# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 12:32:57 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-(1H-benzimidazol-2-yl)-N-[(2-methylfuran-3-yl)carbonyl]-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1occc1C(=O)N[C@H](Cc2[nH]c3ccccc3n2)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
 4D7  4D7  3-(1H-benzimidazol-2-yl)-N-[(2-methylfuran-3-yl)carbonyl]-D-alanine  ligand  37  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4D7
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
 4D7  C1    C  CR16   0  -0.280   4.8399   1.8910   0.5700
 4D7  C2    C  CR16   0  -0.273   4.3069   2.5169  -0.5669
 4D7  C3    C  CR16   0  -0.337   3.3104   1.9194  -1.3189
 4D7  C4    C  CR16   0  -0.310   4.3905   0.6503   0.9906
 4D7  N5    N  NR15   0  -0.693   2.7115  -1.1260   0.3407
 4D7  C6    C  CR56   0   0.331   3.3869   0.0602   0.2319
 4D7  C7    C  CR56   0   0.142   2.8442   0.6700  -0.9123
 4D7  N8    N  N      0  -0.477   1.8780  -0.1399  -1.4618
 4D7  C9    C  CR5    0   0.452   1.8284  -1.1934  -0.6892
 4D7  C10   C  CH2    0  -0.587   0.8613  -2.3134  -0.8332
 4D7  C11   C  CH1    0  -0.171  -0.3647  -2.1255   0.0755
 4D7  C12   C  C      0   0.413  -1.3632  -3.2902  -0.1625
 4D7  O13   O  OC    -1  -0.615  -0.9483  -4.4062   0.2075
 4D7  O14   O  O      0  -0.584  -2.4438  -3.0218  -0.7071
 4D7  N15   N  NH1    0  -0.642  -0.9204  -0.8194  -0.1616
 4D7  C16   C  C      0   0.492  -1.7671  -0.2199   0.6869
 4D7  C17   C  CR5    0  -0.168  -2.2040   1.1284   0.2772
 4D7  O18   O  O      0  -0.503  -2.1255  -0.7289   1.7443
 4D7  C19   C  CR5    0   0.377  -3.2821   1.8026   0.7720
 4D7  O20   O  O      0  -0.406  -3.3582   3.0102   0.1851
 4D7  C21   C  CR15   0   0.000  -2.3296   3.1288  -0.6862
 4D7  C22   C  CR15   0  -0.366  -1.5867   2.0048  -0.6785
 4D7  C23   C  CH3    0  -0.747  -4.3212   1.4758   1.7761
 4D7  H1    H  HCR6   0   0.253   5.6177   2.3909   1.1322
 4D7  H2    H  HCR6   0   0.251   4.6843   3.4888  -0.8572
 4D7  H3    H  HCR6   0   0.252   2.9007   2.4063  -2.1949
 4D7  H4    H  HCR6   0   0.264   4.8010   0.1682   1.8681
 4D7  H10   H  HCH2   0   0.271   0.5469  -2.3608  -1.8781
 4D7  H10A  H  HCH2   0   0.281   1.3300  -3.2658  -0.5881
 4D7  H11   H  HCH1   0   0.248  -0.0296  -2.1751   1.1158
 4D7  HN15  H  HNH1   0   0.396  -0.7543  -0.3951  -1.0596
 4D7  H21   H  HCR5   0   0.285  -2.2559   4.0583  -1.2264
 4D7  H22   H  HCR5   0   0.258  -0.6939   1.8308  -1.2596
 4D7  H23   H  HCH3   0   0.259  -4.0496   1.8521   2.7646
 4D7  H23A  H  HCH3   0   0.255  -5.2780   1.9194   1.5025
 4D7  H23B  H  HCH3   0   0.263  -4.4477   0.4006   1.8591
 4D7  HN5   H  HNR5   0   0.418   2.8507  -1.8327   1.0460

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
 4D7  C2   C1    aromatic  1.403  0.020  1.403
 4D7  C1   C4    aromatic  1.385  0.020  1.385
 4D7  C1   H1    single    0.930  0.020  1.080
 4D7  C3   C2    aromatic  1.384  0.020  1.384
 4D7  C2   H2    single    0.930  0.020  1.080
 4D7  C3   C7    aromatic  1.394  0.020  1.394
 4D7  C3   H3    single    0.930  0.020  1.080
 4D7  C6   C4    aromatic  1.390  0.020  1.390
 4D7  C4   H4    single    0.930  0.020  1.080
 4D7  C9   N5    aromatic  1.358  0.020  1.358
 4D7  C6   N5    aromatic  1.369  0.020  1.369
 4D7  C7   C6    aromatic  1.406  0.020  1.406
 4D7  N8   C7    aromatic  1.375  0.020  1.375
 4D7  N8   C9    aromatic  1.307  0.020  1.307
 4D7  C10  C9    single    1.487  0.020  1.487
 4D7  C11  C10   single    1.538  0.020  1.538
 4D7  C10  H10   single    0.970  0.020  1.090
 4D7  C10  H10A  single    0.970  0.020  1.090
 4D7  N15  C11   single    1.439  0.020  1.439
 4D7  C12  C11   single    1.552  0.020  1.552
 4D7  C11  H11   single    0.970  0.020  1.090
 4D7  O14  C12   deloc     1.240  0.020  1.240
 4D7  C12  O13   deloc     1.247  0.020  1.247
 4D7  C16  N15   single    1.340  0.020  1.340
 4D7  N15  HN15  single    0.860  0.020  1.020
 4D7  C17  C16   single    1.475  0.020  1.475
 4D7  C16  O18   double    1.227  0.020  1.227
 4D7  C19  C17   aromatic  1.364  0.020  1.364
 4D7  C22  C17   aromatic  1.436  0.020  1.436
 4D7  O20  C19   aromatic  1.345  0.020  1.345
 4D7  C19  C23   single    1.481  0.020  1.481
 4D7  O20  C21   aromatic  1.353  0.020  1.353
 4D7  C21  C22   aromatic  1.347  0.020  1.347
 4D7  C21  H21   single    0.930  0.020  1.080
 4D7  C22  H22   single    0.930  0.020  1.080
 4D7  C23  H23   single    0.970  0.020  1.090
 4D7  C23  H23A  single    0.970  0.020  1.090
 4D7  C23  H23B  single    0.970  0.020  1.090
 4D7  N5   HN5   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
 4D7  H1    C1   C4    119.29  3.000
 4D7  H1    C1   C2    119.21  3.000
 4D7  C4    C1   C2    121.50  3.000
 4D7  H2    C2   C3    119.54  3.000
 4D7  H2    C2   C1    119.05  3.000
 4D7  C3    C2   C1    121.41  3.000
 4D7  H3    C3   C7    120.82  3.000
 4D7  H3    C3   C2    121.19  3.000
 4D7  C7    C3   C2    117.98  3.000
 4D7  H4    C4   C6    121.84  3.000
 4D7  H4    C4   C1    121.49  3.000
 4D7  C6    C4   C1    116.68  3.000
 4D7  HN5   N5   C9    125.84  3.000
 4D7  HN5   N5   C6    126.49  3.000
 4D7  C9    N5   C6    107.66  3.000
 4D7  C7    C6   N5    104.48  3.000
 4D7  C7    C6   C4    122.62  3.000
 4D7  N5    C6   C4    132.90  3.000
 4D7  N8    C7   C6    109.94  3.000
 4D7  N8    C7   C3    130.25  3.000
 4D7  C6    C7   C3    119.81  3.000
 4D7  C9    N8   C7    105.37  3.000
 4D7  C10   C9   N8    125.07  3.000
 4D7  C10   C9   N5    122.25  3.000
 4D7  N8    C9   N5    112.55  3.000
 4D7  H10A  C10  H10   107.52  3.000
 4D7  H10A  C10  C11   108.48  3.000
 4D7  H10   C10  C11   109.95  3.000
 4D7  H10A  C10  C9    110.92  3.000
 4D7  H10   C10  C9    108.22  3.000
 4D7  C11   C10  C9    111.68  3.000
 4D7  H11   C11  N15   108.43  3.000
 4D7  H11   C11  C12   107.98  3.000
 4D7  N15   C11  C12   114.03  3.000
 4D7  H11   C11  C10   108.19  3.000
 4D7  C12   C11  C10   109.30  3.000
 4D7  N15   C11  C10   108.75  3.000
 4D7  O14   C12  O13   127.90  3.000
 4D7  O13   C12  C11   114.33  3.000
 4D7  O14   C12  C11   117.75  3.000
 4D7  HN15  N15  C16   118.71  3.000
 4D7  HN15  N15  C11   117.75  3.000
 4D7  C16   N15  C11   123.06  3.000
 4D7  O18   C16  C17   122.13  3.000
 4D7  O18   C16  N15   123.00  3.000
 4D7  C17   C16  N15   114.83  3.000
 4D7  C22   C17  C19   106.23  3.000
 4D7  C22   C17  C16   127.97  3.000
 4D7  C19   C17  C16   125.79  3.000
 4D7  C23   C19  O20   117.01  3.000
 4D7  C23   C19  C17   133.71  3.000
 4D7  O20   C19  C17   109.28  3.000
 4D7  C21   O20  C19   108.46  3.000
 4D7  H21   C21  C22   133.22  3.000
 4D7  H21   C21  O20   116.77  3.000
 4D7  C22   C21  O20   110.02  3.000
 4D7  H22   C22  C21   125.98  3.000
 4D7  H22   C22  C17   127.98  3.000
 4D7  C21   C22  C17   106.02  3.000
 4D7  H23B  C23  H23A  108.67  3.000
 4D7  H23B  C23  H23   107.52  3.000
 4D7  H23A  C23  H23   107.79  3.000
 4D7  H23B  C23  C19   110.61  3.000
 4D7  H23A  C23  C19   110.85  3.000
 4D7  H23   C23  C19   111.29  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
 4D7  CONST_01  C7    C3   C2   C1     0.00   0.0  0
 4D7  CONST_02  N5    C6   C4   C1   180.00   0.0  0
 4D7  CONST_03  C7    C6   C4   C1     0.00   0.0  0
 4D7  CONST_04  C6    C4   C1   C2     0.00   0.0  0
 4D7  CONST_05  C6    C7   C3   C2     0.00   0.0  0
 4D7  CONST_06  N8    C7   C3   C2   180.00   0.0  0
 4D7  CONST_07  C4    C1   C2   C3     0.00   0.0  0
 4D7  CONST_08  C4    C6   C7   C3     0.00   0.0  0
 4D7  CONST_09  N5    C6   C7   C3   180.00   0.0  0
 4D7  CONST_10  C9    N8   C7   C3   180.00   0.0  0
 4D7  CONST_11  C9    N5   C6   C4   180.00   0.0  0
 4D7  CONST_12  N8    C7   C6   C4   180.00   0.0  0
 4D7  CONST_13  C7    N8   C9   N5     0.00   0.0  0
 4D7  CONST_14  N8    C7   C6   N5     0.00   0.0  0
 4D7  CONST_15  N8    C9   N5   C6     0.00   0.0  0
 4D7  CONST_16  C9    N8   C7   C6     0.00   0.0  0
 4D7  CONST_17  C9    N5   C6   C7     0.00   0.0  0
 4D7  CONST_18  C21   O20  C19  C17    0.00   0.0  0
 4D7  CONST_19  O20   C21  C22  C17    0.00   0.0  0
 4D7  CONST_20  C21   C22  C17  C19    0.00   0.0  0
 4D7  CONST_21  C22   C21  O20  C19    0.00   0.0  0
 4D7  CONST_22  C22   C17  C19  O20    0.00   0.0  0
 4D7  CONST_23  C10   C9   N5   C6   180.00   0.0  0
 4D7  CONST_24  C10   C9   N8   C7   180.00   0.0  0
 4D7  CONST_25  O20   C19  C17  C16  180.00   0.0  0
 4D7  CONST_26  C21   C22  C17  C16  180.00   0.0  0
 4D7  CONST_27  C23   C19  O20  C21  180.00   0.0  0
 4D7  CONST_28  C23   C19  C17  C22  180.00   0.0  0
 4D7  CONST_29  H3    C3   C2   C1   180.00   0.0  0
 4D7  CONST_30  H4    C4   C1   C2   180.00   0.0  0
 4D7  CONST_31  H1    C1   C2   C3   180.00   0.0  0
 4D7  CONST_32  H2    C2   C1   C4   180.00   0.0  0
 4D7  CONST_33  HN5   N5   C6   C4     0.00   0.0  0
 4D7  CONST_34  H21   C21  C22  C17  180.00   0.0  0
 4D7  CONST_35  H22   C22  C17  C19  180.00   0.0  0
 4D7  CONST_36  C17   C16  N15  C11  180.00   0.0  0
 4D7  CONST_37  HN15  N15  C16  C17    0.00   0.0  0
 4D7  CONST_38  O18   C16  N15  C11    0.00   0.0  0
 4D7  Var_01    C11   C10  C9   N5    80.27  30.0  2
 4D7  Var_02    C19   C17  C16  N15  163.04  30.0  1
 4D7  Var_03    H23   C23  C19  C17   94.35  30.0  2

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
 4D7  chir_01  C11  C10  N15  C12  negativ

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
 4D7  plan-1  C16   0.020
 4D7  plan-1  C17   0.020
 4D7  plan-1  C19   0.020
 4D7  plan-1  O20   0.020
 4D7  plan-1  C21   0.020
 4D7  plan-1  C22   0.020
 4D7  plan-1  C23   0.020
 4D7  plan-1  H21   0.020
 4D7  plan-1  H22   0.020
 4D7  plan-2  C1    0.020
 4D7  plan-2  C2    0.020
 4D7  plan-2  C3    0.020
 4D7  plan-2  C4    0.020
 4D7  plan-2  N5    0.020
 4D7  plan-2  C6    0.020
 4D7  plan-2  C7    0.020
 4D7  plan-2  N8    0.020
 4D7  plan-2  C9    0.020
 4D7  plan-2  C10   0.020
 4D7  plan-2  H1    0.020
 4D7  plan-2  H2    0.020
 4D7  plan-2  H3    0.020
 4D7  plan-2  H4    0.020
 4D7  plan-2  HN5   0.020
 4D7  plan-3  C11   0.020
 4D7  plan-3  N15   0.020
 4D7  plan-3  C16   0.020
 4D7  plan-3  C17   0.020
 4D7  plan-3  O18   0.020
 4D7  plan-3  HN15  0.020
 4D7  plan-4  C11   0.020
 4D7  plan-4  C12   0.020
 4D7  plan-4  O13   0.020
 4D7  plan-4  O14   0.020

