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About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: ZV89N

Calculation Name: 3PVE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PVE

Chain ID: A

ChEMBL ID:

UniProt ID: A2ASQ1

Base Structure: X-ray

Registration Date: 2023-09-23

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1810769.940108
FMO2-HF: Nuclear repulsion 1744934.689882
FMO2-HF: Total energy -65835.250226
FMO2-MP2: Total energy -66031.002018


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:1454:SER)


Summations of interaction energy for fragment #1(A:1454: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.
-12.686-7.059.697-8.004-7.33-0.054
Interaction energy analysis for fragmet #1(A:1454:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.002
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].
3A1456PRO00.0330.0073.827-1.3380.075-0.008-0.590-0.8160.003
4A1457PHE0-0.040-0.0216.1100.6780.6780.0000.0000.0000.000
5A1458LEU00.0070.0259.122-0.204-0.2040.0000.0000.0000.000
6A1459ALA0-0.0060.00712.4810.0790.0790.0000.0000.0000.000
7A1460ASP-1-0.797-0.88814.0430.1080.1080.0000.0000.0000.000
8A1461PHE0-0.002-0.02214.9340.0330.0330.0000.0000.0000.000
9A1462ASN00.057-0.00520.037-0.038-0.0380.0000.0000.0000.000
10A1463GLY00.0050.01723.352-0.009-0.0090.0000.0000.0000.000
11A1464PHE0-0.064-0.03824.758-0.021-0.0210.0000.0000.0000.000
12A1465SER00.0150.01319.4240.0010.0010.0000.0000.0000.000
13A1466TYR0-0.036-0.02418.110-0.030-0.0300.0000.0000.0000.000
14A1467LEU00.0030.01711.7340.0600.0600.0000.0000.0000.000
15A1468GLU-1-0.792-0.86214.7520.0460.0460.0000.0000.0000.000
16A1469LEU00.0300.01110.2390.0600.0600.0000.0000.0000.000
17A1470LYS10.9890.98411.8570.2360.2360.0000.0000.0000.000
18A1471GLY00.0680.03214.064-0.035-0.0350.0000.0000.0000.000
19A1472LEU00.0140.00315.493-0.063-0.0630.0000.0000.0000.000
20A1473HIS0-0.045-0.01516.930-0.066-0.0660.0000.0000.0000.000
21A1474THR0-0.082-0.05113.5770.0200.0200.0000.0000.0000.000
22A1475PHE0-0.0040.00710.013-0.060-0.0600.0000.0000.0000.000
23A1483MET0-0.038-0.02319.8410.0030.0030.0000.0000.0000.000
24A1484ALA00.012-0.00119.1740.0270.0270.0000.0000.0000.000
25A1485LEU0-0.022-0.00316.433-0.061-0.0610.0000.0000.0000.000
26A1486GLU-1-0.889-0.93515.701-0.402-0.4020.0000.0000.0000.000
27A1487MET0-0.019-0.01115.595-0.033-0.0330.0000.0000.0000.000
28A1488VAL00.0060.01515.7440.0230.0230.0000.0000.0000.000
29A1489PHE00.000-0.01416.6560.0150.0150.0000.0000.0000.000
30A1490LEU00.0270.03019.170-0.007-0.0070.0000.0000.0000.000
31A1491ALA0-0.031-0.00921.9450.0180.0180.0000.0000.0000.000
32A1492ARG10.8020.85321.898-0.136-0.1360.0000.0000.0000.000
33A1493GLY00.0650.04626.5950.0000.0000.0000.0000.0000.000
34A1494PRO0-0.049-0.03527.672-0.011-0.0110.0000.0000.0000.000
35A1495SER0-0.014-0.02729.158-0.015-0.0150.0000.0000.0000.000
36A1496GLY00.0380.03626.1780.0130.0130.0000.0000.0000.000
37A1497LEU0-0.079-0.03522.307-0.017-0.0170.0000.0000.0000.000
38A1498LEU00.0290.01220.1310.0120.0120.0000.0000.0000.000
39A1499LEU0-0.011-0.00516.785-0.007-0.0070.0000.0000.0000.000
40A1500TYR00.0550.02919.7140.0040.0040.0000.0000.0000.000
41A1501ASN00.0290.00818.679-0.028-0.0280.0000.0000.0000.000
42A1502GLY00.0570.02821.469-0.004-0.0040.0000.0000.0000.000
43A1503GLN0-0.0110.00623.8870.0000.0000.0000.0000.0000.000
44A1504LYS10.8940.93926.6370.0570.0570.0000.0000.0000.000
45A1505THR00.0350.04127.001-0.001-0.0010.0000.0000.0000.000
46A1506ASP-1-0.754-0.88529.555-0.037-0.0370.0000.0000.0000.000
47A1507GLY00.0240.01631.7770.0010.0010.0000.0000.0000.000
48A1508LYS10.8100.88533.1550.0280.0280.0000.0000.0000.000
49A1509GLY00.0100.00830.9830.0000.0000.0000.0000.0000.000
50A1510ASP-1-0.781-0.88328.135-0.125-0.1250.0000.0000.0000.000
51A1511PHE0-0.049-0.03425.7570.0060.0060.0000.0000.0000.000
52A1512VAL0-0.020-0.00621.871-0.008-0.0080.0000.0000.0000.000
53A1513SER00.017-0.00623.3110.0090.0090.0000.0000.0000.000
54A1514LEU0-0.0180.00220.834-0.010-0.0100.0000.0000.0000.000
55A1515ALA00.0120.01023.3960.0120.0120.0000.0000.0000.000
56A1516LEU00.0160.01924.571-0.011-0.0110.0000.0000.0000.000
57A1517HIS00.0710.03627.5200.0060.0060.0000.0000.0000.000
58A1518ASN00.008-0.01431.279-0.010-0.0100.0000.0000.0000.000
59A1519ARG10.9400.95630.0040.0200.0200.0000.0000.0000.000
60A1520HIS10.8210.93630.2190.0510.0510.0000.0000.0000.000
61A1521LEU00.0420.03524.0760.0040.0040.0000.0000.0000.000
62A1522GLU-1-0.785-0.87927.435-0.066-0.0660.0000.0000.0000.000
63A1523PHE0-0.024-0.00524.325-0.004-0.0040.0000.0000.0000.000
64A1524ARG10.8250.88826.7950.0750.0750.0000.0000.0000.000
65A1525TYR0-0.008-0.03526.813-0.016-0.0160.0000.0000.0000.000
66A1526ASP-1-0.819-0.89128.576-0.085-0.0850.0000.0000.0000.000
67A1527LEU0-0.069-0.03328.834-0.008-0.0080.0000.0000.0000.000
68A1528GLY00.0560.02431.456-0.002-0.0020.0000.0000.0000.000
69A1529LYS10.8340.93434.4400.0850.0850.0000.0000.0000.000
70A1530GLY00.0410.01435.3720.0050.0050.0000.0000.0000.000
71A1531ALA0-0.039-0.03432.335-0.008-0.0080.0000.0000.0000.000
72A1532ALA0-0.0110.00531.1420.0050.0050.0000.0000.0000.000
73A1533ILE0-0.029-0.02431.665-0.001-0.0010.0000.0000.0000.000
74A1534ILE0-0.0130.01629.5060.0030.0030.0000.0000.0000.000
75A1535ARG10.8630.91430.0900.0500.0500.0000.0000.0000.000
76A1536SER00.000-0.01429.252-0.002-0.0020.0000.0000.0000.000
77A1537LYS10.9230.95831.1820.0910.0910.0000.0000.0000.000
78A1538GLU-1-0.843-0.91432.513-0.070-0.0700.0000.0000.0000.000
79A1539PRO0-0.082-0.02431.924-0.005-0.0050.0000.0000.0000.000
80A1540ILE00.0510.01526.070-0.002-0.0020.0000.0000.0000.000
81A1541ALA00.0210.01429.4430.0100.0100.0000.0000.0000.000
82A1542LEU0-0.018-0.01627.993-0.006-0.0060.0000.0000.0000.000
83A1543GLY00.0160.01026.3830.0010.0010.0000.0000.0000.000
84A1544THR0-0.048-0.02325.677-0.002-0.0020.0000.0000.0000.000
85A1545TRP00.0370.01217.682-0.011-0.0110.0000.0000.0000.000
86A1546VAL0-0.018-0.00121.911-0.012-0.0120.0000.0000.0000.000
87A1547ARG10.9430.98418.9720.2310.2310.0000.0000.0000.000
88A1548VAL0-0.018-0.00720.2470.0200.0200.0000.0000.0000.000
89A1549PHE00.0260.01119.032-0.032-0.0320.0000.0000.0000.000
90A1550LEU0-0.018-0.00821.1470.0350.0350.0000.0000.0000.000
91A1551GLU-1-0.837-0.89721.885-0.294-0.2940.0000.0000.0000.000
92A1552ARG10.8870.93524.3150.2440.2440.0000.0000.0000.000
93A1553ASN0-0.0030.01325.613-0.027-0.0270.0000.0000.0000.000
94A1554GLY00.0580.02628.3240.0160.0160.0000.0000.0000.000
95A1555ARG10.8420.88830.0080.1160.1160.0000.0000.0000.000
96A1556LYS10.8330.92831.6280.1390.1390.0000.0000.0000.000
97A1557GLY00.0460.02028.572-0.018-0.0180.0000.0000.0000.000
98A1558ALA0-0.029-0.02827.5050.0130.0130.0000.0000.0000.000
99A1559LEU0-0.0050.01225.463-0.017-0.0170.0000.0000.0000.000
100A1560GLN00.0010.00325.0810.0160.0160.0000.0000.0000.000
101A1561VAL00.0160.00124.675-0.013-0.0130.0000.0000.0000.000
102A1562GLY0-0.007-0.01024.2760.0120.0120.0000.0000.0000.000
103A1563ASP-1-0.923-0.96125.219-0.152-0.1520.0000.0000.0000.000
104A1564GLY00.0090.02127.4690.0060.0060.0000.0000.0000.000
105A1565PRO0-0.005-0.02429.412-0.012-0.0120.0000.0000.0000.000
106A1566ARG10.8110.88627.1080.2150.2150.0000.0000.0000.000
107A1567VAL0-0.020-0.00230.2370.0100.0100.0000.0000.0000.000
108A1568LEU0-0.007-0.01230.880-0.012-0.0120.0000.0000.0000.000
109A1569GLY00.0340.01232.6090.0120.0120.0000.0000.0000.000
110A1570GLU-1-0.804-0.87433.087-0.129-0.1290.0000.0000.0000.000
111A1571SER00.0630.05732.8580.0040.0040.0000.0000.0000.000
112A1572PRO00.0130.00534.796-0.003-0.0030.0000.0000.0000.000
113A1573VAL00.0220.00937.381-0.006-0.0060.0000.0000.0000.000
114A1574PRO0-0.056-0.01338.9100.0050.0050.0000.0000.0000.000
115A1575HIS00.1000.04034.254-0.007-0.0070.0000.0000.0000.000
116A1576THR00.017-0.00732.480-0.002-0.0020.0000.0000.0000.000
117A1577MET0-0.031-0.02429.333-0.019-0.0190.0000.0000.0000.000
118A1578LEU00.0120.02023.7810.0080.0080.0000.0000.0000.000
119A1579ASN0-0.030-0.01226.093-0.029-0.0290.0000.0000.0000.000
120A1580LEU0-0.010-0.00320.9590.0160.0160.0000.0000.0000.000
121A1581LYS10.8520.90222.7750.1610.1610.0000.0000.0000.000
122A1582GLU-1-0.842-0.90321.922-0.027-0.0270.0000.0000.0000.000
123A1583PRO00.001-0.00617.316-0.042-0.0420.0000.0000.0000.000
124A1584LEU0-0.0330.00813.530-0.012-0.0120.0000.0000.0000.000
125A1585TYR0-0.077-0.05416.1170.0250.0250.0000.0000.0000.000
126A1586VAL0-0.004-0.01614.071-0.042-0.0420.0000.0000.0000.000
127A1587GLY00.0330.00416.8860.0490.0490.0000.0000.0000.000
128A1588GLY00.0570.02919.1540.0160.0160.0000.0000.0000.000
129A1589ALA0-0.048-0.03220.820-0.016-0.0160.0000.0000.0000.000
130A1590PRO0-0.0020.01421.3430.0080.0080.0000.0000.0000.000
131A1591ASP-1-0.779-0.86623.9720.0430.0430.0000.0000.0000.000
132A1592PHE00.0310.00125.018-0.015-0.0150.0000.0000.0000.000
133A1593SER0-0.043-0.03928.758-0.014-0.0140.0000.0000.0000.000
134A1594LYS10.8750.95424.838-0.013-0.0130.0000.0000.0000.000
135A1595LEU0-0.052-0.01724.704-0.011-0.0110.0000.0000.0000.000
136A1596ALA00.0070.00128.2990.0040.0040.0000.0000.0000.000
137A1597ARG10.8810.91330.4150.0160.0160.0000.0000.0000.000
138A1598GLY0-0.0070.00832.9270.0010.0010.0000.0000.0000.000
139A1599ALA0-0.011-0.00627.817-0.006-0.0060.0000.0000.0000.000
140A1600ALA0-0.053-0.02029.8330.0000.0000.0000.0000.0000.000
141A1601VAL00.0020.00526.6940.0020.0020.0000.0000.0000.000
142A1602ALA0-0.011-0.02329.7820.0020.0020.0000.0000.0000.000
143A1603SER00.0290.02428.2640.0060.0060.0000.0000.0000.000
144A1604GLY00.0650.03424.157-0.015-0.0150.0000.0000.0000.000
145A1605PHE0-0.081-0.03719.574-0.008-0.0080.0000.0000.0000.000
146A1606ASP-1-0.775-0.87722.8930.1100.1100.0000.0000.0000.000
147A1607GLY00.0350.00222.036-0.021-0.0210.0000.0000.0000.000
148A1608ALA00.0010.02317.4840.0270.0270.0000.0000.0000.000
149A1609ILE0-0.037-0.03014.237-0.048-0.0480.0000.0000.0000.000
150A1610GLN00.001-0.01013.2800.0320.0320.0000.0000.0000.000
151A1611LEU0-0.017-0.00311.504-0.078-0.0780.0000.0000.0000.000
152A1612VAL00.0270.00411.3420.0910.0910.0000.0000.0000.000
153A1613SER0-0.0240.00111.264-0.165-0.1650.0000.0000.0000.000
154A1614LEU00.0470.01612.5460.1430.1430.0000.0000.0000.000
155A1615ARG10.9170.93313.6040.3750.3750.0000.0000.0000.000
156A1616GLY00.0640.04013.280-0.032-0.0320.0000.0000.0000.000
157A1617HIS00.0070.0266.808-0.002-0.0020.0000.0000.0000.000
158A1618GLN00.031-0.0066.3810.3700.3700.0000.0000.0000.000
159A1619LEU0-0.001-0.0156.927-0.413-0.4130.0000.0000.0000.000
160A1620LEU0-0.049-0.0017.7450.1410.1410.0000.0000.0000.000
161A1621THR0-0.009-0.0352.6030.0340.7900.451-0.462-0.7460.001
162A1622GLN00.0300.0053.818-0.2830.2900.024-0.226-0.3710.001
163A1623GLU-1-0.832-0.9042.296-13.575-10.6849.231-6.714-5.407-0.059
164A1624HIS10.7760.8874.7201.3061.309-0.001-0.0120.0100.000
165A1625VAL0-0.0290.0037.362-0.170-0.1700.0000.0000.0000.000
166A1626LEU0-0.039-0.0129.8160.1050.1050.0000.0000.0000.000
167A1627ARG10.8310.88113.094-0.151-0.1510.0000.0000.0000.000
168A1628ALA00.0060.00213.175-0.048-0.0480.0000.0000.0000.000
169A1629VAL0-0.026-0.00715.2470.0350.0350.0000.0000.0000.000
170A1630ASP-1-0.796-0.90418.9370.2220.2220.0000.0000.0000.000
171A1631VAL0-0.0330.01214.259-0.031-0.0310.0000.0000.0000.000
172A1632ALA00.0160.01916.5740.0700.0700.0000.0000.0000.000
173A1633PRO0-0.020-0.01014.153-0.016-0.0160.0000.0000.0000.000
174A1634PHE0-0.005-0.01415.485-0.048-0.0480.0000.0000.0000.000
175A1635ALA0-0.015-0.00217.7150.0280.0280.0000.0000.0000.000
176A1636GLY00.0100.01020.487-0.020-0.0200.0000.0000.0000.000