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: J3Z19

Calculation Name: 5GKJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GKJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5JER9

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 OptHSide
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 -2134356.90487
FMO2-HF: Nuclear repulsion 2050244.258246
FMO2-HF: Total energy -84112.646624
FMO2-MP2: Total energy -84361.467379


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:5:LYS)


Summations of interaction energy for fragment #1(A:5: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.
-52.16-45.3973.041-3.351-6.452-0.015
Interaction energy analysis for fragmet #1(A:5:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.976 / q_NPA : 0.978
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].
3A7THR0-0.0040.0123.8060.4052.632-0.029-1.100-1.098-0.001
4A8VAL0-0.001-0.0076.2840.3570.3570.0000.0000.0000.000
5A9ILE00.0420.0219.7070.5180.5180.0000.0000.0000.000
6A10THR0-0.022-0.01813.144-0.089-0.0890.0000.0000.0000.000
7A11SER0-0.021-0.01916.4020.3420.3420.0000.0000.0000.000
8A12PRO0-0.0370.00716.5390.2360.2360.0000.0000.0000.000
9A13SER00.0430.02218.7580.6040.6040.0000.0000.0000.000
10A14THR00.035-0.01719.831-0.449-0.4490.0000.0000.0000.000
11A15GLU-1-0.936-0.95819.106-13.187-13.1870.0000.0000.0000.000
12A16GLU-1-0.821-0.91715.752-14.711-14.7110.0000.0000.0000.000
13A17LEU0-0.033-0.01015.617-0.871-0.8710.0000.0000.0000.000
14A18VAL00.024-0.00716.426-0.757-0.7570.0000.0000.0000.000
15A19SER0-0.0140.02015.126-0.725-0.7250.0000.0000.0000.000
16A20LEU00.0350.0039.990-0.922-0.9220.0000.0000.0000.000
17A21VAL0-0.028-0.01812.175-1.166-1.1660.0000.0000.0000.000
18A22ASN0-0.041-0.03314.371-0.298-0.2980.0000.0000.0000.000
19A23SER0-0.024-0.0079.4770.2260.2260.0000.0000.0000.000
20A24ALA0-0.038-0.0239.909-1.309-1.3090.0000.0000.0000.000
21A25LEU0-0.062-0.03610.952-0.481-0.4810.0000.0000.0000.000
22A26LEU0-0.049-0.01113.0290.2500.2500.0000.0000.0000.000
23A27GLU-1-0.866-0.9237.026-27.819-27.8190.0000.0000.0000.000
24A28GLU-1-0.962-0.9669.459-23.303-23.3030.0000.0000.0000.000
25A29ALA0-0.036-0.0166.634-3.267-3.2670.0000.0000.0000.000
26A30MET0-0.059-0.0427.1932.5032.5030.0000.0000.0000.000
27A31LEU00.0080.0178.525-1.180-1.1800.0000.0000.0000.000
28A32THR0-0.031-0.01910.6491.3481.3480.0000.0000.0000.000
29A33ILE00.0000.01412.436-0.248-0.2480.0000.0000.0000.000
30A34PHE0-0.020-0.00714.1910.4850.4850.0000.0000.0000.000
31A35ALA00.0610.01717.9600.1500.1500.0000.0000.0000.000
32A36ARG10.8850.95521.40410.77010.7700.0000.0000.0000.000
33A37CYS0-0.039-0.00723.9050.0450.0450.0000.0000.0000.000
34A38LYS10.9180.96026.1119.4649.4640.0000.0000.0000.000
35A39VAL0-0.047-0.02925.753-0.269-0.2690.0000.0000.0000.000
36A40HIS10.8780.92928.4069.9879.9870.0000.0000.0000.000
37A41TYR0-0.041-0.03627.715-0.490-0.4900.0000.0000.0000.000
38A42ASP-1-0.891-0.94630.506-9.042-9.0420.0000.0000.0000.000
39A43GLY00.0890.02332.301-0.282-0.2820.0000.0000.0000.000
40A44ARG10.8820.94234.8387.9977.9970.0000.0000.0000.000
41A45ALA0-0.034-0.00833.5580.2430.2430.0000.0000.0000.000
42A46LYS10.9170.95134.5017.8117.8110.0000.0000.0000.000
43A47SER0-0.0130.00030.9730.1320.1320.0000.0000.0000.000
44A48GLU-1-0.760-0.86232.499-9.337-9.3370.0000.0000.0000.000
45A49LEU0-0.028-0.01228.9220.1000.1000.0000.0000.0000.000
46A50GLY00.013-0.00131.203-0.078-0.0780.0000.0000.0000.000
47A51SER0-0.026-0.03529.982-0.375-0.3750.0000.0000.0000.000
48A52GLY00.0250.00828.6230.2320.2320.0000.0000.0000.000
49A53ASP-1-0.834-0.87424.046-11.631-11.6310.0000.0000.0000.000
50A54ARG10.7550.86222.53811.29411.2940.0000.0000.0000.000
51A55VAL00.0090.01516.176-0.311-0.3110.0000.0000.0000.000
52A56ILE0-0.015-0.01117.4880.3580.3580.0000.0000.0000.000
53A57ILE00.003-0.00212.402-0.836-0.8360.0000.0000.0000.000
54A58VAL00.007-0.00313.7781.1761.1760.0000.0000.0000.000
55A59LYS10.8280.89911.89618.70218.7020.0000.0000.0000.000
56A60PRO00.1040.0529.7261.6541.6540.0000.0000.0000.000
57A61ASP-1-0.752-0.82112.922-18.385-18.3850.0000.0000.0000.000
58A62GLY00.005-0.01415.5031.3341.3340.0000.0000.0000.000
59A63SER0-0.100-0.07116.0700.9420.9420.0000.0000.0000.000
60A64PHE0-0.005-0.00716.853-0.774-0.7740.0000.0000.0000.000
61A65LEU00.004-0.00215.5650.7520.7520.0000.0000.0000.000
62A66ILE00.0370.03218.693-0.381-0.3810.0000.0000.0000.000
63A67HIS00.0570.02817.9751.1191.1190.0000.0000.0000.000
64A68GLN00.0370.02021.5570.2920.2920.0000.0000.0000.000
65A69SER00.0450.01323.140-0.251-0.2510.0000.0000.0000.000
66A70LYS10.9190.95324.91510.78310.7830.0000.0000.0000.000
67A71LYS10.9430.97025.82710.23510.2350.0000.0000.0000.000
68A72ARG10.9480.97423.73712.22412.2240.0000.0000.0000.000
69A73GLU-1-0.862-0.92222.790-12.206-12.2060.0000.0000.0000.000
70A74PRO00.0060.00320.7710.0910.0910.0000.0000.0000.000
71A75VAL0-0.087-0.03623.2180.5070.5070.0000.0000.0000.000
72A76ASN0-0.008-0.01224.5740.6250.6250.0000.0000.0000.000
73A77TRP0-0.027-0.00921.685-0.451-0.4510.0000.0000.0000.000
74A78GLN0-0.006-0.01221.7860.7240.7240.0000.0000.0000.000
75A79PRO0-0.036-0.00921.147-0.651-0.6510.0000.0000.0000.000
76A80PRO00.0800.03718.794-0.018-0.0180.0000.0000.0000.000
77A81GLY0-0.0090.01819.8280.7130.7130.0000.0000.0000.000
78A82SER0-0.089-0.04920.8901.0761.0760.0000.0000.0000.000
79A83ARG10.9490.96221.09511.13811.1380.0000.0000.0000.000
80A84VAL0-0.0010.01618.6370.5960.5960.0000.0000.0000.000
81A85ARG10.8350.90219.74910.80610.8060.0000.0000.0000.000
82A86LEU00.0220.02019.0130.2680.2680.0000.0000.0000.000
83A87GLU-1-0.800-0.86121.705-10.295-10.2950.0000.0000.0000.000
84A88LEU00.013-0.00125.067-0.074-0.0740.0000.0000.0000.000
85A89ARG10.7700.84726.61710.21110.2110.0000.0000.0000.000
86A90GLU-1-0.893-0.94529.831-9.129-9.1290.0000.0000.0000.000
87A91ASN0-0.044-0.01127.551-0.101-0.1010.0000.0000.0000.000
88A92PRO0-0.021-0.01023.2180.0110.0110.0000.0000.0000.000
89A93VAL00.0470.01724.903-0.217-0.2170.0000.0000.0000.000
90A94LEU0-0.009-0.00118.221-0.201-0.2010.0000.0000.0000.000
91A95VAL00.0170.00822.6060.2910.2910.0000.0000.0000.000
92A96SER00.0130.01221.935-0.257-0.2570.0000.0000.0000.000
93A97ILE0-0.063-0.04823.7030.6240.6240.0000.0000.0000.000
94A98ARG10.9971.02525.23810.28310.2830.0000.0000.0000.000
95A99ARG10.9180.93726.91510.80110.8010.0000.0000.0000.000
96A100LYS10.9180.98629.0068.9598.9590.0000.0000.0000.000
97A101PRO00.0890.03130.626-0.125-0.1250.0000.0000.0000.000
98A102ARG10.9180.93430.6219.3989.3980.0000.0000.0000.000
99A103GLU-1-0.813-0.88130.233-9.208-9.2080.0000.0000.0000.000
100A104THR0-0.016-0.01128.256-0.539-0.5390.0000.0000.0000.000
101A105LEU0-0.0150.00523.6920.2410.2410.0000.0000.0000.000
102A106GLU-1-0.843-0.90025.342-10.496-10.4960.0000.0000.0000.000
103A107VAL0-0.004-0.01222.0550.2170.2170.0000.0000.0000.000
104A108GLU-1-0.833-0.91124.877-9.984-9.9840.0000.0000.0000.000
105A109LEU0-0.047-0.04020.536-0.129-0.1290.0000.0000.0000.000
106A110GLU-1-0.837-0.89524.660-9.879-9.8790.0000.0000.0000.000
107A111GLU-1-0.873-0.94424.932-11.273-11.2730.0000.0000.0000.000
108A112VAL0-0.032-0.01918.550-0.452-0.4520.0000.0000.0000.000
109A113TYR0-0.043-0.04819.3140.0270.0270.0000.0000.0000.000
110A114MET0-0.013-0.00512.065-0.157-0.1570.0000.0000.0000.000
111A115VAL0-0.0010.00512.6330.1180.1180.0000.0000.0000.000
112A116SER0-0.044-0.0448.977-1.096-1.0960.0000.0000.0000.000
113A117VAL00.0510.0316.0210.2740.2740.0000.0000.0000.000
114A118PHE0-0.002-0.0062.769-7.513-6.1750.252-0.524-1.066-0.004
115A119ARG10.8170.8912.21736.90439.6562.807-1.652-3.906-0.009
116A120ALA0-0.025-0.0373.736-0.990-0.5940.012-0.071-0.336-0.001
117A121GLU-1-0.873-0.8944.832-32.552-32.502-0.001-0.004-0.0460.000
118A122ASP-1-0.917-0.9197.529-32.466-32.4660.0000.0000.0000.000
119A123TYR0-0.135-0.1118.6654.1114.1110.0000.0000.0000.000
120A134GLU-1-0.787-0.86828.214-11.214-11.2140.0000.0000.0000.000
121A135MET0-0.004-0.01126.979-0.107-0.1070.0000.0000.0000.000
122A136ALA00.0250.00630.3790.0400.0400.0000.0000.0000.000
123A137GLU-1-0.865-0.93033.190-8.739-8.7390.0000.0000.0000.000
124A138LEU0-0.020-0.00927.3370.0360.0360.0000.0000.0000.000
125A139ILE0-0.062-0.02831.596-0.001-0.0010.0000.0000.0000.000
126A140PHE0-0.052-0.03533.9940.2040.2040.0000.0000.0000.000
127A141GLU-1-0.859-0.91433.523-9.311-9.3110.0000.0000.0000.000
128A142ASN0-0.056-0.02932.4720.1590.1590.0000.0000.0000.000
129A143PRO00.0030.00533.827-0.217-0.2170.0000.0000.0000.000
130A144GLU-1-0.847-0.93234.803-8.340-8.3400.0000.0000.0000.000
131A145VAL0-0.053-0.02029.855-0.215-0.2150.0000.0000.0000.000
132A146ILE0-0.085-0.02631.812-0.228-0.2280.0000.0000.0000.000
133A147GLU-1-0.801-0.90834.106-8.485-8.4850.0000.0000.0000.000
134A148PRO0-0.0060.00936.1050.0180.0180.0000.0000.0000.000
135A149GLY00.000-0.00338.2060.1960.1960.0000.0000.0000.000
136A150PHE00.0080.00137.7110.1840.1840.0000.0000.0000.000
137A151LYS10.9020.93640.5417.6007.6000.0000.0000.0000.000
138A152PRO00.0230.02938.7500.1130.1130.0000.0000.0000.000
139A153LEU0-0.051-0.02541.3340.1880.1880.0000.0000.0000.000
140A154PHE00.0430.02941.440-0.067-0.0670.0000.0000.0000.000
141A165ALA0-0.039-0.02937.9840.0490.0490.0000.0000.0000.000
142A166VAL0-0.022-0.01036.9320.0020.0020.0000.0000.0000.000
143A167LEU00.0080.01439.5190.0060.0060.0000.0000.0000.000
144A168GLY00.0270.00641.918-0.059-0.0590.0000.0000.0000.000
145A169ARG10.9040.94442.9136.7236.7230.0000.0000.0000.000
146A170ASP-1-0.772-0.87242.774-7.365-7.3650.0000.0000.0000.000
147A171SER00.0330.02044.0210.1840.1840.0000.0000.0000.000
148A172ASP-1-0.864-0.88845.919-6.381-6.3810.0000.0000.0000.000
149A173GLY0-0.056-0.03047.8800.1470.1470.0000.0000.0000.000
150A174ASN0-0.079-0.06146.3630.2690.2690.0000.0000.0000.000
151A175ILE00.0090.00145.798-0.152-0.1520.0000.0000.0000.000
152A176VAL00.0220.00540.060-0.043-0.0430.0000.0000.0000.000
153A177VAL0-0.013-0.02440.707-0.061-0.0610.0000.0000.0000.000
154A178LEU00.0250.00935.687-0.214-0.2140.0000.0000.0000.000
155A179GLU-1-0.808-0.90135.730-8.774-8.7740.0000.0000.0000.000
156A180LEU00.0100.01231.619-0.293-0.2930.0000.0000.0000.000
157A181LYS10.7900.87329.2139.6679.6670.0000.0000.0000.000
158A182ARG10.8730.90124.48311.81711.8170.0000.0000.0000.000
159A183ARG10.8710.90419.88114.68614.6860.0000.0000.0000.000
160A184ARG10.9220.95521.05214.47014.4700.0000.0000.0000.000
161A185ALA00.0270.00824.8230.2500.2500.0000.0000.0000.000
162A186GLU-1-0.906-0.96328.321-10.996-10.9960.0000.0000.0000.000
163A187LEU0-0.018-0.02230.4680.1730.1730.0000.0000.0000.000
164A188HIS00.0150.00034.2150.2070.2070.0000.0000.0000.000
165A189ALA00.0650.01634.0890.2490.2490.0000.0000.0000.000
166A190VAL00.0000.02234.3590.0810.0810.0000.0000.0000.000
167A191ARG10.9560.98337.0318.3418.3410.0000.0000.0000.000
168A192GLN0-0.010-0.00337.199-0.034-0.0340.0000.0000.0000.000
169A193LEU0-0.0130.01936.9140.1800.1800.0000.0000.0000.000
170A194LYS10.8280.91440.1647.1507.1500.0000.0000.0000.000
171A195SER00.010-0.02142.7540.1240.1240.0000.0000.0000.000
172A196TYR0-0.061-0.02539.9060.1730.1730.0000.0000.0000.000
173A197VAL00.0170.00343.2970.1260.1260.0000.0000.0000.000
174A198GLU-1-0.808-0.88845.254-6.652-6.6520.0000.0000.0000.000
175A199ILE00.0460.02047.4290.1120.1120.0000.0000.0000.000
176A200LEU0-0.035-0.00746.3150.0890.0890.0000.0000.0000.000
177A201ARG10.7720.90146.8786.7786.7780.0000.0000.0000.000
178A202GLU-1-0.969-0.97950.818-5.832-5.8320.0000.0000.0000.000
179A203GLU-1-0.969-0.98351.736-6.106-6.1060.0000.0000.0000.000
180A204TYR0-0.065-0.04550.7840.1080.1080.0000.0000.0000.000
181A205GLY0-0.0030.01952.8150.0130.0130.0000.0000.0000.000
182A206ASP-1-0.854-0.94950.403-6.606-6.6060.0000.0000.0000.000
183A207LYS10.8250.89747.9636.4096.4090.0000.0000.0000.000
184A208VAL0-0.0180.01546.283-0.170-0.1700.0000.0000.0000.000
185A209ARG10.7940.85339.7747.8527.8520.0000.0000.0000.000
186A210GLY00.0180.01740.706-0.024-0.0240.0000.0000.0000.000
187A211ILE0-0.001-0.01134.664-0.112-0.1120.0000.0000.0000.000
188A212LEU0-0.051-0.03131.542-0.080-0.0800.0000.0000.0000.000
189A213VAL00.0160.01630.791-0.228-0.2280.0000.0000.0000.000
190A214ALA00.0310.00027.108-0.004-0.0040.0000.0000.0000.000
191A215PRO00.0110.02921.932-0.062-0.0620.0000.0000.0000.000
192A216SER0-0.023-0.02022.404-0.302-0.3020.0000.0000.0000.000
193A217LEU00.0360.05624.4640.2260.2260.0000.0000.0000.000
194A218THR00.0180.01126.013-0.336-0.3360.0000.0000.0000.000
195A219SER00.0300.00728.1280.2900.2900.0000.0000.0000.000
196A220GLY00.0540.02430.1250.3050.3050.0000.0000.0000.000
197A221ALA00.0080.00530.8810.3160.3160.0000.0000.0000.000
198A222LYS10.8590.93130.5609.7039.7030.0000.0000.0000.000
199A223ARG10.8720.91332.3669.6699.6690.0000.0000.0000.000
200A224LEU0-0.019-0.00735.6410.2210.2210.0000.0000.0000.000
201A225LEU0-0.021-0.01933.3210.1780.1780.0000.0000.0000.000
202A226GLU-1-0.815-0.89536.085-8.935-8.9350.0000.0000.0000.000
203A227LYS10.8010.89138.0617.7327.7320.0000.0000.0000.000
204A228GLU-1-0.830-0.91840.881-7.268-7.2680.0000.0000.0000.000
205A229GLY00.0080.02341.3120.1450.1450.0000.0000.0000.000
206A230LEU0-0.063-0.00838.464-0.038-0.0380.0000.0000.0000.000
207A231GLU-1-0.785-0.86936.535-8.328-8.3280.0000.0000.0000.000
208A232PHE0-0.025-0.03527.294-0.163-0.1630.0000.0000.0000.000
209A233ARG10.8590.92730.7039.3789.3780.0000.0000.0000.000
210A234LYS10.9280.97024.69012.20812.2080.0000.0000.0000.000
211A235LEU00.0500.02426.340-0.010-0.0100.0000.0000.0000.000
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