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: 171QZ

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 OptAll
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 -12510860.962947
FMO2-HF: Nuclear repulsion 12278815.304725
FMO2-HF: Total energy -232045.658223
FMO2-MP2: Total energy -232713.754018


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.
-24.258-32.48334.03-12.301-13.5030.009
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 : 0.082 / q_NPA : 0.087
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].
3A1328SER0-0.030-0.0522.124-8.228-22.19631.146-9.794-7.3830.037
4A1329HIS10.8730.9332.551-3.449-2.4140.4070.403-1.8450.000
5A1330PRO00.0290.0362.349-10.522-7.0322.303-2.797-2.996-0.029
6A1331PRO0-0.011-0.0172.8200.6241.1710.171-0.049-0.6690.001
7A1332ILE00.0130.0245.4820.1270.1270.0000.0000.0000.000
8A1333PRO00.0330.0198.9380.1090.1090.0000.0000.0000.000
9A1334ILE0-0.014-0.02411.835-0.001-0.0010.0000.0000.0000.000
10A1335THR0-0.051-0.03415.1120.0230.0230.0000.0000.0000.000
11A1336ASP-1-0.832-0.90913.200-0.164-0.1640.0000.0000.0000.000
12A1337MET0-0.089-0.04513.491-0.028-0.0280.0000.0000.0000.000
13A1338ALA00.0360.01314.483-0.003-0.0030.0000.0000.0000.000
14A1339GLU-1-0.782-0.88314.438-0.159-0.1590.0000.0000.0000.000
15A1340HIS00.0130.0099.7370.0370.0370.0000.0000.0000.000
16A1341MET0-0.036-0.00514.1620.0050.0050.0000.0000.0000.000
17A1342GLU-1-0.856-0.91816.304-0.083-0.0830.0000.0000.0000.000
18A1343ARG10.7770.85911.8530.1870.1870.0000.0000.0000.000
19A1344LEU0-0.087-0.03111.7230.0220.0220.0000.0000.0000.000
20A1345LYS10.8440.90715.8730.1250.1250.0000.0000.0000.000
21A1346ALA0-0.033-0.00419.3730.0120.0120.0000.0000.0000.000
22A1347ASN0-0.077-0.05120.3120.0060.0060.0000.0000.0000.000
23A1348ASP-1-0.871-0.93122.102-0.051-0.0510.0000.0000.0000.000
24A1349SER00.0040.00419.261-0.005-0.0050.0000.0000.0000.000
25A1350LEU00.0140.03418.168-0.013-0.0130.0000.0000.0000.000
26A1351LYS10.8650.91914.564-0.060-0.0600.0000.0000.0000.000
27A1352LEU00.0070.00813.648-0.014-0.0140.0000.0000.0000.000
28A1353SER0-0.005-0.01814.105-0.034-0.0340.0000.0000.0000.000
29A1354GLN00.0390.01113.2470.0060.0060.0000.0000.0000.000
30A1355GLU-1-0.832-0.8888.700-0.488-0.4880.0000.0000.0000.000
31A1356TYR0-0.046-0.05810.180-0.112-0.1120.0000.0000.0000.000
32A1357GLU-1-0.933-0.97312.327-0.213-0.2130.0000.0000.0000.000
33A1358SER0-0.059-0.0187.4430.0680.0680.0000.0000.0000.000
34A1359ILE0-0.073-0.0147.256-0.249-0.2490.0000.0000.0000.000
35A1360ASP-1-0.834-0.9237.465-0.746-0.7460.0000.0000.0000.000
36A1361PRO0-0.058-0.0306.661-0.441-0.4410.0000.0000.0000.000
37A1362GLY0-0.0040.0137.906-0.129-0.1290.0000.0000.0000.000
38A1363GLN0-0.085-0.0578.7720.1390.1390.0000.0000.0000.000
39A1364GLN0-0.022-0.00812.1520.0140.0140.0000.0000.0000.000
40A1365PHE0-0.014-0.00712.9710.0130.0130.0000.0000.0000.000
41A1366THR0-0.013-0.01618.4790.0090.0090.0000.0000.0000.000
42A1367TRP00.0410.00519.408-0.014-0.0140.0000.0000.0000.000
43A1368GLU-1-0.800-0.90724.517-0.128-0.1280.0000.0000.0000.000
44A1369HIS0-0.072-0.04627.3330.0170.0170.0000.0000.0000.000
45A1370SER00.0390.02626.5660.0050.0050.0000.0000.0000.000
46A1371ASN0-0.050-0.01428.3740.0090.0090.0000.0000.0000.000
47A1372LEU00.0200.02030.2310.0070.0070.0000.0000.0000.000
48A1373GLU-1-0.879-0.94933.511-0.070-0.0700.0000.0000.0000.000
49A1374ALA0-0.016-0.01736.6240.0000.0000.0000.0000.0000.000
50A1375ASN0-0.013-0.02232.3000.0060.0060.0000.0000.0000.000
51A1376LYS10.8510.94532.6250.0870.0870.0000.0000.0000.000
52A1377PRO00.0220.00733.618-0.004-0.0040.0000.0000.0000.000
53A1378LYS10.8160.90733.0760.0690.0690.0000.0000.0000.000
54A1379ASN0-0.0330.00529.137-0.011-0.0110.0000.0000.0000.000
55A1380ARG10.7410.85330.8060.0830.0830.0000.0000.0000.000
56A1381TYR0-0.016-0.02528.1720.0060.0060.0000.0000.0000.000
57A1382ALA00.0400.02128.488-0.007-0.0070.0000.0000.0000.000
58A1383ASN00.0120.01224.9450.0060.0060.0000.0000.0000.000
59A1384VAL0-0.075-0.02823.128-0.018-0.0180.0000.0000.0000.000
60A1385ILE00.0210.04221.4050.0140.0140.0000.0000.0000.000
61A1386ALA00.017-0.00522.794-0.010-0.0100.0000.0000.0000.000
62A1387TYR0-0.031-0.02015.5120.0280.0280.0000.0000.0000.000
63A1388ASP-1-0.736-0.85521.603-0.123-0.1230.0000.0000.0000.000
64A1389HIS0-0.057-0.02616.1070.0430.0430.0000.0000.0000.000
65A1390SER0-0.011-0.02318.4870.0120.0120.0000.0000.0000.000
66A1391ARG10.7660.88320.6370.1010.1010.0000.0000.0000.000
67A1392VAL0-0.010-0.01023.8880.0100.0100.0000.0000.0000.000
68A1393ILE0-0.037-0.01226.442-0.002-0.0020.0000.0000.0000.000
69A1394LEU0-0.058-0.02029.3420.0060.0060.0000.0000.0000.000
70A1395GLN0-0.018-0.02532.8130.0020.0020.0000.0000.0000.000
71A1396PRO00.0110.02135.525-0.001-0.0010.0000.0000.0000.000
72A1397LEU00.011-0.00237.6340.0040.0040.0000.0000.0000.000
73A1398GLU-1-0.918-0.96341.026-0.031-0.0310.0000.0000.0000.000
74A1399GLY00.0000.00042.9830.0010.0010.0000.0000.0000.000
75A1400ILE0-0.044-0.01840.502-0.001-0.0010.0000.0000.0000.000
76A1401MET00.0150.01838.409-0.001-0.0010.0000.0000.0000.000
77A1402GLY00.0500.02435.0780.0000.0000.0000.0000.0000.000
78A1403SER0-0.014-0.01235.378-0.003-0.0030.0000.0000.0000.000
79A1404ASP-1-0.817-0.89632.234-0.070-0.0700.0000.0000.0000.000
80A1405TYR0-0.025-0.01927.570-0.002-0.0020.0000.0000.0000.000
81A1406ILE00.0540.01829.0820.0050.0050.0000.0000.0000.000
82A1407ASN0-0.0070.00326.254-0.012-0.0120.0000.0000.0000.000
83A1408ALA0-0.0010.00225.1820.0000.0000.0000.0000.0000.000
84A1409ASN00.0020.00820.3250.0000.0000.0000.0000.0000.000
85A1410TYR0-0.008-0.01520.5130.0050.0050.0000.0000.0000.000
86A1411VAL0-0.025-0.01815.733-0.028-0.0280.0000.0000.0000.000
87A1412ASP-1-0.780-0.86413.574-0.024-0.0240.0000.0000.0000.000
88A1413GLY00.0160.01314.979-0.038-0.0380.0000.0000.0000.000
89A1414TYR0-0.031-0.01210.3790.0510.0510.0000.0000.0000.000
90A1415ARG10.8490.91310.628-0.486-0.4860.0000.0000.0000.000
91A1416ARG10.8360.92714.659-0.091-0.0910.0000.0000.0000.000
92A1417GLN00.0470.01415.886-0.001-0.0010.0000.0000.0000.000
93A1418ASN0-0.017-0.01917.581-0.017-0.0170.0000.0000.0000.000
94A1419ALA00.0100.01518.723-0.001-0.0010.0000.0000.0000.000
95A1420TYR0-0.065-0.06517.1270.0030.0030.0000.0000.0000.000
96A1421ILE00.008-0.00121.221-0.006-0.0060.0000.0000.0000.000
97A1422ALA0-0.0080.01920.6120.0050.0050.0000.0000.0000.000
98A1423THR0-0.030-0.05022.670-0.001-0.0010.0000.0000.0000.000
99A1424GLN0-0.0030.00225.887-0.008-0.0080.0000.0000.0000.000
100A1425GLY00.022-0.00228.0870.0060.0060.0000.0000.0000.000
101A1426PRO00.0200.00931.1730.0000.0000.0000.0000.0000.000
102A1427LEU00.0430.02833.7440.0020.0020.0000.0000.0000.000
103A1428PRO00.0520.02636.3010.0010.0010.0000.0000.0000.000
104A1429GLU-1-0.900-0.95438.436-0.056-0.0560.0000.0000.0000.000
105A1430THR0-0.090-0.05834.134-0.002-0.0020.0000.0000.0000.000
106A1431PHE00.0070.01936.0070.0000.0000.0000.0000.0000.000
107A1432GLY00.0290.00637.6330.0010.0010.0000.0000.0000.000
108A1433ASP-1-0.784-0.89434.484-0.056-0.0560.0000.0000.0000.000
109A1434PHE00.0050.00430.200-0.001-0.0010.0000.0000.0000.000
110A1435TRP0-0.003-0.02233.4530.0010.0010.0000.0000.0000.000
111A1436ARG10.7670.86335.8670.0530.0530.0000.0000.0000.000
112A1437MET00.0000.01628.5740.0010.0010.0000.0000.0000.000
113A1438VAL00.0090.00431.5330.0030.0030.0000.0000.0000.000
114A1439TRP0-0.012-0.00232.5820.0030.0030.0000.0000.0000.000
115A1440GLU-1-0.817-0.91833.544-0.038-0.0380.0000.0000.0000.000
116A1441GLN00.0100.02028.0680.0040.0040.0000.0000.0000.000
117A1442ARG10.9100.95829.4850.0260.0260.0000.0000.0000.000
118A1443SER0-0.0220.00728.1130.0030.0030.0000.0000.0000.000
119A1444ALA00.0360.01930.3480.0000.0000.0000.0000.0000.000
120A1445THR0-0.044-0.04628.3980.0010.0010.0000.0000.0000.000
121A1446VAL0-0.021-0.00529.137-0.004-0.0040.0000.0000.0000.000
122A1447VAL0-0.003-0.00625.8810.0030.0030.0000.0000.0000.000
123A1448MET0-0.0320.00428.251-0.005-0.0050.0000.0000.0000.000
124A1449MET0-0.045-0.01824.1850.0070.0070.0000.0000.0000.000
125A1450THR0-0.013-0.03728.204-0.007-0.0070.0000.0000.0000.000
126A1451ARG10.9160.95931.3270.0700.0700.0000.0000.0000.000
127A1452LEU00.0220.02434.515-0.004-0.0040.0000.0000.0000.000
128A1453GLU-1-0.871-0.93536.891-0.058-0.0580.0000.0000.0000.000
129A1454GLU-1-0.747-0.84732.361-0.085-0.0850.0000.0000.0000.000
130A1455LYS10.8960.93836.5620.0620.0620.0000.0000.0000.000
131A1456SER0-0.0230.00338.4030.0010.0010.0000.0000.0000.000
132A1457ARG10.8630.93031.7990.0870.0870.0000.0000.0000.000
133A1458ILE00.0420.02036.624-0.002-0.0020.0000.0000.0000.000
134A1459LYS10.7810.89331.1300.0820.0820.0000.0000.0000.000
135A1460CYS0-0.0240.00432.667-0.007-0.0070.0000.0000.0000.000
136A1461ASP-1-0.761-0.84834.690-0.061-0.0610.0000.0000.0000.000
137A1462GLN0-0.050-0.04637.252-0.002-0.0020.0000.0000.0000.000
138A1463TYR0-0.002-0.01632.5540.0040.0040.0000.0000.0000.000
139A1464TRP00.0480.00735.9450.0000.0000.0000.0000.0000.000
140A1465PRO00.0500.05340.8620.0000.0000.0000.0000.0000.000
141A1466ASN00.014-0.00244.139-0.001-0.0010.0000.0000.0000.000
142A1467ARG10.9360.95146.3130.0300.0300.0000.0000.0000.000
143A1468GLY00.0330.03447.8050.0000.0000.0000.0000.0000.000
144A1469THR0-0.008-0.00746.519-0.001-0.0010.0000.0000.0000.000
145A1470GLU-1-0.835-0.86445.066-0.036-0.0360.0000.0000.0000.000
146A1471THR0-0.051-0.03844.8480.0010.0010.0000.0000.0000.000
147A1472TYR0-0.003-0.02140.789-0.001-0.0010.0000.0000.0000.000
148A1473GLY00.0190.00741.763-0.001-0.0010.0000.0000.0000.000
149A1474PHE0-0.008-0.00841.6100.0020.0020.0000.0000.0000.000
150A1475ILE0-0.005-0.00538.7110.0020.0020.0000.0000.0000.000
151A1476GLN00.0050.00242.1640.0000.0000.0000.0000.0000.000
152A1477VAL00.0330.00040.1520.0000.0000.0000.0000.0000.000
153A1478THR0-0.049-0.03942.7980.0000.0000.0000.0000.0000.000
154A1479LEU0-0.0080.00541.6300.0000.0000.0000.0000.0000.000
155A1480LEU0-0.070-0.04642.7280.0020.0020.0000.0000.0000.000
156A1481ASP-1-0.810-0.89441.524-0.027-0.0270.0000.0000.0000.000
157A1482THR0-0.067-0.03941.183-0.003-0.0030.0000.0000.0000.000
158A1483MET00.0390.06639.4900.0010.0010.0000.0000.0000.000
159A1484GLU-1-0.785-0.90039.073-0.043-0.0430.0000.0000.0000.000
160A1485LEU0-0.054-0.02836.9310.0030.0030.0000.0000.0000.000
161A1486ALA0-0.037-0.00538.311-0.002-0.0020.0000.0000.0000.000
162A1487THR00.013-0.00833.333-0.002-0.0020.0000.0000.0000.000
163A1488PHE00.003-0.00832.594-0.005-0.0050.0000.0000.0000.000
164A1489CYS0-0.086-0.02934.6520.0040.0040.0000.0000.0000.000
165A1490VAL0-0.0150.00034.327-0.003-0.0030.0000.0000.0000.000
166A1491ARG10.8620.92836.4950.0480.0480.0000.0000.0000.000
167A1492THR0-0.036-0.03437.299-0.001-0.0010.0000.0000.0000.000
168A1493PHE00.0400.00537.5750.0010.0010.0000.0000.0000.000
169A1494SER0-0.0020.01139.9200.0020.0020.0000.0000.0000.000
170A1495LEU00.0260.01637.150-0.001-0.0010.0000.0000.0000.000
171A1496HIS0-0.048-0.03441.2690.0020.0020.0000.0000.0000.000
172A1497LYS10.9050.96938.2070.0320.0320.0000.0000.0000.000
173A1498ASN0-0.012-0.00943.3990.0010.0010.0000.0000.0000.000
174A1499GLY00.0240.02146.5580.0000.0000.0000.0000.0000.000
175A1500SER0-0.021-0.00743.1670.0020.0020.0000.0000.0000.000
176A1501SER00.021-0.00746.2090.0000.0000.0000.0000.0000.000
177A1502GLU-1-0.876-0.90039.140-0.019-0.0190.0000.0000.0000.000
178A1503LYS10.8920.93042.8760.0190.0190.0000.0000.0000.000
179A1504ARG10.7910.87735.4030.0260.0260.0000.0000.0000.000
180A1505GLU-1-0.851-0.90338.307-0.023-0.0230.0000.0000.0000.000
181A1506VAL0-0.031-0.01533.6730.0000.0000.0000.0000.0000.000
182A1507ARG10.8370.90933.8850.0260.0260.0000.0000.0000.000
183A1508HIS0-0.012-0.00732.9180.0000.0000.0000.0000.0000.000
184A1509PHE00.0420.01130.3220.0030.0030.0000.0000.0000.000
185A1510GLN00.0280.00830.859-0.002-0.0020.0000.0000.0000.000
186A1511PHE00.0030.00228.7110.0020.0020.0000.0000.0000.000
187A1512THR0-0.018-0.02531.252-0.003-0.0030.0000.0000.0000.000
188A1513ALA00.0220.01732.1700.0000.0000.0000.0000.0000.000
189A1514TRP0-0.055-0.03922.777-0.004-0.0040.0000.0000.0000.000
190A1515PRO00.0140.02329.1290.0040.0040.0000.0000.0000.000
191A1516ASP-1-0.771-0.87430.678-0.073-0.0730.0000.0000.0000.000
192A1517HIS0-0.048-0.02930.3210.0020.0020.0000.0000.0000.000
193A1518GLY00.0800.05326.6220.0040.0040.0000.0000.0000.000
194A1519VAL0-0.010-0.00122.795-0.005-0.0050.0000.0000.0000.000
195A1520PRO00.007-0.00925.5960.0080.0080.0000.0000.0000.000
196A1521GLU-1-0.827-0.85626.626-0.067-0.0670.0000.0000.0000.000
197A1522TYR00.001-0.03027.024-0.001-0.0010.0000.0000.0000.000
198A1523PRO00.0020.01223.4200.0010.0010.0000.0000.0000.000
199A1524THR0-0.004-0.03025.5140.0020.0020.0000.0000.0000.000
200A1525PRO00.0290.00927.8720.0030.0030.0000.0000.0000.000
201A1526PHE00.0080.01122.0400.0020.0020.0000.0000.0000.000
202A1527LEU00.0140.00621.8540.0020.0020.0000.0000.0000.000
203A1528ALA0-0.052-0.01525.6170.0060.0060.0000.0000.0000.000
204A1529PHE00.0170.01527.0570.0030.0030.0000.0000.0000.000
205A1530LEU00.0040.00421.4120.0040.0040.0000.0000.0000.000
206A1531ARG10.8900.92525.7490.0570.0570.0000.0000.0000.000
207A1532ARG10.8630.91827.3720.0390.0390.0000.0000.0000.000
208A1533VAL0-0.014-0.01126.8770.0030.0030.0000.0000.0000.000
209A1534LYS10.7460.82921.5670.0400.0400.0000.0000.0000.000
210A1535THR0-0.035-0.02127.0510.0060.0060.0000.0000.0000.000
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