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: 14R1Z

Calculation Name: 2JA9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2JA9

Chain ID: A

ChEMBL ID:

UniProt ID: Q08285

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptAll
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 175
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1782374.749183
FMO2-HF: Nuclear repulsion 1712824.558199
FMO2-HF: Total energy -69550.190984
FMO2-MP2: Total energy -69749.865029


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:62:LYS)


Summations of interaction energy for fragment #1(A:62: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.
-39.336-36.6580.531-0.882-2.327-0.001
Interaction energy analysis for fragmet #1(A:62:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.953 / q_NPA : 0.964
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].
3A64TYR0-0.014-0.0353.754-3.514-2.1130.006-0.563-0.8440.001
4A65ILE0-0.0010.0045.6722.7492.7490.0000.0000.0000.000
5A66PRO00.012-0.0048.243-0.843-0.8430.0000.0000.0000.000
6A67SER0-0.029-0.01610.6300.4410.4410.0000.0000.0000.000
7A68VAL00.0560.01512.5990.1730.1730.0000.0000.0000.000
8A69ASN0-0.026-0.01716.0610.3360.3360.0000.0000.0000.000
9A70ASP-1-0.767-0.81810.849-26.459-26.4590.0000.0000.0000.000
10A71PHE00.0240.01614.2691.0281.0280.0000.0000.0000.000
11A72VAL0-0.021-0.01812.123-1.912-1.9120.0000.0000.0000.000
12A73ILE0-0.0100.00414.2511.2491.2490.0000.0000.0000.000
13A74GLY00.0110.00214.966-1.276-1.2760.0000.0000.0000.000
14A75VAL0-0.036-0.00417.2660.5020.5020.0000.0000.0000.000
15A76ILE0-0.0040.00420.299-0.282-0.2820.0000.0000.0000.000
16A77ILE0-0.007-0.01719.3950.2310.2310.0000.0000.0000.000
17A78GLY00.002-0.00223.2430.3420.3420.0000.0000.0000.000
18A79THR0-0.021-0.01126.041-0.233-0.2330.0000.0000.0000.000
19A80PHE00.0160.01625.6030.2210.2210.0000.0000.0000.000
20A81SER00.001-0.01630.3070.1150.1150.0000.0000.0000.000
21A82ASP-1-0.887-0.91329.575-9.537-9.5370.0000.0000.0000.000
22A83SER00.001-0.01026.155-0.216-0.2160.0000.0000.0000.000
23A84TYR0-0.037-0.02324.8060.3110.3110.0000.0000.0000.000
24A85LYS10.8030.89720.97212.51612.5160.0000.0000.0000.000
25A86VAL00.0190.01218.2480.1730.1730.0000.0000.0000.000
26A87SER0-0.0010.01215.621-0.801-0.8010.0000.0000.0000.000
27A88LEU00.0740.02712.331-0.102-0.1020.0000.0000.0000.000
28A89GLN0-0.028-0.0379.0900.4090.4090.0000.0000.0000.000
29A90ASN00.0550.04412.3751.1391.1390.0000.0000.0000.000
30A91PHE00.002-0.00111.208-1.482-1.4820.0000.0000.0000.000
31A92SER0-0.033-0.0219.919-2.222-2.2220.0000.0000.0000.000
32A93SER00.0270.02012.1870.8590.8590.0000.0000.0000.000
33A94SER0-0.082-0.05014.102-0.693-0.6930.0000.0000.0000.000
34A95VAL0-0.007-0.00115.173-0.472-0.4720.0000.0000.0000.000
35A96SER00.0070.01017.9550.6380.6380.0000.0000.0000.000
36A97LEU00.0650.02721.211-0.344-0.3440.0000.0000.0000.000
37A98SER00.0360.02323.3900.5630.5630.0000.0000.0000.000
38A99TYR0-0.048-0.07026.953-0.060-0.0600.0000.0000.0000.000
39A100MET0-0.023-0.02429.8590.3880.3880.0000.0000.0000.000
40A101ALA00.0350.03725.3060.0860.0860.0000.0000.0000.000
41A102PHE00.0300.00026.093-0.436-0.4360.0000.0000.0000.000
42A103PRO00.0470.02628.8100.2840.2840.0000.0000.0000.000
43A104ASN0-0.030-0.01331.6040.1700.1700.0000.0000.0000.000
44A105ALA00.0020.04031.9680.3060.3060.0000.0000.0000.000
45A106SER00.015-0.00633.8940.1980.1980.0000.0000.0000.000
46A107LYS10.9010.93335.2058.4248.4240.0000.0000.0000.000
47A108LYS10.9290.97037.9287.1117.1110.0000.0000.0000.000
48A109ASN0-0.042-0.01735.2060.0740.0740.0000.0000.0000.000
49A110ARG10.9100.95931.9768.9748.9740.0000.0000.0000.000
50A111PRO00.0220.02929.8180.1280.1280.0000.0000.0000.000
51A112THR00.012-0.00732.1510.0840.0840.0000.0000.0000.000
52A113LEU00.0140.03025.7980.0590.0590.0000.0000.0000.000
53A114GLN0-0.055-0.03128.9330.5600.5600.0000.0000.0000.000
54A115VAL0-0.022-0.02525.900-0.406-0.4060.0000.0000.0000.000
55A116GLY00.0070.00424.9900.2940.2940.0000.0000.0000.000
56A117ASP-1-0.773-0.86624.848-11.014-11.0140.0000.0000.0000.000
57A118LEU0-0.018-0.01220.727-0.552-0.5520.0000.0000.0000.000
58A119VAL0-0.010-0.01220.2090.5320.5320.0000.0000.0000.000
59A120TYR0-0.004-0.02016.739-0.808-0.8080.0000.0000.0000.000
60A121ALA00.0250.00318.6090.8630.8630.0000.0000.0000.000
61A122ARG10.8050.89517.96712.23412.2340.0000.0000.0000.000
62A123VAL0-0.035-0.01513.8060.6750.6750.0000.0000.0000.000
63A124CYS0-0.054-0.01617.276-0.054-0.0540.0000.0000.0000.000
64A125THR0-0.001-0.03319.261-0.028-0.0280.0000.0000.0000.000
65A126ALA0-0.008-0.03414.188-0.585-0.5850.0000.0000.0000.000
66A127GLU-1-0.911-0.94115.566-14.812-14.8120.0000.0000.0000.000
67A128LYS10.8010.87314.06516.16816.1680.0000.0000.0000.000
68A129DGL-1-0.824-0.89313.373-16.457-16.4570.0000.0000.0000.000
69A130LEU0-0.0230.00216.7150.8470.8470.0000.0000.0000.000
70A131GLU-1-0.837-0.87716.789-14.238-14.2380.0000.0000.0000.000
71A132ALA00.0120.01415.4440.3340.3340.0000.0000.0000.000
72A133GLU-1-0.875-0.90417.435-12.199-12.1990.0000.0000.0000.000
73A134ILE0-0.015-0.01916.926-0.751-0.7510.0000.0000.0000.000
74A135GLU-1-0.820-0.91319.875-11.538-11.5380.0000.0000.0000.000
75A136CYS0-0.047-0.03022.067-0.595-0.5950.0000.0000.0000.000
76A137PHE0-0.002-0.00124.5000.4710.4710.0000.0000.0000.000
77A138ASP-1-0.733-0.82524.867-11.938-11.9380.0000.0000.0000.000
78A139SER0-0.011-0.01725.5360.2860.2860.0000.0000.0000.000
79A140THR0-0.080-0.04227.3960.3200.3200.0000.0000.0000.000
80A141THR0-0.069-0.07329.7120.4410.4410.0000.0000.0000.000
81A142GLY0-0.0040.01130.5260.3340.3340.0000.0000.0000.000
82A143ARG10.8450.90430.9459.7839.7830.0000.0000.0000.000
83A144ASP-1-0.762-0.88328.307-10.685-10.6850.0000.0000.0000.000
84A145ALA0-0.026-0.01326.007-0.442-0.4420.0000.0000.0000.000
85A146GLY00.0150.01525.228-0.424-0.4240.0000.0000.0000.000
86A147PHE0-0.063-0.01219.707-0.456-0.4560.0000.0000.0000.000
87A148GLY00.006-0.00423.5090.6440.6440.0000.0000.0000.000
88A149ILE0-0.0110.00123.829-0.678-0.6780.0000.0000.0000.000
89A150LEU0-0.042-0.02020.154-0.126-0.1260.0000.0000.0000.000
90A151GLU-1-0.895-0.95424.645-10.343-10.3430.0000.0000.0000.000
91A152ASP-1-0.876-0.95027.540-10.291-10.2910.0000.0000.0000.000
92A153GLY0-0.026-0.01024.4840.0690.0690.0000.0000.0000.000
93A154MET0-0.078-0.03522.0850.0770.0770.0000.0000.0000.000
94A155ILE00.0300.00716.310-0.431-0.4310.0000.0000.0000.000
95A156ILE0-0.054-0.02314.5730.4000.4000.0000.0000.0000.000
96A157ASP-1-0.781-0.86811.991-23.632-23.6320.0000.0000.0000.000
97A158VAL0-0.032-0.0309.5340.1470.1470.0000.0000.0000.000
98A159ASN00.009-0.0075.194-7.867-7.8670.0000.0000.0000.000
99A160LEU00.0350.0012.407-0.9020.1600.526-0.300-1.288-0.002
100A161ASN0-0.0190.0084.0244.1184.333-0.001-0.019-0.1950.000
101A162PHE00.0240.0125.6595.6235.6230.0000.0000.0000.000
102A163ALA00.0290.0138.2593.0453.0450.0000.0000.0000.000
103A164ARG10.8920.9327.76233.51133.5110.0000.0000.0000.000
104A165GLN0-0.033-0.0268.3995.1235.1230.0000.0000.0000.000
105A166LEU0-0.024-0.01411.3162.1272.1270.0000.0000.0000.000
106A167LEU00.0010.01213.3801.3801.3800.0000.0000.0000.000
107A168PHE0-0.006-0.00412.3610.9600.9600.0000.0000.0000.000
108A169ASN0-0.048-0.02413.1492.0322.0320.0000.0000.0000.000
109A170ASN00.0410.00915.4240.3310.3310.0000.0000.0000.000
110A171ASP-1-0.870-0.91417.945-15.032-15.0320.0000.0000.0000.000
111A172PHE0-0.017-0.01011.8520.0590.0590.0000.0000.0000.000
112A173PRO00.0080.00616.4170.5050.5050.0000.0000.0000.000
113A174LEU0-0.0080.00615.2390.8840.8840.0000.0000.0000.000
114A175LEU00.0650.02818.4800.7920.7920.0000.0000.0000.000
115A176LYS10.8610.91619.33316.46416.4640.0000.0000.0000.000
116A177VAL0-0.031-0.01821.3390.6740.6740.0000.0000.0000.000
117A178LEU00.0180.01020.3210.4900.4900.0000.0000.0000.000
118A179ALA00.0200.02324.0160.5140.5140.0000.0000.0000.000
119A180ALA0-0.058-0.02426.5730.4760.4760.0000.0000.0000.000
120A181HIS0-0.077-0.04626.0950.5380.5380.0000.0000.0000.000
121A182THR0-0.026-0.01326.9620.5020.5020.0000.0000.0000.000
122A183LYS10.8760.93028.3718.9498.9490.0000.0000.0000.000
123A184PHE0-0.035-0.02322.221-0.123-0.1230.0000.0000.0000.000
124A185GLU-1-0.814-0.89225.285-11.242-11.2420.0000.0000.0000.000
125A186VAL0-0.034-0.04518.720-0.348-0.3480.0000.0000.0000.000
126A187ALA00.0230.03519.2380.3180.3180.0000.0000.0000.000
127A188ILE0-0.011-0.01513.295-0.661-0.6610.0000.0000.0000.000
128A189GLY00.0430.03713.5530.4400.4400.0000.0000.0000.000
129A190LEU0-0.013-0.0149.931-2.242-2.2420.0000.0000.0000.000
130A191ASN0-0.043-0.0368.131-3.694-3.6940.0000.0000.0000.000
131A192GLY0-0.026-0.0218.416-1.359-1.3590.0000.0000.0000.000
132A193LYS10.7740.8828.95722.52722.5270.0000.0000.0000.000
133A194ILE00.0000.00512.668-0.030-0.0300.0000.0000.0000.000
134A195TRP0-0.0130.00415.1930.0370.0370.0000.0000.0000.000
135A196VAL00.001-0.00318.873-0.034-0.0340.0000.0000.0000.000
136A197LYS10.8670.95021.72211.36111.3610.0000.0000.0000.000
137A198CYS0-0.083-0.03925.550-0.204-0.2040.0000.0000.0000.000
138A199GLU-1-0.810-0.88328.604-9.027-9.0270.0000.0000.0000.000
139A200GLU-1-0.823-0.91031.366-8.812-8.8120.0000.0000.0000.000
140A201LEU00.0170.02129.208-0.489-0.4890.0000.0000.0000.000
141A202SER00.0390.00729.374-0.330-0.3300.0000.0000.0000.000
142A203ASN00.0450.00128.906-0.227-0.2270.0000.0000.0000.000
143A204THR00.0290.01925.269-0.581-0.5810.0000.0000.0000.000
144A205LEU00.0240.00324.593-0.681-0.6810.0000.0000.0000.000
145A206ALA00.0210.02624.469-0.552-0.5520.0000.0000.0000.000
146A207CYS0-0.0190.01122.299-0.610-0.6100.0000.0000.0000.000
147A208TYR00.0040.00319.970-0.785-0.7850.0000.0000.0000.000
148A209ARG10.7860.85119.66810.89910.8990.0000.0000.0000.000
149A210THR0-0.024-0.03019.963-0.556-0.5560.0000.0000.0000.000
150A211ILE00.0180.00515.469-0.887-0.8870.0000.0000.0000.000
151A212MET00.0250.02115.379-1.460-1.4600.0000.0000.0000.000
152A213GLU-1-0.738-0.82615.172-15.826-15.8260.0000.0000.0000.000
153A214CYS0-0.056-0.02815.390-0.269-0.2690.0000.0000.0000.000
154A215CYS0-0.050-0.00310.136-2.342-2.3420.0000.0000.0000.000
155A216GLN0-0.043-0.02010.721-2.743-2.7430.0000.0000.0000.000
156A217LYS10.8800.94512.78716.30316.3030.0000.0000.0000.000
157A218ASN0-0.045-0.0278.454-3.520-3.5200.0000.0000.0000.000
158A219ASP-1-0.850-0.92511.703-19.801-19.8010.0000.0000.0000.000
159A220THR0-0.012-0.01813.6241.2411.2410.0000.0000.0000.000
160A221ALA0-0.0020.00016.0530.8750.8750.0000.0000.0000.000
161A222ALA00.0090.00918.1200.9120.9120.0000.0000.0000.000
162A223PHE00.0350.00713.1960.6730.6730.0000.0000.0000.000
163A224LYS10.9800.99419.35412.08512.0850.0000.0000.0000.000
164A225ASP-1-0.807-0.90622.869-11.173-11.1730.0000.0000.0000.000
165A226ILE0-0.034-0.01118.2970.4030.4030.0000.0000.0000.000
166A227ALA00.0210.01622.4390.4260.4260.0000.0000.0000.000
167A228LYS10.8210.90224.11611.53411.5340.0000.0000.0000.000
168A229ARG10.7860.86522.20413.69913.6990.0000.0000.0000.000
169A230GLN0-0.019-0.02422.2850.7310.7310.0000.0000.0000.000
170A231PHE00.0740.04024.3760.0120.0120.0000.0000.0000.000
171A232LYS10.8370.92528.73810.02110.0210.0000.0000.0000.000
172A233GLU-1-0.820-0.88830.620-10.271-10.2710.0000.0000.0000.000
173A234ILE0-0.0150.00129.7270.1980.1980.0000.0000.0000.000
174A235LEU0-0.029-0.00233.675-0.029-0.0290.0000.0000.0000.000
175A236THR0-0.030-0.02631.5600.1880.1880.0000.0000.0000.000