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: N1KYQ

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2136720.280339
FMO2-HF: Nuclear repulsion 2060672.473604
FMO2-HF: Total energy -76047.806735
FMO2-MP2: Total energy -76268.958104


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.
-12.118-6.1292.271-3.6-4.6590.022
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 : 0.012 / q_NPA : 0.003
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].
3A2ALA00.0110.0152.933-2.1471.1530.157-1.733-1.7240.005
4A3ASN0-0.060-0.0382.261-6.222-4.0772.109-1.623-2.6310.018
5A4ARG10.8960.9403.675-1.583-1.0390.005-0.244-0.304-0.001
6A5ILE0-0.055-0.0165.7780.7460.7460.0000.0000.0000.000
7A6ARG10.9200.9459.5151.0461.0460.0000.0000.0000.000
8A7LEU0-0.0220.00112.1930.1340.1340.0000.0000.0000.000
9A8HIS00.0660.04015.661-0.058-0.0580.0000.0000.0000.000
10A9ILE0-0.012-0.01818.8120.0450.0450.0000.0000.0000.000
11A10TRP00.012-0.01021.420-0.014-0.0140.0000.0000.0000.000
12A11GLY00.0220.00624.9880.0120.0120.0000.0000.0000.000
13A12ASP-1-0.893-0.93628.379-0.144-0.1440.0000.0000.0000.000
14A13TYR0-0.064-0.04431.1880.0030.0030.0000.0000.0000.000
15A14ALA0-0.008-0.00127.407-0.008-0.0080.0000.0000.0000.000
16A15CYS0-0.010-0.01229.1290.0100.0100.0000.0000.0000.000
17A16PHE00.0430.03724.4030.0030.0030.0000.0000.0000.000
18A17THR0-0.028-0.02027.8150.0020.0020.0000.0000.0000.000
19A18ARG10.9050.94729.6340.1530.1530.0000.0000.0000.000
20A19PRO0-0.0020.01029.4300.0110.0110.0000.0000.0000.000
21A20GLU-1-0.781-0.89432.056-0.127-0.1270.0000.0000.0000.000
22A21MET0-0.0240.00434.8870.0040.0040.0000.0000.0000.000
23A22LYS10.8770.92935.2600.0890.0890.0000.0000.0000.000
24A23VAL0-0.0100.00739.0350.0030.0030.0000.0000.0000.000
25A24GLU-1-0.917-0.96039.159-0.089-0.0890.0000.0000.0000.000
26A25ARG10.8790.94433.9940.1020.1020.0000.0000.0000.000
27A26VAL00.0800.02534.1020.0010.0010.0000.0000.0000.000
28A27SER0-0.012-0.00629.313-0.004-0.0040.0000.0000.0000.000
29A28TYR00.010-0.00726.7660.0020.0020.0000.0000.0000.000
30A29ASP-1-0.817-0.90727.196-0.193-0.1930.0000.0000.0000.000
31A30VAL0-0.022-0.01422.613-0.005-0.0050.0000.0000.0000.000
32A31ILE0-0.034-0.00319.8580.0170.0170.0000.0000.0000.000
33A32THR00.0240.01821.194-0.025-0.0250.0000.0000.0000.000
34A33PRO00.0390.01216.453-0.013-0.0130.0000.0000.0000.000
35A34SER0-0.021-0.01217.942-0.003-0.0030.0000.0000.0000.000
36A35ALA0-0.019-0.01820.4300.0120.0120.0000.0000.0000.000
37A36ALA00.0110.00816.6490.0120.0120.0000.0000.0000.000
38A37ARG10.8990.93515.7380.2200.2200.0000.0000.0000.000
39A38GLY00.0210.02117.1330.0320.0320.0000.0000.0000.000
40A39ILE0-0.029-0.01418.9640.0290.0290.0000.0000.0000.000
41A40LEU0-0.023-0.01512.8700.0230.0230.0000.0000.0000.000
42A41SER0-0.028-0.04216.9030.0450.0450.0000.0000.0000.000
43A42ALA0-0.0310.00118.6440.0360.0360.0000.0000.0000.000
44A43ILE00.0140.01918.1300.0310.0310.0000.0000.0000.000
45A44HIS0-0.042-0.03814.4760.0260.0260.0000.0000.0000.000
46A45TRP00.0580.04116.503-0.021-0.0210.0000.0000.0000.000
47A46LYS10.9320.95817.069-0.048-0.0480.0000.0000.0000.000
48A47PRO00.0620.03917.294-0.007-0.0070.0000.0000.0000.000
49A48ALA00.0430.02515.692-0.007-0.0070.0000.0000.0000.000
50A49ILE0-0.033-0.01211.8710.0380.0380.0000.0000.0000.000
51A50ASN00.0190.01012.867-0.018-0.0180.0000.0000.0000.000
52A51TRP0-0.028-0.0229.708-0.029-0.0290.0000.0000.0000.000
53A52VAL0-0.009-0.0199.3570.0990.0990.0000.0000.0000.000
54A53ILE0-0.015-0.0129.948-0.221-0.2210.0000.0000.0000.000
55A54ASP-1-0.804-0.8787.259-2.138-2.1380.0000.0000.0000.000
56A55LYS10.8220.8849.6111.2491.2490.0000.0000.0000.000
57A56ILE0-0.020-0.00812.6610.0050.0050.0000.0000.0000.000
58A57TYR0-0.042-0.03711.4490.0710.0710.0000.0000.0000.000
59A58VAL00.018-0.00517.6710.0350.0350.0000.0000.0000.000
60A59LEU00.0090.00519.8860.0100.0100.0000.0000.0000.000
61A60LYS10.9420.98923.3400.2230.2230.0000.0000.0000.000
62A61PRO00.0040.00226.948-0.006-0.0060.0000.0000.0000.000
63A62ILE0-0.063-0.01526.1450.0050.0050.0000.0000.0000.000
64A63ARG10.8350.89529.8960.1750.1750.0000.0000.0000.000
65A64PHE00.009-0.00131.291-0.004-0.0040.0000.0000.0000.000
66A65GLU-1-0.777-0.84835.167-0.104-0.1040.0000.0000.0000.000
67A66SER00.0010.00637.513-0.001-0.0010.0000.0000.0000.000
68A67VAL00.0250.01737.3080.0040.0040.0000.0000.0000.000
69A68ARG10.9280.94740.4660.0620.0620.0000.0000.0000.000
70A69ARG10.9350.95937.9180.0820.0820.0000.0000.0000.000
71A70ASN00.0380.02640.9460.0060.0060.0000.0000.0000.000
72A104ARG10.9870.99242.1270.0640.0640.0000.0000.0000.000
73A105ALA0-0.002-0.00341.8780.0000.0000.0000.0000.0000.000
74A106ALA0-0.023-0.00736.4820.0010.0010.0000.0000.0000.000
75A107THR00.0050.01935.8370.0010.0010.0000.0000.0000.000
76A108VAL0-0.055-0.03233.206-0.006-0.0060.0000.0000.0000.000
77A109LEU00.0060.00727.6190.0030.0030.0000.0000.0000.000
78A110LYS10.8360.89831.6160.1260.1260.0000.0000.0000.000
79A111ASP-1-0.885-0.94330.755-0.156-0.1560.0000.0000.0000.000
80A112VAL00.0000.01625.872-0.011-0.0110.0000.0000.0000.000
81A113ALA0-0.019-0.03823.7250.0100.0100.0000.0000.0000.000
82A114TYR00.018-0.00519.4110.0050.0050.0000.0000.0000.000
83A115VAL00.0300.02714.3850.0140.0140.0000.0000.0000.000
84A116ILE0-0.0250.00213.460-0.024-0.0240.0000.0000.0000.000
85A117GLU-1-0.744-0.8448.354-2.018-2.0180.0000.0000.0000.000
86A118ALA00.0300.0229.2050.0920.0920.0000.0000.0000.000
87A119HIS10.8470.9205.0861.5041.5040.0000.0000.0000.000
88A120ALA00.0040.0066.9320.3770.3770.0000.0000.0000.000
89A121VAL0-0.0040.0027.317-0.028-0.0280.0000.0000.0000.000
90A122MET00.0170.0149.8180.0160.0160.0000.0000.0000.000
91A123THR0-0.020-0.01212.220-0.035-0.0350.0000.0000.0000.000
92A124SER00.0470.00715.8060.0350.0350.0000.0000.0000.000
93A125LYS10.8490.93018.667-0.056-0.0560.0000.0000.0000.000
94A126ALA0-0.037-0.00215.449-0.007-0.0070.0000.0000.0000.000
95A127GLY00.0170.00417.417-0.011-0.0110.0000.0000.0000.000
96A128VAL00.0110.00316.6750.0430.0430.0000.0000.0000.000
97A129ASP-1-0.869-0.92715.9030.4310.4310.0000.0000.0000.000
98A130GLU-1-0.911-0.92813.6580.4290.4290.0000.0000.0000.000
99A131ASN00.036-0.0018.846-0.135-0.1350.0000.0000.0000.000
100A132THR00.044-0.0045.5510.0820.0820.0000.0000.0000.000
101A133THR0-0.0040.0197.655-0.152-0.1520.0000.0000.0000.000
102A134LYS10.9110.9379.181-0.586-0.5860.0000.0000.0000.000
103A135HIS0-0.042-0.02411.274-0.152-0.1520.0000.0000.0000.000
104A136ILE00.0320.0246.818-0.164-0.1640.0000.0000.0000.000
105A137GLU-1-0.824-0.91010.2460.0930.0930.0000.0000.0000.000
106A138MET0-0.073-0.03212.630-0.099-0.0990.0000.0000.0000.000
107A139PHE0-0.003-0.00812.837-0.050-0.0500.0000.0000.0000.000
108A140LYS10.9060.95210.4860.0190.0190.0000.0000.0000.000
109A141ARG10.8870.93914.866-0.220-0.2200.0000.0000.0000.000
110A142ARG10.8770.92317.836-0.017-0.0170.0000.0000.0000.000
111A143ALA00.0620.03117.148-0.009-0.0090.0000.0000.0000.000
112A144LEU00.0040.00116.927-0.009-0.0090.0000.0000.0000.000
113A145LYS10.8370.92920.2190.0360.0360.0000.0000.0000.000
114A146GLY00.0390.03222.6580.0050.0050.0000.0000.0000.000
115A147GLN0-0.052-0.01322.972-0.001-0.0010.0000.0000.0000.000
116A148CYS0-0.041-0.03022.308-0.017-0.0170.0000.0000.0000.000
117A149PHE0-0.054-0.01622.9420.0180.0180.0000.0000.0000.000
118A150GLN0-0.0040.00524.5200.0100.0100.0000.0000.0000.000
119A151GLN00.005-0.01625.092-0.002-0.0020.0000.0000.0000.000
120A152PRO00.0230.02622.4880.0020.0020.0000.0000.0000.000
121A153CYS0-0.029-0.01424.6090.0130.0130.0000.0000.0000.000
122A154MET00.0200.02423.438-0.024-0.0240.0000.0000.0000.000
123A155GLY00.004-0.00325.7970.0060.0060.0000.0000.0000.000
124A156VAL0-0.067-0.02627.0830.0120.0120.0000.0000.0000.000
125A157ARG10.9490.97028.2100.1010.1010.0000.0000.0000.000
126A158GLU-1-0.919-0.97031.449-0.099-0.0990.0000.0000.0000.000
127A159PHE0-0.0080.00430.3090.0030.0030.0000.0000.0000.000
128A160PRO0-0.0080.00328.642-0.010-0.0100.0000.0000.0000.000
129A161ALA0-0.006-0.00623.598-0.006-0.0060.0000.0000.0000.000
130A162HIS00.0360.01825.2430.0120.0120.0000.0000.0000.000
131A163PHE0-0.015-0.03020.300-0.029-0.0290.0000.0000.0000.000
132A164ALA00.0120.01320.2980.0320.0320.0000.0000.0000.000
133A165LEU0-0.053-0.02313.648-0.044-0.0440.0000.0000.0000.000
134A166ILE0-0.029-0.00514.4850.0270.0270.0000.0000.0000.000
135A167ASP-1-0.811-0.91413.457-0.257-0.2570.0000.0000.0000.000
136A168ASP-1-0.907-0.9709.718-1.030-1.0300.0000.0000.0000.000
137A169ASN0-0.068-0.03812.524-0.056-0.0560.0000.0000.0000.000
138A170ASP-1-0.872-0.91015.719-0.235-0.2350.0000.0000.0000.000
139A171PRO0-0.044-0.02316.054-0.079-0.0790.0000.0000.0000.000
140A172LEU0-0.019-0.01613.839-0.008-0.0080.0000.0000.0000.000
141A173PRO0-0.003-0.00817.6880.0400.0400.0000.0000.0000.000
142A174LEU00.0020.01420.474-0.031-0.0310.0000.0000.0000.000
143A175SER00.011-0.00422.148-0.005-0.0050.0000.0000.0000.000
144A176GLN0-0.083-0.05523.7210.0170.0170.0000.0000.0000.000
145A177LEU0-0.0130.00223.6400.0150.0150.0000.0000.0000.000
146A178SER00.0290.01727.3450.0050.0050.0000.0000.0000.000
147A179GLU-1-0.846-0.92128.506-0.235-0.2350.0000.0000.0000.000
148A180SER0-0.036-0.02628.582-0.007-0.0070.0000.0000.0000.000
149A181GLU-1-0.929-0.98127.522-0.203-0.2030.0000.0000.0000.000
150A182PHE00.0140.01521.795-0.021-0.0210.0000.0000.0000.000
151A183ASN0-0.004-0.00423.411-0.048-0.0480.0000.0000.0000.000
152A184ARG10.9150.95524.6280.2330.2330.0000.0000.0000.000
153A185ASP-1-0.755-0.82824.794-0.229-0.2290.0000.0000.0000.000
154A186LEU0-0.025-0.02422.7390.0150.0150.0000.0000.0000.000
155A187GLY00.0150.02026.3710.0150.0150.0000.0000.0000.000
156A188TRP0-0.031-0.03124.310-0.021-0.0210.0000.0000.0000.000
157A189MET0-0.023-0.01123.2830.0070.0070.0000.0000.0000.000
158A190LEU0-0.016-0.00323.595-0.005-0.0050.0000.0000.0000.000
159A191HIS0-0.030-0.03115.767-0.005-0.0050.0000.0000.0000.000
160A192ASP-1-0.745-0.87919.124-0.255-0.2550.0000.0000.0000.000
161A193ILE0-0.036-0.01621.5150.0120.0120.0000.0000.0000.000
162A194ASP-1-0.848-0.91022.268-0.107-0.1070.0000.0000.0000.000
163A195PHE0-0.012-0.03224.6260.0050.0050.0000.0000.0000.000
164A196GLU-1-0.942-0.97224.544-0.036-0.0360.0000.0000.0000.000
165A197HIS0-0.034-0.00427.6930.0040.0040.0000.0000.0000.000
166A198GLY00.007-0.00430.5160.0030.0030.0000.0000.0000.000
167A199ASN0-0.049-0.03629.585-0.010-0.0100.0000.0000.0000.000
168A200THR00.0040.01327.0130.0040.0040.0000.0000.0000.000
169A201PRO0-0.018-0.00926.031-0.009-0.0090.0000.0000.0000.000
170A202HIS00.0430.04920.2010.0200.0200.0000.0000.0000.000
171A203PHE0-0.008-0.00923.306-0.018-0.0180.0000.0000.0000.000
172A204PHE00.019-0.00418.580-0.003-0.0030.0000.0000.0000.000
173A205ARG10.7800.86221.8230.2060.2060.0000.0000.0000.000
174A206ALA0-0.0090.00920.783-0.031-0.0310.0000.0000.0000.000
175A207GLU-1-0.775-0.88520.374-0.280-0.2800.0000.0000.0000.000
176A208LEU0-0.063-0.01319.849-0.047-0.0470.0000.0000.0000.000
177A209LYS10.8570.88918.2920.3770.3770.0000.0000.0000.000
178A210ASN0-0.012-0.01619.038-0.020-0.0200.0000.0000.0000.000
179A211GLY00.0570.02719.673-0.032-0.0320.0000.0000.0000.000
180A212VAL0-0.064-0.03214.261-0.028-0.0280.0000.0000.0000.000
181A213ILE0-0.0100.01617.0890.0420.0420.0000.0000.0000.000
182A214ASP-1-0.792-0.87812.315-1.000-1.0000.0000.0000.0000.000
183A215VAL0-0.036-0.02113.2610.1180.1180.0000.0000.0000.000
184A216PRO0-0.0020.01712.877-0.077-0.0770.0000.0000.0000.000
185A217PRO00.025-0.01111.779-0.001-0.0010.0000.0000.0000.000
186A218PHE0-0.048-0.00514.0070.0280.0280.0000.0000.0000.000
187A219TYR0-0.044-0.02416.2620.0280.0280.0000.0000.0000.000
188A220ALA00.0160.02017.783-0.002-0.0020.0000.0000.0000.000