# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 07:37:08 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-[2-(propan-2-yloxy)-1H-benzimidazol-1-yl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Oc1nc2ccccc2n1c3ccc(O)cc3
#
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
 YJD  YJD  4-[2-(propan-2-yloxy)-1H-benzimidazol-1-yl]phenol  ligand  36  20  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YJD
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
 YJD  CA    C  CR6   0   0.365  -3.8770   0.2957   0.1322
 YJD  CB    C  CR16  0  -0.342  -3.1366  -0.2526   1.1795
 YJD  CC    C  CR16  0  -0.252  -1.7545  -0.2455   1.1287
 YJD  CD    C  CR6   0   0.258  -1.0964   0.2918   0.0292
 YJD  CE    C  CR16  0  -0.254  -1.8311   0.8312  -1.0167
 YJD  CF    C  CR16  0  -0.386  -3.2155   0.8409  -0.9660
 YJD  N1    N  N     0  -0.525   2.4190  -0.4431  -0.1579
 YJD  C6    C  CR5   0   0.684   1.1581  -0.7546  -0.1382
 YJD  O2    O  O2    0  -0.462   0.6172  -1.9448  -0.2372
 YJD  O4    O  OH1   0  -0.626  -5.2173   0.2733   0.2344
 YJD  C2    C  CR56  0   0.149   2.4392   0.9319  -0.0509
 YJD  C3    C  CR16  0  -0.330   3.5149   1.8119  -0.0180
 YJD  C7    C  CR16  0  -0.273   3.2451   3.1685   0.1018
 YJD  C8    C  CR16  0  -0.283   1.9342   3.6463   0.1894
 YJD  C20   C  CH1   0   0.007   1.5012  -3.0896  -0.3041
 YJD  C9    C  CR16  0  -0.301   0.8471   2.7817   0.1590
 YJD  C10   C  CR56  0   0.323   1.1305   1.4325   0.0369
 YJD  C11   C  CH3   0  -0.675   1.9583  -3.4713   1.0897
 YJD  N13   N  NR5   0  -0.678   0.3173   0.3155  -0.0167
 YJD  C13   C  CH3   0  -0.671   0.7169  -4.1893  -0.9855
 YJD  HB    H  HCR6  0   0.273  -3.6463  -0.6760   2.0353
 YJD  HF    H  HCR6  0   0.280  -3.7769   1.2687  -1.7882
 YJD  H4    H  HOH1  0   0.477  -5.6242   0.6718  -0.5434
 YJD  HC    H  HCR6  0   0.271  -1.1876  -0.6579   1.9532
 YJD  HE    H  HCR6  0   0.277  -1.3237   1.2467  -1.8778
 YJD  H20   H  HCH1  0   0.244   2.3643  -2.8192  -0.9167
 YJD  H3    H  HCR6  0   0.252   4.5321   1.4475  -0.0850
 YJD  H7    H  HCR6  0   0.251   4.0659   3.8730   0.1288
 YJD  H8    H  HCR6  0   0.253   1.7615   4.7105   0.2815
 YJD  H9    H  HCR6  0   0.265  -0.1683   3.1508   0.2252
 YJD  H111  H  HCH3  0   0.231   1.1131  -3.7717   1.7110
 YJD  H112  H  HCH3  0   0.240   2.6463  -4.3144   1.0274
 YJD  H113  H  HCH3  0   0.243   2.4822  -2.6528   1.5823
 YJD  H131  H  HCH3  0   0.244   0.4050  -3.8957  -1.9877
 YJD  H132  H  HCH3  0   0.238   1.3431  -5.0764  -1.0768
 YJD  H133  H  HCH3  0   0.233  -0.1686  -4.4633  -0.4099

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
 YJD  CA   CB    aromatic  1.395  0.020  1.395
 YJD  CA   CF    aromatic  1.393  0.020  1.393
 YJD  CA   O4    single    1.344  0.020  1.344
 YJD  CB   CC    aromatic  1.383  0.020  1.383
 YJD  CC   CD    aromatic  1.389  0.020  1.389
 YJD  CD   CE    aromatic  1.387  0.020  1.387
 YJD  CD   N13   single    1.415  0.020  1.415
 YJD  CE   CF    aromatic  1.385  0.020  1.385
 YJD  N1   C6    aromatic  1.299  0.020  1.299
 YJD  N1   C2    aromatic  1.379  0.020  1.379
 YJD  C6   O2    single    1.311  0.020  1.311
 YJD  C6   N13   aromatic  1.366  0.020  1.366
 YJD  O2   C20   single    1.448  0.020  1.448
 YJD  C2   C3    aromatic  1.390  0.020  1.390
 YJD  C2   C10   aromatic  1.404  0.020  1.404
 YJD  C3   C7    aromatic  1.388  0.020  1.388
 YJD  C7   C8    aromatic  1.398  0.020  1.398
 YJD  C8   C9    aromatic  1.389  0.020  1.389
 YJD  C9   C10   aromatic  1.384  0.020  1.384
 YJD  C10  N13   aromatic  1.383  0.020  1.383
 YJD  C20  C11   single    1.516  0.020  1.516
 YJD  C20  C13   single    1.513  0.020  1.513
 YJD  CB   HB    single    0.930  0.020  1.080
 YJD  CF   HF    single    0.930  0.020  1.080
 YJD  O4   H4    single    0.850  0.020  0.980
 YJD  CC   HC    single    0.930  0.020  1.080
 YJD  CE   HE    single    0.930  0.020  1.080
 YJD  C20  H20   single    0.970  0.020  1.090
 YJD  C3   H3    single    0.930  0.020  1.080
 YJD  C7   H7    single    0.930  0.020  1.080
 YJD  C8   H8    single    0.930  0.020  1.080
 YJD  C9   H9    single    0.930  0.020  1.080
 YJD  C11  H111  single    0.970  0.020  1.090
 YJD  C11  H112  single    0.970  0.020  1.090
 YJD  C11  H113  single    0.970  0.020  1.090
 YJD  C13  H131  single    0.970  0.020  1.090
 YJD  C13  H132  single    0.970  0.020  1.090
 YJD  C13  H133  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
 YJD  O4    CA   CF    122.67  3.000
 YJD  O4    CA   CB    117.75  3.000
 YJD  CF    CA   CB    119.58  3.000
 YJD  HB    CB   CC    120.11  3.000
 YJD  HB    CB   CA    119.83  3.000
 YJD  CC    CB   CA    120.06  3.000
 YJD  HC    CC   CD    120.14  3.000
 YJD  HC    CC   CB    119.57  3.000
 YJD  CD    CC   CB    120.29  3.000
 YJD  N13   CD   CE    119.89  3.000
 YJD  N13   CD   CC    120.36  3.000
 YJD  CE    CD   CC    119.74  3.000
 YJD  HE    CE   CF    119.66  3.000
 YJD  HE    CE   CD    120.05  3.000
 YJD  CF    CE   CD    120.29  3.000
 YJD  HF    CF   CE    119.53  3.000
 YJD  HF    CF   CA    120.43  3.000
 YJD  CE    CF   CA    120.04  3.000
 YJD  C2    N1   C6    104.60  3.000
 YJD  N13   C6   O2    117.63  3.000
 YJD  N13   C6   N1    114.26  3.000
 YJD  O2    C6   N1    128.10  3.000
 YJD  C20   O2   C6    117.99  3.000
 YJD  H4    O4   CA    110.65  3.000
 YJD  C10   C2   C3    119.62  3.000
 YJD  C10   C2   N1    110.28  3.000
 YJD  C3    C2   N1    130.10  3.000
 YJD  H3    C3   C7    121.12  3.000
 YJD  H3    C3   C2    120.84  3.000
 YJD  C7    C3   C2    118.04  3.000
 YJD  H7    C7   C8    119.16  3.000
 YJD  H7    C7   C3    119.40  3.000
 YJD  C8    C7   C3    121.44  3.000
 YJD  H8    C8   C9    119.28  3.000
 YJD  H8    C8   C7    119.42  3.000
 YJD  C9    C8   C7    121.31  3.000
 YJD  H20   C20  C13   109.69  3.000
 YJD  H20   C20  C11   109.86  3.000
 YJD  C13   C20  C11   112.79  3.000
 YJD  H20   C20  O2    108.22  3.000
 YJD  C13   C20  O2    106.20  3.000
 YJD  C11   C20  O2    109.92  3.000
 YJD  H9    C9   C10   122.00  3.000
 YJD  H9    C9   C8    121.36  3.000
 YJD  C10   C9   C8    116.64  3.000
 YJD  N13   C10  C9    132.11  3.000
 YJD  N13   C10  C2    104.94  3.000
 YJD  C9    C10  C2    122.95  3.000
 YJD  H113  C11  H112  107.66  3.000
 YJD  H113  C11  H111  108.77  3.000
 YJD  H112  C11  H111  107.97  3.000
 YJD  H113  C11  C20   111.81  3.000
 YJD  H112  C11  C20   109.43  3.000
 YJD  H111  C11  C20   111.06  3.000
 YJD  C10   N13  C6    105.92  3.000
 YJD  C10   N13  CD    126.87  3.000
 YJD  C6    N13  CD    127.21  3.000
 YJD  H133  C13  H132  107.83  3.000
 YJD  H133  C13  H131  108.69  3.000
 YJD  H132  C13  H131  107.86  3.000
 YJD  H133  C13  C20   111.45  3.000
 YJD  H132  C13  C20   109.37  3.000
 YJD  H131  C13  C20   111.51  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
 YJD  CONST_01  CD    CC   CB   CA      0.00   0.0  0
 YJD  CONST_02  CD    CE   CF   CA      0.00   0.0  0
 YJD  CONST_03  CE    CF   CA   CB      0.00   0.0  0
 YJD  CONST_04  CE    CD   CC   CB      0.00   0.0  0
 YJD  CONST_05  N13   CD   CC   CB    180.00   0.0  0
 YJD  CONST_06  CF    CA   CB   CC      0.00   0.0  0
 YJD  CONST_07  CF    CE   CD   CC      0.00   0.0  0
 YJD  CONST_10  N1    C6   N13  CD    180.00   0.0  0
 YJD  CONST_11  C2    C10  N13  CD    180.00   0.0  0
 YJD  CONST_12  C9    C10  N13  CD      0.00   0.0  0
 YJD  CONST_15  N13   CD   CE   CF    180.00   0.0  0
 YJD  CONST_16  C10   N13  C6   N1      0.00   0.0  0
 YJD  CONST_17  C7    C3   C2   N1    180.00   0.0  0
 YJD  CONST_18  C9    C10  C2   N1    180.00   0.0  0
 YJD  CONST_19  N13   C10  C2   N1      0.00   0.0  0
 YJD  CONST_20  C3    C2   N1   C6    180.00   0.0  0
 YJD  CONST_21  C10   C2   N1   C6      0.00   0.0  0
 YJD  CONST_22  C2    C10  N13  C6      0.00   0.0  0
 YJD  CONST_23  C9    C10  N13  C6    180.00   0.0  0
 YJD  CONST_24  N13   C6   N1   C2      0.00   0.0  0
 YJD  CONST_25  C8    C7   C3   C2      0.00   0.0  0
 YJD  CONST_26  C8    C9   C10  C2      0.00   0.0  0
 YJD  CONST_27  C9    C10  C2   C3      0.00   0.0  0
 YJD  CONST_28  N13   C10  C2   C3    180.00   0.0  0
 YJD  CONST_29  C9    C8   C7   C3      0.00   0.0  0
 YJD  CONST_30  C10   C2   C3   C7      0.00   0.0  0
 YJD  CONST_31  C10   C9   C8   C7      0.00   0.0  0
 YJD  CONST_32  N13   C10  C9   C8    180.00   0.0  0
 YJD  CONST_33  O4    CA   CB   CC    180.00   0.0  0
 YJD  CONST_34  O2    C6   N13  CD      0.00   0.0  0
 YJD  CONST_35  O4    CA   CF   CE    180.00   0.0  0
 YJD  CONST_36  C2    N1   C6   O2    180.00   0.0  0
 YJD  CONST_37  C10   N13  C6   O2    180.00   0.0  0
 YJD  CONST_38  HC    CC   CB   CA    180.00   0.0  0
 YJD  CONST_39  HE    CE   CF   CA    180.00   0.0  0
 YJD  CONST_40  HF    CF   CA   CB    180.00   0.0  0
 YJD  CONST_41  HB    CB   CC   CD    180.00   0.0  0
 YJD  CONST_42  H3    C3   C2   N1      0.00   0.0  0
 YJD  CONST_43  H7    C7   C3   C2    180.00   0.0  0
 YJD  CONST_44  H9    C9   C10  C2    180.00   0.0  0
 YJD  CONST_45  H8    C8   C7   C3    180.00   0.0  0
 YJD  Var_01    N13   C6   O2   C20  -177.20  30.0  1
 YJD  Var_02    C11   C20  O2   C6     81.33  30.0  3
 YJD  Var_03    H111  C11  C20  O2     62.58  30.0  3
 YJD  Var_04    H131  C13  C20  O2     59.94  30.0  3

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
 YJD  plan-1  CA   0.020
 YJD  plan-1  CB   0.020
 YJD  plan-1  CC   0.020
 YJD  plan-1  CD   0.020
 YJD  plan-1  CE   0.020
 YJD  plan-1  CF   0.020
 YJD  plan-1  O4   0.020
 YJD  plan-1  N13  0.020
 YJD  plan-1  HB   0.020
 YJD  plan-1  HF   0.020
 YJD  plan-1  HC   0.020
 YJD  plan-1  HE   0.020
 YJD  plan-2  CD   0.020
 YJD  plan-2  N1   0.020
 YJD  plan-2  C6   0.020
 YJD  plan-2  O2   0.020
 YJD  plan-2  C2   0.020
 YJD  plan-2  C3   0.020
 YJD  plan-2  C7   0.020
 YJD  plan-2  C8   0.020
 YJD  plan-2  C9   0.020
 YJD  plan-2  C10  0.020
 YJD  plan-2  N13  0.020
 YJD  plan-2  H3   0.020
 YJD  plan-2  H7   0.020
 YJD  plan-2  H8   0.020
 YJD  plan-2  H9   0.020

