Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: NNK8Q

Calculation Name: 5KBC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KBC

Chain ID: A

ChEMBL ID:

UniProt ID: G4NNC6

Base Structure: X-ray

Registration Date: 2023-09-23

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2238573.77175
FMO2-HF: Nuclear repulsion 2160375.842539
FMO2-HF: Total energy -78197.929211
FMO2-MP2: Total energy -78425.373514


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:6:PRO)


Summations of interaction energy for fragment #1(A:6:PRO)
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.
-0.7241.394-0.014-1.137-0.9680.006
Interaction energy analysis for fragmet #1(A:6:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.013
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].
3A8LYS10.9590.9773.821-0.3491.769-0.014-1.137-0.9680.006
4A9THR00.0220.0136.1820.2460.2460.0000.0000.0000.000
5A10HIS00.014-0.0018.311-0.113-0.1130.0000.0000.0000.000
6A11ILE00.0140.00210.626-0.036-0.0360.0000.0000.0000.000
7A12PRO0-0.066-0.04014.4280.0440.0440.0000.0000.0000.000
8A13THR0-0.023-0.02017.668-0.029-0.0290.0000.0000.0000.000
9A14THR00.0350.03118.5830.0030.0030.0000.0000.0000.000
10A15ALA00.0370.02120.5000.0020.0020.0000.0000.0000.000
11A16LYS10.9711.00121.5770.0170.0170.0000.0000.0000.000
12A17TYR0-0.024-0.03715.8460.0020.0020.0000.0000.0000.000
13A18PHE0-0.0570.00120.4640.0210.0210.0000.0000.0000.000
14A19PRO00.0270.01522.475-0.006-0.0060.0000.0000.0000.000
15A20THR00.0200.00524.327-0.015-0.0150.0000.0000.0000.000
16A21ILE0-0.030-0.00926.1150.0100.0100.0000.0000.0000.000
17A22GLY00.0810.03128.838-0.007-0.0070.0000.0000.0000.000
18A23ASP-1-0.883-0.94028.7280.0350.0350.0000.0000.0000.000
19A24PRO0-0.050-0.01825.058-0.003-0.0030.0000.0000.0000.000
20A25TYR0-0.037-0.02727.064-0.007-0.0070.0000.0000.0000.000
21A26ALA00.0220.03229.410-0.004-0.0040.0000.0000.0000.000
22A27PRO0-0.039-0.00731.372-0.003-0.0030.0000.0000.0000.000
23A28ILE00.0030.00633.311-0.004-0.0040.0000.0000.0000.000
24A29ASN00.011-0.00228.9810.0090.0090.0000.0000.0000.000
25A30ILE00.0170.01431.754-0.004-0.0040.0000.0000.0000.000
26A31THR0-0.051-0.01627.9290.0030.0030.0000.0000.0000.000
27A32VAL00.0530.02030.698-0.005-0.0050.0000.0000.0000.000
28A33PHE0-0.038-0.00727.2980.0070.0070.0000.0000.0000.000
29A34GLU-1-0.740-0.92230.7340.0470.0470.0000.0000.0000.000
30A35GLU-1-0.709-0.84430.9670.0670.0670.0000.0000.0000.000
31A36PRO0-0.047-0.02230.644-0.001-0.0010.0000.0000.0000.000
32A37SER0-0.048-0.05733.4030.0000.0000.0000.0000.0000.000
33A38CYS0-0.083-0.00536.376-0.005-0.0050.0000.0000.0000.000
34A39SER0-0.010-0.01738.1090.0010.0010.0000.0000.0000.000
35A40ALA00.0760.04441.0590.0000.0000.0000.0000.0000.000
36A42GLU-1-0.940-0.95639.1400.0450.0450.0000.0000.0000.000
37A43GLU-1-0.909-0.95841.1860.0310.0310.0000.0000.0000.000
38A44PHE00.0440.01836.0060.0000.0000.0000.0000.0000.000
39A45SER00.006-0.02437.4120.0010.0010.0000.0000.0000.000
40A46SER0-0.073-0.03839.0970.0030.0030.0000.0000.0000.000
41A47GLU-1-0.922-0.95142.4260.0330.0330.0000.0000.0000.000
42A48VAL0-0.024-0.00740.435-0.001-0.0010.0000.0000.0000.000
43A49PHE0-0.028-0.02232.8530.0000.0000.0000.0000.0000.000
44A50PRO0-0.015-0.01838.4860.0010.0010.0000.0000.0000.000
45A51LEU00.0010.00040.0560.0000.0000.0000.0000.0000.000
46A52ILE0-0.0130.00536.481-0.002-0.0020.0000.0000.0000.000
47A53LYS10.9330.96534.369-0.060-0.0600.0000.0000.0000.000
48A54LYS10.9741.00337.494-0.032-0.0320.0000.0000.0000.000
49A55HIS0-0.004-0.00940.597-0.001-0.0010.0000.0000.0000.000
50A56PHE00.0100.00737.960-0.003-0.0030.0000.0000.0000.000
51A57VAL0-0.035-0.01032.991-0.001-0.0010.0000.0000.0000.000
52A58ASP-1-0.914-0.96735.0970.0450.0450.0000.0000.0000.000
53A59THR0-0.104-0.05037.189-0.001-0.0010.0000.0000.0000.000
54A60GLY00.0400.03135.071-0.002-0.0020.0000.0000.0000.000
55A61GLU-1-0.986-0.98735.5760.0070.0070.0000.0000.0000.000
56A62ALA0-0.044-0.03834.280-0.004-0.0040.0000.0000.0000.000
57A63SER0-0.025-0.02129.0340.0020.0020.0000.0000.0000.000
58A64LEU00.0190.00630.284-0.003-0.0030.0000.0000.0000.000
59A65THR0-0.049-0.03725.7120.0050.0050.0000.0000.0000.000
60A66LEU0-0.0010.02627.868-0.004-0.0040.0000.0000.0000.000
61A67VAL0-0.027-0.02425.0540.0120.0120.0000.0000.0000.000
62A68PRO0-0.0500.00224.865-0.004-0.0040.0000.0000.0000.000
63A69VAL00.006-0.00826.2250.0030.0030.0000.0000.0000.000
64A70CYS0-0.033-0.03627.8620.0060.0060.0000.0000.0000.000
65A71PHE0-0.025-0.00829.599-0.001-0.0010.0000.0000.0000.000
66A72ILE0-0.0140.01032.376-0.002-0.0020.0000.0000.0000.000
67A73ARG10.9320.94433.730-0.048-0.0480.0000.0000.0000.000
68A74GLY00.0500.01133.963-0.002-0.0020.0000.0000.0000.000
69A75SER00.0340.02431.8660.0040.0040.0000.0000.0000.000
70A76MET0-0.0300.00325.7140.0110.0110.0000.0000.0000.000
71A77PRO00.017-0.00427.7860.0110.0110.0000.0000.0000.000
72A78ALA00.0690.03028.8960.0090.0090.0000.0000.0000.000
73A79ALA00.0300.01926.4350.0050.0050.0000.0000.0000.000
74A80GLN0-0.013-0.01822.3600.0260.0260.0000.0000.0000.000
75A81ALA00.0170.01524.4450.0180.0180.0000.0000.0000.000
76A82LEU00.0190.04426.5020.0100.0100.0000.0000.0000.000
77A83LEU00.005-0.00120.4160.0070.0070.0000.0000.0000.000
78A84CYS0-0.125-0.06421.8170.0420.0420.0000.0000.0000.000
79A85VAL00.0010.00523.0450.0170.0170.0000.0000.0000.000
80A86TYR0-0.002-0.00319.9790.0050.0050.0000.0000.0000.000
81A87HIS0-0.049-0.01917.5110.0230.0230.0000.0000.0000.000
82A88HIS0-0.113-0.05120.3150.0450.0450.0000.0000.0000.000
83A89ASP-1-0.841-0.91221.0090.2750.2750.0000.0000.0000.000
84A90PRO0-0.040-0.03216.6260.0110.0110.0000.0000.0000.000
85A91LYS10.8970.95916.595-0.221-0.2210.0000.0000.0000.000
86A92ARG10.9550.95917.256-0.174-0.1740.0000.0000.0000.000
87A93PRO00.0600.03917.909-0.006-0.0060.0000.0000.0000.000
88A94ASP-1-0.779-0.90820.8820.1460.1460.0000.0000.0000.000
89A95PRO0-0.0010.00223.9940.0020.0020.0000.0000.0000.000
90A96GLU-1-0.900-0.94426.3140.0840.0840.0000.0000.0000.000
91A97ALA00.0180.02927.589-0.006-0.0060.0000.0000.0000.000
92A98TYR0-0.063-0.05325.9310.0010.0010.0000.0000.0000.000
93A99MET00.001-0.01028.142-0.005-0.0050.0000.0000.0000.000
94A100GLU-1-0.838-0.88830.9520.0730.0730.0000.0000.0000.000
95A101TYR0-0.001-0.03429.0480.0000.0000.0000.0000.0000.000
96A102PHE00.001-0.02529.218-0.002-0.0020.0000.0000.0000.000
97A103HIS00.0730.06232.289-0.004-0.0040.0000.0000.0000.000
98A104ARG10.7460.82235.457-0.092-0.0920.0000.0000.0000.000
99A105ILE0-0.072-0.03731.497-0.002-0.0020.0000.0000.0000.000
100A106LEU0-0.016-0.00634.709-0.002-0.0020.0000.0000.0000.000
101A107THR00.0080.02237.375-0.003-0.0030.0000.0000.0000.000
102A108TYR0-0.0410.00638.881-0.001-0.0010.0000.0000.0000.000
103A109LYS11.0280.99540.668-0.044-0.0440.0000.0000.0000.000
104A110LYS10.8300.91737.484-0.058-0.0580.0000.0000.0000.000
105A111THR0-0.008-0.00942.098-0.001-0.0010.0000.0000.0000.000
106A112LYS10.9340.97140.875-0.070-0.0700.0000.0000.0000.000
107A113GLY00.0550.04341.8120.0000.0000.0000.0000.0000.000
108A114SER0-0.003-0.02137.5400.0030.0030.0000.0000.0000.000
109A115HIS0-0.029-0.00336.9980.0080.0080.0000.0000.0000.000
110A116TRP00.0280.01434.8890.0000.0000.0000.0000.0000.000
111A117ALA00.0120.02033.5800.0020.0020.0000.0000.0000.000
112A118THR0-0.011-0.01034.0090.0040.0040.0000.0000.0000.000
113A119PRO00.0590.01031.7320.0010.0010.0000.0000.0000.000
114A120GLU-1-0.871-0.94333.3660.1040.1040.0000.0000.0000.000
115A121VAL0-0.0250.00436.530-0.001-0.0010.0000.0000.0000.000
116A122LEU00.0270.01430.7280.0000.0000.0000.0000.0000.000
117A123ALA00.0000.00032.8760.0040.0040.0000.0000.0000.000
118A124LYS10.9170.96533.785-0.080-0.0800.0000.0000.0000.000
119A125LEU0-0.032-0.02235.006-0.003-0.0030.0000.0000.0000.000
120A126ALA0-0.0260.00131.371-0.001-0.0010.0000.0000.0000.000
121A127GLU-1-0.917-0.95333.2610.0990.0990.0000.0000.0000.000
122A128LYS10.9480.97836.008-0.082-0.0820.0000.0000.0000.000
123A129ILE00.0080.02331.411-0.006-0.0060.0000.0000.0000.000
124A130PRO0-0.0060.00432.7570.0060.0060.0000.0000.0000.000
125A131THR0-0.019-0.01428.6670.0060.0060.0000.0000.0000.000
126A132HIS0-0.236-0.00927.1260.0010.0010.0000.0000.0000.000
127A133SER00.1740.02223.336-0.018-0.0180.0000.0000.0000.000
128A134GLY00.1120.03024.3390.0020.0020.0000.0000.0000.000
129A135ARG10.8130.85623.408-0.245-0.2450.0000.0000.0000.000
130A136GLU-1-0.870-0.90527.0840.1170.1170.0000.0000.0000.000
131A137ILE0-0.0060.01327.6570.0160.0160.0000.0000.0000.000
132A138ASN00.0350.01828.290-0.006-0.0060.0000.0000.0000.000
133A139PRO00.0790.03029.1690.0090.0090.0000.0000.0000.000
134A140LYS10.9840.98930.113-0.138-0.1380.0000.0000.0000.000
135A141GLY00.0060.00426.2450.0070.0070.0000.0000.0000.000
136A142LEU00.0170.01525.3800.0180.0180.0000.0000.0000.000
137A143ILE00.016-0.01026.9270.0020.0020.0000.0000.0000.000
138A144GLN0-0.031-0.01224.0670.0080.0080.0000.0000.0000.000
139A146ILE00.0270.00723.5670.0030.0030.0000.0000.0000.000
140A147ASN0-0.063-0.03426.045-0.013-0.0130.0000.0000.0000.000
141A148SER0-0.072-0.01420.9170.0120.0120.0000.0000.0000.000
142A149GLN0-0.018-0.02022.1020.0000.0000.0000.0000.0000.000
143A150ARG10.9960.99515.783-0.423-0.4230.0000.0000.0000.000
144A151PHE00.023-0.00517.2680.0090.0090.0000.0000.0000.000
145A152THR00.0050.00219.982-0.026-0.0260.0000.0000.0000.000
146A153GLU-1-0.897-0.95817.7200.0780.0780.0000.0000.0000.000
147A154GLN0-0.035-0.00616.803-0.009-0.0090.0000.0000.0000.000
148A155LEU00.0350.00819.021-0.020-0.0200.0000.0000.0000.000
149A156LYS10.9350.98621.789-0.112-0.1120.0000.0000.0000.000
150A157LYS10.9600.97214.734-0.110-0.1100.0000.0000.0000.000
151A158ASN00.0130.00821.129-0.014-0.0140.0000.0000.0000.000
152A159ASN0-0.001-0.01023.322-0.006-0.0060.0000.0000.0000.000
153A160ILE0-0.035-0.00822.060-0.007-0.0070.0000.0000.0000.000
154A161TYR00.004-0.00822.881-0.004-0.0040.0000.0000.0000.000
155A162GLY00.0530.01524.885-0.006-0.0060.0000.0000.0000.000
156A163SER00.0110.00428.183-0.004-0.0040.0000.0000.0000.000
157A164GLN00.0100.00226.2810.0020.0020.0000.0000.0000.000
158A165ILE0-0.066-0.02826.730-0.004-0.0040.0000.0000.0000.000
159A166MET0-0.0250.00030.209-0.001-0.0010.0000.0000.0000.000
160A167GLY00.0230.03032.2250.0000.0000.0000.0000.0000.000
161A168GLY0-0.077-0.04332.718-0.001-0.0010.0000.0000.0000.000
162A169GLN0-0.080-0.05634.1030.0020.0020.0000.0000.0000.000
163A170LEU0-0.062-0.03831.0360.0030.0030.0000.0000.0000.000
164A171ALA00.0280.03534.8540.0020.0020.0000.0000.0000.000
165A172THR0-0.123-0.03333.5330.0020.0020.0000.0000.0000.000
166A173PRO00.1120.01735.9310.0010.0010.0000.0000.0000.000
167A174THR00.020-0.01534.489-0.004-0.0040.0000.0000.0000.000
168A175ALA0-0.034-0.01134.1590.0040.0040.0000.0000.0000.000
169A176VAL0-0.023-0.01831.874-0.004-0.0040.0000.0000.0000.000
170A177VAL00.0340.02233.5470.0020.0020.0000.0000.0000.000
171A178GLY00.0180.00333.821-0.003-0.0030.0000.0000.0000.000
172A179ASP-1-0.988-1.00433.131-0.027-0.0270.0000.0000.0000.000
173A180TYR0-0.038-0.00434.914-0.001-0.0010.0000.0000.0000.000
174A181LEU0-0.020-0.01534.9520.0030.0030.0000.0000.0000.000
175A182ILE0-0.0080.00137.243-0.001-0.0010.0000.0000.0000.000
176A183GLU-1-0.839-0.92438.3370.0140.0140.0000.0000.0000.000
177A184ASP-1-0.956-0.96239.6090.0230.0230.0000.0000.0000.000
178A185PRO0-0.041-0.00938.277-0.001-0.0010.0000.0000.0000.000
179A186THR00.0350.00941.5920.0030.0030.0000.0000.0000.000
180A187PHE0-0.002-0.03142.534-0.001-0.0010.0000.0000.0000.000
181A188ASP-1-0.898-0.94644.4030.0080.0080.0000.0000.0000.000
182A189GLU-1-0.847-0.92543.6230.0090.0090.0000.0000.0000.000
183A190ILE0-0.020-0.01739.130-0.002-0.0020.0000.0000.0000.000
184A191GLU-1-0.928-0.95341.8290.0110.0110.0000.0000.0000.000
185A192ARG10.9890.97944.102-0.003-0.0030.0000.0000.0000.000
186A193VAL0-0.038-0.00739.837-0.002-0.0020.0000.0000.0000.000
187A194ILE00.0020.00938.014-0.003-0.0030.0000.0000.0000.000
188A195THR0-0.051-0.03041.299-0.002-0.0020.0000.0000.0000.000
189A196GLN00.0400.02743.775-0.001-0.0010.0000.0000.0000.000
190A197LEU0-0.033-0.02337.498-0.003-0.0030.0000.0000.0000.000
191A198ARG10.9150.96040.952-0.008-0.0080.0000.0000.0000.000
192A199HIS0-0.049-0.02342.0250.0000.0000.0000.0000.0000.000
193A200LEU0-0.063-0.02340.428-0.002-0.0020.0000.0000.0000.000
194A201GLN00.014-0.01236.766-0.002-0.0020.0000.0000.0000.000
195A202ALA0-0.0380.02441.082-0.001-0.0010.0000.0000.0000.000
196A203ILE0-0.059-0.03942.254-0.001-0.0010.0000.0000.0000.000