# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:39:46 2022
#   Inital geometry file: a 151 line input string
#   Ligand name: (2R)-2-[[4-(1,3-benzodioxol-5-yl)phenyl]methyl]-N'-hydroxy-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)C[C@@H](Cc1ccc(cc1)c2ccc3OCOc3c2)C(=O)N[C@@H]4[C@H](O)Cc5ccccc45
#
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
 LA3  LA3  (2R)-2-[[4-(1,3-benzodioxol-5-yl)phenyl]methyl]-N'-hydroxy-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide  ligand  61  35  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LA3
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
 LA3  C1    C  CR16  0  -0.290  -1.4273   0.7756  -1.8804
 LA3  C2    C  CR16  0  -0.291  -0.5511   2.2434   0.2883
 LA3  C3    C  CR6   0   0.065  -2.1653   0.7347  -0.6978
 LA3  C4    C  CR16  0  -0.276  -0.2652   1.5260  -1.9702
 LA3  C5    C  CR6   0   0.095   0.1992   2.2614  -0.8847
 LA3  C6    C  CR16  0  -0.290  -1.7095   1.4908   0.3838
 LA3  C7    C  CR6   0   0.080  -3.3775  -0.0999  -0.5877
 LA3  C8    C  CH2   0  -0.495   1.5278   2.9608  -0.9332
 LA3  C9    C  CR56  0   0.289  -5.6447  -1.6651  -0.4062
 LA3  C10   C  CR16  0  -0.407  -3.6407  -0.7888   0.6119
 LA3  C11   C  CR16  0  -0.330  -4.2590  -0.2195  -1.6588
 LA3  C12   C  CR16  0  -0.326  -5.4116  -1.0089  -1.5886
 LA3  C13   C  CR56  0   0.320  -4.7759  -1.5547   0.6683
 LA3  O14   O  O     0  -0.486  -5.2224  -2.3282   1.6870
 LA3  O15   O  O     0  -0.484  -6.6569  -2.5051  -0.0814
 LA3  C16   C  CH2   0   0.067  -6.5231  -2.7618   1.3103
 LA3  C17   C  CH1   0  -0.389   2.6086   2.1762  -0.1593
 LA3  C18   C  C     0   0.590   2.5921   0.7387  -0.6491
 LA3  C19   C  CH2   0  -0.577   3.9928   2.7906  -0.3516
 LA3  C20   C  C     0   0.520   4.0685   4.1790   0.2417
 LA3  O21   O  O     0  -0.475   3.7105   4.4360   1.3777
 LA3  N22   N  NH1   0  -0.371   4.5466   5.1008  -0.6143
 LA3  O23   O  OH1   0  -0.544   4.8586   6.3482  -0.1653
 LA3  O24   O  O     0  -0.497   3.0705   0.4204  -1.7293
 LA3  N25   N  NH1   0  -0.629   1.9728  -0.1267   0.1668
 LA3  C26   C  CR15  0  -0.129   1.6375  -1.4736  -0.2023
 LA3  C27   C  CR56  0   0.117   2.5899  -2.5462   0.2671
 LA3  C28   C  CR15  0  -0.013   0.2950  -1.9313   0.3998
 LA3  O29   O  OH1   0  -0.668   0.2468  -1.4330   1.7187
 LA3  C30   C  CH2   0  -0.512   0.4056  -3.4624   0.3812
 LA3  C31   C  CR16  0  -0.258   3.9283  -4.7956   1.1400
 LA3  C32   C  CR16  0  -0.326   3.9687  -2.5073   0.3687
 LA3  C33   C  CR56  0   0.102   1.8765  -3.6951   0.5921
 LA3  C34   C  CR16  0  -0.337   2.5403  -4.8282   1.0320
 LA3  C35   C  CR16  0  -0.260   4.6375  -3.6453   0.8114
 LA3  H1    H  HCR6  0   0.251  -1.7449   0.1897  -2.7342
 LA3  H2    H  HCR6  0   0.249  -0.2211   2.8194   1.1462
 LA3  H4    H  HCR6  0   0.248   0.3017   1.5176  -2.8935
 LA3  H6    H  HCR6  0   0.250  -2.2728   1.5062   1.3087
 LA3  H8    H  HCH2  0   0.253   1.8510   3.0879  -1.9691
 LA3  H8A   H  HCH2  0   0.268   1.4425   3.9603  -0.5002
 LA3  H10   H  HCR6  0   0.263  -2.9600  -0.7375   1.4519
 LA3  H11   H  HCR6  0   0.257  -4.0636   0.3275  -2.5721
 LA3  H12   H  HCR6  0   0.275  -6.0861  -1.0907  -2.4299
 LA3  H16   H  HCH2  0   0.248  -6.6261  -3.8296   1.5007
 LA3  H16A  H  HCH2  0   0.234  -7.2788  -2.1968   1.8665
 LA3  H17   H  HCH1  0   0.270   2.3604   2.2025   0.9057
 LA3  H19   H  HCH2  0   0.292   4.7441   2.1840   0.1631
 LA3  H19A  H  HCH2  0   0.265   4.2573   2.7888  -1.4107
 LA3  HN22  H  HNH1  0   0.417   4.9858   4.8450  -1.4872
 LA3  HO23  H  HOH1  0   0.479   4.1153   6.9144  -0.4098
 LA3  HN25  H  HNH1  0   0.399   1.5822   0.2103   1.0330
 LA3  H26   H  HCR5  0   0.278   1.5541  -1.5221  -1.2929
 LA3  H28   H  HCR5  0   0.246  -0.5490  -1.5619  -0.1916
 LA3  HO29  H  HOH1  0   0.458  -0.6346  -1.5760   2.0740
 LA3  H30   H  HCH2  0   0.261  -0.2318  -3.9368   1.1300
 LA3  H30A  H  HCH2  0   0.257   0.0937  -3.8477  -0.5948
 LA3  H31   H  HCR6  0   0.253   4.4593  -5.6718   1.4895
 LA3  H32   H  HCR6  0   0.245   4.5220  -1.6108   0.1161
 LA3  H34   H  HCR6  0   0.248   1.9938  -5.7245   1.2999
 LA3  H35   H  HCR6  0   0.253   5.7159  -3.6339   0.9043

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
 LA3  C4   C1    aromatic  1.386  0.020  1.386
 LA3  C3   C1    aromatic  1.395  0.020  1.395
 LA3  C1   H1    single    0.930  0.020  1.080
 LA3  C2   C5    aromatic  1.393  0.020  1.393
 LA3  C2   C6    aromatic  1.385  0.020  1.385
 LA3  C2   H2    single    0.930  0.020  1.080
 LA3  C6   C3    aromatic  1.396  0.020  1.396
 LA3  C3   C7    single    1.476  0.020  1.476
 LA3  C5   C4    aromatic  1.391  0.020  1.391
 LA3  C4   H4    single    0.930  0.020  1.080
 LA3  C8   C5    single    1.502  0.020  1.502
 LA3  C6   H6    single    0.930  0.020  1.080
 LA3  C10  C7    aromatic  1.408  0.020  1.408
 LA3  C7   C11   aromatic  1.392  0.020  1.392
 LA3  C17  C8    single    1.544  0.020  1.544
 LA3  C8   H8    single    0.970  0.020  1.090
 LA3  C8   H8A   single    0.970  0.020  1.090
 LA3  C13  C9    aromatic  1.386  0.020  1.386
 LA3  C9   C12   aromatic  1.372  0.020  1.372
 LA3  C9   O15   single    1.355  0.020  1.355
 LA3  C10  C13   aromatic  1.371  0.020  1.371
 LA3  C10  H10   single    0.930  0.020  1.080
 LA3  C11  C12   aromatic  1.399  0.020  1.399
 LA3  C11  H11   single    0.930  0.020  1.080
 LA3  C12  H12   single    0.930  0.020  1.080
 LA3  C13  O14   single    1.355  0.020  1.355
 LA3  O14  C16   single    1.422  0.020  1.422
 LA3  C16  O15   single    1.422  0.020  1.422
 LA3  C16  H16   single    0.970  0.020  1.090
 LA3  C16  H16A  single    0.970  0.020  1.090
 LA3  C18  C17   single    1.519  0.020  1.519
 LA3  C19  C17   single    1.527  0.020  1.527
 LA3  C17  H17   single    0.970  0.020  1.090
 LA3  O24  C18   double    1.224  0.020  1.224
 LA3  C18  N25   single    1.341  0.020  1.341
 LA3  C19  C20   single    1.512  0.020  1.512
 LA3  C19  H19   single    0.970  0.020  1.090
 LA3  C19  H19A  single    0.970  0.020  1.090
 LA3  N22  C20   single    1.346  0.020  1.346
 LA3  C20  O21   double    1.219  0.020  1.219
 LA3  N22  O23   single    1.362  0.020  1.362
 LA3  N22  HN22  single    0.890  0.020  1.040
 LA3  O23  HO23  single    0.850  0.020  0.980
 LA3  C26  N25   single    1.436  0.020  1.436
 LA3  N25  HN25  single    0.860  0.020  1.020
 LA3  C27  C26   single    1.509  0.020  1.509
 LA3  C26  C28   single    1.541  0.020  1.541
 LA3  C26  H26   single    0.970  0.020  1.090
 LA3  C33  C27   aromatic  1.391  0.020  1.391
 LA3  C32  C27   aromatic  1.383  0.020  1.383
 LA3  C30  C28   single    1.535  0.020  1.535
 LA3  C28  O29   single    1.411  0.020  1.411
 LA3  C28  H28   single    0.970  0.020  1.090
 LA3  O29  HO29  single    0.850  0.020  0.980
 LA3  C33  C30   single    1.504  0.020  1.504
 LA3  C30  H30   single    0.970  0.020  1.090
 LA3  C30  H30A  single    0.970  0.020  1.090
 LA3  C31  C34   aromatic  1.393  0.020  1.393
 LA3  C31  C35   aromatic  1.391  0.020  1.391
 LA3  C31  H31   single    0.930  0.020  1.080
 LA3  C35  C32   aromatic  1.392  0.020  1.392
 LA3  C32  H32   single    0.930  0.020  1.080
 LA3  C34  C33   aromatic  1.385  0.020  1.385
 LA3  C34  H34   single    0.930  0.020  1.080
 LA3  C35  H35   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
 LA3  H1    C1   C4   119.18  3.000
 LA3  H1    C1   C3   119.83  3.000
 LA3  C4    C1   C3   120.96  3.000
 LA3  H2    C2   C6   119.25  3.000
 LA3  H2    C2   C5   119.70  3.000
 LA3  C6    C2   C5   121.05  3.000
 LA3  C7    C3   C6   121.10  3.000
 LA3  C7    C3   C1   120.96  3.000
 LA3  C6    C3   C1   117.93  3.000
 LA3  H4    C4   C5   119.63  3.000
 LA3  H4    C4   C1   119.32  3.000
 LA3  C5    C4   C1   121.03  3.000
 LA3  C8    C5   C4   121.08  3.000
 LA3  C8    C5   C2   120.65  3.000
 LA3  C4    C5   C2   118.07  3.000
 LA3  H6    C6   C3   119.96  3.000
 LA3  H6    C6   C2   119.10  3.000
 LA3  C3    C6   C2   120.93  3.000
 LA3  C11   C7   C10  119.67  3.000
 LA3  C11   C7   C3   120.74  3.000
 LA3  C10   C7   C3   119.59  3.000
 LA3  H8A   C8   H8   107.00  3.000
 LA3  H8A   C8   C17  108.72  3.000
 LA3  H8    C8   C17  109.11  3.000
 LA3  H8A   C8   C5   110.13  3.000
 LA3  H8    C8   C5   110.27  3.000
 LA3  C17   C8   C5   111.50  3.000
 LA3  O15   C9   C13  109.38  3.000
 LA3  O15   C9   C12  129.05  3.000
 LA3  C13   C9   C12  121.56  3.000
 LA3  H10   C10  C13  121.03  3.000
 LA3  H10   C10  C7   121.35  3.000
 LA3  C13   C10  C7   117.60  3.000
 LA3  H11   C11  C12  118.45  3.000
 LA3  H11   C11  C7   119.43  3.000
 LA3  C12   C11  C7   122.11  3.000
 LA3  H12   C12  C11  121.17  3.000
 LA3  H12   C12  C9   121.88  3.000
 LA3  C11   C12  C9   116.94  3.000
 LA3  O14   C13  C10  128.53  3.000
 LA3  O14   C13  C9   109.32  3.000
 LA3  C10   C13  C9   122.12  3.000
 LA3  C16   O14  C13  106.04  3.000
 LA3  C16   O15  C9   106.04  3.000
 LA3  H16A  C16  H16  110.58  3.000
 LA3  H16A  C16  O15  109.82  3.000
 LA3  H16   C16  O15  109.82  3.000
 LA3  H16A  C16  O14  109.83  3.000
 LA3  H16   C16  O14  109.82  3.000
 LA3  O15   C16  O14  106.89  3.000
 LA3  H17   C17  C19  108.58  3.000
 LA3  H17   C17  C18  109.53  3.000
 LA3  C19   C17  C18  110.50  3.000
 LA3  H17   C17  C8   108.48  3.000
 LA3  C19   C17  C8   111.54  3.000
 LA3  C18   C17  C8   108.17  3.000
 LA3  N25   C18  O24  123.36  3.000
 LA3  N25   C18  C17  114.81  3.000
 LA3  O24   C18  C17  121.78  3.000
 LA3  H19A  C19  H19  106.80  3.000
 LA3  H19A  C19  C20  111.72  3.000
 LA3  H19   C19  C20  106.87  3.000
 LA3  H19A  C19  C17  109.95  3.000
 LA3  H19   C19  C17  109.89  3.000
 LA3  C20   C19  C17  111.44  3.000
 LA3  N22   C20  O21  123.57  3.000
 LA3  O21   C20  C19  123.01  3.000
 LA3  N22   C20  C19  113.40  3.000
 LA3  HN22  N22  O23  114.66  3.000
 LA3  HN22  N22  C20  122.05  3.000
 LA3  O23   N22  C20  119.93  3.000
 LA3  HO23  O23  N22  106.09  3.000
 LA3  HN25  N25  C26  116.35  3.000
 LA3  HN25  N25  C18  119.08  3.000
 LA3  C26   N25  C18  123.82  3.000
 LA3  H26   C26  C28  108.04  3.000
 LA3  H26   C26  C27  109.06  3.000
 LA3  C28   C26  C27  102.54  3.000
 LA3  H26   C26  N25  108.38  3.000
 LA3  C28   C26  N25  112.43  3.000
 LA3  C27   C26  N25  116.05  3.000
 LA3  C33   C27  C32  121.16  3.000
 LA3  C32   C27  C26  129.19  3.000
 LA3  C33   C27  C26  109.64  3.000
 LA3  H28   C28  C30  112.67  3.000
 LA3  H28   C28  O29  111.06  3.000
 LA3  C30   C28  O29  111.47  3.000
 LA3  H28   C28  C26  111.13  3.000
 LA3  O29   C28  C26  106.87  3.000
 LA3  C30   C28  C26  103.23  3.000
 LA3  HO29  O29  C28  108.94  3.000
 LA3  H30A  C30  H30  106.99  3.000
 LA3  H30A  C30  C33  110.44  3.000
 LA3  H30   C30  C33  114.05  3.000
 LA3  H30A  C30  C28  109.96  3.000
 LA3  H30   C30  C28  112.52  3.000
 LA3  C33   C30  C28  102.88  3.000
 LA3  H31   C31  C35  119.72  3.000
 LA3  H31   C31  C34  119.67  3.000
 LA3  C35   C31  C34  120.62  3.000
 LA3  H32   C32  C35  120.35  3.000
 LA3  H32   C32  C27  121.02  3.000
 LA3  C35   C32  C27  118.63  3.000
 LA3  C34   C33  C30  129.78  3.000
 LA3  C34   C33  C27  120.28  3.000
 LA3  C30   C33  C27  109.94  3.000
 LA3  H34   C34  C33  120.91  3.000
 LA3  H34   C34  C31  120.20  3.000
 LA3  C33   C34  C31  118.89  3.000
 LA3  H35   C35  C32  119.81  3.000
 LA3  H35   C35  C31  119.77  3.000
 LA3  C32   C35  C31  120.42  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
 LA3  CONST_01  C2    C5   C4   C1      0.00   0.0  0
 LA3  CONST_02  C2    C6   C3   C1      0.00   0.0  0
 LA3  CONST_05  C7    C3   C6   C2    180.00   0.0  0
 LA3  CONST_06  C5    C4   C1   C3      0.00   0.0  0
 LA3  CONST_07  C5    C2   C6   C3      0.00   0.0  0
 LA3  CONST_08  C13   C10  C7   C3    180.00   0.0  0
 LA3  CONST_09  C12   C11  C7   C3    180.00   0.0  0
 LA3  CONST_10  C6    C3   C1   C4      0.00   0.0  0
 LA3  CONST_11  C7    C3   C1   C4    180.00   0.0  0
 LA3  CONST_12  C6    C2   C5   C4      0.00   0.0  0
 LA3  CONST_15  C9    C13  C10  C7      0.00   0.0  0
 LA3  CONST_16  C9    C12  C11  C7      0.00   0.0  0
 LA3  CONST_17  C12   C11  C7   C10     0.00   0.0  0
 LA3  CONST_18  C12   C9   C13  C10     0.00   0.0  0
 LA3  CONST_19  C13   C10  C7   C11     0.00   0.0  0
 LA3  CONST_20  C13   C9   C12  C11     0.00   0.0  0
 LA3  CONST_21  C31   C34  C33  C27     0.00   0.0  0
 LA3  CONST_22  C31   C35  C32  C27     0.00   0.0  0
 LA3  CONST_23  C34   C33  C27  C32     0.00   0.0  0
 LA3  CONST_24  C34   C31  C35  C32     0.00   0.0  0
 LA3  CONST_25  C35   C32  C27  C33     0.00   0.0  0
 LA3  CONST_26  C35   C31  C34  C33     0.00   0.0  0
 LA3  CONST_27  C8    C5   C4   C1    180.00   0.0  0
 LA3  CONST_28  C8    C5   C2   C6    180.00   0.0  0
 LA3  CONST_29  H6    C6   C3   C1    180.00   0.0  0
 LA3  CONST_30  H4    C4   C5   C2    180.00   0.0  0
 LA3  CONST_31  H2    C2   C6   C3    180.00   0.0  0
 LA3  CONST_32  H10   C10  C7   C3      0.00   0.0  0
 LA3  CONST_33  H11   C11  C7   C3      0.00   0.0  0
 LA3  CONST_34  H1    C1   C4   C5    180.00   0.0  0
 LA3  CONST_35  H12   C12  C11  C7    180.00   0.0  0
 LA3  CONST_36  H32   C32  C27  C26     0.00   0.0  0
 LA3  CONST_37  H34   C34  C33  C27   180.00   0.0  0
 LA3  CONST_38  H35   C35  C32  C27   180.00   0.0  0
 LA3  CONST_39  H31   C31  C35  C32   180.00   0.0  0
 LA3  CONST_40  C26   N25  C18  C17   180.00   0.0  0
 LA3  CONST_41  C26   N25  C18  O24     0.00   0.0  0
 LA3  CONST_42  O23   N22  C20  C19   180.00   0.0  0
 LA3  CONST_43  O23   N22  C20  O21     0.00   0.0  0
 LA3  CONST_44  HN25  N25  C18  C17     0.00   0.0  0
 LA3  CONST_45  HN22  N22  C20  C19     0.00   0.0  0
 LA3  Var_01    O14   C16  O15  C9    -14.78  30.0  1
 LA3  Var_02    O15   C16  O14  C13    14.95  30.0  1
 LA3  Var_03    C28   C30  C33  C27   -20.18  30.0  1
 LA3  Var_04    C17   C8   C5   C2     72.67  30.0  2
 LA3  Var_05    N22   C20  C19  C17  -128.58  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
 LA3  chir_01  C17  C8   C18  C19  negativ
 LA3  chir_02  C26  N25  C27  C28  negativ
 LA3  chir_03  C28  O29  C26  C30  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
 LA3  plan-1  C1    0.020
 LA3  plan-1  C2    0.020
 LA3  plan-1  C3    0.020
 LA3  plan-1  C4    0.020
 LA3  plan-1  C5    0.020
 LA3  plan-1  C6    0.020
 LA3  plan-1  C7    0.020
 LA3  plan-1  C8    0.020
 LA3  plan-1  H1    0.020
 LA3  plan-1  H2    0.020
 LA3  plan-1  H4    0.020
 LA3  plan-1  H6    0.020
 LA3  plan-2  C3    0.020
 LA3  plan-2  C7    0.020
 LA3  plan-2  C9    0.020
 LA3  plan-2  C10   0.020
 LA3  plan-2  C11   0.020
 LA3  plan-2  C12   0.020
 LA3  plan-2  C13   0.020
 LA3  plan-2  O14   0.020
 LA3  plan-2  O15   0.020
 LA3  plan-2  H10   0.020
 LA3  plan-2  H11   0.020
 LA3  plan-2  H12   0.020
 LA3  plan-3  C26   0.020
 LA3  plan-3  C27   0.020
 LA3  plan-3  C30   0.020
 LA3  plan-3  C31   0.020
 LA3  plan-3  C32   0.020
 LA3  plan-3  C33   0.020
 LA3  plan-3  C34   0.020
 LA3  plan-3  C35   0.020
 LA3  plan-3  H31   0.020
 LA3  plan-3  H32   0.020
 LA3  plan-3  H34   0.020
 LA3  plan-3  H35   0.020
 LA3  plan-4  C17   0.020
 LA3  plan-4  C18   0.020
 LA3  plan-4  O24   0.020
 LA3  plan-4  N25   0.020
 LA3  plan-4  C26   0.020
 LA3  plan-4  HN25  0.020
 LA3  plan-5  C19   0.020
 LA3  plan-5  C20   0.020
 LA3  plan-5  O21   0.020
 LA3  plan-5  N22   0.020
 LA3  plan-5  O23   0.020
 LA3  plan-5  HN22  0.020

