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: G5GM1

Calculation Name: 4JG2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JG2

Chain ID: A

ChEMBL ID:

UniProt ID: Q73EI2

Base Structure: X-ray

Registration Date: 2023-09-23

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1810683.331698
FMO2-HF: Nuclear repulsion 1740743.646183
FMO2-HF: Total energy -69939.685515
FMO2-MP2: Total energy -70146.909064


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:-11:LYS)


Summations of interaction energy for fragment #1(A:-11:LYS)
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.
-29.802-16.88824.572-16.786-20.705-0.12
Interaction energy analysis for fragmet #1(A:-11:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.979 / q_NPA : 1.001
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].
3A-9THR00.022-0.0033.817-0.3042.607-0.013-1.506-1.3920.009
4A-8GLU-1-0.820-0.8501.759-85.321-88.26818.163-8.261-6.955-0.072
5A-7ASN00.0590.0174.5282.7142.828-0.001-0.010-0.1030.000
6A-6LEU00.0380.0084.956-2.086-2.0860.0000.0000.0000.000
7A-5TYR0-0.0230.0026.139-0.166-0.1660.0000.0000.0000.000
8A-4PHE0-0.040-0.0307.6460.6560.6560.0000.0000.0000.000
9A-3GLN0-0.067-0.0122.611-3.384-2.2980.839-0.671-1.2550.000
10A-2SER0-0.036-0.0622.476-5.306-0.4561.687-2.922-3.615-0.029
11A-1ASN0-0.008-0.0064.3102.2142.537-0.001-0.027-0.2960.000
12A0ALA00.0010.0085.0134.7114.7110.0000.0000.0000.000
13A4GLN00.0590.0222.519-21.426-16.3501.703-2.623-4.157-0.024
14A5ASN0-0.058-0.0292.218-0.7000.4862.185-0.803-2.569-0.004
15A6ARG10.9030.9233.70430.84531.0050.0110.043-0.2150.000
16A7THR00.0740.0497.0062.5282.5280.0000.0000.0000.000
17A8LYS10.9160.9734.75345.72745.882-0.001-0.006-0.1480.000
18A9VAL00.0080.0056.867-0.419-0.4190.0000.0000.0000.000
19A10VAL0-0.042-0.0267.8460.3280.3280.0000.0000.0000.000
20A11THR00.0290.00910.3110.2360.2360.0000.0000.0000.000
21A12SER00.0870.06013.764-0.327-0.3270.0000.0000.0000.000
22A13VAL00.013-0.01415.5280.1370.1370.0000.0000.0000.000
23A14ASN0-0.035-0.01218.0630.8870.8870.0000.0000.0000.000
24A15THR0-0.0210.00517.6110.2580.2580.0000.0000.0000.000
25A16ARG10.8670.93520.18510.45410.4540.0000.0000.0000.000
26A17LEU0-0.017-0.00220.476-0.372-0.3720.0000.0000.0000.000
27A18SER00.0550.04123.9460.5990.5990.0000.0000.0000.000
28A19TYR00.014-0.01025.782-0.379-0.3790.0000.0000.0000.000
29A20PHE0-0.023-0.02222.374-0.496-0.4960.0000.0000.0000.000
30A21HIS0-0.0020.00724.8560.5050.5050.0000.0000.0000.000
31A22GLY00.0320.00022.468-0.443-0.4430.0000.0000.0000.000
32A23TRP0-0.010-0.01523.006-0.493-0.4930.0000.0000.0000.000
33A24GLU-1-0.867-0.93025.658-10.249-10.2490.0000.0000.0000.000
34A25PRO0-0.063-0.01024.791-0.213-0.2130.0000.0000.0000.000
35A26VAL00.0910.02726.4360.4020.4020.0000.0000.0000.000
36A27SER0-0.009-0.00627.656-0.327-0.3270.0000.0000.0000.000
37A28ILE0-0.014-0.01426.3930.1860.1860.0000.0000.0000.000
38A29ASN0-0.033-0.02730.197-0.154-0.1540.0000.0000.0000.000
39A30GLY00.1020.06033.0680.0840.0840.0000.0000.0000.000
40A31GLY0-0.060-0.01828.920-0.089-0.0890.0000.0000.0000.000
41A32ALA0-0.034-0.02126.1020.0250.0250.0000.0000.0000.000
42A33GLU-1-0.861-0.92626.702-11.044-11.0440.0000.0000.0000.000
43A34LYS10.7810.88521.52512.28112.2810.0000.0000.0000.000
44A35TYR00.0980.06820.6430.3820.3820.0000.0000.0000.000
45A36SER0-0.063-0.05521.386-0.385-0.3850.0000.0000.0000.000
46A37VAL00.0230.02020.2080.2310.2310.0000.0000.0000.000
47A38SER0-0.017-0.01221.810-0.365-0.3650.0000.0000.0000.000
48A39VAL0-0.028-0.01317.5300.2140.2140.0000.0000.0000.000
49A40LEU00.0140.00820.956-0.084-0.0840.0000.0000.0000.000
50A41ILE0-0.006-0.01917.605-0.337-0.3370.0000.0000.0000.000
51A42PRO00.0830.04620.3210.3200.3200.0000.0000.0000.000
52A43LYS10.8250.88621.41110.13710.1370.0000.0000.0000.000
53A44THR0-0.030-0.02622.781-0.124-0.1240.0000.0000.0000.000
54A45ASP-1-0.798-0.86316.558-15.853-15.8530.0000.0000.0000.000
55A46LYS10.9310.94317.73111.38511.3850.0000.0000.0000.000
56A47GLU-1-0.914-0.93511.203-18.601-18.6010.0000.0000.0000.000
57A48THR0-0.025-0.04913.198-1.436-1.4360.0000.0000.0000.000
58A49ILE0-0.033-0.01214.185-0.622-0.6220.0000.0000.0000.000
59A50ASN0-0.027-0.01614.5170.1190.1190.0000.0000.0000.000
60A51ALA00.0140.0139.972-0.513-0.5130.0000.0000.0000.000
61A52ILE00.001-0.00311.599-1.073-1.0730.0000.0000.0000.000
62A53ASN0-0.011-0.00513.791-0.114-0.1140.0000.0000.0000.000
63A54ALA00.0070.01111.5180.1430.1430.0000.0000.0000.000
64A55ALA00.0130.00910.344-0.622-0.6220.0000.0000.0000.000
65A56VAL0-0.047-0.03211.811-0.149-0.1490.0000.0000.0000.000
66A57ASP-1-0.796-0.88215.361-15.632-15.6320.0000.0000.0000.000
67A58ALA0-0.018-0.00210.9930.1800.1800.0000.0000.0000.000
68A59ALA00.0070.00612.866-0.251-0.2510.0000.0000.0000.000
69A60ILE0-0.042-0.02513.6720.8660.8660.0000.0000.0000.000
70A61GLU-1-0.912-0.96014.601-18.741-18.7410.0000.0000.0000.000
71A62GLU-1-0.916-0.9539.045-30.917-30.9170.0000.0000.0000.000
72A63GLY0-0.023-0.01113.8550.4780.4780.0000.0000.0000.000
73A64ILE0-0.072-0.03716.9790.7810.7810.0000.0000.0000.000
74A65ALA0-0.007-0.00314.8350.6370.6370.0000.0000.0000.000
75A66LYS10.8860.96415.66718.65218.6520.0000.0000.0000.000
76A67PHE0-0.022-0.03117.5300.4310.4310.0000.0000.0000.000
77A68GLY00.0190.03620.6240.7430.7430.0000.0000.0000.000
78A69GLY00.0250.00922.5360.1110.1110.0000.0000.0000.000
79A70LYS10.9270.96223.9629.8869.8860.0000.0000.0000.000
80A71LYS11.0251.00220.47114.52014.5200.0000.0000.0000.000
81A72PRO0-0.0150.00822.1690.5850.5850.0000.0000.0000.000
82A73ASN00.0420.01524.782-0.428-0.4280.0000.0000.0000.000
83A74LYS10.9060.91019.93214.62514.6250.0000.0000.0000.000
84A75ALA00.0340.02525.265-0.082-0.0820.0000.0000.0000.000
85A76ALA0-0.059-0.01828.0080.2550.2550.0000.0000.0000.000
86A77ILE0-0.070-0.03721.914-0.018-0.0180.0000.0000.0000.000
87A78LYS10.9700.99923.70012.38812.3880.0000.0000.0000.000
88A79LEU00.040-0.00520.708-0.712-0.7120.0000.0000.0000.000
89A80PRO0-0.021-0.01217.6140.6260.6260.0000.0000.0000.000
90A81LEU0-0.0020.01418.3480.0970.0970.0000.0000.0000.000
91A82ARG10.7700.88120.84612.15112.1510.0000.0000.0000.000
92A83ASP-1-0.774-0.89224.234-10.750-10.7500.0000.0000.0000.000
93A84GLY0-0.016-0.02026.5790.2850.2850.0000.0000.0000.000
94A85ASP-1-0.795-0.87628.303-9.575-9.5750.0000.0000.0000.000
95A86VAL0-0.038-0.02830.4770.3110.3110.0000.0000.0000.000
96A87GLU-1-0.835-0.89627.732-10.837-10.8370.0000.0000.0000.000
97A88ARG10.8390.91728.91710.15110.1510.0000.0000.0000.000
98A89ASP-1-0.871-0.91532.662-8.301-8.3010.0000.0000.0000.000
99A90ASP-1-0.891-0.95032.237-9.068-9.0680.0000.0000.0000.000
100A91GLU-1-0.899-0.97732.787-8.533-8.5330.0000.0000.0000.000
101A92ALA0-0.059-0.01729.411-0.158-0.1580.0000.0000.0000.000
102A93TYR0-0.039-0.05026.957-0.556-0.5560.0000.0000.0000.000
103A94LYS10.9781.01028.5958.6268.6260.0000.0000.0000.000
104A95GLY0-0.0080.00728.500-0.151-0.1510.0000.0000.0000.000
105A96HIS0-0.099-0.05623.621-0.688-0.6880.0000.0000.0000.000
106A97TYR00.0330.01521.4150.2630.2630.0000.0000.0000.000
107A98PHE0-0.013-0.01522.060-0.119-0.1190.0000.0000.0000.000
108A99VAL00.0000.00917.477-0.120-0.1200.0000.0000.0000.000
109A100ASN0-0.0140.00620.7010.2340.2340.0000.0000.0000.000
110A101ALA00.0090.01417.193-0.311-0.3110.0000.0000.0000.000
111A102ASN0-0.030-0.03018.2560.3920.3920.0000.0000.0000.000
112A103SER00.0400.02716.774-1.137-1.1370.0000.0000.0000.000
113A104LYS10.9600.97118.50513.96413.9640.0000.0000.0000.000
114A105THR0-0.0040.01016.5610.6810.6810.0000.0000.0000.000
115A106PRO00.0280.01518.821-0.387-0.3870.0000.0000.0000.000
116A107PRO0-0.0210.01616.768-0.876-0.8760.0000.0000.0000.000
117A108GLN0-0.001-0.01313.9980.0690.0690.0000.0000.0000.000
118A109ILE0-0.009-0.00316.966-0.752-0.7520.0000.0000.0000.000
119A110VAL0-0.0060.00715.6430.4530.4530.0000.0000.0000.000
120A111ASP-1-0.696-0.83718.960-13.809-13.8090.0000.0000.0000.000
121A112LYS10.9580.95718.49212.54112.5410.0000.0000.0000.000
122A113ALA0-0.057-0.02018.337-0.433-0.4330.0000.0000.0000.000
123A114VAL0-0.057-0.02913.642-0.555-0.5550.0000.0000.0000.000
124A115ARG10.8950.93916.93012.41912.4190.0000.0000.0000.000
125A116PRO0-0.004-0.01319.4620.0370.0370.0000.0000.0000.000
126A117ILE0-0.0010.00721.1010.4920.4920.0000.0000.0000.000
127A118LEU0-0.035-0.02423.769-0.059-0.0590.0000.0000.0000.000
128A119ASP-1-0.814-0.89827.090-9.541-9.5410.0000.0000.0000.000
129A120ARG10.8930.93027.72310.60910.6090.0000.0000.0000.000
130A121ASN00.002-0.00528.726-0.209-0.2090.0000.0000.0000.000
131A122GLU-1-0.922-0.94326.613-10.483-10.4830.0000.0000.0000.000
132A123VAL0-0.093-0.05722.927-0.429-0.4290.0000.0000.0000.000
133A124TYR00.0450.01926.0630.0850.0850.0000.0000.0000.000
134A125SER00.019-0.00827.197-0.487-0.4870.0000.0000.0000.000
135A126GLY00.0590.04227.3280.4070.4070.0000.0000.0000.000
136A127CYS0-0.0640.01324.958-0.113-0.1130.0000.0000.0000.000
137A128TYR00.008-0.00922.560-0.245-0.2450.0000.0000.0000.000
138A129ALA00.0530.00119.5930.0340.0340.0000.0000.0000.000
139A130ARG10.8280.93510.34720.75520.7550.0000.0000.0000.000
140A131VAL00.0410.01015.120-0.016-0.0160.0000.0000.0000.000
141A132SER0-0.033-0.01210.142-1.929-1.9290.0000.0000.0000.000
142A133LEU0-0.022-0.00111.2351.2241.2240.0000.0000.0000.000
143A134ASN00.0130.0067.882-5.833-5.8330.0000.0000.0000.000
144A135PHE0-0.0030.00010.7392.5142.5140.0000.0000.0000.000
145A136TYR00.0300.00411.651-1.339-1.3390.0000.0000.0000.000
146A137ALA00.0330.02013.9541.3041.3040.0000.0000.0000.000
147A138PHE0-0.047-0.02117.166-0.111-0.1110.0000.0000.0000.000
148A139ASN0-0.014-0.02819.9720.6760.6760.0000.0000.0000.000
149A140SER00.0560.02523.441-0.042-0.0420.0000.0000.0000.000
150A141ASN00.002-0.00225.8020.2530.2530.0000.0000.0000.000
151A142GLY00.0240.02328.7490.1510.1510.0000.0000.0000.000
152A143ASN0-0.0320.00126.2130.2110.2110.0000.0000.0000.000
153A144LYS10.9990.97723.92910.67910.6790.0000.0000.0000.000
154A145GLY00.0030.01621.9550.4580.4580.0000.0000.0000.000
155A146VAL0-0.037-0.00416.025-0.504-0.5040.0000.0000.0000.000
156A147ALA0-0.0060.00917.4660.7430.7430.0000.0000.0000.000
157A148CYS0-0.003-0.01814.841-1.041-1.0410.0000.0000.0000.000
158A149GLY00.0020.01214.0130.9860.9860.0000.0000.0000.000
159A150LEU0-0.023-0.02013.797-1.174-1.1740.0000.0000.0000.000
160A151GLY00.0160.00712.407-0.577-0.5770.0000.0000.0000.000
161A152ASN00.000-0.01811.4852.3792.3790.0000.0000.0000.000
162A153ILE00.0390.02414.704-0.289-0.2890.0000.0000.0000.000
163A154GLN0-0.038-0.01215.328-0.421-0.4210.0000.0000.0000.000
164A155LYS10.8500.92117.38611.76611.7660.0000.0000.0000.000
165A156ILE0-0.117-0.05617.670-0.135-0.1350.0000.0000.0000.000
166A157ARG10.9400.95621.70511.53411.5340.0000.0000.0000.000
167A158ASP-1-0.757-0.86325.295-10.729-10.7290.0000.0000.0000.000
168A159GLY0-0.030-0.03228.378-0.095-0.0950.0000.0000.0000.000
169A160GLU-1-0.925-0.95029.665-8.529-8.5290.0000.0000.0000.000
170A161PRO00.0500.02331.552-0.324-0.3240.0000.0000.0000.000
171A162LEU0-0.059-0.02328.9330.1670.1670.0000.0000.0000.000
172A163GLY00.0280.01932.734-0.051-0.0510.0000.0000.0000.000
173A164GLY0-0.023-0.01832.949-0.300-0.3000.0000.0000.0000.000
174A165ARG10.9570.96627.38010.87410.8740.0000.0000.0000.000
175A166THR0-0.012-0.01334.6910.0090.0090.0000.0000.0000.000
176A167ASN0-0.013-0.00533.8570.3370.3370.0000.0000.0000.000
177A168ALA00.1100.06037.623-0.020-0.0200.0000.0000.0000.000
178A169ALA0-0.041-0.02440.7400.0980.0980.0000.0000.0000.000
179A170ASP-1-0.952-0.96835.935-8.651-8.6510.0000.0000.0000.000
180A171ASP-1-0.963-0.95938.522-8.338-8.3380.0000.0000.0000.000
181A172PHE0-0.106-0.06040.9650.1700.1700.0000.0000.0000.000
182A173THR00.0370.02244.514-0.086-0.0860.0000.0000.0000.000
183A174THR0-0.019-0.01547.0900.0200.0200.0000.0000.0000.000
184A175ILE0-0.037-0.01750.2840.0200.0200.0000.0000.0000.000
185A176GLU-1-0.967-0.98252.782-5.930-5.9300.0000.0000.0000.000