Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: VQQ61

Calculation Name: 5GI4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GI4

Chain ID: A

ChEMBL ID:

UniProt ID: P0A9P6

Base Structure: X-ray

Registration Date: 2023-09-21

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

DOI:


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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2485827.00114
FMO2-HF: Nuclear repulsion 2399602.38775
FMO2-HF: Total energy -86224.613389
FMO2-MP2: Total energy -86478.235573


3D Structure
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:PRO)


Summations of interaction energy for fragment #1(A:218:PRO)
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.
-1.9662.1582.857-2.339-4.641-0.013
Interaction energy analysis for fragmet #1(A:218:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.022
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].
3A220ILE0-0.094-0.0382.3680.1762.1290.768-0.928-1.7920.001
4A221SER00.0820.0475.675-0.034-0.0340.0000.0000.0000.000
5A222GLN00.0090.0067.7830.3960.3960.0000.0000.0000.000
6A223SER0-0.0070.00211.1540.1170.1170.0000.0000.0000.000
7A224TYR0-0.086-0.08714.892-0.013-0.0130.0000.0000.0000.000
8A225TRP00.0730.04317.7880.0230.0230.0000.0000.0000.000
9A226THR0-0.024-0.04721.2220.0000.0000.0000.0000.0000.000
10A227VAL0-0.084-0.03924.3750.0130.0130.0000.0000.0000.000
11A228TRP0-0.011-0.01726.2810.0130.0130.0000.0000.0000.000
12A229GLY00.0000.00829.215-0.003-0.0030.0000.0000.0000.000
13A230MET00.0260.03628.1620.0030.0030.0000.0000.0000.000
14A231ARG10.9600.97528.9840.1230.1230.0000.0000.0000.000
15A232LYS10.8930.93923.1220.2400.2400.0000.0000.0000.000
16A233ASN00.0180.01824.841-0.012-0.0120.0000.0000.0000.000
17A234GLU-1-0.893-0.95426.117-0.134-0.1340.0000.0000.0000.000
18A235ALA00.0540.01724.576-0.001-0.0010.0000.0000.0000.000
19A236LEU0-0.028-0.01219.577-0.016-0.0160.0000.0000.0000.000
20A237VAL00.0110.00722.170-0.008-0.0080.0000.0000.0000.000
21A238ARG10.8360.91324.2720.1490.1490.0000.0000.0000.000
22A239PHE00.023-0.02519.2670.0000.0000.0000.0000.0000.000
23A240LEU0-0.066-0.01118.452-0.014-0.0140.0000.0000.0000.000
24A241GLU-1-0.749-0.85120.652-0.110-0.1100.0000.0000.0000.000
25A242ALA0-0.038-0.01521.4950.0150.0150.0000.0000.0000.000
26A243GLU-1-0.895-0.95315.550-0.363-0.3630.0000.0000.0000.000
27A244ASP-1-0.780-0.85117.979-0.116-0.1160.0000.0000.0000.000
28A245PHE0-0.026-0.01215.096-0.047-0.0470.0000.0000.0000.000
29A246ASP-1-0.865-0.90714.242-0.033-0.0330.0000.0000.0000.000
30A247ALA00.0250.01714.5870.0130.0130.0000.0000.0000.000
31A248ALA0-0.024-0.01613.811-0.058-0.0580.0000.0000.0000.000
32A249ILE0-0.027-0.00812.4700.0430.0430.0000.0000.0000.000
33A250ILE00.003-0.00614.788-0.052-0.0520.0000.0000.0000.000
34A251PHE00.013-0.00412.4270.0330.0330.0000.0000.0000.000
35A252VAL00.001-0.00617.600-0.004-0.0040.0000.0000.0000.000
36A253ARG10.8150.89821.0080.2400.2400.0000.0000.0000.000
37A254THR0-0.018-0.01923.2310.0080.0080.0000.0000.0000.000
38A255LYS10.9040.91925.5840.1200.1200.0000.0000.0000.000
39A256ASN00.0510.02626.8750.0020.0020.0000.0000.0000.000
40A257ALA00.0330.02525.5610.0050.0050.0000.0000.0000.000
41A258THR0-0.044-0.03222.938-0.005-0.0050.0000.0000.0000.000
42A259LEU0-0.011-0.01624.9930.0020.0020.0000.0000.0000.000
43A260GLU-1-0.986-0.97028.196-0.143-0.1430.0000.0000.0000.000
44A261VAL00.027-0.00322.9650.0020.0020.0000.0000.0000.000
45A262ALA0-0.0130.00225.3530.0010.0010.0000.0000.0000.000
46A263GLU-1-0.855-0.93826.334-0.089-0.0890.0000.0000.0000.000
47A264ALA0-0.033-0.01327.4500.0060.0060.0000.0000.0000.000
48A265LEU0-0.038-0.02622.0270.0000.0000.0000.0000.0000.000
49A266GLU-1-0.791-0.87726.261-0.091-0.0910.0000.0000.0000.000
50A267ARG10.9561.00228.7320.1090.1090.0000.0000.0000.000
51A268ASN0-0.144-0.08527.7910.0060.0060.0000.0000.0000.000
52A269GLY0-0.001-0.00428.229-0.003-0.0030.0000.0000.0000.000
53A270TYR0-0.042-0.02523.0090.0010.0010.0000.0000.0000.000
54A271ASN00.0130.02224.3200.0090.0090.0000.0000.0000.000
55A272SER0-0.065-0.05422.884-0.016-0.0160.0000.0000.0000.000
56A273ALA00.0390.01622.9280.0130.0130.0000.0000.0000.000
57A274ALA0-0.009-0.00122.725-0.016-0.0160.0000.0000.0000.000
58A275LEU00.0460.01218.9130.0120.0120.0000.0000.0000.000
59A276ASN00.029-0.02022.011-0.013-0.0130.0000.0000.0000.000
60A277GLY0-0.009-0.02724.5790.0060.0060.0000.0000.0000.000
61A278ASP-1-0.861-0.91126.187-0.098-0.0980.0000.0000.0000.000
62A279MET0-0.0130.02225.1250.0030.0030.0000.0000.0000.000
63A280ASN0-0.0230.01325.707-0.005-0.0050.0000.0000.0000.000
64A281GLN00.012-0.00822.845-0.005-0.0050.0000.0000.0000.000
65A282ALA00.0680.01726.088-0.002-0.0020.0000.0000.0000.000
66A283LEU00.0290.01927.1960.0000.0000.0000.0000.0000.000
67A284ARG10.8620.90920.2710.1080.1080.0000.0000.0000.000
68A285GLU-1-0.831-0.89722.387-0.044-0.0440.0000.0000.0000.000
69A286GLN0-0.0090.00123.2440.0040.0040.0000.0000.0000.000
70A287THR0-0.041-0.03222.1220.0020.0020.0000.0000.0000.000
71A288LEU00.0270.00217.454-0.006-0.0060.0000.0000.0000.000
72A289GLU-1-0.805-0.86919.7960.0050.0050.0000.0000.0000.000
73A290ARG10.8740.94621.9170.0720.0720.0000.0000.0000.000
74A291LEU0-0.023-0.00416.188-0.002-0.0020.0000.0000.0000.000
75A292LYS10.8130.88216.826-0.018-0.0180.0000.0000.0000.000
76A293ASP-1-0.830-0.90018.758-0.010-0.0100.0000.0000.0000.000
77A294GLY00.0200.01521.0880.0070.0070.0000.0000.0000.000
78A295ARG10.7680.85822.1260.0210.0210.0000.0000.0000.000
79A296LEU0-0.064-0.02522.043-0.004-0.0040.0000.0000.0000.000
80A297ASP-1-0.756-0.86019.552-0.091-0.0910.0000.0000.0000.000
81A298ILE0-0.028-0.02118.285-0.029-0.0290.0000.0000.0000.000
82A299LEU00.0040.01517.6090.0220.0220.0000.0000.0000.000
83A300ILE00.0210.03018.268-0.036-0.0360.0000.0000.0000.000
84A301ALA00.0070.01217.4880.0270.0270.0000.0000.0000.000
85A302THR00.006-0.00219.533-0.008-0.0080.0000.0000.0000.000
86A303ASP-1-0.781-0.87916.850-0.337-0.3370.0000.0000.0000.000
87A304VAL0-0.022-0.01518.5360.0070.0070.0000.0000.0000.000
88A305ALA0-0.037-0.01020.2660.0060.0060.0000.0000.0000.000
89A306ALA00.0630.04016.0460.0110.0110.0000.0000.0000.000
90A307ARG10.9160.97615.5890.1680.1680.0000.0000.0000.000
91A308GLY0-0.035-0.00614.923-0.009-0.0090.0000.0000.0000.000
92A309LEU00.0150.0259.668-0.019-0.0190.0000.0000.0000.000
93A310ASP-1-0.892-0.99010.257-0.107-0.1070.0000.0000.0000.000
94A311VAL0-0.070-0.02912.3820.0390.0390.0000.0000.0000.000
95A312GLU-1-0.918-0.9478.9500.1710.1710.0000.0000.0000.000
96A313ARG10.8570.89211.8080.1160.1160.0000.0000.0000.000
97A314ILE0-0.048-0.01710.487-0.014-0.0140.0000.0000.0000.000
98A315SER00.0460.0409.538-0.074-0.0740.0000.0000.0000.000
99A316LEU0-0.035-0.01010.293-0.114-0.1140.0000.0000.0000.000
100A317VAL00.0090.0149.1080.0820.0820.0000.0000.0000.000
101A318VAL00.0230.00411.894-0.041-0.0410.0000.0000.0000.000
102A319ASN0-0.018-0.00812.7200.0870.0870.0000.0000.0000.000
103A320TYR00.0850.04616.2010.0160.0160.0000.0000.0000.000
104A321ASP-1-0.836-0.91819.745-0.209-0.2090.0000.0000.0000.000
105A322ILE00.0050.01818.764-0.030-0.0300.0000.0000.0000.000
106A323PRO00.0110.00015.4360.0380.0380.0000.0000.0000.000
107A324MET0-0.026-0.01918.6950.0090.0090.0000.0000.0000.000
108A325ASP-1-0.861-0.93117.274-0.323-0.3230.0000.0000.0000.000
109A326SER00.0160.00213.550-0.025-0.0250.0000.0000.0000.000
110A327GLU-1-0.829-0.89413.112-0.392-0.3920.0000.0000.0000.000
111A328SER0-0.021-0.01012.835-0.053-0.0530.0000.0000.0000.000
112A329TYR0-0.021-0.04410.6750.0410.0410.0000.0000.0000.000
113A330VAL00.0320.0077.523-0.101-0.1010.0000.0000.0000.000
114A331HIS0-0.054-0.0338.672-0.152-0.1520.0000.0000.0000.000
115A332ARG10.7260.84210.0190.3810.3810.0000.0000.0000.000
116A333ILE0-0.001-0.0066.2570.0310.0310.0000.0000.0000.000
117A334GLY00.0230.0125.296-0.177-0.1770.0000.0000.0000.000
118A335ARG10.7710.8686.2100.5780.5780.0000.0000.0000.000
119A336THR0-0.015-0.0216.1680.1480.1480.0000.0000.0000.000
120A337GLY00.0140.0132.942-0.920-0.5750.103-0.142-0.3060.000
121A338ARG00.0220.0282.458-1.345-0.1251.957-1.138-2.038-0.014
122A339ALA00.027-0.0084.7120.1740.205-0.001-0.004-0.0270.000
123A340GLY0-0.040-0.0173.165-0.0060.3180.032-0.092-0.2640.000
124A341ARG10.9160.9724.187-0.557-0.433-0.001-0.029-0.0940.000
125A342ALA00.0100.0134.711-0.453-0.326-0.001-0.006-0.1200.000
126A343GLY00.0080.0026.3850.1230.1230.0000.0000.0000.000
127A344ARG10.8600.9387.4580.1610.1610.0000.0000.0000.000
128A345ALA00.012-0.0038.9530.0450.0450.0000.0000.0000.000
129A346LEU00.0050.01410.6730.0250.0250.0000.0000.0000.000
130A347LEU0-0.048-0.03014.4030.0250.0250.0000.0000.0000.000
131A348PHE0-0.0050.00516.5640.0300.0300.0000.0000.0000.000
132A349VAL0-0.006-0.00720.0390.0000.0000.0000.0000.0000.000
133A350GLU-1-0.772-0.86222.500-0.170-0.1700.0000.0000.0000.000
134A351ASN00.0460.01126.093-0.014-0.0140.0000.0000.0000.000
135A352ARG10.8270.89028.5320.1750.1750.0000.0000.0000.000
136A353GLU-1-0.878-0.95124.333-0.239-0.2390.0000.0000.0000.000
137A354ARG10.9690.97724.2000.2240.2240.0000.0000.0000.000
138A355ARG10.9580.98323.9380.1790.1790.0000.0000.0000.000
139A356LEU00.0010.00121.919-0.007-0.0070.0000.0000.0000.000
140A357LEU00.0950.05618.184-0.019-0.0190.0000.0000.0000.000
141A358ARG10.8900.92919.2780.2710.2710.0000.0000.0000.000
142A359ASN0-0.062-0.03520.4200.0010.0010.0000.0000.0000.000
143A360ILE00.0120.02014.734-0.003-0.0030.0000.0000.0000.000
144A361GLU-1-0.760-0.86815.782-0.436-0.4360.0000.0000.0000.000
145A362ARG10.8470.90716.6130.2430.2430.0000.0000.0000.000
146A363THR0-0.034-0.02515.9850.0080.0080.0000.0000.0000.000
147A364MET00.0050.0189.5170.0320.0320.0000.0000.0000.000
148A365LYS10.8740.94712.5640.4590.4590.0000.0000.0000.000
149A366LEU0-0.035-0.01410.6000.0360.0360.0000.0000.0000.000
150A367THR00.0010.00614.5010.0250.0250.0000.0000.0000.000
151A368ILE0-0.019-0.01213.536-0.072-0.0720.0000.0000.0000.000
152A369PRO0-0.017-0.00914.5100.0740.0740.0000.0000.0000.000
153A370GLU-1-0.747-0.80817.494-0.300-0.3000.0000.0000.0000.000
154A371VAL0-0.032-0.01717.9260.0050.0050.0000.0000.0000.000
155A372GLU-1-0.901-0.95320.896-0.187-0.1870.0000.0000.0000.000
156A373LEU0-0.050-0.02322.790-0.017-0.0170.0000.0000.0000.000
157A374PRO00.0170.00722.0630.0160.0160.0000.0000.0000.000
158A375ASN00.0640.03524.8650.0090.0090.0000.0000.0000.000
159A376ALA00.0480.01428.5500.0010.0010.0000.0000.0000.000
160A377GLU-1-0.925-0.95831.277-0.090-0.0900.0000.0000.0000.000
161A378LEU00.0110.00323.6320.0060.0060.0000.0000.0000.000
162A379LEU0-0.011-0.00226.9040.0030.0030.0000.0000.0000.000
163A380GLY00.0360.01128.5780.0060.0060.0000.0000.0000.000
164A381LYS10.8680.92426.6750.0860.0860.0000.0000.0000.000
165A382ARG10.7840.86921.4830.1440.1440.0000.0000.0000.000
166A383ARG10.7660.85327.6120.1080.1080.0000.0000.0000.000
167A384LEU00.0200.00630.2490.0070.0070.0000.0000.0000.000
168A385GLU-1-0.874-0.91926.673-0.070-0.0700.0000.0000.0000.000
169A386LYS10.8610.91522.7980.1000.1000.0000.0000.0000.000
170A387PHE0-0.0060.00529.2670.0070.0070.0000.0000.0000.000
171A388ALA00.0260.00632.9810.0060.0060.0000.0000.0000.000
172A389ALA00.0250.02030.1200.0060.0060.0000.0000.0000.000
173A390LYS10.9390.96531.4490.0410.0410.0000.0000.0000.000
174A391VAL0-0.024-0.01733.7910.0040.0040.0000.0000.0000.000
175A392GLN0-0.043-0.03234.5540.0000.0000.0000.0000.0000.000
176A393GLN00.0120.00432.150-0.001-0.0010.0000.0000.0000.000
177A394GLN0-0.034-0.01536.3270.0020.0020.0000.0000.0000.000
178A395LEU0-0.048-0.01539.2810.0010.0010.0000.0000.0000.000
179A396GLU-1-0.912-0.93536.8100.0080.0080.0000.0000.0000.000
180A397SER0-0.064-0.02640.7100.0030.0030.0000.0000.0000.000
181A398SER00.003-0.01741.9740.0000.0000.0000.0000.0000.000
182A399ASP-1-0.867-0.92844.996-0.003-0.0030.0000.0000.0000.000
183A400LEU00.0210.02144.159-0.002-0.0020.0000.0000.0000.000
184A401ASP-1-0.831-0.91147.064-0.004-0.0040.0000.0000.0000.000
185A402GLN0-0.019-0.01850.4270.0000.0000.0000.0000.0000.000
186A403TYR0-0.019-0.01245.700-0.002-0.0020.0000.0000.0000.000
187A404ARG10.8430.90949.5620.0030.0030.0000.0000.0000.000
188A405ALA0-0.011-0.00751.471-0.001-0.0010.0000.0000.0000.000
189A406LEU0-0.040-0.03051.3140.0000.0000.0000.0000.0000.000
190A407LEU00.0190.02049.582-0.001-0.0010.0000.0000.0000.000
191A408SER0-0.015-0.01453.659-0.001-0.0010.0000.0000.0000.000
192A409LYS10.9030.96156.6040.0080.0080.0000.0000.0000.000
193A410ILE00.0140.02751.6800.0000.0000.0000.0000.0000.000
194A411GLN0-0.063-0.02655.9910.0000.0000.0000.0000.0000.000
195A420ASP-1-0.798-0.87754.308-0.021-0.0210.0000.0000.0000.000
196A421LEU0-0.023-0.02650.359-0.001-0.0010.0000.0000.0000.000
197A422GLU-1-0.911-0.93849.041-0.026-0.0260.0000.0000.0000.000
198A423THR0-0.027-0.05049.506-0.003-0.0030.0000.0000.0000.000
199A424LEU0-0.030-0.01450.224-0.002-0.0020.0000.0000.0000.000
200A425ALA00.016-0.00346.639-0.001-0.0010.0000.0000.0000.000
201A426ALA00.0210.02645.511-0.002-0.0020.0000.0000.0000.000
202A427ALA0-0.018-0.01345.104-0.003-0.0030.0000.0000.0000.000
203A428LEU00.015-0.00745.513-0.001-0.0010.0000.0000.0000.000
204A429LEU0-0.0010.01139.162-0.001-0.0010.0000.0000.0000.000
205A430LYS10.9220.95240.8700.0440.0440.0000.0000.0000.000
206A431MET0-0.045-0.02741.306-0.002-0.0020.0000.0000.0000.000
207A432ALA0-0.0110.00040.0900.0000.0000.0000.0000.0000.000
208A433GLN0-0.040-0.00336.686-0.002-0.0020.0000.0000.0000.000
209A434GLY0-0.0040.00535.358-0.003-0.0030.0000.0000.0000.000
210A435GLU-1-0.893-0.95633.441-0.063-0.0630.0000.0000.0000.000
211A436ARG10.7730.88726.1310.1050.1050.0000.0000.0000.000
212A437THR0-0.028-0.01032.7690.0050.0050.0000.0000.0000.000
213A438LEU00.0690.01833.850-0.006-0.0060.0000.0000.0000.000
214A439ILE0-0.052-0.00835.669-0.001-0.0010.0000.0000.0000.000
215A440VAL0-0.028-0.01432.169-0.001-0.0010.0000.0000.0000.000
216A441PRO0-0.0130.00435.3960.0020.0020.0000.0000.0000.000
217A442PRO00.026-0.00835.281-0.006-0.0060.0000.0000.0000.000
218A443ASP-1-0.916-0.93431.561-0.117-0.1170.0000.0000.0000.000