FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 9MGQ2

Calculation Name: 3FB2-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3FB2

Chain ID: A

ChEMBL ID:
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UniProt ID: Q13813

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptH
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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1817610.439513
FMO2-HF: Nuclear repulsion 1740365.405756
FMO2-HF: Total energy -77245.033757
FMO2-MP2: Total energy -77469.571528


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:1334:HIS)


Summations of interaction energy for fragment #1(A:1334:HIS)
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.
-17.251-11.5832.527-2.69-5.505-0.015
Interaction energy analysis for fragmet #1(A:1334:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.008
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].
3A1336HIS0-0.0020.0012.856-5.655-2.1920.170-1.173-2.4610.008
4A1337ASP-1-0.796-0.8934.110-0.555-0.2270.003-0.049-0.2810.000
5A1338SER0-0.034-0.0126.836-0.341-0.3410.0000.0000.0000.000
6A1339HIS00.008-0.0222.457-10.524-8.6472.354-1.468-2.763-0.023
7A1340ASP-1-0.858-0.9216.953-0.424-0.4240.0000.0000.0000.000
8A1341LEU0-0.031-0.0119.5180.0680.0680.0000.0000.0000.000
9A1342GLN0-0.022-0.0168.169-0.385-0.3850.0000.0000.0000.000
10A1343ARG10.9550.97510.7710.8820.8820.0000.0000.0000.000
11A1344PHE00.0100.01812.3750.1180.1180.0000.0000.0000.000
12A1345LEU0-0.011-0.02814.8140.0760.0760.0000.0000.0000.000
13A1346SER0-0.0020.00714.5770.0340.0340.0000.0000.0000.000
14A1347ASP-1-0.866-0.92716.336-0.606-0.6060.0000.0000.0000.000
15A1348PHE0-0.021-0.02218.2890.0610.0610.0000.0000.0000.000
16A1349ARG10.9170.95919.7010.4110.4110.0000.0000.0000.000
17A1350ASP-1-0.849-0.92819.148-0.561-0.5610.0000.0000.0000.000
18A1351LEU0-0.046-0.02721.9170.0440.0440.0000.0000.0000.000
19A1352MET0-0.044-0.01724.0680.0360.0360.0000.0000.0000.000
20A1353SER0-0.036-0.02024.3370.0280.0280.0000.0000.0000.000
21A1354TRP0-0.0180.00826.4300.0210.0210.0000.0000.0000.000
22A1355ILE00.0230.00328.2920.0200.0200.0000.0000.0000.000
23A1356ASN0-0.020-0.00828.8100.0290.0290.0000.0000.0000.000
24A1357GLY00.0070.00930.9560.0150.0150.0000.0000.0000.000
25A1358ILE00.0160.00932.5300.0160.0160.0000.0000.0000.000
26A1359ARG10.9690.99134.1350.1620.1620.0000.0000.0000.000
27A1360GLY00.0110.00535.5350.0100.0100.0000.0000.0000.000
28A1361LEU0-0.0520.00936.9570.0110.0110.0000.0000.0000.000
29A1362VAL0-0.047-0.05138.5890.0090.0090.0000.0000.0000.000
30A1363SER0-0.125-0.07040.1670.0080.0080.0000.0000.0000.000
31A1364SER0-0.032-0.00641.8820.0070.0070.0000.0000.0000.000
32A1365ASP-1-0.826-0.92044.459-0.098-0.0980.0000.0000.0000.000
33A1366GLU-1-1.030-1.00647.484-0.097-0.0970.0000.0000.0000.000
34A1367LEU00.0070.00049.6180.0000.0000.0000.0000.0000.000
35A1368ALA0-0.052-0.02252.6140.0000.0000.0000.0000.0000.000
36A1369LYS10.8950.94554.9380.0790.0790.0000.0000.0000.000
37A1370ASP-1-0.834-0.92457.622-0.068-0.0680.0000.0000.0000.000
38A1371VAL00.0420.02058.2700.0000.0000.0000.0000.0000.000
39A1372THR00.0290.01956.363-0.001-0.0010.0000.0000.0000.000
40A1373GLY0-0.003-0.01254.367-0.003-0.0030.0000.0000.0000.000
41A1374ALA00.013-0.01652.931-0.004-0.0040.0000.0000.0000.000
42A1375GLU-1-0.929-0.95852.577-0.072-0.0720.0000.0000.0000.000
43A1376ALA00.0270.01950.713-0.003-0.0030.0000.0000.0000.000
44A1377LEU0-0.065-0.03648.498-0.006-0.0060.0000.0000.0000.000
45A1378LEU00.0140.01047.365-0.006-0.0060.0000.0000.0000.000
46A1379GLU-1-0.956-0.96647.024-0.097-0.0970.0000.0000.0000.000
47A1380ARG10.9620.97544.0750.1120.1120.0000.0000.0000.000
48A1381HIS0-0.046-0.02542.366-0.011-0.0110.0000.0000.0000.000
49A1382GLN00.0500.00342.361-0.002-0.0020.0000.0000.0000.000
50A1383GLU-1-0.895-0.94040.847-0.127-0.1270.0000.0000.0000.000
51A1384HIS10.8890.93738.3150.1340.1340.0000.0000.0000.000
52A1385ARG10.8000.88237.6180.1070.1070.0000.0000.0000.000
53A1386THR00.015-0.00137.315-0.002-0.0020.0000.0000.0000.000
54A1387GLU-1-0.960-0.97233.300-0.205-0.2050.0000.0000.0000.000
55A1388ILE0-0.004-0.02233.185-0.015-0.0150.0000.0000.0000.000
56A1389ASP-1-0.854-0.93632.740-0.135-0.1350.0000.0000.0000.000
57A1390ALA0-0.064-0.02332.127-0.001-0.0010.0000.0000.0000.000
58A1391ARG10.8870.94427.7380.2120.2120.0000.0000.0000.000
59A1392ALA0-0.0060.01127.995-0.011-0.0110.0000.0000.0000.000
60A1393GLY00.0260.00127.4060.0010.0010.0000.0000.0000.000
61A1394THR0-0.003-0.00423.044-0.001-0.0010.0000.0000.0000.000
62A1395PHE00.0280.00523.338-0.019-0.0190.0000.0000.0000.000
63A1396GLN0-0.0140.00024.3660.0010.0010.0000.0000.0000.000
64A1397ALA0-0.0140.00520.5710.0120.0120.0000.0000.0000.000
65A1398PHE0-0.0040.00018.704-0.002-0.0020.0000.0000.0000.000
66A1399GLU-1-0.873-0.94520.231-0.134-0.1340.0000.0000.0000.000
67A1400GLN0-0.0080.00219.7450.0200.0200.0000.0000.0000.000
68A1401PHE0-0.061-0.03312.1630.0320.0320.0000.0000.0000.000
69A1402GLY00.0690.01316.9470.0250.0250.0000.0000.0000.000
70A1403GLN0-0.024-0.00618.7790.0520.0520.0000.0000.0000.000
71A1404GLN0-0.016-0.01015.5600.0610.0610.0000.0000.0000.000
72A1405LEU0-0.0190.00912.4290.0720.0720.0000.0000.0000.000
73A1406LEU0-0.008-0.01115.0250.0510.0510.0000.0000.0000.000
74A1407ALA0-0.040-0.01317.7110.0300.0300.0000.0000.0000.000
75A1408HIS0-0.107-0.05512.7430.0630.0630.0000.0000.0000.000
76A1409GLY0-0.0100.00213.2590.0590.0590.0000.0000.0000.000
77A1410HIS00.0300.01810.2030.0430.0430.0000.0000.0000.000
78A1411TYR00.0390.0188.247-0.052-0.0520.0000.0000.0000.000
79A1412ALA00.0050.01213.217-0.017-0.0170.0000.0000.0000.000
80A1413SER0-0.009-0.03615.354-0.035-0.0350.0000.0000.0000.000
81A1414PRO0-0.035-0.01217.620-0.017-0.0170.0000.0000.0000.000
82A1415GLU-1-0.873-0.95118.332-0.143-0.1430.0000.0000.0000.000
83A1416ILE00.0030.00114.812-0.031-0.0310.0000.0000.0000.000
84A1417LYS10.9950.98519.3790.0420.0420.0000.0000.0000.000
85A1418GLN0-0.0080.00122.500-0.019-0.0190.0000.0000.0000.000
86A1419LYS10.8340.92620.2060.2620.2620.0000.0000.0000.000
87A1420LEU00.0060.00821.785-0.009-0.0090.0000.0000.0000.000
88A1421ASP-1-0.854-0.91224.559-0.103-0.1030.0000.0000.0000.000
89A1422ILE0-0.073-0.03825.438-0.001-0.0010.0000.0000.0000.000
90A1423LEU00.007-0.00523.823-0.002-0.0020.0000.0000.0000.000
91A1424ASP-1-0.901-0.94527.253-0.132-0.1320.0000.0000.0000.000
92A1425GLN0-0.061-0.02629.7820.0110.0110.0000.0000.0000.000
93A1426GLU-1-0.932-0.98429.163-0.182-0.1820.0000.0000.0000.000
94A1427ARG10.9080.95828.0720.1650.1650.0000.0000.0000.000
95A1428ALA0-0.0070.00532.0430.0080.0080.0000.0000.0000.000
96A1429ASP-1-0.904-0.96735.052-0.116-0.1160.0000.0000.0000.000
97A1430LEU0-0.031-0.00832.8650.0030.0030.0000.0000.0000.000
98A1431GLU-1-0.798-0.84336.048-0.108-0.1080.0000.0000.0000.000
99A1432LYS10.9300.95037.9520.1000.1000.0000.0000.0000.000
100A1433ALA0-0.021-0.00138.8630.0050.0050.0000.0000.0000.000
101A1434TRP0-0.003-0.00639.2700.0050.0050.0000.0000.0000.000
102A1435VAL00.0120.00541.1840.0050.0050.0000.0000.0000.000
103A1436GLN0-0.032-0.01343.8990.0060.0060.0000.0000.0000.000
104A1437ARG10.9180.96643.8420.1080.1080.0000.0000.0000.000
105A1438ARG10.8750.93745.4640.0850.0850.0000.0000.0000.000
106A1439MET00.0130.00747.0610.0030.0030.0000.0000.0000.000
107A1440MET00.0120.00549.1110.0040.0040.0000.0000.0000.000
108A1441LEU0-0.028-0.02446.9460.0020.0020.0000.0000.0000.000
109A1442ASP-1-0.845-0.91450.845-0.074-0.0740.0000.0000.0000.000
110A1443GLN00.0120.00153.0420.0010.0010.0000.0000.0000.000
111A1444CYS0-0.0350.01453.6590.0020.0020.0000.0000.0000.000
112A1445LEU00.0730.01854.8920.0020.0020.0000.0000.0000.000
113A1446GLU-1-0.892-0.95856.654-0.057-0.0570.0000.0000.0000.000
114A1447LEU0-0.047-0.01858.7300.0020.0020.0000.0000.0000.000
115A1448GLN0-0.009-0.01057.7980.0030.0030.0000.0000.0000.000
116A1449LEU0-0.008-0.02259.8200.0010.0010.0000.0000.0000.000
117A1450PHE00.0280.01962.6200.0020.0020.0000.0000.0000.000
118A1451HIS00.0310.00562.9070.0030.0030.0000.0000.0000.000
119A1452ARG10.9691.00263.0120.0560.0560.0000.0000.0000.000
120A1453ASP-1-0.923-0.95866.577-0.046-0.0460.0000.0000.0000.000
121A1454CYS0-0.100-0.05868.5490.0020.0020.0000.0000.0000.000
122A1455GLU-1-0.905-0.94967.474-0.052-0.0520.0000.0000.0000.000
123A1456GLN0-0.081-0.03569.0550.0000.0000.0000.0000.0000.000
124A1457ALA0-0.002-0.01572.5320.0010.0010.0000.0000.0000.000
125A1458GLU-1-0.897-0.94573.010-0.042-0.0420.0000.0000.0000.000
126A1459ASN0-0.014-0.01872.3250.0010.0010.0000.0000.0000.000
127A1460TRP0-0.031-0.01076.1680.0010.0010.0000.0000.0000.000
128A1461MET0-0.020-0.00577.1900.0020.0020.0000.0000.0000.000
129A1462ALA00.0350.01078.9510.0010.0010.0000.0000.0000.000
130A1463ALA0-0.047-0.01880.7540.0010.0010.0000.0000.0000.000
131A1464ARG10.9370.90681.6470.0350.0350.0000.0000.0000.000
132A1465GLU-1-0.865-0.91882.213-0.034-0.0340.0000.0000.0000.000
133A1466ALA0-0.0220.01584.9420.0000.0000.0000.0000.0000.000
134A1467PHE0-0.108-0.00285.5050.0010.0010.0000.0000.0000.000
135A1468LEU00.0010.00388.5580.0010.0010.0000.0000.0000.000
136A1488GLU-1-0.953-0.98692.962-0.024-0.0240.0000.0000.0000.000
137A1489ASP-1-0.933-0.96588.215-0.028-0.0280.0000.0000.0000.000
138A1490PHE0-0.014-0.02587.614-0.001-0.0010.0000.0000.0000.000
139A1491ASP-1-0.889-0.95287.341-0.026-0.0260.0000.0000.0000.000
140A1492LYS10.9970.98185.2630.0260.0260.0000.0000.0000.000
141A1493ALA0-0.012-0.00283.110-0.001-0.0010.0000.0000.0000.000
142A1494ILE0-0.022-0.00182.961-0.001-0.0010.0000.0000.0000.000
143A1495ASN0-0.029-0.02382.9850.0000.0000.0000.0000.0000.000
144A1496VAL00.0130.01578.510-0.001-0.0010.0000.0000.0000.000
145A1497GLN0-0.010-0.00476.320-0.001-0.0010.0000.0000.0000.000
146A1498GLU-1-0.855-0.93878.382-0.032-0.0320.0000.0000.0000.000
147A1499GLU-1-0.916-0.96375.616-0.035-0.0350.0000.0000.0000.000
148A1500LYS10.9210.96373.6930.0370.0370.0000.0000.0000.000
149A1501ILE0-0.0020.00773.493-0.001-0.0010.0000.0000.0000.000
150A1502ALA0-0.0090.00874.9750.0000.0000.0000.0000.0000.000
151A1503ALA0-0.012-0.00570.3590.0000.0000.0000.0000.0000.000
152A1504LEU00.012-0.00369.298-0.001-0.0010.0000.0000.0000.000
153A1505GLN0-0.034-0.02270.2580.0000.0000.0000.0000.0000.000
154A1506ALA00.0240.01469.9450.0000.0000.0000.0000.0000.000
155A1507PHE0-0.018-0.00962.189-0.001-0.0010.0000.0000.0000.000
156A1508ALA00.0610.01965.499-0.001-0.0010.0000.0000.0000.000
157A1509ASP-1-0.919-0.96866.434-0.039-0.0390.0000.0000.0000.000
158A1510GLN0-0.048-0.01761.410-0.002-0.0020.0000.0000.0000.000
159A1511LEU00.0290.02060.514-0.001-0.0010.0000.0000.0000.000
160A1512ILE0-0.041-0.02261.632-0.001-0.0010.0000.0000.0000.000
161A1513ALA0-0.051-0.02463.4160.0000.0000.0000.0000.0000.000
162A1514ALA0-0.0090.00658.6550.0000.0000.0000.0000.0000.000
163A1515GLY0-0.102-0.05658.052-0.002-0.0020.0000.0000.0000.000
164A1516HIS00.0310.02057.522-0.001-0.0010.0000.0000.0000.000
165A1517TYR00.0470.00855.0660.0010.0010.0000.0000.0000.000
166A1518ALA00.0180.00857.5870.0000.0000.0000.0000.0000.000
167A1519LYS10.9240.98260.6600.0510.0510.0000.0000.0000.000
168A1520GLY0-0.045-0.02163.2860.0020.0020.0000.0000.0000.000
169A1521ASP-1-0.843-0.93363.901-0.051-0.0510.0000.0000.0000.000
170A1522ILE0-0.031-0.00761.8620.0010.0010.0000.0000.0000.000
171A1523SER0-0.038-0.02965.9750.0020.0020.0000.0000.0000.000
172A1524SER00.001-0.00268.5320.0020.0020.0000.0000.0000.000
173A1525ARG11.0021.00267.5190.0500.0500.0000.0000.0000.000
174A1526ARG10.9340.98770.1720.0400.0400.0000.0000.0000.000
175A1527ASN0-0.035-0.02671.8550.0010.0010.0000.0000.0000.000
176A1528GLU-1-0.953-0.95873.461-0.041-0.0410.0000.0000.0000.000
177A1529VAL00.0350.01373.3430.0010.0010.0000.0000.0000.000
178A1530LEU0-0.011-0.01974.7630.0010.0010.0000.0000.0000.000
179A1531ASP-1-0.905-0.96777.635-0.032-0.0320.0000.0000.0000.000
180A1532ARG10.7930.89677.4900.0390.0390.0000.0000.0000.000
181A1533TRP00.0280.00679.3260.0000.0000.0000.0000.0000.000
182A1534ARG10.8460.93181.2010.0320.0320.0000.0000.0000.000
183A1535ARG10.9390.98280.4220.0340.0340.0000.0000.0000.000
184A1536LEU00.0270.02183.1280.0010.0010.0000.0000.0000.000
185A1537LYS10.8970.94284.1890.0290.0290.0000.0000.0000.000
186A1538ALA0-0.054-0.02186.6290.0010.0010.0000.0000.0000.000
187A1539GLN0-0.025-0.01088.8740.0000.0000.0000.0000.0000.000
188A1540MET0-0.0410.01485.4200.0010.0010.0000.0000.0000.000