FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: V5341

Calculation Name: 3SR9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SR9

Chain ID: A

ChEMBL ID:

UniProt ID: B0V2N1

Base Structure: X-ray

Registration Date: 2023-09-20

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 568
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12495249.034918
FMO2-HF: Nuclear repulsion 12263204.803551
FMO2-HF: Total energy -232044.231367
FMO2-MP2: Total energy -232712.316065


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:1326:MET)


Summations of interaction energy for fragment #1(A:1326:MET)
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.
-22.192-29.10326.549-7.454-12.183-0.014
Interaction energy analysis for fragmet #1(A:1326:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : 0.023
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].
3A1328SER00.009-0.0272.192-4.892-16.18223.744-5.696-6.7570.006
4A1329HIS10.8870.9412.622-5.602-5.1211.0910.400-1.972-0.001
5A1330PRO00.0290.0382.259-7.775-4.9241.572-2.069-2.354-0.020
6A1331PRO0-0.012-0.0212.6680.4941.0580.141-0.050-0.6550.001
7A1332ILE00.0080.0105.5170.4100.4100.0000.0000.0000.000
8A1333PRO00.0290.0199.059-0.018-0.0180.0000.0000.0000.000
9A1334ILE00.0290.00011.530-0.011-0.0110.0000.0000.0000.000
10A1335THR0-0.111-0.07314.9290.0520.0520.0000.0000.0000.000
11A1336ASP-1-0.816-0.88913.4410.0790.0790.0000.0000.0000.000
12A1337MET0-0.060-0.03014.087-0.037-0.0370.0000.0000.0000.000
13A1338ALA00.011-0.00915.083-0.011-0.0110.0000.0000.0000.000
14A1339GLU-1-0.781-0.88714.7230.0300.0300.0000.0000.0000.000
15A1340HIS00.0600.03510.2140.0900.0900.0000.0000.0000.000
16A1341MET0-0.046-0.02014.710-0.008-0.0080.0000.0000.0000.000
17A1342GLU-1-0.898-0.94116.787-0.052-0.0520.0000.0000.0000.000
18A1343ARG10.7980.87912.250-0.031-0.0310.0000.0000.0000.000
19A1344LEU0-0.103-0.04212.0230.0210.0210.0000.0000.0000.000
20A1345LYS10.9190.94916.1690.1270.1270.0000.0000.0000.000
21A1346ALA0-0.045-0.00819.7410.0070.0070.0000.0000.0000.000
22A1347ASN0-0.087-0.06120.8950.0050.0050.0000.0000.0000.000
23A1348ASP-1-0.876-0.93122.871-0.031-0.0310.0000.0000.0000.000
24A1349SER0-0.007-0.00319.556-0.010-0.0100.0000.0000.0000.000
25A1350LEU00.0650.05518.477-0.015-0.0150.0000.0000.0000.000
26A1351LYS10.8780.91614.278-0.216-0.2160.0000.0000.0000.000
27A1352LEU0-0.0060.00313.703-0.001-0.0010.0000.0000.0000.000
28A1353SER00.009-0.00214.555-0.047-0.0470.0000.0000.0000.000
29A1354GLN00.0340.01413.0090.0170.0170.0000.0000.0000.000
30A1355GLU-1-0.899-0.9239.030-0.428-0.4280.0000.0000.0000.000
31A1356TYR0-0.022-0.04610.439-0.133-0.1330.0000.0000.0000.000
32A1357GLU-1-0.938-0.96612.629-0.251-0.2510.0000.0000.0000.000
33A1358SER0-0.106-0.0478.1700.0470.0470.0000.0000.0000.000
34A1359ILE0-0.096-0.0408.038-0.199-0.1990.0000.0000.0000.000
35A1360ASP-1-0.812-0.9167.331-0.926-0.9260.0000.0000.0000.000
36A1361PRO0-0.087-0.0346.632-0.474-0.4740.0000.0000.0000.000
37A1362GLY00.0050.0148.230-0.138-0.1380.0000.0000.0000.000
38A1363GLN0-0.099-0.0589.1610.1380.1380.0000.0000.0000.000
39A1364GLN0-0.017-0.00312.4550.0310.0310.0000.0000.0000.000
40A1365PHE0-0.009-0.00212.9290.0040.0040.0000.0000.0000.000
41A1366THR0-0.007-0.01918.4600.0220.0220.0000.0000.0000.000
42A1367TRP00.0470.00819.561-0.028-0.0280.0000.0000.0000.000
43A1368GLU-1-0.864-0.94624.612-0.219-0.2190.0000.0000.0000.000
44A1369HIS0-0.063-0.04227.4320.0300.0300.0000.0000.0000.000
45A1370SER00.0450.03126.7410.0070.0070.0000.0000.0000.000
46A1371ASN00.0030.00528.7900.0170.0170.0000.0000.0000.000
47A1372LEU00.0330.03830.6680.0150.0150.0000.0000.0000.000
48A1373GLU-1-0.903-0.95833.728-0.129-0.1290.0000.0000.0000.000
49A1374ALA0-0.004-0.00636.6150.0030.0030.0000.0000.0000.000
50A1375ASN0-0.021-0.03832.2770.0090.0090.0000.0000.0000.000
51A1376LYS10.8600.94532.7730.1560.1560.0000.0000.0000.000
52A1377PRO00.0200.00833.772-0.006-0.0060.0000.0000.0000.000
53A1378LYS10.8670.94533.5230.1590.1590.0000.0000.0000.000
54A1379ASN0-0.0420.00329.628-0.023-0.0230.0000.0000.0000.000
55A1380ARG10.7480.86330.8090.1760.1760.0000.0000.0000.000
56A1381TYR0-0.026-0.02728.1630.0130.0130.0000.0000.0000.000
57A1382ALA00.0500.02328.707-0.012-0.0120.0000.0000.0000.000
58A1383ASN0-0.001-0.00425.1290.0040.0040.0000.0000.0000.000
59A1384VAL0-0.058-0.01923.366-0.025-0.0250.0000.0000.0000.000
60A1385ILE0-0.0140.01521.8570.0210.0210.0000.0000.0000.000
61A1386ALA00.003-0.00623.042-0.026-0.0260.0000.0000.0000.000
62A1387TYR0-0.026-0.01215.7870.0550.0550.0000.0000.0000.000
63A1388ASP-1-0.734-0.85521.489-0.265-0.2650.0000.0000.0000.000
64A1389HIS0-0.049-0.02516.1670.0770.0770.0000.0000.0000.000
65A1390SER0-0.006-0.01618.6320.0170.0170.0000.0000.0000.000
66A1391ARG10.7880.89920.7790.2310.2310.0000.0000.0000.000
67A1392VAL0-0.010-0.01224.1430.0100.0100.0000.0000.0000.000
68A1393ILE0-0.049-0.01626.6740.0100.0100.0000.0000.0000.000
69A1394LEU0-0.061-0.01729.5590.0070.0070.0000.0000.0000.000
70A1395GLN0-0.012-0.02133.0030.0080.0080.0000.0000.0000.000
71A1396PRO00.0200.02735.7260.0010.0010.0000.0000.0000.000
72A1397LEU0-0.005-0.00637.8020.0070.0070.0000.0000.0000.000
73A1398GLU-1-0.917-0.96441.159-0.090-0.0900.0000.0000.0000.000
74A1399GLY00.0150.00842.9250.0040.0040.0000.0000.0000.000
75A1400ILE0-0.049-0.02540.7780.0010.0010.0000.0000.0000.000
76A1401MET00.0060.02438.760-0.004-0.0040.0000.0000.0000.000
77A1402GLY00.0550.02035.3630.0000.0000.0000.0000.0000.000
78A1403SER0-0.048-0.03435.416-0.009-0.0090.0000.0000.0000.000
79A1404ASP-1-0.809-0.89432.179-0.177-0.1770.0000.0000.0000.000
80A1405TYR0-0.057-0.03827.778-0.011-0.0110.0000.0000.0000.000
81A1406ILE00.0410.00628.9990.0120.0120.0000.0000.0000.000
82A1407ASN0-0.025-0.00826.414-0.033-0.0330.0000.0000.0000.000
83A1408ALA00.003-0.00225.3070.0000.0000.0000.0000.0000.000
84A1409ASN0-0.0010.00620.4390.0140.0140.0000.0000.0000.000
85A1410TYR0-0.010-0.01720.4950.0060.0060.0000.0000.0000.000
86A1411VAL0-0.027-0.01715.919-0.046-0.0460.0000.0000.0000.000
87A1412ASP-1-0.793-0.87413.662-0.578-0.5780.0000.0000.0000.000
88A1413GLY00.005-0.00615.140-0.032-0.0320.0000.0000.0000.000
89A1414TYR0-0.018-0.0069.603-0.048-0.0480.0000.0000.0000.000
90A1415ARG10.8270.88010.5500.0940.0940.0000.0000.0000.000
91A1416ARG10.9130.96813.6810.3460.3460.0000.0000.0000.000
92A1417GLN00.0550.03415.747-0.070-0.0700.0000.0000.0000.000
93A1418ASN0-0.012-0.01117.5320.0120.0120.0000.0000.0000.000
94A1419ALA00.0260.01918.3650.0370.0370.0000.0000.0000.000
95A1420TYR0-0.078-0.06917.2510.0220.0220.0000.0000.0000.000
96A1421ILE00.0270.01321.329-0.016-0.0160.0000.0000.0000.000
97A1422ALA0-0.0230.00421.0550.0160.0160.0000.0000.0000.000
98A1423THR0-0.025-0.04523.0540.0060.0060.0000.0000.0000.000
99A1424GLN0-0.0040.00626.122-0.011-0.0110.0000.0000.0000.000
100A1425GLY00.001-0.02028.2690.0060.0060.0000.0000.0000.000
101A1426PRO00.0120.00331.4090.0030.0030.0000.0000.0000.000
102A1427LEU00.0410.02333.9750.0030.0030.0000.0000.0000.000
103A1428PRO00.0240.01636.6720.0000.0000.0000.0000.0000.000
104A1429GLU-1-0.884-0.94638.872-0.121-0.1210.0000.0000.0000.000
105A1430THR0-0.027-0.02534.531-0.002-0.0020.0000.0000.0000.000
106A1431PHE0-0.0060.00836.136-0.006-0.0060.0000.0000.0000.000
107A1432GLY00.0290.00337.727-0.002-0.0020.0000.0000.0000.000
108A1433ASP-1-0.809-0.89934.529-0.149-0.1490.0000.0000.0000.000
109A1434PHE00.0090.00230.410-0.007-0.0070.0000.0000.0000.000
110A1435TRP00.003-0.02033.675-0.007-0.0070.0000.0000.0000.000
111A1436ARG10.7970.88736.1910.1430.1430.0000.0000.0000.000
112A1437MET0-0.0040.02228.691-0.004-0.0040.0000.0000.0000.000
113A1438VAL00.0090.00231.733-0.002-0.0020.0000.0000.0000.000
114A1439TRP00.000-0.00232.7690.0010.0010.0000.0000.0000.000
115A1440GLU-1-0.855-0.95233.724-0.136-0.1360.0000.0000.0000.000
116A1441GLN00.0120.03027.946-0.010-0.0100.0000.0000.0000.000
117A1442ARG10.9070.95829.7840.1320.1320.0000.0000.0000.000
118A1443SER00.0040.01028.1910.0020.0020.0000.0000.0000.000
119A1444ALA00.0210.00830.1040.0110.0110.0000.0000.0000.000
120A1445THR0-0.022-0.03028.5510.0130.0130.0000.0000.0000.000
121A1446VAL0-0.035-0.01429.233-0.013-0.0130.0000.0000.0000.000
122A1447VAL0-0.016-0.01225.9400.0110.0110.0000.0000.0000.000
123A1448MET0-0.0400.00028.150-0.010-0.0100.0000.0000.0000.000
124A1449MET0-0.050-0.03124.7470.0130.0130.0000.0000.0000.000
125A1450THR0-0.001-0.01828.515-0.004-0.0040.0000.0000.0000.000
126A1451ARG10.8940.95631.4210.1370.1370.0000.0000.0000.000
127A1452LEU00.0020.00134.784-0.007-0.0070.0000.0000.0000.000
128A1453GLU-1-0.878-0.94037.141-0.107-0.1070.0000.0000.0000.000
129A1454GLU-1-0.751-0.83732.471-0.169-0.1690.0000.0000.0000.000
130A1455LYS10.9240.94836.7500.1060.1060.0000.0000.0000.000
131A1456SER0-0.0110.00138.8190.0020.0020.0000.0000.0000.000
132A1457ARG10.8890.95131.9330.1600.1600.0000.0000.0000.000
133A1458ILE00.0340.01437.041-0.005-0.0050.0000.0000.0000.000
134A1459LYS10.7970.90031.2930.1590.1590.0000.0000.0000.000
135A1460CYS0-0.033-0.00232.932-0.017-0.0170.0000.0000.0000.000
136A1461ASP-1-0.778-0.85935.015-0.128-0.1280.0000.0000.0000.000
137A1462GLN0-0.067-0.04937.426-0.006-0.0060.0000.0000.0000.000
138A1463TYR00.006-0.01332.7720.0060.0060.0000.0000.0000.000
139A1464TRP00.0310.00736.112-0.004-0.0040.0000.0000.0000.000
140A1465PRO00.0520.04440.9220.0020.0020.0000.0000.0000.000
141A1466ASN00.001-0.00944.034-0.003-0.0030.0000.0000.0000.000
142A1467ARG10.9690.97546.1980.0730.0730.0000.0000.0000.000
143A1468GLY00.0220.02348.0100.0000.0000.0000.0000.0000.000
144A1469THR00.011-0.00646.694-0.004-0.0040.0000.0000.0000.000
145A1470GLU-1-0.854-0.87845.028-0.091-0.0910.0000.0000.0000.000
146A1471THR0-0.0200.00444.945-0.002-0.0020.0000.0000.0000.000
147A1472TYR00.006-0.03141.025-0.002-0.0020.0000.0000.0000.000
148A1473GLY00.008-0.00141.848-0.004-0.0040.0000.0000.0000.000
149A1474PHE0-0.008-0.01241.5170.0040.0040.0000.0000.0000.000
150A1475ILE0-0.003-0.00838.8270.0030.0030.0000.0000.0000.000
151A1476GLN0-0.010-0.00742.2990.0000.0000.0000.0000.0000.000
152A1477VAL00.0240.00840.173-0.001-0.0010.0000.0000.0000.000
153A1478THR0-0.053-0.04542.8350.0030.0030.0000.0000.0000.000
154A1479LEU0-0.021-0.00141.938-0.003-0.0030.0000.0000.0000.000
155A1480LEU0-0.070-0.04742.4670.0050.0050.0000.0000.0000.000
156A1481ASP-1-0.887-0.95142.184-0.082-0.0820.0000.0000.0000.000
157A1482THR0-0.048-0.03341.590-0.007-0.0070.0000.0000.0000.000
158A1483MET00.0550.05939.6160.0030.0030.0000.0000.0000.000
159A1484GLU-1-0.963-0.99839.449-0.099-0.0990.0000.0000.0000.000
160A1485LEU0-0.039-0.00336.8020.0050.0050.0000.0000.0000.000
161A1486ALA0-0.0100.00738.384-0.003-0.0030.0000.0000.0000.000
162A1487THR00.009-0.01133.419-0.002-0.0020.0000.0000.0000.000
163A1488PHE00.0190.00532.861-0.012-0.0120.0000.0000.0000.000
164A1489CYS0-0.0430.01234.9300.0090.0090.0000.0000.0000.000
165A1490VAL0-0.020-0.01234.730-0.009-0.0090.0000.0000.0000.000
166A1491ARG10.9340.96836.8460.1280.1280.0000.0000.0000.000
167A1492THR0-0.0050.00437.423-0.008-0.0080.0000.0000.0000.000
168A1493PHE00.0260.00337.5560.0050.0050.0000.0000.0000.000
169A1494SER00.0000.00739.8710.0010.0010.0000.0000.0000.000
170A1495LEU00.0240.00137.1350.0000.0000.0000.0000.0000.000
171A1496HIS0-0.046-0.01741.2850.0040.0040.0000.0000.0000.000
172A1497LYS10.9040.98438.5960.1150.1150.0000.0000.0000.000
173A1498ASN00.033-0.00343.6320.0040.0040.0000.0000.0000.000
174A1499GLY0-0.0040.02646.4470.0000.0000.0000.0000.0000.000
175A1500SER0-0.010-0.02743.6950.0020.0020.0000.0000.0000.000
176A1501SER00.0370.00946.136-0.001-0.0010.0000.0000.0000.000
177A1502GLU-1-0.890-0.90139.215-0.100-0.1000.0000.0000.0000.000
178A1503LYS10.9200.95142.9330.0800.0800.0000.0000.0000.000
179A1504ARG10.7840.86835.6780.1180.1180.0000.0000.0000.000
180A1505GLU-1-0.828-0.90037.648-0.095-0.0950.0000.0000.0000.000
181A1506VAL0-0.037-0.01933.572-0.006-0.0060.0000.0000.0000.000
182A1507ARG10.8550.92733.8170.1110.1110.0000.0000.0000.000
183A1508HIS0-0.008-0.00232.949-0.007-0.0070.0000.0000.0000.000
184A1509PHE00.0350.00530.4750.0090.0090.0000.0000.0000.000
185A1510GLN00.0400.00631.084-0.006-0.0060.0000.0000.0000.000
186A1511PHE00.0180.00828.9450.0090.0090.0000.0000.0000.000
187A1512THR0-0.024-0.03731.515-0.006-0.0060.0000.0000.0000.000
188A1513ALA00.0350.01732.4770.0060.0060.0000.0000.0000.000
189A1514TRP0-0.064-0.03323.054-0.007-0.0070.0000.0000.0000.000
190A1515PRO00.0060.01729.2660.0070.0070.0000.0000.0000.000
191A1516ASP-1-0.788-0.89231.121-0.136-0.1360.0000.0000.0000.000
192A1517HIS0-0.039-0.01830.8430.0040.0040.0000.0000.0000.000
193A1518GLY00.0730.04027.1270.0050.0050.0000.0000.0000.000
194A1519VAL0-0.019-0.00523.017-0.009-0.0090.0000.0000.0000.000
195A1520PRO00.000-0.01425.5980.0160.0160.0000.0000.0000.000
196A1521GLU-1-0.821-0.86126.699-0.106-0.1060.0000.0000.0000.000
197A1522TYR00.007-0.02327.4810.0010.0010.0000.0000.0000.000
198A1523PRO0-0.0090.00723.851-0.004-0.0040.0000.0000.0000.000
199A1524THR0-0.008-0.04025.970-0.004-0.0040.0000.0000.0000.000
200A1525PRO00.0290.01128.325-0.001-0.0010.0000.0000.0000.000
201A1526PHE00.0000.00622.365-0.002-0.0020.0000.0000.0000.000
202A1527LEU00.0080.00122.134-0.007-0.0070.0000.0000.0000.000
203A1528ALA0-0.026-0.01425.8720.0020.0020.0000.0000.0000.000
204A1529PHE0-0.025-0.00327.1890.0030.0030.0000.0000.0000.000
205A1530LEU0-0.013-0.00621.3410.0010.0010.0000.0000.0000.000
206A1531ARG10.9430.96225.9800.1390.1390.0000.0000.0000.000
207A1532ARG10.8710.93227.2750.1160.1160.0000.0000.0000.000
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