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: NL85Q

Calculation Name: 2MKK-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2MKK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BZB8

Base Structure: SolutionNMR

Registration Date: 2025-10-05

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
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 213
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2402351.771967
FMO2-HF: Nuclear repulsion 2318661.106148
FMO2-HF: Total energy -83690.665819
FMO2-MP2: Total energy -83934.431112


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:218:MET)


Summations of interaction energy for fragment #1(A:218: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.
72.06676.4851.58-1.847-4.151-0.011
Interaction energy analysis for fragmet #1(A:218:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.847 / q_NPA : 0.917
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].
3A220TRP0-0.0170.0003.8232.2683.872-0.023-0.613-0.9670.000
156A373LEU0-0.034-0.0182.488-3.267-2.2230.744-0.308-1.481-0.001
157A374PHE0-0.064-0.0452.711-5.108-3.8240.860-0.833-1.311-0.010
158A375GLY00.0200.0155.2901.7271.769-0.001-0.001-0.0390.000
193A410ALA0-0.034-0.0134.157-0.255-0.1510.000-0.012-0.0920.000
194A411ALA00.0040.0224.553-6.134-6.074-0.001-0.008-0.0510.000
196A413VAL0-0.010-0.0054.106-0.798-0.5170.001-0.072-0.2100.000
4A221SER0-0.022-0.0156.9741.9381.9380.0000.0000.0000.000
5A222GLY00.0310.01110.7740.2440.2440.0000.0000.0000.000
6A223GLN0-0.026-0.0078.3850.3240.3240.0000.0000.0000.000
7A224LEU0-0.020-0.00312.479-0.230-0.2300.0000.0000.0000.000
8A225PRO00.0100.00014.5370.4660.4660.0000.0000.0000.000
9A226PRO00.0340.01917.4740.2540.2540.0000.0000.0000.000
10A227ARG10.8990.97020.49312.11812.1180.0000.0000.0000.000
11A228ASN00.0260.00322.255-0.152-0.1520.0000.0000.0000.000
12A229TYR0-0.046-0.03624.3960.7240.7240.0000.0000.0000.000
13A230LYS10.9340.94228.55910.22210.2220.0000.0000.0000.000
14A231ASN00.0260.03231.5240.2670.2670.0000.0000.0000.000
15A232PRO0-0.0290.00330.2010.2520.2520.0000.0000.0000.000
16A233ILE00.0220.01433.406-0.055-0.0550.0000.0000.0000.000
17A234TYR00.008-0.01430.056-0.343-0.3430.0000.0000.0000.000
18A235SER0-0.014-0.01431.7080.3620.3620.0000.0000.0000.000
19A236CYS0-0.023-0.00533.6610.0020.0020.0000.0000.0000.000
20A237LYS10.8140.93729.63410.07010.0700.0000.0000.0000.000
21A238VAL0-0.007-0.00631.207-0.236-0.2360.0000.0000.0000.000
22A239PHE0-0.025-0.01126.6580.0820.0820.0000.0000.0000.000
23A240LEU00.012-0.00430.5150.1090.1090.0000.0000.0000.000
24A241GLY00.0580.03628.976-0.053-0.0530.0000.0000.0000.000
25A242GLY0-0.058-0.05029.7110.2540.2540.0000.0000.0000.000
26A243VAL00.0280.00231.1700.0010.0010.0000.0000.0000.000
27A244PRO0-0.052-0.01732.3240.0240.0240.0000.0000.0000.000
28A245TRP0-0.059-0.05834.2810.0330.0330.0000.0000.0000.000
29A246ASP-1-0.867-0.93537.365-7.978-7.9780.0000.0000.0000.000
30A247ILE0-0.0350.00738.0180.1810.1810.0000.0000.0000.000
31A248THR00.0590.02037.827-0.206-0.2060.0000.0000.0000.000
32A249GLU-1-0.855-0.94637.667-8.069-8.0690.0000.0000.0000.000
33A250ALA00.0260.01039.0100.1020.1020.0000.0000.0000.000
34A251GLY00.0120.01340.8300.1610.1610.0000.0000.0000.000
35A252LEU0-0.0110.00636.0660.1090.1090.0000.0000.0000.000
36A253VAL00.0470.02940.0860.0750.0750.0000.0000.0000.000
37A254ASN0-0.068-0.03042.8380.3550.3550.0000.0000.0000.000
38A255THR0-0.037-0.03140.1530.0720.0720.0000.0000.0000.000
39A256PHE00.010-0.00337.295-0.014-0.0140.0000.0000.0000.000
40A257ARG10.8700.93842.5416.7476.7470.0000.0000.0000.000
41A258VAL0-0.020-0.01044.7590.0310.0310.0000.0000.0000.000
42A259PHE0-0.001-0.00947.4100.0400.0400.0000.0000.0000.000
43A260GLY00.0180.01747.4600.1030.1030.0000.0000.0000.000
44A261SER00.0020.00643.675-0.029-0.0290.0000.0000.0000.000
45A262LEU00.010-0.01440.571-0.121-0.1210.0000.0000.0000.000
46A263SER0-0.0350.00339.5290.1590.1590.0000.0000.0000.000
47A264VAL00.0060.00238.425-0.183-0.1830.0000.0000.0000.000
48A265GLU-1-0.814-0.91732.056-9.559-9.5590.0000.0000.0000.000
49A266TRP00.0740.02333.292-0.208-0.2080.0000.0000.0000.000
50A267PRO0-0.013-0.01529.3750.1650.1650.0000.0000.0000.000
51A268GLY00.0340.02231.761-0.014-0.0140.0000.0000.0000.000
52A269LYS10.7870.89631.0069.9549.9540.0000.0000.0000.000
53A270ASP-1-0.882-0.94229.985-9.891-9.8910.0000.0000.0000.000
54A271GLY00.0020.01732.1420.1280.1280.0000.0000.0000.000
55A272LYS10.9740.98728.38810.49410.4940.0000.0000.0000.000
56A273HIS0-0.010-0.00633.655-0.110-0.1100.0000.0000.0000.000
57A274PRO00.0170.01229.3190.0570.0570.0000.0000.0000.000
58A275ARG10.9530.96028.08210.69210.6920.0000.0000.0000.000
59A276CYS00.0200.01132.106-0.056-0.0560.0000.0000.0000.000
60A277PRO0-0.017-0.00530.4300.0900.0900.0000.0000.0000.000
61A278PRO00.0780.05333.6280.0120.0120.0000.0000.0000.000
62A279LYS10.9190.95226.98111.65211.6520.0000.0000.0000.000
63A280GLY00.0090.00230.702-0.117-0.1170.0000.0000.0000.000
64A281TYR0-0.049-0.02426.039-0.129-0.1290.0000.0000.0000.000
65A282VAL0-0.0120.00530.5400.1170.1170.0000.0000.0000.000
66A283TYR00.0340.01426.654-0.227-0.2270.0000.0000.0000.000
67A284LEU0-0.0220.00032.9500.2940.2940.0000.0000.0000.000
68A285VAL00.004-0.00234.660-0.225-0.2250.0000.0000.0000.000
69A286PHE0-0.005-0.02236.5740.2770.2770.0000.0000.0000.000
70A287GLU-1-0.874-0.94638.886-7.139-7.1390.0000.0000.0000.000
71A288LEU0-0.045-0.00341.0820.0850.0850.0000.0000.0000.000
72A289GLU-1-0.728-0.83937.509-8.177-8.1770.0000.0000.0000.000
73A290LYS10.9750.96739.6546.6486.6480.0000.0000.0000.000
74A291SER0-0.007-0.00541.6140.0570.0570.0000.0000.0000.000
75A292VAL00.0190.02334.965-0.082-0.0820.0000.0000.0000.000
76A293ARG10.8500.88937.4497.8217.8210.0000.0000.0000.000
77A294SER0-0.0160.01538.7400.0330.0330.0000.0000.0000.000
78A295LEU00.0270.00435.681-0.016-0.0160.0000.0000.0000.000
79A296LEU0-0.030-0.02432.677-0.130-0.1300.0000.0000.0000.000
80A297GLN0-0.071-0.02736.6190.0140.0140.0000.0000.0000.000
81A298ALA0-0.034-0.00139.4660.0990.0990.0000.0000.0000.000
82A299CYS0-0.089-0.03635.601-0.010-0.0100.0000.0000.0000.000
83A300SER0-0.017-0.01335.0950.0210.0210.0000.0000.0000.000
84A301HIS0-0.050-0.04226.9290.0140.0140.0000.0000.0000.000
85A302ASP-1-0.770-0.86327.695-11.872-11.8720.0000.0000.0000.000
86A303PRO00.0350.04130.117-0.194-0.1940.0000.0000.0000.000
87A304LEU00.001-0.00626.1610.1150.1150.0000.0000.0000.000
88A305SER0-0.037-0.04126.2110.4660.4660.0000.0000.0000.000
89A306PRO00.0310.01426.978-0.348-0.3480.0000.0000.0000.000
90A307ASP-1-0.859-0.91622.222-13.579-13.5790.0000.0000.0000.000
91A308GLY00.0220.01022.278-0.611-0.6110.0000.0000.0000.000
92A309LEU0-0.055-0.02422.044-0.286-0.2860.0000.0000.0000.000
93A310SER0-0.099-0.03724.0510.2230.2230.0000.0000.0000.000
94A311GLU-1-0.827-0.92425.691-13.114-13.1140.0000.0000.0000.000
95A312TYR0-0.012-0.01028.4720.4170.4170.0000.0000.0000.000
96A313TYR0-0.0070.00026.759-0.156-0.1560.0000.0000.0000.000
97A314PHE00.1110.05833.3530.3130.3130.0000.0000.0000.000
98A315LYS10.9620.98436.0437.5707.5700.0000.0000.0000.000
99A316MET00.0230.01537.6980.1630.1630.0000.0000.0000.000
100A317SER00.001-0.01640.5690.2870.2870.0000.0000.0000.000
101A318SER00.0380.00841.820-0.109-0.1090.0000.0000.0000.000
102A319ARG10.9320.96644.2086.6726.6720.0000.0000.0000.000
103A320ARG10.9860.99842.9347.4127.4120.0000.0000.0000.000
104A321MET00.0510.03436.2860.0010.0010.0000.0000.0000.000
105A322ARG10.9220.96737.7837.1417.1410.0000.0000.0000.000
106A323CYS0-0.0150.00336.0740.1180.1180.0000.0000.0000.000
107A324LYS10.9070.94230.66210.04010.0400.0000.0000.0000.000
108A325GLU-1-0.893-0.93133.025-9.080-9.0800.0000.0000.0000.000
109A326VAL0-0.095-0.05132.494-0.336-0.3360.0000.0000.0000.000
110A327GLN0-0.020-0.01224.8860.0530.0530.0000.0000.0000.000
111A328VAL0-0.021-0.01930.5660.0990.0990.0000.0000.0000.000
112A329ILE00.0140.00225.147-0.195-0.1950.0000.0000.0000.000
113A330PRO00.0100.01828.8860.1810.1810.0000.0000.0000.000
114A331TRP00.0710.02622.962-0.633-0.6330.0000.0000.0000.000
115A332VAL00.0280.01027.5980.4570.4570.0000.0000.0000.000
116A333LEU0-0.065-0.02529.648-0.027-0.0270.0000.0000.0000.000
117A334ALA0-0.007-0.00127.0640.1690.1690.0000.0000.0000.000
118A335ASP-1-0.799-0.90226.247-10.965-10.9650.0000.0000.0000.000
119A336SER0-0.046-0.02923.456-0.168-0.1680.0000.0000.0000.000
120A337ASN0-0.068-0.01920.742-0.793-0.7930.0000.0000.0000.000
121A338PHE00.0400.00118.9430.3330.3330.0000.0000.0000.000
122A339VAL0-0.013-0.01015.813-0.832-0.8320.0000.0000.0000.000
123A340ARG10.9460.98016.71515.04115.0410.0000.0000.0000.000
124A341SER0-0.012-0.00815.9520.1550.1550.0000.0000.0000.000
125A342PRO00.0080.01218.5760.3880.3880.0000.0000.0000.000
126A343SER00.0230.01120.756-0.381-0.3810.0000.0000.0000.000
127A344GLN00.0570.01820.744-0.213-0.2130.0000.0000.0000.000
128A345ARG10.8610.91323.3829.9209.9200.0000.0000.0000.000
129A346LEU00.0300.01320.969-0.351-0.3510.0000.0000.0000.000
130A347ASP-1-0.768-0.85622.599-10.023-10.0230.0000.0000.0000.000
131A348PRO00.0390.01322.342-0.518-0.5180.0000.0000.0000.000
132A349SER00.0100.00622.343-0.346-0.3460.0000.0000.0000.000
133A350ARG10.7800.88618.17811.71111.7110.0000.0000.0000.000
134A351THR00.0060.00917.641-0.535-0.5350.0000.0000.0000.000
135A352VAL00.0060.01514.5360.0110.0110.0000.0000.0000.000
136A353PHE00.0590.03317.9480.0080.0080.0000.0000.0000.000
137A354VAL0-0.035-0.02013.695-0.722-0.7220.0000.0000.0000.000
138A355GLY00.0650.03716.3130.7440.7440.0000.0000.0000.000
139A356ALA0-0.043-0.03914.581-1.136-1.1360.0000.0000.0000.000
140A357LEU00.0390.02714.879-0.426-0.4260.0000.0000.0000.000
141A358HIS0-0.008-0.00916.5540.0640.0640.0000.0000.0000.000
142A359GLY00.0090.01719.7370.6260.6260.0000.0000.0000.000
143A360MET00.0020.00621.0210.4880.4880.0000.0000.0000.000
144A361LEU0-0.004-0.02514.295-0.833-0.8330.0000.0000.0000.000
145A362ASN0-0.0020.00718.3330.4830.4830.0000.0000.0000.000
146A363ALA00.0350.01916.998-0.938-0.9380.0000.0000.0000.000
147A364GLU-1-0.887-0.94916.645-14.802-14.8020.0000.0000.0000.000
148A365ALA0-0.0010.00214.429-0.811-0.8110.0000.0000.0000.000
149A366LEU0-0.014-0.01012.495-1.577-1.5770.0000.0000.0000.000
150A367ALA00.0080.00411.897-1.056-1.0560.0000.0000.0000.000
151A368ALA0-0.012-0.00211.826-0.492-0.4920.0000.0000.0000.000
152A369ILE0-0.012-0.0167.420-1.564-1.5640.0000.0000.0000.000
153A370LEU0-0.050-0.0377.057-2.476-2.4760.0000.0000.0000.000
154A371ASN0-0.0120.0049.2121.8161.8160.0000.0000.0000.000
155A372ASP-1-0.886-0.9245.707-35.397-35.3970.0000.0000.0000.000
159A376GLY00.0210.0269.076-0.347-0.3470.0000.0000.0000.000
160A377VAL0-0.033-0.00712.0860.3400.3400.0000.0000.0000.000
161A378VAL00.004-0.00213.8940.4250.4250.0000.0000.0000.000
162A379TYR00.013-0.00116.8440.4710.4710.0000.0000.0000.000
163A380ALA00.0120.01114.733-0.745-0.7450.0000.0000.0000.000
164A381GLY00.0340.02216.4160.6760.6760.0000.0000.0000.000
165A382ILE0-0.065-0.03517.973-0.474-0.4740.0000.0000.0000.000
166A383ASP-1-0.777-0.88120.655-11.145-11.1450.0000.0000.0000.000
167A384THR0-0.085-0.05223.6090.0290.0290.0000.0000.0000.000
168A385ASP-1-0.810-0.89127.094-10.053-10.0530.0000.0000.0000.000
169A386LYS10.8720.92629.0279.8119.8110.0000.0000.0000.000
170A387HIS0-0.0010.00531.8730.2220.2220.0000.0000.0000.000
171A388LYS10.9620.97232.9857.4387.4380.0000.0000.0000.000
172A389TYR00.0000.00633.0980.0740.0740.0000.0000.0000.000
173A390PRO00.016-0.01428.137-0.109-0.1090.0000.0000.0000.000
174A391ILE00.0320.02223.0980.0220.0220.0000.0000.0000.000
175A392GLY00.0610.03524.7170.4590.4590.0000.0000.0000.000
176A393SER0-0.036-0.01722.069-0.162-0.1620.0000.0000.0000.000
177A394GLY00.0150.02217.9920.1320.1320.0000.0000.0000.000
178A395ARG10.8550.90717.84312.53712.5370.0000.0000.0000.000
179A396VAL0-0.031-0.01012.700-0.589-0.5890.0000.0000.0000.000
180A397THR0-0.0120.00615.9230.4970.4970.0000.0000.0000.000
181A398PHE00.0110.01310.4010.0310.0310.0000.0000.0000.000
182A399ASN00.006-0.01716.1340.2300.2300.0000.0000.0000.000
183A400ASN00.0670.04214.2540.8050.8050.0000.0000.0000.000
184A401GLN00.0680.01714.524-0.694-0.6940.0000.0000.0000.000
185A402ARG10.9520.97810.63918.79118.7910.0000.0000.0000.000
186A403SER00.021-0.0169.918-0.839-0.8390.0000.0000.0000.000
187A404TYR0-0.038-0.0299.881-1.534-1.5340.0000.0000.0000.000
188A405LEU00.0420.03211.383-0.862-0.8620.0000.0000.0000.000
189A406LYS10.8970.9645.00728.83728.8370.0000.0000.0000.000
190A407ALA00.0310.0105.762-2.775-2.7750.0000.0000.0000.000
191A408VAL00.016-0.0026.614-2.382-2.3820.0000.0000.0000.000
192A409SER0-0.025-0.0049.0730.5090.5090.0000.0000.0000.000
195A412PHE0-0.029-0.0256.0432.0562.0560.0000.0000.0000.000
197A414GLU-1-0.903-0.9446.981-24.485-24.4850.0000.0000.0000.000
198A415ILE00.0110.0219.411-0.132-0.1320.0000.0000.0000.000
199A416LYS10.9620.97410.96926.70426.7040.0000.0000.0000.000
200A417THR00.0400.00813.084-0.923-0.9230.0000.0000.0000.000
201A418THR0-0.014-0.00415.8640.7750.7750.0000.0000.0000.000
202A419LYS10.8750.95517.69713.58613.5860.0000.0000.0000.000
203A420PHE00.0350.01915.4010.4410.4410.0000.0000.0000.000
204A421THR0-0.001-0.02013.579-1.589-1.5890.0000.0000.0000.000
205A422LYS10.8050.91114.15218.07718.0770.0000.0000.0000.000
206A423LYS10.8680.9289.87925.64925.6490.0000.0000.0000.000
207A424VAL00.0320.0189.5331.9451.9450.0000.0000.0000.000
208A425GLN0-0.035-0.02610.221-0.834-0.8340.0000.0000.0000.000
209A426ILE00.002-0.00312.4310.8760.8760.0000.0000.0000.000
210A427ASP-1-0.892-0.94114.144-13.926-13.9260.0000.0000.0000.000
211A428PRO0-0.027-0.00917.909-0.064-0.0640.0000.0000.0000.000
212A429TYR0-0.036-0.03720.0250.2870.2870.0000.0000.0000.000
213A430LEU-1-0.929-0.94323.316-11.072-11.0720.0000.0000.0000.000