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: 4L8JN

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 OptH
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 -464942.741112
FMO2-HF: Nuclear repulsion 425878.081207
FMO2-HF: Total energy -39064.659905
FMO2-MP2: Total energy -39179.884648


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.
-0.0221.615-0.017-0.838-0.7820
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 : 0.034 / q_NPA : -0.002
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].
3G22LEU0-0.1100.1253.918-0.5480.006-0.001-0.336-0.2170.000
4G23ILE00.063-0.0993.8150.5041.587-0.016-0.502-0.5650.000
5G23ILE0-0.0190.1426.0550.0110.0110.0000.0000.0000.000
6G24LYS00.054-0.0906.538-0.100-0.1000.0000.0000.0000.000
7G24LYS10.9421.0598.6800.1800.1800.0000.0000.0000.000
8G25SER00.013-0.0537.933-0.083-0.0830.0000.0000.0000.000
9G25SER0-0.0140.0567.0620.1060.1060.0000.0000.0000.000
10G26LEU00.123-0.0968.814-0.173-0.1730.0000.0000.0000.000
11G26LEU0-0.0670.1249.5340.0500.0500.0000.0000.0000.000
12G27ALA00.146-0.06910.351-0.061-0.0610.0000.0000.0000.000
13G27ALA0-0.0960.09610.9930.0070.0070.0000.0000.0000.000
14G28GLU00.011-0.11012.258-0.022-0.0220.0000.0000.0000.000
15G28GLU-1-0.872-0.82012.2980.1450.1450.0000.0000.0000.000
16G29LYS00.030-0.09213.620-0.065-0.0650.0000.0000.0000.000
17G29LYS10.9251.07313.757-0.007-0.0070.0000.0000.0000.000
18G30GLU00.096-0.13314.915-0.052-0.0520.0000.0000.0000.000
19G30GLU-1-0.967-0.80215.5760.3610.3610.0000.0000.0000.000
20G31LYS0-0.001-0.11516.828-0.023-0.0230.0000.0000.0000.000
21G31LYS10.8221.00314.726-0.196-0.1960.0000.0000.0000.000
22G32GLN00.111-0.06318.730-0.015-0.0150.0000.0000.0000.000
23G32GLN0-0.1650.04316.891-0.019-0.0190.0000.0000.0000.000
24G33LEU00.050-0.10919.520-0.020-0.0200.0000.0000.0000.000
25G33LEU0-0.0710.09518.057-0.001-0.0010.0000.0000.0000.000
26G34LEU00.080-0.11220.805-0.014-0.0140.0000.0000.0000.000
27G34LEU0-0.0410.13521.0810.0020.0020.0000.0000.0000.000
28G35GLU00.083-0.11822.528-0.002-0.0020.0000.0000.0000.000
29G35GLU-1-0.977-0.82722.7030.0660.0660.0000.0000.0000.000
30G36ARG00.080-0.10223.899-0.009-0.0090.0000.0000.0000.000
31G36ARG10.8601.05624.474-0.018-0.0180.0000.0000.0000.000
32G37LEU00.019-0.13825.295-0.011-0.0110.0000.0000.0000.000
33G37LEU0-0.1040.10323.9410.0010.0010.0000.0000.0000.000
34G38GLU00.094-0.12027.024-0.005-0.0050.0000.0000.0000.000
35G38GLU-1-1.007-0.83427.2610.0820.0820.0000.0000.0000.000
36G39ALA00.079-0.12528.743-0.002-0.0020.0000.0000.0000.000
37G39ALA0-0.0650.12129.463-0.001-0.0010.0000.0000.0000.000
38G40ALA00.089-0.08929.996-0.006-0.0060.0000.0000.0000.000
39G40ALA0-0.0920.08830.1180.0010.0010.0000.0000.0000.000
40G41LYS00.024-0.10731.480-0.004-0.0040.0000.0000.0000.000
41G41LYS10.8881.07630.676-0.066-0.0660.0000.0000.0000.000
42G42LYS00.067-0.05733.109-0.001-0.0010.0000.0000.0000.000
43G42LYS10.9051.06130.997-0.045-0.0450.0000.0000.0000.000
44G43GLU00.089-0.10734.9200.0000.0000.0000.0000.0000.000
45G43GLU-1-1.008-0.84335.8590.0140.0140.0000.0000.0000.000
46G44ALA00.138-0.09936.040-0.004-0.0040.0000.0000.0000.000
47G44ALA0-0.1230.08635.7750.0010.0010.0000.0000.0000.000
48G45GLU00.090-0.08037.487-0.002-0.0020.0000.0000.0000.000
49G45GLU-1-0.981-0.89337.9290.0360.0360.0000.0000.0000.000
50G46GLU00.044-0.11038.939-0.002-0.0020.0000.0000.0000.000
51G46GLU-1-0.985-0.85139.0880.0240.0240.0000.0000.0000.000
52G47ARG00.003-0.14140.734-0.003-0.0030.0000.0000.0000.000
53G47ARG10.8311.06540.837-0.016-0.0160.0000.0000.0000.000
54G48VAL00.093-0.10941.745-0.003-0.0030.0000.0000.0000.000
55G48VAL0-0.0380.14541.6410.0000.0000.0000.0000.0000.000
56G49LYS00.168-0.06543.329-0.001-0.0010.0000.0000.0000.000
57G49LYS10.8231.05242.288-0.027-0.0270.0000.0000.0000.000
58G50ARG00.048-0.07345.072-0.001-0.0010.0000.0000.0000.000
59G50ARG10.7911.00641.076-0.016-0.0160.0000.0000.0000.000
60G51ALA00.134-0.07546.782-0.002-0.0020.0000.0000.0000.000
61G51ALA0-0.0680.10047.4040.0000.0000.0000.0000.0000.000
62G52GLU00.053-0.12448.162-0.002-0.0020.0000.0000.0000.000
63G52GLU-1-1.000-0.84247.0250.0280.0280.0000.0000.0000.000
64G53ALA00.059-0.11449.4160.0000.0000.0000.0000.0000.000
65G53ALA0-0.1070.08449.6390.0000.0000.0000.0000.0000.000
66G54GLU00.038-0.13950.937-0.001-0.0010.0000.0000.0000.000
67G54GLU-1-1.012-0.85350.9890.0120.0120.0000.0000.0000.000
68G55ALA00.124-0.10252.669-0.001-0.0010.0000.0000.0000.000
69G55ALA0-0.0920.11353.1150.0000.0000.0000.0000.0000.000
70G56LYS00.118-0.06654.185-0.001-0.0010.0000.0000.0000.000
71G56LYS10.8231.03954.579-0.016-0.0160.0000.0000.0000.000
72G57ALA00.093-0.11955.5540.0000.0000.0000.0000.0000.000
73G57ALA0-0.0680.11955.9460.0000.0000.0000.0000.0000.000
74G58LEU00.091-0.07957.101-0.001-0.0010.0000.0000.0000.000
75G58LEU0-0.0930.09157.3330.0000.0000.0000.0000.0000.000
76G59LEU00.031-0.11158.837-0.001-0.0010.0000.0000.0000.000
77G59LEU0-0.0690.09358.5410.0000.0000.0000.0000.0000.000
78G60GLU00.062-0.10560.3260.0000.0000.0000.0000.0000.000
79G60GLU-1-1.018-0.86660.0140.0120.0120.0000.0000.0000.000
80G61GLU00.136-0.11161.6850.0000.0000.0000.0000.0000.000
81G61GLU-1-1.032-0.84262.0750.0080.0080.0000.0000.0000.000
82G62ALA00.046-0.14863.026-0.001-0.0010.0000.0000.0000.000
83G62ALA0-0.1120.10863.1550.0000.0000.0000.0000.0000.000
84G63GLU00.041-0.11664.8460.0000.0000.0000.0000.0000.000
85G63GLU-1-0.994-0.84265.6630.0120.0120.0000.0000.0000.000
86G64ALA00.059-0.13766.3290.0000.0000.0000.0000.0000.000
87G64ALA0-0.0170.14866.4560.0000.0000.0000.0000.0000.000
88G65LYS00.058-0.08467.747-0.001-0.0010.0000.0000.0000.000
89G65LYS10.8831.07468.251-0.007-0.0070.0000.0000.0000.000
90G66ALA00.104-0.12569.282-0.001-0.0010.0000.0000.0000.000
91G66ALA0-0.0220.15969.7320.0000.0000.0000.0000.0000.000
92G67LYS00.109-0.08070.9000.0000.0000.0000.0000.0000.000
93G67LYS10.8191.01568.623-0.011-0.0110.0000.0000.0000.000
94G68ALA00.073-0.13172.1070.0000.0000.0000.0000.0000.000
95G68ALA0-0.0730.13172.2290.0000.0000.0000.0000.0000.000
96G69LEU00.024-0.13573.646-0.001-0.0010.0000.0000.0000.000
97G69LEU0-0.1320.09573.2470.0000.0000.0000.0000.0000.000
98G70GLU00.126-0.10975.3030.0000.0000.0000.0000.0000.000
99G70GLU-1-0.986-0.84774.5670.0090.0090.0000.0000.0000.000
100G71ALA0-0.011-0.12776.8130.0000.0000.0000.0000.0000.000
101G71ALA0-0.0360.12376.9070.0000.0000.0000.0000.0000.000
102G72GLN00.056-0.08078.3440.0000.0000.0000.0000.0000.000
103G72GLN0-0.1150.07777.0820.0000.0000.0000.0000.0000.000
104G73TYR00.075-0.11179.9590.0000.0000.0000.0000.0000.000
105G73TYR0-0.1120.09178.6370.0000.0000.0000.0000.0000.000
106G74ARG00.162-0.07381.2800.0000.0000.0000.0000.0000.000
107G74ARG10.8571.05678.239-0.008-0.0080.0000.0000.0000.000
108G75GLU00.054-0.12182.9970.0000.0000.0000.0000.0000.000
109G75GLU-1-0.978-0.84983.7270.0050.0050.0000.0000.0000.000
110G76ARG00.090-0.04784.2510.0000.0000.0000.0000.0000.000
111G76ARG10.7861.00980.209-0.006-0.0060.0000.0000.0000.000
112G77GLU00.098-0.10885.8340.0000.0000.0000.0000.0000.000
113G77GLU-1-0.991-0.83786.4110.0070.0070.0000.0000.0000.000
114G78ARG00.106-0.03987.5970.0000.0000.0000.0000.0000.000
115G78ARG10.8921.06988.135-0.005-0.0050.0000.0000.0000.000
116G79ALA00.070-0.14388.9150.0000.0000.0000.0000.0000.000
117G79ALA0-0.0530.14689.1730.0000.0000.0000.0000.0000.000
118G80GLU00.029-0.13890.5470.0000.0000.0000.0000.0000.000
119G80GLU-1-1.010-0.84188.7690.0050.0050.0000.0000.0000.000
120G81THR0-0.120-0.13791.6200.0000.0000.0000.0000.0000.000
121G81THR0-0.0400.03891.0190.0000.0000.0000.0000.0000.000
122G82GLU00.098-0.11593.4520.0000.0000.0000.0000.0000.000
123G82GLU-1-1.002-0.83693.6810.0040.0040.0000.0000.0000.000
124G83ALA00.147-0.09494.8670.0000.0000.0000.0000.0000.000
125G83ALA0-0.0600.12795.0540.0000.0000.0000.0000.0000.000
126G84LEU00.057-0.12795.8520.0000.0000.0000.0000.0000.000
127G84LEU0-0.0950.10794.7160.0000.0000.0000.0000.0000.000
128G85LEU00.020-0.13697.4420.0000.0000.0000.0000.0000.000
129G85LEU0-0.0630.10896.8510.0000.0000.0000.0000.0000.000
130G86ALA00.086-0.12099.0890.0000.0000.0000.0000.0000.000
131G86ALA0-0.0190.13799.5130.0000.0000.0000.0000.0000.000
132G87ARG00.047-0.074100.3700.0000.0000.0000.0000.0000.000
133G87ARG10.8781.04799.716-0.004-0.0040.0000.0000.0000.000
134G88TYR00.081-0.089101.7700.0000.0000.0000.0000.0000.000
135G88TYR0-0.1010.07099.0570.0000.0000.0000.0000.0000.000
136G89ARG00.017-0.098103.6590.0000.0000.0000.0000.0000.000
137G89ARG10.9441.064101.690-0.004-0.0040.0000.0000.0000.000
138G90GLU00.132-0.087105.3370.0000.0000.0000.0000.0000.000
139G90GLU-1-1.013-0.832104.6750.0030.0030.0000.0000.0000.000
140G91ARG00.107-0.091106.2590.0000.0000.0000.0000.0000.000
141G91ARG10.8351.051105.120-0.004-0.0040.0000.0000.0000.000
142G92ALA00.074-0.101107.5210.0000.0000.0000.0000.0000.000
143G92ALA0-0.0990.096107.3500.0000.0000.0000.0000.0000.000
144G93GLU00.049-0.127109.0340.0000.0000.0000.0000.0000.000
145G93GLU-1-0.972-0.833109.6970.0030.0030.0000.0000.0000.000
146G94ALA00.067-0.140111.0780.0000.0000.0000.0000.0000.000
147G94ALA0-0.0440.143111.1950.0000.0000.0000.0000.0000.000
148G95GLU00.018-0.161111.8840.0000.0000.0000.0000.0000.000
149G95GLU-1-1.010-0.839110.3740.0040.0040.0000.0000.0000.000
150G96ALA00.105-0.099113.3350.0000.0000.0000.0000.0000.000
151G96ALA0-0.1170.098113.6500.0000.0000.0000.0000.0000.000
152G97LYS00.027-0.136115.1060.0000.0000.0000.0000.0000.000
153G97LYS10.8881.087116.095-0.003-0.0030.0000.0000.0000.000
154G98ALA00.110-0.094116.2270.0000.0000.0000.0000.0000.000
155G98ALA0-0.0700.113115.8150.0000.0000.0000.0000.0000.000
156G99VAL0-0.023-0.130117.6040.0000.0000.0000.0000.0000.000
157G99VAL0-0.0280.123116.0310.0000.0000.0000.0000.0000.000
158G100ARG00.056-0.089119.0200.0000.0000.0000.0000.0000.000
159G100ARG10.9121.055116.345-0.003-0.0030.0000.0000.0000.000
160G101GLU00.099-0.113121.3760.0000.0000.0000.0000.0000.000
161G101GLU-1-0.991-0.829121.2870.0030.0030.0000.0000.0000.000
162G102LYS00.069-0.085122.2200.0000.0000.0000.0000.0000.000
163G102LYS10.7950.993117.908-0.003-0.0030.0000.0000.0000.000
164G103ALA00.090-0.090123.5720.0000.0000.0000.0000.0000.000
165G103ALA0-0.0900.105123.7450.0000.0000.0000.0000.0000.000
166G104MET00.031-0.084125.3650.0000.0000.0000.0000.0000.000
167G104MET0-0.1110.080125.5100.0000.0000.0000.0000.0000.000
168G105ALA00.136-0.086127.4660.0000.0000.0000.0000.0000.000
169G105ALA0-0.1070.091128.8660.0000.0000.0000.0000.0000.000
170G106ARG00.049-0.090128.9120.0000.0000.0000.0000.0000.000
171G106ARG10.7951.046128.667-0.003-0.0030.0000.0000.0000.000
172G107LEU00.133-0.093129.9100.0000.0000.0000.0000.0000.000
173G107LEU0-0.0870.111128.2740.0000.0000.0000.0000.0000.000
174G108ASP00.169-0.108130.9790.0000.0000.0000.0000.0000.000
175G108ASP-1-0.971-0.827134.9390.0030.0030.0000.0000.0000.000
176G109GLU0-0.007-0.138133.8900.0000.0000.0000.0000.0000.000
177G109GLU-1-0.922-0.828132.8520.0030.0030.0000.0000.0000.000
178G110ALA00.134-0.077131.0420.0000.0000.0000.0000.0000.000
179G110ALA0-0.0760.097130.3930.0000.0000.0000.0000.0000.000
180G111VAL00.039-0.134132.4190.0000.0000.0000.0000.0000.000
181G111VAL0-0.0770.109133.2250.0000.0000.0000.0000.0000.000
182G112ALA00.074-0.102134.6930.0000.0000.0000.0000.0000.000
183G112ALA0-0.1010.092137.0240.0000.0000.0000.0000.0000.000
184G113LEU00.070-0.102134.6410.0000.0000.0000.0000.0000.000
185G113LEU0-0.0900.101132.1640.0000.0000.0000.0000.0000.000
186G114VAL00.084-0.082134.5790.0000.0000.0000.0000.0000.000
187G114VAL0-0.0970.072132.5160.0000.0000.0000.0000.0000.000
188G115LEU00.115-0.062135.5050.0000.0000.0000.0000.0000.000
189G115LEU0-0.0960.078137.9520.0000.0000.0000.0000.0000.000
190G116LYS00.017-0.115138.9280.0000.0000.0000.0000.0000.000
191G116LYS10.8921.058139.356-0.003-0.0030.0000.0000.0000.000
192G117GLU00.089-0.110137.5800.0000.0000.0000.0000.0000.000
193G117GLU-1-1.012-0.841136.3450.0030.0030.0000.0000.0000.000
194G118VAL00.022-0.125139.0170.0000.0000.0000.0000.0000.000
195G118VAL0-0.1100.068137.3320.0000.0000.0000.0000.0000.000
196G119LEU00.009-0.082139.8840.0000.0000.0000.0000.0000.000
197G119LEU0-0.1250.061142.4580.0000.0000.0000.0000.0000.000
198G120PRO0-0.030-0.096141.7400.0000.0000.0000.0000.0000.000