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: K3VG3

Calculation Name: 3CUQ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CUQ

Chain ID: B

ChEMBL ID:

UniProt ID: Q96H20

Base Structure: X-ray

Registration Date: 2023-03-14

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2021023.23391
FMO2-HF: Nuclear repulsion 1938514.139135
FMO2-HF: Total energy -82509.094775
FMO2-MP2: Total energy -82741.000526


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:172:LYS)


Summations of interaction energy for fragment #1(B:172:LYS)
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.
-33.366-28.1671.692-3.111-3.7780
Interaction energy analysis for fragmet #1(B:172:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.948 / q_NPA : 0.948
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].
3B174ILE00.0620.0432.681-1.3803.3051.690-2.959-3.4150.000
4B175SER0-0.021-0.0253.6490.9431.3740.003-0.147-0.2870.000
5B176GLU-1-0.854-0.9085.322-26.582-26.499-0.001-0.005-0.0760.000
6B177ALA00.0010.0037.2902.1362.1360.0000.0000.0000.000
7B178PHE0-0.033-0.0387.3971.2971.2970.0000.0000.0000.000
8B179GLU-1-0.888-0.9229.671-16.458-16.4580.0000.0000.0000.000
9B180ASP-1-0.800-0.89911.092-17.022-17.0220.0000.0000.0000.000
10B181LEU0-0.037-0.01612.5691.1071.1070.0000.0000.0000.000
11B182SER0-0.002-0.01114.1371.2751.2750.0000.0000.0000.000
12B183LYS10.8240.90613.65318.09318.0930.0000.0000.0000.000
13B184LEU0-0.022-0.01016.8800.8280.8280.0000.0000.0000.000
14B185MET00.002-0.00218.4120.8270.8270.0000.0000.0000.000
15B186ILE0-0.0130.00620.4580.5760.5760.0000.0000.0000.000
16B187LYS10.9740.98121.45211.98411.9840.0000.0000.0000.000
17B188ALA00.0330.02523.3040.4150.4150.0000.0000.0000.000
18B189LYS10.8400.89524.89910.26810.2680.0000.0000.0000.000
19B190GLU-1-0.894-0.93826.543-9.762-9.7620.0000.0000.0000.000
20B191MET0-0.028-0.01326.6050.3710.3710.0000.0000.0000.000
21B192VAL0-0.0220.00828.2300.3210.3210.0000.0000.0000.000
22B193GLU-1-0.843-0.92729.967-8.947-8.9470.0000.0000.0000.000
23B194LEU0-0.0050.00132.6690.3140.3140.0000.0000.0000.000
24B195SER0-0.056-0.04833.4700.0880.0880.0000.0000.0000.000
25B196LYS10.9260.96033.3288.4778.4770.0000.0000.0000.000
26B197SER00.0340.01137.6550.1350.1350.0000.0000.0000.000
27B198ILE0-0.068-0.01938.4100.1670.1670.0000.0000.0000.000
28B199ALA00.0090.01740.8950.0980.0980.0000.0000.0000.000
29B200ASN0-0.049-0.01942.6300.0310.0310.0000.0000.0000.000
30B201LYS11.0091.01545.8676.0646.0640.0000.0000.0000.000
31B212ASP-1-0.854-0.91645.533-6.471-6.4710.0000.0000.0000.000
32B213GLU-1-0.902-0.93847.550-6.059-6.0590.0000.0000.0000.000
33B214THR00.0290.00943.349-0.139-0.1390.0000.0000.0000.000
34B215ILE0-0.003-0.00542.752-0.133-0.1330.0000.0000.0000.000
35B216ARG10.8810.89340.3256.6136.6130.0000.0000.0000.000
36B217PHE00.0470.01437.502-0.181-0.1810.0000.0000.0000.000
37B218LYS10.8530.95437.8356.6506.6500.0000.0000.0000.000
38B219SER00.0100.00836.219-0.138-0.1380.0000.0000.0000.000
39B220TYR0-0.073-0.01032.974-0.231-0.2310.0000.0000.0000.000
40B221LEU0-0.013-0.01433.342-0.204-0.2040.0000.0000.0000.000
41B222LEU0-0.053-0.03032.927-0.186-0.1860.0000.0000.0000.000
42B223SER0-0.020-0.01930.573-0.181-0.1810.0000.0000.0000.000
43B224MET0-0.060-0.01327.094-0.349-0.3490.0000.0000.0000.000
44B225GLY00.0540.03228.116-0.294-0.2940.0000.0000.0000.000
45B226ILE0-0.053-0.01630.2350.0170.0170.0000.0000.0000.000
46B227ALA00.0180.01032.2680.2520.2520.0000.0000.0000.000
47B228ASN00.042-0.00235.3770.1220.1220.0000.0000.0000.000
48B229PRO00.0580.02638.2980.1510.1510.0000.0000.0000.000
49B230VAL00.0330.02341.4620.1190.1190.0000.0000.0000.000
50B231THR00.004-0.01641.0130.0820.0820.0000.0000.0000.000
51B232ARG10.8140.89138.0747.3587.3580.0000.0000.0000.000
52B233GLU-1-0.852-0.91742.339-6.788-6.7880.0000.0000.0000.000
53B234THR0-0.0360.00545.2990.1160.1160.0000.0000.0000.000
54B235TYR00.0270.01146.4160.1700.1700.0000.0000.0000.000
55B236GLY00.0220.00645.630-0.140-0.1400.0000.0000.0000.000
56B237SER0-0.036-0.01644.982-0.116-0.1160.0000.0000.0000.000
57B238GLY00.0860.04042.340-0.105-0.1050.0000.0000.0000.000
58B239THR0-0.011-0.01038.193-0.003-0.0030.0000.0000.0000.000
59B240GLN00.0670.01041.462-0.050-0.0500.0000.0000.0000.000
60B241TYR0-0.040-0.02734.8060.1460.1460.0000.0000.0000.000
61B242HIS00.0370.00236.8680.1990.1990.0000.0000.0000.000
62B243MET00.0300.01540.9210.1240.1240.0000.0000.0000.000
63B244GLN0-0.034-0.02541.1070.2200.2200.0000.0000.0000.000
64B245LEU00.0140.01537.8900.0450.0450.0000.0000.0000.000
65B246ALA00.0180.01041.5790.0330.0330.0000.0000.0000.000
66B247LYS10.9190.94444.7896.3786.3780.0000.0000.0000.000
67B248GLN0-0.036-0.01138.8160.1070.1070.0000.0000.0000.000
68B249LEU00.0180.00240.9100.0350.0350.0000.0000.0000.000
69B250ALA0-0.0070.00144.5830.0660.0660.0000.0000.0000.000
70B251GLY00.0210.01347.4760.0910.0910.0000.0000.0000.000
71B252ILE0-0.055-0.02641.9570.0300.0300.0000.0000.0000.000
72B253LEU00.014-0.00743.866-0.009-0.0090.0000.0000.0000.000
73B254GLN0-0.044-0.01247.3260.0260.0260.0000.0000.0000.000
74B255VAL00.0450.01550.3650.0590.0590.0000.0000.0000.000
75B256PRO00.0350.02246.3960.0400.0400.0000.0000.0000.000
76B257LEU00.005-0.00349.2060.0340.0340.0000.0000.0000.000
77B258GLU-1-0.857-0.90851.276-5.413-5.4130.0000.0000.0000.000
78B259GLU-1-0.898-0.93849.693-6.050-6.0500.0000.0000.0000.000
79B260ARG10.7590.85746.7716.2496.2490.0000.0000.0000.000
80B261GLY00.0300.02852.6300.0090.0090.0000.0000.0000.000
81B262GLY0-0.055-0.04454.3130.0760.0760.0000.0000.0000.000
82B263ILE0-0.035-0.03452.0390.0060.0060.0000.0000.0000.000
83B264MET0-0.0040.01645.066-0.031-0.0310.0000.0000.0000.000
84B265SER00.015-0.02045.471-0.056-0.0560.0000.0000.0000.000
85B266LEU00.041-0.01542.392-0.094-0.0940.0000.0000.0000.000
86B267THR0-0.048-0.00640.264-0.164-0.1640.0000.0000.0000.000
87B268GLU-1-0.787-0.86640.548-6.547-6.5470.0000.0000.0000.000
88B269VAL00.0130.00442.170-0.065-0.0650.0000.0000.0000.000
89B270TYR0-0.031-0.03032.827-0.125-0.1250.0000.0000.0000.000
90B271CYS0-0.073-0.04337.376-0.226-0.2260.0000.0000.0000.000
91B272LEU0-0.058-0.01538.387-0.099-0.0990.0000.0000.0000.000
92B273VAL00.012-0.00337.577-0.038-0.0380.0000.0000.0000.000
93B274ASN0-0.003-0.01333.499-0.076-0.0760.0000.0000.0000.000
94B275ARG10.9861.00234.0147.3527.3520.0000.0000.0000.000
95B276ALA0-0.049-0.01135.612-0.086-0.0860.0000.0000.0000.000
96B277ARG10.8810.93933.3868.3378.3370.0000.0000.0000.000
97B278GLY00.0170.02631.056-0.126-0.1260.0000.0000.0000.000
98B279MET0-0.006-0.01623.605-0.296-0.2960.0000.0000.0000.000
99B280GLU-1-0.901-0.95628.493-9.163-9.1630.0000.0000.0000.000
100B281LEU0-0.047-0.00229.5280.3380.3380.0000.0000.0000.000
101B282LEU0-0.015-0.00831.7400.0380.0380.0000.0000.0000.000
102B283SER00.0740.04031.751-0.007-0.0070.0000.0000.0000.000
103B284PRO00.0400.00232.9970.2340.2340.0000.0000.0000.000
104B285GLU-1-0.858-0.94033.500-8.360-8.3600.0000.0000.0000.000
105B286ASP-1-0.808-0.87034.555-8.049-8.0490.0000.0000.0000.000
106B287LEU00.0000.01237.1370.2130.2130.0000.0000.0000.000
107B288VAL00.0340.01939.3790.2270.2270.0000.0000.0000.000
108B289ASN0-0.042-0.03138.6100.3450.3450.0000.0000.0000.000
109B290ALA0-0.038-0.02641.0890.1570.1570.0000.0000.0000.000
110B291CYS0-0.040-0.02642.8300.1830.1830.0000.0000.0000.000
111B292LYS10.9040.96144.0466.7766.7760.0000.0000.0000.000
112B293MET0-0.061-0.01444.0500.1280.1280.0000.0000.0000.000
113B294LEU0-0.020-0.01146.9980.0790.0790.0000.0000.0000.000
114B295GLU-1-0.828-0.89849.507-5.420-5.4200.0000.0000.0000.000
115B296ALA00.0000.00451.4110.0920.0920.0000.0000.0000.000
116B297LEU0-0.049-0.02647.5050.0380.0380.0000.0000.0000.000
117B298LYS10.8660.92452.1505.3085.3080.0000.0000.0000.000
118B299LEU0-0.029-0.00348.9530.0650.0650.0000.0000.0000.000
119B300PRO00.0320.01352.7700.0140.0140.0000.0000.0000.000
120B301LEU00.0030.01948.2670.0390.0390.0000.0000.0000.000
121B302ARG10.9490.96551.6985.4475.4470.0000.0000.0000.000
122B303LEU0-0.020-0.00446.209-0.037-0.0370.0000.0000.0000.000
123B304ARG10.7800.85949.8355.5915.5910.0000.0000.0000.000
124B305VAL0-0.021-0.02148.522-0.140-0.1400.0000.0000.0000.000
125B306PHE00.0200.01650.8260.1410.1410.0000.0000.0000.000
126B307ASP-1-0.822-0.92151.642-5.464-5.4640.0000.0000.0000.000
127B308SER0-0.077-0.06350.480-0.063-0.0630.0000.0000.0000.000
128B309GLY0-0.007-0.00248.095-0.107-0.1070.0000.0000.0000.000
129B310VAL0-0.045-0.01546.792-0.175-0.1750.0000.0000.0000.000
130B311MET0-0.008-0.00344.6030.0630.0630.0000.0000.0000.000
131B312VAL0-0.016-0.00246.841-0.086-0.0860.0000.0000.0000.000
132B313ILE0-0.014-0.01146.2020.0040.0040.0000.0000.0000.000
133B314GLU-1-0.754-0.84949.407-5.453-5.4530.0000.0000.0000.000
134B315LEU00.0080.01052.829-0.029-0.0290.0000.0000.0000.000
135B316GLN0-0.016-0.00854.8130.0530.0530.0000.0000.0000.000
136B317SER0-0.045-0.03357.4830.0340.0340.0000.0000.0000.000
137B318HIS10.8290.92656.6615.4075.4070.0000.0000.0000.000
138B319LYS10.8700.91658.4914.7854.7850.0000.0000.0000.000
139B320GLU-1-0.744-0.86256.715-5.295-5.2950.0000.0000.0000.000
140B321GLU-1-0.833-0.90559.815-4.868-4.8680.0000.0000.0000.000
141B322GLU-1-0.872-0.93663.183-4.692-4.6920.0000.0000.0000.000
142B323MET0-0.084-0.03459.8910.0120.0120.0000.0000.0000.000
143B324VAL0-0.0010.00063.0610.0060.0060.0000.0000.0000.000
144B325ALA00.0220.02464.8820.0300.0300.0000.0000.0000.000
145B326SER0-0.011-0.00664.5150.0010.0010.0000.0000.0000.000
146B327ALA00.0290.00662.934-0.008-0.0080.0000.0000.0000.000
147B328LEU00.0050.00364.691-0.004-0.0040.0000.0000.0000.000
148B329GLU-1-0.885-0.95167.990-4.274-4.2740.0000.0000.0000.000
149B330THR0-0.066-0.02663.531-0.008-0.0080.0000.0000.0000.000
150B331VAL0-0.018-0.02564.9710.0090.0090.0000.0000.0000.000
151B332SER0-0.024-0.02467.2260.0440.0440.0000.0000.0000.000
152B333GLU-1-0.905-0.92169.148-4.457-4.4570.0000.0000.0000.000
153B334LYS10.7770.87565.7974.6044.6040.0000.0000.0000.000
154B335GLY0-0.0100.02868.943-0.014-0.0140.0000.0000.0000.000
155B336SER0-0.036-0.03667.203-0.003-0.0030.0000.0000.0000.000
156B337LEU0-0.041-0.01462.117-0.030-0.0300.0000.0000.0000.000
157B338THR00.018-0.02158.675-0.055-0.0550.0000.0000.0000.000
158B339SER00.012-0.02455.837-0.005-0.0050.0000.0000.0000.000
159B340GLU-1-0.901-0.95852.086-5.859-5.8590.0000.0000.0000.000
160B341GLU-1-0.851-0.88055.889-5.034-5.0340.0000.0000.0000.000
161B342PHE00.0250.01458.3940.0140.0140.0000.0000.0000.000
162B343ALA00.005-0.00554.2110.0140.0140.0000.0000.0000.000
163B344LYS10.9180.95054.9235.5075.5070.0000.0000.0000.000
164B345LEU0-0.043-0.01356.8310.0150.0150.0000.0000.0000.000
165B346VAL0-0.013-0.00558.8610.0390.0390.0000.0000.0000.000
166B347GLY0-0.0230.01455.581-0.012-0.0120.0000.0000.0000.000
167B348MET0-0.050-0.01653.427-0.011-0.0110.0000.0000.0000.000
168B349SER00.0250.00449.1870.0120.0120.0000.0000.0000.000
169B350VAL00.0770.02050.4170.0710.0710.0000.0000.0000.000
170B351LEU0-0.034-0.01346.7510.0810.0810.0000.0000.0000.000
171B352LEU00.032-0.00249.9440.0670.0670.0000.0000.0000.000
172B353ALA00.0280.03152.8880.1060.1060.0000.0000.0000.000
173B354LYS10.9740.98352.8265.6835.6830.0000.0000.0000.000
174B355GLU-1-0.855-0.89752.615-5.621-5.6210.0000.0000.0000.000
175B356ARG10.8730.92455.8975.3065.3060.0000.0000.0000.000
176B357LEU00.0220.00658.6950.0930.0930.0000.0000.0000.000
177B358LEU00.0140.00656.1470.0680.0680.0000.0000.0000.000
178B359LEU0-0.065-0.01359.6870.0630.0630.0000.0000.0000.000
179B360ALA00.0550.01061.4050.0770.0770.0000.0000.0000.000
180B361GLU-1-0.800-0.85762.368-4.844-4.8440.0000.0000.0000.000
181B362LYS10.8590.93159.0805.2165.2160.0000.0000.0000.000
182B363MET0-0.091-0.03564.7090.0270.0270.0000.0000.0000.000
183B364GLY00.0050.00767.3570.0720.0720.0000.0000.0000.000
184B365HIS00.0180.00467.8360.0820.0820.0000.0000.0000.000
185B366LEU0-0.036-0.01364.3070.0300.0300.0000.0000.0000.000
186B367CYS0-0.030-0.00867.5340.0030.0030.0000.0000.0000.000
187B368ARG10.7700.84359.9774.9714.9710.0000.0000.0000.000
188B369ASP-1-0.883-0.94765.151-4.575-4.5750.0000.0000.0000.000
189B370ASP-1-0.852-0.93160.862-5.163-5.1630.0000.0000.0000.000
190B371SER0-0.0020.00162.8260.0460.0460.0000.0000.0000.000
191B372VAL0-0.007-0.01760.879-0.080-0.0800.0000.0000.0000.000
192B373GLU-1-0.894-0.92960.262-4.815-4.8150.0000.0000.0000.000
193B374GLY0-0.0090.00559.437-0.062-0.0620.0000.0000.0000.000
194B375LEU0-0.071-0.02457.9690.0630.0630.0000.0000.0000.000
195B376ARG10.8410.91060.6684.7614.7610.0000.0000.0000.000
196B377PHE0-0.038-0.01659.6520.0150.0150.0000.0000.0000.000
197B378TYR00.0350.00864.9760.0400.0400.0000.0000.0000.000
198B379PRO00.0500.02468.651-0.022-0.0220.0000.0000.0000.000
199B380ASN0-0.027-0.02670.8110.0450.0450.0000.0000.0000.000
200B381LEU00.003-0.01672.3410.0520.0520.0000.0000.0000.000
201B382PHE0-0.0080.00472.0210.0610.0610.0000.0000.0000.000
202B383MET0-0.066-0.02073.8070.0490.0490.0000.0000.0000.000
203B384THR0-0.041-0.01576.6300.0250.0250.0000.0000.0000.000
204B385GLN00.0000.00879.1280.0120.0120.0000.0000.0000.000