V9  C21  C  CR16  0  -0.382   5.2172   0.3429   0.3295
 3V9  C17  C  CR56  0   0.316   6.2383   0.1895  -0.5711
 3V9  O18  O  O     0  -0.487   6.8396   1.1338  -1.3355
 3V9  C19  C  CH2   0   0.069   7.9501   0.4969  -1.9532
 3V9  O20  O  O     0  -0.486   7.7754  -0.9029  -1.7778
 3V9  C16  C  CR56  0   0.290   6.8086  -1.0474  -0.8385
 3V9  C15  C  CR16  0  -0.333   6.3788  -2.1882  -0.2119
 3V9  C14  C  CR16  0  -0.325   5.3318  -2.0448   0.7099
 3V9  H1   H  HOH1  0   0.504  -5.8630  -4.2214  -1.0377
 3V9  H2   H  HOH1  0   0.495  -3.3114  -3.2165   0.6136
 3V9  H3   H  HCH2  0   0.243  -5.1042   0.3530   0.3875
 3V9  H4   H  HCH2  0   0.244  -3.4013  -0.1350   0.4554
 3V9  H5   H  HCH3  0   0.250  -3.0118  -0.2271  -2.7628
 3V9  H6   H  HCH3  0   0.236  -2.3884   1.4111  -2.7818
 3V9  H7   H  HCH3  0   0.235  -1.8835   0.2855  -1.5177
 3V9  H8   H  HCH3  0   0.237  -6.0078   1.6134  -1.6414
 3V9  H9   H  HCH3  0   0.231  -4.9040   2.0527  -2.9438
 3V9  H10  H  HCH3  0   0.239  -5.3844   0.3750  -2.7322
 3V9  H11  H  HCH1  0   0.258  -3.3974   3.1428  -1.3952
 3V9  H12  H  HOH1  0   0.446  -4.5460   2.6647   1.0728
 3V9  H13  H  HNH1  0   0.410  -1.1424   2.7474  -1.2156
 3V9  H14  H  HCH2  0   0.264   0.7959   3.0507  -0.0401
 3V9  H15  H  HCH2  0   0.254  -0.0618   2.9098   1.4826
 3V9  H16  H  HCH2  0   0.281  -0.2287   0.4212   1.1549
 3V9  H17  H  HCH2  0   0.272   0.6165   0.5631  -0.3707
 3V9  H18  H  HNH1  0   0.401   1.8988  -1.0656   0.8151
 3V9  H19  H  HCH2  0   0.265   3.8450   0.0417   2.7325
 3V9  H20  H  HCH2  0   0.270   3.4955  -1.6585   2.4888
 3V9  H21  H  HCR6  0   0.268   4.7849   1.3140   0.5336
 3V9  H22  H  HCH2  0   0.246   7.9691   0.7364  -3.0162
 3V9  H23  H  HCH2  0   0.233   8.8789   0.8191  -1.4707
 3V9  H24  H  HCR6  0   0.272   6.8186  -3.1548  -0.4175
 3V9  H25  H  HCR6  0   0.256   4.9669  -2.9255   1.2239

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
 3V9  O2   P    double    1.475  0.020  1.475
 3V9  O3   P    single    1.599  0.020  1.599
 3V9  P    O1   single    1.594  0.020  1.594
 3V9  P    O01  single    1.593  0.020  1.593
 3V9  O24  C05  single    1.401  0.020  1.401
 3V9  O01  C02  single    1.434  0.020  1.434
 3V9  C05  C06  single    1.531  0.020  1.531
 3V9  C05  C03  single    1.556  0.020  1.556
 3V9  O23  C06  double    1.227  0.020  1.227
 3V9  C06  N07  single    1.334  0.020  1.334
 3V9  N07  C08  single    1.448  0.020  1.448
 3V9  C08  C09  single    1.523  0.020  1.523
 3V9  C02  C03  single    1.528  0.020  1.528
 3V9  C03  C04  single    1.530  0.020  1.530
 3V9  C03  C25  single    1.531  0.020  1.531
 3V9  O22  C10  double    1.224  0.020  1.224
 3V9  C10  C09  single    1.515  0.020  1.515
 3V9  C10  N11  single    1.344  0.020  1.344
 3V9  C12  N11  single    1.447  0.020  1.447
 3V9  C12  C13  single    1.508  0.020  1.508
 3V9  C14  C13  aromatic  1.386  0.020  1.386
 3V9  C14  C15  aromatic  1.402  0.020  1.402
 3V9  C13  C21  aromatic  1.406  0.020  1.406
 3V9  C15  C16  aromatic  1.371  0.020  1.371
 3V9  C21  C17  aromatic  1.370  0.020  1.370
 3V9  C16  C17  aromatic  1.388  0.020  1.388
 3V9  C16  O20  single    1.356  0.020  1.356
 3V9  C17  O18  single    1.356  0.020  1.356
 3V9  O20  C19  single    1.421  0.020  1.421
 3V9  O18  C19  single    1.421  0.020  1.421
 3V9  O1   H1   single    0.850  0.020  0.980
 3V9  O3   H2   single    0.850  0.020  0.980
 3V9  C02  H3   single    0.970  0.020  1.090
 3V9  C02  H4   single    0.970  0.020  1.090
 3V9  C04  H5   single    0.970  0.020  1.090
 3V9  C04  H6   single    0.970  0.020  1.090
 3V9  C04  H7   single    0.970  0.020  1.090
 3V9  C25  H8   single    0.970  0.020  1.090
 3V9  C25  H9   single    0.970  0.020  1.090
 3V9  C25  H10  single    0.970  0.020  1.090
 3V9  C05  H11  single    0.970  0.020  1.090
 3V9  O24  H12  single    0.850  0.020  0.980
 3V9  N07  H13  single    0.860  0.020  1.020
 3V9  C08  H14  single    0.970  0.020  1.090
 3V9  C08  H15  single    0.970  0.020  1.090
 3V9  C09  H16  single    0.970  0.020  1.090
 3V9  C09  H17  single    0.970  0.020  1.090
 3V9  N11  H18  single    0.860  0.020  1.020
 3V9  C12  H19  single    0.970  0.020  1.090
 3V9  C12  H20  single    0.970  0.020  1.090
 3V9  C21  H21  single    0.930  0.020  1.080
 3V9  C19  H22  single    0.970  0.020  1.090
 3V9  C19  H23  single    0.970  0.020  1.090
 3V9  C15  H24  single    0.930  0.020  1.080
 3V9  C14  H25  single    0.930  0.020  1.080

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
 3V9  H1   O1   P    113.84  3.000
 3V9  H2   O3   P    115.89  3.000
 3V9  O01  P    O3   107.05  3.000
 3V9  O01  P    O2   117.03  3.000
 3V9  O3   P    O2   109.32  3.000
 3V9  O01  P    O1    96.86  3.000
 3V9  O3   P    O1   107.90  3.000
 3V9  O2   P    O1   117.62  3.000
 3V9  C02  O01  P    119.88  3.000
 3V9  H4   C02  H3   108.34  3.000
 3V9  H4   C02  C03  111.07  3.000
 3V9  H3   C02  C03  110.37  3.000
 3V9  H4   C02  O01  108.73  3.000
 3V9  H3   C02  O01  109.68  3.000
 3V9  C03  C02  O01  108.62  3.000
 3V9  C05  C03  C25  107.62  3.000
 3V9  C25  C03  C04  109.02  3.000
 3V9  C05  C03  C04  110.25  3.000
 3V9  C25  C03  C02  110.24  3.000
 3V9  C04  C03  C02  110.38  3.000
 3V9  C05  C03  C02  109.28  3.000
 3V9  H7   C04  H6   107.95  3.000
 3V9  H7   C04  H5   107.32  3.000
 3V9  H6   C04  H5   106.90  3.000
 3V9  H7   C04  C03  112.80  3.000
 3V9  H6   C04  C03  110.88  3.000
 3V9  H5   C04  C03  110.74  3.000
 3V9  H10  C25  H9   107.37  3.000
 3V9  H10  C25  H8   108.08  3.000
 3V9  H9   C25  H8   107.82  3.000
 3V9  H10  C25  C03  111.05  3.000
 3V9  H9   C25  C03  110.40  3.000
 3V9  H8   C25  C03  111.94  3.000
 3V9  H11  C05  C06  108.96  3.000
 3V9  H11  C05  O24  107.64  3.000
 3V9  C06  C05  O24  108.32  3.000
 3V9  H11  C05  C03  106.39  3.000
 3V9  C06  C05  C03  113.09  3.000
 3V9  O24  C05  C03  112.25  3.000
 3V9  H12  O24  C05  107.54  3.000
 3V9  N07  C06  O23  123.54  3.000
 3V9  N07  C06  C05  116.85  3.000
 3V9  O23  C06  C05  119.61  3.000
 3V9  H13  N07  C08  117.69  3.000
 3V9  H13  N07  C06  118.87  3.000
 3V9  C08  N07  C06  123.32  3.000
 3V9  H15  C08  H14  107.27  3.000
 3V9  H15  C08  C09  110.74  3.000
 3V9  H14  C08  C09  110.52  3.000
 3V9  H15  C08  N07  109.04  3.000
 3V9  H14  C08  N07  107.21  3.000
 3V9  C09  C08  N07  111.89  3.000
 3V9  H17  C09  H16  106.24  3.000
 3V9  H17  C09  C10  109.20  3.000
 3V9  H16  C09  C10  108.58  3.000
 3V9  H17  C09  C08  110.06  3.000
 3V9  H16  C09  C08  110.11  3.000
 3V9  C10  C09  C08  112.45  3.000
 3V9  N11  C10  O22  123.33  3.000
 3V9  N11  C10  C09  114.41  3.000
 3V9  O22  C10  C09  122.26  3.000
 3V9  H18  N11  C12  117.15  3.000
 3V9  H18  N11  C10  118.37  3.000
 3V9  C12  N11  C10  124.26  3.000
 3V9  H20  C12  H19  107.03  3.000
 3V9  H20  C12  C13  109.63  3.000
 3V9  H19  C12  C13  110.67  3.000
 3V9  H20  C12  N11  108.47  3.000
 3V9  H19  C12  N11  107.98  3.000
 3V9  C13  C12  N11  112.87  3.000
 3V9  C14  C13  C21  120.16  3.000
 3V9  C21  C13  C12  119.52  3.000
 3V9  C14  C13  C12  120.32  3.000
 3V9  H21  C21  C17  121.47  3.000
 3V9  H21  C21  C13  121.28  3.000
 3V9  C17  C21  C13  117.25  3.000
 3V9  C16  C17  O18  109.26  3.000
 3V9  O18  C17  C21  128.55  3.000
 3V9  C16  C17  C21  122.18  3.000
 3V9  C19  O18  C17  106.23  3.000
 3V9  H23  C19  H22  110.50  3.000
 3V9  H23  C19  O20  109.86  3.000
 3V9  H22  C19  O20  109.81  3.000
 3V9  H23  C19  O18  109.83  3.000
 3V9  H22  C19  O18  109.82  3.000
 3V9  O20  C19  O18  106.95  3.000
 3V9  C16  O20  C19  106.15  3.000
 3V9  C15  C16  O20  128.98  3.000
 3V9  O20  C16  C17  109.36  3.000
 3V9  C15  C16  C17  121.65  3.000
 3V9  H24  C15  C14  121.33  3.000
 3V9  H24  C15  C16  121.96  3.000
 3V9  C14  C15  C16  116.71  3.000
 3V9  H25  C14  C15  118.71  3.000
 3V9  H25  C14  C13  119.25  3.000
 3V9  C15  C14  C13  122.05  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
 3V9  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 3V9  CONST_02  C16  C17  C21  C13     0.00   0.0  0
 3V9  CONST_03  C15  C14  C13  C21     0.00   0.0  0
 3V9  CONST_04  C15  C16  C17  C21     0.00   0.0  0
 3V9  CONST_05  C14  C13  C21  C17     0.00   0.0  0
 3V9  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 3V9  CONST_07  C15  C14  C13  C12   180.00   0.0  0
 3V9  CONST_08  C17  C21  C13  C12   180.00   0.0  0
 3V9  CONST_09  H24  C15  C14  C13   180.00   0.0  0
 3V9  CONST_10  H25  C14  C13  C21   180.00   0.0  0
 3V9  CONST_11  H21  C21  C17  O18     0.00   0.0  0
 3V9  CONST_12  C08  N07  C06  C05   180.00   0.0  0
 3V9  CONST_13  C08  N07  C06  O23     0.00   0.0  0
 3V9  CONST_14  C12  N11  C10  C09   180.00   0.0  0
 3V9  CONST_15  C12  N11  C10  O22     0.00   0.0  0
 3V9  CONST_16  H13  N07  C06  C05     0.00   0.0  0
 3V9  CONST_17  H18  N11  C10  C09     0.00   0.0  0
 3V9  Var_01    O20  C19  O18  C17    13.90  30.0  1
 3V9  Var_02    C15  C16  O20  C19  -172.08  30.0  1
 3V9  Var_03    C16  C17  O18  C19    -8.62  30.0  1
 3V9  Var_04    C14  C13  C12  N11  -111.97  30.0  2
 3V9  Var_05    C13  C12  N11  C10  -100.66  30.0  1
 3V9  Var_06    C03  C02  O01  P    -167.10  30.0  3
 3V9  Var_07    C05  C03  C02  O01   179.06  30.0  3
 3V9  Var_08    C09  C08  N07  C06    81.42  30.0  3
 3V9  Var_09    C10  C09  C08  N07   178.79  30.0  3
 3V9  Var_10    O22  C10  C09  C08     7.93  30.0  2
 3V9  Var_11    H5   C04  C03  C02    70.46  30.0  3
 3V9  Var_12    H8   C25  C03  C02    58.40  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
 3V9  chir_01  C05  O24  C06  C03  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
 3V9  plan-1  C05  0.020
 3V9  plan-1  C06  0.020
 3V9  plan-1  O23  0.020
 3V9  plan-1  N07  0.020
 3V9  plan-1  C08  0.020
 3V9  plan-1  H13  0.020
 3V9  plan-2  C12  0.020
 3V9  plan-2  C13  0.020
 3V9  plan-2  C21  0.020
 3V9  plan-2  C17  0.020
 3V9  plan-2  O18  0.020
 3V9  plan-2  O20  0.020
 3V9  plan-2  C16  0.020
 3V9  plan-2  C15  0.020
 3V9  plan-2  C14  0.020
 3V9  plan-2  H21  0.020
 3V9  plan-2  H24  0.020
 3V9  plan-2  H25  0.020
 3V9  plan-3  C09  0.020
 3V9  plan-3  C10  0.020
 3V9  plan-3  O22  0.020
 3V9  plan-3  N11  0.020
 3V9  plan-3  C12  0.020
 3V9  plan-3  H18  0.020

