Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: MVGJZ

Calculation Name: 2B9U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B9U

Chain ID: A

ChEMBL ID:

UniProt ID: Q96Z62

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1975447.572562
FMO2-HF: Nuclear repulsion 1903837.169778
FMO2-HF: Total energy -71610.402783
FMO2-MP2: Total energy -71819.68103


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-3.0662.433.958-3.729-5.724-0.012
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.001
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].
3A3PHE0-0.039-0.0222.692-0.3201.6810.314-0.978-1.3360.001
4A4GLU-1-0.890-0.9342.629-8.085-5.1650.907-1.921-1.907-0.019
5A5PHE00.000-0.0115.1190.3160.342-0.001-0.004-0.0210.000
6A6GLU-1-0.809-0.8968.301-0.764-0.7640.0000.0000.0000.000
7A7ASN0-0.032-0.02111.596-0.017-0.0170.0000.0000.0000.000
8A8LEU00.0320.01314.8470.0330.0330.0000.0000.0000.000
9A9GLY00.0120.01817.7070.0440.0440.0000.0000.0000.000
10A10MET0-0.037-0.02520.357-0.007-0.0070.0000.0000.0000.000
11A11GLY00.0300.00918.8300.0160.0160.0000.0000.0000.000
12A12ILE0-0.0080.01717.772-0.031-0.0310.0000.0000.0000.000
13A13ILE0-0.047-0.02211.708-0.009-0.0090.0000.0000.0000.000
14A14LEU00.0110.01912.4500.0200.0200.0000.0000.0000.000
15A15ILE0-0.035-0.0298.080-0.103-0.1030.0000.0000.0000.000
16A16LYS10.8600.9337.5761.2201.2200.0000.0000.0000.000
17A17PRO00.0170.0156.469-0.715-0.7150.0000.0000.0000.000
18A18LYS10.8450.9212.1546.0306.5792.738-0.826-2.4600.006
19A19VAL00.0080.0057.7340.2600.2600.0000.0000.0000.000
20A20PHE0-0.033-0.0216.5310.0350.0350.0000.0000.0000.000
21A21PRO00.0240.01311.6350.0740.0740.0000.0000.0000.000
22A22ASP-1-0.801-0.88414.724-0.178-0.1780.0000.0000.0000.000
23A23LYS10.9740.97717.4400.0770.0770.0000.0000.0000.000
24A24ARG10.7900.86317.2420.2020.2020.0000.0000.0000.000
25A25GLY00.0220.02819.9740.0060.0060.0000.0000.0000.000
26A26PHE0-0.040-0.02115.207-0.003-0.0030.0000.0000.0000.000
27A27PHE0-0.0060.00312.1450.0320.0320.0000.0000.0000.000
28A28LEU00.0400.01411.262-0.098-0.0980.0000.0000.0000.000
29A29GLU-1-0.824-0.8838.723-0.655-0.6550.0000.0000.0000.000
30A30VAL00.0170.01210.053-0.231-0.2310.0000.0000.0000.000
31A31PHE00.0430.00211.077-0.102-0.1020.0000.0000.0000.000
32A32LYS10.7980.8937.0900.7300.7300.0000.0000.0000.000
33A33SER00.0260.0179.978-0.046-0.0460.0000.0000.0000.000
34A34GLU-1-0.827-0.8908.9870.1820.1820.0000.0000.0000.000
35A35ASP-1-0.819-0.9315.369-0.756-0.7560.0000.0000.0000.000
36A36PHE00.0400.0037.250-0.059-0.0590.0000.0000.0000.000
37A37THR00.0210.00710.1650.0720.0720.0000.0000.0000.000
38A38LYS10.7780.8856.3820.0640.0640.0000.0000.0000.000
39A39MET0-0.054-0.0287.2290.1400.1400.0000.0000.0000.000
40A40ARG10.8590.93211.1860.4490.4490.0000.0000.0000.000
41A41ILE0-0.0170.00812.0670.0340.0340.0000.0000.0000.000
42A42PRO0-0.016-0.00214.6680.0050.0050.0000.0000.0000.000
43A43ASN00.007-0.01116.787-0.057-0.0570.0000.0000.0000.000
44A44VAL0-0.014-0.00816.9560.0070.0070.0000.0000.0000.000
45A45ILE0-0.058-0.03119.6260.0210.0210.0000.0000.0000.000
46A46GLN00.0400.02323.0990.0250.0250.0000.0000.0000.000
47A47THR0-0.018-0.00721.815-0.037-0.0370.0000.0000.0000.000
48A48ASN0-0.0040.02023.8040.0300.0300.0000.0000.0000.000
49A49MET00.0300.01124.319-0.030-0.0300.0000.0000.0000.000
50A50SER0-0.0530.00126.3600.0230.0230.0000.0000.0000.000
51A51PHE00.0290.01127.245-0.014-0.0140.0000.0000.0000.000
52A52SER0-0.025-0.00728.8870.0190.0190.0000.0000.0000.000
53A53ARG11.0031.01130.5070.1370.1370.0000.0000.0000.000
54A54LYS10.9650.97231.7500.1850.1850.0000.0000.0000.000
55A55GLY00.0180.01032.1340.0110.0110.0000.0000.0000.000
56A56VAL0-0.048-0.01631.8960.0050.0050.0000.0000.0000.000
57A57VAL0-0.013-0.00331.557-0.014-0.0140.0000.0000.0000.000
58A58ARG10.8600.93729.3760.2110.2110.0000.0000.0000.000
59A59GLY00.0070.01129.859-0.018-0.0180.0000.0000.0000.000
60A60LEU0-0.047-0.00729.3130.0090.0090.0000.0000.0000.000
61A61HIS0-0.032-0.05029.5860.0000.0000.0000.0000.0000.000
62A62TYR0-0.036-0.04828.712-0.020-0.0200.0000.0000.0000.000
63A63GLN0-0.036-0.02129.5710.0120.0120.0000.0000.0000.000
64A64ARG10.9050.95330.6540.1050.1050.0000.0000.0000.000
65A65THR00.0630.01130.945-0.001-0.0010.0000.0000.0000.000
66A66PRO0-0.117-0.05932.2100.0070.0070.0000.0000.0000.000
67A67LYS10.8930.93530.7110.1290.1290.0000.0000.0000.000
68A68GLU-1-0.791-0.87427.047-0.158-0.1580.0000.0000.0000.000
69A69GLN0-0.051-0.04725.225-0.006-0.0060.0000.0000.0000.000
70A70GLY00.0080.01821.2250.0000.0000.0000.0000.0000.000
71A71LYS10.8950.94720.7020.2670.2670.0000.0000.0000.000
72A72ILE00.0070.00814.460-0.030-0.0300.0000.0000.0000.000
73A73ILE0-0.0230.00917.6270.0280.0280.0000.0000.0000.000
74A74PHE00.0470.00915.055-0.054-0.0540.0000.0000.0000.000
75A75VAL00.0140.00817.8620.0600.0600.0000.0000.0000.000
76A76PRO0-0.0160.00719.189-0.015-0.0150.0000.0000.0000.000
77A77LYS10.8480.89920.1260.2920.2920.0000.0000.0000.000
78A78GLY00.0420.02623.3780.0090.0090.0000.0000.0000.000
79A79ARG10.8310.87522.7810.2630.2630.0000.0000.0000.000
80A80ILE0-0.039-0.00421.9800.0340.0340.0000.0000.0000.000
81A81LEU0-0.0120.00023.090-0.023-0.0230.0000.0000.0000.000
82A82ASP-1-0.754-0.89821.262-0.345-0.3450.0000.0000.0000.000
83A83VAL0-0.006-0.01823.163-0.005-0.0050.0000.0000.0000.000
84A84ALA00.0110.01122.6180.0020.0020.0000.0000.0000.000
85A85VAL00.014-0.00524.6040.0020.0020.0000.0000.0000.000
86A86ASP-1-0.710-0.79826.952-0.187-0.1870.0000.0000.0000.000
87A87VAL00.0130.00728.1450.0130.0130.0000.0000.0000.000
88A88ARG10.8510.90424.3140.2160.2160.0000.0000.0000.000
89A89LYS10.9950.97931.5020.1040.1040.0000.0000.0000.000
90A90SER0-0.036-0.01733.2230.0010.0010.0000.0000.0000.000
91A91SER0-0.032-0.02628.3930.0040.0040.0000.0000.0000.000
92A92PRO0-0.022-0.01028.6470.0040.0040.0000.0000.0000.000
93A93THR0-0.086-0.07426.6930.0010.0010.0000.0000.0000.000
94A94PHE00.0260.02829.494-0.011-0.0110.0000.0000.0000.000
95A95GLY00.0360.02131.3120.0070.0070.0000.0000.0000.000
96A96LYS10.9080.96827.9390.1500.1500.0000.0000.0000.000
97A97TYR00.016-0.00626.233-0.008-0.0080.0000.0000.0000.000
98A98VAL0-0.0060.01019.7900.0020.0020.0000.0000.0000.000
99A99LYS10.8960.95222.9830.2280.2280.0000.0000.0000.000
100A100ALA00.0180.00218.382-0.017-0.0170.0000.0000.0000.000
101A101GLU-1-0.793-0.85020.407-0.330-0.3300.0000.0000.0000.000
102A102LEU0-0.041-0.00116.359-0.050-0.0500.0000.0000.0000.000
103A103ASN0-0.002-0.02818.2260.0170.0170.0000.0000.0000.000
104A104GLU-1-0.756-0.84718.073-0.378-0.3780.0000.0000.0000.000
105A105GLU-1-0.964-0.97017.888-0.457-0.4570.0000.0000.0000.000
106A106ASN00.006-0.00814.863-0.071-0.0710.0000.0000.0000.000
107A107HIS0-0.0150.00013.456-0.164-0.1640.0000.0000.0000.000
108A108TYR0-0.005-0.01911.427-0.158-0.1580.0000.0000.0000.000
109A109MET0-0.055-0.02110.5980.1410.1410.0000.0000.0000.000
110A110LEU00.0170.02513.770-0.059-0.0590.0000.0000.0000.000
111A111TRP0-0.001-0.00814.6880.0410.0410.0000.0000.0000.000
112A112ILE0-0.022-0.02116.3210.0190.0190.0000.0000.0000.000
113A113PRO0-0.0020.01319.0930.0190.0190.0000.0000.0000.000
114A114PRO00.0410.00221.2420.0120.0120.0000.0000.0000.000
115A115GLY0-0.022-0.01024.9290.0010.0010.0000.0000.0000.000
116A116PHE00.003-0.01323.3490.0040.0040.0000.0000.0000.000
117A117ALA0-0.047-0.01126.6290.0010.0010.0000.0000.0000.000
118A118HIS0-0.093-0.07123.4070.0100.0100.0000.0000.0000.000
119A119GLY00.0700.01226.2830.0200.0200.0000.0000.0000.000
120A120PHE0-0.045-0.01025.155-0.019-0.0190.0000.0000.0000.000
121A121GLN00.0090.01127.1620.0130.0130.0000.0000.0000.000
122A122ALA0-0.024-0.00527.532-0.021-0.0210.0000.0000.0000.000
123A123LEU00.017-0.00825.3040.0210.0210.0000.0000.0000.000
124A124GLU-1-0.921-0.97527.060-0.247-0.2470.0000.0000.0000.000
125A125ASP-1-0.835-0.92128.940-0.190-0.1900.0000.0000.0000.000
126A126SER0-0.029-0.03325.287-0.018-0.0180.0000.0000.0000.000
127A127ILE0-0.062-0.02624.0600.0220.0220.0000.0000.0000.000
128A128VAL00.0220.02222.237-0.028-0.0280.0000.0000.0000.000
129A129ILE0-0.011-0.01619.9730.0360.0360.0000.0000.0000.000
130A130TYR0-0.012-0.03020.667-0.027-0.0270.0000.0000.0000.000
131A131PHE00.018-0.00316.5980.0270.0270.0000.0000.0000.000
132A132ILE0-0.009-0.00120.124-0.017-0.0170.0000.0000.0000.000
133A133THR00.0710.00918.2600.0000.0000.0000.0000.0000.000
134A134HIS0-0.0030.01220.745-0.001-0.0010.0000.0000.0000.000
135A135ASN0-0.012-0.00624.2520.0300.0300.0000.0000.0000.000
136A136GLU-1-0.875-0.92827.173-0.159-0.1590.0000.0000.0000.000
137A137TYR0-0.071-0.04128.9010.0050.0050.0000.0000.0000.000
138A138SER0-0.001-0.00831.3240.0120.0120.0000.0000.0000.000
139A139PRO00.0660.02434.2530.0000.0000.0000.0000.0000.000
140A140PRO0-0.0200.00137.0410.0010.0010.0000.0000.0000.000
141A141HIS0-0.011-0.00534.3590.0030.0030.0000.0000.0000.000
142A142GLU-1-0.805-0.86733.665-0.151-0.1510.0000.0000.0000.000
143A143ARG10.8590.93434.0140.1260.1260.0000.0000.0000.000
144A144CYS0-0.0540.00333.638-0.007-0.0070.0000.0000.0000.000
145A145ILE00.0390.02632.1070.0090.0090.0000.0000.0000.000
146A146SER0-0.012-0.00334.545-0.009-0.0090.0000.0000.0000.000
147A147TYR00.1100.03633.512-0.005-0.0050.0000.0000.0000.000
148A148SER0-0.038-0.01134.277-0.005-0.0050.0000.0000.0000.000
149A149TYR0-0.072-0.04731.8010.0060.0060.0000.0000.0000.000
150A150ILE0-0.049-0.02229.680-0.005-0.0050.0000.0000.0000.000
151A151ASP-1-0.927-0.94432.601-0.153-0.1530.0000.0000.0000.000
152A152TRP0-0.057-0.05328.001-0.020-0.0200.0000.0000.0000.000
153A153PRO00.0230.01429.3930.0080.0080.0000.0000.0000.000
154A154ILE0-0.070-0.02731.5540.0090.0090.0000.0000.0000.000
155A155LYS10.9300.95734.5760.1280.1280.0000.0000.0000.000
156A156GLU-1-0.879-0.93838.101-0.130-0.1300.0000.0000.0000.000
157A157VAL0-0.0020.00235.778-0.007-0.0070.0000.0000.0000.000
158A158ILE0-0.049-0.01936.1800.0080.0080.0000.0000.0000.000
159A159ILE00.0290.00735.834-0.010-0.0100.0000.0000.0000.000
160A160SER00.0000.01036.8060.0090.0090.0000.0000.0000.000
161A161ASP-1-0.827-0.92938.923-0.109-0.1090.0000.0000.0000.000
162A162LYS10.8720.91336.0850.1420.1420.0000.0000.0000.000
163A163ASP-1-0.803-0.90934.249-0.166-0.1660.0000.0000.0000.000
164A164LEU0-0.052-0.02437.6130.0000.0000.0000.0000.0000.000
165A165GLN0-0.019-0.00540.6550.0050.0050.0000.0000.0000.000
166A167PRO00.0140.02138.8560.0020.0020.0000.0000.0000.000
167A168SER00.0330.00138.476-0.007-0.0070.0000.0000.0000.000
168A169LEU00.0510.01834.0440.0010.0010.0000.0000.0000.000
169A170GLU-1-0.928-0.97337.334-0.116-0.1160.0000.0000.0000.000
170A171LYS10.8560.93340.3660.0930.0930.0000.0000.0000.000
171A172ALA0-0.0090.01337.3850.0030.0030.0000.0000.0000.000
172A173GLU-1-0.923-0.94238.953-0.094-0.0940.0000.0000.0000.000
173A174VAL0-0.079-0.03234.499-0.008-0.0080.0000.0000.0000.000
174A175PHE00.0330.01829.4280.0030.0030.0000.0000.0000.000
175A176ASP-1-0.935-0.94532.131-0.112-0.1120.0000.0000.0000.000