FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 7286K

Calculation Name: 4KMS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KMS

Chain ID: A

ChEMBL ID:

UniProt ID: Q4UN54

Base Structure: X-ray

Registration Date: 2023-09-20

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 242
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2961958.339832
FMO2-HF: Nuclear repulsion 2867800.716604
FMO2-HF: Total energy -94157.623228
FMO2-MP2: Total energy -94427.474177


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:-2:HIS)


Summations of interaction energy for fragment #1(A:-2:HIS)
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.
-9.613-3.8682.207-2.943-5.009-0.005
Interaction energy analysis for fragmet #1(A:-2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / 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].
3A0HIS00.0440.0303.104-3.4700.2801.407-2.141-3.016-0.001
4A1MET0-0.013-0.0152.624-4.935-3.3740.784-0.652-1.694-0.005
5A2SER00.0280.0365.4070.3740.3740.0000.0000.0000.000
6A3GLU-1-0.787-0.8678.917-1.657-1.6570.0000.0000.0000.000
7A4ILE00.0160.00610.0140.1270.1270.0000.0000.0000.000
8A5ALA00.009-0.00513.4500.0110.0110.0000.0000.0000.000
9A6ILE00.0070.02017.1340.0550.0550.0000.0000.0000.000
10A7VAL0-0.004-0.00319.883-0.004-0.0040.0000.0000.0000.000
11A8THR00.0390.01622.8830.0280.0280.0000.0000.0000.000
12A9GLY00.0340.03025.898-0.001-0.0010.0000.0000.0000.000
13A10GLY00.013-0.00724.7150.0000.0000.0000.0000.0000.000
14A11THR00.0420.01225.387-0.003-0.0030.0000.0000.0000.000
15A12ARG10.8030.89527.2770.1380.1380.0000.0000.0000.000
16A13GLY00.0190.00230.164-0.011-0.0110.0000.0000.0000.000
17A14ILE00.0350.00229.802-0.008-0.0080.0000.0000.0000.000
18A15GLY00.0180.02527.263-0.018-0.0180.0000.0000.0000.000
19A16LYS10.8540.94025.6790.0630.0630.0000.0000.0000.000
20A17ALA00.0340.01125.440-0.010-0.0100.0000.0000.0000.000
21A18THR0-0.027-0.03623.587-0.020-0.0200.0000.0000.0000.000
22A19ALA00.0170.01121.529-0.033-0.0330.0000.0000.0000.000
23A20LEU0-0.030-0.01720.632-0.023-0.0230.0000.0000.0000.000
24A21GLU-1-0.819-0.90921.414-0.327-0.3270.0000.0000.0000.000
25A22LEU0-0.014-0.01818.622-0.031-0.0310.0000.0000.0000.000
26A23LYS10.9220.96216.4110.1130.1130.0000.0000.0000.000
27A24ASN0-0.097-0.04816.714-0.039-0.0390.0000.0000.0000.000
28A25LYS10.8060.90918.0460.3610.3610.0000.0000.0000.000
29A26GLY00.0170.01914.085-0.070-0.0700.0000.0000.0000.000
30A27LEU0-0.037-0.00912.453-0.137-0.1370.0000.0000.0000.000
31A28THR0-0.009-0.0259.9100.1240.1240.0000.0000.0000.000
32A29VAL0-0.052-0.02413.066-0.020-0.0200.0000.0000.0000.000
33A30VAL00.0000.00215.7440.0580.0580.0000.0000.0000.000
34A31ALA0-0.014-0.01018.307-0.016-0.0160.0000.0000.0000.000
35A32ASN00.0290.00021.9460.0250.0250.0000.0000.0000.000
36A33PHE0-0.061-0.03623.663-0.002-0.0020.0000.0000.0000.000
37A34PHE00.0120.01226.7140.0050.0050.0000.0000.0000.000
38A35SER00.0680.01229.5440.0060.0060.0000.0000.0000.000
39A36ASN0-0.0110.00131.1990.0160.0160.0000.0000.0000.000
40A37TYR00.1350.04125.553-0.007-0.0070.0000.0000.0000.000
41A38ASP-1-0.888-0.92128.2740.0220.0220.0000.0000.0000.000
42A39ALA0-0.055-0.03829.8150.0000.0000.0000.0000.0000.000
43A40ALA00.0060.00725.027-0.009-0.0090.0000.0000.0000.000
44A41LYS10.8670.91425.216-0.048-0.0480.0000.0000.0000.000
45A42GLU-1-0.798-0.88625.994-0.041-0.0410.0000.0000.0000.000
46A43MET0-0.047-0.01522.786-0.010-0.0100.0000.0000.0000.000
47A44GLU-1-0.825-0.89620.6410.0220.0220.0000.0000.0000.000
48A45GLU-1-0.854-0.91521.8120.0620.0620.0000.0000.0000.000
49A46LYS10.7930.89524.0790.0340.0340.0000.0000.0000.000
50A47TYR0-0.010-0.01122.017-0.006-0.0060.0000.0000.0000.000
51A48GLY00.0120.03218.595-0.027-0.0270.0000.0000.0000.000
52A49ILE0-0.062-0.02817.277-0.022-0.0220.0000.0000.0000.000
53A50LYS10.8550.91613.8050.0050.0050.0000.0000.0000.000
54A51THR0-0.059-0.04818.346-0.047-0.0470.0000.0000.0000.000
55A52LYS10.8370.90817.6620.0970.0970.0000.0000.0000.000
56A53CYS0-0.100-0.02521.136-0.023-0.0230.0000.0000.0000.000
57A54TRP00.0730.01120.6320.0000.0000.0000.0000.0000.000
58A55ASN00.0230.00725.612-0.016-0.0160.0000.0000.0000.000
59A56VAL00.008-0.00726.176-0.004-0.0040.0000.0000.0000.000
60A57ALA0-0.034-0.02528.343-0.010-0.0100.0000.0000.0000.000
61A58ASP-1-0.871-0.92529.022-0.066-0.0660.0000.0000.0000.000
62A59PHE0-0.0030.00027.237-0.014-0.0140.0000.0000.0000.000
63A60GLU-1-0.828-0.93625.805-0.109-0.1090.0000.0000.0000.000
64A61GLU-1-0.859-0.93024.387-0.063-0.0630.0000.0000.0000.000
65A62CYS0-0.099-0.03623.233-0.011-0.0110.0000.0000.0000.000
66A63ARG10.9190.96321.5850.1630.1630.0000.0000.0000.000
67A64GLN0-0.012-0.01619.068-0.032-0.0320.0000.0000.0000.000
68A65ALA0-0.002-0.00718.644-0.001-0.0010.0000.0000.0000.000
69A66VAL00.016-0.00316.973-0.019-0.0190.0000.0000.0000.000
70A67LYS10.8350.91515.356-0.002-0.0020.0000.0000.0000.000
71A68GLU-1-0.814-0.88713.824-0.056-0.0560.0000.0000.0000.000
72A69ILE0-0.048-0.02413.1600.0050.0050.0000.0000.0000.000
73A70GLU-1-0.834-0.91611.228-0.632-0.6320.0000.0000.0000.000
74A71GLU-1-0.837-0.8989.328-0.225-0.2250.0000.0000.0000.000
75A72GLU-1-0.838-0.8878.448-0.015-0.0150.0000.0000.0000.000
76A73PHE0-0.012-0.0127.1850.0070.0070.0000.0000.0000.000
77A74LYS10.7690.8703.3510.0450.4790.016-0.150-0.2990.001
78A75LYS10.8260.9136.4882.0042.0040.0000.0000.0000.000
79A76PRO00.0380.0299.2690.1700.1700.0000.0000.0000.000
80A77VAL0-0.033-0.01113.053-0.090-0.0900.0000.0000.0000.000
81A78SER0-0.012-0.02413.5310.0530.0530.0000.0000.0000.000
82A79ILE0-0.012-0.00816.4010.0580.0580.0000.0000.0000.000
83A80LEU0-0.0190.00618.9270.0180.0180.0000.0000.0000.000
84A81VAL00.0110.00521.9280.0130.0130.0000.0000.0000.000
85A82ASN0-0.033-0.02324.6000.0210.0210.0000.0000.0000.000
86A83ASN0-0.035-0.04327.6560.0140.0140.0000.0000.0000.000
87A84ALA00.0240.02829.7920.0100.0100.0000.0000.0000.000
88A85GLY00.004-0.00832.331-0.004-0.0040.0000.0000.0000.000
89A86ILE0-0.031-0.00335.9770.0060.0060.0000.0000.0000.000
90A87THR00.0200.00138.977-0.004-0.0040.0000.0000.0000.000
91A88LYS10.8680.92042.2750.0570.0570.0000.0000.0000.000
92A89ASP-1-0.801-0.87245.421-0.069-0.0690.0000.0000.0000.000
93A90LYS10.8920.92648.4170.0500.0500.0000.0000.0000.000
94A91MET00.0070.01151.584-0.004-0.0040.0000.0000.0000.000
95A92LEU00.0710.02751.6780.0010.0010.0000.0000.0000.000
96A93HIS00.0320.01553.873-0.001-0.0010.0000.0000.0000.000
97A94ARG10.8640.92355.3710.0410.0410.0000.0000.0000.000
98A95MET0-0.0590.00248.8130.0000.0000.0000.0000.0000.000
99A96SER0-0.009-0.02049.1010.0010.0010.0000.0000.0000.000
100A97HIS00.0430.00245.2910.0000.0000.0000.0000.0000.000
101A98GLN00.0210.00642.482-0.001-0.0010.0000.0000.0000.000
102A99ASP-1-0.804-0.87444.208-0.051-0.0510.0000.0000.0000.000
103A100TRP00.0230.00544.663-0.005-0.0050.0000.0000.0000.000
104A101ASN00.016-0.01541.346-0.003-0.0030.0000.0000.0000.000
105A102ASP-1-0.754-0.84739.881-0.060-0.0600.0000.0000.0000.000
106A103VAL0-0.0150.00038.947-0.005-0.0050.0000.0000.0000.000
107A104ILE0-0.028-0.00938.902-0.008-0.0080.0000.0000.0000.000
108A105ASN00.0060.00934.716-0.013-0.0130.0000.0000.0000.000
109A106VAL00.0120.00434.139-0.007-0.0070.0000.0000.0000.000
110A107ASN0-0.0210.00033.984-0.007-0.0070.0000.0000.0000.000
111A108LEU0-0.0070.00134.843-0.010-0.0100.0000.0000.0000.000
112A109ASN0-0.020-0.02233.589-0.015-0.0150.0000.0000.0000.000
113A110SER00.0190.01030.173-0.013-0.0130.0000.0000.0000.000
114A111CYS0-0.0140.00728.937-0.017-0.0170.0000.0000.0000.000
115A112PHE00.0360.02928.700-0.022-0.0220.0000.0000.0000.000
116A113ASN0-0.011-0.01927.722-0.013-0.0130.0000.0000.0000.000
117A114MET00.0100.02321.8280.0020.0020.0000.0000.0000.000
118A115SER00.006-0.01523.649-0.033-0.0330.0000.0000.0000.000
119A116SER0-0.068-0.04524.264-0.020-0.0200.0000.0000.0000.000
120A117SER0-0.076-0.04821.568-0.010-0.0100.0000.0000.0000.000
121A118VAL00.0500.02718.993-0.014-0.0140.0000.0000.0000.000
122A119MET0-0.0080.01419.754-0.053-0.0530.0000.0000.0000.000
123A120GLU-1-0.954-0.97219.783-0.294-0.2940.0000.0000.0000.000
124A121GLN00.022-0.01513.415-0.016-0.0160.0000.0000.0000.000
125A122MET0-0.0220.01217.126-0.050-0.0500.0000.0000.0000.000
126A123ARG10.8260.88319.1710.2840.2840.0000.0000.0000.000
127A124ASN0-0.078-0.03617.0710.0180.0180.0000.0000.0000.000
128A125GLN0-0.052-0.02913.647-0.119-0.1190.0000.0000.0000.000
129A126ASP-1-0.854-0.91216.227-0.585-0.5850.0000.0000.0000.000
130A127TYR00.0180.00615.987-0.015-0.0150.0000.0000.0000.000
131A128GLY00.0480.01817.977-0.011-0.0110.0000.0000.0000.000
132A129ARG10.7200.87919.7930.6030.6030.0000.0000.0000.000
133A130ILE00.0140.00521.9340.0010.0010.0000.0000.0000.000
134A131VAL0-0.003-0.00124.6380.0190.0190.0000.0000.0000.000
135A132ASN0-0.001-0.00926.9290.0040.0040.0000.0000.0000.000
136A133ILE00.0200.00927.9880.0070.0070.0000.0000.0000.000
137A134SER00.0110.00531.5730.0130.0130.0000.0000.0000.000
138A135SER00.0320.00035.205-0.004-0.0040.0000.0000.0000.000
139A136ILE0-0.0340.00837.2910.0040.0040.0000.0000.0000.000
140A137ASN0-0.032-0.02540.5690.0000.0000.0000.0000.0000.000
141A138ALA00.011-0.00142.5320.0010.0010.0000.0000.0000.000
142A139GLN00.0040.01544.1960.0060.0060.0000.0000.0000.000
143A140ALA00.010-0.03647.588-0.002-0.0020.0000.0000.0000.000
144A141GLY00.0190.00949.7660.0010.0010.0000.0000.0000.000
145A142GLN0-0.033-0.05450.3390.0020.0020.0000.0000.0000.000
146A143VAL0-0.0520.04451.0520.0000.0000.0000.0000.0000.000
147A144GLY00.0050.00451.712-0.003-0.0030.0000.0000.0000.000
148A145GLN00.0590.00645.0870.0020.0020.0000.0000.0000.000
149A146THR00.014-0.00247.000-0.004-0.0040.0000.0000.0000.000
150A147ASN00.002-0.00944.422-0.005-0.0050.0000.0000.0000.000
151A148TYR0-0.018-0.02639.036-0.004-0.0040.0000.0000.0000.000
152A149SER0-0.023-0.01742.230-0.007-0.0070.0000.0000.0000.000
153A150ALA00.0140.01943.528-0.005-0.0050.0000.0000.0000.000
154A151ALA00.0200.01539.005-0.006-0.0060.0000.0000.0000.000
155A152LYS10.9320.97838.3120.1290.1290.0000.0000.0000.000
156A153ALA0-0.015-0.01438.975-0.009-0.0090.0000.0000.0000.000
157A154GLY00.0180.01139.440-0.006-0.0060.0000.0000.0000.000
158A155ILE00.0210.01533.613-0.008-0.0080.0000.0000.0000.000
159A156ILE0-0.0110.01335.120-0.012-0.0120.0000.0000.0000.000
160A157GLY0-0.027-0.01836.635-0.008-0.0080.0000.0000.0000.000
161A158PHE0-0.005-0.00829.592-0.004-0.0040.0000.0000.0000.000
162A159THR00.0150.00031.453-0.014-0.0140.0000.0000.0000.000
163A160LYS10.9420.98332.4570.1610.1610.0000.0000.0000.000
164A161ALA0-0.054-0.02834.383-0.005-0.0050.0000.0000.0000.000
165A162LEU00.0540.02727.629-0.004-0.0040.0000.0000.0000.000
166A163ALA00.0120.03129.685-0.017-0.0170.0000.0000.0000.000
167A164ARG10.9010.94030.3820.1740.1740.0000.0000.0000.000
168A165GLU-1-0.902-0.93329.230-0.250-0.2500.0000.0000.0000.000
169A166THR0-0.010-0.02925.928-0.011-0.0110.0000.0000.0000.000
170A167ALA00.0210.02226.572-0.025-0.0250.0000.0000.0000.000
171A168SER0-0.083-0.03227.682-0.016-0.0160.0000.0000.0000.000
172A169LYS10.8410.92821.4720.4720.4720.0000.0000.0000.000
173A170ASN00.0580.04519.3390.0570.0570.0000.0000.0000.000
174A171ILE0-0.010-0.02020.974-0.046-0.0460.0000.0000.0000.000
175A172THR0-0.040-0.00423.1860.0300.0300.0000.0000.0000.000
176A173VAL00.0230.01125.210-0.007-0.0070.0000.0000.0000.000
177A174ASN0-0.001-0.01227.4780.0390.0390.0000.0000.0000.000
178A175CYS0-0.080-0.03629.7850.0060.0060.0000.0000.0000.000
179A176ILE00.0270.02828.9450.0040.0040.0000.0000.0000.000
180A177ALA0-0.007-0.01832.9450.0070.0070.0000.0000.0000.000
181A178PRO0-0.0030.00133.8440.0060.0060.0000.0000.0000.000
182A179GLY0-0.002-0.01236.6540.0070.0070.0000.0000.0000.000
183A180TYR00.0490.01039.304-0.002-0.0020.0000.0000.0000.000
184A181ILE0-0.0240.00434.871-0.001-0.0010.0000.0000.0000.000
185A182ALA00.0210.00037.9370.0050.0050.0000.0000.0000.000
186A183THR0-0.024-0.03933.7830.0040.0040.0000.0000.0000.000
187A184GLU-1-0.779-0.86334.271-0.111-0.1110.0000.0000.0000.000
188A185MET0-0.036-0.01137.9860.0010.0010.0000.0000.0000.000
189A186VAL0-0.038-0.01437.6670.0060.0060.0000.0000.0000.000
190A187GLY00.0290.01340.6640.0040.0040.0000.0000.0000.000
191A188ALA0-0.036-0.01343.7120.0040.0040.0000.0000.0000.000
192A189VAL0-0.028-0.01445.538-0.001-0.0010.0000.0000.0000.000
193A190PRO00.0280.01947.8020.0010.0010.0000.0000.0000.000
194A191GLU-1-0.860-0.93549.751-0.053-0.0530.0000.0000.0000.000
195A192ASP-1-0.922-0.95851.467-0.051-0.0510.0000.0000.0000.000
196A193VAL0-0.014-0.01650.424-0.002-0.0020.0000.0000.0000.000
197A194LEU00.0370.01745.157-0.005-0.0050.0000.0000.0000.000
198A195ALA00.0240.01249.140-0.004-0.0040.0000.0000.0000.000
199A196LYS10.9160.96951.5060.0570.0570.0000.0000.0000.000
200A197ILE00.0220.00546.249-0.002-0.0020.0000.0000.0000.000
201A198ILE00.0310.03246.181-0.005-0.0050.0000.0000.0000.000
202A199ASN00.0080.00948.471-0.004-0.0040.0000.0000.0000.000
203A200SER0-0.100-0.05749.534-0.001-0.0010.0000.0000.0000.000
204A201ILE00.0310.03244.232-0.003-0.0030.0000.0000.0000.000
205A202PRO0-0.0230.00246.9660.0020.0020.0000.0000.0000.000
206A203LYS10.9060.93543.3920.1140.1140.0000.0000.0000.000
207A204LYS10.8080.91746.4610.0760.0760.0000.0000.0000.000
208A205ARG10.7770.85238.7350.1250.1250.0000.0000.0000.000
209A206LEU00.0260.02041.193-0.003-0.0030.0000.0000.0000.000
210A207GLY00.0070.00038.377-0.002-0.0020.0000.0000.0000.000
211A208GLN00.024-0.00235.0260.0080.0080.0000.0000.0000.000
212A209PRO00.0380.01831.345-0.010-0.0100.0000.0000.0000.000
213A210GLU-1-0.806-0.91929.312-0.162-0.1620.0000.0000.0000.000
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