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: 89LGY

Calculation Name: 2FJR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FJR

Chain ID: A

ChEMBL ID:

UniProt ID: P08707

Base Structure: X-ray

Registration Date: 2023-09-24

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1866847.387073
FMO2-HF: Nuclear repulsion 1794436.731368
FMO2-HF: Total energy -72410.655705
FMO2-MP2: Total energy -72623.746919


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:4:ASP)


Summations of interaction energy for fragment #1(A:4:ASP)
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.
8.78314.7470.253-3.148-3.0660.026
Interaction energy analysis for fragmet #1(A:4:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.904 / q_NPA : -0.963
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].
3A6LEU0-0.027-0.0453.753-9.599-6.4440.011-1.673-1.4920.008
4A7GLY0-0.0040.0205.172-0.274-0.109-0.001-0.013-0.1510.000
5A8TRP00.009-0.0055.671-0.682-0.6820.0000.0000.0000.000
6A9SER00.0230.0017.1051.3331.3330.0000.0000.0000.000
7A10ASN00.001-0.0228.389-0.227-0.2270.0000.0000.0000.000
8A11VAL0-0.003-0.0039.903-1.343-1.3430.0000.0000.0000.000
9A12ASP-1-0.839-0.90112.95518.74318.7430.0000.0000.0000.000
10A13VAL0-0.057-0.0119.593-0.568-0.5680.0000.0000.0000.000
11A14LEU0-0.047-0.02212.830-0.965-0.9650.0000.0000.0000.000
12A15ASP-1-0.732-0.83415.03314.59214.5920.0000.0000.0000.000
13A16ARG10.8970.97712.488-21.920-21.9200.0000.0000.0000.000
14A17ILE0-0.014-0.00913.601-0.493-0.4930.0000.0000.0000.000
15A18CYS0-0.082-0.04517.880-0.889-0.8890.0000.0000.0000.000
16A19GLU-1-0.916-0.96120.56413.55813.5580.0000.0000.0000.000
17A20ALA0-0.047-0.02820.043-0.562-0.5620.0000.0000.0000.000
18A21TYR0-0.052-0.06519.456-0.054-0.0540.0000.0000.0000.000
19A22GLY00.0180.02423.874-0.580-0.5800.0000.0000.0000.000
20A23PHE0-0.098-0.04822.612-0.458-0.4580.0000.0000.0000.000
21A24SER00.0190.00724.8560.2890.2890.0000.0000.0000.000
22A25GLN0-0.048-0.03325.7600.0650.0650.0000.0000.0000.000
23A26LYS10.8670.91119.107-14.781-14.7810.0000.0000.0000.000
24A27ILE00.000-0.00322.7480.3730.3730.0000.0000.0000.000
25A28GLN00.0640.02825.2710.0800.0800.0000.0000.0000.000
26A29LEU00.0650.04817.5530.0400.0400.0000.0000.0000.000
27A30ALA0-0.075-0.04621.5030.3200.3200.0000.0000.0000.000
28A31ASN0-0.025-0.02022.4520.1580.1580.0000.0000.0000.000
29A32HIS0-0.041-0.01921.656-0.572-0.5720.0000.0000.0000.000
30A33PHE0-0.049-0.03518.3130.1950.1950.0000.0000.0000.000
31A34ASP-1-0.953-0.96021.91212.12712.1270.0000.0000.0000.000
32A35ILE0-0.054-0.01318.6200.3990.3990.0000.0000.0000.000
33A36ALA00.0210.00822.857-0.442-0.4420.0000.0000.0000.000
34A37SER00.1030.02622.4360.5570.5570.0000.0000.0000.000
35A38SER0-0.034-0.01722.0390.5480.5480.0000.0000.0000.000
36A39SER00.0250.00519.5300.3380.3380.0000.0000.0000.000
37A40LEU00.0430.03017.0841.1261.1260.0000.0000.0000.000
38A41SER0-0.017-0.01617.3130.5900.5900.0000.0000.0000.000
39A42ASN0-0.015-0.00415.3480.7460.7460.0000.0000.0000.000
40A43ARG10.7760.86713.407-19.560-19.5600.0000.0000.0000.000
41A44TYR00.007-0.03612.4681.5001.5000.0000.0000.0000.000
42A45THR0-0.054-0.01613.2460.1230.1230.0000.0000.0000.000
43A46ARG10.8140.9189.436-26.782-26.7820.0000.0000.0000.000
44A47GLY00.0670.0257.0310.0740.0740.0000.0000.0000.000
45A48ALA0-0.022-0.0095.5202.3512.3510.0000.0000.0000.000
46A49ILE00.1020.0574.721-5.227-5.158-0.001-0.003-0.0630.000
47A50SER0-0.028-0.0107.1430.3900.3900.0000.0000.0000.000
48A51TYR00.0530.0152.611-17.239-14.6640.244-1.459-1.3600.018
49A52ASP-1-0.796-0.8549.35821.60521.6050.0000.0000.0000.000
50A53PHE00.0530.01012.643-1.308-1.3080.0000.0000.0000.000
51A54ALA00.0560.03611.255-1.203-1.2030.0000.0000.0000.000
52A55ALA0-0.024-0.00912.467-1.165-1.1650.0000.0000.0000.000
53A56HIS0-0.037-0.03214.082-1.791-1.7910.0000.0000.0000.000
54A57CYS00.0260.04516.586-1.059-1.0590.0000.0000.0000.000
55A58ALA00.0130.02015.826-0.990-0.9900.0000.0000.0000.000
56A59LEU0-0.049-0.02917.236-1.054-1.0540.0000.0000.0000.000
57A60GLU-1-0.820-0.87820.08813.58613.5860.0000.0000.0000.000
58A61THR0-0.005-0.02220.724-0.688-0.6880.0000.0000.0000.000
59A62GLY0-0.088-0.05121.594-0.552-0.5520.0000.0000.0000.000
60A63ALA00.0010.01719.119-0.034-0.0340.0000.0000.0000.000
61A64ASN00.001-0.00617.0681.7381.7380.0000.0000.0000.000
62A65LEU00.0550.00611.4020.5280.5280.0000.0000.0000.000
63A66GLN0-0.018-0.00412.2252.8192.8190.0000.0000.0000.000
64A67TRP00.0330.04613.4131.4181.4180.0000.0000.0000.000
65A68LEU00.0010.00713.8640.3840.3840.0000.0000.0000.000
66A69LEU0-0.021-0.0317.9670.6410.6410.0000.0000.0000.000
67A70THR0-0.033-0.02310.4560.6850.6850.0000.0000.0000.000
68A71GLY0-0.044-0.02012.486-0.804-0.8040.0000.0000.0000.000
69A72GLU-1-0.920-0.95614.01620.60520.6050.0000.0000.0000.000
70A73GLY0-0.055-0.03217.3280.1750.1750.0000.0000.0000.000
71A74GLU-1-0.944-0.98620.38112.03212.0320.0000.0000.0000.000
72A75ALA0-0.0020.01620.2760.3500.3500.0000.0000.0000.000
73A76PHE00.013-0.01221.3280.3610.3610.0000.0000.0000.000
74A77VAL0-0.0110.00824.111-0.162-0.1620.0000.0000.0000.000
75A78ASN00.014-0.00226.508-0.377-0.3770.0000.0000.0000.000
76A79ASN00.011-0.00328.673-0.424-0.4240.0000.0000.0000.000
77A80ARG10.7920.90723.108-12.652-12.6520.0000.0000.0000.000
78A81GLU-1-0.855-0.92726.82110.94510.9450.0000.0000.0000.000
79A82SER00.0340.04926.275-0.426-0.4260.0000.0000.0000.000
80A83SER0-0.129-0.09427.2400.1910.1910.0000.0000.0000.000
81A84ASP-1-0.806-0.92229.5249.4089.4080.0000.0000.0000.000
82A85ALA0-0.0110.00629.3940.2670.2670.0000.0000.0000.000
83A86LYS10.8670.92828.883-9.991-9.9910.0000.0000.0000.000
84A87ARG10.8390.91526.927-11.832-11.8320.0000.0000.0000.000
85A88ILE00.0210.02728.9810.2560.2560.0000.0000.0000.000
86A89GLU-1-0.802-0.89528.34811.01611.0160.0000.0000.0000.000
87A90GLY00.0410.01531.075-0.269-0.2690.0000.0000.0000.000
88A91PHE00.005-0.01431.7770.1330.1330.0000.0000.0000.000
89A92THR0-0.026-0.00337.038-0.236-0.2360.0000.0000.0000.000
90A93LEU0-0.020-0.00240.5640.1240.1240.0000.0000.0000.000
91A94SER0-0.075-0.07442.822-0.198-0.1980.0000.0000.0000.000
92A95GLU-1-0.864-0.91445.6487.0077.0070.0000.0000.0000.000
93A96GLU-1-0.921-0.96045.7896.6246.6240.0000.0000.0000.000
94A97ILE00.0200.01741.7680.1520.1520.0000.0000.0000.000
95A98LEU0-0.001-0.00536.854-0.067-0.0670.0000.0000.0000.000
96A99LYS10.8740.94137.605-7.317-7.3170.0000.0000.0000.000
97A100SER00.0640.02932.492-0.052-0.0520.0000.0000.0000.000
98A101ASP-1-0.817-0.87834.5788.2378.2370.0000.0000.0000.000
99A102LYS10.8240.89733.318-8.086-8.0860.0000.0000.0000.000
100A103GLN00.0160.01127.253-0.157-0.1570.0000.0000.0000.000
101A104LEU0-0.043-0.01632.585-0.238-0.2380.0000.0000.0000.000
102A105SER0-0.024-0.02232.7780.3600.3600.0000.0000.0000.000
103A106VAL0-0.040-0.02433.434-0.334-0.3340.0000.0000.0000.000
104A107ASP-1-0.807-0.88333.6319.4229.4220.0000.0000.0000.000
105A108ALA00.0390.01732.171-0.107-0.1070.0000.0000.0000.000
106A109GLN0-0.012-0.01233.965-0.290-0.2900.0000.0000.0000.000
107A110PHE0-0.094-0.04737.119-0.276-0.2760.0000.0000.0000.000
108A111PHE0-0.040-0.02534.647-0.206-0.2060.0000.0000.0000.000
109A112THR00.0110.01636.6220.0400.0400.0000.0000.0000.000
110A113LYS10.8990.95435.838-7.976-7.9760.0000.0000.0000.000
111A114PRO00.1050.04230.389-0.085-0.0850.0000.0000.0000.000
112A115LEU0-0.093-0.02131.615-0.117-0.1170.0000.0000.0000.000
113A116THR00.0700.03426.4650.0030.0030.0000.0000.0000.000
114A117ASP-1-0.773-0.85627.18511.46511.4650.0000.0000.0000.000
115A118GLY00.026-0.00229.052-0.373-0.3730.0000.0000.0000.000
116A119MET0-0.066-0.01731.2540.1850.1850.0000.0000.0000.000
117A120ALA0-0.0140.00533.979-0.249-0.2490.0000.0000.0000.000
118A121ILE00.001-0.01636.5900.0350.0350.0000.0000.0000.000
119A122ARG10.8850.94638.243-8.334-8.3340.0000.0000.0000.000
120A123SER00.011-0.02942.1980.0250.0250.0000.0000.0000.000
121A124GLU-1-0.779-0.85245.2416.6016.6010.0000.0000.0000.000
122A125GLY0-0.0070.00147.730-0.099-0.0990.0000.0000.0000.000
123A126LYS10.8260.92046.358-6.591-6.5910.0000.0000.0000.000
124A127ILE0-0.019-0.02239.8220.1130.1130.0000.0000.0000.000
125A128TYR0-0.029-0.03341.583-0.087-0.0870.0000.0000.0000.000
126A129PHE00.0190.00236.3620.1970.1970.0000.0000.0000.000
127A130VAL0-0.032-0.02036.347-0.176-0.1760.0000.0000.0000.000
128A131ASP-1-0.820-0.91533.4689.6819.6810.0000.0000.0000.000
129A132LYS10.8140.85628.928-11.101-11.1010.0000.0000.0000.000
130A133GLN00.0050.00628.896-0.083-0.0830.0000.0000.0000.000
131A134ALA0-0.0510.00932.522-0.108-0.1080.0000.0000.0000.000
132A135SER00.0280.01836.007-0.027-0.0270.0000.0000.0000.000
133A136LEU00.017-0.00637.548-0.174-0.1740.0000.0000.0000.000
134A137SER0-0.084-0.06440.740-0.078-0.0780.0000.0000.0000.000
135A138ASP-1-0.797-0.88543.6956.6846.6840.0000.0000.0000.000
136A139GLY00.0100.01245.2220.1220.1220.0000.0000.0000.000
137A140LEU00.0460.03844.984-0.048-0.0480.0000.0000.0000.000
138A141TRP0-0.065-0.04138.3240.2680.2680.0000.0000.0000.000
139A142LEU00.0060.02537.667-0.187-0.1870.0000.0000.0000.000
140A143VAL0-0.019-0.02740.5000.1630.1630.0000.0000.0000.000
141A144ASP-1-0.871-0.93839.9127.8877.8870.0000.0000.0000.000
142A145ILE00.004-0.01242.364-0.038-0.0380.0000.0000.0000.000
143A146LYS10.9290.94745.042-6.544-6.5440.0000.0000.0000.000
144A147GLY00.0360.02842.502-0.081-0.0810.0000.0000.0000.000
145A148ALA0-0.0280.01443.1620.0940.0940.0000.0000.0000.000
146A149ILE0-0.002-0.00839.2710.0480.0480.0000.0000.0000.000
147A150SER0-0.017-0.00643.488-0.199-0.1990.0000.0000.0000.000
148A151ILE00.0040.00542.8310.1690.1690.0000.0000.0000.000
149A152ARG10.8700.93045.480-6.748-6.7480.0000.0000.0000.000
150A153GLU-1-0.864-0.93446.6426.7916.7910.0000.0000.0000.000
151A154LEU0-0.039-0.02044.128-0.088-0.0880.0000.0000.0000.000
152A155THR0-0.016-0.00948.130-0.022-0.0220.0000.0000.0000.000
153A156LYS10.8750.93543.157-7.305-7.3050.0000.0000.0000.000
154A157LEU0-0.0130.00648.795-0.134-0.1340.0000.0000.0000.000
155A158PRO00.000-0.01650.3020.1210.1210.0000.0000.0000.000
156A159GLY0-0.013-0.00950.877-0.043-0.0430.0000.0000.0000.000
157A160ARG10.8990.95345.287-6.641-6.6410.0000.0000.0000.000
158A161LYS10.9410.96747.654-5.892-5.8920.0000.0000.0000.000
159A162LEU00.0030.00544.8390.0880.0880.0000.0000.0000.000
160A163HIS0-0.028-0.02149.461-0.117-0.1170.0000.0000.0000.000
161A164VAL0-0.006-0.00448.7040.1240.1240.0000.0000.0000.000
162A165ALA00.0470.01050.984-0.150-0.1500.0000.0000.0000.000
163A166GLY00.0420.01650.9850.1470.1470.0000.0000.0000.000
164A167GLY0-0.0070.00952.5320.0130.0130.0000.0000.0000.000
165A168LYS10.9210.94453.389-5.674-5.6740.0000.0000.0000.000
166A169VAL00.0090.00956.417-0.107-0.1070.0000.0000.0000.000
167A170PRO0-0.0120.01054.8510.1000.1000.0000.0000.0000.000
168A171PHE0-0.034-0.02249.365-0.095-0.0950.0000.0000.0000.000
169A172GLU-1-0.798-0.88852.8285.8575.8570.0000.0000.0000.000
170A173CYS0-0.082-0.03148.091-0.060-0.0600.0000.0000.0000.000
171A174GLY00.0420.01748.392-0.016-0.0160.0000.0000.0000.000
172A175ILE0-0.060-0.04742.2490.0570.0570.0000.0000.0000.000
173A176ASP-1-0.922-0.96442.9807.1847.1840.0000.0000.0000.000
174A177ASP-1-0.862-0.90944.0446.6306.6300.0000.0000.0000.000
175A178ILE0-0.085-0.04744.265-0.067-0.0670.0000.0000.0000.000
176A179LYS10.9630.99534.718-8.857-8.8570.0000.0000.0000.000
177A180THR0-0.019-0.01238.549-0.130-0.1300.0000.0000.0000.000
178A181LEU0-0.041-0.03636.1190.2240.2240.0000.0000.0000.000
179A182GLY00.0830.03735.4810.3190.3190.0000.0000.0000.000
180A183ARG10.8920.96137.193-8.314-8.3140.0000.0000.0000.000
181A184VAL0-0.007-0.00538.6580.1920.1920.0000.0000.0000.000
182A185VAL0-0.059-0.03937.069-0.174-0.1740.0000.0000.0000.000
183A186GLY00.0320.02240.413-0.076-0.0760.0000.0000.0000.000
184A187VAL0-0.038-0.01941.7660.0980.0980.0000.0000.0000.000
185A188TYR00.0090.01742.969-0.080-0.0800.0000.0000.0000.000
186A189SER00.009-0.00944.765-0.012-0.0120.0000.0000.0000.000
187A190GLU-1-0.935-0.95147.1076.7546.7540.0000.0000.0000.000
188A191VAL0-0.037-0.02349.407-0.078-0.0780.0000.0000.0000.000
189A192ASN0-0.0050.00553.069-0.183-0.1830.0000.0000.0000.000