# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 00:27:39 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (2~{S})-4-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)N[C@@H](CCN)C(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
 JC2  JC2  '(2~{S})-4-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]butanoic acid'  ligand  60  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JC2
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
 JC2  C10  C  C      0   0.413    6.5489   0.2175  -0.3690
 JC2  C11  C  CH2    0  -0.556   -1.3553  -0.2500  -1.3374
 JC2  C12  C  C      0   0.747   -3.4570   0.8219  -0.6764
 JC2  C13  C  CH2    0  -0.233   -5.5720   1.5507   0.0864
 JC2  C14  C  CR6    0   0.075   -6.9425   0.9671   0.2556
 JC2  C15  C  CR16   0  -0.284   -7.7119   0.6508  -0.8625
 JC2  C16  C  CR16   0  -0.242   -8.9737   0.0949  -0.7153
 JC2  C19  C  CR16   0  -0.300   -7.4584   0.7178   1.5222
 JC2  O01  O  OP    -1  -0.811   -1.0797  -2.3490   0.3332
 JC2  N01  N  NH1    0  -0.788    1.1040  -1.0407  -0.5248
 JC2  C01  C  CH1    0  -0.201    2.2464  -0.9990   0.3710
 JC2  C02  C  CH2    0  -0.416    2.5406  -2.3459   1.0394
 JC2  C03  C  CH1    0  -0.273    3.6839  -2.3376   2.0553
 JC2  C04  C  CH3    0  -0.656    3.3386  -1.5027   3.2853
 JC2  C05  C  CH3    0  -0.650    4.0298  -3.7662   2.4641
 JC2  C06  C  C      0   0.573    3.4515  -0.5493  -0.4504
 JC2  N02  N  NH1    0  -0.624    4.0903   0.5371  -0.0059
 JC2  C07  C  CH1    0  -0.183    5.2786   1.0666  -0.6336
 JC2  O02  O  OC    -1  -0.619    7.5237   0.5007  -1.0945
 JC2  O03  O  O      0  -0.581    6.5092  -0.6351   0.5338
 JC2  O04  O  O      0  -0.518    3.7730  -1.1441  -1.4736
 JC2  O05  O  O      0  -0.808   -0.4740   0.0105   1.2594
 JC2  N04  N  NH1    0  -0.646   -2.7868  -0.2527  -1.1217
 JC2  O06  O  O2     0  -0.485   -4.7169   0.4921  -0.3509
 JC2  C17  C  CR16   0  -0.262   -9.4828  -0.1503   0.5552
 JC2  C18  C  CR16   0  -0.241   -8.7244   0.1647   1.6738
 JC2  O07  O  O      0  -0.527   -3.0189   1.9530  -0.5997
 JC2  C08  C  CH2    0  -0.472    5.5008   2.5102  -0.1852
 JC2  C09  C  CH2    0  -0.269    4.3699   3.4533  -0.5714
 JC2  N03  N  NH2    0  -0.801    4.6825   4.8168  -0.1623
 JC2  H1   H  HCH2   0   0.253   -1.0225   0.7688  -1.5275
 JC2  H2   H  HCH2   0   0.249   -1.1349  -0.8294  -2.2377
 JC2  H3   H  HCH2   0   0.244   -5.5854   2.3557  -0.6518
 JC2  H4   H  HCH2   0   0.245   -5.2089   1.9649   1.0303
 JC2  H5   H  HCR6   0   0.254   -7.3246   0.8466  -1.8555
 JC2  H6   H  HCR6   0   0.257   -9.5626  -0.1437  -1.5915
 JC2  H7   H  HCR6   0   0.255   -6.8697   0.9590   2.3993
 JC2  H9   H  HNH1   0   0.353    1.2217  -1.7640  -1.2248
 JC2  H10  H  HCH1   0   0.243    2.0266  -0.2527   1.1377
 JC2  H11  H  HCH2   0   0.224    1.6227  -2.6886   1.5286
 JC2  H12  H  HCH2   0   0.213    2.7541  -3.0757   0.2504
 JC2  H13  H  HCH1   0   0.249    4.5703  -1.8967   1.5868
 JC2  H14  H  HCH3   0   0.225    4.1577  -1.5104   4.0062
 JC2  H15  H  HCH3   0   0.220    3.1375  -0.4594   3.0374
 JC2  H16  H  HCH3   0   0.212    2.4508  -1.8962   3.7878
 JC2  H17  H  HCH3   0   0.222    4.3321  -4.3649   1.6025
 JC2  H18  H  HCH3   0   0.222    4.8505  -3.7867   3.1838
 JC2  H19  H  HCH3   0   0.210    3.1725  -4.2626   2.9258
 JC2  H20  H  HNH1   0   0.386    3.8239   0.9123   0.8904
 JC2  H21  H  HCH1   0   0.229    5.1095   1.0725  -1.7148
 JC2  H23  H  HNH1   0   0.391   -3.2230  -1.1553  -1.0144
 JC2  H24  H  HCR6   0   0.258  -10.4681  -0.5833   0.6714
 JC2  H25  H  HCR6   0   0.258   -9.1159  -0.0208   2.6655
 JC2  H26  H  HCH2   0   0.220    5.6495   2.5380   0.9018
 JC2  H27  H  HCH2   0   0.238    6.4276   2.8685  -0.6355
 JC2  H28  H  HCH2   0   0.213    4.2567   3.4374  -1.6593
 JC2  H29  H  HCH2   0   0.193    3.4211   3.0854  -0.1591
 JC2  H30  H  HNH2   0   0.345    3.9348   5.4332  -0.4547
 JC2  H31  H  HNH2   0   0.337    4.6875   4.8643   0.8498
 JC2  P01  P  P      0   1.219   -0.4820  -0.9761   0.1172

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
 JC2  C16  C15  aromatic  1.387  0.020  1.387
 JC2  C16  C17  aromatic  1.390  0.020  1.390
 JC2  C15  C14  aromatic  1.394  0.020  1.394
 JC2  C17  C18  aromatic  1.388  0.020  1.388
 JC2  C14  C13  single    1.499  0.020  1.499
 JC2  C14  C19  aromatic  1.390  0.020  1.390
 JC2  C13  O06  single    1.429  0.020  1.429
 JC2  C18  C19  aromatic  1.390  0.020  1.390
 JC2  O06  C12  single    1.342  0.020  1.342
 JC2  O07  C12  double    1.215  0.020  1.215
 JC2  C12  N04  single    1.342  0.020  1.342
 JC2  N04  C11  single    1.448  0.020  1.448
 JC2  C11  P01  single    1.845  0.020  1.845
 JC2  O05  P01  deloc     1.509  0.020  1.509
 JC2  O01  P01  deloc     1.513  0.020  1.513
 JC2  O03  C10  deloc     1.242  0.020  1.242
 JC2  P01  N01  single    1.712  0.020  1.712
 JC2  O02  C10  deloc     1.248  0.020  1.248
 JC2  C10  C07  single    1.551  0.020  1.551
 JC2  N01  C01  single    1.452  0.020  1.452
 JC2  C07  N02  single    1.444  0.020  1.444
 JC2  C07  C08  single    1.528  0.020  1.528
 JC2  N02  C06  single    1.336  0.020  1.336
 JC2  C06  O04  double    1.226  0.020  1.226
 JC2  C06  C01  single    1.526  0.020  1.526
 JC2  C01  C02  single    1.532  0.020  1.532
 JC2  C08  C09  single    1.522  0.020  1.522
 JC2  C09  N03  single    1.457  0.020  1.457
 JC2  C02  C03  single    1.530  0.020  1.530
 JC2  C05  C03  single    1.526  0.020  1.526
 JC2  C03  C04  single    1.526  0.020  1.526
 JC2  C11  H1   single    0.970  0.020  1.090
 JC2  C11  H2   single    0.970  0.020  1.090
 JC2  C13  H3   single    0.970  0.020  1.090
 JC2  C13  H4   single    0.970  0.020  1.090
 JC2  C15  H5   single    0.930  0.020  1.080
 JC2  C16  H6   single    0.930  0.020  1.080
 JC2  C19  H7   single    0.930  0.020  1.080
 JC2  N01  H9   single    0.890  0.020  1.040
 JC2  C01  H10  single    0.970  0.020  1.090
 JC2  C02  H11  single    0.970  0.020  1.090
 JC2  C02  H12  single    0.970  0.020  1.090
 JC2  C03  H13  single    0.970  0.020  1.090
 JC2  C04  H14  single    0.970  0.020  1.090
 JC2  C04  H15  single    0.970  0.020  1.090
 JC2  C04  H16  single    0.970  0.020  1.090
 JC2  C05  H17  single    0.970  0.020  1.090
 JC2  C05  H18  single    0.970  0.020  1.090
 JC2  C05  H19  single    0.970  0.020  1.090
 JC2  N02  H20  single    0.860  0.020  1.020
 JC2  C07  H21  single    0.970  0.020  1.090
 JC2  N04  H23  single    0.890  0.020  1.040
 JC2  C17  H24  single    0.930  0.020  1.080
 JC2  C18  H25  single    0.930  0.020  1.080
 JC2  C08  H26  single    0.970  0.020  1.090
 JC2  C08  H27  single    0.970  0.020  1.090
 JC2  C09  H28  single    0.970  0.020  1.090
 JC2  C09  H29  single    0.970  0.020  1.090
 JC2  N03  H30  single    0.890  0.020  1.040
 JC2  N03  H31  single    0.890  0.020  1.040

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
 JC2  O03  C10  O02  127.10  3.000
 JC2  O02  C10  C07  114.61  3.000
 JC2  O03  C10  C07  118.27  3.000
 JC2  H2   C11  H1   106.90  3.000
 JC2  H2   C11  N04  108.73  3.000
 JC2  H1   C11  N04  109.28  3.000
 JC2  H2   C11  P01  110.19  3.000
 JC2  H1   C11  P01  111.17  3.000
 JC2  N04  C11  P01  110.47  3.000
 JC2  O07  C12  O06  123.48  3.000
 JC2  O07  C12  N04  125.87  3.000
 JC2  O06  C12  N04  110.63  3.000
 JC2  H4   C13  H3   107.97  3.000
 JC2  H4   C13  O06  110.25  3.000
 JC2  H3   C13  O06  110.27  3.000
 JC2  H4   C13  C14  110.72  3.000
 JC2  H3   C13  C14  110.60  3.000
 JC2  O06  C13  C14  107.04  3.000
 JC2  C19  C14  C15  119.04  3.000
 JC2  C19  C14  C13  120.79  3.000
 JC2  C15  C14  C13  120.17  3.000
 JC2  H5   C15  C16  119.67  3.000
 JC2  H5   C15  C14  119.79  3.000
 JC2  C16  C15  C14  120.54  3.000
 JC2  H6   C16  C17  120.11  3.000
 JC2  H6   C16  C15  119.83  3.000
 JC2  C17  C16  C15  120.06  3.000
 JC2  H7   C19  C18  119.69  3.000
 JC2  H7   C19  C14  119.73  3.000
 JC2  C18  C19  C14  120.58  3.000
 JC2  H9   N01  C01  110.81  3.000
 JC2  H9   N01  P01  113.17  3.000
 JC2  C01  N01  P01  119.76  3.000
 JC2  H10  C01  C06  109.59  3.000
 JC2  H10  C01  C02  109.46  3.000
 JC2  C06  C01  C02  110.02  3.000
 JC2  H10  C01  N01  107.11  3.000
 JC2  C02  C01  N01  113.26  3.000
 JC2  C06  C01  N01  107.31  3.000
 JC2  H12  C02  H11  106.05  3.000
 JC2  H12  C02  C03  109.64  3.000
 JC2  H11  C02  C03  109.36  3.000
 JC2  H12  C02  C01  107.99  3.000
 JC2  H11  C02  C01  108.00  3.000
 JC2  C03  C02  C01  115.37  3.000
 JC2  H13  C03  C05  107.94  3.000
 JC2  H13  C03  C04  107.92  3.000
 JC2  C05  C03  C04  110.34  3.000
 JC2  H13  C03  C02  108.85  3.000
 JC2  C04  C03  C02  111.66  3.000
 JC2  C05  C03  C02  110.02  3.000
 JC2  H16  C04  H15  107.39  3.000
 JC2  H16  C04  H14  107.66  3.000
 JC2  H15  C04  H14  107.17  3.000
 JC2  H16  C04  C03  110.93  3.000
 JC2  H15  C04  C03  112.44  3.000
 JC2  H14  C04  C03  111.02  3.000
 JC2  H19  C05  H18  107.62  3.000
 JC2  H19  C05  H17  107.55  3.000
 JC2  H18  C05  H17  107.57  3.000
 JC2  H19  C05  C03  111.14  3.000
 JC2  H18  C05  C03  111.39  3.000
 JC2  H17  C05  C03  111.39  3.000
 JC2  O04  C06  N02  123.12  3.000
 JC2  O04  C06  C01  120.87  3.000
 JC2  N02  C06  C01  115.98  3.000
 JC2  H20  N02  C07  117.88  3.000
 JC2  H20  N02  C06  118.18  3.000
 JC2  C07  N02  C06  123.14  3.000
 JC2  H21  C07  C08  107.90  3.000
 JC2  H21  C07  N02  107.71  3.000
 JC2  C08  C07  N02  109.78  3.000
 JC2  H21  C07  C10  107.35  3.000
 JC2  C08  C07  C10  110.37  3.000
 JC2  N02  C07  C10  113.52  3.000
 JC2  H23  N04  C12  117.73  3.000
 JC2  H23  N04  C11  116.44  3.000
 JC2  C12  N04  C11  122.79  3.000
 JC2  C13  O06  C12  116.98  3.000
 JC2  H24  C17  C18  120.11  3.000
 JC2  H24  C17  C16  120.12  3.000
 JC2  C18  C17  C16  119.76  3.000
 JC2  H25  C18  C17  120.14  3.000
 JC2  H25  C18  C19  119.85  3.000
 JC2  C17  C18  C19  120.02  3.000
 JC2  H27  C08  H26  106.58  3.000
 JC2  H27  C08  C09  108.83  3.000
 JC2  H26  C08  C09  109.65  3.000
 JC2  H27  C08  C07  108.23  3.000
 JC2  H26  C08  C07  109.54  3.000
 JC2  C09  C08  C07  113.76  3.000
 JC2  H29  C09  H28  106.21  3.000
 JC2  H29  C09  N03  113.17  3.000
 JC2  H28  C09  N03  108.36  3.000
 JC2  H29  C09  C08  109.82  3.000
 JC2  H28  C09  C08  108.67  3.000
 JC2  N03  C09  C08  110.43  3.000
 JC2  H31  N03  H30  105.29  3.000
 JC2  H31  N03  C09  108.99  3.000
 JC2  H30  N03  C09  109.28  3.000
 JC2  O05  P01  N01  107.67  3.000
 JC2  N01  P01  O01  112.66  3.000
 JC2  O05  P01  O01  119.16  3.000
 JC2  N01  P01  C11   99.07  3.000
 JC2  O01  P01  C11  106.42  3.000
 JC2  O05  P01  C11  109.99  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
 JC2  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 JC2  CONST_02  C17  C18  C19  C14     0.00   0.0  0
 JC2  CONST_03  C18  C17  C16  C15     0.00   0.0  0
 JC2  CONST_04  C18  C19  C14  C15     0.00   0.0  0
 JC2  CONST_05  C19  C14  C15  C16     0.00   0.0  0
 JC2  CONST_06  C19  C18  C17  C16     0.00   0.0  0
 JC2  CONST_07  C16  C15  C14  C13   180.00   0.0  0
 JC2  CONST_08  C18  C19  C14  C13   180.00   0.0  0
 JC2  CONST_09  H6   C16  C15  C14   180.00   0.0  0
 JC2  CONST_10  H25  C18  C19  C14   180.00   0.0  0
 JC2  CONST_11  H24  C17  C16  C15   180.00   0.0  0
 JC2  CONST_12  H7   C19  C14  C15   180.00   0.0  0
 JC2  CONST_13  H5   C15  C14  C19   180.00   0.0  0
 JC2  CONST_14  C07  N02  C06  C01   180.00   0.0  0
 JC2  CONST_15  O04  C06  N02  C07     0.00   0.0  0
 JC2  CONST_16  H20  N02  C06  C01     0.00   0.0  0
 JC2  Var_01    O06  C13  C14  C15   -73.80  30.0  2
 JC2  Var_02    C14  C13  O06  C12   174.44  30.0  2
 JC2  Var_03    O06  C12  N04  C11  -169.61  30.0  2
 JC2  Var_04    C01  N01  P01  C11   153.74  30.0  3
 JC2  Var_05    P01  C11  N04  C12    97.32  30.0  3
 JC2  Var_06    N04  C11  P01  O01    55.23  30.0  2
 JC2  Var_07    C05  C03  C02  C01  -170.34  30.0  3
 JC2  Var_08    N03  C09  C08  C07  -177.49  30.0  3
 JC2  Var_09    H17  C05  C03  C02    59.42  30.0  3
 JC2  Var_10    H14  C04  C03  C02   179.55  30.0  3
 JC2  Var_11    H30  N03  C09  C08   178.11  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
 JC2  chir_02  C01  N01  C06  C02  positiv
 JC2  chir_03  C07  N02  C08  C10  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
 JC2  plan-1  C13  0.020
 JC2  plan-1  C14  0.020
 JC2  plan-1  C15  0.020
 JC2  plan-1  C16  0.020
 JC2  plan-1  C19  0.020
 JC2  plan-1  C17  0.020
 JC2  plan-1  C18  0.020
 JC2  plan-1  H5   0.020
 JC2  plan-1  H6   0.020
 JC2  plan-1  H7   0.020
 JC2  plan-1  H24  0.020
 JC2  plan-1  H25  0.020
 JC2  plan-2  C01  0.020
 JC2  plan-2  C06  0.020
 JC2  plan-2  N02  0.020
 JC2  plan-2  C07  0.020
 JC2  plan-2  O04  0.020
 JC2  plan-2  H20  0.020
 JC2  plan-3  C10  0.020
 JC2  plan-3  C07  0.020
 JC2  plan-3  O02  0.020
 JC2  plan-3  O03  0.020
 JC2  plan-4  C12  0.020
 JC2  plan-4  N04  0.020
 JC2  plan-4  O06  0.020
 JC2  plan-4  O07  0.020

