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: 6Y17Z

Calculation Name: 1B89-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B89

Chain ID: A

ChEMBL ID:

UniProt ID: P49951

Base Structure: X-ray

Registration Date: 2023-09-24

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 319
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4241205.226915
FMO2-HF: Nuclear repulsion 4110185.223593
FMO2-HF: Total energy -131020.003322
FMO2-MP2: Total energy -131403.595222


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:1182:ARG)


Summations of interaction energy for fragment #1(A:1182:ARG)
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.
-189.466-186.44630.787-16.37-17.437-0.152
Interaction energy analysis for fragmet #1(A:1182:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.835 / q_NPA : 0.890
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].
3A1184ALA0-0.020-0.0142.339-0.1142.3911.008-1.206-2.3070.002
4A1185GLU-1-0.834-0.9283.345-35.661-35.0560.005-0.100-0.5100.000
5A1186LEU0-0.073-0.0253.8260.6981.1630.001-0.101-0.3640.000
6A1187GLU-1-0.878-0.9536.199-26.088-26.0880.0000.0000.0000.000
7A1188GLU-1-0.950-0.9618.042-17.814-17.8140.0000.0000.0000.000
8A1189PHE00.056-0.0029.0121.9981.9980.0000.0000.0000.000
9A1190ILE0-0.095-0.04110.1181.5691.5690.0000.0000.0000.000
10A1191ASN0-0.076-0.01411.9061.5581.5580.0000.0000.0000.000
11A1192GLY00.0000.00113.8351.3481.3480.0000.0000.0000.000
12A1193PRO0-0.045-0.01015.451-0.794-0.7940.0000.0000.0000.000
13A1210MET0-0.011-0.0117.6830.6780.6780.0000.0000.0000.000
14A1211TYR00.0710.0145.1012.7472.7470.0000.0000.0000.000
15A1212ASP-1-0.734-0.8691.802-130.540-135.63527.462-12.436-9.930-0.140
16A1213ALA0-0.0340.0002.790-12.889-10.8340.510-1.172-1.393-0.015
17A1214ALA00.0550.0195.0972.2432.260-0.001-0.001-0.0160.000
18A1215LYS10.9110.9962.12067.01867.9791.736-0.901-1.7960.002
19A1216LEU0-0.035-0.0373.1691.5362.4700.067-0.235-0.7660.000
20A1217LEU00.0290.0366.3574.4504.4500.0000.0000.0000.000
21A1218TYR00.002-0.0189.4223.8003.8000.0000.0000.0000.000
22A1219ASN0-0.039-0.0078.6872.7142.7140.0000.0000.0000.000
23A1220ASN00.0310.01310.625-0.067-0.0670.0000.0000.0000.000
24A1221VAL0-0.048-0.01512.6051.6471.6470.0000.0000.0000.000
25A1222SER0-0.0100.00113.7611.4481.4480.0000.0000.0000.000
26A1223ASN0-0.0070.00014.2350.6620.6620.0000.0000.0000.000
27A1224PHE00.045-0.00913.995-0.840-0.8400.0000.0000.0000.000
28A1225GLY0-0.0080.00514.860-0.304-0.3040.0000.0000.0000.000
29A1226ARG10.9350.95513.13118.48118.4810.0000.0000.0000.000
30A1227LEU00.0050.0278.740-1.079-1.0790.0000.0000.0000.000
31A1228ALA0-0.001-0.00310.086-2.115-2.1150.0000.0000.0000.000
32A1229SER0-0.0120.01512.345-1.069-1.0690.0000.0000.0000.000
33A1230THR0-0.029-0.0438.339-1.385-1.3850.0000.0000.0000.000
34A1231LEU00.0360.0216.772-1.878-1.8780.0000.0000.0000.000
35A1232VAL00.0410.0338.896-0.743-0.7430.0000.0000.0000.000
36A1233HIS0-0.108-0.0309.9301.4851.4850.0000.0000.0000.000
37A1234LEU0-0.052-0.0293.750-0.844-0.4270.000-0.188-0.230-0.001
38A1235GLY0-0.003-0.0037.481-1.947-1.9470.0000.0000.0000.000
39A1236GLU-1-0.926-0.9604.246-51.958-51.802-0.001-0.030-0.1250.000
40A1237TYR00.048-0.0058.9760.8280.8280.0000.0000.0000.000
41A1238GLN00.0340.00712.6950.0200.0200.0000.0000.0000.000
42A1239ALA00.0400.0319.9240.9430.9430.0000.0000.0000.000
43A1240ALA00.0040.00211.6660.7130.7130.0000.0000.0000.000
44A1241VAL0-0.016-0.01512.7701.3681.3680.0000.0000.0000.000
45A1242ASP-1-0.917-0.96614.089-18.424-18.4240.0000.0000.0000.000
46A1243GLY0-0.041-0.02913.8080.8320.8320.0000.0000.0000.000
47A1244ALA00.0550.01714.6870.8460.8460.0000.0000.0000.000
48A1245ARG10.9370.98017.67616.06116.0610.0000.0000.0000.000
49A1246LYS10.8730.94315.29719.59619.5960.0000.0000.0000.000
50A1247ALA0-0.029-0.02217.3830.5410.5410.0000.0000.0000.000
51A1248ASN0-0.050-0.01419.2660.6660.6660.0000.0000.0000.000
52A1249SER00.0200.01921.5460.8210.8210.0000.0000.0000.000
53A1250THR00.0790.02522.830-0.442-0.4420.0000.0000.0000.000
54A1251ARG10.9700.98222.85712.43012.4300.0000.0000.0000.000
55A1252THR00.0150.00818.085-0.095-0.0950.0000.0000.0000.000
56A1253TRP00.0640.00819.692-0.886-0.8860.0000.0000.0000.000
57A1254LYS10.8410.93821.55411.13511.1350.0000.0000.0000.000
58A1255GLU-1-0.947-0.95517.778-16.621-16.6210.0000.0000.0000.000
59A1256VAL00.012-0.01016.052-0.364-0.3640.0000.0000.0000.000
60A1257CYS0-0.062-0.02718.022-0.066-0.0660.0000.0000.0000.000
61A1258PHE00.014-0.00121.0110.1510.1510.0000.0000.0000.000
62A1259ALA00.0570.04116.5080.0340.0340.0000.0000.0000.000
63A1260CYS0-0.088-0.05017.266-0.423-0.4230.0000.0000.0000.000
64A1261VAL00.0120.01618.2140.2320.2320.0000.0000.0000.000
65A1262ASP-1-0.834-0.89019.119-14.184-14.1840.0000.0000.0000.000
66A1263GLY0-0.078-0.04517.2150.1130.1130.0000.0000.0000.000
67A1264LYS10.8280.89718.17614.08714.0870.0000.0000.0000.000
68A1265GLU-1-0.925-0.93816.287-17.224-17.2240.0000.0000.0000.000
69A1266PHE00.0790.01119.7090.0820.0820.0000.0000.0000.000
70A1267ARG10.9500.97222.37212.53912.5390.0000.0000.0000.000
71A1268LEU00.0140.00516.3310.2070.2070.0000.0000.0000.000
72A1269ALA00.0630.02320.5230.2140.2140.0000.0000.0000.000
73A1270GLN00.0440.03221.8980.5020.5020.0000.0000.0000.000
74A1271MET0-0.041-0.01221.6830.1520.1520.0000.0000.0000.000
75A1272CYS0-0.113-0.03020.236-0.231-0.2310.0000.0000.0000.000
76A1273GLY00.0740.03022.391-0.133-0.1330.0000.0000.0000.000
77A1274LEU0-0.045-0.03425.5740.4630.4630.0000.0000.0000.000
78A1275HIS0-0.053-0.01923.5290.5390.5390.0000.0000.0000.000
79A1276ILE0-0.026-0.00824.3420.1030.1030.0000.0000.0000.000
80A1277VAL00.0640.03428.3980.3260.3260.0000.0000.0000.000
81A1278VAL0-0.015-0.01130.7450.3290.3290.0000.0000.0000.000
82A1279HIS0-0.063-0.02428.4690.3870.3870.0000.0000.0000.000
83A1280ALA00.0400.03033.084-0.096-0.0960.0000.0000.0000.000
84A1281ASP-1-0.913-0.96334.049-8.671-8.6710.0000.0000.0000.000
85A1282GLU-1-0.911-0.97929.213-10.751-10.7510.0000.0000.0000.000
86A1283LEU0-0.085-0.03131.705-0.158-0.1580.0000.0000.0000.000
87A1284GLU-1-0.892-0.94833.103-8.527-8.5270.0000.0000.0000.000
88A1285GLU-1-0.854-0.92627.992-11.132-11.1320.0000.0000.0000.000
89A1286LEU0-0.014-0.01027.101-0.278-0.2780.0000.0000.0000.000
90A1287ILE00.008-0.00629.592-0.189-0.1890.0000.0000.0000.000
91A1288ASN0-0.016-0.03832.2670.0500.0500.0000.0000.0000.000
92A1289TYR0-0.031-0.00422.9100.0580.0580.0000.0000.0000.000
93A1290TYR00.011-0.02625.321-0.193-0.1930.0000.0000.0000.000
94A1291GLN0-0.046-0.01529.4140.3040.3040.0000.0000.0000.000
95A1292ASP-1-0.861-0.91430.891-9.516-9.5160.0000.0000.0000.000
96A1293ARG10.7920.92125.52611.47011.4700.0000.0000.0000.000
97A1294GLY00.014-0.01629.099-0.130-0.1300.0000.0000.0000.000
98A1295TYR0-0.0370.00325.516-0.043-0.0430.0000.0000.0000.000
99A1296PHE00.038-0.00930.323-0.060-0.0600.0000.0000.0000.000
100A1297GLU-1-0.849-0.93232.496-8.706-8.7060.0000.0000.0000.000
101A1298GLU-1-0.841-0.90227.642-10.596-10.5960.0000.0000.0000.000
102A1299LEU0-0.0350.00130.2810.0070.0070.0000.0000.0000.000
103A1300ILE00.006-0.02631.3500.1360.1360.0000.0000.0000.000
104A1301THR0-0.036-0.03030.8920.2210.2210.0000.0000.0000.000
105A1302MET0-0.074-0.02726.7200.0080.0080.0000.0000.0000.000
106A1303LEU00.003-0.01530.7790.0610.0610.0000.0000.0000.000
107A1304GLU-1-0.851-0.86534.020-8.176-8.1760.0000.0000.0000.000
108A1305ALA0-0.022-0.00331.5150.1530.1530.0000.0000.0000.000
109A1306ALA0-0.002-0.01132.6090.1120.1120.0000.0000.0000.000
110A1307LEU0-0.017-0.00833.6880.1160.1160.0000.0000.0000.000
111A1308GLY0-0.024-0.00336.1150.1890.1890.0000.0000.0000.000
112A1309LEU0-0.075-0.03331.2160.0210.0210.0000.0000.0000.000
113A1310GLU-1-0.882-0.94835.076-8.250-8.2500.0000.0000.0000.000
114A1311ARG10.8610.93930.7249.9249.9240.0000.0000.0000.000
115A1312ALA00.0310.03036.419-0.098-0.0980.0000.0000.0000.000
116A1313HIS00.024-0.02135.5400.5320.5320.0000.0000.0000.000
117A1314MET00.0110.00339.804-0.025-0.0250.0000.0000.0000.000
118A1315GLY00.0110.00639.4910.0930.0930.0000.0000.0000.000
119A1316MET0-0.0090.01335.362-0.130-0.1300.0000.0000.0000.000
120A1317PHE00.0580.02638.186-0.014-0.0140.0000.0000.0000.000
121A1318THR0-0.022-0.00741.3410.1920.1920.0000.0000.0000.000
122A1319GLU-1-0.797-0.91037.934-7.789-7.7890.0000.0000.0000.000
123A1320LEU0-0.0030.03137.264-0.058-0.0580.0000.0000.0000.000
124A1321ALA00.0020.00839.6070.0680.0680.0000.0000.0000.000
125A1322ILE00.0290.00541.5860.0730.0730.0000.0000.0000.000
126A1323LEU0-0.0170.00335.9350.0820.0820.0000.0000.0000.000
127A1324TYR0-0.002-0.08238.9330.1450.1450.0000.0000.0000.000
128A1325SER0-0.032-0.01942.0710.1310.1310.0000.0000.0000.000
129A1326LYS10.9130.96440.2347.7957.7950.0000.0000.0000.000
130A1327PHE0-0.027-0.01738.963-0.129-0.1290.0000.0000.0000.000
131A1328LYS10.7610.88937.5418.1808.1800.0000.0000.0000.000
132A1329PRO00.0930.04842.7260.0360.0360.0000.0000.0000.000
133A1330GLN00.001-0.00644.5290.0700.0700.0000.0000.0000.000
134A1331LYS10.9470.98239.5507.9297.9290.0000.0000.0000.000
135A1332MET0-0.0410.01045.007-0.013-0.0130.0000.0000.0000.000
136A1333ARG10.8860.94846.3015.9985.9980.0000.0000.0000.000
137A1334GLU-1-0.921-0.97246.453-6.852-6.8520.0000.0000.0000.000
138A1335HIS00.0200.02241.833-0.038-0.0380.0000.0000.0000.000
139A1336LEU0-0.021-0.01445.9150.0070.0070.0000.0000.0000.000
140A1337GLU-1-0.892-0.95248.738-5.892-5.8920.0000.0000.0000.000
141A1338LEU0-0.026-0.00445.6020.0850.0850.0000.0000.0000.000
142A1339PHE0-0.034-0.03642.517-0.002-0.0020.0000.0000.0000.000
143A1340TRP00.0380.01046.878-0.041-0.0410.0000.0000.0000.000
144A1341SER00.0020.00149.582-0.010-0.0100.0000.0000.0000.000
145A1342ARG10.8460.93641.7177.3527.3520.0000.0000.0000.000
146A1343VAL00.0250.00744.709-0.216-0.2160.0000.0000.0000.000
147A1344ASN0-0.0010.00845.8590.2710.2710.0000.0000.0000.000
148A1345ILE00.0800.02147.691-0.053-0.0530.0000.0000.0000.000
149A1346PRO00.0260.01850.602-0.008-0.0080.0000.0000.0000.000
150A1347LYS10.8350.90941.7977.5537.5530.0000.0000.0000.000
151A1348VAL00.0430.00945.935-0.043-0.0430.0000.0000.0000.000
152A1349LEU00.0230.02848.0920.0070.0070.0000.0000.0000.000
153A1350ARG10.8980.96649.7266.0906.0900.0000.0000.0000.000
154A1351ALA00.012-0.00746.245-0.022-0.0220.0000.0000.0000.000
155A1352ALA00.0410.01548.254-0.059-0.0590.0000.0000.0000.000
156A1353GLU-1-0.993-1.00250.537-5.619-5.6190.0000.0000.0000.000
157A1354GLN0-0.066-0.04948.6180.1110.1110.0000.0000.0000.000
158A1355ALA00.0080.02047.964-0.024-0.0240.0000.0000.0000.000
159A1356HIS0-0.057-0.03049.9220.0130.0130.0000.0000.0000.000
160A1357LEU00.0200.02148.1870.0160.0160.0000.0000.0000.000
161A1358TRP0-0.009-0.00852.8540.0400.0400.0000.0000.0000.000
162A1359ALA00.0410.02255.0390.0700.0700.0000.0000.0000.000
163A1360GLU-1-0.843-0.94250.526-6.090-6.0900.0000.0000.0000.000
164A1361LEU00.0010.00153.8230.0200.0200.0000.0000.0000.000
165A1362VAL0-0.025-0.00355.1840.0540.0540.0000.0000.0000.000
166A1363PHE0-0.0210.00052.3570.0630.0630.0000.0000.0000.000
167A1364LEU00.0290.00750.4600.0230.0230.0000.0000.0000.000
168A1365TYR0-0.025-0.00954.9920.0450.0450.0000.0000.0000.000
169A1366ASP-1-0.948-0.96658.056-5.208-5.2080.0000.0000.0000.000
170A1367LYS10.9260.98054.8315.7095.7090.0000.0000.0000.000
171A1368TYR0-0.126-0.06455.679-0.024-0.0240.0000.0000.0000.000
172A1369GLU-1-0.937-0.97757.253-5.143-5.1430.0000.0000.0000.000
173A1370GLU-1-0.919-0.95458.111-5.455-5.4550.0000.0000.0000.000
174A1371TYR00.077-0.00561.5040.0270.0270.0000.0000.0000.000
175A1372ASP-1-0.775-0.88264.211-4.734-4.7340.0000.0000.0000.000
176A1373ASN0-0.005-0.00860.7330.0490.0490.0000.0000.0000.000
177A1374ALA00.0440.03761.234-0.024-0.0240.0000.0000.0000.000
178A1375ILE00.0190.00662.1870.0080.0080.0000.0000.0000.000
179A1376ILE0-0.029-0.02064.0870.0270.0270.0000.0000.0000.000
180A1377THR0-0.014-0.01059.222-0.005-0.0050.0000.0000.0000.000
181A1378MET0-0.085-0.03362.4050.0010.0010.0000.0000.0000.000
182A1379MET0-0.051-0.01964.0010.0370.0370.0000.0000.0000.000
183A1380ASN0-0.0100.00163.3830.1170.1170.0000.0000.0000.000
184A1381HIS10.8630.94260.0905.3165.3160.0000.0000.0000.000
185A1382PRO00.015-0.00762.045-0.059-0.0590.0000.0000.0000.000
186A1383THR0-0.007-0.00260.8410.0190.0190.0000.0000.0000.000
187A1384ASP-1-0.925-0.95757.143-5.538-5.5380.0000.0000.0000.000
188A1385ALA0-0.0020.00059.682-0.007-0.0070.0000.0000.0000.000
189A1386TRP0-0.0380.00960.5490.0110.0110.0000.0000.0000.000
190A1387LYS10.9620.98059.9955.2715.2710.0000.0000.0000.000
191A1388GLU-1-0.906-0.97065.079-4.496-4.4960.0000.0000.0000.000
192A1389GLY0-0.009-0.01267.7270.0420.0420.0000.0000.0000.000
193A1390GLN00.1170.04460.8230.0050.0050.0000.0000.0000.000
194A1391PHE00.005-0.00165.9150.0070.0070.0000.0000.0000.000
195A1392LYS10.9340.95167.9074.4544.4540.0000.0000.0000.000
196A1393ASP-1-0.903-0.92966.924-4.678-4.6780.0000.0000.0000.000
197A1394ILE0-0.071-0.04062.8760.0140.0140.0000.0000.0000.000
198A1395ILE00.002-0.01267.1430.0310.0310.0000.0000.0000.000
199A1396THR0-0.0050.00070.1260.0580.0580.0000.0000.0000.000
200A1397LYS10.8850.94566.0084.8924.8920.0000.0000.0000.000
201A1398VAL0-0.0280.01968.561-0.014-0.0140.0000.0000.0000.000
202A1399ALA00.0130.00869.0650.0730.0730.0000.0000.0000.000
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