# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:17:15 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(2-methylpropyl)-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CNC(=O)[C@H](CC(C)C)N[P](O)(=O)CNC(=O)OCc1ccccc1
#
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
 2G7  2G7  N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(2-methylpropyl)-L-leucinamide  ligand  59  28  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2G7
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
 2G7  C7   C  CH2    0  -0.235  -2.4909   0.9106   0.9331
 2G7  C6   C  CR6    0   0.075  -3.9711   0.9319   1.1682
 2G7  C1   C  CR16   0  -0.282  -4.7451   1.9790   0.6720
 2G7  C2   C  CR16   0  -0.243  -6.1175   1.9962   0.8702
 2G7  C3   C  CR16   0  -0.263  -6.7327   0.9648   1.5711
 2G7  C4   C  CR16   0  -0.241  -5.9690  -0.0810   2.0696
 2G7  C5   C  CR16   0  -0.301  -4.5946  -0.0969   1.8653
 2G7  C9   C  C      0   0.779  -1.0288   0.4843  -0.8735
 2G7  O10  O  O      0  -0.527  -0.0675   0.6846  -0.1498
 2G7  O8   O  O2     0  -0.481  -2.2916   0.5505  -0.4369
 2G7  N11  N  NH1    0  -0.629  -0.9826   0.2379  -2.1916
 2G7  C12  C  CH2    0  -0.599   0.2225  -0.2479  -2.8259
 2G7  P13  P  P      0   1.228   0.5139  -2.0780  -2.5317
 2G7  O14  O  O      0  -0.800  -0.4002  -2.4733  -1.3999
 2G7  O15  O  OP    -1  -0.815   0.4586  -2.7795  -3.8658
 2G7  N16  N  NH1    0  -0.785   2.1158  -2.2270  -1.9778
 2G7  C17  C  CH1    0  -0.191   2.5266  -1.7185  -0.6833
 2G7  C22  C  C      0   0.542   3.4420  -0.5102  -0.8722
 2G7  O23  O  O      0  -0.511   4.5810  -0.6462  -1.3069
 2G7  C18  C  CH2    0  -0.388   3.2259  -2.7975   0.1406
 2G7  C19  C  CH1    0  -0.254   3.6854  -2.3672   1.5349
 2G7  C20  C  CH3    0  -0.662   2.5382  -1.8142   2.3770
 2G7  C21  C  CH3    0  -0.647   4.3567  -3.5401   2.2428
 2G7  C28  C  CH3    0  -0.663   4.7158   1.7353   1.5612
 2G7  C26  C  CH1    0  -0.242   3.8506   2.6129   0.6665
 2G7  C29  C  CH3    0  -0.657   4.5000   3.9723   0.4320
 2G7  C25  C  CH2    0  -0.270   3.5701   1.9459  -0.6815
 2G7  N24  N  NH1    0  -0.660   2.8980   0.6739  -0.5576
 2G7  H25  H  HCH2   0   0.245  -2.0544   1.8924   1.1308
 2G7  H26  H  HCH2   0   0.247  -2.0051   0.1868   1.5907
 2G7  H27  H  HCR6   0   0.255  -4.2701   2.7904   0.1333
 2G7  H28  H  HCR6   0   0.258  -6.7078   2.8158   0.4814
 2G7  H29  H  HCR6   0   0.258  -7.8032   0.9800   1.7303
 2G7  H30  H  HCR6   0   0.258  -6.4415  -0.8864   2.6165
 2G7  H31  H  HCR6   0   0.256  -4.0039  -0.9165   2.2570
 2G7  H32  H  HNH1   0   0.394  -1.8522  -0.0282  -2.6268
 2G7  H23  H  HCH2   0   0.260   0.1312  -0.0655  -3.8968
 2G7  H24  H  HCH2   0   0.253   1.0714   0.3447  -2.4863
 2G7  H1   H  HNH1   0   0.357   2.8456  -2.2285  -2.6763
 2G7  H2   H  HCH1   0   0.247   1.6213  -1.4121  -0.1544
 2G7  H3   H  HCH2   0   0.218   2.5246  -3.6325   0.2356
 2G7  H4   H  HCH2   0   0.215   4.0846  -3.1717  -0.4250
 2G7  H5   H  HCH1   0   0.219   4.4368  -1.5763   1.4225
 2G7  H6   H  HCH3   0   0.228   2.8725  -1.5880   3.3910
 2G7  H7   H  HCH3   0   0.218   2.1273  -0.8917   1.9638
 2G7  H8   H  HCH3   0   0.218   1.7204  -2.5360   2.4492
 2G7  H9   H  HCH3   0   0.223   5.2043  -3.9166   1.6672
 2G7  H10  H  HCH3   0   0.224   4.7273  -3.2521   3.2280
 2G7  H11  H  HCH3   0   0.212   3.6555  -4.3672   2.3790
 2G7  H19  H  HCH3   0   0.236   4.2257   0.7899   1.7981
 2G7  H20  H  HCH3   0   0.214   5.6683   1.5039   1.0789
 2G7  H21  H  HCH3   0   0.229   4.9331   2.2369   2.5055
 2G7  H15  H  HCH1   0   0.218   2.8894   2.7762   1.1682
 2G7  H16  H  HCH3   0   0.216   5.4700   3.8635  -0.0600
 2G7  H17  H  HCH3   0   0.226   3.8780   4.6119  -0.1970
 2G7  H18  H  HCH3   0   0.230   4.6675   4.4957   1.3742
 2G7  H13  H  HCH2   0   0.241   2.9552   2.6113  -1.2945
 2G7  H14  H  HCH2   0   0.234   4.5071   1.7907  -1.2176
 2G7  H12  H  HNH1   0   0.417   1.9195   0.6888  -0.2943

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
 2G7  C2   C1   aromatic  1.387  0.020  1.387
 2G7  C2   C3   aromatic  1.390  0.020  1.390
 2G7  C1   C6   aromatic  1.393  0.020  1.393
 2G7  C3   C4   aromatic  1.388  0.020  1.388
 2G7  C6   C7   single    1.499  0.020  1.499
 2G7  C6   C5   aromatic  1.390  0.020  1.390
 2G7  C4   C5   aromatic  1.390  0.020  1.390
 2G7  C7   O8   single    1.430  0.020  1.430
 2G7  O8   C9   single    1.338  0.020  1.338
 2G7  C9   O10  double    1.220  0.020  1.220
 2G7  C9   N11  single    1.342  0.020  1.342
 2G7  N11  C12  single    1.446  0.020  1.446
 2G7  C12  P13  single    1.876  0.020  1.876
 2G7  O14  P13  deloc     1.508  0.020  1.508
 2G7  O15  P13  deloc     1.508  0.020  1.508
 2G7  P13  N16  single    1.702  0.020  1.702
 2G7  N16  C17  single    1.450  0.020  1.450
 2G7  C25  N24  single    1.444  0.020  1.444
 2G7  C25  C26  single    1.530  0.020  1.530
 2G7  N24  C22  single    1.341  0.020  1.341
 2G7  O23  C22  double    1.227  0.020  1.227
 2G7  C22  C17  single    1.528  0.020  1.528
 2G7  C17  C18  single    1.527  0.020  1.527
 2G7  C29  C26  single    1.525  0.020  1.525
 2G7  C26  C28  single    1.523  0.020  1.523
 2G7  C18  C19  single    1.530  0.020  1.530
 2G7  C20  C19  single    1.527  0.020  1.527
 2G7  C19  C21  single    1.526  0.020  1.526
 2G7  N16  H1   single    0.890  0.020  1.040
 2G7  C17  H2   single    0.970  0.020  1.090
 2G7  C18  H3   single    0.970  0.020  1.090
 2G7  C18  H4   single    0.970  0.020  1.090
 2G7  C19  H5   single    0.970  0.020  1.090
 2G7  C20  H6   single    0.970  0.020  1.090
 2G7  C20  H7   single    0.970  0.020  1.090
 2G7  C20  H8   single    0.970  0.020  1.090
 2G7  C21  H9   single    0.970  0.020  1.090
 2G7  C21  H10  single    0.970  0.020  1.090
 2G7  C21  H11  single    0.970  0.020  1.090
 2G7  N24  H12  single    0.860  0.020  1.020
 2G7  C25  H13  single    0.970  0.020  1.090
 2G7  C25  H14  single    0.970  0.020  1.090
 2G7  C26  H15  single    0.970  0.020  1.090
 2G7  C29  H16  single    0.970  0.020  1.090
 2G7  C29  H17  single    0.970  0.020  1.090
 2G7  C29  H18  single    0.970  0.020  1.090
 2G7  C28  H19  single    0.970  0.020  1.090
 2G7  C28  H20  single    0.970  0.020  1.090
 2G7  C28  H21  single    0.970  0.020  1.090
 2G7  C12  H23  single    0.970  0.020  1.090
 2G7  C12  H24  single    0.970  0.020  1.090
 2G7  C7   H25  single    0.970  0.020  1.090
 2G7  C7   H26  single    0.970  0.020  1.090
 2G7  C1   H27  single    0.930  0.020  1.080
 2G7  C2   H28  single    0.930  0.020  1.080
 2G7  C3   H29  single    0.930  0.020  1.080
 2G7  C4   H30  single    0.930  0.020  1.080
 2G7  C5   H31  single    0.930  0.020  1.080
 2G7  N11  H32  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
 2G7  H26  C7   H25  107.99  3.000
 2G7  H26  C7   O8   110.37  3.000
 2G7  H25  C7   O8   110.11  3.000
 2G7  H26  C7   C6   110.75  3.000
 2G7  H25  C7   C6   110.69  3.000
 2G7  O8   C7   C6   106.94  3.000
 2G7  C5   C6   C1   119.04  3.000
 2G7  C5   C6   C7   120.73  3.000
 2G7  C1   C6   C7   120.22  3.000
 2G7  H27  C1   C2   119.71  3.000
 2G7  H27  C1   C6   119.75  3.000
 2G7  C2   C1   C6   120.54  3.000
 2G7  H28  C2   C3   120.10  3.000
 2G7  H28  C2   C1   119.86  3.000
 2G7  C3   C2   C1   120.04  3.000
 2G7  H29  C3   C4   120.13  3.000
 2G7  H29  C3   C2   120.09  3.000
 2G7  C4   C3   C2   119.78  3.000
 2G7  H30  C4   C5   119.84  3.000
 2G7  H30  C4   C3   120.15  3.000
 2G7  C5   C4   C3   120.01  3.000
 2G7  H31  C5   C4   119.65  3.000
 2G7  H31  C5   C6   119.77  3.000
 2G7  C4   C5   C6   120.58  3.000
 2G7  N11  C9   O8   111.23  3.000
 2G7  N11  C9   O10  125.87  3.000
 2G7  O8   C9   O10  122.83  3.000
 2G7  C9   O8   C7   117.16  3.000
 2G7  H32  N11  C12  116.16  3.000
 2G7  H32  N11  C9   116.28  3.000
 2G7  C12  N11  C9   121.43  3.000
 2G7  H24  C12  H23  106.28  3.000
 2G7  H24  C12  P13  111.14  3.000
 2G7  H23  C12  P13  109.29  3.000
 2G7  H24  C12  N11  109.26  3.000
 2G7  H23  C12  N11  107.76  3.000
 2G7  P13  C12  N11  112.85  3.000
 2G7  N16  P13  O15  106.36  3.000
 2G7  N16  P13  O14  107.67  3.000
 2G7  O15  P13  O14  121.32  3.000
 2G7  N16  P13  C12  106.42  3.000
 2G7  O15  P13  C12  108.02  3.000
 2G7  O14  P13  C12  106.22  3.000
 2G7  H1   N16  C17  114.40  3.000
 2G7  H1   N16  P13  117.08  3.000
 2G7  C17  N16  P13  121.77  3.000
 2G7  H2   C17  C18  108.45  3.000
 2G7  H2   C17  C22  109.55  3.000
 2G7  C18  C17  C22  110.56  3.000
 2G7  H2   C17  N16  107.21  3.000
 2G7  C18  C17  N16  111.32  3.000
 2G7  C22  C17  N16  109.68  3.000
 2G7  N24  C22  O23  123.91  3.000
 2G7  O23  C22  C17  120.83  3.000
 2G7  N24  C22  C17  115.24  3.000
 2G7  H4   C18  H3   106.66  3.000
 2G7  H4   C18  C19  109.36  3.000
 2G7  H3   C18  C19  109.14  3.000
 2G7  H4   C18  C17  108.79  3.000
 2G7  H3   C18  C17  107.01  3.000
 2G7  C19  C18  C17  115.50  3.000
 2G7  H5   C19  C21  107.49  3.000
 2G7  H5   C19  C20  108.07  3.000
 2G7  C21  C19  C20  110.68  3.000
 2G7  H5   C19  C18  108.37  3.000
 2G7  C21  C19  C18  109.80  3.000
 2G7  C20  C19  C18  112.26  3.000
 2G7  H8   C20  H7   107.55  3.000
 2G7  H8   C20  H6   107.74  3.000
 2G7  H7   C20  H6   106.98  3.000
 2G7  H8   C20  C19  111.07  3.000
 2G7  H7   C20  C19  112.35  3.000
 2G7  H6   C20  C19  110.94  3.000
 2G7  H11  C21  H10  107.76  3.000
 2G7  H11  C21  H9   107.63  3.000
 2G7  H10  C21  H9   107.66  3.000
 2G7  H11  C21  C19  110.94  3.000
 2G7  H10  C21  C19  111.43  3.000
 2G7  H9   C21  C19  111.24  3.000
 2G7  H21  C28  H20  107.81  3.000
 2G7  H21  C28  H19  107.46  3.000
 2G7  H20  C28  H19  107.70  3.000
 2G7  H21  C28  C26  110.89  3.000
 2G7  H20  C28  C26  110.98  3.000
 2G7  H19  C28  C26  111.82  3.000
 2G7  H15  C26  C25  107.90  3.000
 2G7  H15  C26  C29  108.12  3.000
 2G7  C25  C26  C29  109.35  3.000
 2G7  H15  C26  C28  108.36  3.000
 2G7  C29  C26  C28  111.24  3.000
 2G7  C25  C26  C28  111.75  3.000
 2G7  H18  C29  H17  107.71  3.000
 2G7  H18  C29  H16  107.48  3.000
 2G7  H17  C29  H16  107.74  3.000
 2G7  H18  C29  C26  111.12  3.000
 2G7  H17  C29  C26  111.61  3.000
 2G7  H16  C29  C26  111.00  3.000
 2G7  H14  C25  H13  107.10  3.000
 2G7  H14  C25  N24  108.46  3.000
 2G7  H13  C25  N24  108.80  3.000
 2G7  H14  C25  C26  109.73  3.000
 2G7  H13  C25  C26  109.36  3.000
 2G7  N24  C25  C26  113.19  3.000
 2G7  H12  N24  C25  117.31  3.000
 2G7  H12  N24  C22  117.76  3.000
 2G7  C25  N24  C22  124.68  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
 2G7  CONST_01  C3   C2   C1   C6      0.00   0.0  0
 2G7  CONST_02  C3   C4   C5   C6      0.00   0.0  0
 2G7  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 2G7  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 2G7  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 2G7  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 2G7  CONST_07  C2   C1   C6   C7    180.00   0.0  0
 2G7  CONST_08  C4   C5   C6   C7    180.00   0.0  0
 2G7  CONST_09  H28  C2   C1   C6    180.00   0.0  0
 2G7  CONST_10  H30  C4   C5   C6    180.00   0.0  0
 2G7  CONST_11  H29  C3   C2   C1    180.00   0.0  0
 2G7  CONST_12  H31  C5   C6   C1    180.00   0.0  0
 2G7  CONST_13  H27  C1   C2   C3    180.00   0.0  0
 2G7  CONST_14  C25  N24  C22  C17   180.00   0.0  0
 2G7  CONST_15  C25  N24  C22  O23     0.00   0.0  0
 2G7  CONST_16  H12  N24  C22  C17     0.00   0.0  0
 2G7  Var_01    O8   C7   C6   C1    -74.48  30.0  2
 2G7  Var_02    O10  C9   O8   C7      1.78  30.0  3
 2G7  Var_03    P13  C12  N11  C9     77.36  30.0  3
 2G7  Var_04    C12  N11  C9   O10    20.71  30.0  2
 2G7  Var_05    O14  P13  C12  N11   -14.90  30.0  3
 2G7  Var_06    C17  N16  P13  C12    67.89  30.0  3
 2G7  Var_07    C20  C19  C18  C17    56.13  30.0  3
 2G7  Var_08    C26  C25  N24  C22  -112.84  30.0  1
 2G7  Var_09    N24  C25  C26  C28    59.01  30.0  2
 2G7  Var_10    H6   C20  C19  C18   175.52  30.0  3
 2G7  Var_11    H9   C21  C19  C18    57.82  30.0  3
 2G7  Var_12    H16  C29  C26  C28    60.62  30.0  3
 2G7  Var_13    H19  C28  C26  C29   175.61  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
 2G7  chir_02  C17  N16  C22  C18  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
 2G7  plan-1  C7   0.020
 2G7  plan-1  C6   0.020
 2G7  plan-1  C1   0.020
 2G7  plan-1  C2   0.020
 2G7  plan-1  C3   0.020
 2G7  plan-1  C4   0.020
 2G7  plan-1  C5   0.020
 2G7  plan-1  H27  0.020
 2G7  plan-1  H28  0.020
 2G7  plan-1  H29  0.020
 2G7  plan-1  H30  0.020
 2G7  plan-1  H31  0.020
 2G7  plan-2  C17  0.020
 2G7  plan-2  C22  0.020
 2G7  plan-2  O23  0.020
 2G7  plan-2  C25  0.020
 2G7  plan-2  N24  0.020
 2G7  plan-2  H12  0.020
 2G7  plan-3  C9   0.020
 2G7  plan-3  O10  0.020
 2G7  plan-3  O8   0.020
 2G7  plan-3  N11  0.020

