Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 82RYY

Calculation Name: 3KG4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KG4

Chain ID: A

ChEMBL ID:

UniProt ID: Q65TW5

Base Structure: X-ray

Registration Date: 2023-06-19

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2135326.738208
FMO2-HF: Nuclear repulsion 2059279.789099
FMO2-HF: Total energy -76046.949108
FMO2-MP2: Total energy -76268.063402


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-10.301-4.2071.235-3.2-4.1290.021
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.012
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].
3A2ALA00.0190.0192.803-1.8771.3610.111-1.709-1.6390.005
4A3ASN0-0.055-0.0332.511-6.511-4.0511.122-1.322-2.2600.016
5A4ARG11.0211.0043.795-0.518-0.1220.002-0.169-0.2300.000
6A5ILE0-0.087-0.0256.0030.2300.2300.0000.0000.0000.000
7A6ARG10.9200.9479.7580.4920.4920.0000.0000.0000.000
8A7LEU0-0.0240.00412.3600.0500.0500.0000.0000.0000.000
9A8HIS00.0660.03715.931-0.017-0.0170.0000.0000.0000.000
10A9ILE0-0.006-0.01618.9090.0190.0190.0000.0000.0000.000
11A10TRP00.003-0.01321.587-0.005-0.0050.0000.0000.0000.000
12A11GLY00.0220.00725.0830.0050.0050.0000.0000.0000.000
13A12ASP-1-0.874-0.92128.518-0.043-0.0430.0000.0000.0000.000
14A13TYR0-0.044-0.01231.3190.0010.0010.0000.0000.0000.000
15A14ALA0-0.0090.00127.506-0.002-0.0020.0000.0000.0000.000
16A15CYS0-0.017-0.01729.3200.0030.0030.0000.0000.0000.000
17A16PHE00.0300.03024.4990.0020.0020.0000.0000.0000.000
18A17THR0-0.025-0.01927.9510.0000.0000.0000.0000.0000.000
19A18ARG10.9030.94429.7730.0180.0180.0000.0000.0000.000
20A19PRO0-0.0050.00729.4820.0010.0010.0000.0000.0000.000
21A20GLU-1-0.796-0.90732.242-0.008-0.0080.0000.0000.0000.000
22A21MET0-0.0230.00134.9050.0000.0000.0000.0000.0000.000
23A22LYS10.9020.95135.5800.0000.0000.0000.0000.0000.000
24A23VAL0-0.0040.01439.1590.0000.0000.0000.0000.0000.000
25A24GLU-1-0.968-0.98539.562-0.013-0.0130.0000.0000.0000.000
26A25ARG10.9020.95234.2540.0130.0130.0000.0000.0000.000
27A26VAL00.0900.03233.861-0.001-0.0010.0000.0000.0000.000
28A27SER0-0.021-0.01929.2360.0010.0010.0000.0000.0000.000
29A28TYR00.008-0.01126.6710.0020.0020.0000.0000.0000.000
30A29ASP-1-0.817-0.90427.078-0.036-0.0360.0000.0000.0000.000
31A30VAL00.0090.00722.330-0.004-0.0040.0000.0000.0000.000
32A31ILE0-0.044-0.01119.8510.0080.0080.0000.0000.0000.000
33A32THR00.0280.01921.116-0.006-0.0060.0000.0000.0000.000
34A33PRO00.0330.00816.772-0.008-0.0080.0000.0000.0000.000
35A34SER0-0.0160.00718.119-0.003-0.0030.0000.0000.0000.000
36A35ALA0-0.012-0.01420.5830.0020.0020.0000.0000.0000.000
37A36ALA00.0140.00816.8340.0000.0000.0000.0000.0000.000
38A37ARG10.8990.94215.934-0.011-0.0110.0000.0000.0000.000
39A38GLY00.0190.01817.2790.0100.0100.0000.0000.0000.000
40A39ILE0-0.028-0.01419.0910.0050.0050.0000.0000.0000.000
41A40LEU0-0.030-0.01912.9880.0030.0030.0000.0000.0000.000
42A41SER0-0.020-0.03217.0520.0160.0160.0000.0000.0000.000
43A42ALA0-0.0110.01318.7290.0070.0070.0000.0000.0000.000
44A43ILE0-0.0040.01018.3200.0040.0040.0000.0000.0000.000
45A44HIS0-0.056-0.05614.785-0.002-0.0020.0000.0000.0000.000
46A45TRP00.0690.04916.913-0.001-0.0010.0000.0000.0000.000
47A46LYS10.9260.95217.271-0.034-0.0340.0000.0000.0000.000
48A47PRO00.0550.03917.5250.0050.0050.0000.0000.0000.000
49A48ALA00.0550.03115.5290.0020.0020.0000.0000.0000.000
50A49ILE0-0.043-0.01212.1110.0100.0100.0000.0000.0000.000
51A50ASN00.0250.00813.188-0.024-0.0240.0000.0000.0000.000
52A51TRP0-0.039-0.0279.9090.0290.0290.0000.0000.0000.000
53A52VAL0-0.007-0.0189.4590.0110.0110.0000.0000.0000.000
54A53ILE0-0.018-0.01410.100-0.067-0.0670.0000.0000.0000.000
55A54ASP-1-0.794-0.8737.366-0.453-0.4530.0000.0000.0000.000
56A55LYS10.9230.9659.4210.5340.5340.0000.0000.0000.000
57A56ILE0-0.015-0.00412.471-0.008-0.0080.0000.0000.0000.000
58A57TYR0-0.053-0.03411.3990.0270.0270.0000.0000.0000.000
59A58VAL00.018-0.00717.4590.0100.0100.0000.0000.0000.000
60A59LEU00.0100.01119.7010.0020.0020.0000.0000.0000.000
61A60LYS10.9320.97723.1150.0710.0710.0000.0000.0000.000
62A61PRO00.0080.00726.7200.0000.0000.0000.0000.0000.000
63A62ILE0-0.042-0.01026.1050.0020.0020.0000.0000.0000.000
64A63ARG10.8870.94429.6890.0460.0460.0000.0000.0000.000
65A64PHE00.006-0.00331.095-0.001-0.0010.0000.0000.0000.000
66A65GLU-1-0.832-0.92034.982-0.026-0.0260.0000.0000.0000.000
67A66SER0-0.0150.00237.4830.0000.0000.0000.0000.0000.000
68A67VAL00.0400.02337.4930.0000.0000.0000.0000.0000.000
69A68ARG10.9280.94540.5590.0130.0130.0000.0000.0000.000
70A69ARG10.9350.96038.4600.0110.0110.0000.0000.0000.000
71A70ASN00.0350.02441.1530.0020.0020.0000.0000.0000.000
72A104ARG10.9530.96642.2680.0080.0080.0000.0000.0000.000
73A105ALA00.0390.02842.036-0.001-0.0010.0000.0000.0000.000
74A106ALA0-0.028-0.00936.6180.0010.0010.0000.0000.0000.000
75A107THR00.0170.02135.753-0.001-0.0010.0000.0000.0000.000
76A108VAL0-0.048-0.02633.2270.0000.0000.0000.0000.0000.000
77A109LEU00.0100.00827.4200.0000.0000.0000.0000.0000.000
78A110LYS10.8460.91531.5420.0330.0330.0000.0000.0000.000
79A111ASP-1-0.908-0.97430.748-0.045-0.0450.0000.0000.0000.000
80A112VAL0-0.0170.00625.747-0.004-0.0040.0000.0000.0000.000
81A113ALA0-0.010-0.04023.5580.0010.0010.0000.0000.0000.000
82A114TYR00.008-0.00619.2630.0030.0030.0000.0000.0000.000
83A115VAL00.0260.02914.1530.0000.0000.0000.0000.0000.000
84A116ILE0-0.0240.00113.583-0.001-0.0010.0000.0000.0000.000
85A117GLU-1-0.789-0.8928.283-0.884-0.8840.0000.0000.0000.000
86A118ALA00.0340.0299.4470.0550.0550.0000.0000.0000.000
87A119HIS10.8300.9035.2080.0230.0230.0000.0000.0000.000
88A120ALA00.0000.0047.1040.0170.0170.0000.0000.0000.000
89A121VAL0-0.0080.0037.6920.0800.0800.0000.0000.0000.000
90A122MET00.0120.0099.818-0.005-0.0050.0000.0000.0000.000
91A123THR0-0.032-0.02312.1310.0020.0020.0000.0000.0000.000
92A124SER00.035-0.00215.772-0.003-0.0030.0000.0000.0000.000
93A125LYS10.8710.94518.462-0.056-0.0560.0000.0000.0000.000
94A126ALA0-0.035-0.00315.129-0.002-0.0020.0000.0000.0000.000
95A127GLY00.0180.00417.018-0.004-0.0040.0000.0000.0000.000
96A128VAL00.0050.00216.0880.0010.0010.0000.0000.0000.000
97A129ASP-1-0.865-0.92515.0530.0200.0200.0000.0000.0000.000
98A130GLU-1-0.914-0.92813.3680.0620.0620.0000.0000.0000.000
99A131ASN00.037-0.0057.7360.0160.0160.0000.0000.0000.000
100A132THR00.037-0.0065.551-0.068-0.0680.0000.0000.0000.000
101A133THR00.0200.0277.587-0.009-0.0090.0000.0000.0000.000
102A134LYS10.9180.9449.073-0.089-0.0890.0000.0000.0000.000
103A135HIS0-0.037-0.01811.297-0.027-0.0270.0000.0000.0000.000
104A136ILE00.0170.0197.007-0.074-0.0740.0000.0000.0000.000
105A137GLU-1-0.849-0.92410.4100.0030.0030.0000.0000.0000.000
106A138MET0-0.066-0.02912.771-0.051-0.0510.0000.0000.0000.000
107A139PHE0-0.003-0.00613.110-0.023-0.0230.0000.0000.0000.000
108A140LYS11.0081.0029.8450.0230.0230.0000.0000.0000.000
109A141ARG10.9090.96115.018-0.069-0.0690.0000.0000.0000.000
110A142ARG10.8790.93417.995-0.024-0.0240.0000.0000.0000.000
111A143ALA00.0590.02817.335-0.006-0.0060.0000.0000.0000.000
112A144LEU00.0240.00817.562-0.006-0.0060.0000.0000.0000.000
113A145LYS10.8340.93220.3910.0220.0220.0000.0000.0000.000
114A146GLY00.0380.02822.8060.0010.0010.0000.0000.0000.000
115A147GLN0-0.055-0.01223.1570.0020.0020.0000.0000.0000.000
116A148CYS0-0.026-0.02622.583-0.003-0.0030.0000.0000.0000.000
117A149PHE0-0.064-0.02623.3320.0030.0030.0000.0000.0000.000
118A150GLN00.0070.00424.8100.0020.0020.0000.0000.0000.000
119A151GLN0-0.011-0.00525.2220.0000.0000.0000.0000.0000.000
120A152PRO00.0130.02422.6740.0030.0030.0000.0000.0000.000
121A153CYS0-0.054-0.02624.7900.0010.0010.0000.0000.0000.000
122A154MET00.0420.02324.030-0.004-0.0040.0000.0000.0000.000
123A155GLY00.0080.00226.0280.0010.0010.0000.0000.0000.000
124A156VAL0-0.053-0.02027.2950.0050.0050.0000.0000.0000.000
125A157ARG10.9440.96928.6510.0170.0170.0000.0000.0000.000
126A158GLU-1-0.925-0.97131.630-0.018-0.0180.0000.0000.0000.000
127A159PHE0-0.0090.00530.4810.0000.0000.0000.0000.0000.000
128A160PRO0-0.0110.00028.857-0.001-0.0010.0000.0000.0000.000
129A161ALA0-0.006-0.00723.894-0.003-0.0030.0000.0000.0000.000
130A162HIS00.0300.01625.4760.0040.0040.0000.0000.0000.000
131A163PHE0-0.006-0.02720.512-0.007-0.0070.0000.0000.0000.000
132A164ALA00.0070.01320.5790.0090.0090.0000.0000.0000.000
133A165LEU0-0.042-0.02213.816-0.011-0.0110.0000.0000.0000.000
134A166ILE0-0.025-0.00214.4690.0070.0070.0000.0000.0000.000
135A167ASP-1-0.899-0.97013.621-0.155-0.1550.0000.0000.0000.000
136A168ASP-1-1.017-1.0199.460-0.594-0.5940.0000.0000.0000.000
137A169ASN0-0.031-0.01212.524-0.054-0.0540.0000.0000.0000.000
138A170ASP-1-0.872-0.91215.719-0.121-0.1210.0000.0000.0000.000
139A171PRO0-0.049-0.02716.009-0.041-0.0410.0000.0000.0000.000
140A172LEU0-0.029-0.02113.664-0.002-0.0020.0000.0000.0000.000
141A173PRO0-0.004-0.00417.4600.0180.0180.0000.0000.0000.000
142A174LEU00.0100.01520.262-0.011-0.0110.0000.0000.0000.000
143A175SER00.025-0.00422.4300.0020.0020.0000.0000.0000.000
144A176GLN0-0.092-0.05423.5340.0040.0040.0000.0000.0000.000
145A177LEU0-0.0250.00123.4770.0060.0060.0000.0000.0000.000
146A178SER00.0500.01827.1790.0010.0010.0000.0000.0000.000
147A179GLU-1-0.844-0.92228.413-0.063-0.0630.0000.0000.0000.000
148A180SER0-0.040-0.03528.503-0.002-0.0020.0000.0000.0000.000
149A181GLU-1-0.944-0.96027.528-0.050-0.0500.0000.0000.0000.000
150A182PHE00.0050.01421.855-0.006-0.0060.0000.0000.0000.000
151A183ASN0-0.0010.00223.397-0.011-0.0110.0000.0000.0000.000
152A184ARG10.9330.96824.5520.0470.0470.0000.0000.0000.000
153A185ASP-1-0.740-0.82424.709-0.021-0.0210.0000.0000.0000.000
154A186LEU0-0.019-0.02622.7580.0010.0010.0000.0000.0000.000
155A187GLY00.0050.01426.2810.0030.0030.0000.0000.0000.000
156A188TRP0-0.035-0.03124.153-0.002-0.0020.0000.0000.0000.000
157A189MET0-0.030-0.01223.104-0.003-0.0030.0000.0000.0000.000
158A190LEU0-0.009-0.00223.6610.0040.0040.0000.0000.0000.000
159A191HIS0-0.024-0.02515.961-0.013-0.0130.0000.0000.0000.000
160A192ASP-1-0.749-0.90518.998-0.009-0.0090.0000.0000.0000.000
161A193ILE0-0.048-0.01621.6180.0020.0020.0000.0000.0000.000
162A194ASP-1-0.886-0.93022.3840.0420.0420.0000.0000.0000.000
163A195PHE0-0.011-0.03224.626-0.002-0.0020.0000.0000.0000.000
164A196GLU-1-0.952-0.97324.5210.0260.0260.0000.0000.0000.000
165A197HIS0-0.030-0.00627.6770.0010.0010.0000.0000.0000.000
166A198GLY00.004-0.00730.5420.0000.0000.0000.0000.0000.000
167A199ASN0-0.029-0.02129.536-0.002-0.0020.0000.0000.0000.000
168A200THR0-0.030-0.01527.1510.0000.0000.0000.0000.0000.000
169A201PRO00.0020.00526.1080.0020.0020.0000.0000.0000.000
170A202HIS00.0620.05920.2790.0000.0000.0000.0000.0000.000
171A203PHE0-0.017-0.01323.401-0.007-0.0070.0000.0000.0000.000
172A204PHE00.017-0.00818.4910.0080.0080.0000.0000.0000.000
173A205ARG10.7800.86821.7640.0020.0020.0000.0000.0000.000
174A206ALA0-0.0130.00920.686-0.003-0.0030.0000.0000.0000.000
175A207GLU-1-0.897-0.96420.295-0.029-0.0290.0000.0000.0000.000
176A208LEU0-0.064-0.01419.768-0.012-0.0120.0000.0000.0000.000
177A209LYS10.9980.97718.4770.0540.0540.0000.0000.0000.000
178A210ASN0-0.023-0.02918.971-0.011-0.0110.0000.0000.0000.000
179A211GLY00.0430.02019.575-0.017-0.0170.0000.0000.0000.000
180A212VAL0-0.048-0.02514.076-0.015-0.0150.0000.0000.0000.000
181A213ILE0-0.0070.01716.9230.0220.0220.0000.0000.0000.000
182A214ASP-1-0.888-0.95211.970-0.240-0.2400.0000.0000.0000.000
183A215VAL0-0.045-0.02313.1410.0370.0370.0000.0000.0000.000
184A216PRO0-0.0130.01012.7900.0070.0070.0000.0000.0000.000
185A217PRO00.019-0.01911.905-0.012-0.0120.0000.0000.0000.000
186A218PHE0-0.038-0.00313.967-0.007-0.0070.0000.0000.0000.000
187A219TYR0-0.014-0.00115.970-0.004-0.0040.0000.0000.0000.000
188A220ALA00.0060.01217.7640.0150.0150.0000.0000.0000.000