# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:52:20 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  62  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 PERFECT
;

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   0.550    6.2994   0.5013  -0.4111
 JC2  C11  C  CH2   0  -0.568   -1.3645  -0.8276  -1.3084
 JC2  C12  C  C     0   0.763   -3.3058   0.5313  -0.7383
 JC2  C13  C  CH2   0  -0.240   -5.3198   1.6065  -0.1376
 JC2  C14  C  CR6   0   0.075   -6.7350   1.2049   0.1464
 JC2  C15  C  CR16  0  -0.287   -7.6264   0.9885  -0.9013
 JC2  C16  C  CR16  0  -0.242   -8.9307   0.5897  -0.6463
 JC2  C19  C  CR16  0  -0.292   -7.1691   1.0141   1.4544
 JC2  O01  O  OH1   0  -0.751   -1.0072  -2.4283   0.8736
 JC2  N01  N  NH1   0  -0.779    1.1449  -1.3429  -0.3581
 JC2  C01  C  CH1   0  -0.214    2.3120  -1.2395   0.5078
 JC2  C02  C  CH2   0  -0.407    2.7345  -2.5892   1.0848
 JC2  C03  C  CH1   0  -0.265    3.9337  -2.5418   2.0336
 JC2  C04  C  CH3   0  -0.657    3.6449  -1.7152   3.2836
 JC2  C05  C  CH3   0  -0.649    4.3417  -3.9608   2.4169
 JC2  C06  C  C     0   0.593    3.4323  -0.6364  -0.3319
 JC2  N02  N  NH1   0  -0.639    3.9168   0.5412   0.0877
 JC2  C07  C  CH1   0  -0.187    4.9736   1.2199  -0.6138
 JC2  O02  O  OH1   0  -0.591    7.1846   0.8685  -1.3269
 JC2  O03  O  O     0  -0.425    6.5324  -0.2744   0.4777
 JC2  O04  O  O     0  -0.489    3.8366  -1.1942  -1.3405
 JC2  O05  O  O     0  -0.712   -0.4723   0.0048   1.2218
 JC2  N04  N  NH1   0  -0.655   -2.7611  -0.6731  -1.0069
 JC2  O06  O  O2    0  -0.478   -4.5883   0.3997  -0.3903
 JC2  C17  C  CR16  0  -0.261   -9.3566   0.4025   0.6631
 JC2  C18  C  CR16  0  -0.242   -8.4741   0.6165   1.7136
 JC2  O07  O  O     0  -0.514   -2.7263   1.5932  -0.8234
 JC2  C08  C  CH2   0  -0.476    5.0818   2.6754  -0.1516
 JC2  C09  C  CH2   0  -0.272    3.8490   3.4960  -0.5106
 JC2  N03  N  NH2   0  -0.799    4.0377   4.8785  -0.0988
 JC2  H1   H  HCH2  0   0.297   -0.9851   0.0569  -1.8186
 JC2  H2   H  HCH2  0   0.304   -1.2304  -1.6700  -1.9895
 JC2  H3   H  HCH2  0   0.249   -5.2701   2.2634  -1.0081
 JC2  H4   H  HCH2  0   0.249   -4.8869   2.1361   0.7135
 JC2  H5   H  HCR6  0   0.255   -7.2999   1.1388  -1.9236
 JC2  H6   H  HCR6  0   0.258   -9.6156   0.4281  -1.4685
 JC2  H7   H  HCR6  0   0.255   -6.4845   1.1813   2.2777
 JC2  H8   H  HOH1  0   0.484   -0.9143  -3.2288   0.3412
 JC2  H9   H  HNH1  0   0.401    1.2544  -2.0005  -1.1209
 JC2  H10  H  HCH1  0   0.265    2.0473  -0.5586   1.3197
 JC2  H11  H  HCH2  0   0.234    1.8740  -3.0111   1.6135
 JC2  H12  H  HCH2  0   0.232    2.9512  -3.2687   0.2546
 JC2  H13  H  HCH1  0   0.237    4.7791  -2.0817   1.5106
 JC2  H14  H  HCH3  0   0.232    4.4961  -1.7371   3.9653
 JC2  H15  H  HCH3  0   0.221    3.4433  -0.6664   3.0602
 JC2  H16  H  HCH3  0   0.218    2.7794  -2.1106   3.8211
 JC2  H17  H  HCH3  0   0.226    4.6003  -4.5534   1.5375
 JC2  H18  H  HCH3  0   0.228    5.2094  -3.9560   3.0787
 JC2  H19  H  HCH3  0   0.215    3.5306  -4.4759   2.9373
 JC2  H20  H  HNH1  0   0.407    3.5930   0.9307   0.9589
 JC2  H21  H  HCH1  0   0.289    4.7506   1.2141  -1.6850
 JC2  H22  H  HOH1  0   0.485    8.0388   0.4434  -1.1574
 JC2  H23  H  HNH1  0   0.410   -3.3130  -1.5027  -0.8580
 JC2  H24  H  HCR6  0   0.259  -10.3746   0.0951   0.8645
 JC2  H25  H  HCR6  0   0.259   -8.8017   0.4753   2.7353
 JC2  H26  H  HCH2  0   0.246    5.2549   2.7041   0.9296
 JC2  H27  H  HCH2  0   0.263    5.9521   3.1353  -0.6217
 JC2  H28  H  HCH2  0   0.226    3.7197   3.4740  -1.5957
 JC2  H29  H  HCH2  0   0.202    2.9504   3.0325  -0.0834
 JC2  H30  H  HNH2  0   0.351    3.2604   5.4345  -0.4313
 JC2  H31  H  HNH2  0   0.341    3.9965   4.9352   0.9117
 JC2  P01  P  P     0   1.312   -0.3916  -1.0829   0.2127

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  1.388  0.020  1.388
 JC2  C16  C17  aromatic  1.390  0.020  1.390
 JC2  C15  C14  aromatic  1.392  0.020  1.392
 JC2  C17  C18  aromatic  1.389  0.020  1.389
 JC2  C14  C13  single    1.498  0.020  1.498
 JC2  C14  C19  aromatic  1.391  0.020  1.391
 JC2  C13  O06  single    1.434  0.020  1.434
 JC2  C18  C19  aromatic  1.389  0.020  1.389
 JC2  O06  C12  single    1.335  0.020  1.335
 JC2  O07  C12  double    1.213  0.020  1.213
 JC2  C12  N04  single    1.349  0.020  1.349
 JC2  N04  C11  single    1.437  0.020  1.437
 JC2  C11  P01  single    1.824  0.020  1.824
 JC2  O05  P01  double    1.486  0.020  1.486
 JC2  O01  P01  single    1.620  0.020  1.620
 JC2  O03  C10  double    1.203  0.020  1.203
 JC2  P01  N01  single    1.660  0.020  1.660
 JC2  O02  C10  single    1.325  0.020  1.325
 JC2  C10  C07  single    1.522  0.020  1.522
 JC2  N01  C01  single    1.457  0.020  1.457
 JC2  C07  N02  single    1.439  0.020  1.439
 JC2  C07  C08  single    1.531  0.020  1.531
 JC2  N02  C06  single    1.341  0.020  1.341
 JC2  C06  O04  double    1.221  0.020  1.221
 JC2  C06  C01  single    1.524  0.020  1.524
 JC2  C01  C02  single    1.527  0.020  1.527
 JC2  C08  C09  single    1.524  0.020  1.524
 JC2  C09  N03  single    1.455  0.020  1.455
 JC2  C02  C03  single    1.530  0.020  1.530
 JC2  C05  C03  single    1.525  0.020  1.525
 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  O01  H8   single    0.850  0.020  0.980
 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  O02  H22  single    0.850  0.020  0.980
 JC2  N04  H23  single    0.860  0.020  1.020
 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  124.05  3.000
 JC2  O02  C10  C07  111.04  3.000
 JC2  O03  C10  C07  124.88  3.000
 JC2  H2   C11  H1   106.95  3.000
 JC2  H2   C11  N04  109.47  3.000
 JC2  H1   C11  N04  110.45  3.000
 JC2  H2   C11  P01  110.30  3.000
 JC2  H1   C11  P01  108.57  3.000
 JC2  N04  C11  P01  111.01  3.000
 JC2  O07  C12  O06  124.30  3.000
 JC2  O07  C12  N04  125.09  3.000
 JC2  O06  C12  N04  110.59  3.000
 JC2  H4   C13  H3   108.16  3.000
 JC2  H4   C13  O06  110.08  3.000
 JC2  H3   C13  O06  110.04  3.000
 JC2  H4   C13  C14  110.90  3.000
 JC2  H3   C13  C14  110.82  3.000
 JC2  O06  C13  C14  106.84  3.000
 JC2  C19  C14  C15  119.10  3.000
 JC2  C19  C14  C13  120.64  3.000
 JC2  C15  C14  C13  120.25  3.000
 JC2  H5   C15  C16  119.76  3.000
 JC2  H5   C15  C14  119.69  3.000
 JC2  C16  C15  C14  120.54  3.000
 JC2  H6   C16  C17  120.12  3.000
 JC2  H6   C16  C15  119.88  3.000
 JC2  C17  C16  C15  120.00  3.000
 JC2  H7   C19  C18  119.74  3.000
 JC2  H7   C19  C14  119.74  3.000
 JC2  C18  C19  C14  120.53  3.000
 JC2  H8   O01  P01  115.26  3.000
 JC2  H9   N01  C01  114.02  3.000
 JC2  H9   N01  P01  117.44  3.000
 JC2  C01  N01  P01  121.74  3.000
 JC2  H10  C01  C06  109.93  3.000
 JC2  H10  C01  C02  109.70  3.000
 JC2  C06  C01  C02  110.75  3.000
 JC2  H10  C01  N01  106.98  3.000
 JC2  C02  C01  N01  112.55  3.000
 JC2  C06  C01  N01  106.83  3.000
 JC2  H12  C02  H11  106.42  3.000
 JC2  H12  C02  C03  109.54  3.000
 JC2  H11  C02  C03  109.19  3.000
 JC2  H12  C02  C01  108.47  3.000
 JC2  H11  C02  C01  107.80  3.000
 JC2  C03  C02  C01  115.07  3.000
 JC2  H13  C03  C05  107.71  3.000
 JC2  H13  C03  C04  108.04  3.000
 JC2  C05  C03  C04  110.40  3.000
 JC2  H13  C03  C02  108.78  3.000
 JC2  C04  C03  C02  112.11  3.000
 JC2  C05  C03  C02  109.68  3.000
 JC2  H16  C04  H15  107.59  3.000
 JC2  H16  C04  H14  107.65  3.000
 JC2  H15  C04  H14  106.95  3.000
 JC2  H16  C04  C03  110.90  3.000
 JC2  H15  C04  C03  112.82  3.000
 JC2  H14  C04  C03  110.69  3.000
 JC2  H19  C05  H18  107.66  3.000
 JC2  H19  C05  H17  107.68  3.000
 JC2  H18  C05  H17  107.61  3.000
 JC2  H19  C05  C03  111.08  3.000
 JC2  H18  C05  C03  111.16  3.000
 JC2  H17  C05  C03  111.47  3.000
 JC2  O04  C06  N02  122.68  3.000
 JC2  O04  C06  C01  121.16  3.000
 JC2  N02  C06  C01  116.15  3.000
 JC2  H20  N02  C07  118.38  3.000
 JC2  H20  N02  C06  119.60  3.000
 JC2  C07  N02  C06  121.82  3.000
 JC2  H21  C07  C08  108.36  3.000
 JC2  H21  C07  N02  108.98  3.000
 JC2  C08  C07  N02  110.68  3.000
 JC2  H21  C07  C10  107.79  3.000
 JC2  C08  C07  C10  110.31  3.000
 JC2  N02  C07  C10  110.63  3.000
 JC2  H22  O02  C10  110.26  3.000
 JC2  H23  N04  C12  118.99  3.000
 JC2  H23  N04  C11  118.35  3.000
 JC2  C12  N04  C11  122.02  3.000
 JC2  C13  O06  C12  116.93  3.000
 JC2  H24  C17  C18  120.05  3.000
 JC2  H24  C17  C16  120.13  3.000
 JC2  C18  C17  C16  119.82  3.000
 JC2  H25  C18  C17  120.12  3.000
 JC2  H25  C18  C19  119.87  3.000
 JC2  C17  C18  C19  120.01  3.000
 JC2  H27  C08  H26  106.75  3.000
 JC2  H27  C08  C09  108.47  3.000
 JC2  H26  C08  C09  110.26  3.000
 JC2  H27  C08  C07  109.10  3.000
 JC2  H26  C08  C07  109.52  3.000
 JC2  C09  C08  C07  112.56  3.000
 JC2  H29  C09  H28  106.32  3.000
 JC2  H29  C09  N03  113.41  3.000
 JC2  H28  C09  N03  108.39  3.000
 JC2  H29  C09  C08  110.07  3.000
 JC2  H28  C09  C08  108.59  3.000
 JC2  N03  C09  C08  109.89  3.000
 JC2  H31  N03  H30  105.41  3.000
 JC2  H31  N03  C09  109.29  3.000
 JC2  H30  N03  C09  109.24  3.000
 JC2  O05  P01  N01  113.49  3.000
 JC2  N01  P01  O01  111.22  3.000
 JC2  O05  P01  O01  108.07  3.000
 JC2  N01  P01  C11  103.23  3.000
 JC2  O01  P01  C11  104.70  3.000
 JC2  O05  P01  C11  115.79  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  CONST_17  H22  O02  C10  C07   180.00   0.0  0
 JC2  Var_01    O06  C13  C14  C15   -84.25  30.0  2
 JC2  Var_02    C14  C13  O06  C12   176.56  30.0  1
 JC2  Var_03    O06  C12  N04  C11  -175.21  30.0  1
 JC2  Var_04    C01  N01  P01  C11   163.26  30.0  3
 JC2  Var_05    P01  C11  N04  C12    88.86  30.0  3
 JC2  Var_06    N04  C11  P01  O01    59.64  30.0  1
 JC2  Var_07    C05  C03  C02  C01  -173.98  30.0  3
 JC2  Var_08    N03  C09  C08  C07  -177.50  30.0  3
 JC2  Var_09    H17  C05  C03  C02    58.80  30.0  3
 JC2  Var_10    H14  C04  C03  C02   177.22  30.0  3
 JC2  Var_11    H30  N03  C09  C08   173.82  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
 JC2  chir_04  P01  O05  O01  N01  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
 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-3  H22  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

