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: 6GG7Z

Calculation Name: 4I61-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4I61

Chain ID: B

ChEMBL ID:

UniProt ID: F8DQ39

Base Structure: X-ray

Registration Date: 2023-09-27

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2508795.331753
FMO2-HF: Nuclear repulsion 2424238.186936
FMO2-HF: Total energy -84557.144817
FMO2-MP2: Total energy -84799.702473


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(B:11:VAL)


Summations of interaction energy for fragment #1(B:11:VAL)
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.
-5.777-1.4643.211-2.376-5.148-0.018
Interaction energy analysis for fragmet #1(B:11:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.019
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].
3B13GLU-1-0.885-0.9492.323-5.752-3.0742.744-1.861-3.561-0.015
4B14PHE0-0.045-0.0062.6960.1501.7360.466-0.487-1.565-0.003
5B15VAL0-0.059-0.0194.2680.2990.3480.001-0.028-0.0220.000
6B16GLY00.020-0.0037.9170.2260.2260.0000.0000.0000.000
7B17ALA0-0.023-0.0159.192-0.080-0.0800.0000.0000.0000.000
8B18SER00.0200.00910.8350.0890.0890.0000.0000.0000.000
9B19GLU-1-0.927-0.96614.579-0.257-0.2570.0000.0000.0000.000
10B20ILE00.0040.01117.0470.0230.0230.0000.0000.0000.000
11B21GLY00.0720.03717.987-0.033-0.0330.0000.0000.0000.000
12B22ASP-1-0.891-0.92215.439-0.327-0.3270.0000.0000.0000.000
13B23THR00.000-0.00914.395-0.024-0.0240.0000.0000.0000.000
14B24ILE0-0.026-0.0206.664-0.044-0.0440.0000.0000.0000.000
15B25GLY00.0430.0189.8700.0960.0960.0000.0000.0000.000
16B26MET0-0.049-0.0365.150-0.353-0.3530.0000.0000.0000.000
17B27VAL00.007-0.0056.2950.3660.3660.0000.0000.0000.000
18B28ILE00.0200.0266.532-0.308-0.3080.0000.0000.0000.000
19B29PRO00.000-0.0167.4060.2060.2060.0000.0000.0000.000
20B30ARG10.9270.96310.6730.2540.2540.0000.0000.0000.000
21B31VAL00.0140.02111.7580.0000.0000.0000.0000.0000.000
22B32ASP-1-0.843-0.92712.570-0.146-0.1460.0000.0000.0000.000
23B33GLN0-0.055-0.04814.442-0.019-0.0190.0000.0000.0000.000
24B34GLN00.0100.00317.8220.0140.0140.0000.0000.0000.000
25B35LEU0-0.039-0.01612.237-0.001-0.0010.0000.0000.0000.000
26B36LEU0-0.001-0.00116.456-0.008-0.0080.0000.0000.0000.000
27B37ASP-1-0.860-0.91917.631-0.159-0.1590.0000.0000.0000.000
28B38LYS10.8410.92118.5240.1790.1790.0000.0000.0000.000
29B39LEU0-0.044-0.00114.570-0.011-0.0110.0000.0000.0000.000
30B40HIS00.0160.00719.0750.0270.0270.0000.0000.0000.000
31B41VAL0-0.009-0.00318.406-0.015-0.0150.0000.0000.0000.000
32B42THR0-0.023-0.02321.6540.0140.0140.0000.0000.0000.000
33B43LYS10.8380.91522.7100.1940.1940.0000.0000.0000.000
34B44GLN0-0.010-0.00820.306-0.015-0.0150.0000.0000.0000.000
35B45TYR0-0.006-0.01718.0110.0220.0220.0000.0000.0000.000
36B46LYS10.7960.88316.1100.2140.2140.0000.0000.0000.000
37B47THR0-0.060-0.03212.478-0.019-0.0190.0000.0000.0000.000
38B48LEU00.0250.01811.7020.0350.0350.0000.0000.0000.000
39B49GLY00.0180.00010.861-0.130-0.1300.0000.0000.0000.000
40B50ILE0-0.029-0.0139.2530.0790.0790.0000.0000.0000.000
41B51LEU00.026-0.00210.983-0.114-0.1140.0000.0000.0000.000
42B52SER0-0.022-0.00111.6420.0580.0580.0000.0000.0000.000
43B53ASP-1-0.806-0.92413.496-0.419-0.4190.0000.0000.0000.000
44B54ARG10.8140.88715.8680.3410.3410.0000.0000.0000.000
45B55THR0-0.040-0.02918.2420.0470.0470.0000.0000.0000.000
46B56GLY00.0620.03421.072-0.007-0.0070.0000.0000.0000.000
47B57ALA00.0380.02821.217-0.015-0.0150.0000.0000.0000.000
48B58GLY00.0450.01522.958-0.011-0.0110.0000.0000.0000.000
49B59PRO00.0280.02122.904-0.002-0.0020.0000.0000.0000.000
50B60GLN00.0110.00318.1020.0250.0250.0000.0000.0000.000
51B61ILE00.0080.00620.451-0.013-0.0130.0000.0000.0000.000
52B62MET0-0.031-0.01922.5240.0060.0060.0000.0000.0000.000
53B63ALA0-0.0040.01120.3230.0080.0080.0000.0000.0000.000
54B64MET0-0.014-0.01115.7170.0010.0010.0000.0000.0000.000
55B65ASP-1-0.765-0.88520.112-0.184-0.1840.0000.0000.0000.000
56B66GLU-1-0.882-0.94522.705-0.166-0.1660.0000.0000.0000.000
57B67GLY00.0060.00619.3090.0070.0070.0000.0000.0000.000
58B68ILE0-0.063-0.03020.2160.0020.0020.0000.0000.0000.000
59B69LYS10.7920.89422.0280.1900.1900.0000.0000.0000.000
60B70ALA0-0.066-0.01221.4750.0170.0170.0000.0000.0000.000
61B71THR0-0.125-0.07118.326-0.004-0.0040.0000.0000.0000.000
62B72ASN0-0.083-0.04620.7880.0320.0320.0000.0000.0000.000
63B73MET0-0.0500.01415.084-0.002-0.0020.0000.0000.0000.000
64B74GLU-1-0.761-0.83919.811-0.176-0.1760.0000.0000.0000.000
65B75CYS0-0.042-0.01819.742-0.032-0.0320.0000.0000.0000.000
66B76ILE0-0.0160.00117.4540.0210.0210.0000.0000.0000.000
67B77ASH0-0.016-0.06118.7220.0230.0230.0000.0000.0000.000
68B78VAL00.0190.00919.538-0.029-0.0290.0000.0000.0000.000
69B79GLU-1-0.905-0.91019.214-0.282-0.2820.0000.0000.0000.000
70B80TRP00.0380.00420.783-0.015-0.0150.0000.0000.0000.000
71B81PRO00.0220.03718.7000.0230.0230.0000.0000.0000.000
72B82ARG10.8360.93421.7890.1670.1670.0000.0000.0000.000
73B83ASP-1-0.809-0.89819.897-0.272-0.2720.0000.0000.0000.000
74B84THR0-0.039-0.00222.3220.0260.0260.0000.0000.0000.000
75B85LYS10.8030.87319.0910.2760.2760.0000.0000.0000.000
76B86GLY0-0.030-0.00523.5500.0120.0120.0000.0000.0000.000
77B87GLY00.0300.03726.7250.0130.0130.0000.0000.0000.000
78B88GLY0-0.003-0.01728.379-0.002-0.0020.0000.0000.0000.000
79B89GLY00.0620.03227.3570.0070.0070.0000.0000.0000.000
80B90HIS00.0070.01123.9640.0060.0060.0000.0000.0000.000
81B91GLY00.0470.05220.0300.0010.0010.0000.0000.0000.000
82B92CYS0-0.041-0.02918.5510.0260.0260.0000.0000.0000.000
83B93LEU0-0.0170.00613.814-0.052-0.0520.0000.0000.0000.000
84B94ILE00.0290.01615.9250.0460.0460.0000.0000.0000.000
85B95ILE0-0.0040.00214.198-0.076-0.0760.0000.0000.0000.000
86B96ILE0-0.013-0.01114.7330.0520.0520.0000.0000.0000.000
87B97GLY00.008-0.00715.401-0.054-0.0540.0000.0000.0000.000
88B98GLY00.0930.02916.9150.0250.0250.0000.0000.0000.000
89B99ASP-1-0.843-0.94017.552-0.202-0.2020.0000.0000.0000.000
90B100ASP-1-0.815-0.90116.548-0.207-0.2070.0000.0000.0000.000
91B101PRO0-0.010-0.01311.217-0.038-0.0380.0000.0000.0000.000
92B102ALA0-0.091-0.03912.548-0.090-0.0900.0000.0000.0000.000
93B103ASP-1-0.758-0.87314.511-0.274-0.2740.0000.0000.0000.000
94B104ALA00.0770.02512.597-0.015-0.0150.0000.0000.0000.000
95B105ARG10.9050.9358.8540.5540.5540.0000.0000.0000.000
96B106GLN00.0280.02212.279-0.036-0.0360.0000.0000.0000.000
97B107ALA00.0460.02815.8020.0110.0110.0000.0000.0000.000
98B108ILE0-0.028-0.00110.5900.0110.0110.0000.0000.0000.000
99B109ARG10.9010.94311.7670.4200.4200.0000.0000.0000.000
100B110VAL00.0220.02314.9540.0340.0340.0000.0000.0000.000
101B111ALA00.0140.01216.2700.0270.0270.0000.0000.0000.000
102B112LEU0-0.008-0.01811.6900.0200.0200.0000.0000.0000.000
103B113ASP-1-0.908-0.94116.406-0.276-0.2760.0000.0000.0000.000
104B114ASN0-0.080-0.06019.1200.0630.0630.0000.0000.0000.000
105B115LEU00.0290.02516.6760.0190.0190.0000.0000.0000.000
106B116HIS00.0030.00321.1090.0280.0280.0000.0000.0000.000
107B117ARG10.8570.94923.5090.1980.1980.0000.0000.0000.000
108B118THR0-0.069-0.05123.2890.0140.0140.0000.0000.0000.000
109B119PHE00.0340.00821.3570.0030.0030.0000.0000.0000.000
110B120GLY00.0220.03126.0670.0100.0100.0000.0000.0000.000
111B121ASP-1-0.803-0.85929.225-0.103-0.1030.0000.0000.0000.000
112B122VAL00.0110.01526.8170.0020.0020.0000.0000.0000.000
113B123TYR0-0.050-0.03930.0070.0030.0030.0000.0000.0000.000
114B124ASN0-0.006-0.00928.013-0.003-0.0030.0000.0000.0000.000
115B125ALA00.0580.02432.0290.0070.0070.0000.0000.0000.000
116B126LYS10.8360.89533.5870.0760.0760.0000.0000.0000.000
117B127ALA0-0.046-0.01834.708-0.002-0.0020.0000.0000.0000.000
118B128GLY00.0230.00733.8050.0010.0010.0000.0000.0000.000
119B129HIS0-0.021-0.01529.7210.0030.0030.0000.0000.0000.000
120B130LEU0-0.054-0.03133.0250.0050.0050.0000.0000.0000.000
121B131GLU-1-0.804-0.89827.700-0.193-0.1930.0000.0000.0000.000
122B132LEU0-0.081-0.03131.6640.0080.0080.0000.0000.0000.000
123B133GLN0-0.017-0.00527.280-0.005-0.0050.0000.0000.0000.000
124B134PHE00.016-0.01231.4040.0120.0120.0000.0000.0000.000
125B135THR00.0150.01630.331-0.003-0.0030.0000.0000.0000.000
126B136ALA00.008-0.00332.5640.0060.0060.0000.0000.0000.000
127B137ARG10.8830.93332.7750.1040.1040.0000.0000.0000.000
128B138ALA00.0080.02330.106-0.008-0.0080.0000.0000.0000.000
129B139ALA00.0270.02026.3790.0100.0100.0000.0000.0000.000
130B140GLY00.0930.04425.5020.0000.0000.0000.0000.0000.000
131B141ALA00.006-0.00122.134-0.004-0.0040.0000.0000.0000.000
132B142ALA00.0180.00123.9480.0010.0010.0000.0000.0000.000
133B143HIS0-0.091-0.04027.1010.0080.0080.0000.0000.0000.000
134B144LEU0-0.032-0.01022.7840.0060.0060.0000.0000.0000.000
135B145GLY0-0.007-0.00625.0100.0010.0010.0000.0000.0000.000
136B146LEU0-0.028-0.03425.6410.0070.0070.0000.0000.0000.000
137B147GLY00.0250.02929.0360.0110.0110.0000.0000.0000.000
138B148ALA0-0.059-0.02130.5390.0110.0110.0000.0000.0000.000
139B149VAL00.0290.01132.184-0.001-0.0010.0000.0000.0000.000
140B150GLU-1-0.859-0.94428.879-0.157-0.1570.0000.0000.0000.000
141B151GLY0-0.062-0.04232.3040.0090.0090.0000.0000.0000.000
142B152LYS10.8650.93034.1750.0980.0980.0000.0000.0000.000
143B153ALA00.0160.02134.556-0.007-0.0070.0000.0000.0000.000
144B154PHE00.0130.01530.3520.0010.0010.0000.0000.0000.000
145B155GLY00.0260.00534.258-0.001-0.0010.0000.0000.0000.000
146B156LEU0-0.0060.01129.5310.0010.0010.0000.0000.0000.000
147B157ILE0-0.013-0.01733.6450.0010.0010.0000.0000.0000.000
148B158CYS00.0340.02130.9270.0050.0050.0000.0000.0000.000
149B159GLY00.0160.00434.3610.0010.0010.0000.0000.0000.000
150B160CYS0-0.0480.00432.1170.0020.0020.0000.0000.0000.000
151B161PRO00.1000.02735.0570.0010.0010.0000.0000.0000.000
152B162SER0-0.0090.00036.1330.0050.0050.0000.0000.0000.000
153B163GLY0-0.030-0.01137.4160.0010.0010.0000.0000.0000.000
154B164ILE0-0.013-0.01138.6510.0040.0040.0000.0000.0000.000
155B165GLY00.0820.03437.8410.0010.0010.0000.0000.0000.000
156B166VAL0-0.027-0.00538.7210.0010.0010.0000.0000.0000.000
157B167VAL0-0.035-0.01441.7210.0030.0030.0000.0000.0000.000
158B168MET0-0.053-0.00936.6440.0020.0020.0000.0000.0000.000
159B169GLY00.0570.03241.1650.0000.0000.0000.0000.0000.000
160B170ASP-1-0.819-0.89441.725-0.063-0.0630.0000.0000.0000.000
161B171LYS10.9210.95544.4560.0670.0670.0000.0000.0000.000
162B172ALA00.0050.01541.6850.0020.0020.0000.0000.0000.000
163B173LEU00.013-0.00443.0530.0020.0020.0000.0000.0000.000
164B174LYS10.7500.87345.5790.0650.0650.0000.0000.0000.000
165B175THR0-0.085-0.04045.7060.0030.0030.0000.0000.0000.000
166B176ALA0-0.031-0.02645.5960.0020.0020.0000.0000.0000.000
167B177GLY0-0.0130.01246.835-0.001-0.0010.0000.0000.0000.000
168B178VAL0-0.052-0.02542.110-0.001-0.0010.0000.0000.0000.000
169B179GLU-1-0.912-0.95841.955-0.071-0.0710.0000.0000.0000.000
170B180PRO0-0.025-0.01040.541-0.006-0.0060.0000.0000.0000.000
171B181LEU0-0.063-0.02935.0040.0020.0020.0000.0000.0000.000
172B182ASN00.017-0.00334.3870.0060.0060.0000.0000.0000.000
173B183PHE0-0.013-0.00537.3380.0000.0000.0000.0000.0000.000
174B184THR0-0.0200.01432.1420.0030.0030.0000.0000.0000.000
175B185SER00.026-0.00735.1320.0040.0040.0000.0000.0000.000
176B186PRO00.0330.04233.903-0.004-0.0040.0000.0000.0000.000
177B187SER0-0.030-0.02734.023-0.003-0.0030.0000.0000.0000.000
178B188HIS0-0.044-0.02335.6240.0010.0010.0000.0000.0000.000
179B189GLY00.0630.02932.3670.0000.0000.0000.0000.0000.000
180B190THR0-0.037-0.01629.635-0.008-0.0080.0000.0000.0000.000
181B191SER0-0.029-0.04125.3080.0080.0080.0000.0000.0000.000
182B192PHE0-0.039-0.02428.4040.0000.0000.0000.0000.0000.000
183B193SER0-0.055-0.03428.9920.0030.0030.0000.0000.0000.000
184B194ASN0-0.004-0.02230.6440.0120.0120.0000.0000.0000.000
185B195GLU-1-0.750-0.87329.178-0.162-0.1620.0000.0000.0000.000
186B196GLY0-0.022-0.01233.5810.0020.0020.0000.0000.0000.000
187B197CYS0-0.027-0.01531.6450.0000.0000.0000.0000.0000.000
188B198LEU00.0060.01235.0330.0020.0020.0000.0000.0000.000
189B199THR00.0230.01432.640-0.003-0.0030.0000.0000.0000.000
190B200ILE0-0.025-0.00435.8490.0060.0060.0000.0000.0000.000
191B201THR00.019-0.01336.745-0.005-0.0050.0000.0000.0000.000
192B202GLY00.0610.02738.7550.0040.0040.0000.0000.0000.000
193B203ASP-1-0.913-0.96040.665-0.074-0.0740.0000.0000.0000.000
194B204SER00.010-0.01138.8020.0000.0000.0000.0000.0000.000
195B205GLY0-0.071-0.03340.233-0.002-0.0020.0000.0000.0000.000
196B206ALA00.0900.05142.9280.0000.0000.0000.0000.0000.000
197B207VAL00.0420.01337.286-0.001-0.0010.0000.0000.0000.000
198B208ARG10.9270.96938.2050.0830.0830.0000.0000.0000.000
199B209GLN0-0.013-0.01239.7790.0000.0000.0000.0000.0000.000
200B210ALA00.0330.02441.3460.0010.0010.0000.0000.0000.000
201B211VAL00.0210.00035.7290.0000.0000.0000.0000.0000.000
202B212MET0-0.043-0.02038.995-0.001-0.0010.0000.0000.0000.000
203B213ALA00.0230.02240.5550.0010.0010.0000.0000.0000.000
204B214GLY00.002-0.00840.3450.0020.0020.0000.0000.0000.000
205B215ARG10.8780.92335.9550.0980.0980.0000.0000.0000.000
206B216GLU-1-0.877-0.91339.236-0.065-0.0650.0000.0000.0000.000
207B217VAL0-0.020-0.01942.4780.0020.0020.0000.0000.0000.000
208B218GLY00.0690.01839.5800.0010.0010.0000.0000.0000.000
209B219LEU00.0100.00537.1600.0000.0000.0000.0000.0000.000
210B220LYS10.8410.92940.4670.0660.0660.0000.0000.0000.000
211B221LEU0-0.007-0.01042.3060.0030.0030.0000.0000.0000.000
212B222LEU00.0170.01735.8010.0030.0030.0000.0000.0000.000
213B223SER00.012-0.02240.4560.0000.0000.0000.0000.0000.000
214B224GLN0-0.113-0.04142.2010.0050.0050.0000.0000.0000.000
215B225PHE0-0.064-0.03540.8050.0020.0020.0000.0000.0000.000
216B226GLY0-0.051-0.02142.8940.0010.0010.0000.0000.0000.000
217B227GLU-1-0.869-0.91836.354-0.086-0.0860.0000.0000.0000.000
218B228GLU-1-0.951-0.97838.768-0.076-0.0760.0000.0000.0000.000
219B229PRO0-0.060-0.03335.809-0.003-0.0030.0000.0000.0000.000
220B230VAL00.0420.02431.9960.0030.0030.0000.0000.0000.000
221B231ASN0-0.023-0.00830.704-0.001-0.0010.0000.0000.0000.000
222B232ASP-1-0.914-0.95626.721-0.141-0.1410.0000.0000.0000.000
223B233PHE0-0.011-0.01722.886-0.004-0.0040.0000.0000.0000.000
224B234PRO0-0.019-0.02128.6100.0040.0040.0000.0000.0000.000
225B235SER0-0.024-0.01830.660-0.005-0.0050.0000.0000.0000.000
226B236TYR0-0.013-0.04229.3180.0070.0070.0000.0000.0000.000
227B237ILE0-0.091-0.01832.5660.0110.0110.0000.0000.0000.000