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: MN41Z

Calculation Name: 1JYK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JYK

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3141211.293044
FMO2-HF: Nuclear repulsion 3048414.026785
FMO2-HF: Total energy -92797.266259
FMO2-MP2: Total energy -93073.751379


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:3:GLU)


Summations of interaction energy for fragment #1(A:3: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.
43.95847.09725.747-14.291-14.5950.141
Interaction energy analysis for fragmet #1(A:3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.796 / q_NPA : -0.898
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].
3A5ARG10.8070.8882.471-72.957-67.1442.408-3.724-4.4970.039
4A6VAL00.0030.0214.0588.0468.3150.004-0.065-0.2080.000
5A7LYS10.7900.8991.833-127.353-135.68322.308-8.130-5.8490.092
6A8ALA00.0140.0016.365-4.464-4.4640.0000.0000.0000.000
7A9ILE00.0140.0267.470-0.024-0.0240.0000.0000.0000.000
8A10ILE0-0.010-0.01111.095-1.727-1.7270.0000.0000.0000.000
9A11LEU00.0150.00614.822-0.326-0.3260.0000.0000.0000.000
10A12ALA00.002-0.01917.314-1.195-1.1950.0000.0000.0000.000
11A13ALA0-0.045-0.00319.437-0.884-0.8840.0000.0000.0000.000
12A14GLY00.0350.03221.237-0.596-0.5960.0000.0000.0000.000
13A15LEU00.014-0.00724.042-0.121-0.1210.0000.0000.0000.000
14A16GLY00.0590.03027.173-0.192-0.1920.0000.0000.0000.000
15A17THR00.012-0.00128.293-0.156-0.1560.0000.0000.0000.000
16A18ARG10.7720.86626.790-11.898-11.8980.0000.0000.0000.000
17A19LEU0-0.0110.00828.467-0.273-0.2730.0000.0000.0000.000
18A20ARG10.8020.89232.928-8.651-8.6510.0000.0000.0000.000
19A21PRO0-0.041-0.04935.965-0.172-0.1720.0000.0000.0000.000
20A22LEU00.0210.00932.6840.0090.0090.0000.0000.0000.000
21A23THR00.0240.00929.2710.0060.0060.0000.0000.0000.000
22A24GLU-1-0.860-0.86731.9368.5098.5090.0000.0000.0000.000
23A25ASN0-0.049-0.04033.659-0.243-0.2430.0000.0000.0000.000
24A26THR00.0110.01628.620-0.038-0.0380.0000.0000.0000.000
25A27PRO00.0390.04224.852-0.148-0.1480.0000.0000.0000.000
26A28LYS10.8420.87722.139-14.263-14.2630.0000.0000.0000.000
27A29ALA0-0.0100.01321.634-0.108-0.1080.0000.0000.0000.000
28A30LEU0-0.032-0.02123.0260.1810.1810.0000.0000.0000.000
29A31VAL00.0060.01325.959-0.486-0.4860.0000.0000.0000.000
30A32GLN0-0.039-0.02027.8600.3270.3270.0000.0000.0000.000
31A33VAL00.015-0.00128.339-0.305-0.3050.0000.0000.0000.000
32A34ASN0-0.023-0.02030.3610.1460.1460.0000.0000.0000.000
33A35GLN0-0.057-0.02032.3350.0420.0420.0000.0000.0000.000
34A36LYS10.8630.91824.297-12.796-12.7960.0000.0000.0000.000
35A37PRO0-0.034-0.00924.915-0.029-0.0290.0000.0000.0000.000
36A38LEU00.0390.01824.5030.3590.3590.0000.0000.0000.000
37A39ILE00.0370.01417.6740.3210.3210.0000.0000.0000.000
38A40GLU-1-0.759-0.84719.84913.66813.6680.0000.0000.0000.000
39A41TYR00.006-0.01020.9680.3490.3490.0000.0000.0000.000
40A42GLN0-0.037-0.02317.8751.1051.1050.0000.0000.0000.000
41A43ILE00.011-0.00116.0761.0151.0150.0000.0000.0000.000
42A44GLU-1-0.797-0.85716.66214.46614.4660.0000.0000.0000.000
43A45PHE00.0190.00918.6310.2970.2970.0000.0000.0000.000
44A46LEU00.0260.01912.3540.5430.5430.0000.0000.0000.000
45A47LYS10.8620.92114.333-18.958-18.9580.0000.0000.0000.000
46A48GLU-1-0.907-0.94415.59014.68514.6850.0000.0000.0000.000
47A49LYS10.7630.88815.139-17.402-17.4020.0000.0000.0000.000
48A50GLY00.0040.00413.5141.0311.0310.0000.0000.0000.000
49A51ILE0-0.0220.0069.1192.1162.1160.0000.0000.0000.000
50A52ASN0-0.056-0.06110.735-2.267-2.2670.0000.0000.0000.000
51A53ASP-1-0.821-0.8675.93345.56745.5670.0000.0000.0000.000
52A54ILE00.0220.0127.9962.3782.3780.0000.0000.0000.000
53A55ILE0-0.0030.0046.540-1.946-1.9460.0000.0000.0000.000
54A56ILE0-0.001-0.00111.034-0.758-0.7580.0000.0000.0000.000
55A57ILE00.0180.01712.203-0.612-0.6120.0000.0000.0000.000
56A58VAL0-0.007-0.02016.072-1.164-1.1640.0000.0000.0000.000
57A59GLY00.058-0.00219.7280.2850.2850.0000.0000.0000.000
58A60TYR0-0.058-0.03622.762-0.532-0.5320.0000.0000.0000.000
59A61LEU0-0.023-0.01325.0820.3350.3350.0000.0000.0000.000
60A62LYS10.8930.94122.427-12.292-12.2920.0000.0000.0000.000
61A63GLU-1-0.802-0.88623.23612.32012.3200.0000.0000.0000.000
62A64GLN0-0.050-0.04325.748-0.012-0.0120.0000.0000.0000.000
63A65PHE00.0410.00520.3640.0980.0980.0000.0000.0000.000
64A66ASP-1-0.842-0.91021.36414.92714.9270.0000.0000.0000.000
65A67TYR0-0.042-0.04521.6820.4300.4300.0000.0000.0000.000
66A68LEU0-0.0040.00118.8130.1430.1430.0000.0000.0000.000
67A69LYS10.8560.92117.423-14.698-14.6980.0000.0000.0000.000
68A70GLU-1-0.967-0.97918.18113.98513.9850.0000.0000.0000.000
69A71LYS10.7770.89720.950-13.114-13.1140.0000.0000.0000.000
70A72TYR0-0.046-0.06617.132-0.186-0.1860.0000.0000.0000.000
71A73GLY0-0.0010.01215.4190.8920.8920.0000.0000.0000.000
72A74VAL0-0.051-0.00913.0021.4581.4580.0000.0000.0000.000
73A75ARG10.7570.8215.790-44.599-44.5990.0000.0000.0000.000
74A76LEU0-0.017-0.00112.983-0.101-0.1010.0000.0000.0000.000
75A77VAL00.0100.00112.2680.1090.1090.0000.0000.0000.000
76A78PHE0-0.047-0.01715.636-0.649-0.6490.0000.0000.0000.000
77A79ASN00.0510.01218.177-0.098-0.0980.0000.0000.0000.000
78A80ASP-1-0.879-0.96219.59513.54313.5430.0000.0000.0000.000
79A81LYS10.7970.90322.266-12.908-12.9080.0000.0000.0000.000
80A82TYR0-0.040-0.01722.504-0.305-0.3050.0000.0000.0000.000
81A83ALA0-0.036-0.02123.563-0.156-0.1560.0000.0000.0000.000
82A84ASP-1-0.874-0.91326.21211.08811.0880.0000.0000.0000.000
83A85TYR0-0.016-0.02422.071-0.395-0.3950.0000.0000.0000.000
84A86ASN00.0000.01423.4400.4690.4690.0000.0000.0000.000
85A87ASN0-0.028-0.03219.1830.6190.6190.0000.0000.0000.000
86A88PHE00.0590.03817.4141.2721.2720.0000.0000.0000.000
87A89TYR00.000-0.00416.5391.1671.1670.0000.0000.0000.000
88A90SER0-0.024-0.02416.4810.4550.4550.0000.0000.0000.000
89A91LEU00.0330.02910.2641.2011.2010.0000.0000.0000.000
90A92TYR00.005-0.00311.9562.0652.0650.0000.0000.0000.000
91A93LEU0-0.027-0.01612.8321.0941.0940.0000.0000.0000.000
92A94VAL0-0.034-0.0128.9770.4070.4070.0000.0000.0000.000
93A95LYS10.7890.8967.970-19.119-19.1190.0000.0000.0000.000
94A96GLU-1-0.830-0.9096.70431.85931.8590.0000.0000.0000.000
95A97GLU-1-0.829-0.8813.40262.32763.2790.027-0.367-0.6120.003
96A98LEU0-0.024-0.0074.4385.0355.169-0.001-0.014-0.1190.000
97A99ALA00.012-0.0012.717-7.270-5.7450.818-0.923-1.4200.009
98A100ASN0-0.040-0.0463.2146.7858.9240.107-0.918-1.328-0.001
99A101SER00.0190.0155.2971.7571.902-0.001-0.005-0.1390.000
100A102TYR0-0.018-0.0387.134-5.110-5.1100.0000.0000.0000.000
101A103VAL0-0.0120.00410.1972.3762.3760.0000.0000.0000.000
102A104ILE0-0.0140.00012.705-1.571-1.5710.0000.0000.0000.000
103A105ASP-1-0.807-0.90416.08316.05416.0540.0000.0000.0000.000
104A106ALA0-0.022-0.01319.305-0.456-0.4560.0000.0000.0000.000
105A107ASP-1-0.793-0.88320.68112.85712.8570.0000.0000.0000.000
106A108ASN00.0070.01521.746-1.059-1.0590.0000.0000.0000.000
107A109TYR00.0180.00823.2030.4610.4610.0000.0000.0000.000
108A110LEU0-0.010-0.01119.8560.1050.1050.0000.0000.0000.000
109A111PHE00.0120.00924.416-0.132-0.1320.0000.0000.0000.000
110A112LYS10.7950.87724.996-12.275-12.2750.0000.0000.0000.000
111A113ASN0-0.045-0.01518.8361.0411.0410.0000.0000.0000.000
112A114MET0-0.012-0.00919.2600.2060.2060.0000.0000.0000.000
113A115PHE00.0080.02614.6820.4110.4110.0000.0000.0000.000
114A116ARG10.8290.86814.724-18.478-18.4780.0000.0000.0000.000
115A117ASN00.0260.01311.4750.3520.3520.0000.0000.0000.000
116A118ASP-1-0.800-0.86711.43220.57320.5730.0000.0000.0000.000
117A119LEU0-0.0090.00611.937-1.060-1.0600.0000.0000.0000.000
118A120THR0-0.025-0.01810.4451.8631.8630.0000.0000.0000.000
119A121ARG10.8850.95811.184-16.270-16.2700.0000.0000.0000.000
120A122SER00.027-0.00511.0920.9760.9760.0000.0000.0000.000
121A123THR0-0.070-0.03612.738-2.010-2.0100.0000.0000.0000.000
122A124TYR00.018-0.00415.7950.9310.9310.0000.0000.0000.000
123A125PHE00.005-0.01115.014-0.828-0.8280.0000.0000.0000.000
124A126SER0-0.015-0.01920.079-0.279-0.2790.0000.0000.0000.000
125A127VAL0-0.008-0.00323.624-0.345-0.3450.0000.0000.0000.000
126A128TYR0-0.084-0.05927.0520.1500.1500.0000.0000.0000.000
127A129ARG10.7450.82629.143-11.068-11.0680.0000.0000.0000.000
128A130GLU-1-0.816-0.90332.1828.5588.5580.0000.0000.0000.000
129A131ASP-1-0.949-0.97235.3288.2198.2190.0000.0000.0000.000
130A132CYS0-0.086-0.01632.3200.1330.1330.0000.0000.0000.000
131A133THR0-0.038-0.03832.992-0.399-0.3990.0000.0000.0000.000
132A134ASN0-0.062-0.03730.7950.0260.0260.0000.0000.0000.000
133A135GLU-1-0.855-0.91627.81111.71011.7100.0000.0000.0000.000
134A136TRP0-0.032-0.01222.2770.0120.0120.0000.0000.0000.000
135A137PHE0-0.009-0.01426.1150.3030.3030.0000.0000.0000.000
136A138LEU0-0.012-0.00721.8160.2190.2190.0000.0000.0000.000
137A139VAL0-0.021-0.00425.564-0.466-0.4660.0000.0000.0000.000
138A140TYR0-0.035-0.04424.3810.4590.4590.0000.0000.0000.000
139A141GLY00.0340.01725.949-0.485-0.4850.0000.0000.0000.000
140A142ASP-1-0.909-0.96026.64310.20710.2070.0000.0000.0000.000
141A143ASP-1-0.881-0.94523.21312.39612.3960.0000.0000.0000.000
142A144TYR0-0.096-0.04422.3290.5960.5960.0000.0000.0000.000
143A145LYS10.8640.93618.311-14.010-14.0100.0000.0000.0000.000
144A146VAL0-0.042-0.03920.156-0.645-0.6450.0000.0000.0000.000
145A147GLN0-0.030-0.00421.4920.2710.2710.0000.0000.0000.000
146A148ASP-1-0.834-0.93424.22711.55411.5540.0000.0000.0000.000
147A149ILE0-0.030-0.00520.6670.2190.2190.0000.0000.0000.000
148A150ILE0-0.0100.00025.314-0.200-0.2000.0000.0000.0000.000
149A151VAL00.033-0.00528.1980.2520.2520.0000.0000.0000.000
150A152ASP-1-0.982-0.96930.4648.5898.5890.0000.0000.0000.000
151A153SER00.024-0.00533.026-0.228-0.2280.0000.0000.0000.000
152A154LYS10.9350.96334.566-8.269-8.2690.0000.0000.0000.000
153A155ALA0-0.0030.00734.263-0.045-0.0450.0000.0000.0000.000
154A156GLY00.0280.01931.380-0.006-0.0060.0000.0000.0000.000
155A157ARG10.7620.86226.337-11.521-11.5210.0000.0000.0000.000
156A158ILE00.0520.03826.0530.0490.0490.0000.0000.0000.000
157A159LEU00.0150.01320.6130.4140.4140.0000.0000.0000.000
158A160SER0-0.0110.01222.540-0.143-0.1430.0000.0000.0000.000
159A161GLY00.0300.01220.0650.0400.0400.0000.0000.0000.000
160A162VAL0-0.018-0.01616.6740.7960.7960.0000.0000.0000.000
161A163SER0-0.0080.00514.681-0.390-0.3900.0000.0000.0000.000
162A164PHE00.000-0.0068.0891.4131.4130.0000.0000.0000.000
163A165TRP00.0340.0209.006-2.827-2.8270.0000.0000.0000.000
164A166ASP-1-0.749-0.8287.21629.20129.2010.0000.0000.0000.000
165A167ALA00.002-0.0142.921-0.3820.0260.078-0.141-0.345-0.001
166A168PRO00.007-0.0014.921-0.639-0.555-0.001-0.004-0.0780.000
167A169THR00.002-0.0167.938-2.023-2.0230.0000.0000.0000.000
168A170ALA00.000-0.0046.919-1.170-1.1700.0000.0000.0000.000
169A171GLU-1-0.955-0.9707.58124.45224.4520.0000.0000.0000.000
170A172LYS10.8240.9199.195-19.669-19.6690.0000.0000.0000.000
171A173ILE00.0380.03111.915-0.939-0.9390.0000.0000.0000.000
172A174VAL0-0.0030.0018.561-1.380-1.3800.0000.0000.0000.000
173A175SER0-0.038-0.02511.977-1.910-1.9100.0000.0000.0000.000
174A176PHE0-0.046-0.02814.890-1.406-1.4060.0000.0000.0000.000
175A177ILE00.0170.00012.573-1.088-1.0880.0000.0000.0000.000
176A178ASP-1-0.844-0.92313.97420.40620.4060.0000.0000.0000.000
177A179LYS10.9320.96716.851-15.137-15.1370.0000.0000.0000.000
178A180ALA00.0720.04219.618-0.767-0.7670.0000.0000.0000.000
179A181TYR0-0.043-0.02018.691-0.564-0.5640.0000.0000.0000.000
180A182VAL0-0.042-0.03120.226-0.678-0.6780.0000.0000.0000.000
181A183SER0-0.061-0.03522.745-0.735-0.7350.0000.0000.0000.000
182A184GLY0-0.070-0.02324.755-0.498-0.4980.0000.0000.0000.000
183A185GLU-1-0.950-0.97424.18812.09012.0900.0000.0000.0000.000
184A186PHE00.026-0.00421.2910.1750.1750.0000.0000.0000.000
185A187VAL0-0.027-0.00122.9940.3340.3340.0000.0000.0000.000
186A188ASP-1-0.859-0.93724.88911.27111.2710.0000.0000.0000.000
187A189LEU0-0.067-0.00821.988-0.020-0.0200.0000.0000.0000.000
188A190TYR00.0300.01021.1090.2310.2310.0000.0000.0000.000
189A191TRP00.033-0.00914.0920.6550.6550.0000.0000.0000.000
190A192ASP-1-0.791-0.89717.34317.13017.1300.0000.0000.0000.000
191A193ASN0-0.020-0.02518.962-0.343-0.3430.0000.0000.0000.000
192A194MET0-0.035-0.00216.598-0.271-0.2710.0000.0000.0000.000
193A195VAL00.0190.01015.6880.9000.9000.0000.0000.0000.000
194A196LYS10.8900.92118.312-12.555-12.5550.0000.0000.0000.000
195A197ASP-1-0.854-0.90722.16912.20512.2050.0000.0000.0000.000
196A198ASN0-0.043-0.03819.0260.2480.2480.0000.0000.0000.000
197A199ILE00.0000.02219.1090.3120.3120.0000.0000.0000.000
198A200LYS10.8400.92020.123-11.856-11.8560.0000.0000.0000.000
199A201GLU-1-0.927-0.94918.21113.43013.4300.0000.0000.0000.000
200A202LEU0-0.071-0.02214.2521.1101.1100.0000.0000.0000.000
201A203ASP-1-0.890-0.95214.08215.65115.6510.0000.0000.0000.000
202A204VAL00.0150.01514.7330.9350.9350.0000.0000.0000.000
203A205TYR0-0.028-0.01115.501-1.368-1.3680.0000.0000.0000.000
204A206VAL0-0.0140.00318.6190.6420.6420.0000.0000.0000.000
205A207GLU-1-0.887-0.94619.55015.24715.2470.0000.0000.0000.000
206A208GLU-1-0.804-0.89021.63511.10411.1040.0000.0000.0000.000
207A209LEU0-0.0050.01022.096-0.191-0.1910.0000.0000.0000.000
208A210GLU-1-0.775-0.86525.96311.06411.0640.0000.0000.0000.000
209A211GLY00.0250.01228.6300.2990.2990.0000.0000.0000.000
210A212ASN00.0290.01330.5420.1320.1320.0000.0000.0000.000
211A213SER0-0.035-0.02925.1690.0700.0700.0000.0000.0000.000
212A214ILE0-0.026-0.00922.3000.4830.4830.0000.0000.0000.000
213A215TYR0-0.048-0.04025.889-0.653-0.6530.0000.0000.0000.000
214A216GLU-1-0.702-0.81026.35611.82311.8230.0000.0000.0000.000
215A217ILE0-0.052-0.03327.897-0.583-0.5830.0000.0000.0000.000
216A218ASP-1-0.747-0.86228.95911.59111.5910.0000.0000.0000.000
217A219SER0-0.045-0.04931.079-0.334-0.3340.0000.0000.0000.000
218A220VAL0-0.002-0.00434.1010.0810.0810.0000.0000.0000.000
219A221GLN00.000-0.01936.0410.0620.0620.0000.0000.0000.000
220A222ASP-1-0.776-0.84233.0809.3229.3220.0000.0000.0000.000
221A223TYR00.013-0.00332.384-0.029-0.0290.0000.0000.0000.000
222A224ARG10.9230.95533.878-8.200-8.2000.0000.0000.0000.000
223A225LYS10.8520.91636.123-8.986-8.9860.0000.0000.0000.000
224A226LEU00.0120.02729.617-0.091-0.0910.0000.0000.0000.000
225A227GLU-1-0.775-0.87334.0519.5429.5420.0000.0000.0000.000
226A228GLU-1-0.887-0.92835.8877.6697.6690.0000.0000.0000.000
227A229ILE0-0.052-0.02734.224-0.140-0.1400.0000.0000.0000.000
228A230LEU0-0.049-0.01730.680-0.020-0.0200.0000.0000.0000.000
229A231LYS10.7770.89834.833-7.845-7.8450.0000.0000.0000.000