# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 16:07:28 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (1S)-1-(1H-benzimidazol-2-yl)ethyl (3,4-dichlorophenyl)carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](OC(=O)Nc1ccc(Cl)c(Cl)c1)c2[nH]c3ccccc3n2
#
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
 AGX  AGX  '(1S)-1-(1H-benzimidazol-2-yl)ethyl (3,4-dichlorophenyl)carbamate'  ligand  36  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AGX
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
 AGX  C     C   CR16  0  -0.307   5.3717  -0.5037  -2.0674
 AGX  N     N   NR15  0  -0.701   3.4157  -0.1201  -0.5123
 AGX  O     O   O2    0  -0.498   1.1207  -0.3684   0.8917
 AGX  CL    CL  CL    0  -0.093  -5.5232   1.2989   0.6703
 AGX  C1    C   CR16  0  -0.278   6.7549  -0.4568  -2.0635
 AGX  N1    N   N     0  -0.476   4.5554   0.4247   1.3118
 AGX  O1    O   O     0  -0.478  -0.5565   1.0663   1.3492
 AGX  CL1   CL  CL    0  -0.101  -6.6553  -1.0382  -1.1101
 AGX  C2    C   CR16  0  -0.271   7.4751  -0.1038  -0.9116
 AGX  N2    N   NH1   0  -0.777  -0.9004  -0.8964   0.2209
 AGX  C3    C   CR16  0  -0.335   6.8328   0.2114   0.2723
 AGX  C4    C   CR56  0   0.330   4.7350  -0.1811  -0.8746
 AGX  C5    C   CR56  0   0.137   5.4388   0.1706   0.2887
 AGX  C6    C   CR5   0   0.465   3.3740   0.2417   0.7944
 AGX  C7    C   CH1   0  -0.067   2.0873   0.4759   1.5255
 AGX  C9    C   CR6   0   0.385  -2.2643  -0.8617  -0.0549
 AGX  C10   C   CR16  0  -0.341  -2.7747  -1.8971  -0.8413
 AGX  C11   C   CR16  0  -0.205  -4.1165  -1.9478  -1.1581
 AGX  C12   C   CR6   0  -0.029  -4.9838  -0.9663  -0.7016
 AGX  C13   C   CR6   0   0.024  -4.4781   0.0625   0.0801
 AGX  C14   C   CR16  0  -0.281  -3.1317   0.1249   0.4083
 AGX  C15   C   CH3   0  -0.674   2.1978   0.1709   3.0052
 AGX  H     H   HCR6  0   0.267   4.8185  -0.7793  -2.9554
 AGX  H1    H   HCR6  0   0.256   7.2944  -0.6996  -2.9696
 AGX  H2    H   HCR6  0   0.253   8.5562  -0.0800  -0.9545
 AGX  HN2   H   HNH1  0   0.425  -0.4034  -1.6982  -0.1395
 AGX  H3    H   HCR6  0   0.255   7.3906   0.4820   1.1596
 AGX  H7    H   HCH1  0   0.286   1.8025   1.5232   1.3841
 AGX  H10   H   HCR6  0   0.289  -2.1169  -2.6723  -1.2139
 AGX  H11   H   HCR6  0   0.293  -4.4926  -2.7583  -1.7670
 AGX  H14   H   HCR6  0   0.308  -2.7808   0.9418   1.0170
 AGX  H15   H   HCH3  0   0.243   2.4582  -0.8735   3.1733
 AGX  H15A  H   HCH3  0   0.252   2.9721   0.7925   3.4502
 AGX  H15B  H   HCH3  0   0.251   1.2590   0.3900   3.5113
 AGX  HN    H   HNR5  0   0.419   2.6237  -0.3232  -1.1015
 AGX  C8    C   C     0   0.777  -0.1541   0.0347   0.8679

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
 AGX  C    C4    aromatic  1.390  0.020  1.390
 AGX  C    C1    aromatic  1.384  0.020  1.384
 AGX  C    H     single    0.930  0.020  1.080
 AGX  N    C4    aromatic  1.369  0.020  1.369
 AGX  N    C6    aromatic  1.356  0.020  1.356
 AGX  C7   O     single    1.431  0.020  1.431
 AGX  O    C8    single    1.337  0.020  1.337
 AGX  C13  CL    single    1.723  0.020  1.723
 AGX  C1   C2    aromatic  1.404  0.020  1.404
 AGX  C1   H1    single    0.930  0.020  1.080
 AGX  C6   N1    aromatic  1.303  0.020  1.303
 AGX  C5   N1    aromatic  1.375  0.020  1.375
 AGX  C8   O1    double    1.207  0.020  1.207
 AGX  C12  CL1   single    1.722  0.020  1.722
 AGX  C2   C3    aromatic  1.383  0.020  1.383
 AGX  C2   H2    single    0.930  0.020  1.080
 AGX  C8   N2    single    1.357  0.020  1.357
 AGX  N2   C9    single    1.392  0.020  1.392
 AGX  N2   HN2   single    0.860  0.020  1.020
 AGX  C5   C3    aromatic  1.395  0.020  1.395
 AGX  C3   H3    single    0.930  0.020  1.080
 AGX  C4   C5    aromatic  1.404  0.020  1.404
 AGX  C7   C6    single    1.498  0.020  1.498
 AGX  C15  C7    single    1.515  0.020  1.515
 AGX  C7   H7    single    0.970  0.020  1.090
 AGX  C9   C14   aromatic  1.393  0.020  1.393
 AGX  C9   C10   aromatic  1.397  0.020  1.397
 AGX  C10  C11   aromatic  1.380  0.020  1.380
 AGX  C10  H10   single    0.930  0.020  1.080
 AGX  C11  C12   aromatic  1.387  0.020  1.387
 AGX  C11  H11   single    0.930  0.020  1.080
 AGX  C13  C12   aromatic  1.387  0.020  1.387
 AGX  C14  C13   aromatic  1.387  0.020  1.387
 AGX  C14  H14   single    0.930  0.020  1.080
 AGX  C15  H15   single    0.970  0.020  1.090
 AGX  C15  H15A  single    0.970  0.020  1.090
 AGX  C15  H15B  single    0.970  0.020  1.090
 AGX  N    HN    single    0.860  0.020  1.020

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
 AGX  H     C    C4    121.95  3.000
 AGX  H     C    C1    121.46  3.000
 AGX  C4    C    C1    116.59  3.000
 AGX  HN    N    C6    126.36  3.000
 AGX  HN    N    C4    126.40  3.000
 AGX  C6    N    C4    107.23  3.000
 AGX  C8    O    C7    118.28  3.000
 AGX  H1    C1   C2    119.20  3.000
 AGX  H1    C1   C     119.23  3.000
 AGX  C2    C1   C     121.58  3.000
 AGX  C6    N1   C5    105.13  3.000
 AGX  H2    C2   C3    119.53  3.000
 AGX  H2    C2   C1    119.05  3.000
 AGX  C3    C2   C1    121.43  3.000
 AGX  HN2   N2   C9    115.55  3.000
 AGX  HN2   N2   C8    116.37  3.000
 AGX  C9    N2   C8    128.03  3.000
 AGX  H3    C3   C5    120.84  3.000
 AGX  H3    C3   C2    121.28  3.000
 AGX  C5    C3   C2    117.87  3.000
 AGX  C5    C4   N     104.63  3.000
 AGX  C5    C4   C     122.64  3.000
 AGX  N     C4   C     132.74  3.000
 AGX  C4    C5   C3    119.90  3.000
 AGX  C4    C5   N1    109.91  3.000
 AGX  C3    C5   N1    130.19  3.000
 AGX  C7    C6   N1    124.27  3.000
 AGX  C7    C6   N     122.55  3.000
 AGX  N1    C6   N     113.10  3.000
 AGX  H7    C7   C15   109.74  3.000
 AGX  H7    C7   C6    108.06  3.000
 AGX  C15   C7   C6    112.49  3.000
 AGX  H7    C7   O     109.36  3.000
 AGX  C15   C7   O     111.29  3.000
 AGX  C6    C7   O     105.77  3.000
 AGX  C14   C9   C10   118.99  3.000
 AGX  C10   C9   N2    116.81  3.000
 AGX  C14   C9   N2    124.19  3.000
 AGX  H10   C10  C11   119.04  3.000
 AGX  H10   C10  C9    120.16  3.000
 AGX  C11   C10  C9    120.79  3.000
 AGX  H11   C11  C12   119.89  3.000
 AGX  H11   C11  C10   119.68  3.000
 AGX  C12   C11  C10   120.43  3.000
 AGX  C13   C12  C11   118.83  3.000
 AGX  C13   C12  CL1   121.22  3.000
 AGX  C11   C12  CL1   119.95  3.000
 AGX  C14   C13  C12   121.36  3.000
 AGX  C14   C13  CL    118.38  3.000
 AGX  C12   C13  CL    120.26  3.000
 AGX  H14   C14  C13   118.93  3.000
 AGX  H14   C14  C9    121.47  3.000
 AGX  C13   C14  C9    119.60  3.000
 AGX  H15B  C15  H15A  107.97  3.000
 AGX  H15B  C15  H15   109.10  3.000
 AGX  H15A  C15  H15   108.33  3.000
 AGX  H15B  C15  C7    110.52  3.000
 AGX  H15A  C15  C7    109.66  3.000
 AGX  H15   C15  C7    111.17  3.000
 AGX  N2    C8   O1    126.36  3.000
 AGX  N2    C8   O     109.02  3.000
 AGX  O1    C8   O     124.63  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
 AGX  CONST_01  C6   N    C4   C    180.00  0.0  0
 AGX  CONST_02  N1   C5   C4   C    180.00  0.0  0
 AGX  CONST_03  C3   C5   C4   C      0.00  0.0  0
 AGX  CONST_04  C3   C2   C1   C      0.00  0.0  0
 AGX  CONST_05  C1   C    C4   N    180.00  0.0  0
 AGX  CONST_06  N1   C5   C4   N      0.00  0.0  0
 AGX  CONST_07  C3   C5   C4   N    180.00  0.0  0
 AGX  CONST_08  C5   N1   C6   N      0.00  0.0  0
 AGX  CONST_09  C5   C4   C    C1     0.00  0.0  0
 AGX  CONST_10  C5   C3   C2   C1     0.00  0.0  0
 AGX  CONST_11  C4   N    C6   N1     0.00  0.0  0
 AGX  CONST_12  C2   C3   C5   N1   180.00  0.0  0
 AGX  CONST_13  C4   C    C1   C2     0.00  0.0  0
 AGX  CONST_14  C4   C5   C3   C2     0.00  0.0  0
 AGX  CONST_15  C6   N1   C5   C3   180.00  0.0  0
 AGX  CONST_16  C6   N1   C5   C4     0.00  0.0  0
 AGX  CONST_17  C6   N    C4   C5     0.00  0.0  0
 AGX  CONST_18  C12  C13  C14  C9     0.00  0.0  0
 AGX  CONST_19  C12  C11  C10  C9     0.00  0.0  0
 AGX  CONST_20  C13  C14  C9   C10    0.00  0.0  0
 AGX  CONST_21  C13  C12  C11  C10    0.00  0.0  0
 AGX  CONST_22  C14  C9   C10  C11    0.00  0.0  0
 AGX  CONST_23  C14  C13  C12  C11    0.00  0.0  0
 AGX  CONST_24  C11  C12  C13  CL   180.00  0.0  0
 AGX  CONST_25  C9   C14  C13  CL   180.00  0.0  0
 AGX  CONST_26  C10  C11  C12  CL1  180.00  0.0  0
 AGX  CONST_27  C14  C13  C12  CL1  180.00  0.0  0
 AGX  CONST_28  C13  C14  C9   N2   180.00  0.0  0
 AGX  CONST_29  C11  C10  C9   N2   180.00  0.0  0
 AGX  CONST_30  C7   C6   N    C4   180.00  0.0  0
 AGX  CONST_31  C7   C6   N1   C5   180.00  0.0  0
 AGX  CONST_32  HN   N    C4   C      0.00  0.0  0
 AGX  CONST_33  H2   C2   C1   C    180.00  0.0  0
 AGX  CONST_34  H    C    C4   N      0.00  0.0  0
 AGX  CONST_35  H3   C3   C2   C1   180.00  0.0  0
 AGX  CONST_36  H1   C1   C2   C3   180.00  0.0  0
 AGX  CONST_37  H11  C11  C10  C9   180.00  0.0  0
 AGX  CONST_38  H14  C14  C9   C10  180.00  0.0  0
 AGX  CONST_39  H10  C10  C11  C12  180.00  0.0  0
 AGX  CONST_40  C14  C9   N2   C8     0.00  0.0  0
 AGX  CONST_41  C10  C9   N2   C8   180.00  0.0  0
 AGX  CONST_42  HN2  N2   C9   C10    0.00  0.0  0
 AGX  CONST_43  C9   N2   C8   O    180.00  0.0  0
 AGX  CONST_44  C9   N2   C8   O1     0.00  0.0  0

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
 AGX  chir_01  C7  O  C6  C15  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
 AGX  plan-1  CL   0.020
 AGX  plan-1  CL1  0.020
 AGX  plan-1  N2   0.020
 AGX  plan-1  C9   0.020
 AGX  plan-1  C10  0.020
 AGX  plan-1  C11  0.020
 AGX  plan-1  C12  0.020
 AGX  plan-1  C13  0.020
 AGX  plan-1  C14  0.020
 AGX  plan-1  H10  0.020
 AGX  plan-1  H11  0.020
 AGX  plan-1  H14  0.020
 AGX  plan-2  C    0.020
 AGX  plan-2  N    0.020
 AGX  plan-2  C1   0.020
 AGX  plan-2  N1   0.020
 AGX  plan-2  C2   0.020
 AGX  plan-2  C3   0.020
 AGX  plan-2  C4   0.020
 AGX  plan-2  C5   0.020
 AGX  plan-2  C6   0.020
 AGX  plan-2  C7   0.020
 AGX  plan-2  H    0.020
 AGX  plan-2  H1   0.020
 AGX  plan-2  H2   0.020
 AGX  plan-2  H3   0.020
 AGX  plan-2  HN   0.020
 AGX  plan-3  N2   0.020
 AGX  plan-3  C9   0.020
 AGX  plan-3  HN2  0.020
 AGX  plan-3  C8   0.020
 AGX  plan-4  O    0.020
 AGX  plan-4  O1   0.020
 AGX  plan-4  N2   0.020
 AGX  plan-4  C8   0.020

