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

tag_button

FMODB ID: 2JK7R

Calculation Name: 5GPL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GPL

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HGN2

Base Structure: X-ray

Registration Date: 2023-06-21

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2401898.074242
FMO2-HF: Nuclear repulsion 2318561.023551
FMO2-HF: Total energy -83337.05069
FMO2-MP2: Total energy -83585.969553


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:2:GLU)


Summations of interaction energy for fragment #1(A:2:GLU)
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.
111.11117.3241.979-3.176-5.0170.027
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.958 / q_NPA : -0.996
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].
3A4ALA00.0100.0113.680-4.272-2.221-0.016-0.854-1.1810.004
4A5GLN00.0880.0512.782-11.735-8.1021.995-2.202-3.4260.023
5A6ALA0-0.011-0.0043.786-7.537-7.1390.001-0.112-0.2880.000
6A7PHE00.021-0.0095.294-4.628-4.496-0.001-0.008-0.1220.000
7A8GLU-1-0.941-0.9587.53735.21635.2160.0000.0000.0000.000
8A9ASN0-0.044-0.0346.199-5.327-5.3270.0000.0000.0000.000
9A10LEU0-0.013-0.0039.384-2.660-2.6600.0000.0000.0000.000
10A11ALA00.0280.02511.346-2.100-2.1000.0000.0000.0000.000
11A12ASN0-0.028-0.02511.473-3.041-3.0410.0000.0000.0000.000
12A13LEU0-0.022-0.00713.517-1.343-1.3430.0000.0000.0000.000
13A14GLU-1-0.890-0.94915.23915.68015.6800.0000.0000.0000.000
14A15GLN0-0.031-0.01417.377-1.271-1.2710.0000.0000.0000.000
15A16GLU-1-0.844-0.90117.87714.74614.7460.0000.0000.0000.000
16A17PHE00.0150.00616.551-0.816-0.8160.0000.0000.0000.000
17A18GLY00.0280.02421.078-0.741-0.7410.0000.0000.0000.000
18A19LYS10.7620.85520.987-15.393-15.3930.0000.0000.0000.000
19A20ALA00.0070.00523.977-0.546-0.5460.0000.0000.0000.000
20A21GLU-1-0.884-0.94125.20810.67110.6710.0000.0000.0000.000
21A22ILE0-0.029-0.01827.034-0.544-0.5440.0000.0000.0000.000
22A23GLU-1-0.981-0.98628.75410.40310.4030.0000.0000.0000.000
23A24ILE0-0.003-0.00628.630-0.472-0.4720.0000.0000.0000.000
24A25LEU00.0170.01330.538-0.459-0.4590.0000.0000.0000.000
25A26LYS10.8540.93433.099-9.440-9.4400.0000.0000.0000.000
26A27LYS10.8150.90234.303-8.708-8.7080.0000.0000.0000.000
27A28GLN0-0.009-0.00934.828-0.328-0.3280.0000.0000.0000.000
28A29ASN00.019-0.00136.964-0.341-0.3410.0000.0000.0000.000
29A30GLU-1-0.861-0.91238.8537.9037.9030.0000.0000.0000.000
30A31LEU0-0.051-0.02938.525-0.224-0.2240.0000.0000.0000.000
31A32PHE00.006-0.01238.814-0.183-0.1830.0000.0000.0000.000
32A33GLN00.0240.03842.870-0.058-0.0580.0000.0000.0000.000
33A34PRO00.0210.00744.810-0.173-0.1730.0000.0000.0000.000
34A35LEU00.0040.00244.664-0.174-0.1740.0000.0000.0000.000
35A36PHE00.020-0.00942.071-0.147-0.1470.0000.0000.0000.000
36A37GLU-1-0.877-0.90747.7906.2276.2270.0000.0000.0000.000
37A38GLN0-0.013-0.02250.415-0.062-0.0620.0000.0000.0000.000
38A39ARG10.8120.90346.892-6.817-6.8170.0000.0000.0000.000
39A40ARG10.7730.87251.393-6.198-6.1980.0000.0000.0000.000
40A41ASP-1-0.847-0.90953.0655.7145.7140.0000.0000.0000.000
41A42ILE0-0.033-0.01454.655-0.123-0.1230.0000.0000.0000.000
42A43LEU00.0050.00651.763-0.102-0.1020.0000.0000.0000.000
43A44LYS10.9180.99056.227-5.426-5.4260.0000.0000.0000.000
44A45THR0-0.124-0.07458.439-0.115-0.1150.0000.0000.0000.000
45A46ILE0-0.039-0.00657.230-0.095-0.0950.0000.0000.0000.000
46A47ASN0-0.056-0.03459.6030.0490.0490.0000.0000.0000.000
47A48ASN00.038-0.00859.757-0.053-0.0530.0000.0000.0000.000
48A49PHE00.0430.02552.1690.0650.0650.0000.0000.0000.000
49A50TRP00.020-0.01648.9770.1240.1240.0000.0000.0000.000
50A51VAL00.0220.03353.7620.1130.1130.0000.0000.0000.000
51A52VAL00.0560.03455.1690.0450.0450.0000.0000.0000.000
52A53VAL0-0.039-0.02249.7460.0870.0870.0000.0000.0000.000
53A54LEU0-0.065-0.04949.7360.1200.1200.0000.0000.0000.000
54A55GLU-1-0.913-0.95150.9955.6735.6730.0000.0000.0000.000
55A56ALA0-0.0090.00751.472-0.010-0.0100.0000.0000.0000.000
56A57ALA0-0.073-0.02246.8610.1130.1130.0000.0000.0000.000
57A58GLY00.0450.02146.1650.1570.1570.0000.0000.0000.000
58A59ASP-1-0.921-0.97745.0666.6126.6120.0000.0000.0000.000
59A60GLU-1-0.897-0.96041.9207.4657.4650.0000.0000.0000.000
60A61ILE00.000-0.00744.536-0.001-0.0010.0000.0000.0000.000
61A62SER00.0230.00347.814-0.061-0.0610.0000.0000.0000.000
62A63GLN0-0.089-0.02243.461-0.118-0.1180.0000.0000.0000.000
63A64TYR0-0.071-0.03143.596-0.065-0.0650.0000.0000.0000.000
64A65ILE0-0.037-0.01050.496-0.101-0.1010.0000.0000.0000.000
65A66THR0-0.023-0.01353.657-0.085-0.0850.0000.0000.0000.000
66A67PRO0-0.005-0.02456.892-0.020-0.0200.0000.0000.0000.000
67A68GLU-1-0.903-0.96259.3905.2465.2460.0000.0000.0000.000
68A69ASP-1-0.754-0.87454.9555.8085.8080.0000.0000.0000.000
69A70SER00.030-0.00257.8380.0200.0200.0000.0000.0000.000
70A71VAL0-0.051-0.01758.978-0.048-0.0480.0000.0000.0000.000
71A72LEU0-0.060-0.01858.200-0.054-0.0540.0000.0000.0000.000
72A73LEU00.009-0.00954.2430.0060.0060.0000.0000.0000.000
73A74GLU-1-0.835-0.89758.1355.2055.2050.0000.0000.0000.000
74A75LYS10.7860.89860.953-4.986-4.9860.0000.0000.0000.000
75A76LEU0-0.044-0.00553.4650.0020.0020.0000.0000.0000.000
76A77GLU-1-0.911-0.96858.0905.2725.2720.0000.0000.0000.000
77A78ASN0-0.042-0.06253.7540.1030.1030.0000.0000.0000.000
78A79ILE00.0370.05148.4590.0000.0000.0000.0000.0000.000
79A80TYR0-0.040-0.02848.6480.0310.0310.0000.0000.0000.000
80A81VAL00.0300.01842.4460.0250.0250.0000.0000.0000.000
81A82GLU-1-0.880-0.93144.5096.7616.7610.0000.0000.0000.000
82A83ARG10.8520.91935.813-8.500-8.5000.0000.0000.0000.000
83A84PHE0-0.023-0.01641.1150.0250.0250.0000.0000.0000.000
84A85ASN0-0.085-0.04937.439-0.041-0.0410.0000.0000.0000.000
85A86GLU-1-0.832-0.93037.9468.4658.4650.0000.0000.0000.000
86A87LYS10.8600.93731.447-9.732-9.7320.0000.0000.0000.000
87A88GLU-1-0.804-0.87731.53210.54010.5400.0000.0000.0000.000
88A89PRO00.0570.03832.858-0.261-0.2610.0000.0000.0000.000
89A90ARG10.8630.88427.812-10.849-10.8490.0000.0000.0000.000
90A91ASP-1-0.814-0.88034.9808.5378.5370.0000.0000.0000.000
91A92VAL0-0.006-0.00637.947-0.091-0.0910.0000.0000.0000.000
92A93ARG10.7610.85441.070-6.980-6.9800.0000.0000.0000.000
93A94ILE00.0050.00942.837-0.047-0.0470.0000.0000.0000.000
94A95SER0-0.011-0.01346.661-0.064-0.0640.0000.0000.0000.000
95A96LEU00.0370.02349.7340.0000.0000.0000.0000.0000.000
96A97THR0-0.029-0.01152.974-0.039-0.0390.0000.0000.0000.000
97A98PHE00.0330.01355.348-0.009-0.0090.0000.0000.0000.000
98A99GLN0-0.030-0.01759.454-0.121-0.1210.0000.0000.0000.000
99A100PRO00.018-0.00363.0620.0210.0210.0000.0000.0000.000
100A101ASN00.0330.00861.765-0.041-0.0410.0000.0000.0000.000
101A102GLU-1-0.843-0.92165.7084.7634.7630.0000.0000.0000.000
102A103TYR00.0360.00461.761-0.015-0.0150.0000.0000.0000.000
103A104LEU00.0110.02358.4970.0120.0120.0000.0000.0000.000
104A105GLN0-0.0070.00162.652-0.162-0.1620.0000.0000.0000.000
105A106ASP-1-0.858-0.94363.2024.8904.8900.0000.0000.0000.000
106A107ASP-1-0.927-0.94363.1265.1625.1620.0000.0000.0000.000
107A108ASN0-0.015-0.02257.6430.1290.1290.0000.0000.0000.000
108A109LEU00.0410.03259.2620.0380.0380.0000.0000.0000.000
109A110THR0-0.043-0.01654.2020.0510.0510.0000.0000.0000.000
110A111LEU00.0030.01853.2830.0150.0150.0000.0000.0000.000
111A112VAL0-0.001-0.00848.9340.0860.0860.0000.0000.0000.000
112A113LYS10.8230.92045.024-6.986-6.9860.0000.0000.0000.000
113A114GLU-1-0.799-0.87143.7757.2697.2690.0000.0000.0000.000
114A115VAL0-0.0280.00938.8690.0100.0100.0000.0000.0000.000
115A116ARG10.8390.91337.948-7.676-7.6760.0000.0000.0000.000
116A117ILE00.0140.01931.3540.0620.0620.0000.0000.0000.000
117A118LYS10.8230.87931.329-9.942-9.9420.0000.0000.0000.000
118A119GLU-1-0.864-0.91024.31813.26513.2650.0000.0000.0000.000
119A120GLU-1-0.842-0.90528.47310.26310.2630.0000.0000.0000.000
120A121LYS10.8210.88323.838-11.758-11.7580.0000.0000.0000.000
121A122ALA00.0010.01025.646-0.428-0.4280.0000.0000.0000.000
122A123LYS10.9030.96423.714-12.163-12.1630.0000.0000.0000.000
123A124ASP-1-0.792-0.89621.41113.51913.5190.0000.0000.0000.000
124A125ASP-1-0.918-0.97024.70411.06111.0610.0000.0000.0000.000
125A126GLU-1-0.989-0.97818.37514.86714.8670.0000.0000.0000.000
126A127GLY0-0.034-0.00921.8260.1390.1390.0000.0000.0000.000
127A128LEU0-0.067-0.03516.6610.2460.2460.0000.0000.0000.000
128A129GLU-1-0.834-0.92020.55211.97211.9720.0000.0000.0000.000
129A130LYS10.8720.92420.355-12.821-12.8210.0000.0000.0000.000
130A131LYS10.8240.89920.390-15.044-15.0440.0000.0000.0000.000
131A132ILE00.0040.00323.7160.0320.0320.0000.0000.0000.000
132A133THR0-0.0130.00427.145-0.134-0.1340.0000.0000.0000.000
133A134LYS10.8570.92829.324-9.021-9.0210.0000.0000.0000.000
134A135TYR00.0500.01632.4080.0680.0680.0000.0000.0000.000
135A136THR0-0.026-0.00836.185-0.133-0.1330.0000.0000.0000.000
136A137SER0-0.011-0.03739.099-0.080-0.0800.0000.0000.0000.000
137A138GLN0-0.0070.00342.668-0.119-0.1190.0000.0000.0000.000
138A139PRO00.0080.01345.871-0.010-0.0100.0000.0000.0000.000
139A140VAL0-0.018-0.02048.742-0.055-0.0550.0000.0000.0000.000
140A141ASP-1-0.958-0.97851.3475.6245.6240.0000.0000.0000.000
141A142ILE0-0.0100.01053.664-0.037-0.0370.0000.0000.0000.000
142A143HIS0-0.064-0.04156.994-0.132-0.1320.0000.0000.0000.000
143A144TRP00.0170.00556.174-0.108-0.1080.0000.0000.0000.000
144A145LYS10.8020.90362.170-4.931-4.9310.0000.0000.0000.000
145A146PRO0-0.029-0.03465.3880.0380.0380.0000.0000.0000.000
146A147GLY0-0.056-0.02866.068-0.041-0.0410.0000.0000.0000.000
147A148LYS10.8300.91764.051-4.842-4.8420.0000.0000.0000.000
148A149SER0-0.047-0.03059.1520.0730.0730.0000.0000.0000.000
149A150LEU00.0430.03357.221-0.047-0.0470.0000.0000.0000.000
150A151PHE00.0100.03153.4500.0850.0850.0000.0000.0000.000
151A152ARG10.7540.86247.589-6.635-6.6350.0000.0000.0000.000
152A153LYS10.8990.94255.154-5.270-5.2700.0000.0000.0000.000
153A154ASN00.000-0.01953.7920.0210.0210.0000.0000.0000.000
154A155LYS10.9450.98246.859-6.810-6.8100.0000.0000.0000.000
155A156LYS10.8190.88448.055-6.396-6.3960.0000.0000.0000.000
156A157LEU00.0160.01351.5390.0270.0270.0000.0000.0000.000
157A158PRO00.0270.00550.4910.0530.0530.0000.0000.0000.000
158A159PRO0-0.0130.01647.659-0.141-0.1410.0000.0000.0000.000
159A160ASN00.0030.00650.9230.0260.0260.0000.0000.0000.000
160A161PHE00.0660.02048.7160.1250.1250.0000.0000.0000.000
161A162PHE0-0.009-0.02050.3730.1220.1220.0000.0000.0000.000
162A163ASP-1-0.779-0.89549.9626.1136.1130.0000.0000.0000.000
163A164TYR0-0.010-0.00842.7190.0620.0620.0000.0000.0000.000
164A165PHE0-0.004-0.02447.0670.1350.1350.0000.0000.0000.000
165A166GLN0-0.064-0.03749.3480.0350.0350.0000.0000.0000.000
166A167TRP00.0470.06539.1450.0650.0650.0000.0000.0000.000
167A168THR0-0.014-0.03043.5760.0870.0870.0000.0000.0000.000
168A169GLY00.0270.01039.7030.1700.1700.0000.0000.0000.000
169A170GLU-1-0.928-0.97238.4188.5308.5300.0000.0000.0000.000
170A171GLU-1-0.879-0.89540.1766.9576.9570.0000.0000.0000.000
171A172GLU-1-0.986-0.99338.1008.1818.1810.0000.0000.0000.000
172A173ASP-1-0.950-0.98439.4737.4807.4800.0000.0000.0000.000
173A174ASP-1-0.896-0.93941.9376.6416.6410.0000.0000.0000.000
174A175ASP-1-0.814-0.89742.2736.8816.8810.0000.0000.0000.000
175A176PHE0-0.002-0.00443.2570.0680.0680.0000.0000.0000.000
176A177ASP-1-0.789-0.86638.1068.4618.4610.0000.0000.0000.000
177A178GLY00.035-0.00541.040-0.018-0.0180.0000.0000.0000.000
178A179ALA0-0.0330.00136.1540.0020.0020.0000.0000.0000.000
179A180THR0-0.017-0.03437.3180.1820.1820.0000.0000.0000.000
180A181LEU00.0280.03738.539-0.033-0.0330.0000.0000.0000.000
181A182THR0-0.028-0.03639.265-0.128-0.1280.0000.0000.0000.000
182A183ILE0-0.045-0.01434.303-0.028-0.0280.0000.0000.0000.000
183A184PHE00.0380.02738.202-0.020-0.0200.0000.0000.0000.000
184A185LEU00.0150.00240.668-0.111-0.1110.0000.0000.0000.000
185A186ALA0-0.025-0.02139.544-0.107-0.1070.0000.0000.0000.000
186A187GLU-1-0.928-0.96734.9089.0569.0560.0000.0000.0000.000
187A188ASP-1-0.853-0.88639.1197.6197.6190.0000.0000.0000.000
188A189LEU00.0140.01341.401-0.140-0.1400.0000.0000.0000.000
189A190PHE00.0460.01343.819-0.185-0.1850.0000.0000.0000.000
190A191PRO0-0.018-0.00240.782-0.188-0.1880.0000.0000.0000.000
191A192ASN0-0.059-0.03041.219-0.103-0.1030.0000.0000.0000.000
192A193ALA00.0560.04945.389-0.117-0.1170.0000.0000.0000.000
193A194VAL00.022-0.00748.762-0.097-0.0970.0000.0000.0000.000
194A195LYS10.8320.92443.279-7.314-7.3140.0000.0000.0000.000
195A196TYR00.0710.02143.455-0.109-0.1090.0000.0000.0000.000
196A197PHE00.0090.01149.915-0.111-0.1110.0000.0000.0000.000
197A198THR0-0.066-0.06152.711-0.129-0.1290.0000.0000.0000.000
198A199GLU-1-0.965-0.97048.8276.3656.3650.0000.0000.0000.000
199A200ALA00.0530.02452.870-0.070-0.0700.0000.0000.0000.000
200A201MET0-0.037-0.02454.828-0.141-0.1410.0000.0000.0000.000
201A202THR0-0.113-0.06255.285-0.100-0.1000.0000.0000.0000.000
202A203GLU-1-0.901-0.94754.9695.5975.5970.0000.0000.0000.000
203A204GLU-1-0.966-0.97057.0915.2855.2850.0000.0000.0000.000
204A205ALA0-0.088-0.04460.147-0.113-0.1130.0000.0000.0000.000
205A206SER0-0.097-0.04359.556-0.064-0.0640.0000.0000.0000.000
206A207ASP-1-1.016-0.99860.7215.1145.1140.0000.0000.0000.000