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: 9G932

Calculation Name: 2YIN-A-Xray372

Preferred Name: Dedicator of cytokinesis protein 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2YIN

Chain ID: A

ChEMBL ID: CHEMBL4105810

UniProt ID: Q92608

Base Structure: X-ray

Registration Date: 2023-06-20

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 411
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7323524.928741
FMO2-HF: Nuclear repulsion 7150163.593215
FMO2-HF: Total energy -173361.335526
FMO2-MP2: Total energy -173860.35139


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:1196:SER)


Summations of interaction energy for fragment #1(A:1196:SER)
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.
-0.5763.3441.018-1.922-3.016-0.004
Interaction energy analysis for fragmet #1(A:1196:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.015
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].
3A1198ASP-1-0.708-0.8563.876-0.3291.2320.001-0.628-0.9330.002
4A1199ASN00.0080.0092.446-1.687-0.3501.009-0.992-1.354-0.006
5A1200ARG10.8090.8963.608-1.251-0.6310.004-0.226-0.3990.000
6A1201MET00.0280.0365.9330.1960.1960.0000.0000.0000.000
7A1202SER00.0360.0007.567-0.130-0.1300.0000.0000.0000.000
8A1203CYS0-0.019-0.0068.003-0.082-0.0820.0000.0000.0000.000
9A1204THR0-0.026-0.0169.730-0.026-0.0260.0000.0000.0000.000
10A1205VAL00.0360.01411.774-0.012-0.0120.0000.0000.0000.000
11A1206ASN0-0.013-0.00211.8950.0240.0240.0000.0000.0000.000
12A1207LEU0-0.015-0.01313.084-0.013-0.0130.0000.0000.0000.000
13A1208LEU0-0.0150.00915.665-0.002-0.0020.0000.0000.0000.000
14A1209ASN00.0070.00216.927-0.004-0.0040.0000.0000.0000.000
15A1210PHE00.0460.03018.520-0.008-0.0080.0000.0000.0000.000
16A1211TYR0-0.027-0.03517.295-0.011-0.0110.0000.0000.0000.000
17A1212LYS10.8470.90521.661-0.083-0.0830.0000.0000.0000.000
18A1213ASP-1-0.851-0.90022.7680.0510.0510.0000.0000.0000.000
19A1214ASN0-0.097-0.05023.220-0.003-0.0030.0000.0000.0000.000
20A1215ASN0-0.025-0.01226.276-0.003-0.0030.0000.0000.0000.000
21A1216ARG10.9320.98424.0160.0490.0490.0000.0000.0000.000
22A1217GLU-1-0.855-0.94924.1950.0330.0330.0000.0000.0000.000
23A1218GLU-1-0.892-0.94124.344-0.031-0.0310.0000.0000.0000.000
24A1219MET0-0.036-0.02320.406-0.003-0.0030.0000.0000.0000.000
25A1220TYR0-0.012-0.00819.8920.0050.0050.0000.0000.0000.000
26A1221ILE00.0610.02620.2840.0190.0190.0000.0000.0000.000
27A1222ARG10.8990.95317.5040.1160.1160.0000.0000.0000.000
28A1223TYR0-0.029-0.04213.906-0.020-0.0200.0000.0000.0000.000
29A1224LEU0-0.0040.02316.0010.0370.0370.0000.0000.0000.000
30A1225TYR0-0.005-0.00917.4840.0460.0460.0000.0000.0000.000
31A1226LYS10.9310.97012.5550.0810.0810.0000.0000.0000.000
32A1227LEU0-0.007-0.00111.8790.0490.0490.0000.0000.0000.000
33A1228ARG10.8710.92113.774-0.098-0.0980.0000.0000.0000.000
34A1229ASP-1-0.813-0.89514.3230.2520.2520.0000.0000.0000.000
35A1230LEU0-0.054-0.0228.0590.0620.0620.0000.0000.0000.000
36A1231HIS00.023-0.00810.8210.3580.3580.0000.0000.0000.000
37A1232LEU0-0.021-0.00613.2180.0490.0490.0000.0000.0000.000
38A1233ASP-1-0.826-0.8939.3950.6580.6580.0000.0000.0000.000
39A1234CYS0-0.086-0.0329.5430.3330.3330.0000.0000.0000.000
40A1235ASP-1-0.807-0.87211.9690.5110.5110.0000.0000.0000.000
41A1236ASN0-0.129-0.05811.527-0.015-0.0150.0000.0000.0000.000
42A1237TYR00.046-0.02715.667-0.059-0.0590.0000.0000.0000.000
43A1238THR0-0.042-0.02618.817-0.042-0.0420.0000.0000.0000.000
44A1239GLU-1-0.772-0.86414.9340.6070.6070.0000.0000.0000.000
45A1240ALA00.006-0.00117.063-0.038-0.0380.0000.0000.0000.000
46A1241ALA00.0200.03018.166-0.044-0.0440.0000.0000.0000.000
47A1242TYR0-0.007-0.03920.134-0.019-0.0190.0000.0000.0000.000
48A1243THR0-0.094-0.06516.294-0.023-0.0230.0000.0000.0000.000
49A1244LEU00.0250.01019.749-0.030-0.0300.0000.0000.0000.000
50A1245LEU00.0350.01822.783-0.021-0.0210.0000.0000.0000.000
51A1246LEU0-0.045-0.01319.887-0.015-0.0150.0000.0000.0000.000
52A1247HIS00.0540.03423.915-0.010-0.0100.0000.0000.0000.000
53A1248THR00.0260.00525.536-0.011-0.0110.0000.0000.0000.000
54A1249TRP0-0.019-0.00327.524-0.005-0.0050.0000.0000.0000.000
55A1250LEU0-0.043-0.01926.565-0.006-0.0060.0000.0000.0000.000
56A1251LEU0-0.055-0.00429.616-0.009-0.0090.0000.0000.0000.000
57A1252LYS10.8420.89632.537-0.038-0.0380.0000.0000.0000.000
58A1253TRP00.0340.01034.490-0.002-0.0020.0000.0000.0000.000
59A1254SER0-0.045-0.05238.610-0.002-0.0020.0000.0000.0000.000
60A1255ASP-1-0.878-0.94239.4500.0370.0370.0000.0000.0000.000
61A1256GLU-1-0.791-0.84638.3320.0380.0380.0000.0000.0000.000
62A1271GLN0-0.019-0.01532.0850.0010.0010.0000.0000.0000.000
63A1272THR0-0.034-0.03235.9180.0000.0000.0000.0000.0000.000
64A1273HIS00.021-0.00134.0000.0090.0090.0000.0000.0000.000
65A1274ARG10.8570.91634.934-0.052-0.0520.0000.0000.0000.000
66A1275GLN00.0920.06936.1110.0030.0030.0000.0000.0000.000
67A1276LEU0-0.0320.00229.5400.0050.0050.0000.0000.0000.000
68A1277LYS10.8860.94531.293-0.085-0.0850.0000.0000.0000.000
69A1278GLU-1-0.830-0.88931.8370.0840.0840.0000.0000.0000.000
70A1279THR00.0280.00431.2320.0100.0100.0000.0000.0000.000
71A1280LEU0-0.037-0.01626.6070.0130.0130.0000.0000.0000.000
72A1281TYR0-0.061-0.07427.9800.0190.0190.0000.0000.0000.000
73A1282GLU-1-0.915-0.95029.7300.1170.1170.0000.0000.0000.000
74A1283THR0-0.079-0.04124.5960.0130.0130.0000.0000.0000.000
75A1284ILE0-0.061-0.03124.8690.0240.0240.0000.0000.0000.000
76A1285ILE00.0040.00426.0730.0210.0210.0000.0000.0000.000
77A1286GLY00.0290.01827.6650.0090.0090.0000.0000.0000.000
78A1287TYR0-0.063-0.04320.4410.0240.0240.0000.0000.0000.000
79A1288PHE00.0390.00123.5090.0330.0330.0000.0000.0000.000
80A1289ASP-1-0.829-0.89325.5090.1940.1940.0000.0000.0000.000
81A1290LYS10.9160.95921.371-0.299-0.2990.0000.0000.0000.000
82A1291GLY0-0.048-0.02722.2950.0250.0250.0000.0000.0000.000
83A1292LYS10.8110.89123.215-0.320-0.3200.0000.0000.0000.000
84A1293MET0-0.0410.00223.614-0.005-0.0050.0000.0000.0000.000
85A1294TRP00.0570.00026.998-0.008-0.0080.0000.0000.0000.000
86A1295GLU-1-0.765-0.84929.8870.1950.1950.0000.0000.0000.000
87A1296GLU-1-0.780-0.82626.5240.2000.2000.0000.0000.0000.000
88A1297ALA00.0050.01329.415-0.011-0.0110.0000.0000.0000.000
89A1298ILE00.0150.00030.670-0.013-0.0130.0000.0000.0000.000
90A1299SER0-0.092-0.05031.361-0.011-0.0110.0000.0000.0000.000
91A1300LEU00.0450.01828.310-0.008-0.0080.0000.0000.0000.000
92A1301CYS0-0.035-0.01032.976-0.009-0.0090.0000.0000.0000.000
93A1302LYS10.8700.92735.630-0.119-0.1190.0000.0000.0000.000
94A1303GLU-1-0.783-0.85233.9260.1040.1040.0000.0000.0000.000
95A1304LEU0-0.007-0.00534.184-0.005-0.0050.0000.0000.0000.000
96A1305ALA0-0.020-0.00838.071-0.005-0.0050.0000.0000.0000.000
97A1306GLU-1-0.915-0.95541.0730.0720.0720.0000.0000.0000.000
98A1307GLN0-0.001-0.01039.206-0.007-0.0070.0000.0000.0000.000
99A1308TYR0-0.052-0.07138.351-0.002-0.0020.0000.0000.0000.000
100A1309GLU-1-0.960-0.98543.7450.0640.0640.0000.0000.0000.000
101A1310MET0-0.068-0.04445.994-0.004-0.0040.0000.0000.0000.000
102A1311GLU-1-0.868-0.90043.4290.0550.0550.0000.0000.0000.000
103A1312ILE0-0.057-0.04041.697-0.003-0.0030.0000.0000.0000.000
104A1313PHE0-0.061-0.02246.159-0.002-0.0020.0000.0000.0000.000
105A1314ASP-1-0.797-0.87744.0280.0600.0600.0000.0000.0000.000
106A1315TYR0-0.005-0.02245.0490.0030.0030.0000.0000.0000.000
107A1316GLU-1-0.904-0.93845.7080.0560.0560.0000.0000.0000.000
108A1317LEU0-0.0030.00539.8790.0050.0050.0000.0000.0000.000
109A1318LEU0-0.0250.00341.3820.0070.0070.0000.0000.0000.000
110A1319SER0-0.079-0.05242.9290.0050.0050.0000.0000.0000.000
111A1320GLN00.0310.00839.5830.0060.0060.0000.0000.0000.000
112A1321ASN0-0.019-0.00338.0560.0100.0100.0000.0000.0000.000
113A1322LEU00.0240.00438.8900.0070.0070.0000.0000.0000.000
114A1323ILE0-0.0050.00639.7170.0040.0040.0000.0000.0000.000
115A1324GLN00.0530.03332.7050.0080.0080.0000.0000.0000.000
116A1325GLN00.0300.00636.4920.0100.0100.0000.0000.0000.000
117A1326ALA0-0.0160.00037.9630.0050.0050.0000.0000.0000.000
118A1327LYS10.8320.90432.023-0.155-0.1550.0000.0000.0000.000
119A1328PHE0-0.029-0.00531.8430.0090.0090.0000.0000.0000.000
120A1329TYR00.0330.00535.0470.0060.0060.0000.0000.0000.000
121A1330GLU-1-0.769-0.86237.7100.1170.1170.0000.0000.0000.000
122A1331SER0-0.051-0.04432.8030.0040.0040.0000.0000.0000.000
123A1332ILE0-0.044-0.02732.7800.0080.0080.0000.0000.0000.000
124A1333MET0-0.049-0.02234.4880.0030.0030.0000.0000.0000.000
125A1334LYS10.8070.88836.770-0.116-0.1160.0000.0000.0000.000
126A1335ILE0-0.0120.01130.8460.0010.0010.0000.0000.0000.000
127A1336LEU0-0.017-0.01631.8880.0080.0080.0000.0000.0000.000
128A1337ARG10.7660.85727.444-0.208-0.2080.0000.0000.0000.000
129A1338PRO0-0.018-0.00624.466-0.006-0.0060.0000.0000.0000.000
130A1339LYS10.8160.90524.703-0.302-0.3020.0000.0000.0000.000
131A1340PRO00.0120.01620.7260.0070.0070.0000.0000.0000.000
132A1341ASP-1-0.850-0.91420.5960.3110.3110.0000.0000.0000.000
133A1342TYR00.014-0.01618.9680.0590.0590.0000.0000.0000.000
134A1343PHE0-0.023-0.01515.249-0.059-0.0590.0000.0000.0000.000
135A1344ALA00.0220.03116.9470.0460.0460.0000.0000.0000.000
136A1345VAL0-0.019-0.02012.945-0.002-0.0020.0000.0000.0000.000
137A1346GLY00.0180.01416.101-0.013-0.0130.0000.0000.0000.000
138A1347TYR00.0070.00610.5900.0160.0160.0000.0000.0000.000
139A1348TYR00.021-0.01115.214-0.047-0.0470.0000.0000.0000.000
140A1349GLY00.0560.03517.418-0.004-0.0040.0000.0000.0000.000
141A1350GLN0-0.031-0.02617.7960.0150.0150.0000.0000.0000.000
142A1351GLY00.0260.03316.029-0.028-0.0280.0000.0000.0000.000
143A1352PHE0-0.0250.00310.730-0.047-0.0470.0000.0000.0000.000
144A1353PRO00.0380.0269.902-0.017-0.0170.0000.0000.0000.000
145A1354SER00.023-0.01613.2520.0610.0610.0000.0000.0000.000
146A1355PHE0-0.026-0.0107.650-0.005-0.0050.0000.0000.0000.000
147A1356LEU0-0.002-0.0078.7620.0620.0620.0000.0000.0000.000
148A1357ARG10.9200.95313.4630.0150.0150.0000.0000.0000.000
149A1358ASN0-0.025-0.03516.3960.0080.0080.0000.0000.0000.000
150A1359LYS10.8000.92215.938-0.167-0.1670.0000.0000.0000.000
151A1360VAL00.018-0.00117.3430.0230.0230.0000.0000.0000.000
152A1361PHE0-0.012-0.00414.0680.0000.0000.0000.0000.0000.000
153A1362ILE0-0.0080.00716.6300.0120.0120.0000.0000.0000.000
154A1363TYR00.018-0.0038.912-0.159-0.1590.0000.0000.0000.000
155A1364ARG10.8680.92115.398-0.517-0.5170.0000.0000.0000.000
156A1365GLY00.0220.02015.5820.0920.0920.0000.0000.0000.000
157A1366LYS10.8480.89613.380-0.949-0.9490.0000.0000.0000.000
158A1367GLU-1-0.831-0.90316.6030.3180.3180.0000.0000.0000.000
159A1368TYR0-0.006-0.01619.3640.0040.0040.0000.0000.0000.000
160A1369GLU-1-0.858-0.89912.9491.0711.0710.0000.0000.0000.000
161A1370ARG10.9330.94517.729-0.351-0.3510.0000.0000.0000.000
162A1371ARG10.8210.89616.958-0.303-0.3030.0000.0000.0000.000
163A1372GLU-1-0.799-0.87316.4910.4080.4080.0000.0000.0000.000
164A1373ASP-1-0.831-0.92015.0240.5260.5260.0000.0000.0000.000
165A1374PHE00.0030.00811.0110.1030.1030.0000.0000.0000.000
166A1375GLN00.0340.01111.6040.1300.1300.0000.0000.0000.000
167A1376MET0-0.020-0.00412.213-0.003-0.0030.0000.0000.0000.000
168A1377GLN0-0.036-0.0158.2340.2290.2290.0000.0000.0000.000
169A1378LEU0-0.024-0.0137.5970.2160.2160.0000.0000.0000.000
170A1379MET0-0.009-0.0198.321-0.056-0.0560.0000.0000.0000.000
171A1380THR0-0.044-0.0227.075-0.235-0.2350.0000.0000.0000.000
172A1381GLN0-0.107-0.0543.7160.4690.8040.005-0.075-0.2660.000
173A1382PHE0-0.060-0.0265.369-0.606-0.539-0.001-0.001-0.0640.000
174A1383PRO00.0280.0117.7870.0550.0550.0000.0000.0000.000
175A1384ASN0-0.034-0.01411.023-0.016-0.0160.0000.0000.0000.000
176A1385ALA0-0.032-0.00512.5430.0080.0080.0000.0000.0000.000
177A1386GLU-1-0.871-0.93414.1430.1290.1290.0000.0000.0000.000
178A1387LYS10.8640.93516.501-0.143-0.1430.0000.0000.0000.000
179A1388MET00.0400.02117.845-0.017-0.0170.0000.0000.0000.000
180A1389ASN0-0.033-0.01520.7460.0280.0280.0000.0000.0000.000
181A1390THR0-0.009-0.01323.321-0.008-0.0080.0000.0000.0000.000
182A1391THR00.0380.00623.1930.0080.0080.0000.0000.0000.000
183A1392SER0-0.0140.00124.9110.0050.0050.0000.0000.0000.000
184A1393ALA00.0420.03025.0200.0090.0090.0000.0000.0000.000
185A1394PRO00.0050.01622.307-0.013-0.0130.0000.0000.0000.000
186A1395GLY00.0720.03825.610-0.003-0.0030.0000.0000.0000.000
187A1396ASP-1-0.850-0.94226.1730.0550.0550.0000.0000.0000.000
188A1397ASP-1-0.875-0.92526.6830.0400.0400.0000.0000.0000.000
189A1398VAL00.005-0.00321.699-0.008-0.0080.0000.0000.0000.000
190A1399LYS10.8090.89321.888-0.081-0.0810.0000.0000.0000.000
191A1400ASN0-0.079-0.03922.100-0.012-0.0120.0000.0000.0000.000
192A1401ALA00.0270.03222.690-0.017-0.0170.0000.0000.0000.000
193A1402PRO0-0.015-0.01820.8230.0060.0060.0000.0000.0000.000
194A1403GLY00.0200.02218.192-0.025-0.0250.0000.0000.0000.000
195A1404GLN0-0.051-0.03311.1230.0310.0310.0000.0000.0000.000
196A1405TYR00.013-0.00215.828-0.007-0.0070.0000.0000.0000.000
197A1406ILE00.0170.01111.2320.0170.0170.0000.0000.0000.000
198A1407GLN0-0.044-0.02515.586-0.006-0.0060.0000.0000.0000.000
199A1408CYS0-0.015-0.01415.6100.0630.0630.0000.0000.0000.000
200A1409PHE0-0.034-0.01317.612-0.029-0.0290.0000.0000.0000.000
201A1410THR00.0420.01120.1560.0370.0370.0000.0000.0000.000
202A1411VAL0-0.049-0.01821.195-0.037-0.0370.0000.0000.0000.000
203A1412GLN00.0180.00323.7110.0160.0160.0000.0000.0000.000
204A1413PRO00.003-0.00324.636-0.006-0.0060.0000.0000.0000.000
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