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: G5Z41

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2205311.710231
FMO2-HF: Nuclear repulsion 2124182.697068
FMO2-HF: Total energy -81129.013162
FMO2-MP2: Total energy -81366.621918


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.
-15.206-16.16320.976-8.115-11.9010.024
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 : 0.035 / q_NPA : 0.045
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].
3A11PRO00.0920.0273.483-0.7021.7580.020-1.252-1.2290.004
4A12TRP00.0550.0265.9781.1301.1300.0000.0000.0000.000
5A13LYS10.9400.9812.257-4.881-3.7872.976-0.987-3.0820.000
6A14ILE00.0150.0173.0390.3741.4360.155-0.237-0.979-0.001
7A15GLU-1-0.796-0.8785.1670.0480.103-0.001-0.003-0.0500.000
8A16GLU-1-0.830-0.8987.5461.7771.7770.0000.0000.0000.000
9A17VAL00.0240.0074.596-0.518-0.3160.002-0.039-0.1650.000
10A18LYS10.8370.9087.797-0.741-0.7410.0000.0000.0000.000
11A19THR0-0.072-0.04810.713-0.251-0.2510.0000.0000.0000.000
12A20LEU0-0.042-0.0138.261-0.174-0.1740.0000.0000.0000.000
13A21LYS10.7980.8669.104-1.436-1.4360.0000.0000.0000.000
14A22GLY00.0000.00712.688-0.129-0.1290.0000.0000.0000.000
15A23LEU0-0.056-0.02615.364-0.082-0.0820.0000.0000.0000.000
16A24ILE00.0070.01211.921-0.066-0.0660.0000.0000.0000.000
17A25LYS10.8730.92214.602-0.567-0.5670.0000.0000.0000.000
18A26SER0-0.093-0.04018.330-0.056-0.0560.0000.0000.0000.000
19A27LYS10.7600.85321.017-0.254-0.2540.0000.0000.0000.000
20A28PRO00.0310.03721.8820.0180.0180.0000.0000.0000.000
21A29VAL00.0010.01823.0800.0010.0010.0000.0000.0000.000
22A30VAL0-0.017-0.01516.4650.0260.0260.0000.0000.0000.000
23A31ALA00.0200.00218.873-0.024-0.0240.0000.0000.0000.000
24A32ILE0-0.040-0.01113.7330.0610.0610.0000.0000.0000.000
25A33VAL00.0230.00817.313-0.043-0.0430.0000.0000.0000.000
26A34ASP-1-0.740-0.87517.9210.3420.3420.0000.0000.0000.000
27A35MET0-0.063-0.03218.590-0.015-0.0150.0000.0000.0000.000
28A36MET0-0.015-0.02320.251-0.006-0.0060.0000.0000.0000.000
29A37ASP-1-0.840-0.89621.8330.1750.1750.0000.0000.0000.000
30A38VAL00.0080.01524.735-0.018-0.0180.0000.0000.0000.000
31A39PRO0-0.015-0.00726.4520.0070.0070.0000.0000.0000.000
32A40ALA00.0340.01028.7320.0010.0010.0000.0000.0000.000
33A41PRO00.002-0.00129.6670.0020.0020.0000.0000.0000.000
34A42GLN00.0640.02430.3500.0040.0040.0000.0000.0000.000
35A43LEU0-0.0020.00024.1080.0050.0050.0000.0000.0000.000
36A44GLN0-0.046-0.01528.3210.0150.0150.0000.0000.0000.000
37A45GLU-1-0.784-0.88331.0800.1330.1330.0000.0000.0000.000
38A46ILE0-0.017-0.00626.4550.0000.0000.0000.0000.0000.000
39A47ARG10.8980.94226.517-0.198-0.1980.0000.0000.0000.000
40A48ASP-1-0.819-0.90429.0960.1410.1410.0000.0000.0000.000
41A49LYS10.8220.92531.376-0.148-0.1480.0000.0000.0000.000
42A50ILE00.0210.00225.438-0.002-0.0020.0000.0000.0000.000
43A51ARG10.8100.90328.508-0.144-0.1440.0000.0000.0000.000
44A52ASP-1-0.833-0.89628.8130.1630.1630.0000.0000.0000.000
45A53LYS10.8280.90529.097-0.155-0.1550.0000.0000.0000.000
46A54VAL00.0040.01923.8410.0050.0050.0000.0000.0000.000
47A55LYS10.8860.95321.147-0.334-0.3340.0000.0000.0000.000
48A56LEU00.0200.01118.9080.0130.0130.0000.0000.0000.000
49A57ARG10.8790.93613.734-0.636-0.6360.0000.0000.0000.000
50A58MET00.0550.03914.7710.0270.0270.0000.0000.0000.000
51A59SER0-0.021-0.0529.5880.1240.1240.0000.0000.0000.000
52A60ARG10.9720.9927.544-1.384-1.3840.0000.0000.0000.000
53A61ASN00.0640.0327.8880.2810.2810.0000.0000.0000.000
54A62THR00.014-0.0033.360-0.1330.1170.016-0.040-0.2250.000
55A63LEU0-0.063-0.0243.243-0.6390.1840.314-0.231-0.906-0.001
56A64ILE00.0490.0285.079-0.0170.014-0.001-0.002-0.0270.000
57A65ILE00.003-0.0036.329-0.065-0.0650.0000.0000.0000.000
58A66ARG10.7810.8412.245-9.314-16.26617.496-5.323-5.2220.022
59A67ALA00.0150.0015.258-0.0130.005-0.001-0.001-0.0160.000
60A68LEU00.0360.0168.169-0.170-0.1700.0000.0000.0000.000
61A69LYS10.9480.9787.932-0.399-0.3990.0000.0000.0000.000
62A70GLU-1-0.727-0.8366.7862.4912.4910.0000.0000.0000.000
63A71ALA0-0.023-0.01710.228-0.119-0.1190.0000.0000.0000.000
64A72ALA00.0100.01013.010-0.083-0.0830.0000.0000.0000.000
65A73GLU-1-0.945-0.96311.8790.2930.2930.0000.0000.0000.000
66A74GLU-1-0.819-0.88612.1020.6930.6930.0000.0000.0000.000
67A75LEU0-0.042-0.01815.816-0.031-0.0310.0000.0000.0000.000
68A76ASN0-0.058-0.02318.302-0.043-0.0430.0000.0000.0000.000
69A77ASN00.0150.02418.459-0.029-0.0290.0000.0000.0000.000
70A78PRO00.0800.02116.6730.0310.0310.0000.0000.0000.000
71A79LYS10.8550.92416.691-0.165-0.1650.0000.0000.0000.000
72A80LEU00.0210.01715.0320.0100.0100.0000.0000.0000.000
73A81ALA00.005-0.00812.8390.0420.0420.0000.0000.0000.000
74A82GLU-1-0.858-0.91713.2600.2150.2150.0000.0000.0000.000
75A83LEU00.0330.01914.648-0.006-0.0060.0000.0000.0000.000
76A84ALA0-0.026-0.02610.0140.0170.0170.0000.0000.0000.000
77A85ASN0-0.070-0.03811.901-0.003-0.0030.0000.0000.0000.000
78A86TYR00.0200.02214.382-0.030-0.0300.0000.0000.0000.000
79A87VAL0-0.059-0.01310.2880.0190.0190.0000.0000.0000.000
80A88GLU-1-0.820-0.88312.8810.2660.2660.0000.0000.0000.000
81A89ARG10.8300.86915.513-0.236-0.2360.0000.0000.0000.000
82A90GLY0-0.0010.01615.3390.0500.0500.0000.0000.0000.000
83A91ALA0-0.033-0.01513.194-0.007-0.0070.0000.0000.0000.000
84A92ALA0-0.031-0.02214.0600.0800.0800.0000.0000.0000.000
85A93ILE00.0120.00811.122-0.025-0.0250.0000.0000.0000.000
86A94LEU00.004-0.00115.434-0.007-0.0070.0000.0000.0000.000
87A95VAL0-0.027-0.01318.1980.0040.0040.0000.0000.0000.000
88A96THR00.000-0.03320.965-0.019-0.0190.0000.0000.0000.000
89A97ASP-1-0.747-0.86924.7320.2130.2130.0000.0000.0000.000
90A98MET0-0.085-0.00727.683-0.018-0.0180.0000.0000.0000.000
91A99ASN00.0780.02027.7090.0160.0160.0000.0000.0000.000
92A100PRO00.024-0.00325.4290.0020.0020.0000.0000.0000.000
93A101PHE00.0450.04327.2700.0070.0070.0000.0000.0000.000
94A102LYS10.9670.98630.517-0.144-0.1440.0000.0000.0000.000
95A103LEU0-0.025-0.02123.6530.0020.0020.0000.0000.0000.000
96A104TYR00.030-0.00226.9510.0020.0020.0000.0000.0000.000
97A105LYS10.7990.88328.856-0.113-0.1130.0000.0000.0000.000
98A106LEU0-0.052-0.02028.661-0.002-0.0020.0000.0000.0000.000
99A107LEU0-0.060-0.03724.4160.0030.0030.0000.0000.0000.000
100A108GLU-1-0.815-0.89726.4650.1930.1930.0000.0000.0000.000
101A109GLU-1-0.890-0.94530.1680.1190.1190.0000.0000.0000.000
102A110ASN0-0.068-0.02932.796-0.011-0.0110.0000.0000.0000.000
103A111LYS10.8090.91228.369-0.170-0.1700.0000.0000.0000.000
104A112SER0-0.015-0.03531.561-0.008-0.0080.0000.0000.0000.000
105A113PRO0-0.025-0.00633.1670.0030.0030.0000.0000.0000.000
106A114ALA00.0130.00832.4830.0030.0030.0000.0000.0000.000
107A115PRO00.0090.01034.289-0.004-0.0040.0000.0000.0000.000
108A116VAL0-0.0170.00234.2840.0070.0070.0000.0000.0000.000
109A117ARG10.8380.88327.451-0.164-0.1640.0000.0000.0000.000
110A118GLY00.014-0.01134.451-0.003-0.0030.0000.0000.0000.000
111A119GLY0-0.023-0.00834.3590.0040.0040.0000.0000.0000.000
112A120GLN00.0000.01530.9770.0010.0010.0000.0000.0000.000
113A121ILE00.0120.00432.411-0.007-0.0070.0000.0000.0000.000
114A122ALA00.0320.02133.4890.0070.0070.0000.0000.0000.000
115A123PRO00.0180.01132.355-0.002-0.0020.0000.0000.0000.000
116A124CYS0-0.052-0.04334.3540.0010.0010.0000.0000.0000.000
117A125ASP-1-0.779-0.89237.9140.0750.0750.0000.0000.0000.000
118A126ILE0-0.021-0.00137.6680.0030.0030.0000.0000.0000.000
119A127LYS10.8940.94142.089-0.068-0.0680.0000.0000.0000.000
120A128VAL0-0.026-0.01145.1270.0020.0020.0000.0000.0000.000
121A129GLU-1-0.922-0.96747.9630.0680.0680.0000.0000.0000.000
122A130LYS10.8330.91850.857-0.047-0.0470.0000.0000.0000.000
123A131GLY00.0620.02354.5430.0000.0000.0000.0000.0000.000
124A132SER0-0.056-0.03155.0520.0000.0000.0000.0000.0000.000
125A133THR00.010-0.01751.5880.0010.0010.0000.0000.0000.000
126A134GLY00.0160.01752.1570.0020.0020.0000.0000.0000.000
127A135MET0-0.012-0.00550.490-0.001-0.0010.0000.0000.0000.000
128A136PRO00.0440.01254.537-0.002-0.0020.0000.0000.0000.000
129A137PRO0-0.011-0.00156.7580.0010.0010.0000.0000.0000.000
130A138GLY00.0650.02656.6170.0000.0000.0000.0000.0000.000
131A139PRO00.0330.00853.5230.0000.0000.0000.0000.0000.000
132A140PHE00.0750.03048.1000.0000.0000.0000.0000.0000.000
133A141LEU00.0030.01152.7670.0010.0010.0000.0000.0000.000
134A142GLY0-0.002-0.01054.986-0.001-0.0010.0000.0000.0000.000
135A143GLU-1-0.898-0.94548.6300.0580.0580.0000.0000.0000.000
136A144LEU00.0520.04249.5850.0010.0010.0000.0000.0000.000
137A145LYS10.9210.98050.941-0.042-0.0420.0000.0000.0000.000
138A146SER0-0.050-0.03250.3770.0000.0000.0000.0000.0000.000
139A147VAL0-0.030-0.01546.1130.0010.0010.0000.0000.0000.000
140A148GLY00.0520.03348.0720.0020.0020.0000.0000.0000.000
141A149ILE00.0130.00547.335-0.001-0.0010.0000.0000.0000.000
142A150PRO0-0.053-0.02251.717-0.001-0.0010.0000.0000.0000.000
143A151ALA00.0390.02354.6600.0010.0010.0000.0000.0000.000
144A152ALA0-0.061-0.05556.727-0.002-0.0020.0000.0000.0000.000
145A153ILE00.0090.01158.9750.0010.0010.0000.0000.0000.000
146A154GLU-1-0.848-0.91360.6850.0420.0420.0000.0000.0000.000
147A155LYS10.9130.93861.621-0.041-0.0410.0000.0000.0000.000
148A156GLY00.0410.02962.9340.0000.0000.0000.0000.0000.000
149A157LYS10.8480.92657.628-0.043-0.0430.0000.0000.0000.000
150A158ILE00.0020.00754.316-0.001-0.0010.0000.0000.0000.000
151A159ALA0-0.0050.01455.7650.0020.0020.0000.0000.0000.000
152A160ILE00.0500.02850.373-0.002-0.0020.0000.0000.0000.000
153A161LYS10.9100.94954.841-0.041-0.0410.0000.0000.0000.000
154A162GLU-1-0.783-0.90354.6700.0480.0480.0000.0000.0000.000
155A163ASP-1-0.798-0.88451.8620.0570.0570.0000.0000.0000.000
156A164LYS10.8320.92350.142-0.051-0.0510.0000.0000.0000.000
157A165VAL00.0340.02445.2280.0020.0020.0000.0000.0000.000
158A166VAL0-0.063-0.04744.077-0.003-0.0030.0000.0000.0000.000
159A167VAL0-0.023-0.00940.504-0.001-0.0010.0000.0000.0000.000
160A168LYS10.8650.91642.083-0.063-0.0630.0000.0000.0000.000
161A169LYS10.8840.93334.823-0.099-0.0990.0000.0000.0000.000
162A170GLY0-0.009-0.00335.939-0.003-0.0030.0000.0000.0000.000
163A171GLU-1-0.799-0.86837.0260.0670.0670.0000.0000.0000.000
164A172VAL0-0.009-0.00335.8990.0050.0050.0000.0000.0000.000
165A173VAL00.0100.01137.184-0.005-0.0050.0000.0000.0000.000
166A174SER00.0300.01738.2270.0030.0030.0000.0000.0000.000
167A175PRO00.0750.00337.9950.0010.0010.0000.0000.0000.000
168A176LYS10.8880.95939.855-0.055-0.0550.0000.0000.0000.000
169A177LEU00.0340.02042.3890.0000.0000.0000.0000.0000.000
170A178ALA00.0160.01138.0450.0000.0000.0000.0000.0000.000
171A179ALA00.0080.00640.0910.0010.0010.0000.0000.0000.000
172A180VAL0-0.041-0.02841.696-0.001-0.0010.0000.0000.0000.000
173A181LEU00.000-0.00241.191-0.001-0.0010.0000.0000.0000.000
174A182ASP-1-0.812-0.90438.9020.1000.1000.0000.0000.0000.000
175A183ARG10.8160.90741.345-0.062-0.0620.0000.0000.0000.000
176A184LEU0-0.064-0.03144.639-0.003-0.0030.0000.0000.0000.000
177A185GLY00.0180.01343.246-0.001-0.0010.0000.0000.0000.000
178A186ILE0-0.017-0.00341.9490.0040.0040.0000.0000.0000.000
179A187LYS10.8100.88437.566-0.096-0.0960.0000.0000.0000.000
180A188PRO00.0000.00837.7930.0020.0020.0000.0000.0000.000
181A189ILE0-0.0120.00331.8200.0010.0010.0000.0000.0000.000
182A190LYS10.9140.94932.747-0.124-0.1240.0000.0000.0000.000
183A191VAL0-0.0080.00128.2070.0050.0050.0000.0000.0000.000
184A192GLY00.037-0.01327.093-0.009-0.0090.0000.0000.0000.000
185A193LEU0-0.028-0.00121.6210.0110.0110.0000.0000.0000.000
186A194ASN00.0150.01623.322-0.021-0.0210.0000.0000.0000.000
187A195ILE00.0350.01821.9530.0260.0260.0000.0000.0000.000
188A196LEU0-0.062-0.02117.152-0.015-0.0150.0000.0000.0000.000
189A197ALA00.003-0.00818.529-0.016-0.0160.0000.0000.0000.000
190A198VAL0-0.015-0.00820.0810.0260.0260.0000.0000.0000.000
191A199TYR0-0.005-0.01019.290-0.012-0.0120.0000.0000.0000.000
192A200GLU-1-0.740-0.88121.2750.1800.1800.0000.0000.0000.000
193A201ASP-1-0.866-0.92424.1720.1590.1590.0000.0000.0000.000
194A202GLY00.0030.00522.976-0.012-0.0120.0000.0000.0000.000
195A203ILE0-0.044-0.02223.987-0.007-0.0070.0000.0000.0000.000
196A204ILE0-0.053-0.03618.7300.0210.0210.0000.0000.0000.000
197A205TYR0-0.026-0.02422.630-0.019-0.0190.0000.0000.0000.000
198A206THR00.0320.00322.9240.0150.0150.0000.0000.0000.000
199A207PRO00.031-0.00623.231-0.009-0.0090.0000.0000.0000.000
200A208ASP-1-0.844-0.92126.3080.1320.1320.0000.0000.0000.000
201A209VAL00.0260.03128.030-0.006-0.0060.0000.0000.0000.000
202A210LEU0-0.041-0.02225.424-0.005-0.0050.0000.0000.0000.000
203A211LYS10.7630.87329.760-0.142-0.1420.0000.0000.0000.000
204A212VAL0-0.047-0.01332.218-0.006-0.0060.0000.0000.0000.000
205A213ASP-1-0.872-0.94033.0900.1100.1100.0000.0000.0000.000
206A214GLU-1-0.903-0.91734.2430.0990.0990.0000.0000.0000.000
207A215GLU-1-0.897-0.96234.3580.1140.1140.0000.0000.0000.000
208A216LYS10.8120.92229.670-0.151-0.1510.0000.0000.0000.000
209A217LEU00.0430.01134.031-0.006-0.0060.0000.0000.0000.000
210A218LEU0-0.056-0.04036.2610.0020.0020.0000.0000.0000.000
211A219ALA00.0070.01536.562-0.001-0.0010.0000.0000.0000.000
212A220ASP-1-0.886-0.93033.3890.1440.1440.0000.0000.0000.000
213A221ILE0-0.028-0.00631.869-0.008-0.0080.0000.0000.0000.000