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: 2284R

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2278463.056302
FMO2-HF: Nuclear repulsion 2201588.547874
FMO2-HF: Total energy -76874.508429
FMO2-MP2: Total energy -77098.920498


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.
-1.2080.16713.092-4.395-10.072-0.021
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 : 0.037 / q_NPA : 0.016
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].
3A3LEU00.0750.0323.299-0.0891.7650.006-0.664-1.1960.003
4A4GLY0-0.0230.0025.861-0.003-0.0030.0000.0000.0000.000
5A5ARG10.8630.9249.143-0.520-0.5200.0000.0000.0000.000
6A6ILE00.0080.0107.4530.1080.1080.0000.0000.0000.000
7A7LEU0-0.023-0.00411.452-0.049-0.0490.0000.0000.0000.000
8A8ALA00.0380.01013.3850.0170.0170.0000.0000.0000.000
9A9VAL0-0.027-0.00915.2280.0060.0060.0000.0000.0000.000
10A10GLY00.0390.01918.2310.0090.0090.0000.0000.0000.000
11A11ARG10.8720.93220.3960.0450.0450.0000.0000.0000.000
12A12ASN0-0.0060.01719.214-0.004-0.0040.0000.0000.0000.000
13A13SER0-0.022-0.02122.5560.0100.0100.0000.0000.0000.000
14A14ASN0-0.055-0.03322.8900.0190.0190.0000.0000.0000.000
15A15GLY00.0910.05025.0510.0050.0050.0000.0000.0000.000
16A16SER0-0.0270.00723.656-0.001-0.0010.0000.0000.0000.000
17A17PHE0-0.028-0.02316.787-0.008-0.0080.0000.0000.0000.000
18A18VAL00.0180.00919.6950.0180.0180.0000.0000.0000.000
19A19ALA0-0.0070.00315.677-0.018-0.0180.0000.0000.0000.000
20A20TYR00.023-0.02115.4670.0340.0340.0000.0000.0000.000
21A21ARG10.8440.9006.6361.6321.6320.0000.0000.0000.000
22A22VAL0-0.0210.00612.7400.0720.0720.0000.0000.0000.000
23A23SER00.0460.0268.494-0.256-0.2560.0000.0000.0000.000
24A24SER0-0.088-0.05810.5540.2470.2470.0000.0000.0000.000
25A25ARG10.9690.9895.881-1.103-1.1030.0000.0000.0000.000
26A26SER00.018-0.00112.376-0.007-0.0070.0000.0000.0000.000
27A27PHE0-0.016-0.00315.762-0.001-0.0010.0000.0000.0000.000
28A28PRO00.031-0.00115.112-0.013-0.0130.0000.0000.0000.000
29A29ASN0-0.0020.02116.681-0.056-0.0560.0000.0000.0000.000
30A30ARG10.8490.91715.7730.0920.0920.0000.0000.0000.000
31A31THR0-0.003-0.03319.492-0.029-0.0290.0000.0000.0000.000
32A32THR0-0.014-0.01019.3260.0300.0300.0000.0000.0000.000
33A33SER0-0.029-0.00122.315-0.008-0.0080.0000.0000.0000.000
34A34ILE00.0400.00625.9220.0100.0100.0000.0000.0000.000
35A35GLN0-0.045-0.03227.1450.0130.0130.0000.0000.0000.000
36A36GLU-1-0.880-0.95430.225-0.067-0.0670.0000.0000.0000.000
37A37GLU-1-0.951-0.96430.264-0.042-0.0420.0000.0000.0000.000
38A38ARG10.8850.91727.7700.0580.0580.0000.0000.0000.000
39A39VAL0-0.0140.01322.622-0.009-0.0090.0000.0000.0000.000
40A40ALA0-0.0130.00024.3180.0110.0110.0000.0000.0000.000
41A41VAL0-0.0100.00719.258-0.025-0.0250.0000.0000.0000.000
42A42VAL0-0.015-0.02922.2820.0280.0280.0000.0000.0000.000
43A43PRO0-0.009-0.01523.062-0.020-0.0200.0000.0000.0000.000
44A44VAL00.0140.03122.017-0.002-0.0020.0000.0000.0000.000
45A45GLU-1-0.934-0.97124.910-0.103-0.1030.0000.0000.0000.000
46A46GLY00.0110.01228.051-0.004-0.0040.0000.0000.0000.000
47A47HIS0-0.016-0.01724.8300.0180.0180.0000.0000.0000.000
48A48GLU-1-0.869-0.93926.520-0.045-0.0450.0000.0000.0000.000
49A49ARG10.9200.94228.8010.0170.0170.0000.0000.0000.000
50A50ASP-1-0.900-0.95823.686-0.014-0.0140.0000.0000.0000.000
51A51VAL00.0230.00125.0300.0150.0150.0000.0000.0000.000
52A52PHE0-0.053-0.01526.3930.0100.0100.0000.0000.0000.000
53A53ARG10.8700.95824.303-0.027-0.0270.0000.0000.0000.000
54A54ASN00.014-0.00819.5220.0170.0170.0000.0000.0000.000
55A55PRO00.0340.01423.605-0.016-0.0160.0000.0000.0000.000
56A56TYR00.0470.03720.061-0.001-0.0010.0000.0000.0000.000
57A57ILE0-0.103-0.04118.832-0.011-0.0110.0000.0000.0000.000
58A58ALA00.0240.00820.838-0.028-0.0280.0000.0000.0000.000
59A59TYR0-0.0050.02017.7010.0060.0060.0000.0000.0000.000
60A60ASN00.0750.05423.561-0.033-0.0330.0000.0000.0000.000
61A61CYS0-0.061-0.00519.6460.0070.0070.0000.0000.0000.000
62A62ILE00.0540.01320.363-0.001-0.0010.0000.0000.0000.000
63A63ARG10.8120.91223.8300.0140.0140.0000.0000.0000.000
64A64ILE0-0.0210.00326.586-0.003-0.0030.0000.0000.0000.000
65A65VAL00.000-0.00329.4590.0040.0040.0000.0000.0000.000
66A66GLY00.0460.02232.4330.0040.0040.0000.0000.0000.000
67A67ASP-1-0.858-0.94232.725-0.031-0.0310.0000.0000.0000.000
68A68THR0-0.036-0.02728.3260.0000.0000.0000.0000.0000.000
69A69ALA0-0.0090.01724.761-0.002-0.0020.0000.0000.0000.000
70A70VAL0-0.027-0.02924.4010.0090.0090.0000.0000.0000.000
71A71VAL00.0160.00718.721-0.014-0.0140.0000.0000.0000.000
72A72SER0-0.031-0.06318.9530.0340.0340.0000.0000.0000.000
73A73ASN00.0430.01315.871-0.040-0.0400.0000.0000.0000.000
74A74GLY00.0380.01117.8750.0190.0190.0000.0000.0000.000
75A75SER00.014-0.00121.244-0.010-0.0100.0000.0000.0000.000
76A76HIS00.0080.02919.796-0.011-0.0110.0000.0000.0000.000
77A77THR00.0220.02722.8190.0020.0020.0000.0000.0000.000
78A78ASP-1-0.814-0.90124.874-0.009-0.0090.0000.0000.0000.000
79A79THR0-0.025-0.00627.761-0.004-0.0040.0000.0000.0000.000
80A80ILE0-0.006-0.00324.1390.0010.0010.0000.0000.0000.000
81A81ALA0-0.0040.00228.206-0.004-0.0040.0000.0000.0000.000
82A82ASP-1-0.840-0.92929.6940.0080.0080.0000.0000.0000.000
83A83LYS10.8980.94431.528-0.045-0.0450.0000.0000.0000.000
84A84VAL00.0130.02129.7600.0000.0000.0000.0000.0000.000
85A85ALA0-0.0110.00032.896-0.003-0.0030.0000.0000.0000.000
86A86LEU0-0.085-0.04835.4810.0000.0000.0000.0000.0000.000
87A87GLY00.0000.00836.3480.0010.0010.0000.0000.0000.000
88A88MET0-0.106-0.02732.7910.0040.0040.0000.0000.0000.000
89A89ASN0-0.009-0.02632.2140.0000.0000.0000.0000.0000.000
90A90LEU00.0800.01927.3040.0070.0070.0000.0000.0000.000
91A91ARG10.9150.97827.354-0.074-0.0740.0000.0000.0000.000
92A92ASP-1-0.796-0.89727.9350.0810.0810.0000.0000.0000.000
93A93ALA0-0.0070.00729.1090.0060.0060.0000.0000.0000.000
94A94ILE00.0230.01822.9870.0050.0050.0000.0000.0000.000
95A95GLY00.0040.00025.7700.0150.0150.0000.0000.0000.000
96A96LEU0-0.017-0.01627.1210.0100.0100.0000.0000.0000.000
97A97SER0-0.027-0.03626.5000.0010.0010.0000.0000.0000.000
98A98LEU0-0.026-0.00621.1670.0040.0040.0000.0000.0000.000
99A99LEU0-0.0050.00824.8190.0140.0140.0000.0000.0000.000
100A100ALA0-0.043-0.01727.2640.0040.0040.0000.0000.0000.000
101A101MET0-0.091-0.04025.017-0.005-0.0050.0000.0000.0000.000
102A102ASP-1-0.848-0.92824.0410.2330.2330.0000.0000.0000.000
103A103TYR0-0.057-0.01919.272-0.006-0.0060.0000.0000.0000.000
104A104GLU-1-0.947-0.98318.5600.1650.1650.0000.0000.0000.000
105A105LYS10.8580.92020.145-0.183-0.1830.0000.0000.0000.000
106A106ASP-1-0.791-0.83117.0990.3620.3620.0000.0000.0000.000
107A107GLU-1-0.969-0.99616.9280.3520.3520.0000.0000.0000.000
108A108LEU0-0.078-0.04411.7090.0500.0500.0000.0000.0000.000
109A109ASN0-0.0220.00815.4020.0260.0260.0000.0000.0000.000
110A110THR0-0.060-0.08814.3230.0800.0800.0000.0000.0000.000
111A111PRO00.0340.02513.893-0.083-0.0830.0000.0000.0000.000
112A112ARG10.8580.95016.652-0.184-0.1840.0000.0000.0000.000
113A113ILE0-0.010-0.01413.3840.0110.0110.0000.0000.0000.000
114A114ALA00.018-0.02417.449-0.037-0.0370.0000.0000.0000.000
115A115ALA00.0200.01419.3210.0180.0180.0000.0000.0000.000
116A116ALA0-0.0150.00521.187-0.010-0.0100.0000.0000.0000.000
117A117ILE00.0230.00623.1560.0080.0080.0000.0000.0000.000
118A118ASN00.0520.06925.940-0.008-0.0080.0000.0000.0000.000
119A119GLY00.0470.01028.701-0.006-0.0060.0000.0000.0000.000
120A120SER0-0.052-0.03430.730-0.001-0.0010.0000.0000.0000.000
121A121GLU-1-0.922-0.97528.1690.0250.0250.0000.0000.0000.000
122A122ALA00.0370.00723.478-0.010-0.0100.0000.0000.0000.000
123A123PHE0-0.068-0.01523.6970.0130.0130.0000.0000.0000.000
124A124ILE00.0520.02216.046-0.019-0.0190.0000.0000.0000.000
125A125GLY0-0.033-0.02019.7490.0120.0120.0000.0000.0000.000
126A126ILE00.0030.00214.488-0.008-0.0080.0000.0000.0000.000
127A127VAL0-0.0300.00618.595-0.008-0.0080.0000.0000.0000.000
128A128THR00.021-0.01016.1620.0050.0050.0000.0000.0000.000
129A129ALA00.007-0.00218.819-0.037-0.0370.0000.0000.0000.000
130A130ASP-1-0.927-0.96117.9490.4670.4670.0000.0000.0000.000
131A131GLY0-0.024-0.01220.782-0.019-0.0190.0000.0000.0000.000
132A132LEU0-0.030-0.00521.4760.0050.0050.0000.0000.0000.000
133A133MET0-0.0160.00118.686-0.002-0.0020.0000.0000.0000.000
134A134VAL00.008-0.00120.888-0.004-0.0040.0000.0000.0000.000
135A135SER0-0.014-0.01520.8640.0080.0080.0000.0000.0000.000
136A136ARG10.8820.93422.755-0.050-0.0500.0000.0000.0000.000
137A137VAL0-0.011-0.00219.8960.0130.0130.0000.0000.0000.000
138A138PRO0-0.029-0.00919.517-0.005-0.0050.0000.0000.0000.000
139A139GLU-1-0.950-0.99422.058-0.034-0.0340.0000.0000.0000.000
140A140GLU-1-0.983-0.97520.6630.0060.0060.0000.0000.0000.000
141A141THR0-0.013-0.01816.571-0.030-0.0300.0000.0000.0000.000
142A142PRO0-0.052-0.01116.1150.0250.0250.0000.0000.0000.000
143A143VAL00.0090.00214.4430.0090.0090.0000.0000.0000.000
144A144TYR0-0.011-0.0096.570-0.110-0.1100.0000.0000.0000.000
145A145ILE0-0.0010.01011.5730.0720.0720.0000.0000.0000.000
146A146SER0-0.006-0.0237.908-0.196-0.1960.0000.0000.0000.000
147A147THR00.0020.00410.5420.0220.0220.0000.0000.0000.000
148A148TYR0-0.064-0.0567.432-0.040-0.0400.0000.0000.0000.000
149A149GLU-1-0.899-0.9473.9144.0644.4170.009-0.102-0.2610.001
150A150GLN0-0.028-0.0057.193-0.192-0.1920.0000.0000.0000.000
151A151THR0-0.014-0.0158.688-0.225-0.2250.0000.0000.0000.000
152A152GLU-1-0.910-0.96312.0280.4120.4120.0000.0000.0000.000
153A153PRO0-0.043-0.01712.6910.0070.0070.0000.0000.0000.000
154A154ALA00.0320.02710.7520.0400.0400.0000.0000.0000.000
155A155ALA00.005-0.00312.696-0.075-0.0750.0000.0000.0000.000
156A156THR0-0.016-0.02110.709-0.054-0.0540.0000.0000.0000.000
157A157GLU-1-0.911-0.94112.765-0.238-0.2380.0000.0000.0000.000
158A158PHE0-0.015-0.01812.874-0.067-0.0670.0000.0000.0000.000
159A159LYS10.8810.96015.3410.3390.3390.0000.0000.0000.000
160A160ALA00.027-0.00317.329-0.034-0.0340.0000.0000.0000.000
161A161GLY00.0000.00519.9890.0250.0250.0000.0000.0000.000
162A162SER00.0180.01522.6400.0130.0130.0000.0000.0000.000
163A163PRO00.0180.01922.031-0.026-0.0260.0000.0000.0000.000
164A164GLU-1-0.843-0.95120.809-0.237-0.2370.0000.0000.0000.000
165A165GLU-1-0.900-0.95019.675-0.311-0.3110.0000.0000.0000.000
166A166ALA0-0.001-0.00117.584-0.058-0.0580.0000.0000.0000.000
167A167ALA0-0.005-0.00716.100-0.053-0.0530.0000.0000.0000.000
168A168GLU-1-0.897-0.97215.181-0.624-0.6240.0000.0000.0000.000
169A169PHE00.0510.02112.089-0.141-0.1410.0000.0000.0000.000
170A170ILE0-0.0180.00811.282-0.136-0.1360.0000.0000.0000.000
171A171LEU0-0.049-0.03610.327-0.166-0.1660.0000.0000.0000.000
172A172LYS10.8040.8919.9670.4470.4470.0000.0000.0000.000
173A173GLY0-0.0120.00810.256-0.091-0.0910.0000.0000.0000.000
174A174GLY00.0300.0029.354-0.150-0.1500.0000.0000.0000.000
175A175GLU-1-0.862-0.9425.694-1.031-1.0310.0000.0000.0000.000
176A176PHE00.001-0.0104.585-1.065-0.954-0.001-0.003-0.1060.000
177A177ALA0-0.0240.0066.131-0.315-0.3150.0000.0000.0000.000
178A178ALA0-0.043-0.0191.9782.150-2.1898.259-1.659-2.262-0.003
179A179PHE00.0160.0302.209-6.289-3.7124.217-1.867-4.927-0.022
180A180THR00.0360.0212.5391.4542.1960.603-0.092-1.2530.000
181A181HIS0-0.052-0.0314.8600.4140.491-0.001-0.008-0.0670.000
182A182PRO00.0560.0297.8910.2410.2410.0000.0000.0000.000
183A183VAL0-0.049-0.01510.4120.0880.0880.0000.0000.0000.000
184A184THR0-0.008-0.01013.9740.0220.0220.0000.0000.0000.000
185A185ALA0-0.0010.00214.485-0.028-0.0280.0000.0000.0000.000
186A186ALA00.0160.00416.4450.0340.0340.0000.0000.0000.000
187A187ALA0-0.037-0.01718.187-0.021-0.0210.0000.0000.0000.000
188A188ALA00.0260.02120.4490.0150.0150.0000.0000.0000.000
189A189PHE0-0.008-0.01721.990-0.009-0.0090.0000.0000.0000.000
190A190ASN00.0480.02524.6690.0070.0070.0000.0000.0000.000
191A191ASP-1-0.859-0.93827.502-0.112-0.1120.0000.0000.0000.000
192A192GLY0-0.043-0.02729.0550.0050.0050.0000.0000.0000.000
193A193GLU-1-0.998-0.98331.762-0.071-0.0710.0000.0000.0000.000
194A194GLY0-0.027-0.01631.9930.0050.0050.0000.0000.0000.000
195A195TRP0-0.094-0.04524.524-0.014-0.0140.0000.0000.0000.000
196A196ASN00.0160.01927.7500.0070.0070.0000.0000.0000.000
197A197LEU0-0.023-0.01825.209-0.011-0.0110.0000.0000.0000.000
198A198ALA00.0190.01322.7940.0000.0000.0000.0000.0000.000
199A199THR0-0.023-0.00720.667-0.006-0.0060.0000.0000.0000.000
200A200ARG10.9100.95617.6860.3530.3530.0000.0000.0000.000
201A201GLU-1-0.786-0.84217.958-0.304-0.3040.0000.0000.0000.000
202A202MET00.0170.01512.143-0.026-0.0260.0000.0000.0000.000