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: QNJVY

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 OptHSide
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 -465665.740077
FMO2-HF: Nuclear repulsion 426599.239517
FMO2-HF: Total energy -39066.500561
FMO2-MP2: Total energy -39181.764673


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.
0.3531.769-0.017-0.69-0.7090
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].
3G22LEU0-0.0640.1074.253-0.1990.146-0.001-0.192-0.1520.000
4G23ILE00.050-0.0833.8150.5371.608-0.016-0.498-0.5570.000
5G23ILE0-0.0250.1436.0270.0110.0110.0000.0000.0000.000
6G24LYS00.060-0.0846.538-0.102-0.1020.0000.0000.0000.000
7G24LYS10.9241.0668.7430.1540.1540.0000.0000.0000.000
8G25SER00.032-0.0557.937-0.084-0.0840.0000.0000.0000.000
9G25SER0-0.0230.0546.6800.1210.1210.0000.0000.0000.000
10G26LEU00.125-0.1098.823-0.174-0.1740.0000.0000.0000.000
11G26LEU0-0.0710.1249.4830.0510.0510.0000.0000.0000.000
12G27ALA00.135-0.06610.351-0.064-0.0640.0000.0000.0000.000
13G27ALA0-0.0950.09310.9770.0090.0090.0000.0000.0000.000
14G28GLU0-0.008-0.10812.258-0.022-0.0220.0000.0000.0000.000
15G28GLU-1-0.887-0.82212.3720.1600.1600.0000.0000.0000.000
16G29LYS00.070-0.09813.627-0.056-0.0560.0000.0000.0000.000
17G29LYS10.8501.04713.874-0.001-0.0010.0000.0000.0000.000
18G30GLU00.087-0.13914.919-0.054-0.0540.0000.0000.0000.000
19G30GLU-1-0.969-0.81515.4590.3580.3580.0000.0000.0000.000
20G31LYS00.024-0.10916.833-0.024-0.0240.0000.0000.0000.000
21G31LYS10.7971.01014.748-0.208-0.2080.0000.0000.0000.000
22G32GLN00.122-0.07718.717-0.016-0.0160.0000.0000.0000.000
23G32GLN0-0.0770.10217.589-0.015-0.0150.0000.0000.0000.000
24G33LEU00.048-0.10019.523-0.020-0.0200.0000.0000.0000.000
25G33LEU0-0.0670.09118.020-0.001-0.0010.0000.0000.0000.000
26G34LEU00.080-0.09920.812-0.015-0.0150.0000.0000.0000.000
27G34LEU0-0.0370.12821.1580.0030.0030.0000.0000.0000.000
28G35GLU00.059-0.13322.536-0.003-0.0030.0000.0000.0000.000
29G35GLU-1-0.974-0.82422.8140.0710.0710.0000.0000.0000.000
30G36ARG00.093-0.08923.906-0.009-0.0090.0000.0000.0000.000
31G36ARG10.8521.05324.416-0.020-0.0200.0000.0000.0000.000
32G37LEU00.036-0.13125.300-0.011-0.0110.0000.0000.0000.000
33G37LEU0-0.1000.10224.1050.0010.0010.0000.0000.0000.000
34G38GLU00.100-0.14027.031-0.004-0.0040.0000.0000.0000.000
35G38GLU-1-0.921-0.79727.1520.0730.0730.0000.0000.0000.000
36G39ALA00.048-0.09128.750-0.002-0.0020.0000.0000.0000.000
37G39ALA0-0.0650.10929.392-0.001-0.0010.0000.0000.0000.000
38G40ALA00.096-0.07430.001-0.006-0.0060.0000.0000.0000.000
39G40ALA0-0.0940.07930.2000.0000.0000.0000.0000.0000.000
40G41LYS00.001-0.12231.488-0.004-0.0040.0000.0000.0000.000
41G41LYS10.9021.06830.945-0.064-0.0640.0000.0000.0000.000
42G42LYS00.128-0.01133.116-0.001-0.0010.0000.0000.0000.000
43G42LYS10.8011.00230.270-0.054-0.0540.0000.0000.0000.000
44G43GLU00.031-0.11734.9250.0000.0000.0000.0000.0000.000
45G43GLU-1-0.918-0.78836.0100.0140.0140.0000.0000.0000.000
46G44ALA00.163-0.09936.040-0.004-0.0040.0000.0000.0000.000
47G44ALA0-0.1260.07535.9230.0010.0010.0000.0000.0000.000
48G45GLU00.113-0.08537.493-0.002-0.0020.0000.0000.0000.000
49G45GLU-1-1.032-0.87737.8900.0370.0370.0000.0000.0000.000
50G46GLU00.081-0.12038.947-0.002-0.0020.0000.0000.0000.000
51G46GLU-1-0.908-0.81139.0960.0260.0260.0000.0000.0000.000
52G47ARG0-0.001-0.10740.728-0.003-0.0030.0000.0000.0000.000
53G47ARG10.7491.00640.981-0.016-0.0160.0000.0000.0000.000
54G48VAL00.078-0.10241.749-0.003-0.0030.0000.0000.0000.000
55G48VAL0-0.0450.12941.9770.0000.0000.0000.0000.0000.000
56G49LYS00.173-0.06243.339-0.001-0.0010.0000.0000.0000.000
57G49LYS10.7260.99741.753-0.028-0.0280.0000.0000.0000.000
58G50ARG00.039-0.06745.081-0.001-0.0010.0000.0000.0000.000
59G50ARG10.7080.92440.938-0.017-0.0170.0000.0000.0000.000
60G51ALA00.172-0.05346.778-0.002-0.0020.0000.0000.0000.000
61G51ALA0-0.0850.08647.3880.0000.0000.0000.0000.0000.000
62G52GLU00.037-0.14448.167-0.002-0.0020.0000.0000.0000.000
63G52GLU-1-0.996-0.84247.2940.0280.0280.0000.0000.0000.000
64G53ALA00.048-0.09549.4220.0000.0000.0000.0000.0000.000
65G53ALA0-0.1010.07649.6180.0000.0000.0000.0000.0000.000
66G54GLU00.019-0.12650.941-0.001-0.0010.0000.0000.0000.000
67G54GLU-1-0.885-0.81449.3550.0140.0140.0000.0000.0000.000
68G55ALA00.119-0.08652.679-0.001-0.0010.0000.0000.0000.000
69G55ALA0-0.0900.11253.2170.0000.0000.0000.0000.0000.000
70G56LYS00.090-0.08054.193-0.001-0.0010.0000.0000.0000.000
71G56LYS10.7130.96254.687-0.015-0.0150.0000.0000.0000.000
72G57ALA00.104-0.09855.5610.0000.0000.0000.0000.0000.000
73G57ALA0-0.0790.10455.8920.0000.0000.0000.0000.0000.000
74G58LEU00.072-0.08257.112-0.001-0.0010.0000.0000.0000.000
75G58LEU0-0.0970.08957.4140.0000.0000.0000.0000.0000.000
76G59LEU00.041-0.11658.844-0.001-0.0010.0000.0000.0000.000
77G59LEU0-0.0650.09558.2610.0000.0000.0000.0000.0000.000
78G60GLU00.114-0.07760.3260.0000.0000.0000.0000.0000.000
79G60GLU-1-0.896-0.79259.0230.0140.0140.0000.0000.0000.000
80G61GLU00.110-0.11061.6920.0000.0000.0000.0000.0000.000
81G61GLU-1-1.016-0.84762.1080.0080.0080.0000.0000.0000.000
82G62ALA00.044-0.13863.035-0.001-0.0010.0000.0000.0000.000
83G62ALA0-0.1090.09863.1520.0000.0000.0000.0000.0000.000
84G63GLU00.062-0.11864.8530.0000.0000.0000.0000.0000.000
85G63GLU-1-0.960-0.82065.5540.0120.0120.0000.0000.0000.000
86G64ALA00.047-0.13866.3390.0000.0000.0000.0000.0000.000
87G64ALA0-0.0290.14566.4380.0000.0000.0000.0000.0000.000
88G65LYS00.059-0.08267.752-0.001-0.0010.0000.0000.0000.000
89G65LYS10.8781.07668.330-0.007-0.0070.0000.0000.0000.000
90G66ALA00.109-0.11969.288-0.001-0.0010.0000.0000.0000.000
91G66ALA0-0.0450.14169.6880.0000.0000.0000.0000.0000.000
92G67LYS00.118-0.09570.9050.0000.0000.0000.0000.0000.000
93G67LYS10.7901.02868.926-0.011-0.0110.0000.0000.0000.000
94G68ALA00.072-0.12772.1080.0000.0000.0000.0000.0000.000
95G68ALA0-0.0660.12472.2370.0000.0000.0000.0000.0000.000
96G69LEU00.011-0.13473.659-0.001-0.0010.0000.0000.0000.000
97G69LEU0-0.1340.08572.7480.0000.0000.0000.0000.0000.000
98G70GLU00.084-0.14375.3100.0000.0000.0000.0000.0000.000
99G70GLU-1-0.839-0.77875.3540.0090.0090.0000.0000.0000.000
100G71ALA00.015-0.08076.8240.0000.0000.0000.0000.0000.000
101G71ALA0-0.0440.12376.9130.0000.0000.0000.0000.0000.000
102G72GLN00.072-0.06978.3510.0000.0000.0000.0000.0000.000
103G72GLN0-0.1140.06376.3580.0000.0000.0000.0000.0000.000
104G73TYR00.062-0.11079.9720.0000.0000.0000.0000.0000.000
105G73TYR0-0.0970.09178.5290.0000.0000.0000.0000.0000.000
106G74ARG00.160-0.07881.2860.0000.0000.0000.0000.0000.000
107G74ARG10.7530.98077.074-0.008-0.0080.0000.0000.0000.000
108G75GLU00.064-0.09183.0040.0000.0000.0000.0000.0000.000
109G75GLU-1-0.942-0.82783.4610.0050.0050.0000.0000.0000.000
110G76ARG00.092-0.06184.2560.0000.0000.0000.0000.0000.000
111G76ARG10.7601.00580.331-0.006-0.0060.0000.0000.0000.000
112G77GLU00.104-0.10485.8410.0000.0000.0000.0000.0000.000
113G77GLU-1-0.989-0.84585.8430.0070.0070.0000.0000.0000.000
114G78ARG00.090-0.03987.6020.0000.0000.0000.0000.0000.000
115G78ARG10.7250.97487.989-0.005-0.0050.0000.0000.0000.000
116G79ALA00.089-0.12888.9200.0000.0000.0000.0000.0000.000
117G79ALA0-0.0610.13089.1070.0000.0000.0000.0000.0000.000
118G80GLU00.020-0.13990.5570.0000.0000.0000.0000.0000.000
119G80GLU-1-0.993-0.84788.6270.0050.0050.0000.0000.0000.000
120G81THR0-0.123-0.13391.6280.0000.0000.0000.0000.0000.000
121G81THR0-0.0410.05191.0530.0000.0000.0000.0000.0000.000
122G82GLU00.095-0.10293.4590.0000.0000.0000.0000.0000.000
123G82GLU-1-0.894-0.79393.6860.0050.0050.0000.0000.0000.000
124G83ALA00.144-0.09094.8710.0000.0000.0000.0000.0000.000
125G83ALA0-0.0640.12195.0070.0000.0000.0000.0000.0000.000
126G84LEU00.061-0.12495.8620.0000.0000.0000.0000.0000.000
127G84LEU0-0.0900.10795.0190.0000.0000.0000.0000.0000.000
128G85LEU00.039-0.12197.4490.0000.0000.0000.0000.0000.000
129G85LEU0-0.0690.10496.8390.0000.0000.0000.0000.0000.000
130G86ALA00.064-0.12299.0950.0000.0000.0000.0000.0000.000
131G86ALA0-0.0120.12699.5640.0000.0000.0000.0000.0000.000
132G87ARG00.083-0.071100.3770.0000.0000.0000.0000.0000.000
133G87ARG10.8821.06199.384-0.004-0.0040.0000.0000.0000.000
134G88TYR00.076-0.091101.7740.0000.0000.0000.0000.0000.000
135G88TYR0-0.1090.07399.3430.0000.0000.0000.0000.0000.000
136G89ARG00.016-0.114103.6630.0000.0000.0000.0000.0000.000
137G89ARG10.9461.065101.520-0.004-0.0040.0000.0000.0000.000
138G90GLU00.132-0.087105.3440.0000.0000.0000.0000.0000.000
139G90GLU-1-1.025-0.822105.1370.0030.0030.0000.0000.0000.000
140G91ARG00.072-0.098106.2660.0000.0000.0000.0000.0000.000
141G91ARG10.7100.955104.996-0.004-0.0040.0000.0000.0000.000
142G92ALA00.088-0.092107.5020.0000.0000.0000.0000.0000.000
143G92ALA0-0.1040.088107.3000.0000.0000.0000.0000.0000.000
144G93GLU00.048-0.123109.0410.0000.0000.0000.0000.0000.000
145G93GLU-1-0.984-0.842109.8950.0040.0040.0000.0000.0000.000
146G94ALA00.080-0.137111.0850.0000.0000.0000.0000.0000.000
147G94ALA0-0.0440.138111.1740.0000.0000.0000.0000.0000.000
148G95GLU00.008-0.151111.8960.0000.0000.0000.0000.0000.000
149G95GLU-1-0.868-0.758109.7020.0040.0040.0000.0000.0000.000
150G96ALA00.117-0.080113.3450.0000.0000.0000.0000.0000.000
151G96ALA0-0.1190.088113.6060.0000.0000.0000.0000.0000.000
152G97LYS00.040-0.142115.1120.0000.0000.0000.0000.0000.000
153G97LYS10.7981.019116.154-0.003-0.0030.0000.0000.0000.000
154G98ALA00.091-0.087116.2340.0000.0000.0000.0000.0000.000
155G98ALA0-0.0570.108115.8330.0000.0000.0000.0000.0000.000
156G99VAL0-0.029-0.137117.6160.0000.0000.0000.0000.0000.000
157G99VAL0-0.0550.123116.4300.0000.0000.0000.0000.0000.000
158G100ARG00.070-0.067119.0260.0000.0000.0000.0000.0000.000
159G100ARG10.8961.045116.067-0.004-0.0040.0000.0000.0000.000
160G101GLU00.122-0.112121.3770.0000.0000.0000.0000.0000.000
161G101GLU-1-0.914-0.780120.8500.0030.0030.0000.0000.0000.000
162G102LYS00.074-0.086122.2260.0000.0000.0000.0000.0000.000
163G102LYS10.8041.011118.200-0.003-0.0030.0000.0000.0000.000
164G103ALA00.086-0.077123.5780.0000.0000.0000.0000.0000.000
165G103ALA0-0.0870.097123.7440.0000.0000.0000.0000.0000.000
166G104MET00.043-0.087125.3720.0000.0000.0000.0000.0000.000
167G104MET0-0.1090.076125.5000.0000.0000.0000.0000.0000.000
168G105ALA00.121-0.072127.4900.0000.0000.0000.0000.0000.000
169G105ALA0-0.1100.076128.8020.0000.0000.0000.0000.0000.000
170G106ARG00.046-0.095128.9180.0000.0000.0000.0000.0000.000
171G106ARG10.7100.975128.590-0.003-0.0030.0000.0000.0000.000
172G107LEU00.116-0.079129.9170.0000.0000.0000.0000.0000.000
173G107LEU0-0.0670.105128.2230.0000.0000.0000.0000.0000.000
174G108ASP00.139-0.106130.9850.0000.0000.0000.0000.0000.000
175G108ASP-1-0.970-0.833134.7660.0030.0030.0000.0000.0000.000
176G109GLU00.009-0.131133.9350.0000.0000.0000.0000.0000.000
177G109GLU-1-0.835-0.768132.8670.0030.0030.0000.0000.0000.000
178G110ALA00.134-0.064131.0040.0000.0000.0000.0000.0000.000
179G110ALA0-0.0760.090130.3840.0000.0000.0000.0000.0000.000
180G111VAL00.050-0.132132.4260.0000.0000.0000.0000.0000.000
181G111VAL0-0.0870.110133.0650.0000.0000.0000.0000.0000.000
182G112ALA00.091-0.091134.7000.0000.0000.0000.0000.0000.000
183G112ALA0-0.1040.085137.1020.0000.0000.0000.0000.0000.000
184G113LEU00.076-0.106134.6590.0000.0000.0000.0000.0000.000
185G113LEU0-0.0940.102132.1840.0000.0000.0000.0000.0000.000
186G114VAL00.102-0.081134.5390.0000.0000.0000.0000.0000.000
187G114VAL0-0.1150.078132.4230.0000.0000.0000.0000.0000.000
188G115LEU00.126-0.061135.5110.0000.0000.0000.0000.0000.000
189G115LEU0-0.1040.072137.7950.0000.0000.0000.0000.0000.000
190G116LYS00.002-0.120138.9350.0000.0000.0000.0000.0000.000
191G116LYS10.8921.056139.343-0.003-0.0030.0000.0000.0000.000
192G117GLU00.081-0.097137.5790.0000.0000.0000.0000.0000.000
193G117GLU-1-1.004-0.851136.3160.0030.0030.0000.0000.0000.000
194G118VAL00.022-0.119139.0230.0000.0000.0000.0000.0000.000
195G118VAL0-0.1240.069137.2460.0000.0000.0000.0000.0000.000
196G119LEU00.061-0.076139.8900.0000.0000.0000.0000.0000.000
197G119LEU0-0.1260.061142.7190.0000.0000.0000.0000.0000.000
198G120PRO0-0.051-0.110141.7590.0000.0000.0000.0000.0000.000