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: G5R61

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2050164.254537
FMO2-HF: Nuclear repulsion 1970775.305986
FMO2-HF: Total energy -79388.948551
FMO2-MP2: Total energy -79618.709233


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.
-6.393-0.0200000000000010.133-2.88-3.6280.007
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 : -0.007 / 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].
3X18TYR00.012-0.0112.901-1.7692.6950.030-2.139-2.3560.009
4X19PHE00.0110.0333.1712.1843.4060.089-0.519-0.793-0.004
5X20GLN00.0470.0263.5070.4151.1000.015-0.221-0.4790.002
6X21MET0-0.024-0.0065.196-1.330-1.328-0.001-0.0010.0000.000
7X22LYS10.8540.9127.330-4.083-4.0830.0000.0000.0000.000
8X23GLY00.0460.0219.954-0.357-0.3570.0000.0000.0000.000
9X24LYS10.9150.96913.532-0.779-0.7790.0000.0000.0000.000
10X25VAL00.0380.03314.1680.0390.0390.0000.0000.0000.000
11X26GLN00.0350.01216.421-0.059-0.0590.0000.0000.0000.000
12X27LYS10.9310.95718.267-0.746-0.7460.0000.0000.0000.000
13X28ILE00.0050.01417.7020.1330.1330.0000.0000.0000.000
14X29LEU0-0.064-0.03917.198-0.095-0.0950.0000.0000.0000.000
15X30ILE00.0380.02717.300-0.066-0.0660.0000.0000.0000.000
16X31TRP0-0.044-0.02116.8960.1410.1410.0000.0000.0000.000
17X32LYS10.9861.00312.211-0.450-0.4500.0000.0000.0000.000
18X33TRP00.0370.02616.2100.0400.0400.0000.0000.0000.000
19X34GLY0-0.021-0.01513.7150.0070.0070.0000.0000.0000.000
20X35GLN0-0.035-0.02512.9290.0510.0510.0000.0000.0000.000
21X36PRO00.0130.02511.8070.0040.0040.0000.0000.0000.000
22X37PRO0-0.010-0.0048.488-0.277-0.2770.0000.0000.0000.000
23X38SER00.0380.0159.2360.2630.2630.0000.0000.0000.000
24X39PRO00.006-0.0078.649-0.638-0.6380.0000.0000.0000.000
25X40THR0-0.014-0.0139.479-0.267-0.2670.0000.0000.0000.000
26X41PRO0-0.029-0.0155.4490.1430.1430.0000.0000.0000.000
27X42VAL0-0.0120.0126.436-0.705-0.7050.0000.0000.0000.000
28X43PRO0-0.032-0.0197.0420.4310.4310.0000.0000.0000.000
29X44ARG10.9090.94910.2451.0631.0630.0000.0000.0000.000
30X45PRO00.0010.01213.976-0.029-0.0290.0000.0000.0000.000
31X46PRO0-0.014-0.03416.3390.0230.0230.0000.0000.0000.000
32X47ASP-1-0.921-0.95118.806-0.580-0.5800.0000.0000.0000.000
33X48ALA0-0.0380.00419.5120.0240.0240.0000.0000.0000.000
34X49ASP-1-0.805-0.93021.349-0.460-0.4600.0000.0000.0000.000
35X50PRO0-0.094-0.01122.333-0.045-0.0450.0000.0000.0000.000
36X51ASN0-0.046-0.03618.4840.0490.0490.0000.0000.0000.000
37X52THR00.0350.01721.296-0.017-0.0170.0000.0000.0000.000
38X53PRO00.0130.02321.7370.0040.0040.0000.0000.0000.000
39X54SER0-0.021-0.02318.676-0.028-0.0280.0000.0000.0000.000
40X55PRO00.001-0.01316.831-0.079-0.0790.0000.0000.0000.000
41X56LYS10.9790.97716.0520.5940.5940.0000.0000.0000.000
42X57PRO0-0.0140.01514.1810.0900.0900.0000.0000.0000.000
43X58LEU00.004-0.00217.5270.0010.0010.0000.0000.0000.000
44X59GLU-1-0.899-0.93717.658-0.637-0.6370.0000.0000.0000.000
45X60GLY00.000-0.00617.0000.0630.0630.0000.0000.0000.000
46X61ARG10.9570.96718.0810.1320.1320.0000.0000.0000.000
47X62PRO00.0150.01116.483-0.021-0.0210.0000.0000.0000.000
48X63GLU-1-0.937-0.98212.511-0.028-0.0280.0000.0000.0000.000
49X64ARG10.8380.92315.510-0.197-0.1970.0000.0000.0000.000
50X65GLN0-0.026-0.00910.9660.1640.1640.0000.0000.0000.000
51X66PHE00.000-0.01712.948-0.080-0.0800.0000.0000.0000.000
52X67PHE00.0420.03911.9240.3120.3120.0000.0000.0000.000
53X68VAL00.0070.00012.245-0.228-0.2280.0000.0000.0000.000
54X69LYS10.8830.94614.010-0.811-0.8110.0000.0000.0000.000
55X70TRP00.0690.0229.742-0.167-0.1670.0000.0000.0000.000
56X71GLN0-0.032-0.05215.482-0.127-0.1270.0000.0000.0000.000
57X72GLY0-0.0250.00017.6480.0670.0670.0000.0000.0000.000
58X73MET0-0.0220.01212.3550.0650.0650.0000.0000.0000.000
59X74SER0-0.002-0.02217.338-0.041-0.0410.0000.0000.0000.000
60X75TYR00.021-0.03516.1650.1740.1740.0000.0000.0000.000
61X76TRP00.0750.05014.9580.0970.0970.0000.0000.0000.000
62X77HIS0-0.053-0.03811.7790.5370.5370.0000.0000.0000.000
63X78CYS0-0.0740.00811.1180.4300.4300.0000.0000.0000.000
64X79SER00.0250.0087.8040.1810.1810.0000.0000.0000.000
65X80TRP00.0150.0008.542-0.468-0.4680.0000.0000.0000.000
66X81VAL0-0.039-0.0118.4620.7970.7970.0000.0000.0000.000
67X82SER00.0670.03210.302-0.457-0.4570.0000.0000.0000.000
68X83GLU-1-0.779-0.91311.8190.4050.4050.0000.0000.0000.000
69X84LEU00.0570.04013.5050.0250.0250.0000.0000.0000.000
70X85GLN0-0.032-0.0298.149-0.113-0.1130.0000.0000.0000.000
71X86LEU00.011-0.00613.7940.0140.0140.0000.0000.0000.000
72X87GLU-1-0.946-0.97516.3790.2850.2850.0000.0000.0000.000
73X88LEU0-0.071-0.03415.258-0.036-0.0360.0000.0000.0000.000
74X89HIS0-0.013-0.00114.110-0.030-0.0300.0000.0000.0000.000
75X90CYS0-0.089-0.03817.2570.0220.0220.0000.0000.0000.000
76X91GLN00.1130.06819.788-0.063-0.0630.0000.0000.0000.000
77X92VAL00.0080.00222.385-0.029-0.0290.0000.0000.0000.000
78X93MET0-0.052-0.03419.251-0.028-0.0280.0000.0000.0000.000
79X94PHE00.0570.02119.639-0.003-0.0030.0000.0000.0000.000
80X95ARG10.9550.97022.103-0.364-0.3640.0000.0000.0000.000
81X96ASN0-0.068-0.04025.572-0.063-0.0630.0000.0000.0000.000
82X97TYR0-0.005-0.00121.620-0.023-0.0230.0000.0000.0000.000
83X98GLN00.0990.02322.954-0.011-0.0110.0000.0000.0000.000
84X99ARG10.9000.96525.407-0.295-0.2950.0000.0000.0000.000
85X100LYS10.8880.94627.786-0.385-0.3850.0000.0000.0000.000
86X101ASN0-0.065-0.02625.242-0.017-0.0170.0000.0000.0000.000
87X102ASP-1-0.770-0.87927.2690.1600.1600.0000.0000.0000.000
88X103MET0-0.049-0.02623.0040.0460.0460.0000.0000.0000.000
89X104ASP-1-0.921-0.95723.6710.1060.1060.0000.0000.0000.000
90X105GLU-1-0.929-0.95224.7170.0910.0910.0000.0000.0000.000
91X106PRO0-0.072-0.02621.2030.0300.0300.0000.0000.0000.000
92X107PRO0-0.027-0.02521.528-0.014-0.0140.0000.0000.0000.000
93X108SER00.0100.01023.257-0.008-0.0080.0000.0000.0000.000
94X109GLY0-0.005-0.00123.6780.0270.0270.0000.0000.0000.000
95X110ASP-1-0.884-0.93724.6120.3550.3550.0000.0000.0000.000
96X111PHE0-0.001-0.01227.358-0.021-0.0210.0000.0000.0000.000
97X112GLY00.026-0.00230.6140.0070.0070.0000.0000.0000.000
98X113GLY00.0150.00834.071-0.012-0.0120.0000.0000.0000.000
99X114ASP-1-0.949-0.97034.6630.2040.2040.0000.0000.0000.000
100X115GLU-1-0.849-0.90329.6310.2930.2930.0000.0000.0000.000
101X116GLU-1-0.747-0.85230.9270.1490.1490.0000.0000.0000.000
102X117LYS10.8950.91931.563-0.102-0.1020.0000.0000.0000.000
103X118SER00.003-0.01232.859-0.019-0.0190.0000.0000.0000.000
104X119ARG10.8520.91725.680-0.304-0.3040.0000.0000.0000.000
105X120LYS10.7750.89528.176-0.168-0.1680.0000.0000.0000.000
106X121ARG10.9150.94629.824-0.148-0.1480.0000.0000.0000.000
107X122LYS10.8970.97327.315-0.241-0.2410.0000.0000.0000.000
108X123ASN00.0620.01524.3340.0340.0340.0000.0000.0000.000
109X124LYS10.9130.95826.000-0.083-0.0830.0000.0000.0000.000
110X125ASP-1-0.871-0.93125.7200.1950.1950.0000.0000.0000.000
111X126PRO00.0610.02223.0470.0250.0250.0000.0000.0000.000
112X127LYS10.9060.95518.155-0.473-0.4730.0000.0000.0000.000
113X128PHE0-0.028-0.02521.0940.0570.0570.0000.0000.0000.000
114X129ALA00.0120.00021.7020.0340.0340.0000.0000.0000.000
115X130GLU-1-0.943-0.96916.0150.3810.3810.0000.0000.0000.000
116X131MET0-0.0170.00017.1120.1100.1100.0000.0000.0000.000
117X132GLU-1-0.915-0.96018.7880.3980.3980.0000.0000.0000.000
118X133GLU-1-0.976-0.99414.1150.3660.3660.0000.0000.0000.000
119X134ARG10.9920.9979.571-1.697-1.6970.0000.0000.0000.000
120X135PHE0-0.055-0.04613.4830.1890.1890.0000.0000.0000.000
121X136TYR00.0130.00217.092-0.001-0.0010.0000.0000.0000.000
122X137ARG10.9170.98016.214-0.348-0.3480.0000.0000.0000.000
123X138TYR0-0.072-0.02915.134-0.039-0.0390.0000.0000.0000.000
124X139GLY00.0270.02119.4740.0440.0440.0000.0000.0000.000
125X140ILE0-0.119-0.04916.9490.0290.0290.0000.0000.0000.000
126X141LYS10.9440.96721.428-0.395-0.3950.0000.0000.0000.000
127X142PRO00.0530.01223.3360.0460.0460.0000.0000.0000.000
128X143GLU-1-0.874-0.94724.1680.3840.3840.0000.0000.0000.000
129X144TRP0-0.030-0.00922.0980.0190.0190.0000.0000.0000.000
130X145MET0-0.0150.00218.1960.0880.0880.0000.0000.0000.000
131X146MET00.0010.00521.778-0.012-0.0120.0000.0000.0000.000
132X147ILE00.0340.03723.8060.0040.0040.0000.0000.0000.000
133X148HIS0-0.044-0.02226.271-0.023-0.0230.0000.0000.0000.000
134X149ARG10.9540.94929.017-0.312-0.3120.0000.0000.0000.000
135X150ILE00.0180.03526.8220.0260.0260.0000.0000.0000.000
136X151LEU0-0.061-0.03128.684-0.031-0.0310.0000.0000.0000.000
137X152ASN00.0180.00128.916-0.025-0.0250.0000.0000.0000.000
138X153HIS00.0390.05827.0820.0300.0300.0000.0000.0000.000
139X154SER0-0.032-0.00824.885-0.030-0.0300.0000.0000.0000.000
140X155VAL00.0330.02025.3110.0180.0180.0000.0000.0000.000
141X156ASP-1-0.832-0.89020.5600.5140.5140.0000.0000.0000.000
142X157LYS10.9470.95023.104-0.296-0.2960.0000.0000.0000.000
143X158LYS10.8000.88617.774-0.556-0.5560.0000.0000.0000.000
144X159GLY00.0600.03223.795-0.025-0.0250.0000.0000.0000.000
145X160HIS00.0350.02818.587-0.016-0.0160.0000.0000.0000.000
146X161VAL0-0.031-0.00322.3790.0070.0070.0000.0000.0000.000
147X162HIS0-0.054-0.02418.0590.1010.1010.0000.0000.0000.000
148X163TYR00.0670.01322.706-0.069-0.0690.0000.0000.0000.000
149X164LEU0-0.0270.00823.2660.0580.0580.0000.0000.0000.000
150X165ILE00.0300.00122.063-0.058-0.0580.0000.0000.0000.000
151X166LYS10.8610.94025.384-0.354-0.3540.0000.0000.0000.000
152X167TRP00.0470.00720.494-0.027-0.0270.0000.0000.0000.000
153X168ARG10.9120.94626.109-0.357-0.3570.0000.0000.0000.000
154X169ASP-1-0.885-0.94327.4890.3530.3530.0000.0000.0000.000
155X170LEU0-0.045-0.00623.7970.0060.0060.0000.0000.0000.000
156X171PRO0-0.013-0.01328.298-0.015-0.0150.0000.0000.0000.000
157X172TYR00.0350.00528.6560.0240.0240.0000.0000.0000.000
158X173ASP-1-0.897-0.95328.9500.4230.4230.0000.0000.0000.000
159X174GLN0-0.056-0.02825.0080.0530.0530.0000.0000.0000.000
160X175ALA0-0.008-0.00124.4430.0400.0400.0000.0000.0000.000
161X176SER0-0.018-0.01220.4700.0250.0250.0000.0000.0000.000
162X177TRP0-0.049-0.01520.447-0.033-0.0330.0000.0000.0000.000
163X178GLU-1-0.790-0.86817.0101.2181.2180.0000.0000.0000.000
164X179SER00.0520.03316.887-0.127-0.1270.0000.0000.0000.000
165X180GLU-1-0.838-0.93319.0080.4090.4090.0000.0000.0000.000
166X181ASP-1-0.922-0.95517.2640.4670.4670.0000.0000.0000.000
167X182VAL0-0.065-0.02315.4020.0300.0300.0000.0000.0000.000
168X183GLU-1-0.836-0.90016.6830.4890.4890.0000.0000.0000.000
169X184ILE00.0020.00318.6100.0410.0410.0000.0000.0000.000
170X185GLN00.020-0.00620.984-0.047-0.0470.0000.0000.0000.000
171X186ASP-1-0.897-0.95524.2980.3070.3070.0000.0000.0000.000
172X187TYR0-0.045-0.02720.780-0.036-0.0360.0000.0000.0000.000
173X188ASP-1-0.868-0.95924.9800.3330.3330.0000.0000.0000.000
174X189LEU00.0370.02727.414-0.021-0.0210.0000.0000.0000.000
175X190PHE0-0.042-0.03327.851-0.016-0.0160.0000.0000.0000.000
176X191LYS10.8620.94423.175-0.422-0.4220.0000.0000.0000.000
177X192GLN0-0.0010.00329.328-0.004-0.0040.0000.0000.0000.000
178X193SER0-0.016-0.00132.666-0.016-0.0160.0000.0000.0000.000
179X194TYR0-0.091-0.08331.132-0.008-0.0080.0000.0000.0000.000
180X195TRP0-0.011-0.03629.204-0.013-0.0130.0000.0000.0000.000
181X196ASN00.0440.02534.382-0.012-0.0120.0000.0000.0000.000
182X197HIS0-0.107-0.04236.809-0.020-0.0200.0000.0000.0000.000
183X198ARG10.9330.97134.468-0.240-0.2400.0000.0000.0000.000
184X199GLU-1-0.923-0.95638.0720.1780.1780.0000.0000.0000.000
185X200LEU0-0.066-0.01941.154-0.008-0.0080.0000.0000.0000.000