# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 16:42:22 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(2-phenylethyl)-L-leucinamide
#   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)NCCc2ccccc2
#
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
 2GC  2GC  N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(2-phenylethyl)-L-leucinamide  peptide  63  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2GC
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
 2GC  C7   C  CH2    0  -0.229  -2.7301   2.4340   0.2700
 2GC  C6   C  CR6    0   0.075  -4.1487   2.7983   0.5883
 2GC  C1   C  CR16   0  -0.302  -4.8127   3.7768  -0.1430
 2GC  C2   C  CR16   0  -0.241  -6.1287   4.1108   0.1538
 2GC  C3   C  CR16   0  -0.264  -6.7939   3.4603   1.1832
 2GC  C4   C  CR16   0  -0.242  -6.1383   2.4782   1.9175
 2GC  C5   C  CR16   0  -0.283  -4.8236   2.1515   1.6219
 2GC  C9   C  C      0   0.753  -1.5583   0.6051  -0.6498
 2GC  O10  O  O      0  -0.501  -0.4998   1.1612  -0.4365
 2GC  O8   O  O2     0  -0.486  -2.7495   1.1371  -0.3314
 2GC  N11  N  NH1    0  -0.649  -1.7121  -0.5803  -1.2638
 2GC  C12  C  CH2    0  -0.571  -0.5979  -1.4785  -1.4829
 2GC  P13  P  P      0   1.241  -0.4384  -2.6757  -0.0817
 2GC  O14  O  O      0  -0.800  -0.1707  -1.8885   1.1850
 2GC  O15  O  OP    -1  -0.799  -1.6340  -3.5902  -0.1660
 2GC  N16  N  NH1    0  -0.777   0.9784  -3.5487  -0.4291
 2GC  C17  C  CH1    0  -0.219   2.2620  -3.2640   0.1801
 2GC  C22  C  C      0   0.567   2.9283  -2.0479  -0.4745
 2GC  O23  O  O      0  -0.508   3.7801  -2.1437  -1.3499
 2GC  C18  C  CH2    0  -0.409   3.1736  -4.4827   0.1589
 2GC  C19  C  CH1    0  -0.218   2.5758  -5.7249   0.8225
 2GC  C20  C  CH3    0  -0.652   3.5965  -6.8588   0.7955
 2GC  C21  C  CH3    0  -0.671   2.1159  -5.4509   2.2507
 2GC  C27  C  CR6    0   0.112   3.1326   2.8418  -0.0813
 2GC  C32  C  CR16   0  -0.308   4.4380   3.3203  -0.1676
 2GC  C31  C  CR16   0  -0.241   4.7080   4.5526  -0.7490
 2GC  C30  C  CR16   0  -0.272   3.6719   5.3266  -1.2552
 2GC  C29  C  CR16   0  -0.240   2.3660   4.8591  -1.1753
 2GC  C28  C  CR16   0  -0.312   2.1008   3.6262  -0.5947
 2GC  C26  C  CH2    0  -0.531   2.8430   1.4906   0.5096
 2GC  C25  C  CH2    0  -0.249   2.8315   0.4101  -0.5691
 2GC  N24  N  NH1    0  -0.660   2.4725  -0.8715  -0.0078
 2GC  H16  H  HCH2   0   0.244  -2.2890   3.1638  -0.4123
 2GC  H17  H  HCH2   0   0.243  -2.1233   2.4177   1.1781
 2GC  H18  H  HCR6   0   0.255  -4.2977   4.2857  -0.9494
 2GC  H19  H  HCR6   0   0.258  -6.6336   4.8771  -0.4199
 2GC  H20  H  HCR6   0   0.258  -7.8190   3.7179   1.4158
 2GC  H21  H  HCR6   0   0.258  -6.6529   1.9706   2.7230
 2GC  H22  H  HCR6   0   0.255  -4.3154   1.3915   2.2039
 2GC  H32  H  HNH1   0   0.393  -2.6363  -0.9819  -1.2879
 2GC  H14  H  HCH2   0   0.249  -0.7542  -2.0125  -2.4228
 2GC  H15  H  HCH2   0   0.259   0.3088  -0.8872  -1.6000
 2GC  H1   H  HNH1   0   0.363   1.0294  -4.0236  -1.3199
 2GC  H2   H  HCH1   0   0.253   2.0710  -3.0019   1.2218
 2GC  H3   H  HCH2   0   0.222   3.4499  -4.7211  -0.8727
 2GC  H4   H  HCH2   0   0.218   4.1070  -4.2227   0.6709
 2GC  H5   H  HCH1   0   0.215   1.7024  -6.0362   0.2407
 2GC  H6   H  HCH3   0   0.210   4.4918  -6.5891   1.3617
 2GC  H7   H  HCH3   0   0.223   3.1906  -7.7718   1.2342
 2GC  H8   H  HCH3   0   0.222   3.9093  -7.0932  -0.2237
 2GC  H9   H  HCH3   0   0.210   2.9352  -5.0556   2.8576
 2GC  H10  H  HCH3   0   0.232   1.2947  -4.7337   2.2863
 2GC  H11  H  HCH3   0   0.225   1.7649  -6.3665   2.7302
 2GC  H31  H  HCR6   0   0.246   5.2530   2.7255   0.2295
 2GC  H30  H  HCR6   0   0.252   5.7286   4.9092  -0.8047
 2GC  H29  H  HCR6   0   0.252   3.8812   6.2880  -1.7063
 2GC  H28  H  HCR6   0   0.251   1.5509   5.4573  -1.5631
 2GC  H27  H  HCR6   0   0.258   1.0812   3.2639  -0.5351
 2GC  H25  H  HCH2   0   0.245   3.5930   1.2396   1.2631
 2GC  H26  H  HCH2   0   0.249   1.8716   1.5070   1.0091
 2GC  H23  H  HCH2   0   0.233   2.1313   0.6956  -1.3603
 2GC  H24  H  HCH2   0   0.240   3.8182   0.3306  -1.0246
 2GC  H12  H  HNH1   0   0.396   1.6481  -0.9057   0.5862

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
 2GC  C2   C1   aromatic  1.390  0.020  1.390
 2GC  C2   C3   aromatic  1.388  0.020  1.388
 2GC  C1   C6   aromatic  1.390  0.020  1.390
 2GC  C3   C4   aromatic  1.390  0.020  1.390
 2GC  C6   C7   single    1.499  0.020  1.499
 2GC  C6   C5   aromatic  1.394  0.020  1.394
 2GC  C4   C5   aromatic  1.387  0.020  1.387
 2GC  C7   O8   single    1.430  0.020  1.430
 2GC  O8   C9   single    1.343  0.020  1.343
 2GC  C9   O10  double    1.215  0.020  1.215
 2GC  C9   N11  single    1.344  0.020  1.344
 2GC  N11  C12  single    1.448  0.020  1.448
 2GC  C12  P13  single    1.850  0.020  1.850
 2GC  O14  P13  deloc     1.515  0.020  1.515
 2GC  O15  P13  deloc     1.508  0.020  1.508
 2GC  P13  N16  single    1.700  0.020  1.700
 2GC  N16  C17  single    1.449  0.020  1.449
 2GC  C25  N24  single    1.444  0.020  1.444
 2GC  C25  C26  single    1.527  0.020  1.527
 2GC  N24  C22  single    1.345  0.020  1.345
 2GC  O23  C22  double    1.225  0.020  1.225
 2GC  C22  C17  single    1.533  0.020  1.533
 2GC  C32  C31  aromatic  1.389  0.020  1.389
 2GC  C32  C27  aromatic  1.393  0.020  1.393
 2GC  C17  C18  single    1.522  0.020  1.522
 2GC  C31  C30  aromatic  1.389  0.020  1.389
 2GC  C26  C27  single    1.503  0.020  1.503
 2GC  C27  C28  aromatic  1.394  0.020  1.394
 2GC  C30  C29  aromatic  1.389  0.020  1.389
 2GC  C18  C19  single    1.530  0.020  1.530
 2GC  C28  C29  aromatic  1.388  0.020  1.388
 2GC  C20  C19  single    1.526  0.020  1.526
 2GC  C19  C21  single    1.525  0.020  1.525
 2GC  N16  H1   single    0.890  0.020  1.040
 2GC  C17  H2   single    0.970  0.020  1.090
 2GC  C18  H3   single    0.970  0.020  1.090
 2GC  C18  H4   single    0.970  0.020  1.090
 2GC  C19  H5   single    0.970  0.020  1.090
 2GC  C20  H6   single    0.970  0.020  1.090
 2GC  C20  H7   single    0.970  0.020  1.090
 2GC  C20  H8   single    0.970  0.020  1.090
 2GC  C21  H9   single    0.970  0.020  1.090
 2GC  C21  H10  single    0.970  0.020  1.090
 2GC  C21  H11  single    0.970  0.020  1.090
 2GC  N24  H12  single    0.860  0.020  1.020
 2GC  C12  H14  single    0.970  0.020  1.090
 2GC  C12  H15  single    0.970  0.020  1.090
 2GC  C7   H16  single    0.970  0.020  1.090
 2GC  C7   H17  single    0.970  0.020  1.090
 2GC  C1   H18  single    0.930  0.020  1.080
 2GC  C2   H19  single    0.930  0.020  1.080
 2GC  C3   H20  single    0.930  0.020  1.080
 2GC  C4   H21  single    0.930  0.020  1.080
 2GC  C5   H22  single    0.930  0.020  1.080
 2GC  C25  H23  single    0.970  0.020  1.090
 2GC  C25  H24  single    0.970  0.020  1.090
 2GC  C26  H25  single    0.970  0.020  1.090
 2GC  C26  H26  single    0.970  0.020  1.090
 2GC  C28  H27  single    0.930  0.020  1.080
 2GC  C29  H28  single    0.930  0.020  1.080
 2GC  C30  H29  single    0.930  0.020  1.080
 2GC  C31  H30  single    0.930  0.020  1.080
 2GC  C32  H31  single    0.930  0.020  1.080
 2GC  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
 2GC  H17  C7   H16  107.76  3.000
 2GC  H17  C7   O8   110.10  3.000
 2GC  H16  C7   O8   110.42  3.000
 2GC  H17  C7   C6   110.66  3.000
 2GC  H16  C7   C6   110.64  3.000
 2GC  O8   C7   C6   107.27  3.000
 2GC  C5   C6   C1   119.04  3.000
 2GC  C5   C6   C7   120.20  3.000
 2GC  C1   C6   C7   120.75  3.000
 2GC  H18  C1   C2   119.74  3.000
 2GC  H18  C1   C6   119.67  3.000
 2GC  C2   C1   C6   120.59  3.000
 2GC  H19  C2   C3   120.10  3.000
 2GC  H19  C2   C1   119.91  3.000
 2GC  C3   C2   C1   119.99  3.000
 2GC  H20  C3   C4   120.08  3.000
 2GC  H20  C3   C2   120.13  3.000
 2GC  C4   C3   C2   119.79  3.000
 2GC  H21  C4   C5   119.93  3.000
 2GC  H21  C4   C3   120.01  3.000
 2GC  C5   C4   C3   120.06  3.000
 2GC  H22  C5   C4   119.70  3.000
 2GC  H22  C5   C6   119.77  3.000
 2GC  C4   C5   C6   120.52  3.000
 2GC  N11  C9   O8   110.87  3.000
 2GC  N11  C9   O10  125.72  3.000
 2GC  O8   C9   O10  123.37  3.000
 2GC  C9   O8   C7   116.55  3.000
 2GC  H32  N11  C12  117.05  3.000
 2GC  H32  N11  C9   117.86  3.000
 2GC  C12  N11  C9   121.89  3.000
 2GC  H15  C12  H14  106.99  3.000
 2GC  H15  C12  P13  111.17  3.000
 2GC  H14  C12  P13  110.35  3.000
 2GC  H15  C12  N11  108.68  3.000
 2GC  H14  C12  N11  108.87  3.000
 2GC  P13  C12  N11  110.68  3.000
 2GC  N16  P13  O15  109.75  3.000
 2GC  N16  P13  O14  106.88  3.000
 2GC  O15  P13  O14  120.13  3.000
 2GC  N16  P13  C12  104.44  3.000
 2GC  O15  P13  C12  106.37  3.000
 2GC  O14  P13  C12  108.20  3.000
 2GC  H1   N16  C17  114.72  3.000
 2GC  H1   N16  P13  117.61  3.000
 2GC  C17  N16  P13  123.46  3.000
 2GC  H2   C17  C18  108.09  3.000
 2GC  H2   C17  C22  107.05  3.000
 2GC  C18  C17  C22  111.64  3.000
 2GC  H2   C17  N16  107.07  3.000
 2GC  C18  C17  N16  111.55  3.000
 2GC  C22  C17  N16  111.18  3.000
 2GC  N24  C22  O23  123.49  3.000
 2GC  O23  C22  C17  123.04  3.000
 2GC  N24  C22  C17  113.47  3.000
 2GC  H4   C18  H3   106.09  3.000
 2GC  H4   C18  C19  108.83  3.000
 2GC  H3   C18  C19  109.31  3.000
 2GC  H4   C18  C17  108.28  3.000
 2GC  H3   C18  C17  109.80  3.000
 2GC  C19  C18  C17  114.20  3.000
 2GC  H5   C19  C21  107.95  3.000
 2GC  H5   C19  C20  108.24  3.000
 2GC  C21  C19  C20  110.60  3.000
 2GC  H5   C19  C18  108.19  3.000
 2GC  C21  C19  C18  112.22  3.000
 2GC  C20  C19  C18  109.53  3.000
 2GC  H8   C20  H7   107.60  3.000
 2GC  H8   C20  H6   107.57  3.000
 2GC  H7   C20  H6   107.63  3.000
 2GC  H8   C20  C19  111.58  3.000
 2GC  H7   C20  C19  111.46  3.000
 2GC  H6   C20  C19  110.81  3.000
 2GC  H11  C21  H10  107.16  3.000
 2GC  H11  C21  H9   107.48  3.000
 2GC  H10  C21  H9   107.95  3.000
 2GC  H11  C21  C19  110.96  3.000
 2GC  H10  C21  C19  112.07  3.000
 2GC  H9   C21  C19  111.02  3.000
 2GC  C26  C27  C28  120.54  3.000
 2GC  C28  C27  C32  118.52  3.000
 2GC  C26  C27  C32  120.91  3.000
 2GC  H31  C32  C31  119.60  3.000
 2GC  H31  C32  C27  119.55  3.000
 2GC  C31  C32  C27  120.85  3.000
 2GC  H30  C31  C30  120.07  3.000
 2GC  H30  C31  C32  119.80  3.000
 2GC  C30  C31  C32  120.13  3.000
 2GC  H29  C30  C29  120.30  3.000
 2GC  H29  C30  C31  120.18  3.000
 2GC  C29  C30  C31  119.52  3.000
 2GC  H28  C29  C28  119.77  3.000
 2GC  H28  C29  C30  120.07  3.000
 2GC  C28  C29  C30  120.16  3.000
 2GC  H27  C28  C29  119.97  3.000
 2GC  H27  C28  C27  119.21  3.000
 2GC  C29  C28  C27  120.82  3.000
 2GC  H26  C26  H25  107.37  3.000
 2GC  H26  C26  C25  109.08  3.000
 2GC  H25  C26  C25  109.27  3.000
 2GC  H26  C26  C27  109.74  3.000
 2GC  H25  C26  C27  110.21  3.000
 2GC  C25  C26  C27  111.09  3.000
 2GC  H24  C25  H23  107.23  3.000
 2GC  H24  C25  N24  108.83  3.000
 2GC  H23  C25  N24  110.69  3.000
 2GC  H24  C25  C26  109.88  3.000
 2GC  H23  C25  C26  109.33  3.000
 2GC  N24  C25  C26  110.81  3.000
 2GC  H12  N24  C25  117.29  3.000
 2GC  H12  N24  C22  116.62  3.000
 2GC  C25  N24  C22  123.84  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
 2GC  CONST_01  C3   C2   C1   C6      0.00   0.0  0
 2GC  CONST_02  C3   C4   C5   C6      0.00   0.0  0
 2GC  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 2GC  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 2GC  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 2GC  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 2GC  CONST_07  C30  C31  C32  C27     0.00   0.0  0
 2GC  CONST_08  C30  C29  C28  C27     0.00   0.0  0
 2GC  CONST_09  C29  C30  C31  C32     0.00   0.0  0
 2GC  CONST_10  C29  C28  C27  C32     0.00   0.0  0
 2GC  CONST_11  C28  C27  C32  C31     0.00   0.0  0
 2GC  CONST_12  C28  C29  C30  C31     0.00   0.0  0
 2GC  CONST_13  C2   C1   C6   C7    180.00   0.0  0
 2GC  CONST_14  C4   C5   C6   C7    180.00   0.0  0
 2GC  CONST_15  C26  C27  C32  C31   180.00   0.0  0
 2GC  CONST_16  C26  C27  C28  C29   180.00   0.0  0
 2GC  CONST_17  H19  C2   C1   C6    180.00   0.0  0
 2GC  CONST_18  H21  C4   C5   C6    180.00   0.0  0
 2GC  CONST_19  H20  C3   C2   C1    180.00   0.0  0
 2GC  CONST_20  H22  C5   C6   C1    180.00   0.0  0
 2GC  CONST_21  H18  C1   C2   C3    180.00   0.0  0
 2GC  CONST_22  H30  C31  C32  C27   180.00   0.0  0
 2GC  CONST_23  H28  C29  C28  C27   180.00   0.0  0
 2GC  CONST_24  H29  C30  C31  C32   180.00   0.0  0
 2GC  CONST_25  H27  C28  C27  C32   180.00   0.0  0
 2GC  CONST_26  H31  C32  C31  C30   180.00   0.0  0
 2GC  CONST_27  C25  N24  C22  C17   180.00   0.0  0
 2GC  CONST_28  C25  N24  C22  O23     0.00   0.0  0
 2GC  CONST_29  H12  N24  C22  C17     0.00   0.0  0
 2GC  Var_01    O8   C7   C6   C1   -108.39  30.0  2
 2GC  Var_02    C25  C26  C27  C32   -91.55  30.0  2
 2GC  Var_03    N24  C25  C26  C27  -176.50  30.0  1
 2GC  Var_04    O10  C9   O8   C7      0.94  30.0  3
 2GC  Var_05    P13  C12  N11  C9     92.05  30.0  3
 2GC  Var_06    C12  N11  C9   O10    14.09  30.0  2
 2GC  Var_07    O14  P13  C12  N11   -61.57  30.0  3
 2GC  Var_08    C17  N16  P13  C12    99.26  30.0  3
 2GC  Var_09    C20  C19  C18  C17  -177.55  30.0  3
 2GC  Var_10    C26  C25  N24  C22  -148.73  30.0  1
 2GC  Var_11    H6   C20  C19  C18    61.94  30.0  3
 2GC  Var_12    H9   C21  C19  C18   -56.16  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
 2GC  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
 2GC  plan-1  C7   0.020
 2GC  plan-1  C6   0.020
 2GC  plan-1  C1   0.020
 2GC  plan-1  C2   0.020
 2GC  plan-1  C3   0.020
 2GC  plan-1  C4   0.020
 2GC  plan-1  C5   0.020
 2GC  plan-1  H18  0.020
 2GC  plan-1  H19  0.020
 2GC  plan-1  H20  0.020
 2GC  plan-1  H21  0.020
 2GC  plan-1  H22  0.020
 2GC  plan-2  C27  0.020
 2GC  plan-2  C32  0.020
 2GC  plan-2  C31  0.020
 2GC  plan-2  C30  0.020
 2GC  plan-2  C29  0.020
 2GC  plan-2  C28  0.020
 2GC  plan-2  C26  0.020
 2GC  plan-2  H31  0.020
 2GC  plan-2  H30  0.020
 2GC  plan-2  H29  0.020
 2GC  plan-2  H28  0.020
 2GC  plan-2  H27  0.020
 2GC  plan-3  C17  0.020
 2GC  plan-3  C22  0.020
 2GC  plan-3  O23  0.020
 2GC  plan-3  C25  0.020
 2GC  plan-3  N24  0.020
 2GC  plan-3  H12  0.020
 2GC  plan-4  C9   0.020
 2GC  plan-4  O10  0.020
 2GC  plan-4  O8   0.020
 2GC  plan-4  N11  0.020

