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: 3Q87L

Calculation Name: 1K4N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K4N

Chain ID: A

ChEMBL ID:

UniProt ID: P52007

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2010684.202956
FMO2-HF: Nuclear repulsion 1937999.845687
FMO2-HF: Total energy -72684.357269
FMO2-MP2: Total energy -72897.01025


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-1.17-0.389-0.001-0.28-0.5010.001
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.022
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].
3A3MET0-0.003-0.0063.798-0.4570.324-0.001-0.280-0.5010.001
4A4ILE0-0.009-0.0086.0330.6950.6950.0000.0000.0000.000
5A5MET0-0.0030.0198.1770.1510.1510.0000.0000.0000.000
6A6ALA00.0170.01611.6190.0410.0410.0000.0000.0000.000
7A7ASN00.0280.00814.4410.0730.0730.0000.0000.0000.000
8A8TRP00.1050.02416.7110.0360.0360.0000.0000.0000.000
9A9GLN0-0.082-0.04520.1320.0240.0240.0000.0000.0000.000
10A10SER0-0.089-0.04817.1300.0100.0100.0000.0000.0000.000
11A11ILE0-0.0250.00918.0180.0000.0000.0000.0000.0000.000
12A12ASP-1-0.853-0.91920.932-0.205-0.2050.0000.0000.0000.000
13A13GLU-1-0.932-0.97623.657-0.228-0.2280.0000.0000.0000.000
14A14LEU0-0.045-0.02522.5830.0170.0170.0000.0000.0000.000
15A15GLN00.0350.01924.7880.0140.0140.0000.0000.0000.000
16A16ASP-1-0.786-0.87726.734-0.141-0.1410.0000.0000.0000.000
17A17ILE00.0330.00126.4600.0100.0100.0000.0000.0000.000
18A18ALA00.0050.00925.0870.0040.0040.0000.0000.0000.000
19A19SER0-0.051-0.03126.9820.0110.0110.0000.0000.0000.000
20A20ASP-1-0.747-0.84629.918-0.098-0.0980.0000.0000.0000.000
21A21LEU0-0.0100.00927.0840.0080.0080.0000.0000.0000.000
22A22PRO00.0250.00329.7080.0080.0080.0000.0000.0000.000
23A23ARG10.8120.88532.4310.1030.1030.0000.0000.0000.000
24A24PHE0-0.011-0.01032.5020.0060.0060.0000.0000.0000.000
25A25ILE00.0220.01830.0770.0040.0040.0000.0000.0000.000
26A26HIS00.0160.01434.0220.0030.0030.0000.0000.0000.000
27A27ALA00.0080.00437.3760.0040.0040.0000.0000.0000.000
28A28LEU0-0.021-0.01733.9770.0040.0040.0000.0000.0000.000
29A29ASP-1-0.846-0.89236.964-0.056-0.0560.0000.0000.0000.000
30A30GLU-1-0.902-0.96838.600-0.045-0.0450.0000.0000.0000.000
31A31LEU0-0.044-0.02041.1510.0040.0040.0000.0000.0000.000
32A32SER0-0.012-0.02639.3310.0020.0020.0000.0000.0000.000
33A33ARG10.8240.92440.4010.0520.0520.0000.0000.0000.000
34A34ARG10.9010.95044.0230.0510.0510.0000.0000.0000.000
35A35LEU0-0.010-0.01243.8160.0020.0020.0000.0000.0000.000
36A36GLY00.0150.02846.0830.0010.0010.0000.0000.0000.000
37A37LEU0-0.012-0.00440.8920.0010.0010.0000.0000.0000.000
38A38ASN0-0.015-0.01439.651-0.004-0.0040.0000.0000.0000.000
39A39ILE00.0580.01435.067-0.001-0.0010.0000.0000.0000.000
40A40THR0-0.016-0.00434.389-0.005-0.0050.0000.0000.0000.000
41A41PRO0-0.036-0.01634.526-0.003-0.0030.0000.0000.0000.000
42A42LEU0-0.0270.00536.193-0.002-0.0020.0000.0000.0000.000
43A43THR00.0340.01631.172-0.004-0.0040.0000.0000.0000.000
44A44ALA0-0.009-0.00529.7840.0010.0010.0000.0000.0000.000
45A45ASP-1-0.774-0.87630.239-0.135-0.1350.0000.0000.0000.000
46A46HIS10.7730.88529.2320.1180.1180.0000.0000.0000.000
47A47ILE0-0.0020.01428.2960.0140.0140.0000.0000.0000.000
48A48SER0-0.053-0.08030.834-0.010-0.0100.0000.0000.0000.000
49A49LEU00.0170.03029.3250.0080.0080.0000.0000.0000.000
50A50ARG10.8060.88833.7110.1060.1060.0000.0000.0000.000
51A51CYS00.0060.01835.488-0.002-0.0020.0000.0000.0000.000
52A52HIS0-0.069-0.04937.5370.0030.0030.0000.0000.0000.000
53A53GLN0-0.0110.00538.1500.0070.0070.0000.0000.0000.000
54A54ASN00.0670.00337.385-0.007-0.0070.0000.0000.0000.000
55A55ALA0-0.0040.00035.551-0.006-0.0060.0000.0000.0000.000
56A56THR0-0.035-0.03133.545-0.008-0.0080.0000.0000.0000.000
57A57ALA00.0620.02832.285-0.009-0.0090.0000.0000.0000.000
58A58GLU-1-0.915-0.97031.316-0.163-0.1630.0000.0000.0000.000
59A59ARG10.8010.90028.8560.1400.1400.0000.0000.0000.000
60A60TRP00.026-0.01827.670-0.013-0.0130.0000.0000.0000.000
61A61ARG10.7860.89526.6450.1730.1730.0000.0000.0000.000
62A62ARG10.8910.94525.4430.1940.1940.0000.0000.0000.000
63A63GLY00.0500.02523.235-0.023-0.0230.0000.0000.0000.000
64A64PHE00.037-0.02321.922-0.025-0.0250.0000.0000.0000.000
65A65GLU-1-0.913-0.95321.703-0.278-0.2780.0000.0000.0000.000
66A66GLN0-0.067-0.02918.446-0.049-0.0490.0000.0000.0000.000
67A67CYS0-0.090-0.02017.028-0.040-0.0400.0000.0000.0000.000
68A68GLY00.0410.01518.278-0.001-0.0010.0000.0000.0000.000
69A69GLU-1-0.977-0.96718.221-0.457-0.4570.0000.0000.0000.000
70A70LEU0-0.056-0.03221.5520.0210.0210.0000.0000.0000.000
71A71LEU0-0.026-0.01324.617-0.001-0.0010.0000.0000.0000.000
72A72SER0-0.005-0.00826.8410.0160.0160.0000.0000.0000.000
73A73GLU-1-0.777-0.88430.332-0.165-0.1650.0000.0000.0000.000
74A74ASN00.0080.01832.7110.0070.0070.0000.0000.0000.000
75A75MET00.0010.00136.3730.0000.0000.0000.0000.0000.000
76A76ILE00.0050.01238.7500.0070.0070.0000.0000.0000.000
77A77ASN0-0.039-0.03941.4040.0000.0000.0000.0000.0000.000
78A78GLY00.0150.00544.1250.0010.0010.0000.0000.0000.000
79A79ARG10.8590.92739.1870.0990.0990.0000.0000.0000.000
80A80PRO00.0320.02235.3770.0020.0020.0000.0000.0000.000
81A81ILE0-0.036-0.02134.2400.0020.0020.0000.0000.0000.000
82A82CYS0-0.0180.00729.593-0.001-0.0010.0000.0000.0000.000
83A83LEU00.0050.01529.2970.0030.0030.0000.0000.0000.000
84A84PHE00.0430.01324.142-0.002-0.0020.0000.0000.0000.000
85A85LYS10.9900.99220.8370.2850.2850.0000.0000.0000.000
86A86LEU0-0.014-0.02420.213-0.024-0.0240.0000.0000.0000.000
87A87HIS00.003-0.00314.802-0.022-0.0220.0000.0000.0000.000
88A88GLU-1-0.886-0.93313.598-0.618-0.6180.0000.0000.0000.000
89A89PRO0-0.038-0.01817.7390.0200.0200.0000.0000.0000.000
90A90VAL00.0040.02021.436-0.002-0.0020.0000.0000.0000.000
91A91GLN0-0.025-0.02823.517-0.006-0.0060.0000.0000.0000.000
92A92VAL0-0.007-0.01425.3250.0080.0080.0000.0000.0000.000
93A93ALA00.0200.02029.1250.0060.0060.0000.0000.0000.000
94A94HIS00.012-0.00728.335-0.005-0.0050.0000.0000.0000.000
95A95TRP0-0.026-0.02427.862-0.004-0.0040.0000.0000.0000.000
96A96GLN00.0160.00621.853-0.022-0.0220.0000.0000.0000.000
97A97PHE0-0.0080.00025.2110.0000.0000.0000.0000.0000.000
98A98SER00.0670.02722.343-0.024-0.0240.0000.0000.0000.000
99A99ILE0-0.0130.01523.607-0.020-0.0200.0000.0000.0000.000
100A100VAL00.0230.01025.6370.0180.0180.0000.0000.0000.000
101A101GLU-1-0.845-0.89228.107-0.126-0.1260.0000.0000.0000.000
102A102LEU0-0.008-0.01129.2740.0050.0050.0000.0000.0000.000
103A103PRO0-0.062-0.02732.1030.0020.0020.0000.0000.0000.000
104A104TRP00.0470.01631.7500.0010.0010.0000.0000.0000.000
105A105PRO0-0.0210.00637.4160.0050.0050.0000.0000.0000.000
106A106GLY0-0.004-0.00540.6080.0000.0000.0000.0000.0000.000
107A107GLU-1-0.939-0.96043.329-0.064-0.0640.0000.0000.0000.000
108A108LYS10.8750.94945.0450.0740.0740.0000.0000.0000.000
109A109ARG10.9890.98744.4930.0620.0620.0000.0000.0000.000
110A110TYR00.016-0.01041.1790.0040.0040.0000.0000.0000.000
111A111PRO0-0.006-0.02342.171-0.003-0.0030.0000.0000.0000.000
112A112HIS0-0.063-0.01335.9500.0050.0050.0000.0000.0000.000
113A113GLU-1-0.755-0.84935.896-0.110-0.1100.0000.0000.0000.000
114A114GLY00.0490.02133.411-0.003-0.0030.0000.0000.0000.000
115A115TRP0-0.047-0.02727.4650.0030.0030.0000.0000.0000.000
116A116GLU-1-0.808-0.87234.025-0.088-0.0880.0000.0000.0000.000
117A117HIS10.7130.81235.7350.1130.1130.0000.0000.0000.000
118A118ILE00.0390.04432.714-0.009-0.0090.0000.0000.0000.000
119A119GLU-1-0.891-0.94833.982-0.095-0.0950.0000.0000.0000.000
120A120ILE00.0340.01534.021-0.007-0.0070.0000.0000.0000.000
121A121VAL00.0460.01833.2990.0040.0040.0000.0000.0000.000
122A122LEU0-0.045-0.02036.2870.0030.0030.0000.0000.0000.000
123A123PRO00.0360.01136.5100.0030.0030.0000.0000.0000.000
124A124GLY00.0060.00039.2030.0040.0040.0000.0000.0000.000
125A125ASP-1-0.827-0.92242.600-0.051-0.0510.0000.0000.0000.000
126A126PRO0-0.015-0.00542.6060.0000.0000.0000.0000.0000.000
127A127GLU-1-0.913-0.94744.951-0.051-0.0510.0000.0000.0000.000
128A128THR0-0.024-0.00147.6730.0010.0010.0000.0000.0000.000
129A129LEU0-0.053-0.00441.9060.0010.0010.0000.0000.0000.000
130A130ASN00.035-0.01245.722-0.002-0.0020.0000.0000.0000.000
131A131ALA00.0090.00447.8900.0000.0000.0000.0000.0000.000
132A132ARG10.8450.90042.4350.0570.0570.0000.0000.0000.000
133A133ALA00.0100.00544.2780.0000.0000.0000.0000.0000.000
134A134LEU0-0.022-0.02445.5570.0000.0000.0000.0000.0000.000
135A135ALA0-0.0140.00348.4790.0010.0010.0000.0000.0000.000
136A136LEU0-0.056-0.01942.1970.0010.0010.0000.0000.0000.000
137A137LEU0-0.065-0.02144.818-0.001-0.0010.0000.0000.0000.000
138A138SER00.0140.01447.8370.0030.0030.0000.0000.0000.000
139A139ASP-1-0.875-0.95350.456-0.034-0.0340.0000.0000.0000.000
140A140GLU-1-0.953-0.96852.634-0.033-0.0330.0000.0000.0000.000
141A141GLY00.0490.01349.832-0.001-0.0010.0000.0000.0000.000
142A142LEU0-0.062-0.03749.941-0.002-0.0020.0000.0000.0000.000
143A143SER0-0.080-0.04152.1200.0000.0000.0000.0000.0000.000
144A144LEU0-0.0340.00850.2770.0010.0010.0000.0000.0000.000
145A145PRO00.0230.01353.479-0.001-0.0010.0000.0000.0000.000
146A146GLY0-0.060-0.04251.636-0.001-0.0010.0000.0000.0000.000
147A147ILE0-0.0120.00547.374-0.003-0.0030.0000.0000.0000.000
148A148SER0-0.058-0.02249.0230.0010.0010.0000.0000.0000.000
149A149VAL00.0510.01348.039-0.003-0.0030.0000.0000.0000.000
150A150LYS10.9030.95846.6040.0650.0650.0000.0000.0000.000
151A151THR00.0390.02647.477-0.002-0.0020.0000.0000.0000.000
152A152SER0-0.0070.00744.6120.0000.0000.0000.0000.0000.000
153A160ARG11.0031.01440.1540.0670.0670.0000.0000.0000.000
154A161LEU00.0450.01137.5340.0050.0050.0000.0000.0000.000
155A162PRO0-0.056-0.04141.516-0.002-0.0020.0000.0000.0000.000
156A163ASN00.1030.05939.086-0.001-0.0010.0000.0000.0000.000
157A164PRO0-0.0270.01342.046-0.002-0.0020.0000.0000.0000.000
158A165THR00.039-0.01440.811-0.003-0.0030.0000.0000.0000.000
159A166LEU0-0.0340.00143.2250.0020.0020.0000.0000.0000.000
160A167ALA0-0.046-0.03743.176-0.004-0.0040.0000.0000.0000.000
161A168VAL00.0650.03943.3490.0040.0040.0000.0000.0000.000
162A169THR0-0.028-0.01843.604-0.003-0.0030.0000.0000.0000.000
163A170ASP-1-0.717-0.86644.381-0.061-0.0610.0000.0000.0000.000
164A171GLY0-0.059-0.02246.1850.0020.0020.0000.0000.0000.000
165A172LYS10.8090.88542.5670.0610.0610.0000.0000.0000.000
166A173THR00.0170.02538.846-0.007-0.0070.0000.0000.0000.000
167A174THR0-0.062-0.03339.8470.0060.0060.0000.0000.0000.000
168A175ILE00.0390.03138.390-0.006-0.0060.0000.0000.0000.000
169A176LYS10.8920.94338.7020.0930.0930.0000.0000.0000.000
170A177PHE00.0500.03438.725-0.004-0.0040.0000.0000.0000.000
171A178HIS10.8210.89135.0880.1040.1040.0000.0000.0000.000
172A179PRO0-0.018-0.02238.858-0.001-0.0010.0000.0000.0000.000
173A180TRP0-0.0050.02835.9060.0030.0030.0000.0000.0000.000
174A181SER00.0320.03030.847-0.001-0.0010.0000.0000.0000.000
175A182ILE00.007-0.01229.6020.0040.0040.0000.0000.0000.000
176A183GLU-1-0.876-0.95626.158-0.173-0.1730.0000.0000.0000.000
177A184GLU-1-0.893-0.94829.371-0.097-0.0970.0000.0000.0000.000
178A185ILE0-0.025-0.01132.5990.0060.0060.0000.0000.0000.000
179A186VAL00.0080.03029.0050.0030.0030.0000.0000.0000.000
180A187ALA00.0090.00030.9820.0030.0030.0000.0000.0000.000
181A188SER0-0.172-0.10832.3910.0080.0080.0000.0000.0000.000
182A189GLU-1-1.008-0.99834.861-0.101-0.1010.0000.0000.0000.000
183A190GLN0-0.027-0.00230.249-0.011-0.0110.0000.0000.0000.000