# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 23:00:16 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: amino({(4S)-4-amino-6-[(2,6-dimethylbenzoyl)oxy]-5-oxohexyl}amino)methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(C)c1C(=O)OCC(=O)[C@@H](N)CCCNC(N)=[NH2+]
#
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
 4AR  4AR  amino({(4S)-4-amino-6-[(2,6-dimethylbenzoyl)oxy]-5-oxohexyl}amino)methaniminium  L-peptide  48  23  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_4AR
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
 4AR  N1    N  NH2   0  -0.785  -2.0479   2.8506  -1.3289
 4AR  C1    C  CH1   0  -0.219  -1.6387   1.7861  -0.4383
 4AR  C2    C  C     0   0.368  -0.1862   1.4382  -0.7072
 4AR  O1    O  O     0  -0.373   0.2930   1.4715  -1.8117
 4AR  C3    C  CH2   0  -0.443  -2.4561   0.4833  -0.5324
 4AR  C4    C  CH2   0  -0.478  -3.9149   0.6861  -0.1499
 4AR  C5    C  CH2   0  -0.270  -4.6846  -0.6213  -0.2270
 4AR  N2    N  NH1   0  -0.637  -6.0747  -0.4041   0.1353
 4AR  C6    C  C     0   0.829  -6.9730  -1.3692   0.2769
 4AR  N3    N  NH2   0  -0.817  -6.6298  -2.6374   0.1020
 4AR  N4    N  NC2   1  -0.822  -8.2234  -1.0636   0.6000
 4AR  C7    C  CH2   0  -0.275   0.6054   1.0293   0.5091
 4AR  O2    O  O2    0  -0.437   1.8886   0.6099   0.0914
 4AR  C8    C  C     0   0.489   2.7209   0.1377   1.0119
 4AR  C9    C  CR6   0  -0.087   4.0072  -0.3127   0.4099
 4AR  C10   C  CR6   0   0.128   4.0050  -1.3065  -0.5783
 4AR  C11   C  CR16  0  -0.327   5.2288  -1.7245  -1.0924
 4AR  C12   C  CR16  0  -0.217   6.4156  -1.1604  -0.6538
 4AR  C13   C  CR16  0  -0.325   6.3980  -0.1745   0.3195
 4AR  C14   C  CR6   0   0.118   5.1986   0.2581   0.8761
 4AR  O3    O  O     0  -0.426   2.4581   0.0941   2.1864
 4AR  C15   C  CH3   0  -0.742   2.7398  -1.9468  -1.0804
 4AR  C16   C  CH3   0  -0.739   5.2173   1.3269   1.9333
 4AR  H     H  HNH2  0   0.348  -2.1554   2.4994  -2.2729
 4AR  H2    H  HNH2  0   0.361  -2.9515   3.2088  -1.0505
 4AR  HA    H  HCH1  0   0.266  -1.7170   2.1569   0.5896
 4AR  HB2   H  HCH2  0   0.245  -2.3861   0.0940  -1.5529
 4AR  HB3   H  HCH2  0   0.240  -2.0199  -0.2768   0.1229
 4AR  HG2   H  HCH2  0   0.252  -3.9783   1.0847   0.8665
 4AR  HG3   H  HCH2  0   0.245  -4.3818   1.4165  -0.8160
 4AR  HD2   H  HCH2  0   0.260  -4.6181  -1.0327  -1.2384
 4AR  HD3   H  HCH2  0   0.257  -4.2349  -1.3457   0.4573
 4AR  HE    H  HNH1  0   0.427  -6.3918   0.5467   0.2432
 4AR  HH11  H  HNH2  0   0.447  -5.6869  -2.9108  -0.1145
 4AR  HH12  H  HNH2  0   0.434  -7.2916  -3.3788   0.2567
 4AR  HH21  H  HNC2  0   0.432  -8.5168  -0.1073   0.7010
 4AR  HH22  H  HNC2  0   0.431  -8.9311  -1.7731   0.6832
 4AR  H15   H  HCH2  0   0.289   0.6669   1.8905   1.1839
 4AR  H16   H  HCH2  0   0.276   0.0771   0.2394   1.0539
 4AR  H17   H  HCR6  0   0.255   5.2482  -2.5006  -1.8472
 4AR  H18   H  HCR6  0   0.260   7.3581  -1.4898  -1.0719
 4AR  H19   H  HCR6  0   0.254   7.3276   0.2681   0.6551
 4AR  H20   H  HCH3  0   0.258   2.1639  -1.2665  -1.7077
 4AR  H21   H  HCH3  0   0.253   2.9733  -2.8275  -1.6761
 4AR  H22   H  HCH3  0   0.244   2.0892  -2.2688  -0.2658
 4AR  H23   H  HCH3  0   0.256   4.9641   0.9260   2.9148
 4AR  H24   H  HCH3  0   0.252   6.2077   1.7736   2.0034
 4AR  H25   H  HCH3  0   0.245   4.5114   2.1303   1.7194

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
 4AR  N1   C1    single    1.447  0.020  1.447
 4AR  C1   C2    single    1.518  0.020  1.518
 4AR  C1   C3    single    1.541  0.020  1.541
 4AR  C2   O1    double    1.204  0.020  1.204
 4AR  C2   C7    single    1.508  0.020  1.508
 4AR  C3   C4    single    1.522  0.020  1.522
 4AR  C4   C5    single    1.519  0.020  1.519
 4AR  C5   N2    single    1.453  0.020  1.453
 4AR  N2   C6    single    1.326  0.020  1.326
 4AR  C6   N3    single    1.325  0.020  1.325
 4AR  C6   N4    double    1.327  0.020  1.327
 4AR  C7   O2    single    1.413  0.020  1.413
 4AR  O2   C8    single    1.328  0.020  1.328
 4AR  C8   C9    single    1.490  0.020  1.490
 4AR  C9   C10   aromatic  1.401  0.020  1.401
 4AR  C9   C14   aromatic  1.401  0.020  1.401
 4AR  C10  C11   aromatic  1.392  0.020  1.392
 4AR  C11  C12   aromatic  1.385  0.020  1.385
 4AR  C12  C13   aromatic  1.386  0.020  1.386
 4AR  C13  C14   aromatic  1.391  0.020  1.391
 4AR  C8   O3    double    1.204  0.020  1.204
 4AR  C10  C15   single    1.504  0.020  1.504
 4AR  C14  C16   single    1.503  0.020  1.503
 4AR  N1   H     single    0.890  0.020  1.040
 4AR  N1   H2    single    0.890  0.020  1.040
 4AR  C1   HA    single    0.970  0.020  1.090
 4AR  C3   HB2   single    0.970  0.020  1.090
 4AR  C3   HB3   single    0.970  0.020  1.090
 4AR  C4   HG2   single    0.970  0.020  1.090
 4AR  C4   HG3   single    0.970  0.020  1.090
 4AR  C5   HD2   single    0.970  0.020  1.090
 4AR  C5   HD3   single    0.970  0.020  1.090
 4AR  N2   HE    single    0.860  0.020  1.020
 4AR  N3   HH11  single    0.860  0.020  1.020
 4AR  N3   HH12  single    0.860  0.020  1.020
 4AR  N4   HH21  single    0.860  0.020  1.020
 4AR  N4   HH22  single    0.860  0.020  1.020
 4AR  C7   H15   single    0.970  0.020  1.090
 4AR  C7   H16   single    0.970  0.020  1.090
 4AR  C11  H17   single    0.930  0.020  1.080
 4AR  C12  H18   single    0.930  0.020  1.080
 4AR  C13  H19   single    0.930  0.020  1.080
 4AR  C15  H20   single    0.970  0.020  1.090
 4AR  C15  H21   single    0.970  0.020  1.090
 4AR  C15  H22   single    0.970  0.020  1.090
 4AR  C16  H23   single    0.970  0.020  1.090
 4AR  C16  H24   single    0.970  0.020  1.090
 4AR  C16  H25   single    0.970  0.020  1.090

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
 4AR  H2    N1   H     106.54  3.000
 4AR  H2    N1   C1    110.12  3.000
 4AR  H     N1   C1    110.40  3.000
 4AR  HA    C1   C3    107.78  3.000
 4AR  HA    C1   C2    108.20  3.000
 4AR  C3    C1   C2    107.64  3.000
 4AR  HA    C1   N1    107.96  3.000
 4AR  C3    C1   N1    115.74  3.000
 4AR  C2    C1   N1    109.29  3.000
 4AR  C7    C2   O1    122.57  3.000
 4AR  C7    C2   C1    114.95  3.000
 4AR  O1    C2   C1    122.48  3.000
 4AR  HB3   C3   HB2   106.61  3.000
 4AR  HB3   C3   C4    108.91  3.000
 4AR  HB2   C3   C4    110.06  3.000
 4AR  HB3   C3   C1    109.83  3.000
 4AR  HB2   C3   C1    108.89  3.000
 4AR  C4    C3   C1    112.37  3.000
 4AR  HG3   C4   HG2   107.33  3.000
 4AR  HG3   C4   C5    109.13  3.000
 4AR  HG2   C4   C5    109.36  3.000
 4AR  HG3   C4   C3    110.20  3.000
 4AR  HG2   C4   C3    109.74  3.000
 4AR  C5    C4   C3    111.00  3.000
 4AR  HD3   C5   HD2   107.72  3.000
 4AR  HD3   C5   N2    109.67  3.000
 4AR  HD2   C5   N2    110.18  3.000
 4AR  HD3   C5   C4    109.27  3.000
 4AR  HD2   C5   C4    109.87  3.000
 4AR  N2    C5   C4    110.09  3.000
 4AR  HE    N2   C6    117.51  3.000
 4AR  HE    N2   C5    117.94  3.000
 4AR  C6    N2   C5    124.47  3.000
 4AR  N4    C6   N3    119.76  3.000
 4AR  N4    C6   N2    119.78  3.000
 4AR  N3    C6   N2    120.45  3.000
 4AR  HH12  N3   HH11  116.73  3.000
 4AR  HH12  N3   C6    120.97  3.000
 4AR  HH11  N3   C6    122.11  3.000
 4AR  HH22  N4   HH21  117.22  3.000
 4AR  HH22  N4   C6    121.39  3.000
 4AR  HH21  N4   C6    121.22  3.000
 4AR  H16   C7   H15   106.71  3.000
 4AR  H16   C7   O2    111.78  3.000
 4AR  H15   C7   O2    111.36  3.000
 4AR  H16   C7   C2    110.09  3.000
 4AR  H15   C7   C2    108.25  3.000
 4AR  O2    C7   C2    108.59  3.000
 4AR  C8    O2   C7    118.03  3.000
 4AR  O3    C8   C9    124.85  3.000
 4AR  O3    C8   O2    123.52  3.000
 4AR  C9    C8   O2    111.63  3.000
 4AR  C14   C9   C10   121.66  3.000
 4AR  C14   C9   C8    118.46  3.000
 4AR  C10   C9   C8    119.86  3.000
 4AR  C15   C10  C11   119.24  3.000
 4AR  C15   C10  C9    122.58  3.000
 4AR  C11   C10  C9    118.17  3.000
 4AR  H17   C11  C12   119.81  3.000
 4AR  H17   C11  C10   119.25  3.000
 4AR  C12   C11  C10   120.94  3.000
 4AR  H18   C12  C13   119.93  3.000
 4AR  H18   C12  C11   119.98  3.000
 4AR  C13   C12  C11   120.08  3.000
 4AR  H19   C13  C14   119.28  3.000
 4AR  H19   C13  C12   119.84  3.000
 4AR  C14   C13  C12   120.88  3.000
 4AR  C16   C14  C13   119.45  3.000
 4AR  C16   C14  C9    122.30  3.000
 4AR  C13   C14  C9    118.25  3.000
 4AR  H22   C15  H21   107.32  3.000
 4AR  H22   C15  H20   107.39  3.000
 4AR  H21   C15  H20   107.66  3.000
 4AR  H22   C15  C10   112.20  3.000
 4AR  H21   C15  C10   110.28  3.000
 4AR  H20   C15  C10   111.77  3.000
 4AR  H25   C16  H24   107.41  3.000
 4AR  H25   C16  H23   107.29  3.000
 4AR  H24   C16  H23   107.71  3.000
 4AR  H25   C16  C14   112.19  3.000
 4AR  H24   C16  C14   110.38  3.000
 4AR  H23   C16  C14   111.64  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
 4AR  CONST_01  C12   C11  C10  C9      0.00   0.0  0
 4AR  CONST_02  C12   C13  C14  C9      0.00   0.0  0
 4AR  CONST_03  C13   C14  C9   C10     0.00   0.0  0
 4AR  CONST_04  C13   C12  C11  C10     0.00   0.0  0
 4AR  CONST_05  C14   C9   C10  C11     0.00   0.0  0
 4AR  CONST_06  C14   C13  C12  C11     0.00   0.0  0
 4AR  CONST_07  C11   C10  C9   C8    180.00   0.0  0
 4AR  CONST_08  C13   C14  C9   C8    180.00   0.0  0
 4AR  CONST_09  C16   C14  C9   C10   180.00   0.0  0
 4AR  CONST_10  C15   C10  C11  C12   180.00   0.0  0
 4AR  CONST_11  C16   C14  C13  C12   180.00   0.0  0
 4AR  CONST_12  C15   C10  C9   C14   180.00   0.0  0
 4AR  CONST_13  H17   C11  C10  C9    180.00   0.0  0
 4AR  CONST_14  H19   C13  C14  C9    180.00   0.0  0
 4AR  CONST_15  H18   C12  C11  C10   180.00   0.0  0
 4AR  CONST_16  N3    C6   N2   C5      0.00   0.0  0
 4AR  CONST_17  N4    C6   N2   C5    180.00   0.0  0
 4AR  CONST_18  HH11  N3   C6   N2      0.00   0.0  0
 4AR  CONST_19  HH12  N3   C6   N2    180.00   0.0  0
 4AR  CONST_20  HH21  N4   C6   N2      0.00   0.0  0
 4AR  CONST_21  HH22  N4   C6   N2    180.00   0.0  0
 4AR  CONST_22  HE    N2   C6   N3    180.00   0.0  0
 4AR  Var_01    C10   C9   C8   O2    -58.51  30.0  2
 4AR  Var_02    H20   C15  C10  C9     72.48  30.0  2
 4AR  Var_03    H23   C16  C14  C9     71.85  30.0  2
 4AR  Var_04    C9    C8   O2   C7    177.68  30.0  3
 4AR  Var_05    O2    C7   C2   C1    174.24  30.0  3
 4AR  Var_06    C5    C4   C3   C1   -178.88  30.0  3
 4AR  Var_07    N2    C5   C4   C3   -179.72  30.0  3
 4AR  Var_08    C6    N2   C5   C4   -173.84  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
 4AR  chir_01  C1  N1  C2  C3  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
 4AR  plan-1  C8    0.020
 4AR  plan-1  C9    0.020
 4AR  plan-1  C10   0.020
 4AR  plan-1  C11   0.020
 4AR  plan-1  C12   0.020
 4AR  plan-1  C13   0.020
 4AR  plan-1  C14   0.020
 4AR  plan-1  C15   0.020
 4AR  plan-1  C16   0.020
 4AR  plan-1  H17   0.020
 4AR  plan-1  H18   0.020
 4AR  plan-1  H19   0.020
 4AR  plan-2  C1    0.020
 4AR  plan-2  C2    0.020
 4AR  plan-2  O1    0.020
 4AR  plan-2  C7    0.020
 4AR  plan-3  C5    0.020
 4AR  plan-3  N2    0.020
 4AR  plan-3  C6    0.020
 4AR  plan-3  N3    0.020
 4AR  plan-3  N4    0.020
 4AR  plan-3  HE    0.020
 4AR  plan-3  HH11  0.020
 4AR  plan-3  HH12  0.020
 4AR  plan-3  HH21  0.020
 4AR  plan-3  HH22  0.020
 4AR  plan-4  O2    0.020
 4AR  plan-4  C8    0.020
 4AR  plan-4  C9    0.020
 4AR  plan-4  O3    0.020

