FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

tag_button

FMODB ID: 9LJZ2

Calculation Name: 2D4O-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2D4O

Chain ID: A

ChEMBL ID:

UniProt ID: Q72J89

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 130
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1070495.372361
FMO2-HF: Nuclear repulsion 1020634.39014
FMO2-HF: Total energy -49860.982221
FMO2-MP2: Total energy -50007.810234


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-240.506-228.22436.29-20.472-28.102-0.21
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.787 / q_NPA : 0.905
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A3PHE00.0420.0202.244-1.7530.9004.298-2.083-4.868-0.010
4A4ARG10.7380.8355.17226.91026.921-0.001-0.003-0.0070.000
40A40ALA00.0050.0083.252-2.512-2.1290.648-0.250-0.7810.003
41A41GLU-1-0.800-0.8873.864-26.314-25.2920.199-0.353-0.869-0.002
42A42GLU-1-0.792-0.8981.809-165.407-163.54923.940-13.786-12.013-0.169
43A43GLY00.0090.0043.5129.1339.2400.0230.015-0.1440.000
46A46PRO0-0.020-0.0046.039-4.120-3.979-0.001-0.005-0.1350.000
47A47MET00.003-0.0152.3901.4331.8633.432-0.806-3.0560.000
48A48GLY00.0460.0034.5560.5380.603-0.001-0.014-0.0500.000
72A72SER00.0670.0363.436-4.697-4.1880.056-0.212-0.352-0.001
74A74GLU-1-0.938-0.9652.550-81.755-78.2533.052-2.541-4.014-0.029
75A75ALA0-0.017-0.0142.860-2.109-0.6170.628-0.512-1.609-0.002
76A76LEU00.0270.0113.7982.1462.2550.0170.078-0.2040.000
5A5PRO00.0750.0338.8970.1220.1220.0000.0000.0000.000
6A6PHE0-0.057-0.01511.849-0.747-0.7470.0000.0000.0000.000
7A7THR00.006-0.01313.3591.2681.2680.0000.0000.0000.000
8A8GLU-1-0.761-0.86916.850-12.435-12.4350.0000.0000.0000.000
9A9GLU-1-0.872-0.93017.426-13.894-13.8940.0000.0000.0000.000
10A10ASP-1-0.785-0.85213.133-21.471-21.4710.0000.0000.0000.000
11A11LEU00.0160.00714.506-0.522-0.5220.0000.0000.0000.000
12A12ASP-1-0.852-0.92116.392-14.765-14.7650.0000.0000.0000.000
13A13ARG10.8410.91510.10421.99821.9980.0000.0000.0000.000
14A14LEU00.012-0.00111.700-0.665-0.6650.0000.0000.0000.000
15A15ASN0-0.022-0.04413.3290.3890.3890.0000.0000.0000.000
16A16ARG10.8540.91711.26121.96321.9630.0000.0000.0000.000
17A17LEU0-0.049-0.0027.522-0.475-0.4750.0000.0000.0000.000
18A18ALA0-0.0270.01111.6610.2770.2770.0000.0000.0000.000
19A19GLY00.0540.03715.1290.6550.6550.0000.0000.0000.000
20A20LYS10.9310.94816.59812.17612.1760.0000.0000.0000.000
21A21ARG10.9500.98419.00813.56713.5670.0000.0000.0000.000
22A22PRO00.0680.04618.887-0.589-0.5890.0000.0000.0000.000
23A23VAL00.0020.01016.1420.3110.3110.0000.0000.0000.000
24A24SER00.0260.01619.294-0.095-0.0950.0000.0000.0000.000
25A25LEU00.0750.02721.260-0.276-0.2760.0000.0000.0000.000
26A26GLY00.0030.00622.593-0.036-0.0360.0000.0000.0000.000
27A27ALA00.0170.00521.0080.0140.0140.0000.0000.0000.000
28A28LEU0-0.0060.01417.096-0.148-0.1480.0000.0000.0000.000
29A29ARG10.8310.86419.56411.17111.1710.0000.0000.0000.000
30A30PHE0-0.049-0.01022.0140.1270.1270.0000.0000.0000.000
31A31PHE00.016-0.01217.422-0.065-0.0650.0000.0000.0000.000
32A32ALA00.0130.01016.941-0.428-0.4280.0000.0000.0000.000
33A33ARG10.8870.94717.99211.12111.1210.0000.0000.0000.000
34A34THR0-0.026-0.02318.5090.1940.1940.0000.0000.0000.000
35A35GLY0-0.0020.01517.5780.2550.2550.0000.0000.0000.000
36A36HIS0-0.027-0.02915.751-0.005-0.0050.0000.0000.0000.000
37A37SER0-0.023-0.00913.981-0.459-0.4590.0000.0000.0000.000
38A38PHE0-0.043-0.0178.805-0.659-0.6590.0000.0000.0000.000
39A39LEU0-0.026-0.0177.6731.2561.2560.0000.0000.0000.000
44A44GLU-1-0.923-0.9636.053-22.938-22.9380.0000.0000.0000.000
45A45GLU-1-0.807-0.8666.967-22.316-22.3160.0000.0000.0000.000
49A49PHE0-0.037-0.0126.907-0.373-0.3730.0000.0000.0000.000
50A50ALA00.0130.0069.6570.5210.5210.0000.0000.0000.000
51A51LEU0-0.019-0.00612.3270.1050.1050.0000.0000.0000.000
52A52ALA00.0390.00915.9420.4520.4520.0000.0000.0000.000
53A53GLN0-0.0070.00517.7190.2800.2800.0000.0000.0000.000
54A54ALA00.0610.04020.953-0.022-0.0220.0000.0000.0000.000
55A55VAL0-0.027-0.01823.3240.3070.3070.0000.0000.0000.000
56A56TRP0-0.0160.01226.439-0.190-0.1900.0000.0000.0000.000
57A57GLN0-0.051-0.04127.5080.3760.3760.0000.0000.0000.000
58A58GLY0-0.034-0.01231.2370.1810.1810.0000.0000.0000.000
59A59GLU-1-0.900-0.95633.569-7.986-7.9860.0000.0000.0000.000
60A60ALA0-0.006-0.00528.965-0.078-0.0780.0000.0000.0000.000
61A61THR0-0.021-0.01124.5040.1630.1630.0000.0000.0000.000
62A62THR00.005-0.01723.367-0.092-0.0920.0000.0000.0000.000
63A63VAL0-0.021-0.01617.9300.0720.0720.0000.0000.0000.000
64A64LEU00.0010.00820.270-0.262-0.2620.0000.0000.0000.000
65A65VAL0-0.004-0.02414.944-0.209-0.2090.0000.0000.0000.000
66A66THR0-0.060-0.02418.1700.5690.5690.0000.0000.0000.000
67A67ARG10.7010.79715.36315.70515.7050.0000.0000.0000.000
68A68MET00.0180.02511.008-0.710-0.7100.0000.0000.0000.000
69A69GLU-1-0.802-0.86011.178-15.921-15.9210.0000.0000.0000.000
70A70GLY00.024-0.0157.183-1.454-1.4540.0000.0000.0000.000
71A71ARG10.7930.8835.27428.43128.4310.0000.0000.0000.000
73A73VAL00.0670.0385.743-0.844-0.8440.0000.0000.0000.000
77A77ARG10.8700.9226.97526.04226.0420.0000.0000.0000.000
78A78GLY0-0.014-0.0084.8211.4951.4950.0000.0000.0000.000
79A79LEU0-0.035-0.0145.8441.8741.8740.0000.0000.0000.000
80A80LEU0-0.022-0.0027.9901.7781.7780.0000.0000.0000.000
81A81ARG10.8910.9405.82732.68132.6810.0000.0000.0000.000
82A82ALA0-0.0290.0038.4141.1821.1820.0000.0000.0000.000
83A83VAL0-0.008-0.00210.4411.4941.4940.0000.0000.0000.000
84A84VAL00.0470.02413.4391.0951.0950.0000.0000.0000.000
85A85LYS10.8080.89413.33218.42418.4240.0000.0000.0000.000
86A86SER0-0.014-0.00914.4861.0491.0490.0000.0000.0000.000
87A87ALA00.009-0.00516.2830.8170.8170.0000.0000.0000.000
88A88TYR0-0.0070.00118.2770.6510.6510.0000.0000.0000.000
89A89ASP-1-0.823-0.90917.352-15.664-15.6640.0000.0000.0000.000
90A90ALA0-0.054-0.01720.3740.5170.5170.0000.0000.0000.000
91A91GLY0-0.026-0.00522.4310.4910.4910.0000.0000.0000.000
92A92VAL0-0.088-0.04521.6110.4380.4380.0000.0000.0000.000
93A93TYR0-0.0180.00823.515-0.158-0.1580.0000.0000.0000.000
94A94GLU-1-0.846-0.89122.292-11.244-11.2440.0000.0000.0000.000
95A95VAL0-0.001-0.00616.257-0.168-0.1680.0000.0000.0000.000
96A96ALA00.0240.01819.6950.0550.0550.0000.0000.0000.000
97A97LEU0-0.003-0.01815.347-0.359-0.3590.0000.0000.0000.000
98A98HIS00.0190.01119.5880.2910.2910.0000.0000.0000.000
99A99LEU0-0.0130.00216.726-0.515-0.5150.0000.0000.0000.000
100A100ASP-1-0.870-0.93419.058-12.261-12.2610.0000.0000.0000.000
101A101PRO00.032-0.00319.038-0.601-0.6010.0000.0000.0000.000
102A102GLU-1-0.842-0.90420.107-12.300-12.3000.0000.0000.0000.000
103A103ARG10.8200.90512.55916.33316.3330.0000.0000.0000.000
104A104LYS10.8790.91615.31112.34112.3410.0000.0000.0000.000
105A105GLU-1-0.865-0.9378.942-23.869-23.8690.0000.0000.0000.000
106A106LEU0-0.015-0.01411.302-1.066-1.0660.0000.0000.0000.000
107A107GLU-1-0.862-0.92712.862-13.534-13.5340.0000.0000.0000.000
108A108GLU-1-0.937-0.97012.012-20.374-20.3740.0000.0000.0000.000
109A109ALA0-0.016-0.0309.864-0.223-0.2230.0000.0000.0000.000
110A110LEU00.001-0.00611.603-0.087-0.0870.0000.0000.0000.000
111A111LYS10.8860.94314.75314.25714.2570.0000.0000.0000.000
112A112ALA0-0.042-0.02012.3960.3480.3480.0000.0000.0000.000
113A113GLU-1-0.829-0.88310.298-24.929-24.9290.0000.0000.0000.000
114A114GLY0-0.0020.00713.9080.5080.5080.0000.0000.0000.000
115A115PHE0-0.017-0.01414.3450.6370.6370.0000.0000.0000.000
116A116ALA0-0.0050.00418.5670.0970.0970.0000.0000.0000.000
117A117LEU0-0.022-0.02018.498-0.203-0.2030.0000.0000.0000.000
118A118GLY00.0070.03122.6130.3310.3310.0000.0000.0000.000
119A119PRO0-0.018-0.02326.014-0.094-0.0940.0000.0000.0000.000
120A120LEU00.002-0.00728.0020.2220.2220.0000.0000.0000.000
121A121VAL00.0220.00627.164-0.383-0.3830.0000.0000.0000.000
122A122LEU0-0.0260.00025.2430.2400.2400.0000.0000.0000.000
123A123ALA00.0120.01228.2060.0800.0800.0000.0000.0000.000
124A124VAL00.006-0.01228.405-0.068-0.0680.0000.0000.0000.000
125A125ARG10.9650.98531.8007.6097.6090.0000.0000.0000.000
126A126VAL00.0020.00131.172-0.080-0.0800.0000.0000.0000.000
127A127LEU0-0.013-0.01933.8730.2400.2400.0000.0000.0000.000
128A128GLY00.0080.01934.6360.1760.1760.0000.0000.0000.000
129A129SER0-0.084-0.05033.187-0.223-0.2230.0000.0000.0000.000
130A130ARG00.0880.05935.595-0.286-0.2860.0000.0000.0000.000