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: VQJ61

Calculation Name: 3JSY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JSY

Chain ID: A

ChEMBL ID:

UniProt ID: P54049

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2198826.747508
FMO2-HF: Nuclear repulsion 2117699.288714
FMO2-HF: Total energy -81127.458794
FMO2-MP2: Total energy -81365.030307


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:9:MET)


Summations of interaction energy for fragment #1(A:9:MET)
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.
-15.496-12.78719.659-7.826-14.54-0.006
Interaction energy analysis for fragmet #1(A:9:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : 0.017
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].
3A11PRO00.1210.0353.265-2.2630.9810.046-1.721-1.5690.005
4A12TRP00.0560.0245.9070.9430.9430.0000.0000.0000.000
5A13LYS10.9340.9772.070-4.369-3.8575.526-1.688-4.349-0.002
6A14ILE00.0220.0183.1940.2981.2680.073-0.191-0.851-0.001
7A15GLU-1-0.869-0.9424.9990.1060.159-0.001-0.006-0.0460.000
8A16GLU-1-0.850-0.9077.2781.1581.1580.0000.0000.0000.000
9A17VAL00.0170.0014.105-0.593-0.2380.021-0.087-0.2900.000
10A18LYS10.8990.9607.366-0.550-0.5500.0000.0000.0000.000
11A19THR0-0.073-0.04310.395-0.192-0.1920.0000.0000.0000.000
12A20LEU0-0.029-0.0177.722-0.140-0.1400.0000.0000.0000.000
13A21LYS10.7980.8809.178-1.190-1.1900.0000.0000.0000.000
14A22GLY0-0.0090.00712.298-0.102-0.1020.0000.0000.0000.000
15A23LEU0-0.057-0.03314.822-0.065-0.0650.0000.0000.0000.000
16A24ILE00.0060.00711.581-0.047-0.0470.0000.0000.0000.000
17A25LYS10.8510.90814.272-0.497-0.4970.0000.0000.0000.000
18A26SER0-0.113-0.04517.927-0.043-0.0430.0000.0000.0000.000
19A27LYS10.8110.89520.353-0.204-0.2040.0000.0000.0000.000
20A28PRO00.0400.03621.2620.0180.0180.0000.0000.0000.000
21A29VAL00.0110.02322.6480.0050.0050.0000.0000.0000.000
22A30VAL0-0.025-0.01715.9090.0190.0190.0000.0000.0000.000
23A31ALA00.0210.00318.786-0.012-0.0120.0000.0000.0000.000
24A32ILE0-0.028-0.00313.3280.0400.0400.0000.0000.0000.000
25A33VAL00.003-0.00416.733-0.029-0.0290.0000.0000.0000.000
26A34ASP-1-0.790-0.91617.0830.2590.2590.0000.0000.0000.000
27A35MET0-0.079-0.04517.609-0.011-0.0110.0000.0000.0000.000
28A36MET0-0.017-0.01519.2680.0000.0000.0000.0000.0000.000
29A37ASP-1-0.971-0.98320.7860.1460.1460.0000.0000.0000.000
30A38VAL00.002-0.00224.124-0.010-0.0100.0000.0000.0000.000
31A39PRO0-0.0170.00125.7850.0040.0040.0000.0000.0000.000
32A40ALA00.0360.00627.9270.0010.0010.0000.0000.0000.000
33A41PRO00.012-0.00128.9050.0030.0030.0000.0000.0000.000
34A42GLN00.1010.03729.7650.0030.0030.0000.0000.0000.000
35A43LEU00.0190.01823.1860.0030.0030.0000.0000.0000.000
36A44GLN0-0.044-0.02527.5840.0080.0080.0000.0000.0000.000
37A45GLU-1-0.888-0.93629.9130.0990.0990.0000.0000.0000.000
38A46ILE00.0130.03125.913-0.001-0.0010.0000.0000.0000.000
39A47ARG10.9150.95824.641-0.159-0.1590.0000.0000.0000.000
40A48ASP-1-0.861-0.95528.2710.1100.1100.0000.0000.0000.000
41A49LYS10.9060.96730.958-0.112-0.1120.0000.0000.0000.000
42A50ILE00.0200.00324.713-0.002-0.0020.0000.0000.0000.000
43A51ARG10.8330.93827.649-0.112-0.1120.0000.0000.0000.000
44A52ASP-1-0.876-0.93327.6290.1280.1280.0000.0000.0000.000
45A53LYS10.8660.93928.433-0.122-0.1220.0000.0000.0000.000
46A54VAL00.0020.02423.1950.0050.0050.0000.0000.0000.000
47A55LYS10.9170.97120.283-0.263-0.2630.0000.0000.0000.000
48A56LEU00.0280.01818.1750.0120.0120.0000.0000.0000.000
49A57ARG10.8820.93913.379-0.453-0.4530.0000.0000.0000.000
50A58MET00.0450.02914.1570.0070.0070.0000.0000.0000.000
51A59SER00.010-0.0238.8260.1310.1310.0000.0000.0000.000
52A60ARG10.9650.9876.844-1.049-1.0490.0000.0000.0000.000
53A61ASN00.1280.0537.4410.1030.1030.0000.0000.0000.000
54A62THR0-0.020-0.0122.419-0.127-0.0841.051-0.196-0.897-0.001
55A63LEU0-0.060-0.0332.680-1.853-0.4890.790-0.619-1.535-0.005
56A64ILE00.0530.0334.3590.1260.190-0.001-0.008-0.0550.000
57A65ILE00.0260.0165.9930.0000.0000.0000.0000.0000.000
58A66ARG10.8200.8752.423-7.483-11.39912.155-3.309-4.930-0.002
59A67ALA00.0180.0015.1780.1360.156-0.001-0.001-0.0180.000
60A68LEU00.0340.0177.884-0.107-0.1070.0000.0000.0000.000
61A69LYS10.9460.9697.916-0.464-0.4640.0000.0000.0000.000
62A70GLU-1-0.775-0.8727.1052.2152.2150.0000.0000.0000.000
63A71ALA0-0.003-0.00110.353-0.112-0.1120.0000.0000.0000.000
64A72ALA0-0.008-0.00212.878-0.075-0.0750.0000.0000.0000.000
65A73GLU-1-0.961-0.96812.6380.3630.3630.0000.0000.0000.000
66A74GLU-1-0.784-0.87112.2010.5980.5980.0000.0000.0000.000
67A75LEU0-0.040-0.01416.126-0.040-0.0400.0000.0000.0000.000
68A76ASN0-0.0310.00018.518-0.015-0.0150.0000.0000.0000.000
69A77ASN00.008-0.00218.537-0.032-0.0320.0000.0000.0000.000
70A78PRO00.0710.01917.0950.0280.0280.0000.0000.0000.000
71A79LYS10.8660.93417.003-0.162-0.1620.0000.0000.0000.000
72A80LEU00.0260.02214.7500.0060.0060.0000.0000.0000.000
73A81ALA00.012-0.01012.9180.0260.0260.0000.0000.0000.000
74A82GLU-1-0.879-0.93413.3480.2020.2020.0000.0000.0000.000
75A83LEU00.0190.01114.378-0.008-0.0080.0000.0000.0000.000
76A84ALA0-0.039-0.02410.2000.0020.0020.0000.0000.0000.000
77A85ASN0-0.063-0.03911.900-0.001-0.0010.0000.0000.0000.000
78A86TYR00.0190.01514.484-0.021-0.0210.0000.0000.0000.000
79A87VAL0-0.058-0.01510.1430.0070.0070.0000.0000.0000.000
80A88GLU-1-0.893-0.95813.3130.1900.1900.0000.0000.0000.000
81A89ARG10.8640.94214.971-0.177-0.1770.0000.0000.0000.000
82A90GLY00.0240.02114.4190.0330.0330.0000.0000.0000.000
83A91ALA0-0.0140.00212.247-0.006-0.0060.0000.0000.0000.000
84A92ALA0-0.033-0.01513.4270.0490.0490.0000.0000.0000.000
85A93ILE00.0100.00610.724-0.013-0.0130.0000.0000.0000.000
86A94LEU00.0080.00714.972-0.007-0.0070.0000.0000.0000.000
87A95VAL0-0.032-0.00917.5870.0030.0030.0000.0000.0000.000
88A96THR0-0.005-0.04820.279-0.016-0.0160.0000.0000.0000.000
89A97ASP-1-0.759-0.87924.0320.1650.1650.0000.0000.0000.000
90A98MET0-0.105-0.01327.058-0.012-0.0120.0000.0000.0000.000
91A99ASN00.0810.04827.0300.0130.0130.0000.0000.0000.000
92A100PRO00.0640.00925.2970.0010.0010.0000.0000.0000.000
93A101PHE00.0510.04126.8970.0040.0040.0000.0000.0000.000
94A102LYS10.9580.98330.141-0.115-0.1150.0000.0000.0000.000
95A103LEU0-0.022-0.02222.9910.0000.0000.0000.0000.0000.000
96A104TYR00.0540.00726.639-0.001-0.0010.0000.0000.0000.000
97A105LYS10.8220.91728.140-0.094-0.0940.0000.0000.0000.000
98A106LEU0-0.071-0.03027.623-0.003-0.0030.0000.0000.0000.000
99A107LEU0-0.081-0.05123.7920.0000.0000.0000.0000.0000.000
100A108GLU-1-0.870-0.94926.1430.1490.1490.0000.0000.0000.000
101A109GLU-1-0.943-0.96629.6080.0940.0940.0000.0000.0000.000
102A110ASN0-0.082-0.03432.151-0.010-0.0100.0000.0000.0000.000
103A111LYS10.9200.97929.737-0.109-0.1090.0000.0000.0000.000
104A112SER0-0.027-0.03330.930-0.005-0.0050.0000.0000.0000.000
105A113PRO0-0.034-0.01132.3670.0030.0030.0000.0000.0000.000
106A114ALA00.013-0.00331.9580.0010.0010.0000.0000.0000.000
107A115PRO00.0450.02133.784-0.002-0.0020.0000.0000.0000.000
108A116VAL0-0.037-0.00433.7330.0060.0060.0000.0000.0000.000
109A117ARG10.9850.98627.873-0.123-0.1230.0000.0000.0000.000
110A118GLY00.014-0.01133.728-0.002-0.0020.0000.0000.0000.000
111A119GLY0-0.026-0.01533.5100.0030.0030.0000.0000.0000.000
112A120GLN00.0150.02130.9430.0020.0020.0000.0000.0000.000
113A121ILE00.0040.00531.782-0.005-0.0050.0000.0000.0000.000
114A122ALA00.0120.00632.9330.0050.0050.0000.0000.0000.000
115A123PRO00.0010.00732.012-0.001-0.0010.0000.0000.0000.000
116A124CYS0-0.030-0.04133.9310.0010.0010.0000.0000.0000.000
117A125ASP-1-0.827-0.90437.4630.0630.0630.0000.0000.0000.000
118A126ILE0-0.020-0.00537.3040.0020.0020.0000.0000.0000.000
119A127LYS10.8900.96141.499-0.054-0.0540.0000.0000.0000.000
120A128VAL0-0.032-0.01044.5760.0020.0020.0000.0000.0000.000
121A129GLU-1-0.886-0.95447.2150.0550.0550.0000.0000.0000.000
122A130LYS10.8400.91449.969-0.038-0.0380.0000.0000.0000.000
123A131GLY00.0360.02353.4800.0000.0000.0000.0000.0000.000
124A132SER0-0.061-0.03554.1220.0000.0000.0000.0000.0000.000
125A133THR00.0490.00150.9420.0010.0010.0000.0000.0000.000
126A134GLY0-0.010-0.00151.5990.0010.0010.0000.0000.0000.000
127A135MET0-0.031-0.01149.1860.0000.0000.0000.0000.0000.000
128A136PRO00.0300.00553.876-0.001-0.0010.0000.0000.0000.000
129A137PRO00.0190.01755.8410.0010.0010.0000.0000.0000.000
130A138GLY00.0480.01355.7130.0000.0000.0000.0000.0000.000
131A139PRO00.0380.00752.3450.0000.0000.0000.0000.0000.000
132A140PHE00.0230.01547.2660.0000.0000.0000.0000.0000.000
133A141LEU00.0310.02651.7640.0010.0010.0000.0000.0000.000
134A142GLY00.004-0.00853.9910.0000.0000.0000.0000.0000.000
135A143GLU-1-0.942-0.98047.6560.0460.0460.0000.0000.0000.000
136A144LEU00.0390.03948.9690.0010.0010.0000.0000.0000.000
137A145LYS10.9510.97850.428-0.033-0.0330.0000.0000.0000.000
138A146SER0-0.087-0.05049.3860.0000.0000.0000.0000.0000.000
139A147VAL0-0.011-0.00145.4080.0010.0010.0000.0000.0000.000
140A148GLY00.0300.02547.5710.0020.0020.0000.0000.0000.000
141A149ILE00.0210.01546.6680.0000.0000.0000.0000.0000.000
142A150PRO0-0.032-0.00851.051-0.001-0.0010.0000.0000.0000.000
143A151ALA00.0590.02553.9360.0010.0010.0000.0000.0000.000
144A152ALA0-0.060-0.04756.007-0.001-0.0010.0000.0000.0000.000
145A153ILE00.0020.01458.4860.0010.0010.0000.0000.0000.000
146A154GLU-1-0.906-0.95959.7100.0330.0330.0000.0000.0000.000
147A155LYS10.9700.97360.844-0.032-0.0320.0000.0000.0000.000
148A156GLY00.0110.00662.1290.0000.0000.0000.0000.0000.000
149A157LYS10.9030.96156.823-0.034-0.0340.0000.0000.0000.000
150A158ILE0-0.0050.00953.686-0.001-0.0010.0000.0000.0000.000
151A159ALA00.0110.03055.0700.0020.0020.0000.0000.0000.000
152A160ILE00.0330.01149.571-0.001-0.0010.0000.0000.0000.000
153A161LYS10.9270.97054.098-0.034-0.0340.0000.0000.0000.000
154A162GLU-1-0.892-0.96854.3460.0380.0380.0000.0000.0000.000
155A163ASP-1-0.772-0.87250.8300.0470.0470.0000.0000.0000.000
156A164LYS10.8050.87449.219-0.046-0.0460.0000.0000.0000.000
157A165VAL00.0050.01544.3230.0020.0020.0000.0000.0000.000
158A166VAL0-0.037-0.03743.415-0.002-0.0020.0000.0000.0000.000
159A167VAL00.0040.00539.924-0.001-0.0010.0000.0000.0000.000
160A168LYS10.9750.99641.768-0.052-0.0520.0000.0000.0000.000
161A169LYS10.9390.97134.232-0.083-0.0830.0000.0000.0000.000
162A170GLY0-0.044-0.02635.489-0.002-0.0020.0000.0000.0000.000
163A171GLU-1-0.879-0.93536.5750.0580.0580.0000.0000.0000.000
164A172VAL0-0.020-0.00735.1010.0030.0030.0000.0000.0000.000
165A173VAL00.0240.01936.398-0.004-0.0040.0000.0000.0000.000
166A174SER00.0170.01037.4120.0020.0020.0000.0000.0000.000
167A175PRO00.0980.01637.0260.0010.0010.0000.0000.0000.000
168A176LYS10.9260.97839.007-0.044-0.0440.0000.0000.0000.000
169A177LEU00.0270.01741.643-0.001-0.0010.0000.0000.0000.000
170A178ALA00.0070.00037.4970.0000.0000.0000.0000.0000.000
171A179ALA00.0160.01339.5690.0010.0010.0000.0000.0000.000
172A180VAL0-0.022-0.01741.153-0.001-0.0010.0000.0000.0000.000
173A181LEU0-0.012-0.01940.556-0.001-0.0010.0000.0000.0000.000
174A182ASP-1-0.884-0.94437.6910.0760.0760.0000.0000.0000.000
175A183ARG10.8770.95740.745-0.047-0.0470.0000.0000.0000.000
176A184LEU0-0.069-0.03744.019-0.002-0.0020.0000.0000.0000.000
177A185GLY0-0.0020.00942.019-0.001-0.0010.0000.0000.0000.000
178A186ILE0-0.027-0.00940.9330.0020.0020.0000.0000.0000.000
179A187LYS10.8820.93836.785-0.076-0.0760.0000.0000.0000.000
180A188PRO00.0090.00937.2540.0010.0010.0000.0000.0000.000
181A189ILE0-0.0060.00931.3430.0010.0010.0000.0000.0000.000
182A190LYS10.9380.96632.195-0.095-0.0950.0000.0000.0000.000
183A191VAL00.0110.00327.7670.0030.0030.0000.0000.0000.000
184A192GLY00.030-0.03326.466-0.007-0.0070.0000.0000.0000.000
185A193LEU0-0.038-0.01021.2570.0070.0070.0000.0000.0000.000
186A194ASN00.0440.03122.426-0.016-0.0160.0000.0000.0000.000
187A195ILE00.0100.01621.2550.0200.0200.0000.0000.0000.000
188A196LEU0-0.045-0.01416.724-0.009-0.0090.0000.0000.0000.000
189A197ALA00.013-0.00618.435-0.011-0.0110.0000.0000.0000.000
190A198VAL0-0.026-0.01219.6160.0190.0190.0000.0000.0000.000
191A199TYR0-0.0260.01519.144-0.009-0.0090.0000.0000.0000.000
192A200GLU-1-0.841-0.95621.0070.1520.1520.0000.0000.0000.000
193A201ASP-1-0.897-0.93323.9110.1340.1340.0000.0000.0000.000
194A202GLY0-0.020-0.02722.780-0.007-0.0070.0000.0000.0000.000
195A203ILE0-0.014-0.00123.749-0.005-0.0050.0000.0000.0000.000
196A204ILE0-0.063-0.03718.8420.0130.0130.0000.0000.0000.000
197A205TYR00.0210.00722.501-0.015-0.0150.0000.0000.0000.000
198A206THR00.0350.00522.9760.0110.0110.0000.0000.0000.000
199A207PRO00.0460.00123.096-0.008-0.0080.0000.0000.0000.000
200A208ASP-1-0.943-0.96926.1670.1120.1120.0000.0000.0000.000
201A209VAL0-0.015-0.00127.873-0.006-0.0060.0000.0000.0000.000
202A210LEU0-0.031-0.01625.088-0.004-0.0040.0000.0000.0000.000
203A211LYS10.8990.94929.518-0.117-0.1170.0000.0000.0000.000
204A212VAL0-0.071-0.03031.937-0.005-0.0050.0000.0000.0000.000
205A213ASP-1-0.873-0.92932.8200.0960.0960.0000.0000.0000.000
206A214GLU-1-0.876-0.91833.5060.0810.0810.0000.0000.0000.000
207A215GLU-1-0.962-1.00034.4210.0870.0870.0000.0000.0000.000
208A216LYS10.8980.96530.426-0.119-0.1190.0000.0000.0000.000
209A217LEU00.0350.00534.097-0.005-0.0050.0000.0000.0000.000
210A218LEU0-0.048-0.03036.3310.0010.0010.0000.0000.0000.000
211A219ALA0-0.0020.02336.535-0.001-0.0010.0000.0000.0000.000
212A220ASP-1-0.932-0.98633.6440.1110.1110.0000.0000.0000.000
213A221ILE0-0.025-0.00331.880-0.005-0.0050.0000.0000.0000.000