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: NN89Q

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 OptAll
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 -2055274.839169
FMO2-HF: Nuclear repulsion 1975883.652225
FMO2-HF: Total energy -79391.186944
FMO2-MP2: Total energy -79620.994601


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.
-8.688-3.0590.596-2.752-3.472-0.006
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 : -0.005 / q_NPA : -0.006
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].
3X18TYR00.0280.0142.871-0.3122.8350.030-1.570-1.6060.004
4X19PHE00.0080.0172.643-1.2530.3140.533-0.855-1.245-0.013
5X20GLN00.0330.0153.285-1.878-0.9400.034-0.323-0.6490.003
6X21MET0-0.0090.0015.051-1.742-1.765-0.001-0.0040.0280.000
7X22LYS10.8590.9317.614-2.391-2.3910.0000.0000.0000.000
8X23GLY00.0160.0109.889-0.293-0.2930.0000.0000.0000.000
9X24LYS10.9430.98613.455-0.758-0.7580.0000.0000.0000.000
10X25VAL00.0540.02614.5950.0330.0330.0000.0000.0000.000
11X26GLN0-0.023-0.01616.673-0.033-0.0330.0000.0000.0000.000
12X27LYS10.9400.96318.734-0.422-0.4220.0000.0000.0000.000
13X28ILE00.0110.02517.6270.0810.0810.0000.0000.0000.000
14X29LEU0-0.106-0.05217.277-0.044-0.0440.0000.0000.0000.000
15X30ILE00.0410.02517.656-0.042-0.0420.0000.0000.0000.000
16X31TRP0-0.059-0.02417.2310.0690.0690.0000.0000.0000.000
17X32LYS10.9220.97512.2700.3400.3400.0000.0000.0000.000
18X33TRP00.0240.00316.710-0.004-0.0040.0000.0000.0000.000
19X34GLY0-0.037-0.02114.126-0.016-0.0160.0000.0000.0000.000
20X35GLN0-0.008-0.01112.9850.1090.1090.0000.0000.0000.000
21X36PRO00.0120.01812.078-0.091-0.0910.0000.0000.0000.000
22X37PRO0-0.006-0.0098.498-0.279-0.2790.0000.0000.0000.000
23X38SER00.0380.0229.0610.3700.3700.0000.0000.0000.000
24X39PRO00.005-0.0028.679-0.627-0.6270.0000.0000.0000.000
25X40THR0-0.016-0.0239.935-0.131-0.1310.0000.0000.0000.000
26X41PRO0-0.0190.0005.8480.1910.1910.0000.0000.0000.000
27X42VAL0-0.028-0.0107.025-0.345-0.3450.0000.0000.0000.000
28X43PRO0-0.020-0.0137.2800.3200.3200.0000.0000.0000.000
29X44ARG10.8370.91910.4220.9460.9460.0000.0000.0000.000
30X45PRO00.0050.01814.204-0.021-0.0210.0000.0000.0000.000
31X46PRO0-0.033-0.03116.343-0.001-0.0010.0000.0000.0000.000
32X47ASP-1-0.910-0.95718.928-0.452-0.4520.0000.0000.0000.000
33X48ALA00.0010.01119.4470.0240.0240.0000.0000.0000.000
34X49ASP-1-0.866-0.93321.267-0.450-0.4500.0000.0000.0000.000
35X50PRO0-0.024-0.02122.354-0.055-0.0550.0000.0000.0000.000
36X51ASN00.0170.00517.7570.0230.0230.0000.0000.0000.000
37X52THR00.0310.03921.453-0.026-0.0260.0000.0000.0000.000
38X53PRO00.0160.01321.885-0.013-0.0130.0000.0000.0000.000
39X54SER0-0.068-0.02918.173-0.034-0.0340.0000.0000.0000.000
40X55PRO00.0500.01615.849-0.037-0.0370.0000.0000.0000.000
41X56LYS10.9320.93616.5040.7110.7110.0000.0000.0000.000
42X57PRO0-0.0260.01214.4540.0930.0930.0000.0000.0000.000
43X58LEU00.015-0.00117.759-0.012-0.0120.0000.0000.0000.000
44X59GLU-1-0.888-0.93417.392-0.847-0.8470.0000.0000.0000.000
45X60GLY00.000-0.00317.6540.0780.0780.0000.0000.0000.000
46X61ARG10.9310.95718.4120.2660.2660.0000.0000.0000.000
47X62PRO00.0110.01116.615-0.027-0.0270.0000.0000.0000.000
48X63GLU-1-0.925-0.96811.840-0.434-0.4340.0000.0000.0000.000
49X64ARG10.8260.88415.8860.0070.0070.0000.0000.0000.000
50X65GLN0-0.015-0.00811.4570.0780.0780.0000.0000.0000.000
51X66PHE00.012-0.01113.214-0.026-0.0260.0000.0000.0000.000
52X67PHE00.0290.02512.2160.1640.1640.0000.0000.0000.000
53X68VAL00.003-0.01312.619-0.073-0.0730.0000.0000.0000.000
54X69LYS10.9080.95214.158-0.592-0.5920.0000.0000.0000.000
55X70TRP00.0680.0119.758-0.038-0.0380.0000.0000.0000.000
56X71GLN0-0.029-0.02915.597-0.098-0.0980.0000.0000.0000.000
57X72GLY0-0.016-0.00217.5180.0960.0960.0000.0000.0000.000
58X73MET0-0.0150.00812.1130.0110.0110.0000.0000.0000.000
59X74SER00.000-0.02017.380-0.079-0.0790.0000.0000.0000.000
60X75TYR00.021-0.02616.7440.1100.1100.0000.0000.0000.000
61X76TRP00.0690.04115.5320.0330.0330.0000.0000.0000.000
62X77HIS0-0.077-0.05812.2090.3450.3450.0000.0000.0000.000
63X78CYS0-0.072-0.00411.6760.2960.2960.0000.0000.0000.000
64X79SER00.0100.0048.5510.1470.1470.0000.0000.0000.000
65X80TRP00.0170.0048.808-0.155-0.1550.0000.0000.0000.000
66X81VAL0-0.016-0.0028.4930.5110.5110.0000.0000.0000.000
67X82SER00.0570.01810.285-0.190-0.1900.0000.0000.0000.000
68X83GLU-1-0.799-0.90311.8290.1770.1770.0000.0000.0000.000
69X84LEU00.0520.02813.6480.0850.0850.0000.0000.0000.000
70X85GLN0-0.020-0.0147.788-0.217-0.2170.0000.0000.0000.000
71X86LEU00.0200.00813.3930.0880.0880.0000.0000.0000.000
72X87GLU-1-0.930-0.97216.3900.1730.1730.0000.0000.0000.000
73X88LEU0-0.048-0.02714.4580.0010.0010.0000.0000.0000.000
74X89HIS00.0010.00813.7870.0190.0190.0000.0000.0000.000
75X90CYS0-0.087-0.04617.4910.0420.0420.0000.0000.0000.000
76X91GLN00.0500.04319.523-0.081-0.0810.0000.0000.0000.000
77X92VAL0-0.020-0.01022.025-0.042-0.0420.0000.0000.0000.000
78X93MET0-0.033-0.01419.944-0.039-0.0390.0000.0000.0000.000
79X94PHE00.0290.01119.402-0.019-0.0190.0000.0000.0000.000
80X95ARG10.9560.97621.850-0.275-0.2750.0000.0000.0000.000
81X96ASN0-0.030-0.02225.153-0.048-0.0480.0000.0000.0000.000
82X97TYR00.0180.01321.385-0.015-0.0150.0000.0000.0000.000
83X98GLN00.0820.02421.913-0.011-0.0110.0000.0000.0000.000
84X99ARG10.8900.94825.110-0.176-0.1760.0000.0000.0000.000
85X100LYS10.8820.94427.562-0.208-0.2080.0000.0000.0000.000
86X101ASN0-0.069-0.02925.124-0.006-0.0060.0000.0000.0000.000
87X102ASP-1-0.772-0.87227.073-0.019-0.0190.0000.0000.0000.000
88X103MET0-0.040-0.02522.3140.0280.0280.0000.0000.0000.000
89X104ASP-1-0.870-0.92123.298-0.089-0.0890.0000.0000.0000.000
90X105GLU-1-0.897-0.94024.841-0.153-0.1530.0000.0000.0000.000
91X106PRO0-0.075-0.02421.2140.0260.0260.0000.0000.0000.000
92X107PRO0-0.026-0.02522.085-0.001-0.0010.0000.0000.0000.000
93X108SER0-0.0020.00023.251-0.010-0.0100.0000.0000.0000.000
94X109GLY00.0190.01023.952-0.012-0.0120.0000.0000.0000.000
95X110ASP-1-0.871-0.92424.0250.0860.0860.0000.0000.0000.000
96X111PHE0-0.022-0.01926.897-0.022-0.0220.0000.0000.0000.000
97X112GLY00.0330.00430.1870.0140.0140.0000.0000.0000.000
98X113GLY0-0.041-0.02433.666-0.012-0.0120.0000.0000.0000.000
99X114ASP-1-0.867-0.92535.2730.0450.0450.0000.0000.0000.000
100X115GLU-1-0.821-0.89429.0560.0750.0750.0000.0000.0000.000
101X116GLU-1-0.768-0.85431.049-0.049-0.0490.0000.0000.0000.000
102X117LYS10.9120.93331.2910.0380.0380.0000.0000.0000.000
103X118SER0-0.019-0.00432.608-0.010-0.0100.0000.0000.0000.000
104X119ARG10.8150.89325.186-0.059-0.0590.0000.0000.0000.000
105X120LYS10.8110.88728.2360.0330.0330.0000.0000.0000.000
106X121ARG10.8900.94429.837-0.013-0.0130.0000.0000.0000.000
107X122LYS10.8360.91627.353-0.021-0.0210.0000.0000.0000.000
108X123ASN00.0360.01423.9150.0120.0120.0000.0000.0000.000
109X124LYS10.9260.96426.0330.0640.0640.0000.0000.0000.000
110X125ASP-1-0.809-0.87725.491-0.009-0.0090.0000.0000.0000.000
111X126PRO00.0420.01522.7220.0030.0030.0000.0000.0000.000
112X127LYS10.8440.89717.555-0.124-0.1240.0000.0000.0000.000
113X128PHE0-0.004-0.01520.9800.0310.0310.0000.0000.0000.000
114X129ALA00.0130.00121.7570.0090.0090.0000.0000.0000.000
115X130GLU-1-0.883-0.92516.101-0.005-0.0050.0000.0000.0000.000
116X131MET0-0.016-0.00516.8760.0180.0180.0000.0000.0000.000
117X132GLU-1-0.865-0.95318.6720.0390.0390.0000.0000.0000.000
118X133GLU-1-0.892-0.93814.104-0.343-0.3430.0000.0000.0000.000
119X134ARG10.9951.00812.348-0.476-0.4760.0000.0000.0000.000
120X135PHE0-0.046-0.04714.4380.1150.1150.0000.0000.0000.000
121X136TYR00.0000.01017.2830.0240.0240.0000.0000.0000.000
122X137ARG10.8290.91216.1200.2410.2410.0000.0000.0000.000
123X138TYR0-0.080-0.03114.740-0.049-0.0490.0000.0000.0000.000
124X139GLY00.0100.01519.6150.0530.0530.0000.0000.0000.000
125X140ILE0-0.098-0.05917.8790.0520.0520.0000.0000.0000.000
126X141LYS10.9260.96222.205-0.193-0.1930.0000.0000.0000.000
127X142PRO00.0430.01523.5610.0340.0340.0000.0000.0000.000
128X143GLU-1-0.856-0.94124.4980.1860.1860.0000.0000.0000.000
129X144TRP0-0.075-0.03423.2880.0180.0180.0000.0000.0000.000
130X145MET0-0.0150.00718.9100.0770.0770.0000.0000.0000.000
131X146MET00.0060.00522.223-0.008-0.0080.0000.0000.0000.000
132X147ILE00.0390.03423.8890.0080.0080.0000.0000.0000.000
133X148HIS0-0.017-0.00226.746-0.023-0.0230.0000.0000.0000.000
134X149ARG10.9370.95529.383-0.234-0.2340.0000.0000.0000.000
135X150ILE00.0200.03626.6550.0220.0220.0000.0000.0000.000
136X151LEU0-0.073-0.04028.970-0.028-0.0280.0000.0000.0000.000
137X152ASN00.0370.00629.214-0.025-0.0250.0000.0000.0000.000
138X153HIS00.0430.05127.0130.0160.0160.0000.0000.0000.000
139X154SER0-0.029-0.01025.137-0.019-0.0190.0000.0000.0000.000
140X155VAL00.0130.00225.3470.0090.0090.0000.0000.0000.000
141X156ASP-1-0.783-0.86920.3190.6620.6620.0000.0000.0000.000
142X157LYS10.9650.97023.400-0.500-0.5000.0000.0000.0000.000
143X158LYS10.7780.87617.529-0.740-0.7400.0000.0000.0000.000
144X159GLY00.0090.01523.205-0.027-0.0270.0000.0000.0000.000
145X160HIS00.0160.01118.389-0.008-0.0080.0000.0000.0000.000
146X161VAL0-0.040-0.01422.2810.0120.0120.0000.0000.0000.000
147X162HIS0-0.030-0.01618.2220.0580.0580.0000.0000.0000.000
148X163TYR00.0600.00822.565-0.060-0.0600.0000.0000.0000.000
149X164LEU0-0.032-0.00223.4410.0400.0400.0000.0000.0000.000
150X165ILE00.0390.01422.012-0.055-0.0550.0000.0000.0000.000
151X166LYS10.8190.90525.286-0.241-0.2410.0000.0000.0000.000
152X167TRP00.0490.01020.661-0.032-0.0320.0000.0000.0000.000
153X168ARG10.8600.93726.319-0.217-0.2170.0000.0000.0000.000
154X169ASP-1-0.843-0.92927.7450.1940.1940.0000.0000.0000.000
155X170LEU0-0.0030.02024.0700.0050.0050.0000.0000.0000.000
156X171PRO00.003-0.00628.775-0.014-0.0140.0000.0000.0000.000
157X172TYR00.028-0.00129.3350.0180.0180.0000.0000.0000.000
158X173ASP-1-0.885-0.93729.4400.3250.3250.0000.0000.0000.000
159X174GLN0-0.074-0.04725.6430.0360.0360.0000.0000.0000.000
160X175ALA0-0.0040.00524.9840.0140.0140.0000.0000.0000.000
161X176SER0-0.0020.00220.6390.0150.0150.0000.0000.0000.000
162X177TRP0-0.061-0.02420.706-0.041-0.0410.0000.0000.0000.000
163X178GLU-1-0.762-0.83316.9220.9760.9760.0000.0000.0000.000
164X179SER0-0.002-0.02816.866-0.043-0.0430.0000.0000.0000.000
165X180GLU-1-0.830-0.91618.8350.3630.3630.0000.0000.0000.000
166X181ASP-1-0.858-0.89816.0770.5480.5480.0000.0000.0000.000
167X182VAL0-0.061-0.01215.230-0.013-0.0130.0000.0000.0000.000
168X183GLU-1-0.860-0.90816.1690.1600.1600.0000.0000.0000.000
169X184ILE00.0120.00218.2070.0200.0200.0000.0000.0000.000
170X185GLN0-0.040-0.04020.892-0.037-0.0370.0000.0000.0000.000
171X186ASP-1-0.863-0.93124.3520.1670.1670.0000.0000.0000.000
172X187TYR0-0.019-0.02720.374-0.021-0.0210.0000.0000.0000.000
173X188ASP-1-0.789-0.89624.0180.2760.2760.0000.0000.0000.000
174X189LEU00.0380.03626.755-0.008-0.0080.0000.0000.0000.000
175X190PHE0-0.012-0.02827.582-0.006-0.0060.0000.0000.0000.000
176X191LYS10.7930.89022.158-0.334-0.3340.0000.0000.0000.000
177X192GLN00.001-0.00528.797-0.005-0.0050.0000.0000.0000.000
178X193SER0-0.036-0.01132.063-0.006-0.0060.0000.0000.0000.000
179X194TYR0-0.019-0.01630.497-0.005-0.0050.0000.0000.0000.000
180X195TRP00.004-0.02428.971-0.006-0.0060.0000.0000.0000.000
181X196ASN0-0.024-0.01233.9560.0000.0000.0000.0000.0000.000
182X197HIS0-0.079-0.05136.748-0.021-0.0210.0000.0000.0000.000
183X198ARG10.8560.93932.879-0.245-0.2450.0000.0000.0000.000
184X199GLU-1-0.896-0.94837.7250.1650.1650.0000.0000.0000.000
185X200LEU0-0.071-0.01840.801-0.006-0.0060.0000.0000.0000.000