# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 20:50:29 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 5-{[{[(1S)-2-(butylamino)-2-oxo-1-phenylethyl]carbamoyl}(methyl)amino]methyl}-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCNC(=O)[C@@H](NC(=O)N(C)Cc1ccc2OCOc2c1C(O)=O)c3ccccc3
#
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
 7NV  7NV  '5-{[{[(1S)-2-(butylamino)-2-oxo-1-phenylethyl]carbamoyl}(methyl)amino]methyl}-1,3-benzodioxole-4-carboxylic acid'  ligand  58  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7NV
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
 7NV  C15   C  CR16   0  -0.269   -1.6338  -3.3000  -0.6933
 7NV  C16   C  CR16   0  -0.243   -2.1415  -2.6051  -1.7827
 7NV  C17   C  CR16   0  -0.320   -2.3561  -1.2358  -1.6960
 7NV  C23   C  CR16   0  -0.311    2.1117  -0.2328   0.9926
 7NV  C6    C  CH2    0  -0.424   -8.3656  -0.0973   0.4043
 7NV  C24   C  CR16   0  -0.343    2.5686  -1.5137   1.3251
 7NV  C7    C  CH3    0  -0.662   -9.3743  -0.9215  -0.3825
 7NV  C9    C  CH3    0  -0.566    0.7362   2.7885   1.6843
 7NV  C13   C  CH1    0  -0.260   -2.3415   0.9413  -0.4196
 7NV  C30   C  CR6    0  -0.195    4.1759   0.3144  -0.1636
 7NV  C5    C  CH2    0  -0.460   -7.0274   0.0242  -0.3132
 7NV  C18   C  CR6    0   0.169   -2.0702  -0.5491  -0.5232
 7NV  C22   C  CR6    0   0.051    2.8798   0.6745   0.2769
 7NV  C25   C  CR56   0   0.284    3.8255  -1.8448   0.8946
 7NV  C29   C  CR56   0   0.294    4.5936  -0.9578   0.1576
 7NV  C2    C  C      0   0.548   -3.5944   1.1228   0.4425
 7NV  C27   C  CH2    0   0.070    5.7008  -2.8831   0.3199
 7NV  C4    C  CH2    0  -0.243   -6.0314   0.8560   0.4780
 7NV  C19   C  CR16   0  -0.291   -1.5694  -1.2512   0.5686
 7NV  C21   C  CH2    0  -0.340    2.3255   2.0442  -0.0742
 7NV  N3    N  NH1    0  -0.632   -4.7457   0.8967  -0.1910
 7NV  O33   O  O      0  -0.589    5.1988   2.4081  -0.5338
 7NV  O1    O  O      0  -0.489   -3.5119   1.3955   1.6323
 7NV  O32   O  OC    -1  -0.585    5.6617   0.7365  -1.9353
 7NV  O26   O  O      0  -0.491    4.5200  -2.9926   1.1022
 7NV  O28   O  O      0  -0.480    5.7966  -1.5345  -0.1059
 7NV  O11   O  O      0  -0.529    0.1443   1.2481  -1.5078
 7NV  C3    C  CR16   0  -0.237   -1.3470  -2.6180   0.4829
 7NV  N25   N  NH1    0  -0.705   -1.2728   1.6775   0.1955
 7NV  N26   N  NT     0  -0.497    0.9615   2.2644   0.3536
 7NV  H15   H  HCR6   0   0.256   -1.4590  -4.3659  -0.7611
 7NV  H16   H  HCR6   0   0.256   -2.3634  -3.1266  -2.7049
 7NV  H3    H  HCR6   0   0.255   -0.9507  -3.1508   1.3377
 7NV  H17   H  HCR6   0   0.251   -2.7399  -0.6975  -2.5549
 7NV  H23   H  HCR6   0   0.225    1.1146   0.0332   1.3146
 7NV  H24   H  HCR6   0   0.261    1.9551  -2.1987   1.8944
 7NV  H61C  H  HCH2   0   0.219   -8.7729   0.9007   0.5917
 7NV  H62C  H  HCH2   0   0.219   -8.2073  -0.5508   1.3873
 7NV  H71C  H  HCH3   0   0.229  -10.3143  -1.0245   0.1601
 7NV  H72C  H  HCH3   0   0.219   -9.5968  -0.4585  -1.3452
 7NV  H73C  H  HCH3   0   0.219   -8.9942  -1.9254  -0.5797
 7NV  H51C  H  HCH2   0   0.229   -6.6103  -0.9734  -0.4831
 7NV  H52C  H  HCH2   0   0.228   -7.1824   0.4718  -1.3007
 7NV  H91C  H  HCH3   0   0.237    0.5576   2.0111   2.4342
 7NV  H92C  H  HCH3   0   0.268    1.6155   3.3468   1.9952
 7NV  H93C  H  HCH3   0   0.253   -0.1024   3.4853   1.6989
 7NV  H13   H  HCH1   0   0.294   -2.5392   1.3316  -1.4221
 7NV  H25   H  HNH1   0   0.406   -1.4038   1.9050   1.1689
 7NV  H41C  H  HCH2   0   0.235   -6.4192   1.8690   0.6239
 7NV  H42C  H  HCH2   0   0.239   -5.8931   0.4226   1.4698
 7NV  H19   H  HCR6   0   0.246   -1.3438  -0.7331   1.4930
 7NV  H211  H  HCH2   0   0.261    2.9455   2.8154   0.3790
 7NV  H212  H  HCH2   0   0.255    2.3956   2.2027  -1.1504
 7NV  HA    H  HNH1   0   0.403   -4.7295   0.7415  -1.1872
 7NV  H271  H  HCH2   0   0.239    6.5703  -3.1435   0.9249
 7NV  H272  H  HCH2   0   0.227    5.6327  -3.5459  -0.5500
 7NV  C12   C  C      0   0.745   -0.0398   1.6995  -0.3833
 7NV  C31   C  C      0   0.372    5.0930   1.2406  -0.9519

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
 7NV  C15  C16   aromatic  1.388  0.020  1.388
 7NV  C15  C3    aromatic  1.389  0.020  1.389
 7NV  C16  C17   aromatic  1.389  0.020  1.389
 7NV  C17  C18   aromatic  1.389  0.020  1.389
 7NV  C23  C24   aromatic  1.400  0.020  1.400
 7NV  C23  C22   aromatic  1.388  0.020  1.388
 7NV  C6   C7    single    1.522  0.020  1.522
 7NV  C6   C5    single    1.523  0.020  1.523
 7NV  C24  C25   aromatic  1.369  0.020  1.369
 7NV  C9   N26   single    1.448  0.020  1.448
 7NV  C13  C18   single    1.518  0.020  1.518
 7NV  C13  C2    single    1.532  0.020  1.532
 7NV  C13  N25   single    1.436  0.020  1.436
 7NV  C30  C22   aromatic  1.415  0.020  1.415
 7NV  C30  C29   aromatic  1.377  0.020  1.377
 7NV  C30  C31   single    1.523  0.020  1.523
 7NV  C5   C4    single    1.520  0.020  1.520
 7NV  C18  C19   aromatic  1.391  0.020  1.391
 7NV  C22  C21   single    1.519  0.020  1.519
 7NV  C25  C29   aromatic  1.386  0.020  1.386
 7NV  C25  O26   single    1.357  0.020  1.357
 7NV  C29  O28   single    1.360  0.020  1.360
 7NV  C2   N3    single    1.333  0.020  1.333
 7NV  C2   O1    double    1.224  0.020  1.224
 7NV  C31  O33   deloc     1.245  0.020  1.245
 7NV  C31  O32   deloc     1.243  0.020  1.243
 7NV  C27  O26   single    1.421  0.020  1.421
 7NV  C27  O28   single    1.417  0.020  1.417
 7NV  C12  O11   double    1.226  0.020  1.226
 7NV  C12  N25   single    1.362  0.020  1.362
 7NV  C12  N26   single    1.366  0.020  1.366
 7NV  C4   N3    single    1.450  0.020  1.450
 7NV  C19  C3    aromatic  1.387  0.020  1.387
 7NV  C21  N26   single    1.446  0.020  1.446
 7NV  C15  H15   single    0.930  0.020  1.080
 7NV  C16  H16   single    0.930  0.020  1.080
 7NV  C3   H3    single    0.930  0.020  1.080
 7NV  C17  H17   single    0.930  0.020  1.080
 7NV  C23  H23   single    0.930  0.020  1.080
 7NV  C24  H24   single    0.930  0.020  1.080
 7NV  C6   H61C  single    0.970  0.020  1.090
 7NV  C6   H62C  single    0.970  0.020  1.090
 7NV  C7   H71C  single    0.970  0.020  1.090
 7NV  C7   H72C  single    0.970  0.020  1.090
 7NV  C7   H73C  single    0.970  0.020  1.090
 7NV  C5   H51C  single    0.970  0.020  1.090
 7NV  C5   H52C  single    0.970  0.020  1.090
 7NV  C9   H91C  single    0.970  0.020  1.090
 7NV  C9   H92C  single    0.970  0.020  1.090
 7NV  C9   H93C  single    0.970  0.020  1.090
 7NV  C13  H13   single    0.970  0.020  1.090
 7NV  N25  H25   single    0.860  0.020  1.020
 7NV  C4   H41C  single    0.970  0.020  1.090
 7NV  C4   H42C  single    0.970  0.020  1.090
 7NV  C19  H19   single    0.930  0.020  1.080
 7NV  C21  H211  single    0.970  0.020  1.090
 7NV  C21  H212  single    0.970  0.020  1.090
 7NV  N3   HA    single    0.860  0.020  1.020
 7NV  C27  H271  single    0.970  0.020  1.090
 7NV  C27  H272  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
 7NV  H15   C15  C3    120.21  3.000
 7NV  H15   C15  C16   120.19  3.000
 7NV  C3    C15  C16   119.61  3.000
 7NV  H16   C16  C17   119.77  3.000
 7NV  H16   C16  C15   120.16  3.000
 7NV  C17   C16  C15   120.07  3.000
 7NV  H17   C17  C18   119.77  3.000
 7NV  H17   C17  C16   119.66  3.000
 7NV  C18   C17  C16   120.56  3.000
 7NV  H23   C23  C22   120.22  3.000
 7NV  H23   C23  C24   117.09  3.000
 7NV  C22   C23  C24   122.69  3.000
 7NV  H62C  C6   H61C  106.14  3.000
 7NV  H62C  C6   C5    109.22  3.000
 7NV  H61C  C6   C5    109.57  3.000
 7NV  H62C  C6   C7    109.63  3.000
 7NV  H61C  C6   C7    109.63  3.000
 7NV  C5    C6   C7    112.46  3.000
 7NV  H24   C24  C25   122.21  3.000
 7NV  H24   C24  C23   121.29  3.000
 7NV  C25   C24  C23   116.50  3.000
 7NV  H73C  C7   H72C  107.57  3.000
 7NV  H73C  C7   H71C  107.66  3.000
 7NV  H72C  C7   H71C  107.66  3.000
 7NV  H73C  C7   C6    111.14  3.000
 7NV  H72C  C7   C6    111.19  3.000
 7NV  H71C  C7   C6    111.43  3.000
 7NV  H93C  C9   H92C  106.86  3.000
 7NV  H93C  C9   H91C  108.61  3.000
 7NV  H92C  C9   H91C  107.51  3.000
 7NV  H93C  C9   N26   111.30  3.000
 7NV  H92C  C9   N26   108.84  3.000
 7NV  H91C  C9   N26   113.44  3.000
 7NV  H13   C13  N25   110.13  3.000
 7NV  H13   C13  C2    109.01  3.000
 7NV  N25   C13  C2    107.87  3.000
 7NV  H13   C13  C18   108.67  3.000
 7NV  N25   C13  C18   113.54  3.000
 7NV  C2    C13  C18   107.51  3.000
 7NV  C31   C30  C29   119.99  3.000
 7NV  C31   C30  C22   123.90  3.000
 7NV  C29   C30  C22   116.12  3.000
 7NV  H52C  C5   H51C  106.65  3.000
 7NV  H52C  C5   C4    109.78  3.000
 7NV  H51C  C5   C4    109.26  3.000
 7NV  H52C  C5   C6    109.44  3.000
 7NV  H51C  C5   C6    109.58  3.000
 7NV  C4    C5   C6    111.97  3.000
 7NV  C19   C18  C13   120.41  3.000
 7NV  C19   C18  C17   119.16  3.000
 7NV  C13   C18  C17   120.41  3.000
 7NV  C21   C22  C30   119.45  3.000
 7NV  C21   C22  C23   120.46  3.000
 7NV  C30   C22  C23   120.07  3.000
 7NV  O26   C25  C29   109.82  3.000
 7NV  O26   C25  C24   128.75  3.000
 7NV  C29   C25  C24   121.42  3.000
 7NV  O28   C29  C25   108.78  3.000
 7NV  O28   C29  C30   127.95  3.000
 7NV  C25   C29  C30   123.18  3.000
 7NV  O1    C2   N3    123.92  3.000
 7NV  O1    C2   C13   121.24  3.000
 7NV  N3    C2   C13   114.76  3.000
 7NV  H272  C27  H271  110.21  3.000
 7NV  H272  C27  O28   109.95  3.000
 7NV  H271  C27  O28   109.87  3.000
 7NV  H272  C27  O26   109.81  3.000
 7NV  H271  C27  O26   109.80  3.000
 7NV  O28   C27  O26   107.15  3.000
 7NV  H42C  C4   H41C  106.93  3.000
 7NV  H42C  C4   N3    108.55  3.000
 7NV  H41C  C4   N3    110.47  3.000
 7NV  H42C  C4   C5    109.81  3.000
 7NV  H41C  C4   C5    110.11  3.000
 7NV  N3    C4   C5    110.87  3.000
 7NV  H19   C19  C3    119.37  3.000
 7NV  H19   C19  C18   120.21  3.000
 7NV  C3    C19  C18   120.42  3.000
 7NV  H212  C21  H211  105.75  3.000
 7NV  H212  C21  N26   109.30  3.000
 7NV  H211  C21  N26   107.83  3.000
 7NV  H212  C21  C22   109.63  3.000
 7NV  H211  C21  C22   109.57  3.000
 7NV  N26   C21  C22   114.40  3.000
 7NV  HA    N3   C4    117.76  3.000
 7NV  HA    N3   C2    118.79  3.000
 7NV  C4    N3   C2    123.45  3.000
 7NV  C27   O26  C25   106.01  3.000
 7NV  C27   O28  C29   106.59  3.000
 7NV  H3    C3   C19   119.66  3.000
 7NV  H3    C3   C15   120.16  3.000
 7NV  C19   C3   C15   120.18  3.000
 7NV  H25   N25  C12   121.61  3.000
 7NV  H25   N25  C13   115.63  3.000
 7NV  C12   N25  C13   119.99  3.000
 7NV  C21   N26  C12   117.96  3.000
 7NV  C21   N26  C9    118.28  3.000
 7NV  C12   N26  C9    122.11  3.000
 7NV  N26   C12  N25   116.18  3.000
 7NV  N26   C12  O11   122.50  3.000
 7NV  N25   C12  O11   121.32  3.000
 7NV  O32   C31  O33   127.40  3.000
 7NV  O32   C31  C30   116.00  3.000
 7NV  O33   C31  C30   116.60  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
 7NV  CONST_01  C18   C17  C16  C15     0.00   0.0  0
 7NV  CONST_02  C18   C19  C3   C15     0.00   0.0  0
 7NV  CONST_03  C19   C3   C15  C16     0.00   0.0  0
 7NV  CONST_04  C19   C18  C17  C16     0.00   0.0  0
 7NV  CONST_05  C3    C15  C16  C17     0.00   0.0  0
 7NV  CONST_06  C3    C19  C18  C17     0.00   0.0  0
 7NV  CONST_07  C29   C25  C24  C23     0.00   0.0  0
 7NV  CONST_08  C29   C30  C22  C23     0.00   0.0  0
 7NV  CONST_09  C30   C22  C23  C24     0.00   0.0  0
 7NV  CONST_10  C30   C29  C25  C24     0.00   0.0  0
 7NV  CONST_11  C25   C24  C23  C22     0.00   0.0  0
 7NV  CONST_12  C25   C29  C30  C22     0.00   0.0  0
 7NV  CONST_13  C13   C18  C17  C16   180.00   0.0  0
 7NV  CONST_14  C31   C30  C22  C23   180.00   0.0  0
 7NV  CONST_15  C21   C22  C23  C24   180.00   0.0  0
 7NV  CONST_16  C3    C19  C18  C13   180.00   0.0  0
 7NV  CONST_17  C31   C30  C29  C25   180.00   0.0  0
 7NV  CONST_18  C21   C22  C30  C29   180.00   0.0  0
 7NV  CONST_19  O28   C29  C30  C31     0.00   0.0  0
 7NV  CONST_20  H17   C17  C16  C15   180.00   0.0  0
 7NV  CONST_21  H19   C19  C3   C15   180.00   0.0  0
 7NV  CONST_22  H3    C3   C15  C16   180.00   0.0  0
 7NV  CONST_23  H15   C15  C16  C17   180.00   0.0  0
 7NV  CONST_24  H23   C23  C22  C30   180.00   0.0  0
 7NV  CONST_25  H16   C16  C17  C18   180.00   0.0  0
 7NV  CONST_26  H24   C24  C23  C22   180.00   0.0  0
 7NV  CONST_27  O11   C12  N26  C9    180.00   0.0  0
 7NV  CONST_28  C4    N3   C2   C13   180.00   0.0  0
 7NV  CONST_29  O11   C12  N25  C13     0.00   0.0  0
 7NV  CONST_30  O1    C2   N3   C4      0.00   0.0  0
 7NV  CONST_31  O11   C12  N26  C21     0.00   0.0  0
 7NV  CONST_32  N25   C12  N26  C9      0.00   0.0  0
 7NV  CONST_33  N26   C12  N25  C13   180.00   0.0  0
 7NV  CONST_34  N25   C12  N26  C21   180.00   0.0  0
 7NV  CONST_35  HA    N3   C2   C13     0.00   0.0  0
 7NV  CONST_36  H25   N25  C12  O11   180.00   0.0  0
 7NV  Var_01    O28   C27  O26  C25    12.36  30.0  1
 7NV  Var_02    O26   C27  O28  C29   -12.65  30.0  1
 7NV  Var_03    N26   C21  C22  C23    -2.17  30.0  2
 7NV  Var_04    O33   C31  C30  C22    46.06  30.0  2
 7NV  Var_05    C22   C21  N26  C9     88.22  30.0  2
 7NV  Var_06    N3    C4   C5   C6    176.94  30.0  3
 7NV  Var_07    C4    C5   C6   C7    179.66  30.0  3
 7NV  Var_08    C2    N3   C4   C5   -155.52  30.0  3
 7NV  Var_09    H71C  C7   C6   C5    178.17  30.0  3
 7NV  Var_10    H91C  C9   N26  C12    70.82  30.0  3

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
 7NV  chir_01  C13  C18  C2  N25  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
 7NV  plan-1  C15  0.020
 7NV  plan-1  C16  0.020
 7NV  plan-1  C17  0.020
 7NV  plan-1  C13  0.020
 7NV  plan-1  C18  0.020
 7NV  plan-1  C19  0.020
 7NV  plan-1  C3   0.020
 7NV  plan-1  H15  0.020
 7NV  plan-1  H16  0.020
 7NV  plan-1  H3   0.020
 7NV  plan-1  H17  0.020
 7NV  plan-1  H19  0.020
 7NV  plan-2  C23  0.020
 7NV  plan-2  C24  0.020
 7NV  plan-2  C30  0.020
 7NV  plan-2  C22  0.020
 7NV  plan-2  C25  0.020
 7NV  plan-2  C29  0.020
 7NV  plan-2  C21  0.020
 7NV  plan-2  O26  0.020
 7NV  plan-2  O28  0.020
 7NV  plan-2  H23  0.020
 7NV  plan-2  H24  0.020
 7NV  plan-2  C31  0.020
 7NV  plan-3  C13  0.020
 7NV  plan-3  C2   0.020
 7NV  plan-3  C4   0.020
 7NV  plan-3  N3   0.020
 7NV  plan-3  O1   0.020
 7NV  plan-3  HA   0.020
 7NV  plan-4  C9   0.020
 7NV  plan-4  C13  0.020
 7NV  plan-4  C21  0.020
 7NV  plan-4  O11  0.020
 7NV  plan-4  N25  0.020
 7NV  plan-4  N26  0.020
 7NV  plan-4  H25  0.020
 7NV  plan-4  C12  0.020
 7NV  plan-5  C30  0.020
 7NV  plan-5  O33  0.020
 7NV  plan-5  O32  0.020
 7NV  plan-5  C31  0.020

