# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:53:59 2021
#   Inital geometry file: a 74 line input string
#   Ligand name: ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-2-methoxy-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCC(=O)NCc1[nH]c2ccccc2n1
#
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
 LXA  LXA  ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-2-methoxy-ethanamide  ligand  29  16  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LXA
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
 LXA  N1   N  NR15  0  -0.702  -28.6610   -9.3840  -31.6311
 LXA  C4   C  CR5   0   0.455  -28.3487  -10.5433  -32.2642
 LXA  C5   C  CR56  0   0.332  -27.9804   -8.3762  -32.2624
 LXA  C6   C  CR16  0  -0.308  -27.9137   -7.0041  -32.0542
 LXA  C7   C  CR16  0  -0.280  -27.1015   -6.2841  -32.9147
 LXA  C8   C  CR16  0  -0.272  -26.3854   -6.9117  -33.9448
 LXA  C10  C  CR56  0   0.132  -27.2699   -9.0226  -33.2880
 LXA  N    N  NH1   0  -0.623  -28.8234  -12.8753  -32.8053
 LXA  C    C  CH3   0  -0.399  -29.9264  -14.7706  -36.9827
 LXA  O    O  O2    0  -0.475  -30.0917  -13.7447  -36.0352
 LXA  C1   C  CH2   0  -0.245  -29.3271  -13.9553  -34.8917
 LXA  C2   C  C     0   0.500  -29.5986  -12.8351  -33.9040
 LXA  C3   C  CH2   0  -0.396  -28.8993  -11.8563  -31.7989
 LXA  C9   C  CR16  0  -0.336  -26.4594   -8.2794  -34.1449
 LXA  N2   N  N     0  -0.467  -27.5221  -10.3751  -33.2562
 LXA  O1   O  O     0  -0.475  -30.4595  -11.9927  -34.0768
 LXA  H1   H  HNR5  0   0.419  -29.2803   -9.2878  -30.8417
 LXA  H2   H  HCR6  0   0.265  -28.4650   -6.5180  -31.2600
 LXA  H3   H  HCR6  0   0.254  -27.0164   -5.2126  -32.7891
 LXA  H4   H  HCR6  0   0.251  -25.7623   -6.3102  -34.5936
 LXA  H5   H  HNH1  0   0.410  -28.0617  -13.5315  -32.7552
 LXA  H6   H  HCH3  0   0.238  -30.5440  -14.5277  -37.8461
 LXA  H7   H  HCH3  0   0.208  -28.8858  -14.8611  -37.3157
 LXA  H8   H  HCH3  0   0.208  -30.2414  -15.7453  -36.5924
 LXA  H9   H  HCH2  0   0.241  -29.5683  -14.9139  -34.4075
 LXA  H10  H  HCH2  0   0.236  -28.2506  -13.9859  -35.1180
 LXA  H11  H  HCH2  0   0.275  -29.9300  -11.7229  -31.4640
 LXA  H12  H  HCH2  0   0.301  -28.3337  -12.1966  -30.9300
 LXA  H13  H  HCR6  0   0.252  -25.9070   -8.7614  -34.9415

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
 LXA  C    O    single    1.406  0.020  1.406
 LXA  O    C1   single    1.392  0.020  1.392
 LXA  C1   C2   single    1.518  0.020  1.518
 LXA  C9   C8   aromatic  1.384  0.020  1.384
 LXA  C9   C10  aromatic  1.394  0.020  1.394
 LXA  O1   C2   double    1.217  0.020  1.217
 LXA  C8   C7   aromatic  1.403  0.020  1.403
 LXA  C2   N    single    1.345  0.020  1.345
 LXA  C10  N2   aromatic  1.376  0.020  1.376
 LXA  C10  C5   aromatic  1.405  0.020  1.405
 LXA  N2   C4   aromatic  1.302  0.020  1.302
 LXA  C7   C6   aromatic  1.385  0.020  1.385
 LXA  N    C3   single    1.434  0.020  1.434
 LXA  C5   C6   aromatic  1.389  0.020  1.389
 LXA  C5   N1   aromatic  1.370  0.020  1.370
 LXA  C4   C3   single    1.498  0.020  1.498
 LXA  C4   N1   aromatic  1.357  0.020  1.357
 LXA  N1   H1   single    0.860  0.020  1.020
 LXA  C6   H2   single    0.930  0.020  1.080
 LXA  C7   H3   single    0.930  0.020  1.080
 LXA  C8   H4   single    0.930  0.020  1.080
 LXA  N    H5   single    0.860  0.020  1.020
 LXA  C    H6   single    0.970  0.020  1.090
 LXA  C    H7   single    0.970  0.020  1.090
 LXA  C    H8   single    0.970  0.020  1.090
 LXA  C1   H9   single    0.970  0.020  1.090
 LXA  C1   H10  single    0.970  0.020  1.090
 LXA  C3   H11  single    0.970  0.020  1.090
 LXA  C3   H12  single    0.970  0.020  1.090
 LXA  C9   H13  single    0.930  0.020  1.080

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
 LXA  H1   N1   C5   126.57  3.000
 LXA  H1   N1   C4   126.03  3.000
 LXA  C5   N1   C4   107.40  3.000
 LXA  N2   C4   C3   125.68  3.000
 LXA  C3   C4   N1   121.28  3.000
 LXA  N2   C4   N1   113.02  3.000
 LXA  C10  C5   C6   122.64  3.000
 LXA  C6   C5   N1   132.93  3.000
 LXA  C10  C5   N1   104.42  3.000
 LXA  H2   C6   C7   121.41  3.000
 LXA  H2   C6   C5   121.95  3.000
 LXA  C7   C6   C5   116.64  3.000
 LXA  H3   C7   C8   119.21  3.000
 LXA  H3   C7   C6   119.25  3.000
 LXA  C8   C7   C6   121.54  3.000
 LXA  H4   C8   C9   119.56  3.000
 LXA  H4   C8   C7   119.05  3.000
 LXA  C9   C8   C7   121.39  3.000
 LXA  N2   C10  C9   130.14  3.000
 LXA  N2   C10  C5   110.04  3.000
 LXA  C9   C10  C5   119.82  3.000
 LXA  H5   N    C3   117.92  3.000
 LXA  H5   N    C2   119.75  3.000
 LXA  C3   N    C2   121.43  3.000
 LXA  H8   C    H7   107.90  3.000
 LXA  H8   C    H6   108.52  3.000
 LXA  H7   C    H6   108.42  3.000
 LXA  H8   C    O    112.02  3.000
 LXA  H7   C    O    112.12  3.000
 LXA  H6   C    O    107.75  3.000
 LXA  C1   O    C    112.25  3.000
 LXA  H10  C1   H9   106.30  3.000
 LXA  H10  C1   C2   109.22  3.000
 LXA  H9   C1   C2   108.50  3.000
 LXA  H10  C1   O    111.89  3.000
 LXA  H9   C1   O    111.89  3.000
 LXA  C2   C1   O    108.95  3.000
 LXA  O1   C2   C1   123.03  3.000
 LXA  O1   C2   N    122.98  3.000
 LXA  C1   C2   N    113.98  3.000
 LXA  H12  C3   H11  106.45  3.000
 LXA  H12  C3   N    108.05  3.000
 LXA  H11  C3   N    110.61  3.000
 LXA  H12  C3   C4   109.28  3.000
 LXA  H11  C3   C4   109.58  3.000
 LXA  N    C3   C4   112.66  3.000
 LXA  H13  C9   C10  120.77  3.000
 LXA  H13  C9   C8   121.26  3.000
 LXA  C10  C9   C8   117.97  3.000
 LXA  C10  N2   C4   105.12  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
 LXA  CONST_01  C9   C10  C5   N1    180.00   0.0  0
 LXA  CONST_02  N2   C10  C5   N1      0.00   0.0  0
 LXA  CONST_03  C7   C6   C5   N1    180.00   0.0  0
 LXA  CONST_04  C10  N2   C4   N1      0.00   0.0  0
 LXA  CONST_05  C9   C10  N2   C4    180.00   0.0  0
 LXA  CONST_06  C5   C10  N2   C4      0.00   0.0  0
 LXA  CONST_07  C10  C5   N1   C4      0.00   0.0  0
 LXA  CONST_08  C6   C5   N1   C4    180.00   0.0  0
 LXA  CONST_09  C8   C9   C10  C5      0.00   0.0  0
 LXA  CONST_10  C8   C7   C6   C5      0.00   0.0  0
 LXA  CONST_11  N2   C4   N1   C5      0.00   0.0  0
 LXA  CONST_12  C9   C8   C7   C6      0.00   0.0  0
 LXA  CONST_13  C9   C10  C5   C6      0.00   0.0  0
 LXA  CONST_14  N2   C10  C5   C6    180.00   0.0  0
 LXA  CONST_15  C10  C9   C8   C7      0.00   0.0  0
 LXA  CONST_16  C10  C5   C6   C7      0.00   0.0  0
 LXA  CONST_17  N2   C10  C9   C8    180.00   0.0  0
 LXA  CONST_18  C3   C4   N1   C5    180.00   0.0  0
 LXA  CONST_19  C3   C4   N2   C10   180.00   0.0  0
 LXA  CONST_20  H2   C6   C5   N1      0.00   0.0  0
 LXA  CONST_21  H13  C9   C10  C5    180.00   0.0  0
 LXA  CONST_22  H3   C7   C6   C5    180.00   0.0  0
 LXA  CONST_23  H4   C8   C7   C6    180.00   0.0  0
 LXA  CONST_24  H1   N1   C5   C6      0.00   0.0  0
 LXA  CONST_25  C3   N    C2   C1    180.00   0.0  0
 LXA  CONST_26  O1   C2   N    C3      0.00   0.0  0
 LXA  CONST_27  H5   N    C2   C1      0.00   0.0  0
 LXA  Var_01    N    C3   C4   N1    161.12  30.0  2
 LXA  Var_02    C2   N    C3   C4    -70.03  30.0  2
 LXA  Var_03    O    C1   C2   N    -174.56  30.0  2
 LXA  Var_04    C2   C1   O    C    -178.03  30.0  3
 LXA  Var_05    H6   C    O    C1   -179.35  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
 LXA  plan-1  N1   0.020
 LXA  plan-1  C4   0.020
 LXA  plan-1  C5   0.020
 LXA  plan-1  C6   0.020
 LXA  plan-1  C7   0.020
 LXA  plan-1  C8   0.020
 LXA  plan-1  C10  0.020
 LXA  plan-1  C3   0.020
 LXA  plan-1  C9   0.020
 LXA  plan-1  N2   0.020
 LXA  plan-1  H1   0.020
 LXA  plan-1  H2   0.020
 LXA  plan-1  H3   0.020
 LXA  plan-1  H4   0.020
 LXA  plan-1  H13  0.020
 LXA  plan-2  N    0.020
 LXA  plan-2  C1   0.020
 LXA  plan-2  C2   0.020
 LXA  plan-2  C3   0.020
 LXA  plan-2  O1   0.020
 LXA  plan-2  H5   0.020

