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: M3JQZ

Calculation Name: 2FPN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FPN

Chain ID: A

ChEMBL ID:

UniProt ID: O32277

Base Structure: X-ray

Registration Date: 2023-06-19

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2202720.709792
FMO2-HF: Nuclear repulsion 2114527.57116
FMO2-HF: Total energy -88193.138633
FMO2-MP2: Total energy -88448.680583


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:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-8.849-3.1550.892-3.151-3.434-0.016
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.013
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].
3A3PRO00.017-0.0103.819-1.963-0.096-0.014-0.986-0.8660.005
4A4LEU00.0210.0166.6000.4080.4080.0000.0000.0000.000
5A5ALA00.0100.0163.4960.1440.4510.012-0.099-0.2200.000
6A6GLN00.0180.0032.783-2.280-0.6600.667-0.979-1.308-0.011
7A7MET0-0.084-0.0415.7460.6610.6610.0000.0000.0000.000
8A8ALA00.0190.0218.7640.2590.2590.0000.0000.0000.000
9A9GLU-1-0.874-0.9445.661-1.193-1.1930.0000.0000.0000.000
10A10GLY0-0.102-0.0499.1590.2150.2150.0000.0000.0000.000
11A11MET0-0.041-0.02610.8320.1150.1150.0000.0000.0000.000
12A12GLU-1-0.850-0.92412.148-0.516-0.5160.0000.0000.0000.000
13A13ARG10.9200.9648.4390.5510.5510.0000.0000.0000.000
14A14GLN0-0.098-0.03014.7590.0560.0560.0000.0000.0000.000
15A15ASP-1-0.920-0.96916.971-0.169-0.1690.0000.0000.0000.000
16A16VAL0-0.116-0.05316.8520.0160.0160.0000.0000.0000.000
17A17SER00.0180.01217.156-0.039-0.0390.0000.0000.0000.000
18A18ILE0-0.047-0.00613.342-0.011-0.0110.0000.0000.0000.000
19A19ASP-1-0.850-0.91617.766-0.260-0.2600.0000.0000.0000.000
20A20LYS10.8950.93718.9050.3390.3390.0000.0000.0000.000
21A21TRP0-0.021-0.00914.077-0.077-0.0770.0000.0000.0000.000
22A22THR0-0.056-0.04716.1000.0570.0570.0000.0000.0000.000
23A23LEU00.0370.03011.379-0.081-0.0810.0000.0000.0000.000
24A24HIS00.0070.00015.4170.0660.0660.0000.0000.0000.000
25A25ALA00.0590.04316.231-0.038-0.0380.0000.0000.0000.000
26A26LYS10.9350.95318.0100.2470.2470.0000.0000.0000.000
27A27GLN0-0.032-0.02421.081-0.002-0.0020.0000.0000.0000.000
28A28ASN0-0.035-0.02923.2170.0050.0050.0000.0000.0000.000
29A29LEU00.0250.00326.5210.0060.0060.0000.0000.0000.000
30A30SER0-0.050-0.02629.2180.0030.0030.0000.0000.0000.000
31A31LEU00.0040.00631.1780.0040.0040.0000.0000.0000.000
32A32THR0-0.003-0.00334.9760.0000.0000.0000.0000.0000.000
33A33GLU-1-0.834-0.92837.661-0.075-0.0750.0000.0000.0000.000
34A34LYS10.9850.97538.9500.0520.0520.0000.0000.0000.000
35A35GLU-1-0.825-0.90935.238-0.075-0.0750.0000.0000.0000.000
36A36PHE00.0130.00133.406-0.003-0.0030.0000.0000.0000.000
37A37TYR00.0410.00234.656-0.005-0.0050.0000.0000.0000.000
38A38GLN0-0.0390.00135.2410.0000.0000.0000.0000.0000.000
39A39LYS10.9660.98126.8940.1190.1190.0000.0000.0000.000
40A40VAL00.0170.01031.417-0.004-0.0040.0000.0000.0000.000
41A41GLN0-0.020-0.00532.805-0.001-0.0010.0000.0000.0000.000
42A42ARG10.9430.96330.4460.0860.0860.0000.0000.0000.000
43A43LEU00.0050.01426.689-0.001-0.0010.0000.0000.0000.000
44A44LYS10.9280.97029.2530.0910.0910.0000.0000.0000.000
45A45GLN0-0.044-0.02031.9530.0040.0040.0000.0000.0000.000
46A46GLU-1-0.948-0.97525.455-0.095-0.0950.0000.0000.0000.000
47A47TYR0-0.041-0.02122.600-0.004-0.0040.0000.0000.0000.000
48A48ARG10.9420.95427.3530.0820.0820.0000.0000.0000.000
49A49GLN00.0320.02823.6920.0220.0220.0000.0000.0000.000
50A50TYR0-0.058-0.01922.868-0.008-0.0080.0000.0000.0000.000
51A51ASP-1-0.885-0.92229.260-0.110-0.1100.0000.0000.0000.000
52A52TRP0-0.034-0.03828.311-0.008-0.0080.0000.0000.0000.000
53A53VAL00.0180.01933.6960.0080.0080.0000.0000.0000.000
54A54ILE0-0.053-0.03134.896-0.005-0.0050.0000.0000.0000.000
55A55ALA00.0020.00236.4080.0040.0040.0000.0000.0000.000
56A56ARG10.8880.93637.5550.0750.0750.0000.0000.0000.000
57A57GLU-1-0.881-0.93637.314-0.112-0.1120.0000.0000.0000.000
58A58ASP-1-0.872-0.92939.934-0.082-0.0820.0000.0000.0000.000
59A59LYS10.8520.92741.6060.0760.0760.0000.0000.0000.000
60A60MET0-0.018-0.01434.602-0.003-0.0030.0000.0000.0000.000
61A61ILE0-0.001-0.00136.6290.0030.0030.0000.0000.0000.000
62A62LYS10.9850.99231.5920.1440.1440.0000.0000.0000.000
63A63ALA0-0.0130.00832.2320.0060.0060.0000.0000.0000.000
64A64ILE0-0.015-0.02629.384-0.010-0.0100.0000.0000.0000.000
65A65GLY00.0250.01628.9400.0100.0100.0000.0000.0000.000
66A66THR00.007-0.01427.543-0.024-0.0240.0000.0000.0000.000
67A67TYR00.0740.03523.6080.0120.0120.0000.0000.0000.000
68A68THR0-0.046-0.00724.701-0.017-0.0170.0000.0000.0000.000
69A69ASP-1-0.776-0.87521.476-0.190-0.1900.0000.0000.0000.000
70A70LYS10.9730.95323.0370.1130.1130.0000.0000.0000.000
71A71LYS10.9200.98121.6140.1280.1280.0000.0000.0000.000
72A72ASN0-0.052-0.04018.4330.0020.0020.0000.0000.0000.000
73A73ARG10.8670.96717.1440.2390.2390.0000.0000.0000.000
74A74THR00.0060.04718.071-0.042-0.0420.0000.0000.0000.000
75A75SER00.010-0.01120.1860.0440.0440.0000.0000.0000.000
76A76PHE00.0260.01017.934-0.025-0.0250.0000.0000.0000.000
77A77ARG10.8950.95622.7210.2770.2770.0000.0000.0000.000
78A78LEU00.0120.01223.373-0.017-0.0170.0000.0000.0000.000
79A79GLN0-0.038-0.01825.3070.0120.0120.0000.0000.0000.000
80A80LEU00.0040.00727.131-0.006-0.0060.0000.0000.0000.000
81A81VAL0-0.036-0.01329.6770.0070.0070.0000.0000.0000.000
82A82THR00.0130.01131.622-0.001-0.0010.0000.0000.0000.000
83A83THR0-0.008-0.00634.3380.0010.0010.0000.0000.0000.000
84A84LEU00.0230.01336.9230.0030.0030.0000.0000.0000.000
85A85LYS10.9420.96740.1890.0710.0710.0000.0000.0000.000
86A86LYS10.8910.93336.5170.0930.0930.0000.0000.0000.000
87A87HIS00.0370.03141.438-0.003-0.0030.0000.0000.0000.000
88A88ASN00.000-0.01236.850-0.001-0.0010.0000.0000.0000.000
89A89PRO00.0280.04536.559-0.003-0.0030.0000.0000.0000.000
90A90THR00.0120.00032.336-0.001-0.0010.0000.0000.0000.000
91A91SER0-0.012-0.02731.4800.0020.0020.0000.0000.0000.000
92A92TYR0-0.009-0.01126.133-0.001-0.0010.0000.0000.0000.000
93A93LEU00.0100.01724.0730.0110.0110.0000.0000.0000.000
94A94LEU0-0.053-0.02621.429-0.007-0.0070.0000.0000.0000.000
95A95TYR0-0.045-0.03216.7630.0360.0360.0000.0000.0000.000
96A96GLU-1-0.920-0.97719.357-0.343-0.3430.0000.0000.0000.000
97A97GLN00.0360.00615.578-0.011-0.0110.0000.0000.0000.000
98A98MET0-0.028-0.00717.744-0.042-0.0420.0000.0000.0000.000
99A99SER00.004-0.03417.3510.0330.0330.0000.0000.0000.000
100A100LEU0-0.020-0.00718.839-0.026-0.0260.0000.0000.0000.000
101A101GLU-1-0.841-0.91918.842-0.216-0.2160.0000.0000.0000.000
102A102THR00.0150.03314.196-0.038-0.0380.0000.0000.0000.000
103A103PRO0-0.026-0.01011.4310.0700.0700.0000.0000.0000.000
104A104ASP-1-0.904-0.95313.082-0.253-0.2530.0000.0000.0000.000
105A105SER0-0.020-0.0268.392-0.095-0.0950.0000.0000.0000.000
106A106TRP00.0720.0166.861-0.093-0.0930.0000.0000.0000.000
107A107ASN00.0400.0282.879-4.109-2.4730.226-1.028-0.834-0.010
108A108ASP-1-0.818-0.8885.862-0.266-0.2660.0000.0000.0000.000
109A109THR0-0.072-0.0348.9340.0540.0540.0000.0000.0000.000
110A110TYR00.0420.0107.0100.0350.0350.0000.0000.0000.000
111A111GLU-1-0.905-0.9654.070-1.037-0.7730.001-0.059-0.2060.000
112A112GLN0-0.072-0.0497.9780.2240.2240.0000.0000.0000.000
113A113PHE00.0240.04011.6670.0820.0820.0000.0000.0000.000
114A114GLU-1-0.957-0.9937.603-0.547-0.5470.0000.0000.0000.000
115A115ARG10.9200.9668.8310.3970.3970.0000.0000.0000.000
116A116GLU-1-0.840-0.92112.719-0.286-0.2860.0000.0000.0000.000
117A117THR0-0.026-0.00514.2630.0430.0430.0000.0000.0000.000
118A118LEU0-0.032-0.01212.6140.0370.0370.0000.0000.0000.000
119A119GLY0-0.0150.00216.7390.0290.0290.0000.0000.0000.000
120A120ILE0-0.068-0.02019.1470.0200.0200.0000.0000.0000.000
121A121PHE0-0.080-0.06518.3340.0160.0160.0000.0000.0000.000
122A122GLN0-0.043-0.01320.3460.0170.0170.0000.0000.0000.000
123A123GLU-1-0.866-0.91719.341-0.135-0.1350.0000.0000.0000.000
124A124LYS10.9520.98811.7090.2120.2120.0000.0000.0000.000
125A125VAL00.0060.00815.5970.0120.0120.0000.0000.0000.000
126A126VAL0-0.021-0.01814.317-0.035-0.0350.0000.0000.0000.000
127A127ILE00.0040.01110.6750.0390.0390.0000.0000.0000.000
128A128PHE0-0.070-0.03712.795-0.059-0.0590.0000.0000.0000.000
129A129THR00.0420.01010.718-0.072-0.0720.0000.0000.0000.000
130A130CYS0-0.062-0.02613.5570.0350.0350.0000.0000.0000.000
131A131LEU00.0530.02311.4820.0060.0060.0000.0000.0000.000
132A132ASN0-0.063-0.03815.8940.0440.0440.0000.0000.0000.000
133A133GLY00.0640.02118.709-0.025-0.0250.0000.0000.0000.000
134A134HIS0-0.089-0.04519.9300.0300.0300.0000.0000.0000.000
135A135LEU00.004-0.01221.700-0.011-0.0110.0000.0000.0000.000
136A136ASP-1-0.817-0.92223.774-0.133-0.1330.0000.0000.0000.000
137A137ASP-1-0.947-0.96225.460-0.127-0.1270.0000.0000.0000.000
138A138ASN00.0310.01828.5440.0190.0190.0000.0000.0000.000
139A139MET0-0.005-0.01430.2810.0050.0050.0000.0000.0000.000
140A140ASN00.023-0.00432.4830.0040.0040.0000.0000.0000.000
141A141ILE0-0.0050.01726.4420.0100.0100.0000.0000.0000.000
142A142VAL00.0060.00029.1510.0050.0050.0000.0000.0000.000
143A143LEU0-0.044-0.02431.0900.0060.0060.0000.0000.0000.000
144A144GLN00.0690.02231.2570.0080.0080.0000.0000.0000.000
145A145LYS10.9420.99827.8560.0660.0660.0000.0000.0000.000
146A146LYS10.9970.98331.3770.0730.0730.0000.0000.0000.000
147A147ALA00.0290.02334.1970.0050.0050.0000.0000.0000.000
148A148ASN0-0.0040.00032.7490.0100.0100.0000.0000.0000.000
149A149GLN0-0.077-0.04231.2320.0010.0010.0000.0000.0000.000
150A150LEU00.0550.02634.4670.0030.0030.0000.0000.0000.000
151A151LEU00.0000.00537.1030.0030.0030.0000.0000.0000.000
152A152ASN0-0.050-0.03433.6220.0070.0070.0000.0000.0000.000
153A153GLU-1-1.014-0.99537.360-0.030-0.0300.0000.0000.0000.000
154A154PHE0-0.0130.00238.9570.0010.0010.0000.0000.0000.000
155A155GLN0-0.021-0.03940.3770.0030.0030.0000.0000.0000.000
156A156ALA00.0380.00440.7350.0010.0010.0000.0000.0000.000
157A157ARG10.9280.96642.3680.0000.0000.0000.0000.0000.000
158A158SER0-0.112-0.05543.5320.0010.0010.0000.0000.0000.000
159A159VAL00.048-0.00439.1790.0000.0000.0000.0000.0000.000
160A160GLU-1-0.893-0.97041.666-0.011-0.0110.0000.0000.0000.000
161A161HIS00.0460.03838.993-0.003-0.0030.0000.0000.0000.000
162A162VAL0-0.0540.00939.6280.0010.0010.0000.0000.0000.000
163A163VAL0-0.011-0.02435.437-0.002-0.0020.0000.0000.0000.000
164A164GLU-1-0.928-0.96338.793-0.035-0.0350.0000.0000.0000.000
165A165PRO0-0.056-0.03338.278-0.003-0.0030.0000.0000.0000.000
166A166ASN00.0570.03336.592-0.007-0.0070.0000.0000.0000.000
167A167PHE0-0.013-0.02338.6130.0000.0000.0000.0000.0000.000
168A168VAL00.0530.02636.7160.0000.0000.0000.0000.0000.000
169A169SER0-0.001-0.00139.4750.0000.0000.0000.0000.0000.000
170A170ILE0-0.013-0.01038.2140.0010.0010.0000.0000.0000.000
171A171SER0-0.001-0.00142.309-0.001-0.0010.0000.0000.0000.000
172A172ALA0-0.0100.01043.0560.0010.0010.0000.0000.0000.000
173A173PHE00.030-0.01444.7580.0000.0000.0000.0000.0000.000
174A174THR00.0390.05544.4750.0000.0000.0000.0000.0000.000
175A175ASP-1-0.984-0.98246.8460.0000.0000.0000.0000.0000.000
176A176GLU-1-0.912-0.97245.571-0.008-0.0080.0000.0000.0000.000
177A177TRP0-0.064-0.01847.164-0.001-0.0010.0000.0000.0000.000
178A178GLU-1-0.915-0.94752.507-0.005-0.0050.0000.0000.0000.000
179A179GLU-1-0.938-0.96754.242-0.011-0.0110.0000.0000.0000.000
180A180TYR0-0.054-0.04453.3990.0000.0000.0000.0000.0000.000
181A181ILE00.0020.00653.1310.0000.0000.0000.0000.0000.000
182A182MET00.0030.00353.8050.0000.0000.0000.0000.0000.000
183A183THR00.0050.00654.7630.0000.0000.0000.0000.0000.000
184A184SER00.0520.03254.2090.0010.0010.0000.0000.0000.000
185A185LYS10.9170.95248.2420.0040.0040.0000.0000.0000.000
186A186HIS10.8780.93347.8600.0090.0090.0000.0000.0000.000
187A187LYS10.8790.95250.1620.0020.0020.0000.0000.0000.000
188A188MET0-0.0470.01348.0560.0000.0000.0000.0000.0000.000
189A189ASN0-0.027-0.04848.8010.0000.0000.0000.0000.0000.000
190A190LEU00.1170.06943.579-0.001-0.0010.0000.0000.0000.000
191A191GLN00.0550.03645.7410.0000.0000.0000.0000.0000.000
192A192ILE0-0.0170.01140.167-0.002-0.0020.0000.0000.0000.000
193A193ALA0-0.004-0.01942.4040.0000.0000.0000.0000.0000.000
194A194LEU0-0.027-0.00337.558-0.001-0.0010.0000.0000.0000.000
195A195ARG10.9390.96940.6480.0460.0460.0000.0000.0000.000
196A196SER00.0360.01737.035-0.002-0.0020.0000.0000.0000.000
197A197ALA0-0.006-0.00938.6340.0040.0040.0000.0000.0000.000
198A198GLY00.0050.00538.456-0.004-0.0040.0000.0000.0000.000
199A199MET00.000-0.01137.909-0.001-0.0010.0000.0000.0000.000
200A200GLY00.0500.03135.1970.0030.0030.0000.0000.0000.000
201A201GLY0-0.014-0.01436.1950.0030.0030.0000.0000.0000.000
202A202LYS10.8880.93538.5660.0720.0720.0000.0000.0000.000
203A203HIS00.0060.02735.3150.0070.0070.0000.0000.0000.000
204A204THR0-0.0180.00340.1300.0030.0030.0000.0000.0000.000
205A205VAL00.020-0.00440.248-0.001-0.0010.0000.0000.0000.000
206A206THR0-0.072-0.03242.8890.0010.0010.0000.0000.0000.000
207A207VAL00.0330.01143.6570.0000.0000.0000.0000.0000.000
208A208GLY0-0.0120.00846.3310.0000.0000.0000.0000.0000.000
209A209THR00.0400.04749.0840.0000.0000.0000.0000.0000.000
210A210PRO0-0.034-0.02551.6410.0000.0000.0000.0000.0000.000
211A211ILE0-0.003-0.02750.6380.0000.0000.0000.0000.0000.000
212A212VAL00.0060.00548.2180.0000.0000.0000.0000.0000.000
213A213THR0-0.001-0.00151.3670.0000.0000.0000.0000.0000.000
214A214THR0-0.031-0.01253.950-0.002-0.0020.0000.0000.0000.000