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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: 8975Y

Calculation Name: 4O9I-X-Xray372

Preferred Name: Chromodomain-helicase-DNA-binding protein 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4O9I

Chain ID: X

ChEMBL ID: CHEMBL4105742

UniProt ID: Q14839

Base Structure: X-ray

Registration Date: 2023-09-22

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2050692.580851
FMO2-HF: Nuclear repulsion 1971302.242079
FMO2-HF: Total energy -79390.338771
FMO2-MP2: Total energy -79620.075856


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(X:16:ASN)


Summations of interaction energy for fragment #1(X:16:ASN)
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.
-6.932-1.0250.166-2.719-3.3540.002
Interaction energy analysis for fragmet #1(X:16:ASN)
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 : -0.009
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].
3X18TYR00.0390.0142.883-1.4792.6530.037-1.981-2.1890.007
4X19PHE00.0140.0293.0401.1012.3680.122-0.592-0.796-0.006
5X20GLN00.0370.0243.538-0.796-0.2740.008-0.146-0.3840.001
6X21MET0-0.0010.0015.405-1.313-1.327-0.0010.0000.0150.000
7X22LYS10.8490.9277.463-3.004-3.0040.0000.0000.0000.000
8X23GLY00.0530.02210.088-0.269-0.2690.0000.0000.0000.000
9X24LYS10.9250.98013.645-0.737-0.7370.0000.0000.0000.000
10X25VAL00.0370.03214.5080.0160.0160.0000.0000.0000.000
11X26GLN0-0.006-0.01716.741-0.050-0.0500.0000.0000.0000.000
12X27LYS10.9490.96818.674-0.515-0.5150.0000.0000.0000.000
13X28ILE0-0.0040.01317.8180.0960.0960.0000.0000.0000.000
14X29LEU0-0.076-0.04417.453-0.059-0.0590.0000.0000.0000.000
15X30ILE00.0490.03017.440-0.047-0.0470.0000.0000.0000.000
16X31TRP0-0.051-0.02016.9870.0900.0900.0000.0000.0000.000
17X32LYS10.9430.98412.0830.0040.0040.0000.0000.0000.000
18X33TRP00.0300.01416.3530.0100.0100.0000.0000.0000.000
19X34GLY0-0.023-0.01213.901-0.017-0.0170.0000.0000.0000.000
20X35GLN0-0.015-0.01013.0040.0840.0840.0000.0000.0000.000
21X36PRO00.0050.01912.006-0.051-0.0510.0000.0000.0000.000
22X37PRO00.0050.0028.509-0.264-0.2640.0000.0000.0000.000
23X38SER00.0420.0169.2390.2850.2850.0000.0000.0000.000
24X39PRO0-0.006-0.0148.695-0.599-0.5990.0000.0000.0000.000
25X40THR0-0.006-0.0169.517-0.183-0.1830.0000.0000.0000.000
26X41PRO0-0.043-0.0185.5280.1680.1680.0000.0000.0000.000
27X42VAL0-0.0150.0126.475-0.622-0.6220.0000.0000.0000.000
28X43PRO0-0.026-0.0167.0810.3750.3750.0000.0000.0000.000
29X44ARG10.8940.95110.2650.9640.9640.0000.0000.0000.000
30X45PRO0-0.0020.01213.996-0.023-0.0230.0000.0000.0000.000
31X46PRO0-0.018-0.03216.3470.0080.0080.0000.0000.0000.000
32X47ASP-1-0.917-0.95318.815-0.486-0.4860.0000.0000.0000.000
33X48ALA0-0.0360.00319.4290.0200.0200.0000.0000.0000.000
34X49ASP-1-0.819-0.93121.368-0.419-0.4190.0000.0000.0000.000
35X50PRO0-0.016-0.00622.364-0.044-0.0440.0000.0000.0000.000
36X51ASN0-0.085-0.03518.3940.0520.0520.0000.0000.0000.000
37X52THR00.0370.01721.249-0.013-0.0130.0000.0000.0000.000
38X53PRO00.0120.01121.518-0.006-0.0060.0000.0000.0000.000
39X54SER0-0.050-0.02118.359-0.036-0.0360.0000.0000.0000.000
40X55PRO00.0240.00415.926-0.048-0.0480.0000.0000.0000.000
41X56LYS10.9830.97216.0970.6200.6200.0000.0000.0000.000
42X57PRO0-0.0270.00814.2440.0870.0870.0000.0000.0000.000
43X58LEU00.010-0.00117.573-0.013-0.0130.0000.0000.0000.000
44X59GLU-1-0.901-0.94117.583-0.725-0.7250.0000.0000.0000.000
45X60GLY0-0.005-0.01017.2010.0710.0710.0000.0000.0000.000
46X61ARG10.9660.96818.2610.2040.2040.0000.0000.0000.000
47X62PRO00.0070.00616.659-0.025-0.0250.0000.0000.0000.000
48X63GLU-1-0.957-0.98012.306-0.195-0.1950.0000.0000.0000.000
49X64ARG10.8260.90715.653-0.084-0.0840.0000.0000.0000.000
50X65GLN0-0.023-0.00911.0320.1200.1200.0000.0000.0000.000
51X66PHE00.021-0.01312.999-0.039-0.0390.0000.0000.0000.000
52X67PHE00.0390.03912.6050.2050.2050.0000.0000.0000.000
53X68VAL00.0200.00212.780-0.123-0.1230.0000.0000.0000.000
54X69LYS10.8910.95014.495-0.652-0.6520.0000.0000.0000.000
55X70TRP00.0750.0249.968-0.061-0.0610.0000.0000.0000.000
56X71GLN0-0.050-0.05415.803-0.099-0.0990.0000.0000.0000.000
57X72GLY00.0000.00817.8430.0710.0710.0000.0000.0000.000
58X73MET0-0.0230.00912.4490.0470.0470.0000.0000.0000.000
59X74SER00.003-0.02817.596-0.049-0.0490.0000.0000.0000.000
60X75TYR00.017-0.03916.5130.1340.1340.0000.0000.0000.000
61X76TRP00.0860.04915.3460.0420.0420.0000.0000.0000.000
62X77HIS0-0.074-0.05612.1200.3960.3960.0000.0000.0000.000
63X78CYS0-0.0830.00711.5150.3190.3190.0000.0000.0000.000
64X79SER00.016-0.0048.3130.1440.1440.0000.0000.0000.000
65X80TRP00.0210.0048.753-0.289-0.2890.0000.0000.0000.000
66X81VAL0-0.021-0.0108.6880.5760.5760.0000.0000.0000.000
67X82SER00.0410.01010.288-0.247-0.2470.0000.0000.0000.000
68X83GLU-1-0.754-0.89411.8250.2590.2590.0000.0000.0000.000
69X84LEU00.0420.03613.7180.0480.0480.0000.0000.0000.000
70X85GLN0-0.022-0.0188.119-0.147-0.1470.0000.0000.0000.000
71X86LEU00.019-0.00213.7020.0440.0440.0000.0000.0000.000
72X87GLU-1-0.950-0.97616.4490.2160.2160.0000.0000.0000.000
73X88LEU0-0.067-0.03415.202-0.016-0.0160.0000.0000.0000.000
74X89HIS0-0.0030.00514.310-0.009-0.0090.0000.0000.0000.000
75X90CYS0-0.114-0.05617.8920.0320.0320.0000.0000.0000.000
76X91GLN00.1120.07020.055-0.069-0.0690.0000.0000.0000.000
77X92VAL00.0060.00022.598-0.034-0.0340.0000.0000.0000.000
78X93MET0-0.040-0.02819.544-0.036-0.0360.0000.0000.0000.000
79X94PHE00.0490.01719.655-0.012-0.0120.0000.0000.0000.000
80X95ARG10.9350.96922.236-0.295-0.2950.0000.0000.0000.000
81X96ASN0-0.058-0.04125.572-0.051-0.0510.0000.0000.0000.000
82X97TYR00.0040.00621.521-0.020-0.0200.0000.0000.0000.000
83X98GLN00.0960.02722.169-0.017-0.0170.0000.0000.0000.000
84X99ARG10.8990.96325.416-0.211-0.2110.0000.0000.0000.000
85X100LYS10.8870.94728.032-0.265-0.2650.0000.0000.0000.000
86X101ASN0-0.076-0.03825.260-0.012-0.0120.0000.0000.0000.000
87X102ASP-1-0.779-0.87027.3170.0510.0510.0000.0000.0000.000
88X103MET0-0.033-0.02223.0270.0270.0270.0000.0000.0000.000
89X104ASP-1-0.908-0.95123.718-0.007-0.0070.0000.0000.0000.000
90X105GLU-1-0.919-0.95124.860-0.056-0.0560.0000.0000.0000.000
91X106PRO0-0.085-0.02721.3510.0260.0260.0000.0000.0000.000
92X107PRO0-0.028-0.03121.719-0.008-0.0080.0000.0000.0000.000
93X108SER00.0060.00623.401-0.013-0.0130.0000.0000.0000.000
94X109GLY00.0000.00423.8230.0060.0060.0000.0000.0000.000
95X110ASP-1-0.880-0.93324.6690.1750.1750.0000.0000.0000.000
96X111PHE0-0.011-0.01827.411-0.021-0.0210.0000.0000.0000.000
97X112GLY00.027-0.00530.6840.0110.0110.0000.0000.0000.000
98X113GLY0-0.019-0.01034.168-0.011-0.0110.0000.0000.0000.000
99X114ASP-1-0.888-0.94635.5540.1000.1000.0000.0000.0000.000
100X115GLU-1-0.848-0.89329.5400.1470.1470.0000.0000.0000.000
101X116GLU-1-0.739-0.83930.9150.0220.0220.0000.0000.0000.000
102X117LYS10.8860.91531.508-0.010-0.0100.0000.0000.0000.000
103X118SER0-0.007-0.01532.741-0.012-0.0120.0000.0000.0000.000
104X119ARG10.8350.90325.560-0.138-0.1380.0000.0000.0000.000
105X120LYS10.7820.88728.136-0.039-0.0390.0000.0000.0000.000
106X121ARG10.9200.95529.796-0.058-0.0580.0000.0000.0000.000
107X122LYS10.8350.92727.298-0.098-0.0980.0000.0000.0000.000
108X123ASN00.0770.02824.0980.0210.0210.0000.0000.0000.000
109X124LYS10.9210.96125.9890.0150.0150.0000.0000.0000.000
110X125ASP-1-0.821-0.89725.9490.0620.0620.0000.0000.0000.000
111X126PRO00.0510.02622.8480.0100.0100.0000.0000.0000.000
112X127LYS10.8710.92517.695-0.241-0.2410.0000.0000.0000.000
113X128PHE0-0.027-0.01821.0860.0380.0380.0000.0000.0000.000
114X129ALA00.011-0.00221.6780.0150.0150.0000.0000.0000.000
115X130GLU-1-0.902-0.93316.2670.1140.1140.0000.0000.0000.000
116X131MET00.001-0.00517.0880.0480.0480.0000.0000.0000.000
117X132GLU-1-0.891-0.95318.7320.1670.1670.0000.0000.0000.000
118X133GLU-1-0.891-0.94314.353-0.083-0.0830.0000.0000.0000.000
119X134ARG10.9911.00711.239-0.862-0.8620.0000.0000.0000.000
120X135PHE0-0.036-0.04114.0510.1240.1240.0000.0000.0000.000
121X136TYR00.0130.00817.4220.0140.0140.0000.0000.0000.000
122X137ARG10.8060.91016.0070.0310.0310.0000.0000.0000.000
123X138TYR0-0.071-0.02914.923-0.050-0.0500.0000.0000.0000.000
124X139GLY00.0240.02019.6270.0430.0430.0000.0000.0000.000
125X140ILE0-0.127-0.05717.4980.0340.0340.0000.0000.0000.000
126X141LYS10.9330.95821.960-0.261-0.2610.0000.0000.0000.000
127X142PRO00.0530.01223.8110.0370.0370.0000.0000.0000.000
128X143GLU-1-0.863-0.94124.6050.2440.2440.0000.0000.0000.000
129X144TRP0-0.051-0.02022.8680.0190.0190.0000.0000.0000.000
130X145MET0-0.0080.00918.6490.0740.0740.0000.0000.0000.000
131X146MET00.0120.01222.160-0.006-0.0060.0000.0000.0000.000
132X147ILE00.0350.03823.9320.0080.0080.0000.0000.0000.000
133X148HIS0-0.036-0.02626.553-0.021-0.0210.0000.0000.0000.000
134X149ARG10.9490.95129.280-0.247-0.2470.0000.0000.0000.000
135X150ILE00.0020.02626.9430.0210.0210.0000.0000.0000.000
136X151LEU0-0.058-0.02528.826-0.026-0.0260.0000.0000.0000.000
137X152ASN00.0350.00529.007-0.020-0.0200.0000.0000.0000.000
138X153HIS00.0300.04127.0500.0170.0170.0000.0000.0000.000
139X154SER0-0.0030.00124.947-0.023-0.0230.0000.0000.0000.000
140X155VAL00.0070.00725.2060.0150.0150.0000.0000.0000.000
141X156ASP-1-0.837-0.88120.4810.5890.5890.0000.0000.0000.000
142X157LYS10.9670.95623.401-0.400-0.4000.0000.0000.0000.000
143X158LYS10.8180.90417.614-0.665-0.6650.0000.0000.0000.000
144X159GLY00.0540.03023.581-0.026-0.0260.0000.0000.0000.000
145X160HIS00.0080.01118.556-0.007-0.0070.0000.0000.0000.000
146X161VAL0-0.048-0.02322.1170.0090.0090.0000.0000.0000.000
147X162HIS0-0.068-0.04118.3050.0750.0750.0000.0000.0000.000
148X163TYR00.0700.01422.652-0.061-0.0610.0000.0000.0000.000
149X164LEU0-0.0300.01023.3570.0470.0470.0000.0000.0000.000
150X165ILE00.0230.00022.240-0.053-0.0530.0000.0000.0000.000
151X166LYS10.8600.93725.612-0.274-0.2740.0000.0000.0000.000
152X167TRP00.0430.01120.528-0.029-0.0290.0000.0000.0000.000
153X168ARG10.8680.93126.432-0.255-0.2550.0000.0000.0000.000
154X169ASP-1-0.858-0.92527.8910.2370.2370.0000.0000.0000.000
155X170LEU0-0.0370.00024.1580.0040.0040.0000.0000.0000.000
156X171PRO0-0.008-0.01728.681-0.011-0.0110.0000.0000.0000.000
157X172TYR00.0340.00128.9690.0220.0220.0000.0000.0000.000
158X173ASP-1-0.891-0.94829.2000.3450.3450.0000.0000.0000.000
159X174GLN0-0.055-0.02425.3640.0430.0430.0000.0000.0000.000
160X175ALA0-0.015-0.00524.7360.0280.0280.0000.0000.0000.000
161X176SER0-0.016-0.01320.7270.0230.0230.0000.0000.0000.000
162X177TRP0-0.046-0.01820.549-0.033-0.0330.0000.0000.0000.000
163X178GLU-1-0.774-0.84217.1310.9920.9920.0000.0000.0000.000
164X179SER00.0240.02016.678-0.065-0.0650.0000.0000.0000.000
165X180GLU-1-0.805-0.90518.8210.3720.3720.0000.0000.0000.000
166X181ASP-1-0.908-0.94316.5520.4980.4980.0000.0000.0000.000
167X182VAL0-0.059-0.01815.5350.0070.0070.0000.0000.0000.000
168X183GLU-1-0.852-0.91816.8110.2640.2640.0000.0000.0000.000
169X184ILE0-0.0020.00618.8370.0140.0140.0000.0000.0000.000
170X185GLN0-0.021-0.03121.218-0.040-0.0400.0000.0000.0000.000
171X186ASP-1-0.884-0.94524.5610.2070.2070.0000.0000.0000.000
172X187TYR0-0.032-0.02720.558-0.026-0.0260.0000.0000.0000.000
173X188ASP-1-0.803-0.91624.4520.2840.2840.0000.0000.0000.000
174X189LEU00.0340.02727.167-0.012-0.0120.0000.0000.0000.000
175X190PHE0-0.025-0.02827.750-0.011-0.0110.0000.0000.0000.000
176X191LYS10.8090.89822.522-0.352-0.3520.0000.0000.0000.000
177X192GLN00.0040.00829.183-0.005-0.0050.0000.0000.0000.000
178X193SER0-0.0140.00032.390-0.010-0.0100.0000.0000.0000.000
179X194TYR0-0.048-0.03730.820-0.007-0.0070.0000.0000.0000.000
180X195TRP00.005-0.02728.975-0.007-0.0070.0000.0000.0000.000
181X196ASN00.0290.01934.100-0.005-0.0050.0000.0000.0000.000
182X197HIS0-0.116-0.05636.847-0.018-0.0180.0000.0000.0000.000
183X198ARG10.8860.94933.329-0.233-0.2330.0000.0000.0000.000
184X199GLU-1-0.922-0.96237.9630.1620.1620.0000.0000.0000.000
185X200LEU0-0.066-0.01740.941-0.007-0.0070.0000.0000.0000.000