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: 7J84K

Calculation Name: 1KUU-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KUU

Chain ID: A

ChEMBL ID:

UniProt ID: O27099

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 202
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2278182.325165
FMO2-HF: Nuclear repulsion 2201308.682688
FMO2-HF: Total energy -76873.642477
FMO2-MP2: Total energy -77098.03561


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:MET )


Summations of interaction energy for fragment #1(A:1:MET )
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.
-2.869-1.42613.129-4.513-10.058-0.023
Interaction energy analysis for fragmet #1(A:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.015
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].
3A3LEU 00.0660.0273.301-0.1931.6330.010-0.661-1.1750.003
4A4GLY 0-0.0200.0025.861-0.012-0.0120.0000.0000.0000.000
5A5ARG 10.8640.9269.143-0.564-0.5640.0000.0000.0000.000
6A6ILE 00.0080.0107.4530.1040.1040.0000.0000.0000.000
7A7LEU 0-0.019-0.00211.453-0.039-0.0390.0000.0000.0000.000
8A8ALA 00.0360.01013.3850.0100.0100.0000.0000.0000.000
9A9VAL 0-0.029-0.01015.2280.0130.0130.0000.0000.0000.000
10A10GLY 00.0370.01818.2310.0070.0070.0000.0000.0000.000
11A11ARG 10.8730.93120.3960.0650.0650.0000.0000.0000.000
12A12ASN 0-0.0040.01719.214-0.007-0.0070.0000.0000.0000.000
13A13SER 0-0.026-0.02322.5560.0110.0110.0000.0000.0000.000
14A14ASN 0-0.056-0.03322.8900.0220.0220.0000.0000.0000.000
15A15GLY 00.0890.04925.0510.0070.0070.0000.0000.0000.000
16A16SER 0-0.0300.00523.656-0.003-0.0030.0000.0000.0000.000
17A17PHE 0-0.024-0.02016.787-0.007-0.0070.0000.0000.0000.000
18A18VAL 00.0140.00619.6950.0170.0170.0000.0000.0000.000
19A19ALA 0-0.0040.00515.677-0.017-0.0170.0000.0000.0000.000
20A20TYR 00.020-0.02315.4670.0330.0330.0000.0000.0000.000
21A21ARG 10.8480.9056.6331.6961.6960.0000.0000.0000.000
22A22VAL 0-0.0240.00312.7410.0780.0780.0000.0000.0000.000
23A23SER 00.0520.0328.494-0.258-0.2580.0000.0000.0000.000
24A24SER 0-0.090-0.05910.5540.2660.2660.0000.0000.0000.000
25A25ARG 10.9680.9896.029-1.453-1.4530.0000.0000.0000.000
26A26SER 00.013-0.00412.375-0.011-0.0110.0000.0000.0000.000
27A27PHE 0-0.026-0.01015.762-0.008-0.0080.0000.0000.0000.000
28A28PRO 00.0340.00115.111-0.017-0.0170.0000.0000.0000.000
29A29ASN 00.0060.02516.681-0.058-0.0580.0000.0000.0000.000
30A30ARG 10.8420.91315.7720.0740.0740.0000.0000.0000.000
31A31THR 00.004-0.03019.492-0.029-0.0290.0000.0000.0000.000
32A32THR 0-0.015-0.01019.3270.0320.0320.0000.0000.0000.000
33A33SER 0-0.0270.00022.315-0.007-0.0070.0000.0000.0000.000
34A34ILE 00.0410.00625.9220.0100.0100.0000.0000.0000.000
35A35GLN 0-0.047-0.03427.1450.0140.0140.0000.0000.0000.000
36A36GLU -1-0.883-0.95630.225-0.072-0.0720.0000.0000.0000.000
37A37GLU -1-0.956-0.96630.264-0.048-0.0480.0000.0000.0000.000
38A38ARG 10.8850.91727.7700.0610.0610.0000.0000.0000.000
39A39VAL 0-0.0100.01522.622-0.009-0.0090.0000.0000.0000.000
40A40ALA 0-0.016-0.00224.3190.0110.0110.0000.0000.0000.000
41A41VAL 0-0.0060.01019.259-0.025-0.0250.0000.0000.0000.000
42A42VAL 0-0.019-0.03222.2820.0300.0300.0000.0000.0000.000
43A43PRO 0-0.017-0.02023.062-0.019-0.0190.0000.0000.0000.000
44A44VAL 00.0290.03822.017-0.005-0.0050.0000.0000.0000.000
45A45GLU -1-0.939-0.96924.910-0.097-0.0970.0000.0000.0000.000
46A46GLY 00.0160.01728.051-0.003-0.0030.0000.0000.0000.000
47A47HIS 0-0.027-0.02624.8130.0040.0040.0000.0000.0000.000
48A48GLU -1-0.863-0.93526.520-0.037-0.0370.0000.0000.0000.000
49A49ARG 10.9150.93828.8010.0090.0090.0000.0000.0000.000
50A50ASP -1-0.904-0.96123.6870.0040.0040.0000.0000.0000.000
51A51VAL 00.0300.00725.0300.0170.0170.0000.0000.0000.000
52A52PHE 0-0.054-0.01626.3930.0100.0100.0000.0000.0000.000
53A53ARG 10.8670.95624.303-0.043-0.0430.0000.0000.0000.000
54A54ASN 00.011-0.01019.5220.0170.0170.0000.0000.0000.000
55A55PRO 00.0340.01523.605-0.017-0.0170.0000.0000.0000.000
56A56TYR 00.0470.03720.061-0.003-0.0030.0000.0000.0000.000
57A57ILE 0-0.104-0.04118.832-0.012-0.0120.0000.0000.0000.000
58A58ALA 00.0260.01020.838-0.030-0.0300.0000.0000.0000.000
59A59TYR 0-0.0070.01817.6990.0050.0050.0000.0000.0000.000
60A60ASN 00.0760.05423.562-0.033-0.0330.0000.0000.0000.000
61A61CYS 0-0.058-0.00219.6470.0060.0060.0000.0000.0000.000
62A62ILE 00.0530.01420.363-0.003-0.0030.0000.0000.0000.000
63A63ARG 10.8150.91223.8300.0220.0220.0000.0000.0000.000
64A64ILE 0-0.0210.00426.586-0.004-0.0040.0000.0000.0000.000
65A65VAL 0-0.003-0.00529.4590.0060.0060.0000.0000.0000.000
66A66GLY 00.0450.02132.4330.0030.0030.0000.0000.0000.000
67A67ASP -1-0.860-0.94332.725-0.042-0.0420.0000.0000.0000.000
68A68THR 0-0.036-0.02828.327-0.001-0.0010.0000.0000.0000.000
69A69ALA 0-0.0050.01824.761-0.001-0.0010.0000.0000.0000.000
70A70VAL 0-0.031-0.03124.4030.0080.0080.0000.0000.0000.000
71A71VAL 00.0190.01018.721-0.013-0.0130.0000.0000.0000.000
72A72SER 0-0.033-0.06418.9540.0340.0340.0000.0000.0000.000
73A73ASN 00.0440.01515.871-0.042-0.0420.0000.0000.0000.000
74A74GLY 00.0400.01117.8760.0240.0240.0000.0000.0000.000
75A75SER 00.0210.00021.244-0.011-0.0110.0000.0000.0000.000
76A76HIS 00.0030.02719.798-0.009-0.0090.0000.0000.0000.000
77A77THR 00.0250.02922.8200.0000.0000.0000.0000.0000.000
78A78ASP -1-0.815-0.90224.875-0.014-0.0140.0000.0000.0000.000
79A79THR 0-0.027-0.00727.761-0.003-0.0030.0000.0000.0000.000
80A80ILE 0-0.011-0.00524.1400.0010.0010.0000.0000.0000.000
81A81ALA 00.0010.00428.207-0.004-0.0040.0000.0000.0000.000
82A82ASP -1-0.841-0.93029.6940.0040.0040.0000.0000.0000.000
83A83LYS 10.8990.94431.528-0.040-0.0400.0000.0000.0000.000
84A84VAL 00.0140.02329.7610.0000.0000.0000.0000.0000.000
85A85ALA 0-0.0120.00132.897-0.003-0.0030.0000.0000.0000.000
86A86LEU 0-0.087-0.04835.4820.0000.0000.0000.0000.0000.000
87A87GLY 0-0.0030.00836.3490.0020.0020.0000.0000.0000.000
88A88MET 0-0.108-0.02932.7920.0040.0040.0000.0000.0000.000
89A89ASN 0-0.006-0.02632.215-0.001-0.0010.0000.0000.0000.000
90A90LEU 00.0770.01927.3040.0080.0080.0000.0000.0000.000
91A91ARG 10.9140.97827.355-0.061-0.0610.0000.0000.0000.000
92A92ASP -1-0.795-0.89627.9360.0710.0710.0000.0000.0000.000
93A93ALA 0-0.0090.00529.1100.0070.0070.0000.0000.0000.000
94A94ILE 00.0260.02022.9880.0060.0060.0000.0000.0000.000
95A95GLY 00.0080.00125.7710.0150.0150.0000.0000.0000.000
96A96LEU 0-0.020-0.01827.1220.0110.0110.0000.0000.0000.000
97A97SER 0-0.024-0.03526.5010.0020.0020.0000.0000.0000.000
98A98LEU 0-0.024-0.00521.1690.0060.0060.0000.0000.0000.000
99A99LEU 0-0.0070.00824.8190.0150.0150.0000.0000.0000.000
100A100ALA 0-0.049-0.01927.2650.0040.0040.0000.0000.0000.000
101A101MET 0-0.091-0.04025.017-0.003-0.0030.0000.0000.0000.000
102A102ASP -1-0.846-0.92724.0420.2320.2320.0000.0000.0000.000
103A103TYR 0-0.061-0.02119.272-0.005-0.0050.0000.0000.0000.000
104A104GLU -1-0.942-0.98018.5600.1730.1730.0000.0000.0000.000
105A105LYS 10.8540.91820.145-0.185-0.1850.0000.0000.0000.000
106A106ASP -1-0.790-0.83117.0990.3870.3870.0000.0000.0000.000
107A107GLU -1-0.972-0.99717.0260.3860.3860.0000.0000.0000.000
108A108LEU 0-0.076-0.04211.7090.0570.0570.0000.0000.0000.000
109A109ASN 0-0.0260.00615.4020.0210.0210.0000.0000.0000.000
110A110THR 0-0.057-0.08614.3200.0790.0790.0000.0000.0000.000
111A111PRO 00.0320.02313.893-0.087-0.0870.0000.0000.0000.000
112A112ARG 10.8570.95016.652-0.183-0.1830.0000.0000.0000.000
113A113ILE 0-0.008-0.01313.3840.0090.0090.0000.0000.0000.000
114A114ALA 00.020-0.02317.450-0.035-0.0350.0000.0000.0000.000
115A115ALA 00.0200.01419.3220.0150.0150.0000.0000.0000.000
116A116ALA 0-0.0130.00621.188-0.009-0.0090.0000.0000.0000.000
117A117ILE 00.0190.00423.1560.0060.0060.0000.0000.0000.000
118A118ASN 00.0580.07025.940-0.007-0.0070.0000.0000.0000.000
119A119GLY 00.0460.01028.701-0.007-0.0070.0000.0000.0000.000
120A120SER 0-0.056-0.03530.730-0.001-0.0010.0000.0000.0000.000
121A121GLU -1-0.924-0.97628.1690.0110.0110.0000.0000.0000.000
122A122ALA 00.0350.00723.478-0.010-0.0100.0000.0000.0000.000
123A123PHE 0-0.063-0.01423.6970.0140.0140.0000.0000.0000.000
124A124ILE 00.0510.02216.047-0.018-0.0180.0000.0000.0000.000
125A125GLY 0-0.029-0.01919.7500.0140.0140.0000.0000.0000.000
126A126ILE 0-0.0010.00014.489-0.008-0.0080.0000.0000.0000.000
127A127VAL 0-0.0270.00718.596-0.007-0.0070.0000.0000.0000.000
128A128THR 00.021-0.01016.0050.0090.0090.0000.0000.0000.000
129A129ALA 00.007-0.00218.768-0.036-0.0360.0000.0000.0000.000
130A130ASP -1-0.930-0.96117.8110.4590.4590.0000.0000.0000.000
131A131GLY 0-0.027-0.01320.636-0.021-0.0210.0000.0000.0000.000
132A132LEU 0-0.025-0.00421.3810.0050.0050.0000.0000.0000.000
133A133MET 0-0.0160.00118.680-0.004-0.0040.0000.0000.0000.000
134A134VAL 00.004-0.00220.889-0.006-0.0060.0000.0000.0000.000
135A135SER 0-0.016-0.01620.8650.0070.0070.0000.0000.0000.000
136A136ARG 10.8830.93322.756-0.035-0.0350.0000.0000.0000.000
137A137VAL 0-0.010-0.00119.8960.0110.0110.0000.0000.0000.000
138A138PRO 0-0.030-0.01019.517-0.002-0.0020.0000.0000.0000.000
139A139GLU -1-0.950-0.99322.058-0.053-0.0530.0000.0000.0000.000
140A140GLU -1-0.989-0.97720.662-0.022-0.0220.0000.0000.0000.000
141A141THR 0-0.012-0.01816.571-0.032-0.0320.0000.0000.0000.000
142A142PRO 0-0.049-0.01016.1150.0250.0250.0000.0000.0000.000
143A143VAL 00.0100.00214.4420.0060.0060.0000.0000.0000.000
144A144TYR 0-0.006-0.0076.574-0.101-0.1010.0000.0000.0000.000
145A145ILE 0-0.0040.00911.5740.0730.0730.0000.0000.0000.000
146A146SER 0-0.006-0.0227.912-0.197-0.1970.0000.0000.0000.000
147A147THR 0-0.0080.00110.5430.0300.0300.0000.0000.0000.000
148A148TYR 0-0.059-0.0547.432-0.005-0.0050.0000.0000.0000.000
149A149GLU -1-0.899-0.9473.7663.8494.1920.010-0.094-0.2600.000
150A150GLN 0-0.030-0.0057.053-0.210-0.2100.0000.0000.0000.000
151A151THR 0-0.013-0.0138.689-0.210-0.2100.0000.0000.0000.000
152A152GLU -1-0.912-0.96612.0290.3700.3700.0000.0000.0000.000
153A153PRO 0-0.046-0.01712.692-0.007-0.0070.0000.0000.0000.000
154A154ALA 00.0310.02610.7520.0400.0400.0000.0000.0000.000
155A155ALA 00.004-0.00412.696-0.076-0.0760.0000.0000.0000.000
156A156THR 0-0.013-0.01910.709-0.067-0.0670.0000.0000.0000.000
157A157GLU -1-0.912-0.94212.765-0.270-0.2700.0000.0000.0000.000
158A158PHE 0-0.012-0.01612.874-0.069-0.0690.0000.0000.0000.000
159A159LYS 10.8770.95915.3410.3800.3800.0000.0000.0000.000
160A160ALA 00.025-0.00217.329-0.034-0.0340.0000.0000.0000.000
161A161GLY 00.0000.00419.9890.0270.0270.0000.0000.0000.000
162A162SER 00.0130.01122.6400.0150.0150.0000.0000.0000.000
163A163PRO 00.0210.01822.031-0.028-0.0280.0000.0000.0000.000
164A164GLU -1-0.838-0.94920.809-0.254-0.2540.0000.0000.0000.000
165A165GLU -1-0.902-0.94919.675-0.335-0.3350.0000.0000.0000.000
166A166ALA 0-0.005-0.00517.584-0.062-0.0620.0000.0000.0000.000
167A167ALA 0-0.005-0.00816.100-0.058-0.0580.0000.0000.0000.000
168A168GLU -1-0.889-0.96815.181-0.654-0.6540.0000.0000.0000.000
169A169PHE 00.0420.01812.090-0.150-0.1500.0000.0000.0000.000
170A170ILE 0-0.0200.00311.282-0.146-0.1460.0000.0000.0000.000
171A171LEU 0-0.044-0.03110.327-0.182-0.1820.0000.0000.0000.000
172A172LYS 10.8060.8959.9680.4440.4440.0000.0000.0000.000
173A173GLY 0-0.0200.00110.256-0.097-0.0970.0000.0000.0000.000
174A174GLY 00.024-0.0029.354-0.166-0.1660.0000.0000.0000.000
175A175GLU -1-0.869-0.9475.694-1.139-1.1390.0000.0000.0000.000
176A176PHE 0-0.006-0.0144.585-1.141-1.0320.000-0.004-0.1050.000
177A177ALA 0-0.0100.0156.131-0.337-0.3370.0000.0000.0000.000
178A178ALA 0-0.046-0.0221.9782.092-2.2458.282-1.693-2.252-0.003
179A179PHE 00.0100.0252.208-6.669-3.9844.222-1.952-4.954-0.023
180A180THR 00.0340.0212.5391.6722.4160.605-0.100-1.2480.000
181A181HIS 0-0.059-0.0354.8600.5190.5920.000-0.009-0.0640.000
182A182PRO 00.0650.0357.8910.2420.2420.0000.0000.0000.000
183A183VAL 0-0.052-0.01710.4120.1050.1050.0000.0000.0000.000
184A184THR 00.0130.00213.9740.0220.0220.0000.0000.0000.000
185A185ALA 0-0.0030.00314.485-0.029-0.0290.0000.0000.0000.000
186A186ALA 00.0130.00116.4450.0410.0410.0000.0000.0000.000
187A187ALA 0-0.030-0.01518.187-0.024-0.0240.0000.0000.0000.000
188A188ALA 00.0190.01620.4490.0190.0190.0000.0000.0000.000
189A189PHE 0-0.005-0.01521.989-0.011-0.0110.0000.0000.0000.000
190A190ASN 00.0410.02224.6690.0100.0100.0000.0000.0000.000
191A191ASP -1-0.857-0.93627.502-0.126-0.1260.0000.0000.0000.000
192A192GLY 0-0.047-0.02929.0550.0050.0050.0000.0000.0000.000
193A193GLU -1-1.000-0.98531.762-0.080-0.0800.0000.0000.0000.000
194A194GLY 0-0.028-0.01731.9930.0060.0060.0000.0000.0000.000
195A195TRP 0-0.096-0.04524.523-0.015-0.0150.0000.0000.0000.000
196A196ASN 00.0150.01827.7500.0090.0090.0000.0000.0000.000
197A197LEU 0-0.019-0.01725.209-0.012-0.0120.0000.0000.0000.000
198A198ALA 00.0130.01022.7940.0010.0010.0000.0000.0000.000
199A199THR 0-0.024-0.01120.668-0.007-0.0070.0000.0000.0000.000
200A200ARG 10.8970.94917.6860.3740.3740.0000.0000.0000.000
201A201GLU -1-0.816-0.86317.958-0.301-0.3010.0000.0000.0000.000
202A202MET -1-0.869-0.92312.152-0.593-0.5930.0000.0000.0000.000