FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: YM6J2

Calculation Name: 2K4M-A-Other549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2K4M

Chain ID: A

ChEMBL ID:

UniProt ID: O27081

Base Structure: SolutionNMR

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 153
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1454701.581517
FMO2-HF: Nuclear repulsion 1394102.042511
FMO2-HF: Total energy -60599.539006
FMO2-MP2: Total energy -60775.667667


3D Structure Molmil
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.
47.50148.668-0.004-0.584-0.5790
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 : 0.888 / q_NPA : 0.931
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].
3A3SER0-0.014-0.0263.837-2.908-1.741-0.004-0.584-0.5790.000
4A4SER0-0.0040.0096.5331.9621.9620.0000.0000.0000.000
5A5HIS00.0030.0058.8753.5173.5170.0000.0000.0000.000
6A6HIS00.0190.01511.725-0.368-0.3680.0000.0000.0000.000
7A7HIS00.0150.00914.1501.7771.7770.0000.0000.0000.000
8A8HIS00.0010.00017.2160.3960.3960.0000.0000.0000.000
9A9HIS00.0290.01520.324-0.063-0.0630.0000.0000.0000.000
10A10HIS00.005-0.00722.2510.4880.4880.0000.0000.0000.000
11A11SER0-0.031-0.01426.0590.3190.3190.0000.0000.0000.000
12A12SER00.0100.00829.1600.0130.0130.0000.0000.0000.000
13A13GLY00.0150.01232.4370.1170.1170.0000.0000.0000.000
14A14LEU0-0.040-0.01833.1740.2060.2060.0000.0000.0000.000
15A15VAL00.0230.00635.7530.0180.0180.0000.0000.0000.000
16A16PRO0-0.0160.00738.5330.1190.1190.0000.0000.0000.000
17A17ARG11.0151.00242.1706.8346.8340.0000.0000.0000.000
18A18GLY00.0320.01544.0230.0990.0990.0000.0000.0000.000
19A19SER0-0.014-0.00842.5470.1680.1680.0000.0000.0000.000
20A20HIS00.0400.01044.644-0.057-0.0570.0000.0000.0000.000
21A21MET00.0190.00546.199-0.063-0.0630.0000.0000.0000.000
22A22TRP00.0190.01342.885-0.003-0.0030.0000.0000.0000.000
23A23ASN0-0.033-0.00940.808-0.119-0.1190.0000.0000.0000.000
24A24ASP-1-0.801-0.91341.751-7.022-7.0220.0000.0000.0000.000
25A25LEU0-0.037-0.00541.519-0.047-0.0470.0000.0000.0000.000
26A26ALA00.0350.01637.928-0.136-0.1360.0000.0000.0000.000
27A27VAL0-0.003-0.00638.146-0.198-0.1980.0000.0000.0000.000
28A28TYR0-0.063-0.05539.540-0.083-0.0830.0000.0000.0000.000
29A29ILE00.0300.01035.715-0.063-0.0630.0000.0000.0000.000
30A30ILE0-0.0140.00634.291-0.178-0.1780.0000.0000.0000.000
31A31ARG10.9030.93435.4607.3957.3950.0000.0000.0000.000
32A32CYS0-0.097-0.03737.9530.1120.1120.0000.0000.0000.000
33A33SER0-0.048-0.03132.688-0.147-0.1470.0000.0000.0000.000
34A34GLY00.0460.04331.850-0.063-0.0630.0000.0000.0000.000
35A35PRO0-0.045-0.04926.659-0.216-0.2160.0000.0000.0000.000
36A36GLY0-0.0100.00724.5870.0770.0770.0000.0000.0000.000
37A37THR00.0140.01525.625-0.049-0.0490.0000.0000.0000.000
38A38ARG10.8760.93925.51211.55011.5500.0000.0000.0000.000
39A39VAL0-0.014-0.00728.7490.3820.3820.0000.0000.0000.000
40A40VAL0-0.011-0.00331.244-0.250-0.2500.0000.0000.0000.000
41A41GLU-1-0.725-0.81533.632-8.574-8.5740.0000.0000.0000.000
42A42VAL0-0.006-0.00535.555-0.183-0.1830.0000.0000.0000.000
43A43GLY00.0480.02738.2480.2060.2060.0000.0000.0000.000
44A44ALA0-0.0030.00836.0050.0920.0920.0000.0000.0000.000
45A45GLY00.013-0.00638.0320.0870.0870.0000.0000.0000.000
46A46ARG10.9040.95138.1667.2787.2780.0000.0000.0000.000
47A47PHE0-0.057-0.03339.7550.1390.1390.0000.0000.0000.000
48A48LEU00.0570.03433.763-0.018-0.0180.0000.0000.0000.000
49A49TYR00.0130.01335.927-0.158-0.1580.0000.0000.0000.000
50A50VAL00.0050.00337.353-0.067-0.0670.0000.0000.0000.000
51A51SER00.037-0.01232.790-0.151-0.1510.0000.0000.0000.000
52A52ASP-1-0.817-0.88332.348-9.996-9.9960.0000.0000.0000.000
53A53TYR00.0130.00532.962-0.169-0.1690.0000.0000.0000.000
54A54ILE00.010-0.00232.121-0.119-0.1190.0000.0000.0000.000
55A55ARG10.8410.91228.38210.34610.3460.0000.0000.0000.000
56A56LYS10.7980.89328.6529.3019.3010.0000.0000.0000.000
57A57HIS00.0070.01430.938-0.126-0.1260.0000.0000.0000.000
58A58SER0-0.014-0.01829.5790.0400.0400.0000.0000.0000.000
59A59LYS10.9631.00621.44113.98313.9830.0000.0000.0000.000
60A60VAL0-0.004-0.00925.517-0.356-0.3560.0000.0000.0000.000
61A61ASP-1-0.932-0.96224.164-13.144-13.1440.0000.0000.0000.000
62A62LEU0-0.040-0.02126.2170.3310.3310.0000.0000.0000.000
63A63VAL00.0180.01127.621-0.151-0.1510.0000.0000.0000.000
64A64LEU00.0060.00429.7650.4250.4250.0000.0000.0000.000
65A65THR0-0.027-0.02731.811-0.174-0.1740.0000.0000.0000.000
66A66ASP-1-0.817-0.93334.324-7.915-7.9150.0000.0000.0000.000
67A67ILE00.0720.04935.701-0.252-0.2520.0000.0000.0000.000
68A68LYS10.8840.94036.4468.1038.1030.0000.0000.0000.000
69A69PRO00.0050.01733.4900.2080.2080.0000.0000.0000.000
70A70SER0-0.020-0.02035.134-0.080-0.0800.0000.0000.0000.000
71A71HIS0-0.017-0.00933.2490.1520.1520.0000.0000.0000.000
72A72GLY00.0140.01028.864-0.118-0.1180.0000.0000.0000.000
73A73GLY00.012-0.00627.351-0.020-0.0200.0000.0000.0000.000
74A74ILE0-0.071-0.02128.3860.0230.0230.0000.0000.0000.000
75A75VAL00.001-0.00127.964-0.174-0.1740.0000.0000.0000.000
76A76ARG10.9090.94728.86210.88910.8890.0000.0000.0000.000
77A77ASP-1-0.779-0.87432.352-9.645-9.6450.0000.0000.0000.000
78A78ASP-1-0.777-0.89934.010-7.757-7.7570.0000.0000.0000.000
79A79ILE0-0.048-0.03437.244-0.141-0.1410.0000.0000.0000.000
80A80THR0-0.053-0.02439.8970.1770.1770.0000.0000.0000.000
81A81SER0-0.037-0.01839.3730.1760.1760.0000.0000.0000.000
82A82PRO0-0.0380.00037.171-0.239-0.2390.0000.0000.0000.000
83A83ARG10.9270.94231.1279.9119.9110.0000.0000.0000.000
84A84MET0-0.027-0.01633.101-0.173-0.1730.0000.0000.0000.000
85A85GLU-1-0.953-0.98428.264-10.945-10.9450.0000.0000.0000.000
86A86ILE0-0.0130.00429.140-0.342-0.3420.0000.0000.0000.000
87A87TYR00.0240.00930.119-0.176-0.1760.0000.0000.0000.000
88A88ARG10.9630.98830.3939.8319.8310.0000.0000.0000.000
89A89GLY00.0160.00228.424-0.358-0.3580.0000.0000.0000.000
90A90ALA0-0.044-0.01229.448-0.191-0.1910.0000.0000.0000.000
91A91ALA00.0310.02131.5620.2150.2150.0000.0000.0000.000
92A92LEU0-0.052-0.02733.9160.3420.3420.0000.0000.0000.000
93A93ILE00.0330.01634.917-0.292-0.2920.0000.0000.0000.000
94A94TYR0-0.040-0.06235.3030.2050.2050.0000.0000.0000.000
95A95SER00.0310.01138.921-0.227-0.2270.0000.0000.0000.000
96A96ILE0-0.046-0.02340.0720.2290.2290.0000.0000.0000.000
97A97ARG10.9110.96642.8246.5766.5760.0000.0000.0000.000
98A98PRO00.0070.01144.588-0.008-0.0080.0000.0000.0000.000
99A99PRO00.0500.01646.2270.1200.1200.0000.0000.0000.000
100A100ALA00.0550.03049.049-0.089-0.0890.0000.0000.0000.000
101A101GLU-1-0.979-0.99149.340-6.285-6.2850.0000.0000.0000.000
102A102ILE00.0180.00643.648-0.059-0.0590.0000.0000.0000.000
103A103HIS00.0310.02945.532-0.307-0.3070.0000.0000.0000.000
104A104SER00.1040.04046.161-0.126-0.1260.0000.0000.0000.000
105A105SER0-0.017-0.00943.101-0.044-0.0440.0000.0000.0000.000
106A106LEU00.0120.00540.913-0.190-0.1900.0000.0000.0000.000
107A107MET0-0.018-0.00741.816-0.142-0.1420.0000.0000.0000.000
108A108ARG10.9660.98641.2617.4277.4270.0000.0000.0000.000
109A109VAL0-0.029-0.01237.170-0.137-0.1370.0000.0000.0000.000
110A110ALA00.0130.00138.562-0.193-0.1930.0000.0000.0000.000
111A111ASP-1-0.833-0.91139.489-7.329-7.3290.0000.0000.0000.000
112A112ALA0-0.033-0.00438.616-0.038-0.0380.0000.0000.0000.000
113A113VAL0-0.086-0.05234.349-0.202-0.2020.0000.0000.0000.000
114A114GLY00.0040.01935.430-0.196-0.1960.0000.0000.0000.000
115A115ALA0-0.0170.01035.585-0.044-0.0440.0000.0000.0000.000
116A116ARG10.8410.90137.4277.8577.8570.0000.0000.0000.000
117A117LEU00.0470.02639.362-0.179-0.1790.0000.0000.0000.000
118A118ILE0-0.050-0.03641.0300.1860.1860.0000.0000.0000.000
119A119ILE00.0500.02142.755-0.140-0.1400.0000.0000.0000.000
120A120LYS10.8520.93045.0036.7846.7840.0000.0000.0000.000
121A121PRO00.0300.02946.858-0.063-0.0630.0000.0000.0000.000
122A122LEU0-0.018-0.02450.202-0.079-0.0790.0000.0000.0000.000
123A123THR0-0.039-0.02552.865-0.001-0.0010.0000.0000.0000.000
124A124GLY00.0380.02355.1290.0640.0640.0000.0000.0000.000
125A125GLU-1-0.939-0.96253.986-5.855-5.8550.0000.0000.0000.000
126A126ASP-1-0.885-0.94155.034-5.868-5.8680.0000.0000.0000.000
127A127ILE0-0.016-0.02049.397-0.062-0.0620.0000.0000.0000.000
128A128VAL0-0.038-0.01752.839-0.038-0.0380.0000.0000.0000.000
129A129THR0-0.010-0.01451.041-0.061-0.0610.0000.0000.0000.000
130A130GLU-1-0.889-0.93652.848-5.922-5.9220.0000.0000.0000.000
131A131ARG10.9250.95553.4835.3215.3210.0000.0000.0000.000
132A132LYS10.9040.96048.9816.4646.4640.0000.0000.0000.000
133A133MET00.0070.01146.092-0.095-0.0950.0000.0000.0000.000
134A134LYS10.8850.93848.2836.7186.7180.0000.0000.0000.000
135A135LEU00.0100.00850.074-0.134-0.1340.0000.0000.0000.000
136A136VAL0-0.054-0.02647.0190.0530.0530.0000.0000.0000.000
137A137ASN00.014-0.00950.3620.0430.0430.0000.0000.0000.000
138A138TYR00.0170.01643.517-0.051-0.0510.0000.0000.0000.000
139A139GLY00.0840.04348.331-0.019-0.0190.0000.0000.0000.000
140A140ARG10.8680.93849.3896.0396.0390.0000.0000.0000.000
141A141THR0-0.055-0.03646.4910.1270.1270.0000.0000.0000.000
142A142TYR00.011-0.00249.674-0.056-0.0560.0000.0000.0000.000
143A143PHE0-0.041-0.02545.147-0.065-0.0650.0000.0000.0000.000
144A144TYR00.0840.04448.1830.0790.0790.0000.0000.0000.000
145A145GLU-1-0.759-0.84344.752-7.231-7.2310.0000.0000.0000.000
146A146TYR0-0.011-0.03744.2060.2620.2620.0000.0000.0000.000
147A147ILE0-0.027-0.01342.381-0.203-0.2030.0000.0000.0000.000
148A148ALA00.0300.03940.4840.1490.1490.0000.0000.0000.000
149A149GLU-1-0.939-0.95741.610-6.948-6.9480.0000.0000.0000.000
150A150VAL0-0.013-0.01337.962-0.103-0.1030.0000.0000.0000.000
151A151ARG10.8120.89439.6967.6637.6630.0000.0000.0000.000
152A152SER00.0210.00440.684-0.046-0.0460.0000.0000.0000.000
153A153ARG00.0330.03237.8810.4030.4030.0000.0000.0000.000