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: K2MG3

Calculation Name: 3K5B-G-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3K5B

Chain ID: G

ChEMBL ID:

UniProt ID: P74901

Base Structure: X-ray

Registration Date: 2025-07-08

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -466310.389772
FMO2-HF: Nuclear repulsion 427243.271267
FMO2-HF: Total energy -39067.118505
FMO2-MP2: Total energy -39182.303868


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(G:21:GLY)


Summations of interaction energy for fragment #1(G:21: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.
0.0791.46-0.013-0.652-0.7160
Interaction energy analysis for fragmet #1(G:21:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.006
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].
3G22LEU0-0.0690.1184.187-0.1590.1310.000-0.133-0.1570.000
4G23ILE00.085-0.0873.8660.4941.585-0.013-0.519-0.5590.000
5G23ILE0-0.0100.1405.740-0.010-0.0100.0000.0000.0000.000
6G24LYS00.087-0.0746.296-0.111-0.1110.0000.0000.0000.000
7G24LYS10.9191.0648.6360.1560.1560.0000.0000.0000.000
8G25SER00.007-0.0937.674-0.101-0.1010.0000.0000.0000.000
9G25SER0-0.0540.0536.3470.0670.0670.0000.0000.0000.000
10G26LEU00.116-0.0948.634-0.210-0.2100.0000.0000.0000.000
11G26LEU0-0.0760.1259.3810.0660.0660.0000.0000.0000.000
12G27ALA00.156-0.07710.281-0.117-0.1170.0000.0000.0000.000
13G27ALA0-0.0900.10311.0830.0030.0030.0000.0000.0000.000
14G28GLU00.027-0.10412.297-0.034-0.0340.0000.0000.0000.000
15G28GLU-1-0.911-0.83112.4190.1200.1200.0000.0000.0000.000
16G29LYS00.056-0.10113.362-0.058-0.0580.0000.0000.0000.000
17G29LYS10.8461.05313.611-0.070-0.0700.0000.0000.0000.000
18G30GLU00.077-0.12814.590-0.055-0.0550.0000.0000.0000.000
19G30GLU-1-1.003-0.84114.9540.4070.4070.0000.0000.0000.000
20G31LYS00.106-0.08016.490-0.025-0.0250.0000.0000.0000.000
21G31LYS10.7731.01014.810-0.179-0.1790.0000.0000.0000.000
22G32GLN00.163-0.07118.081-0.015-0.0150.0000.0000.0000.000
23G32GLN0-0.0990.09016.886-0.004-0.0040.0000.0000.0000.000
24G33LEU00.037-0.09719.108-0.027-0.0270.0000.0000.0000.000
25G33LEU0-0.0970.08317.632-0.001-0.0010.0000.0000.0000.000
26G34LEU00.101-0.08920.620-0.018-0.0180.0000.0000.0000.000
27G34LEU0-0.0680.11621.0180.0030.0030.0000.0000.0000.000
28G35GLU00.091-0.12722.443-0.006-0.0060.0000.0000.0000.000
29G35GLU-1-0.983-0.83322.0160.0800.0800.0000.0000.0000.000
30G36ARG00.111-0.07323.715-0.012-0.0120.0000.0000.0000.000
31G36ARG10.8481.05324.117-0.048-0.0480.0000.0000.0000.000
32G37LEU00.038-0.12525.035-0.013-0.0130.0000.0000.0000.000
33G37LEU0-0.1000.09323.7470.0010.0010.0000.0000.0000.000
34G38GLU00.098-0.10226.631-0.005-0.0050.0000.0000.0000.000
35G38GLU-1-0.956-0.81826.7990.0750.0750.0000.0000.0000.000
36G39ALA00.119-0.09728.267-0.005-0.0050.0000.0000.0000.000
37G39ALA0-0.1010.09628.859-0.001-0.0010.0000.0000.0000.000
38G40ALA00.096-0.08329.503-0.007-0.0070.0000.0000.0000.000
39G40ALA0-0.1080.07429.7810.0010.0010.0000.0000.0000.000
40G41LYS0-0.024-0.13131.016-0.005-0.0050.0000.0000.0000.000
41G41LYS10.8951.07230.733-0.077-0.0770.0000.0000.0000.000
42G42LYS00.119-0.04432.708-0.002-0.0020.0000.0000.0000.000
43G42LYS10.7721.01230.116-0.062-0.0620.0000.0000.0000.000
44G43GLU00.055-0.10434.665-0.001-0.0010.0000.0000.0000.000
45G43GLU-1-0.908-0.79135.9700.0240.0240.0000.0000.0000.000
46G44ALA00.169-0.08135.915-0.004-0.0040.0000.0000.0000.000
47G44ALA0-0.1180.07636.0660.0010.0010.0000.0000.0000.000
48G45GLU00.110-0.08437.263-0.003-0.0030.0000.0000.0000.000
49G45GLU-1-0.977-0.83237.2860.0420.0420.0000.0000.0000.000
50G46GLU00.121-0.09138.685-0.002-0.0020.0000.0000.0000.000
51G46GLU-1-0.941-0.82638.9940.0310.0310.0000.0000.0000.000
52G47ARG00.033-0.11140.373-0.003-0.0030.0000.0000.0000.000
53G47ARG10.7000.96341.017-0.023-0.0230.0000.0000.0000.000
54G48VAL00.084-0.09041.746-0.003-0.0030.0000.0000.0000.000
55G48VAL0-0.0750.11241.6890.0000.0000.0000.0000.0000.000
56G49LYS00.173-0.08943.303-0.001-0.0010.0000.0000.0000.000
57G49LYS10.7050.98941.202-0.035-0.0350.0000.0000.0000.000
58G50ARG00.045-0.07244.888-0.001-0.0010.0000.0000.0000.000
59G50ARG10.6700.92340.612-0.024-0.0240.0000.0000.0000.000
60G51ALA00.185-0.05246.555-0.002-0.0020.0000.0000.0000.000
61G51ALA0-0.0910.08547.1630.0000.0000.0000.0000.0000.000
62G52GLU00.033-0.13648.094-0.002-0.0020.0000.0000.0000.000
63G52GLU-1-1.002-0.84547.1540.0320.0320.0000.0000.0000.000
64G53ALA00.085-0.08649.443-0.001-0.0010.0000.0000.0000.000
65G53ALA0-0.0940.08549.7880.0000.0000.0000.0000.0000.000
66G54GLU00.035-0.10950.824-0.001-0.0010.0000.0000.0000.000
67G54GLU-1-0.891-0.80048.8220.0200.0200.0000.0000.0000.000
68G55ALA00.121-0.09952.438-0.002-0.0020.0000.0000.0000.000
69G55ALA0-0.0940.10953.0750.0000.0000.0000.0000.0000.000
70G56LYS00.085-0.08753.900-0.001-0.0010.0000.0000.0000.000
71G56LYS10.6930.95854.381-0.017-0.0170.0000.0000.0000.000
72G57ALA00.133-0.08655.364-0.001-0.0010.0000.0000.0000.000
73G57ALA0-0.0980.09855.8070.0000.0000.0000.0000.0000.000
74G58LEU00.071-0.09256.868-0.001-0.0010.0000.0000.0000.000
75G58LEU0-0.0970.08957.2940.0000.0000.0000.0000.0000.000
76G59LEU00.033-0.12158.526-0.001-0.0010.0000.0000.0000.000
77G59LEU0-0.0710.09957.6120.0000.0000.0000.0000.0000.000
78G60GLU00.097-0.08859.9940.0000.0000.0000.0000.0000.000
79G60GLU-1-0.886-0.78558.4780.0160.0160.0000.0000.0000.000
80G61GLU00.123-0.10961.443-0.001-0.0010.0000.0000.0000.000
81G61GLU-1-1.029-0.85161.9680.0110.0110.0000.0000.0000.000
82G62ALA00.105-0.10162.867-0.001-0.0010.0000.0000.0000.000
83G62ALA0-0.1130.09763.1860.0000.0000.0000.0000.0000.000
84G63GLU00.063-0.11664.6150.0000.0000.0000.0000.0000.000
85G63GLU-1-0.921-0.78964.8810.0140.0140.0000.0000.0000.000
86G64ALA00.068-0.11465.9150.0000.0000.0000.0000.0000.000
87G64ALA0-0.0560.12566.1210.0000.0000.0000.0000.0000.000
88G65LYS00.061-0.10567.271-0.001-0.0010.0000.0000.0000.000
89G65LYS10.8351.06467.676-0.010-0.0100.0000.0000.0000.000
90G66ALA00.098-0.12568.771-0.001-0.0010.0000.0000.0000.000
91G66ALA0-0.0580.13169.1830.0000.0000.0000.0000.0000.000
92G67LYS00.115-0.08670.5720.0000.0000.0000.0000.0000.000
93G67LYS10.7431.00169.290-0.013-0.0130.0000.0000.0000.000
94G68ALA00.116-0.11871.8230.0000.0000.0000.0000.0000.000
95G68ALA0-0.1000.10972.0050.0000.0000.0000.0000.0000.000
96G69LEU00.020-0.13273.188-0.001-0.0010.0000.0000.0000.000
97G69LEU0-0.1270.08572.3130.0000.0000.0000.0000.0000.000
98G70GLU00.065-0.14274.9140.0000.0000.0000.0000.0000.000
99G70GLU-1-0.837-0.77274.6670.0110.0110.0000.0000.0000.000
100G71ALA00.045-0.06476.5250.0000.0000.0000.0000.0000.000
101G71ALA0-0.0570.10976.8950.0000.0000.0000.0000.0000.000
102G72GLN00.066-0.07377.8530.0000.0000.0000.0000.0000.000
103G72GLN0-0.0970.08375.6730.0000.0000.0000.0000.0000.000
104G73TYR00.055-0.11379.6860.0000.0000.0000.0000.0000.000
105G73TYR0-0.0880.09778.2910.0000.0000.0000.0000.0000.000
106G74ARG00.197-0.05581.0050.0000.0000.0000.0000.0000.000
107G74ARG10.7340.96776.685-0.010-0.0100.0000.0000.0000.000
108G75GLU00.108-0.08482.7260.0000.0000.0000.0000.0000.000
109G75GLU-1-0.960-0.82583.0490.0060.0060.0000.0000.0000.000
110G76ARG00.098-0.06184.0120.0000.0000.0000.0000.0000.000
111G76ARG10.7420.99280.247-0.008-0.0080.0000.0000.0000.000
112G77GLU00.113-0.10085.4880.0000.0000.0000.0000.0000.000
113G77GLU-1-1.004-0.84884.6680.0090.0090.0000.0000.0000.000
114G78ARG00.114-0.03687.2450.0000.0000.0000.0000.0000.000
115G78ARG10.6920.94887.632-0.006-0.0060.0000.0000.0000.000
116G79ALA00.122-0.11988.6320.0000.0000.0000.0000.0000.000
117G79ALA0-0.0890.11588.8750.0000.0000.0000.0000.0000.000
118G80GLU00.030-0.14489.8050.0000.0000.0000.0000.0000.000
119G80GLU-1-1.002-0.84787.7940.0070.0070.0000.0000.0000.000
120G81THR0-0.024-0.11391.3320.0000.0000.0000.0000.0000.000
121G81THR0-0.0630.04990.9760.0000.0000.0000.0000.0000.000
122G82GLU00.075-0.10093.1230.0000.0000.0000.0000.0000.000
123G82GLU-1-0.901-0.79593.1450.0060.0060.0000.0000.0000.000
124G83ALA00.111-0.10094.4430.0000.0000.0000.0000.0000.000
125G83ALA0-0.0770.11494.5690.0000.0000.0000.0000.0000.000
126G84LEU00.059-0.12695.5530.0000.0000.0000.0000.0000.000
127G84LEU0-0.1060.10695.0150.0000.0000.0000.0000.0000.000
128G85LEU00.052-0.13197.1680.0000.0000.0000.0000.0000.000
129G85LEU0-0.0770.11496.4290.0000.0000.0000.0000.0000.000
130G86ALA00.061-0.11798.8830.0000.0000.0000.0000.0000.000
131G86ALA0-0.0630.11699.5070.0000.0000.0000.0000.0000.000
132G87ARG00.099-0.070100.3420.0000.0000.0000.0000.0000.000
133G87ARG10.8851.06399.095-0.005-0.0050.0000.0000.0000.000
134G88TYR00.051-0.106101.5200.0000.0000.0000.0000.0000.000
135G88TYR0-0.1170.08499.2420.0000.0000.0000.0000.0000.000
136G89ARG00.044-0.082103.2980.0000.0000.0000.0000.0000.000
137G89ARG10.9171.047101.078-0.005-0.0050.0000.0000.0000.000
138G90GLU00.127-0.093105.3490.0000.0000.0000.0000.0000.000
139G90GLU-1-0.997-0.841104.3130.0050.0050.0000.0000.0000.000
140G91ARG00.107-0.070106.0790.0000.0000.0000.0000.0000.000
141G91ARG10.7100.949104.598-0.005-0.0050.0000.0000.0000.000
142G92ALA00.096-0.099107.2420.0000.0000.0000.0000.0000.000
143G92ALA0-0.0800.108107.2250.0000.0000.0000.0000.0000.000
144G93GLU00.040-0.118108.9490.0000.0000.0000.0000.0000.000
145G93GLU-1-1.009-0.852109.3720.0040.0040.0000.0000.0000.000
146G94ALA00.093-0.119110.9190.0000.0000.0000.0000.0000.000
147G94ALA0-0.0720.121110.9410.0000.0000.0000.0000.0000.000
148G95GLU00.051-0.133111.5420.0000.0000.0000.0000.0000.000
149G95GLU-1-0.879-0.751109.2460.0050.0050.0000.0000.0000.000
150G96ALA00.129-0.100112.9660.0000.0000.0000.0000.0000.000
151G96ALA0-0.1020.099113.3430.0000.0000.0000.0000.0000.000
152G97LYS00.022-0.125114.8570.0000.0000.0000.0000.0000.000
153G97LYS10.7631.001115.920-0.004-0.0040.0000.0000.0000.000
154G98ALA00.131-0.084116.1100.0000.0000.0000.0000.0000.000
155G98ALA0-0.0810.099115.6830.0000.0000.0000.0000.0000.000
156G99VAL0-0.023-0.133117.3070.0000.0000.0000.0000.0000.000
157G99VAL0-0.0700.113116.2700.0000.0000.0000.0000.0000.000
158G100ARG00.079-0.077118.8840.0000.0000.0000.0000.0000.000
159G100ARG10.9031.055115.547-0.004-0.0040.0000.0000.0000.000
160G101GLU00.121-0.104121.0290.0000.0000.0000.0000.0000.000
161G101GLU-1-0.921-0.777120.3040.0040.0040.0000.0000.0000.000
162G102LYS00.070-0.093122.0530.0000.0000.0000.0000.0000.000
163G102LYS10.8001.009118.227-0.004-0.0040.0000.0000.0000.000
164G103ALA00.108-0.067123.3720.0000.0000.0000.0000.0000.000
165G103ALA0-0.0990.091123.5010.0000.0000.0000.0000.0000.000
166G104MET00.059-0.080125.1550.0000.0000.0000.0000.0000.000
167G104MET0-0.0970.077125.1110.0000.0000.0000.0000.0000.000
168G105ALA00.102-0.091127.2410.0000.0000.0000.0000.0000.000
169G105ALA0-0.0920.097127.8740.0000.0000.0000.0000.0000.000
170G106ARG00.021-0.116128.7990.0000.0000.0000.0000.0000.000
171G106ARG10.7070.973128.247-0.004-0.0040.0000.0000.0000.000
172G107LEU00.126-0.070129.9290.0000.0000.0000.0000.0000.000
173G107LEU0-0.0870.104128.0910.0000.0000.0000.0000.0000.000
174G108ASP00.110-0.120130.6520.0000.0000.0000.0000.0000.000
175G108ASP-1-0.954-0.834134.2070.0030.0030.0000.0000.0000.000
176G109GLU00.027-0.129133.7550.0000.0000.0000.0000.0000.000
177G109GLU-1-0.835-0.764132.9210.0040.0040.0000.0000.0000.000
178G110ALA00.134-0.067130.7930.0000.0000.0000.0000.0000.000
179G110ALA0-0.0750.097130.2560.0000.0000.0000.0000.0000.000
180G111VAL00.033-0.132132.2700.0000.0000.0000.0000.0000.000
181G111VAL0-0.0850.112132.4820.0000.0000.0000.0000.0000.000
182G112ALA00.106-0.105134.3830.0000.0000.0000.0000.0000.000
183G112ALA0-0.0730.110137.2020.0000.0000.0000.0000.0000.000
184G113LEU00.104-0.082134.8500.0000.0000.0000.0000.0000.000
185G113LEU0-0.0870.108132.3650.0000.0000.0000.0000.0000.000
186G114VAL00.124-0.077134.4190.0000.0000.0000.0000.0000.000
187G114VAL0-0.0870.094132.2880.0000.0000.0000.0000.0000.000
188G115LEU00.036-0.095135.4000.0000.0000.0000.0000.0000.000
189G115LEU0-0.0990.078137.5270.0000.0000.0000.0000.0000.000
190G116LYS0-0.012-0.140138.4490.0000.0000.0000.0000.0000.000
191G116LYS10.7840.997139.218-0.004-0.0040.0000.0000.0000.000
192G117GLU00.132-0.074137.1500.0000.0000.0000.0000.0000.000
193G117GLU-1-1.006-0.856135.6920.0040.0040.0000.0000.0000.000
194G118VAL0-0.015-0.130138.6350.0000.0000.0000.0000.0000.000
195G118VAL0-0.0860.089136.6870.0000.0000.0000.0000.0000.000
196G119LEU00.008-0.091139.2860.0000.0000.0000.0000.0000.000
197G119LEU0-0.0830.083142.1120.0000.0000.0000.0000.0000.000
198G120PRO0-0.011-0.102141.6930.0000.0000.0000.0000.0000.000