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: 668ZZ

Calculation Name: 1KUU-A-Xray372

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: 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2279819.60138
FMO2-HF: Nuclear repulsion 2202944.153564
FMO2-HF: Total energy -76875.447816
FMO2-MP2: Total energy -77099.797853


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.
-9.501-3.1654.544-3.327-7.554-0.018
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 : 0.034 / q_NPA : 0.008
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].
3A3LEU00.0820.0423.780-1.0210.729-0.009-0.622-1.1190.002
4A4GLY0-0.030-0.0015.8800.4420.4420.0000.0000.0000.000
5A5ARG10.8450.9269.143-0.011-0.0110.0000.0000.0000.000
6A6ILE00.0090.0107.541-0.017-0.0170.0000.0000.0000.000
7A7LEU0-0.023-0.00511.4780.0630.0630.0000.0000.0000.000
8A8ALA00.0360.01013.637-0.038-0.0380.0000.0000.0000.000
9A9VAL0-0.028-0.00815.5310.0420.0420.0000.0000.0000.000
10A10GLY00.0550.02318.445-0.007-0.0070.0000.0000.0000.000
11A11ARG10.8580.91920.6290.1850.1850.0000.0000.0000.000
12A12ASN00.0000.00919.685-0.017-0.0170.0000.0000.0000.000
13A13SER0-0.020-0.01222.8270.0120.0120.0000.0000.0000.000
14A14ASN0-0.041-0.04323.4990.0290.0290.0000.0000.0000.000
15A15GLY00.0960.05325.3470.0100.0100.0000.0000.0000.000
16A16SER0-0.0320.00623.943-0.008-0.0080.0000.0000.0000.000
17A17PHE0-0.025-0.01916.9820.0020.0020.0000.0000.0000.000
18A18VAL00.0190.00820.0010.0020.0020.0000.0000.0000.000
19A19ALA0-0.0130.00116.0350.0030.0030.0000.0000.0000.000
20A20TYR00.022-0.01615.744-0.025-0.0250.0000.0000.0000.000
21A21ARG10.8550.9126.8261.8221.8220.0000.0000.0000.000
22A22VAL0-0.0080.00812.771-0.015-0.0150.0000.0000.0000.000
23A23SER00.0560.0248.634-0.146-0.1460.0000.0000.0000.000
24A24SER0-0.089-0.05310.6350.1630.1630.0000.0000.0000.000
25A25ARG10.9550.9815.874-1.868-1.8680.0000.0000.0000.000
26A26SER00.0120.00112.3490.0090.0090.0000.0000.0000.000
27A27PHE00.0010.01015.7950.0030.0030.0000.0000.0000.000
28A28PRO00.0330.00315.110-0.044-0.0440.0000.0000.0000.000
29A29ASN0-0.0270.00416.811-0.042-0.0420.0000.0000.0000.000
30A30ARG10.8520.91816.0730.1990.1990.0000.0000.0000.000
31A31THR0-0.011-0.02419.652-0.019-0.0190.0000.0000.0000.000
32A32THR0-0.010-0.01419.7770.0150.0150.0000.0000.0000.000
33A33SER0-0.0040.01022.4400.0040.0040.0000.0000.0000.000
34A34ILE0-0.006-0.00926.2120.0010.0010.0000.0000.0000.000
35A35GLN0-0.064-0.03927.5760.0140.0140.0000.0000.0000.000
36A36GLU-1-0.843-0.92730.627-0.126-0.1260.0000.0000.0000.000
37A37GLU-1-0.940-0.95830.597-0.121-0.1210.0000.0000.0000.000
38A38ARG10.8430.89427.9930.1310.1310.0000.0000.0000.000
39A39VAL00.0020.01023.1700.0000.0000.0000.0000.0000.000
40A40ALA0-0.0130.00424.349-0.004-0.0040.0000.0000.0000.000
41A41VAL0-0.0010.00719.205-0.017-0.0170.0000.0000.0000.000
42A42VAL0-0.010-0.02522.3200.0250.0250.0000.0000.0000.000
43A43PRO0-0.003-0.00923.221-0.016-0.0160.0000.0000.0000.000
44A44VAL00.0050.02222.259-0.003-0.0030.0000.0000.0000.000
45A45GLU-1-0.932-0.96825.082-0.090-0.0900.0000.0000.0000.000
46A46GLY0-0.015-0.01128.2310.0030.0030.0000.0000.0000.000
47A47HIS0-0.027-0.02324.8500.0190.0190.0000.0000.0000.000
48A48GLU-1-0.815-0.90826.540-0.066-0.0660.0000.0000.0000.000
49A49ARG10.9230.94528.8310.0200.0200.0000.0000.0000.000
50A50ASP-1-0.806-0.89723.649-0.009-0.0090.0000.0000.0000.000
51A51VAL00.010-0.00325.0020.0070.0070.0000.0000.0000.000
52A52PHE0-0.053-0.02026.3930.0030.0030.0000.0000.0000.000
53A53ARG10.7740.89024.114-0.001-0.0010.0000.0000.0000.000
54A54ASN00.0250.00818.9930.0000.0000.0000.0000.0000.000
55A55PRO00.0250.01023.340-0.015-0.0150.0000.0000.0000.000
56A56TYR00.0220.02219.769-0.010-0.0100.0000.0000.0000.000
57A57ILE0-0.076-0.02819.136-0.029-0.0290.0000.0000.0000.000
58A58ALA00.0140.00820.838-0.023-0.0230.0000.0000.0000.000
59A59TYR00.0020.02217.540-0.006-0.0060.0000.0000.0000.000
60A60ASN00.0300.01523.590-0.020-0.0200.0000.0000.0000.000
61A61CYS0-0.062-0.00319.695-0.003-0.0030.0000.0000.0000.000
62A62ILE00.0480.01120.660-0.018-0.0180.0000.0000.0000.000
63A63ARG10.7790.87823.8700.1320.1320.0000.0000.0000.000
64A64ILE0-0.022-0.00426.615-0.012-0.0120.0000.0000.0000.000
65A65VAL00.001-0.00129.7050.0110.0110.0000.0000.0000.000
66A66GLY00.0460.02732.5050.0010.0010.0000.0000.0000.000
67A67ASP-1-0.812-0.91933.076-0.129-0.1290.0000.0000.0000.000
68A68THR0-0.039-0.02728.563-0.008-0.0080.0000.0000.0000.000
69A69ALA0-0.0200.01925.3160.0020.0020.0000.0000.0000.000
70A70VAL0-0.013-0.02624.470-0.003-0.0030.0000.0000.0000.000
71A71VAL00.0190.01018.694-0.006-0.0060.0000.0000.0000.000
72A72SER0-0.018-0.04818.9920.0130.0130.0000.0000.0000.000
73A73ASN00.0300.01915.922-0.014-0.0140.0000.0000.0000.000
74A74GLY00.0340.00617.8990.0210.0210.0000.0000.0000.000
75A75SER00.0410.01521.248-0.006-0.0060.0000.0000.0000.000
76A76HIS0-0.0160.00419.8810.0270.0270.0000.0000.0000.000
77A77THR00.0150.00822.947-0.004-0.0040.0000.0000.0000.000
78A78ASP-1-0.794-0.87324.897-0.121-0.1210.0000.0000.0000.000
79A79THR0-0.028-0.00427.8050.0040.0040.0000.0000.0000.000
80A80ILE0-0.008-0.00324.1400.0060.0060.0000.0000.0000.000
81A81ALA00.0060.00528.2270.0030.0030.0000.0000.0000.000
82A82ASP-1-0.805-0.90329.716-0.085-0.0850.0000.0000.0000.000
83A83LYS10.9100.95331.5560.0640.0640.0000.0000.0000.000
84A84VAL00.0100.01729.7240.0040.0040.0000.0000.0000.000
85A85ALA0-0.0150.00132.9150.0030.0030.0000.0000.0000.000
86A86LEU0-0.082-0.04635.5030.0060.0060.0000.0000.0000.000
87A87GLY00.0000.00836.3590.0060.0060.0000.0000.0000.000
88A88MET0-0.107-0.03232.7520.0020.0020.0000.0000.0000.000
89A89ASN0-0.002-0.01731.985-0.011-0.0110.0000.0000.0000.000
90A90LEU00.0890.02627.5240.0020.0020.0000.0000.0000.000
91A91ARG10.8740.93427.3610.0630.0630.0000.0000.0000.000
92A92ASP-1-0.776-0.87327.946-0.058-0.0580.0000.0000.0000.000
93A93ALA0-0.0050.01329.1990.0050.0050.0000.0000.0000.000
94A94ILE00.0250.01223.0140.0020.0020.0000.0000.0000.000
95A95GLY00.0080.00325.6810.0050.0050.0000.0000.0000.000
96A96LEU0-0.023-0.01926.9770.0080.0080.0000.0000.0000.000
97A97SER0-0.019-0.02526.4620.0080.0080.0000.0000.0000.000
98A98LEU0-0.021-0.00620.9410.0060.0060.0000.0000.0000.000
99A99LEU0-0.0040.00824.4360.0110.0110.0000.0000.0000.000
100A100ALA0-0.056-0.02326.6540.0090.0090.0000.0000.0000.000
101A101MET0-0.080-0.03824.6470.0020.0020.0000.0000.0000.000
102A102ASP-1-0.817-0.89522.9300.0260.0260.0000.0000.0000.000
103A103TYR0-0.024-0.01518.387-0.009-0.0090.0000.0000.0000.000
104A104GLU-1-0.880-0.94518.182-0.073-0.0730.0000.0000.0000.000
105A105LYS10.8140.89819.342-0.008-0.0080.0000.0000.0000.000
106A106ASP-1-0.830-0.89516.2770.0860.0860.0000.0000.0000.000
107A107GLU-1-0.962-0.98716.5310.2390.2390.0000.0000.0000.000
108A108LEU0-0.071-0.03811.2530.0490.0490.0000.0000.0000.000
109A109ASN0-0.0380.00314.572-0.018-0.0180.0000.0000.0000.000
110A110THR0-0.028-0.04013.649-0.011-0.0110.0000.0000.0000.000
111A111PRO00.0410.02813.024-0.021-0.0210.0000.0000.0000.000
112A112ARG10.8050.92215.8880.0390.0390.0000.0000.0000.000
113A113ILE0-0.011-0.01413.2700.0120.0120.0000.0000.0000.000
114A114ALA00.010-0.01917.4590.0000.0000.0000.0000.0000.000
115A115ALA00.0190.01519.295-0.004-0.0040.0000.0000.0000.000
116A116ALA0-0.0140.00321.2050.0040.0040.0000.0000.0000.000
117A117ILE00.0060.00023.2280.0010.0010.0000.0000.0000.000
118A118ASN00.0260.02226.193-0.003-0.0030.0000.0000.0000.000
119A119GLY00.0330.02328.953-0.009-0.0090.0000.0000.0000.000
120A120SER0-0.001-0.00330.953-0.001-0.0010.0000.0000.0000.000
121A121GLU-1-0.918-0.93328.321-0.103-0.1030.0000.0000.0000.000
122A122ALA00.0580.01823.501-0.007-0.0070.0000.0000.0000.000
123A123PHE0-0.049-0.01323.7250.0130.0130.0000.0000.0000.000
124A124ILE00.0520.02216.099-0.015-0.0150.0000.0000.0000.000
125A125GLY0-0.030-0.02019.7650.0260.0260.0000.0000.0000.000
126A126ILE0-0.0010.00313.997-0.031-0.0310.0000.0000.0000.000
127A127VAL0-0.039-0.00118.3230.0180.0180.0000.0000.0000.000
128A128THR0-0.010-0.03015.193-0.014-0.0140.0000.0000.0000.000
129A129ALA00.0210.00517.829-0.003-0.0030.0000.0000.0000.000
130A130ASP-1-0.908-0.95016.7990.1350.1350.0000.0000.0000.000
131A131GLY0-0.018-0.00419.886-0.001-0.0010.0000.0000.0000.000
132A132LEU0-0.028-0.00520.578-0.010-0.0100.0000.0000.0000.000
133A133MET0-0.0220.00218.7980.0080.0080.0000.0000.0000.000
134A134VAL00.010-0.00220.737-0.020-0.0200.0000.0000.0000.000
135A135SER0-0.010-0.01120.8620.0150.0150.0000.0000.0000.000
136A136ARG10.8160.87222.7630.0950.0950.0000.0000.0000.000
137A137VAL0-0.022-0.00819.917-0.002-0.0020.0000.0000.0000.000
138A138PRO0-0.016-0.00519.6560.0150.0150.0000.0000.0000.000
139A139GLU-1-0.966-0.99422.131-0.149-0.1490.0000.0000.0000.000
140A140GLU-1-0.986-0.98120.732-0.163-0.1630.0000.0000.0000.000
141A141THR0-0.006-0.01316.641-0.021-0.0210.0000.0000.0000.000
142A142PRO0-0.042-0.00516.3030.0120.0120.0000.0000.0000.000
143A143VAL0-0.005-0.00614.554-0.006-0.0060.0000.0000.0000.000
144A144TYR0-0.005-0.0077.208-0.103-0.1030.0000.0000.0000.000
145A145ILE00.0020.01011.5750.0540.0540.0000.0000.0000.000
146A146SER0-0.008-0.0277.909-0.089-0.0890.0000.0000.0000.000
147A147THR0-0.0080.00510.2160.0750.0750.0000.0000.0000.000
148A148TYR0-0.033-0.0406.6110.1650.1650.0000.0000.0000.000
149A149GLU-1-0.889-0.9472.918-0.2660.2810.043-0.174-0.415-0.002
150A150GLN0-0.037-0.0086.3650.2260.2260.0000.0000.0000.000
151A151THR0-0.010-0.0128.641-0.054-0.0540.0000.0000.0000.000
152A152GLU-1-0.911-0.95811.6710.0600.0600.0000.0000.0000.000
153A153PRO0-0.030-0.01012.692-0.066-0.0660.0000.0000.0000.000
154A154ALA00.0160.02110.6750.0490.0490.0000.0000.0000.000
155A155ALA00.010-0.00212.630-0.055-0.0550.0000.0000.0000.000
156A156THR0-0.015-0.02511.071-0.137-0.1370.0000.0000.0000.000
157A157GLU-1-0.864-0.91912.894-0.328-0.3280.0000.0000.0000.000
158A158PHE0-0.024-0.01513.468-0.053-0.0530.0000.0000.0000.000
159A159LYS10.8280.93215.6550.4660.4660.0000.0000.0000.000
160A160ALA00.022-0.00117.759-0.033-0.0330.0000.0000.0000.000
161A161GLY0-0.021-0.00720.4180.0200.0200.0000.0000.0000.000
162A162SER00.004-0.01623.1020.0190.0190.0000.0000.0000.000
163A163PRO00.0240.01722.379-0.033-0.0330.0000.0000.0000.000
164A164GLU-1-0.865-0.95421.164-0.301-0.3010.0000.0000.0000.000
165A165GLU-1-0.854-0.89320.006-0.364-0.3640.0000.0000.0000.000
166A166ALA0-0.010-0.00617.960-0.063-0.0630.0000.0000.0000.000
167A167ALA00.006-0.00216.431-0.072-0.0720.0000.0000.0000.000
168A168GLU-1-0.789-0.87915.571-0.610-0.6100.0000.0000.0000.000
169A169PHE00.0280.01112.032-0.110-0.1100.0000.0000.0000.000
170A170ILE0-0.0260.00311.572-0.136-0.1360.0000.0000.0000.000
171A171LEU0-0.059-0.03310.715-0.189-0.1890.0000.0000.0000.000
172A172LYS10.7650.84310.3530.4340.4340.0000.0000.0000.000
173A173GLY0-0.0130.01010.551-0.064-0.0640.0000.0000.0000.000
174A174GLY00.0270.0019.851-0.164-0.1640.0000.0000.0000.000
175A175GLU-1-0.866-0.9455.895-1.245-1.2450.0000.0000.0000.000
176A176PHE00.006-0.0055.038-0.991-0.911-0.0010.000-0.0790.000
177A177ALA0-0.0360.0026.517-0.246-0.2460.0000.0000.0000.000
178A178ALA0-0.049-0.0272.1690.143-0.5032.594-0.606-1.343-0.001
179A179PHE00.0190.0312.444-6.174-2.5341.509-1.653-3.496-0.017
180A180THR00.0310.0052.7131.2782.1830.409-0.266-1.0490.000
181A181HIS0-0.033-0.0225.0280.0740.134-0.001-0.006-0.0530.000
182A182PRO00.0800.0428.3210.0940.0940.0000.0000.0000.000
183A183VAL0-0.070-0.02710.5560.1310.1310.0000.0000.0000.000
184A184THR0-0.003-0.01014.1290.0320.0320.0000.0000.0000.000
185A185ALA0-0.011-0.00314.902-0.069-0.0690.0000.0000.0000.000
186A186ALA00.0200.00616.8820.0570.0570.0000.0000.0000.000
187A187ALA0-0.035-0.01618.564-0.047-0.0470.0000.0000.0000.000
188A188ALA00.0230.01520.8070.0310.0310.0000.0000.0000.000
189A189PHE0-0.018-0.01921.992-0.021-0.0210.0000.0000.0000.000
190A190ASN00.0410.00925.0290.0210.0210.0000.0000.0000.000
191A191ASP-1-0.860-0.93427.870-0.184-0.1840.0000.0000.0000.000
192A192GLY0-0.035-0.01529.4470.0080.0080.0000.0000.0000.000
193A193GLU-1-1.000-0.99132.120-0.116-0.1160.0000.0000.0000.000
194A194GLY0-0.020-0.00732.3970.0070.0070.0000.0000.0000.000
195A195TRP0-0.101-0.05124.886-0.019-0.0190.0000.0000.0000.000
196A196ASN00.0160.02328.0590.0150.0150.0000.0000.0000.000
197A197LEU0-0.016-0.01625.340-0.020-0.0200.0000.0000.0000.000
198A198ALA00.0190.00923.2310.0100.0100.0000.0000.0000.000
199A199THR0-0.018-0.00921.085-0.017-0.0170.0000.0000.0000.000
200A200ARG10.8710.91818.0630.3810.3810.0000.0000.0000.000
201A201GLU-1-0.764-0.84018.350-0.345-0.3450.0000.0000.0000.000
202A202MET00.0080.01711.7970.0000.0000.0000.0000.0000.000