# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:09:51 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  38  23  .  2021-08-05  2021-08-05  
;
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  -0.277   5.1269   1.7957   0.2754
 4D7  C2    C  CR16  0  -0.271   4.3652   2.5568  -0.6252
 4D7  C3    C  CR16  0  -0.333   3.2135   2.0527  -1.2017
 4D7  C4    C  CR16  0  -0.307   4.7597   0.5087   0.6274
 4D7  N5    N  NR15  0  -0.693   2.9437  -1.1867   0.1550
 4D7  C6    C  CR56  0   0.330   3.5991   0.0114   0.0461
 4D7  C7    C  CR56  0   0.153   2.8263   0.7578  -0.8589
 4D7  N8    N  N     0  -0.489   1.7477   0.0134  -1.2745
 4D7  C9    C  CR5   0   0.460   1.8551  -1.1302  -0.6494
 4D7  C10   C  CH2   0  -0.589   0.8570  -2.2300  -0.7452
 4D7  C11   C  CH1   0  -0.149  -0.3569  -1.9638   0.1656
 4D7  C12   C  C     0   0.535  -1.3649  -3.0838  -0.0480
 4D7  O13   O  OH1   0  -0.587  -1.1146  -4.1118   0.7475
 4D7  O14   O  O     0  -0.430  -2.2362  -3.0608  -0.8758
 4D7  N15   N  NH1   0  -0.678  -0.9353  -0.6918  -0.1587
 4D7  C16   C  C     0   0.500  -1.9628  -0.1966   0.5575
 4D7  C17   C  CR5   0  -0.156  -2.3618   1.1774   0.2246
 4D7  O18   O  O     0  -0.490  -2.5121  -0.8606   1.4295
 4D7  C19   C  CR5   0   0.388  -3.5098   1.7930   0.6372
 4D7  O20   O  O     0  -0.403  -3.5351   3.0458   0.1564
 4D7  C21   C  CR15  0   0.004  -2.4084   3.2547  -0.5647
 4D7  C22   C  CR15  0  -0.365  -1.6486   2.1431  -0.5641
 4D7  C23   C  CH3   0  -0.748  -4.6588   1.3688   1.4697
 4D7  H1    H  HCR6  0   0.257   6.0219   2.2262   0.7050
 4D7  H2    H  HCR6  0   0.254   4.6883   3.5600  -0.8704
 4D7  H3    H  HCR6  0   0.256   2.6282   2.6411  -1.8967
 4D7  H4    H  HCR6  0   0.268   5.3462  -0.0772   1.3226
 4D7  H10   H  HCH2  0   0.298   0.5241  -2.3092  -1.7815
 4D7  H10A  H  HCH2  0   0.304   1.3082  -3.1825  -0.4684
 4D7  H11   H  HCH1  0   0.301  -0.0250  -1.9824   1.2084
 4D7  HO13  H  HOH1  0   0.487  -1.7190  -4.8441   0.5509
 4D7  HN15  H  HNH1  0   0.420  -0.4712  -0.1233  -0.8527
 4D7  H21   H  HCR5  0   0.288  -2.2901   4.2286  -1.0101
 4D7  H22   H  HCR5  0   0.255  -0.6912   2.0345  -1.0506
 4D7  H23   H  HCH3  0   0.263  -4.4975   1.6180   2.5206
 4D7  H23A  H  HCH3  0   0.258  -5.5736   1.8646   1.1470
 4D7  H23B  H  HCH3  0   0.265  -4.8031   0.2945   1.4074
 4D7  HN5   H  HNR5  0   0.423   3.2198  -1.9725   0.7229

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  1.404  0.020  1.404
 4D7  C1   C4    aromatic  1.384  0.020  1.384
 4D7  C1   H1    single    0.930  0.020  1.080
 4D7  C3   C2    aromatic  1.383  0.020  1.383
 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  1.355  0.020  1.355
 4D7  C6   N5    aromatic  1.370  0.020  1.370
 4D7  C7   C6    aromatic  1.405  0.020  1.405
 4D7  N8   C7    aromatic  1.375  0.020  1.375
 4D7  N8   C9    aromatic  1.308  0.020  1.308
 4D7  C10  C9    single    1.488  0.020  1.488
 4D7  C11  C10   single    1.541  0.020  1.541
 4D7  C10  H10   single    0.970  0.020  1.090
 4D7  C10  H10A  single    0.970  0.020  1.090
 4D7  N15  C11   single    1.434  0.020  1.434
 4D7  C12  C11   single    1.522  0.020  1.522
 4D7  C11  H11   single    0.970  0.020  1.090
 4D7  O14  C12   double    1.202  0.020  1.202
 4D7  C12  O13   single    1.324  0.020  1.324
 4D7  O13  HO13  single    0.850  0.020  0.980
 4D7  C16  N15   single    1.347  0.020  1.347
 4D7  N15  HN15  single    0.860  0.020  1.020
 4D7  C17  C16   single    1.469  0.020  1.469
 4D7  C16  O18   double    1.226  0.020  1.226
 4D7  C19  C17   aromatic  1.366  0.020  1.366
 4D7  C22  C17   aromatic  1.436  0.020  1.436
 4D7  O20  C19   aromatic  1.342  0.020  1.342
 4D7  C19  C23   single    1.481  0.020  1.481
 4D7  O20  C21   aromatic  1.354  0.020  1.354
 4D7  C21  C22   aromatic  1.346  0.020  1.346
 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    119.24  3.000
 4D7  H1    C1   C2    119.20  3.000
 4D7  C4    C1   C2    121.56  3.000
 4D7  H2    C2   C3    119.47  3.000
 4D7  H2    C2   C1    119.08  3.000
 4D7  C3    C2   C1    121.45  3.000
 4D7  H3    C3   C7    120.83  3.000
 4D7  H3    C3   C2    121.32  3.000
 4D7  C7    C3   C2    117.85  3.000
 4D7  H4    C4   C6    121.85  3.000
 4D7  H4    C4   C1    121.55  3.000
 4D7  C6    C4   C1    116.61  3.000
 4D7  HN5   N5   C9    125.95  3.000
 4D7  HN5   N5   C6    126.55  3.000
 4D7  C9    N5   C6    107.50  3.000
 4D7  C7    C6   N5    104.64  3.000
 4D7  C7    C6   C4    122.60  3.000
 4D7  N5    C6   C4    132.77  3.000
 4D7  N8    C7   C6    109.80  3.000
 4D7  N8    C7   C3    130.27  3.000
 4D7  C6    C7   C3    119.94  3.000
 4D7  C9    N8   C7    105.34  3.000
 4D7  C10   C9   N8    124.08  3.000
 4D7  C10   C9   N5    123.12  3.000
 4D7  N8    C9   N5    112.72  3.000
 4D7  H10A  C10  H10   107.71  3.000
 4D7  H10A  C10  C11   109.09  3.000
 4D7  H10   C10  C11   109.48  3.000
 4D7  H10A  C10  C9    110.61  3.000
 4D7  H10   C10  C9    108.62  3.000
 4D7  C11   C10  C9    111.26  3.000
 4D7  H11   C11  N15   110.66  3.000
 4D7  H11   C11  C12   108.79  3.000
 4D7  N15   C11  C12   110.72  3.000
 4D7  H11   C11  C10   108.74  3.000
 4D7  C12   C11  C10   108.16  3.000
 4D7  N15   C11  C10   109.71  3.000
 4D7  O14   C12  O13   124.45  3.000
 4D7  O13   C12  C11   111.22  3.000
 4D7  O14   C12  C11   124.24  3.000
 4D7  HO13  O13  C12   110.30  3.000
 4D7  HN15  N15  C16   120.60  3.000
 4D7  HN15  N15  C11   117.97  3.000
 4D7  C16   N15  C11   120.90  3.000
 4D7  O18   C16  C17   123.10  3.000
 4D7  O18   C16  N15   121.40  3.000
 4D7  C17   C16  N15   115.51  3.000
 4D7  C22   C17  C19   106.27  3.000
 4D7  C22   C17  C16   128.19  3.000
 4D7  C19   C17  C16   125.54  3.000
 4D7  C23   C19  O20   117.01  3.000
 4D7  C23   C19  C17   133.83  3.000
 4D7  O20   C19  C17   109.16  3.000
 4D7  C21   O20  C19   108.61  3.000
 4D7  H21   C21  C22   133.19  3.000
 4D7  H21   C21  O20   116.81  3.000
 4D7  C22   C21  O20   110.00  3.000
 4D7  H22   C22  C21   125.69  3.000
 4D7  H22   C22  C17   128.34  3.000
 4D7  C21   C22  C17   105.96  3.000
 4D7  H23B  C23  H23A  108.77  3.000
 4D7  H23B  C23  H23   107.49  3.000
 4D7  H23A  C23  H23   107.77  3.000
 4D7  H23B  C23  C19   110.75  3.000
 4D7  H23A  C23  C19   110.77  3.000
 4D7  H23   C23  C19   111.16  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  CONST_39  HO13  O13  C12  C11  180.00   0.0  0
 4D7  Var_01    C11   C10  C9   N5    96.71  30.0  1
 4D7  Var_02    C19   C17  C16  N15  167.45  30.0  3
 4D7  Var_03    H23   C23  C19  C17   91.64  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
 4D7  plan-4  HO13  0.020

