# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 09:50:26 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: (R)-[2-[[(2S)-butan-2-yl]carbamoyl]phenyl]methyl-[(4-carboxy-1,3-benzodioxol-5-yl)methyl]-methyl-azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)NC(=O)c1ccccc1C[NH+](C)Cc2ccc3OCOc3c2C(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
 OM2  OM2  (R)-[2-[[(2S)-butan-2-yl]carbamoyl]phenyl]methyl-[(4-carboxy-1,3-benzodioxol-5-yl)methyl]-methyl-azanium  ligand  55  29  .  2021-08-17  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OM2
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
 OM2  C1    C  CR16   0  -0.246  -4.9317  -2.0052   1.2680
 OM2  C2    C  CR16   0  -0.241  -4.2500  -3.1964   1.0828
 OM2  C3    C  CR16   0  -0.276  -4.4573  -0.8451   0.6745
 OM2  C4    C  CR16   0  -0.284  -3.1012  -3.2114   0.3062
 OM2  C5    C  CR16   0  -0.320   3.3545  -2.1339  -0.5140
 OM2  C6    C  CR16   0  -0.337   4.5807  -1.7622   0.0458
 OM2  C7    C  CR6    0  -0.068  -3.3025  -0.8511  -0.1061
 OM2  C8    C  CR6    0  -0.208   2.4242   0.1001  -0.2213
 OM2  C9    C  CR6    0   0.092  -2.6109  -2.0562  -0.2961
 OM2  C10   C  CR6    0   0.059   2.2972  -1.2468  -0.6463
 OM2  C11   C  CR56   0   0.303   4.6910  -0.4604   0.4546
 OM2  C12   C  CR56   0   0.307   3.6476   0.4462   0.3116
 OM2  C13   C  C      0   0.520  -2.9054   0.4251  -0.7952
 OM2  C15   C  CH2    0   0.068   5.4100   1.5228   1.1435
 OM2  C17   C  CH3    0  -0.659  -3.7606   3.3977  -1.4307
 OM2  C18   C  CH3    0  -0.541   0.1034  -2.5166   0.8524
 OM2  C19   C  CH2    0  -0.405  -1.3517  -2.1676  -1.1123
 OM2  C20   C  CH2    0  -0.402   1.0426  -1.7590  -1.2957
 OM2  C21   C  CH2    0  -0.462  -2.4616   3.7821   0.6847
 OM2  C22   C  CH1    0  -0.050  -2.6669   2.8598  -0.5146
 OM2  N23   N  NC1    0  -0.630  -2.9920   1.5238  -0.0380
 OM2  N24   N  NT1    1  -0.545  -0.1305  -1.7390  -0.3747
 OM2  O26   O  OC     0  -0.493  -2.5846   0.4379  -1.9770
 OM2  O28   O  O      0  -0.483   5.7423   0.1445   1.0502
 OM2  O29   O  O      0  -0.470   4.0321   1.6372   0.8239
 OM2  H1    H  HCR6   0   0.268  -5.8354  -1.9757   1.8619
 OM2  H2    H  HCR6   0   0.268  -4.6091  -4.1118   1.5337
 OM2  H3    H  HCR6   0   0.269  -5.0161   0.0735   0.7996
 OM2  H4    H  HCR6   0   0.267  -2.5721  -4.1456   0.1613
 OM2  H5    H  HCR6   0   0.264   3.2306  -3.1534  -0.8560
 OM2  H6    H  HCR6   0   0.278   5.3903  -2.4705   0.1525
 OM2  H191  H  HCH2   0   0.296  -1.1981  -3.2042  -1.4166
 OM2  H192  H  HCH2   0   0.306  -1.4079  -1.5584  -2.0098
 OM2  H201  H  HCH2   0   0.301   0.7637  -1.1531  -2.1593
 OM2  H202  H  HCH2   0   0.299   1.1911  -2.7810  -1.6451
 OM2  H23   H  HNC1   0   0.403  -3.1630   1.4078   0.9481
 OM2  H151  H  HCH2   0   0.246   5.5851   1.8782   2.1592
 OM2  H152  H  HCH2   0   0.235   6.0069   2.0982   0.4286
 OM2  H161  H  HCH3   0   0.214  -1.4064   2.4194   2.0218
 OM2  H162  H  HCH3   0   0.238  -0.3565   3.3931   1.0123
 OM2  H163  H  HCH3   0   0.221  -1.1848   4.1249   2.3928
 OM2  H211  H  HCH2   0   0.220  -3.3883   3.8178   1.2684
 OM2  H212  H  HCH2   0   0.235  -2.3132   4.7928   0.2973
 OM2  H171  H  HCH3   0   0.237  -3.9234   2.7459  -2.2875
 OM2  H172  H  HCH3   0   0.218  -4.7032   3.4954  -0.8891
 OM2  H173  H  HCH3   0   0.227  -3.4848   4.3826  -1.8105
 OM2  H22   H  HCH1   0   0.242  -1.7250   2.7965  -1.0669
 OM2  H181  H  HCH3   0   0.286   0.9805  -2.1315   1.3642
 OM2  H182  H  HCH3   0   0.285  -0.7534  -2.4217   1.5116
 OM2  H183  H  HCH3   0   0.268   0.2628  -3.5660   0.6071
 OM2  H224  H  HNT1   0   0.484  -0.1600  -0.6566  -0.1416
 OM2  C16   C  CH3    0  -0.662  -1.2873   3.4080   1.5776
 OM2  O25   O  OC     0  -0.585   0.1367   0.7374  -0.1359
 OM2  O27   O  OC    -1  -0.534   1.6570   2.3002  -0.5465
 OM2  C14   C  C      0   0.480   1.3228   1.1400  -0.3174

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
 OM2  C1   C2    aromatic  1.385  0.020  1.385
 OM2  C1   C3    aromatic  1.387  0.020  1.387
 OM2  C2   C4    aromatic  1.387  0.020  1.387
 OM2  C3   C7    aromatic  1.394  0.020  1.394
 OM2  C4   C9    aromatic  1.392  0.020  1.392
 OM2  C5   C6    aromatic  1.398  0.020  1.398
 OM2  C5   C10   aromatic  1.386  0.020  1.386
 OM2  C6   C11   aromatic  1.369  0.020  1.369
 OM2  C7   C9    aromatic  1.402  0.020  1.402
 OM2  C7   C13   aromatic  1.504  0.020  1.504
 OM2  C8   C10   aromatic  1.418  0.020  1.418
 OM2  C8   C12   aromatic  1.379  0.020  1.379
 OM2  C8   C14   aromatic  1.518  0.020  1.518
 OM2  C9   C19   single    1.505  0.020  1.505
 OM2  C10  C20   aromatic  1.503  0.020  1.503
 OM2  C11  C12   aromatic  1.390  0.020  1.390
 OM2  C11  O28   aromatic  1.351  0.020  1.351
 OM2  C12  O29   aromatic  1.352  0.020  1.352
 OM2  C13  N23   single    1.337  0.020  1.337
 OM2  C13  O26   double    1.225  0.020  1.225
 OM2  C14  O25   deloc     1.266  0.020  1.266
 OM2  C14  O27   deloc     1.229  0.020  1.229
 OM2  C15  O28   single    1.421  0.020  1.421
 OM2  C15  O29   single    1.419  0.020  1.419
 OM2  C16  C21   single    1.522  0.020  1.522
 OM2  C17  C22   single    1.525  0.020  1.525
 OM2  C18  N24   single    1.472  0.020  1.472
 OM2  C19  N24   single    1.490  0.020  1.490
 OM2  C20  N24   single    1.492  0.020  1.492
 OM2  C21  C22   single    1.527  0.020  1.527
 OM2  C22  N23   single    1.455  0.020  1.455
 OM2  C1   H1    single    0.930  0.020  1.080
 OM2  C2   H2    single    0.930  0.020  1.080
 OM2  C3   H3    single    0.930  0.020  1.080
 OM2  C4   H4    single    0.930  0.020  1.080
 OM2  C5   H5    single    0.930  0.020  1.080
 OM2  C6   H6    single    0.930  0.020  1.080
 OM2  C19  H191  single    0.970  0.020  1.090
 OM2  C19  H192  single    0.970  0.020  1.090
 OM2  C20  H201  single    0.970  0.020  1.090
 OM2  C20  H202  single    0.970  0.020  1.090
 OM2  N23  H23   single    0.860  0.020  1.020
 OM2  C15  H151  single    0.970  0.020  1.090
 OM2  C15  H152  single    0.970  0.020  1.090
 OM2  C16  H161  single    0.970  0.020  1.090
 OM2  C16  H162  single    0.970  0.020  1.090
 OM2  C16  H163  single    0.970  0.020  1.090
 OM2  C21  H211  single    0.970  0.020  1.090
 OM2  C21  H212  single    0.970  0.020  1.090
 OM2  C17  H171  single    0.970  0.020  1.090
 OM2  C17  H172  single    0.970  0.020  1.090
 OM2  C17  H173  single    0.970  0.020  1.090
 OM2  C22  H22   single    0.970  0.020  1.090
 OM2  C18  H181  single    0.970  0.020  1.090
 OM2  C18  H182  single    0.970  0.020  1.090
 OM2  C18  H183  single    0.970  0.020  1.090
 OM2  N24  H224  single    0.890  0.020  1.040

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
 OM2  H1    C1   C3    119.86  3.000
 OM2  H1    C1   C2    120.54  3.000
 OM2  C3    C1   C2    119.60  3.000
 OM2  H2    C2   C4    119.95  3.000
 OM2  H2    C2   C1    120.58  3.000
 OM2  C4    C2   C1    119.47  3.000
 OM2  H3    C3   C7    119.74  3.000
 OM2  H3    C3   C1    118.94  3.000
 OM2  C7    C3   C1    121.30  3.000
 OM2  H4    C4   C9    119.06  3.000
 OM2  H4    C4   C2    119.26  3.000
 OM2  C9    C4   C2    121.68  3.000
 OM2  H5    C5   C10   119.03  3.000
 OM2  H5    C5   C6    118.50  3.000
 OM2  C10   C5   C6    122.47  3.000
 OM2  H6    C6   C11   122.23  3.000
 OM2  H6    C6   C5    121.47  3.000
 OM2  C11   C6   C5    116.30  3.000
 OM2  C13   C7   C9    122.48  3.000
 OM2  C13   C7   C3    118.15  3.000
 OM2  C9    C7   C3    119.22  3.000
 OM2  C14   C8   C12   119.76  3.000
 OM2  C14   C8   C10   124.53  3.000
 OM2  C12   C8   C10   115.71  3.000
 OM2  C19   C9   C7    123.35  3.000
 OM2  C19   C9   C4    117.91  3.000
 OM2  C7    C9   C4    118.74  3.000
 OM2  C20   C10  C8    121.88  3.000
 OM2  C20   C10  C5    117.38  3.000
 OM2  C8    C10  C5    120.72  3.000
 OM2  O28   C11  C12   109.73  3.000
 OM2  O28   C11  C6    128.32  3.000
 OM2  C12   C11  C6    121.95  3.000
 OM2  O29   C12  C11   108.79  3.000
 OM2  O29   C12  C8    128.31  3.000
 OM2  C11   C12  C8    122.84  3.000
 OM2  O26   C13  N23   123.70  3.000
 OM2  O26   C13  C7    121.35  3.000
 OM2  N23   C13  C7    114.88  3.000
 OM2  H152  C15  H151  110.45  3.000
 OM2  H152  C15  O29   109.88  3.000
 OM2  H151  C15  O29   109.84  3.000
 OM2  H152  C15  O28   109.84  3.000
 OM2  H151  C15  O28   109.87  3.000
 OM2  O29   C15  O28   106.89  3.000
 OM2  H173  C17  H172  108.08  3.000
 OM2  H173  C17  H171  107.72  3.000
 OM2  H172  C17  H171  108.36  3.000
 OM2  H173  C17  C22   110.26  3.000
 OM2  H172  C17  C22   110.66  3.000
 OM2  H171  C17  C22   111.64  3.000
 OM2  H183  C18  H182  109.67  3.000
 OM2  H183  C18  H181  109.24  3.000
 OM2  H182  C18  H181  108.68  3.000
 OM2  H183  C18  N24   110.16  3.000
 OM2  H182  C18  N24   109.56  3.000
 OM2  H181  C18  N24   109.51  3.000
 OM2  H192  C19  H191  108.04  3.000
 OM2  H192  C19  N24   106.87  3.000
 OM2  H191  C19  N24   107.22  3.000
 OM2  H192  C19  C9    111.31  3.000
 OM2  H191  C19  C9    109.84  3.000
 OM2  N24   C19  C9    113.34  3.000
 OM2  H202  C20  H201  107.56  3.000
 OM2  H202  C20  N24   108.51  3.000
 OM2  H201  C20  N24   106.27  3.000
 OM2  H202  C20  C10   110.14  3.000
 OM2  H201  C20  C10   111.48  3.000
 OM2  N24   C20  C10   112.66  3.000
 OM2  H212  C21  H211  105.88  3.000
 OM2  H212  C21  C22   107.37  3.000
 OM2  H211  C21  C22   108.93  3.000
 OM2  H212  C21  C16   109.31  3.000
 OM2  H211  C21  C16   110.37  3.000
 OM2  C22   C21  C16   114.59  3.000
 OM2  H22   C22  N23   107.73  3.000
 OM2  H22   C22  C21   108.41  3.000
 OM2  N23   C22  C21   109.11  3.000
 OM2  H22   C22  C17   109.56  3.000
 OM2  N23   C22  C17   111.13  3.000
 OM2  C21   C22  C17   110.81  3.000
 OM2  H23   N23  C22   117.65  3.000
 OM2  H23   N23  C13   118.08  3.000
 OM2  C22   N23  C13   123.67  3.000
 OM2  H224  N24  C20    99.44  3.000
 OM2  H224  N24  C19   111.32  3.000
 OM2  C20   N24  C19   109.58  3.000
 OM2  H224  N24  C18   110.19  3.000
 OM2  C20   N24  C18   112.50  3.000
 OM2  C19   N24  C18   113.03  3.000
 OM2  C15   O28  C11   106.33  3.000
 OM2  C15   O29  C12   106.88  3.000
 OM2  H163  C16  H162  108.46  3.000
 OM2  H163  C16  H161  107.57  3.000
 OM2  H162  C16  H161  107.00  3.000
 OM2  H163  C16  C21   110.46  3.000
 OM2  H162  C16  C21   111.00  3.000
 OM2  H161  C16  C21   112.18  3.000
 OM2  O27   C14  O25   125.59  3.000
 OM2  O27   C14  C8    117.47  3.000
 OM2  O25   C14  C8    116.93  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
 OM2  CONST_01  C9    C4   C2   C1     0.00   0.0  0
 OM2  CONST_02  C9    C7   C3   C1     0.00   0.0  0
 OM2  CONST_03  C7    C3   C1   C2     0.00   0.0  0
 OM2  CONST_04  C7    C9   C4   C2     0.00   0.0  0
 OM2  CONST_05  C4    C2   C1   C3     0.00   0.0  0
 OM2  CONST_06  C4    C9   C7   C3     0.00   0.0  0
 OM2  CONST_07  C12   C11  C6   C5     0.00   0.0  0
 OM2  CONST_08  O28   C11  C6   C5   180.00   0.0  0
 OM2  CONST_09  C12   C8   C10  C5     0.00   0.0  0
 OM2  CONST_10  C8    C10  C5   C6     0.00   0.0  0
 OM2  CONST_11  C8    C12  C11  C6     0.00   0.0  0
 OM2  CONST_12  O29   C12  C11  C6   180.00   0.0  0
 OM2  CONST_13  O28   C11  C12  C8   180.00   0.0  0
 OM2  CONST_14  C11   C6   C5   C10    0.00   0.0  0
 OM2  CONST_15  C11   C12  C8   C10    0.00   0.0  0
 OM2  CONST_16  O29   C12  C8   C10  180.00   0.0  0
 OM2  CONST_17  O29   C12  C11  O28    0.00   0.0  0
 OM2  CONST_18  C13   C7   C3   C1   180.00   0.0  0
 OM2  CONST_19  C13   C7   C9   C4   180.00   0.0  0
 OM2  CONST_20  C14   C8   C10  C5   180.00   0.0  0
 OM2  CONST_21  C20   C10  C5   C6   180.00   0.0  0
 OM2  CONST_22  C14   C8   C12  C11  180.00   0.0  0
 OM2  CONST_23  C20   C10  C8   C12  180.00   0.0  0
 OM2  CONST_24  O29   C12  C8   C14    0.00   0.0  0
 OM2  CONST_25  C19   C9   C4   C2   180.00   0.0  0
 OM2  CONST_26  C19   C9   C7   C3   180.00   0.0  0
 OM2  CONST_27  H4    C4   C2   C1   180.00   0.0  0
 OM2  CONST_28  H3    C3   C1   C2   180.00   0.0  0
 OM2  CONST_29  H2    C2   C1   C3   180.00   0.0  0
 OM2  CONST_30  H1    C1   C2   C4   180.00   0.0  0
 OM2  CONST_31  H5    C5   C10  C8   180.00   0.0  0
 OM2  CONST_32  H6    C6   C5   C10  180.00   0.0  0
 OM2  CONST_33  C20   C10  C8   C14    0.00   0.0  0
 OM2  CONST_34  C22   N23  C13  C7   180.00   0.0  0
 OM2  CONST_35  H23   N23  C13  C7     0.00   0.0  0
 OM2  CONST_36  O26   C13  N23  C22    0.00   0.0  0
 OM2  Var_01    O29   C15  O28  C11   11.35  30.0  1
 OM2  Var_02    O28   C15  O29  C12  -11.56  30.0  1
 OM2  Var_03    N23   C13  C7   C3    44.27  30.0  1
 OM2  Var_04    N24   C19  C9   C4   -99.07  30.0  2
 OM2  Var_05    N24   C20  C10  C5   117.02  30.0  1
 OM2  Var_06    O25   C14  C8   C10   35.24  30.0  1
 OM2  Var_07    H161  C16  C21  C22  -61.68  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
 OM2  chir_01  C22  C17  C21  N23  negativ
 OM2  chir_02  N24  C20  C19  C18  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
 OM2  plan-1  C1   0.020
 OM2  plan-1  C2   0.020
 OM2  plan-1  C3   0.020
 OM2  plan-1  C4   0.020
 OM2  plan-1  C7   0.020
 OM2  plan-1  C9   0.020
 OM2  plan-1  C13  0.020
 OM2  plan-1  C19  0.020
 OM2  plan-1  H1   0.020
 OM2  plan-1  H2   0.020
 OM2  plan-1  H3   0.020
 OM2  plan-1  H4   0.020
 OM2  plan-2  C5   0.020
 OM2  plan-2  C6   0.020
 OM2  plan-2  C8   0.020
 OM2  plan-2  C10  0.020
 OM2  plan-2  C11  0.020
 OM2  plan-2  C12  0.020
 OM2  plan-2  C20  0.020
 OM2  plan-2  O28  0.020
 OM2  plan-2  O29  0.020
 OM2  plan-2  H5   0.020
 OM2  plan-2  H6   0.020
 OM2  plan-2  C14  0.020
 OM2  plan-3  C7   0.020
 OM2  plan-3  C13  0.020
 OM2  plan-3  C22  0.020
 OM2  plan-3  N23  0.020
 OM2  plan-3  O26  0.020
 OM2  plan-3  H23  0.020
 OM2  plan-4  C8   0.020
 OM2  plan-4  O25  0.020
 OM2  plan-4  O27  0.020
 OM2  plan-4  C14  0.020

