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: 7K5YK

Calculation Name: 3KMQ-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3KMQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9QCE3

Base Structure: X-ray

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 476
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -9143627.267566
FMO2-HF: Nuclear repulsion 8954696.029458
FMO2-HF: Total energy -188931.238108
FMO2-MP2: Total energy -189477.763375


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:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-172.476-170.61628.842-16.403-14.3-0.158
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.797 / q_NPA : 0.906
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].
3A3ILE00.0360.0103.8142.9183.671-0.010-0.255-0.4890.000
60A60HIS0-0.035-0.0162.393-0.3410.5690.313-0.500-0.7230.002
61A61LYS10.9790.9953.97752.60552.814-0.001-0.031-0.1760.000
62A62SER00.008-0.0043.42213.56614.1760.001-0.263-0.349-0.001
63A63ASP-1-0.771-0.8371.874-94.910-96.0927.505-3.281-3.042-0.046
64A64THR0-0.031-0.0033.91310.11210.3030.005-0.069-0.1270.000
246A246ALA0-0.048-0.0223.893-3.959-3.7020.000-0.086-0.1710.000
247A247ASN0-0.053-0.0442.203-44.036-45.8147.401-3.038-2.584-0.035
248A248HIS00.0090.0534.149-0.402-0.291-0.001-0.022-0.0880.000
249A249CYS0-0.0170.0113.301-13.310-12.4390.008-0.410-0.470-0.003
292A292VAL0-0.042-0.0262.979-2.603-2.2950.190-0.191-0.307-0.001
293A293GLU-1-0.896-0.9384.374-28.695-28.542-0.001-0.117-0.0350.000
294A294GLY00.0440.0162.177-20.539-20.3246.935-4.562-2.589-0.044
295A295GLY0-0.030-0.0182.252-16.062-15.9866.484-3.526-3.034-0.029
296A296MET0-0.010-0.0113.4358.5038.6590.013-0.052-0.116-0.001
4A4VAL0-0.019-0.0086.6682.2092.2090.0000.0000.0000.000
5A5ASP-1-0.795-0.8879.175-17.134-17.1340.0000.0000.0000.000
6A6THR0-0.086-0.05611.074-2.119-2.1190.0000.0000.0000.000
7A7ARG10.8520.93413.58919.22219.2220.0000.0000.0000.000
8A8ASP-1-0.833-0.92816.862-16.716-16.7160.0000.0000.0000.000
9A9VAL0-0.003-0.00519.6790.5150.5150.0000.0000.0000.000
10A10GLU-1-0.928-0.96121.792-11.845-11.8450.0000.0000.0000.000
11A11GLU-1-0.925-0.96622.796-12.186-12.1860.0000.0000.0000.000
12A12ARG10.8890.95722.02911.01711.0170.0000.0000.0000.000
13A13VAL00.0230.01318.4630.4580.4580.0000.0000.0000.000
14A14HIS0-0.050-0.02920.551-0.233-0.2330.0000.0000.0000.000
15A15VAL00.0350.03218.395-0.055-0.0550.0000.0000.0000.000
16A16MET0-0.044-0.02221.7150.9240.9240.0000.0000.0000.000
17A17ARG10.8670.90620.04214.22714.2270.0000.0000.0000.000
18A18LYS10.9580.96724.95810.38010.3800.0000.0000.0000.000
19A19THR0-0.002-0.01426.5360.0220.0220.0000.0000.0000.000
20A20LYS10.9570.95627.55611.75911.7590.0000.0000.0000.000
21A21LEU0-0.062-0.02725.6160.3630.3630.0000.0000.0000.000
22A22ALA0-0.023-0.01229.8380.0490.0490.0000.0000.0000.000
23A23PRO00.0300.00832.804-0.138-0.1380.0000.0000.0000.000
24A24THR0-0.042-0.02934.1940.2300.2300.0000.0000.0000.000
25A25VAL00.0410.01836.837-0.063-0.0630.0000.0000.0000.000
26A26ALA00.0430.02636.6950.0880.0880.0000.0000.0000.000
27A27HIS0-0.056-0.01931.8570.0100.0100.0000.0000.0000.000
28A28GLY00.0190.00736.073-0.056-0.0560.0000.0000.0000.000
29A29VAL0-0.0250.00739.0630.1580.1580.0000.0000.0000.000
30A30PHE0-0.017-0.03035.3910.0000.0000.0000.0000.0000.000
31A31ASN0-0.076-0.02135.341-0.175-0.1750.0000.0000.0000.000
32A32PRO00.0090.01930.134-0.179-0.1790.0000.0000.0000.000
33A33GLU-1-0.865-0.92928.167-10.884-10.8840.0000.0000.0000.000
34A34PHE0-0.062-0.05523.833-0.749-0.7490.0000.0000.0000.000
35A35GLY00.0400.01925.6490.5290.5290.0000.0000.0000.000
36A36PRO0-0.046-0.01724.763-0.555-0.5550.0000.0000.0000.000
37A37ALA00.0230.02219.8630.0490.0490.0000.0000.0000.000
38A38ALA00.0600.05320.7150.6440.6440.0000.0000.0000.000
39A39LEU0-0.0020.00820.418-0.714-0.7140.0000.0000.0000.000
40A40SER00.000-0.01322.409-0.102-0.1020.0000.0000.0000.000
41A41ASN00.0740.02320.384-0.240-0.2400.0000.0000.0000.000
42A42LYS10.9430.97423.49210.94510.9450.0000.0000.0000.000
43A43ASP-1-0.791-0.86624.798-11.706-11.7060.0000.0000.0000.000
44A44PRO00.0230.00726.571-0.250-0.2500.0000.0000.0000.000
45A45ARG10.7250.82525.01212.35412.3540.0000.0000.0000.000
46A46LEU0-0.066-0.02321.403-0.334-0.3340.0000.0000.0000.000
47A47ASN00.0050.00122.4610.9270.9270.0000.0000.0000.000
48A48GLU-1-0.918-0.96824.474-11.219-11.2190.0000.0000.0000.000
49A49GLY00.0190.01624.3390.0420.0420.0000.0000.0000.000
50A50VAL0-0.081-0.03418.837-0.689-0.6890.0000.0000.0000.000
51A51VAL00.0490.03818.2690.5210.5210.0000.0000.0000.000
52A52LEU0-0.027-0.02117.213-1.049-1.0490.0000.0000.0000.000
53A53ASP-1-0.899-0.95315.541-18.478-18.4780.0000.0000.0000.000
54A54GLU-1-0.868-0.93513.736-20.145-20.1450.0000.0000.0000.000
55A55VAL0-0.047-0.02512.285-2.421-2.4210.0000.0000.0000.000
56A56ILE0-0.055-0.01111.681-1.839-1.8390.0000.0000.0000.000
57A57PHE00.0230.0038.033-2.149-2.1490.0000.0000.0000.000
58A58SER0-0.053-0.0297.562-4.965-4.9650.0000.0000.0000.000
59A59LYS10.8470.9315.93436.53936.5390.0000.0000.0000.000
65A65LYS10.8820.9256.88932.59232.5920.0000.0000.0000.000
66A66MET0-0.0160.0089.9751.3571.3570.0000.0000.0000.000
67A67SER00.006-0.02712.2811.2621.2620.0000.0000.0000.000
68A68ALA00.006-0.01516.034-0.270-0.2700.0000.0000.0000.000
69A69GLU-1-0.914-0.94718.714-13.764-13.7640.0000.0000.0000.000
70A70ASP-1-0.743-0.82115.128-18.740-18.7400.0000.0000.0000.000
71A71LYS10.8610.91313.06321.55621.5560.0000.0000.0000.000
72A72ALA00.0030.00716.5400.2420.2420.0000.0000.0000.000
73A73LEU0-0.017-0.00718.9170.5700.5700.0000.0000.0000.000
74A74PHE00.0260.00612.5200.0820.0820.0000.0000.0000.000
75A75ARG10.7980.85717.03216.67016.6700.0000.0000.0000.000
76A76ARG10.9460.98518.92613.81713.8170.0000.0000.0000.000
77A77CYS00.0100.02518.5860.5870.5870.0000.0000.0000.000
78A78ALA00.0180.00616.9330.1170.1170.0000.0000.0000.000
79A79ALA0-0.011-0.00418.8990.3400.3400.0000.0000.0000.000
80A80ASP-1-0.799-0.88122.412-12.125-12.1250.0000.0000.0000.000
81A81TYR0-0.037-0.03219.2150.1190.1190.0000.0000.0000.000
82A82ALA0-0.011-0.00421.3400.3460.3460.0000.0000.0000.000
83A83SER0-0.038-0.00822.8530.5720.5720.0000.0000.0000.000
84A84ARG10.9070.94625.14011.75311.7530.0000.0000.0000.000
85A85LEU0-0.006-0.00821.3020.3710.3710.0000.0000.0000.000
86A86HIS10.7990.88223.04113.05713.0570.0000.0000.0000.000
87A87SER0-0.0420.00327.4180.4760.4760.0000.0000.0000.000
88A88VAL0-0.021-0.00928.4290.2840.2840.0000.0000.0000.000
89A89LEU0-0.037-0.01424.9520.1730.1730.0000.0000.0000.000
90A90GLY00.0410.04129.3670.2460.2460.0000.0000.0000.000
91A91THR0-0.007-0.03029.091-0.379-0.3790.0000.0000.0000.000
92A92ALA0-0.0070.01130.5890.0220.0220.0000.0000.0000.000
93A93ASN0-0.066-0.05326.317-0.188-0.1880.0000.0000.0000.000
94A94ALA00.0400.02827.533-0.314-0.3140.0000.0000.0000.000
95A95PRO00.002-0.01027.675-0.004-0.0040.0000.0000.0000.000
96A96LEU0-0.0280.01527.5340.4030.4030.0000.0000.0000.000
97A97SER0-0.0060.00329.729-0.090-0.0900.0000.0000.0000.000
98A98ILE00.0470.00229.886-0.235-0.2350.0000.0000.0000.000
99A99TYR00.0390.02930.988-0.183-0.1830.0000.0000.0000.000
100A100GLU-1-0.825-0.91631.650-9.640-9.6400.0000.0000.0000.000
101A101ALA0-0.0180.00126.905-0.218-0.2180.0000.0000.0000.000
102A102ILE0-0.017-0.00527.715-0.437-0.4370.0000.0000.0000.000
103A103LYS10.8540.92129.7868.6058.6050.0000.0000.0000.000
104A104GLY0-0.0060.01029.9330.0140.0140.0000.0000.0000.000
105A105VAL0-0.065-0.04029.8730.3410.3410.0000.0000.0000.000
106A106ASP-1-0.892-0.94031.650-9.349-9.3490.0000.0000.0000.000
107A107GLY00.0760.04030.004-0.198-0.1980.0000.0000.0000.000
108A108LEU0-0.105-0.06024.493-0.651-0.6510.0000.0000.0000.000
109A109ASP-1-0.818-0.89627.104-10.884-10.8840.0000.0000.0000.000
110A110ALA00.0320.02027.733-0.341-0.3410.0000.0000.0000.000
111A111MET0-0.109-0.04323.918-0.478-0.4780.0000.0000.0000.000
112A112GLU-1-0.899-0.95825.324-11.020-11.0200.0000.0000.0000.000
113A113PRO00.0330.01126.987-0.309-0.3090.0000.0000.0000.000
114A114ASP-1-0.953-0.97629.023-10.137-10.1370.0000.0000.0000.000
115A115THR0-0.041-0.01123.557-0.348-0.3480.0000.0000.0000.000
116A116ALA0-0.001-0.01120.9030.1460.1460.0000.0000.0000.000
117A117PRO0-0.0060.00822.166-0.371-0.3710.0000.0000.0000.000
118A118GLY00.0660.03719.379-0.271-0.2710.0000.0000.0000.000
119A119LEU0-0.0110.00717.0000.8550.8550.0000.0000.0000.000
120A120PRO00.0560.01820.167-0.334-0.3340.0000.0000.0000.000
121A121TRP0-0.029-0.04422.7510.7370.7370.0000.0000.0000.000
122A122ALA0-0.003-0.00922.5380.4840.4840.0000.0000.0000.000
123A123LEU0-0.007-0.00422.0550.2300.2300.0000.0000.0000.000
124A124GLN0-0.018-0.00725.6240.6100.6100.0000.0000.0000.000
125A125GLY0-0.0020.01028.0490.3840.3840.0000.0000.0000.000
126A126LYS10.8490.93728.25110.35010.3500.0000.0000.0000.000
127A127ARG10.9960.98527.5279.0069.0060.0000.0000.0000.000
128A128ARG10.8970.93721.67513.31113.3110.0000.0000.0000.000
129A129GLY00.0630.03428.0820.1170.1170.0000.0000.0000.000
130A130ALA0-0.102-0.03931.1070.3240.3240.0000.0000.0000.000
131A131LEU0-0.035-0.01226.7870.1130.1130.0000.0000.0000.000
132A132ILE0-0.019-0.01526.602-0.075-0.0750.0000.0000.0000.000
133A133ASP-1-0.836-0.89631.096-8.485-8.4850.0000.0000.0000.000
134A134PHE00.028-0.02127.939-0.135-0.1350.0000.0000.0000.000
135A135GLU-1-0.947-0.95233.552-8.237-8.2370.0000.0000.0000.000
136A136ASN00.015-0.00837.3120.1020.1020.0000.0000.0000.000
137A137GLY0-0.0180.00833.7560.0370.0370.0000.0000.0000.000
138A138THR0-0.023-0.02134.162-0.011-0.0110.0000.0000.0000.000
139A139VAL00.017-0.00429.765-0.248-0.2480.0000.0000.0000.000
140A140GLY00.0650.04131.7870.3040.3040.0000.0000.0000.000
141A141PRO00.012-0.01431.876-0.242-0.2420.0000.0000.0000.000
142A142GLU-1-0.848-0.92628.467-9.871-9.8710.0000.0000.0000.000
143A143VAL0-0.004-0.00326.679-0.417-0.4170.0000.0000.0000.000
144A144GLU-1-0.909-0.94627.920-9.754-9.7540.0000.0000.0000.000
145A145ALA0-0.008-0.01129.606-0.145-0.1450.0000.0000.0000.000
146A146ALA00.003-0.00324.137-0.224-0.2240.0000.0000.0000.000
147A147LEU00.0240.00624.921-0.488-0.4880.0000.0000.0000.000
148A148LYS10.8120.89826.64010.04110.0410.0000.0000.0000.000
149A149LEU0-0.018-0.00124.434-0.009-0.0090.0000.0000.0000.000
150A150MET0-0.049-0.02620.979-0.687-0.6870.0000.0000.0000.000
151A151GLU-1-0.889-0.92823.304-10.796-10.7960.0000.0000.0000.000
152A152LYS10.9370.96326.16310.38810.3880.0000.0000.0000.000
153A153ARG10.8420.92821.01813.63513.6350.0000.0000.0000.000
154A154GLU-1-0.912-0.95620.982-12.150-12.1500.0000.0000.0000.000
155A155TYR0-0.099-0.06918.358-0.574-0.5740.0000.0000.0000.000
156A156LYS10.9370.96217.30614.74014.7400.0000.0000.0000.000
157A157PHE0-0.009-0.00812.8770.9940.9940.0000.0000.0000.000
158A158ALA00.0530.03613.751-0.980-0.9800.0000.0000.0000.000
159A159CYS0-0.064-0.02511.0170.9530.9530.0000.0000.0000.000
160A160GLN00.023-0.00313.3980.1930.1930.0000.0000.0000.000
161A161THR00.001-0.01012.360-0.785-0.7850.0000.0000.0000.000
162A162PHE0-0.030-0.02114.5111.3961.3960.0000.0000.0000.000
163A163LEU00.0010.00416.234-0.929-0.9290.0000.0000.0000.000
164A164LYS10.9330.97816.74317.98217.9820.0000.0000.0000.000
165A165ASP-1-0.727-0.84218.953-12.190-12.1900.0000.0000.0000.000
166A166GLU-1-0.811-0.87717.942-16.977-16.9770.0000.0000.0000.000
167A167ILE00.0050.00722.4280.0280.0280.0000.0000.0000.000
168A168ARG10.8700.93215.09417.88617.8860.0000.0000.0000.000
169A169PRO00.0610.03020.5590.4880.4880.0000.0000.0000.000
170A170MET00.037-0.01322.361-0.628-0.6280.0000.0000.0000.000
171A171GLU-1-0.938-0.95221.237-14.159-14.1590.0000.0000.0000.000
172A172LYS10.9510.96416.07517.55417.5540.0000.0000.0000.000
173A173VAL0-0.045-0.01119.218-0.638-0.6380.0000.0000.0000.000
174A174ARG10.9951.00921.57911.50311.5030.0000.0000.0000.000
175A175ALA0-0.010-0.00818.4300.0230.0230.0000.0000.0000.000
176A176GLY00.0780.03417.979-0.791-0.7910.0000.0000.0000.000
177A177LYS10.9200.97513.29720.46520.4650.0000.0000.0000.000
178A178THR0-0.047-0.04415.9140.3660.3660.0000.0000.0000.000
179A179ARG10.8170.87813.59817.75417.7540.0000.0000.0000.000
180A180ILE00.0210.00310.6931.3941.3940.0000.0000.0000.000
181A181VAL0-0.038-0.02113.215-0.665-0.6650.0000.0000.0000.000
182A182ASP-1-0.786-0.8839.603-29.473-29.4730.0000.0000.0000.000
183A183VAL0-0.045-0.02312.3770.2690.2690.0000.0000.0000.000
184A184LEU00.0250.02012.079-0.055-0.0550.0000.0000.0000.000
185A185PRO0-0.0120.00515.9890.6970.6970.0000.0000.0000.000
186A186VAL00.0380.00719.430-0.203-0.2030.0000.0000.0000.000
187A187GLU-1-0.707-0.83422.039-13.560-13.5600.0000.0000.0000.000
188A188HIS10.8710.94415.15418.48518.4850.0000.0000.0000.000
189A189ILE0-0.0440.00018.447-0.314-0.3140.0000.0000.0000.000
190A190LEU00.0210.01020.3440.0770.0770.0000.0000.0000.000
191A191TYR00.1060.02621.4070.0510.0510.0000.0000.0000.000
192A192THR0-0.029-0.03317.753-0.288-0.2880.0000.0000.0000.000
193A193ARG10.7720.86520.77112.29612.2960.0000.0000.0000.000
194A194MET0-0.0240.00223.7190.2990.2990.0000.0000.0000.000
195A195MET0-0.052-0.01522.0830.3080.3080.0000.0000.0000.000
196A196ILE00.0360.01118.6000.0880.0880.0000.0000.0000.000
197A197GLY00.0260.02222.927-0.073-0.0730.0000.0000.0000.000
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