Manual

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: M9NZZ

Calculation Name: 2FQ4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FQ4

Chain ID: A

ChEMBL ID:

UniProt ID: Q81BJ4

Base Structure: X-ray

Registration Date: 2023-09-27

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1893971.595326
FMO2-HF: Nuclear repulsion 1823066.472547
FMO2-HF: Total energy -70905.122779
FMO2-MP2: Total energy -71117.848989


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:9:ARG)


Summations of interaction energy for fragment #1(A:9: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.
25.84329.6270.166-1.594-2.3550.007
Interaction energy analysis for fragmet #1(A:9:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.002 / q_NPA : 0.993
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].
3A11ILE00.1030.0443.8134.3346.442-0.016-0.889-1.2020.000
4A12GLU-1-0.803-0.8865.518-22.130-22.1300.0000.0000.0000.000
5A13THR0-0.024-0.0256.7373.3153.3150.0000.0000.0000.000
6A14GLN0-0.038-0.0094.492-0.225-0.089-0.001-0.012-0.1230.000
7A15LYS10.9360.9537.16724.79924.7990.0000.0000.0000.000
8A16ALA00.0050.02410.0751.8521.8520.0000.0000.0000.000
9A17ILE00.006-0.0068.9601.4051.4050.0000.0000.0000.000
10A18LEU0-0.012-0.0029.2541.1071.1070.0000.0000.0000.000
11A19SER0-0.002-0.01012.7841.0851.0850.0000.0000.0000.000
12A20ALA00.0430.03015.2070.9280.9280.0000.0000.0000.000
13A21SER0-0.078-0.05015.4000.9000.9000.0000.0000.0000.000
14A22TYR00.0310.01617.2360.7290.7290.0000.0000.0000.000
15A23GLU-1-0.843-0.91518.941-13.427-13.4270.0000.0000.0000.000
16A24LEU00.003-0.00619.5660.5740.5740.0000.0000.0000.000
17A25LEU0-0.045-0.01521.2900.5080.5080.0000.0000.0000.000
18A26LEU0-0.016-0.01023.1050.4590.4590.0000.0000.0000.000
19A27GLU-1-0.844-0.87324.509-10.921-10.9210.0000.0000.0000.000
20A28SER0-0.096-0.05225.5420.3660.3660.0000.0000.0000.000
21A29GLY00.0760.05026.6860.2970.2970.0000.0000.0000.000
22A30PHE00.0320.00221.592-0.249-0.2490.0000.0000.0000.000
23A31LYS10.8830.94324.8438.6548.6540.0000.0000.0000.000
24A32ALA00.0180.01426.954-0.043-0.0430.0000.0000.0000.000
25A33VAL00.0430.04520.223-0.198-0.1980.0000.0000.0000.000
26A34THR00.012-0.00222.1110.0820.0820.0000.0000.0000.000
27A35VAL00.0540.00816.323-0.263-0.2630.0000.0000.0000.000
28A36ASP-1-0.849-0.90618.320-12.594-12.5940.0000.0000.0000.000
29A37LYS10.9510.97420.43610.12810.1280.0000.0000.0000.000
30A38ILE00.0110.01515.192-0.177-0.1770.0000.0000.0000.000
31A39ALA0-0.046-0.02815.932-0.611-0.6110.0000.0000.0000.000
32A40GLU-1-0.939-0.96716.993-12.134-12.1340.0000.0000.0000.000
33A41ARG10.7360.82918.76812.11712.1170.0000.0000.0000.000
34A42ALA0-0.011-0.01813.809-0.225-0.2250.0000.0000.0000.000
35A43LYS10.8810.96215.07214.08114.0810.0000.0000.0000.000
36A44VAL0-0.0010.01211.480-1.181-1.1810.0000.0000.0000.000
37A45SER00.0230.01413.3120.8070.8070.0000.0000.0000.000
38A46LYS10.9410.92113.71611.82911.8290.0000.0000.0000.000
39A47ALA0-0.0060.00913.510-0.201-0.2010.0000.0000.0000.000
40A48THR0-0.013-0.0228.356-1.228-1.2280.0000.0000.0000.000
41A49ILE00.0300.0269.548-0.935-0.9350.0000.0000.0000.000
42A50TYR0-0.014-0.01610.950-0.064-0.0640.0000.0000.0000.000
43A51LYS10.8640.9515.38827.17527.1750.0000.0000.0000.000
44A52TRP0-0.067-0.0343.289-3.034-1.4940.183-0.693-1.0300.007
45A53TRP0-0.008-0.0198.236-0.053-0.0530.0000.0000.0000.000
46A54PRO00.0440.01512.1280.3100.3100.0000.0000.0000.000
47A55ASN0-0.010-0.00415.3880.7660.7660.0000.0000.0000.000
48A56LYS10.8670.91316.67310.30510.3050.0000.0000.0000.000
49A57ALA00.0300.02718.231-0.154-0.1540.0000.0000.0000.000
50A58ALA0-0.0100.01414.616-0.165-0.1650.0000.0000.0000.000
51A59VAL0-0.016-0.01012.552-0.339-0.3390.0000.0000.0000.000
52A60VAL00.0240.01414.457-0.255-0.2550.0000.0000.0000.000
53A61MET0-0.0100.00917.3420.2240.2240.0000.0000.0000.000
54A62ASP-1-0.771-0.86711.479-17.516-17.5160.0000.0000.0000.000
55A63GLY0-0.004-0.00313.982-0.551-0.5510.0000.0000.0000.000
56A64PHE0-0.010-0.01515.258-0.014-0.0140.0000.0000.0000.000
57A65LEU0-0.060-0.03815.5670.1740.1740.0000.0000.0000.000
58A66SER0-0.072-0.03012.900-0.605-0.6050.0000.0000.0000.000
59A67ALA0-0.032-0.00114.764-0.160-0.1600.0000.0000.0000.000
60A68ALA00.0180.02317.8600.4760.4760.0000.0000.0000.000
61A69ALA0-0.0030.00419.326-0.490-0.4900.0000.0000.0000.000
62A70ALA00.0450.01420.0760.4540.4540.0000.0000.0000.000
63A71ARG10.8940.96218.10714.56314.5630.0000.0000.0000.000
64A72LEU00.0410.03121.229-0.005-0.0050.0000.0000.0000.000
65A73PRO00.0070.00024.389-0.295-0.2950.0000.0000.0000.000
66A74VAL0-0.015-0.00825.2950.2060.2060.0000.0000.0000.000
67A75PRO0-0.0180.01927.8810.0090.0090.0000.0000.0000.000
68A76ASP-1-0.844-0.94231.585-9.025-9.0250.0000.0000.0000.000
69A77THR0-0.046-0.05633.5860.1460.1460.0000.0000.0000.000
70A78GLY0-0.0060.00336.8300.2000.2000.0000.0000.0000.000
71A79SER0-0.005-0.00238.3070.2150.2150.0000.0000.0000.000
72A80ALA00.003-0.00237.472-0.189-0.1890.0000.0000.0000.000
73A81LEU00.0210.02237.667-0.154-0.1540.0000.0000.0000.000
74A82ASN00.0460.00638.816-0.032-0.0320.0000.0000.0000.000
75A83ASP-1-0.742-0.83434.160-8.736-8.7360.0000.0000.0000.000
76A84ILE0-0.013-0.02233.524-0.257-0.2570.0000.0000.0000.000
77A85LEU00.0280.03434.849-0.142-0.1420.0000.0000.0000.000
78A86ILE00.0070.02032.108-0.099-0.0990.0000.0000.0000.000
79A87HIS00.0080.02327.621-0.075-0.0750.0000.0000.0000.000
80A88ALA00.0240.01130.924-0.207-0.2070.0000.0000.0000.000
81A89THR00.0140.00033.1840.0390.0390.0000.0000.0000.000
82A90SER0-0.041-0.01629.329-0.211-0.2110.0000.0000.0000.000
83A91LEU0-0.041-0.02227.349-0.226-0.2260.0000.0000.0000.000
84A92ALA00.0280.00729.662-0.090-0.0900.0000.0000.0000.000
85A93ASN0-0.040-0.04031.327-0.067-0.0670.0000.0000.0000.000
86A94PHE00.0040.00623.336-0.110-0.1100.0000.0000.0000.000
87A95LEU0-0.0130.00928.037-0.094-0.0940.0000.0000.0000.000
88A96ILE0-0.0100.00929.8720.0690.0690.0000.0000.0000.000
89A97SER0-0.067-0.03827.8780.0140.0140.0000.0000.0000.000
90A98ARG10.9330.94628.6529.0759.0750.0000.0000.0000.000
91A99GLU-1-0.880-0.93923.746-10.706-10.7060.0000.0000.0000.000
92A100GLY00.0140.00325.554-0.149-0.1490.0000.0000.0000.000
93A101THR0-0.026-0.01727.1630.2200.2200.0000.0000.0000.000
94A102ILE00.0380.02123.3370.1140.1140.0000.0000.0000.000
95A103ILE0-0.040-0.01224.126-0.033-0.0330.0000.0000.0000.000
96A104ASN00.012-0.00527.056-0.075-0.0750.0000.0000.0000.000
97A105GLU-1-0.904-0.94428.077-9.245-9.2450.0000.0000.0000.000
98A106LEU0-0.034-0.01722.5840.0150.0150.0000.0000.0000.000
99A107VAL00.0210.00126.6680.0290.0290.0000.0000.0000.000
100A108GLY00.0340.02229.0890.2090.2090.0000.0000.0000.000
101A109GLU-1-0.807-0.93227.798-9.078-9.0780.0000.0000.0000.000
102A110GLY0-0.067-0.03328.0750.0150.0150.0000.0000.0000.000
103A111GLN0-0.089-0.03728.7740.1750.1750.0000.0000.0000.000
104A112PHE0-0.043-0.01931.3700.2000.2000.0000.0000.0000.000
105A113ASP-1-0.839-0.89926.204-10.148-10.1480.0000.0000.0000.000
106A114SER00.0580.01627.319-0.242-0.2420.0000.0000.0000.000
107A115LYS10.8350.89822.8899.9909.9900.0000.0000.0000.000
108A116LEU0-0.007-0.00422.198-0.440-0.4400.0000.0000.0000.000
109A117ALA00.0220.00623.225-0.225-0.2250.0000.0000.0000.000
110A118GLU-1-0.894-0.94022.191-10.625-10.6250.0000.0000.0000.000
111A119GLU-1-0.752-0.86217.260-14.130-14.1300.0000.0000.0000.000
112A120TYR00.0170.00820.191-0.282-0.2820.0000.0000.0000.000
113A121ARG10.8910.95022.3659.6669.6660.0000.0000.0000.000
114A122VAL00.0070.00518.519-0.018-0.0180.0000.0000.0000.000
115A123ARG10.7810.83812.46015.26215.2620.0000.0000.0000.000
116A124TYR0-0.022-0.00818.656-0.258-0.2580.0000.0000.0000.000
117A125PHE00.019-0.00221.361-0.013-0.0130.0000.0000.0000.000
118A126GLN0-0.0170.00019.7460.2280.2280.0000.0000.0000.000
119A127PRO0-0.0100.00219.3090.1750.1750.0000.0000.0000.000
120A128ARG10.8390.91519.77412.27412.2740.0000.0000.0000.000
121A129ARG10.8460.89824.9739.1819.1810.0000.0000.0000.000
122A130LEU0-0.005-0.00322.2670.2470.2470.0000.0000.0000.000
123A131GLN0-0.061-0.04124.0830.1460.1460.0000.0000.0000.000
124A132ALA00.0200.01526.6870.2240.2240.0000.0000.0000.000
125A133LYS10.8690.91528.3599.7569.7560.0000.0000.0000.000
126A134GLN0-0.011-0.00524.5520.1400.1400.0000.0000.0000.000
127A135LEU0-0.042-0.01729.9710.1820.1820.0000.0000.0000.000
128A136LEU00.0220.01232.6170.2680.2680.0000.0000.0000.000
129A137GLU-1-0.803-0.90131.124-8.994-8.9940.0000.0000.0000.000
130A138LYS10.6930.84331.7829.2699.2690.0000.0000.0000.000
131A139GLY00.0400.01235.6480.1840.1840.0000.0000.0000.000
132A140ILE0-0.018-0.00936.8660.2040.2040.0000.0000.0000.000
133A141LYS10.9030.95735.4868.5878.5870.0000.0000.0000.000
134A142ARG10.8330.92536.6657.9007.9000.0000.0000.0000.000
135A143GLY0-0.0180.00341.4760.1540.1540.0000.0000.0000.000
136A144GLU-1-0.786-0.88840.764-7.240-7.2400.0000.0000.0000.000
137A145LEU0-0.066-0.02738.7160.0350.0350.0000.0000.0000.000
138A146LYS10.9630.97443.1556.7646.7640.0000.0000.0000.000
139A147GLU-1-0.917-0.95743.618-6.169-6.1690.0000.0000.0000.000
140A148ASN0-0.046-0.02742.756-0.078-0.0780.0000.0000.0000.000
141A149LEU0-0.0180.00338.1440.0450.0450.0000.0000.0000.000
142A150ASP-1-0.838-0.90737.497-7.722-7.7220.0000.0000.0000.000
143A151ILE00.0110.00332.986-0.007-0.0070.0000.0000.0000.000
144A152GLU-1-0.807-0.91030.824-9.195-9.1950.0000.0000.0000.000
145A153LEU00.0360.02534.232-0.014-0.0140.0000.0000.0000.000
146A154SER0-0.044-0.05737.0230.1510.1510.0000.0000.0000.000
147A155ILE0-0.025-0.00630.7550.0150.0150.0000.0000.0000.000
148A156ASP-1-0.854-0.90934.090-8.238-8.2380.0000.0000.0000.000
149A157LEU0-0.050-0.02235.8280.0970.0970.0000.0000.0000.000
150A158ILE0-0.0110.00734.9270.0780.0780.0000.0000.0000.000
151A159TYR00.005-0.05828.257-0.123-0.1230.0000.0000.0000.000
152A160GLY00.0110.02233.980-0.045-0.0450.0000.0000.0000.000
153A161PRO00.003-0.01336.2880.0230.0230.0000.0000.0000.000
154A162ILE00.0100.02332.9470.0610.0610.0000.0000.0000.000
155A163PHE0-0.005-0.02128.687-0.055-0.0550.0000.0000.0000.000
156A164TYR00.0150.01934.2560.0280.0280.0000.0000.0000.000
157A165ARG10.8370.91037.7456.9646.9640.0000.0000.0000.000
158A166LEU0-0.050-0.01830.9460.0620.0620.0000.0000.0000.000
159A167LEU0-0.044-0.02931.682-0.035-0.0350.0000.0000.0000.000
160A168VAL0-0.041-0.01235.8150.0760.0760.0000.0000.0000.000
161A169THR0-0.011-0.01039.5060.0580.0580.0000.0000.0000.000
162A170GLY00.0270.03039.7090.1270.1270.0000.0000.0000.000
163A171GLU-1-0.927-0.94740.752-6.348-6.3480.0000.0000.0000.000
164A172LYS10.8820.92840.2156.5436.5430.0000.0000.0000.000
165A173LEU00.0180.01434.2590.1030.1030.0000.0000.0000.000
166A174ASP-1-0.814-0.88837.313-7.097-7.0970.0000.0000.0000.000
167A175ASP-1-0.790-0.91337.329-7.913-7.9130.0000.0000.0000.000
168A176SER0-0.053-0.03339.3320.0460.0460.0000.0000.0000.000
169A177TYR00.0230.00739.2820.1070.1070.0000.0000.0000.000
170A178VAL00.011-0.00536.1050.0280.0280.0000.0000.0000.000
171A179HIS00.015-0.00139.396-0.121-0.1210.0000.0000.0000.000
172A180ASP-1-0.883-0.93841.594-6.395-6.3950.0000.0000.0000.000
173A181LEU0-0.073-0.02038.1550.0900.0900.0000.0000.0000.000
174A182VAL0-0.010-0.00837.7910.0010.0010.0000.0000.0000.000
175A183ILE00.0250.00940.6890.0460.0460.0000.0000.0000.000
176A184ASN0-0.035-0.02444.1940.1870.1870.0000.0000.0000.000
177A185ALA0-0.048-0.00441.0940.0850.0850.0000.0000.0000.000
178A186PHE0-0.037-0.02038.969-0.040-0.0400.0000.0000.0000.000
179A187GLU-1-0.879-0.95343.947-6.068-6.0680.0000.0000.0000.000
180A188GLY0-0.035-0.00746.8180.1120.1120.0000.0000.0000.000
181A189ILE00.0390.00148.0860.0680.0680.0000.0000.0000.000
182A190ARG10.8390.92750.8025.6555.6550.0000.0000.0000.000
183A191LEU00.0530.03253.279-0.046-0.0460.0000.0000.0000.000
184A192ARG10.8430.93247.6986.1646.1640.0000.0000.0000.000