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: 7JRLK

Calculation Name: 2NNU-A-Xray311

Preferred Name: Bromodomain-containing protein 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2NNU

Chain ID: A

ChEMBL ID: CHEMBL1163125

UniProt ID: O60885

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 203
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2233635.090461
FMO2-HF: Nuclear repulsion 2149765.856034
FMO2-HF: Total energy -83869.234427
FMO2-MP2: Total energy -84110.039675


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(A:-1:ACE )


Summations of interaction energy for fragment #1(A:-1:ACE )
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.
0.5621.626-0.001-0.444-0.6190
Interaction energy analysis for fragmet #1(A:-1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.003
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].
3A1MET 00.0540.0223.8300.9601.784-0.006-0.370-0.4480.000
4A2GLU -1-0.891-0.9467.056-0.434-0.4340.0000.0000.0000.000
5A3THR 0-0.0030.0063.7540.2780.4920.005-0.065-0.1550.000
6A4LEU 0-0.035-0.0255.4090.3880.3880.0000.0000.0000.000
7A5CYS 0-0.025-0.0067.6120.1210.1210.0000.0000.0000.000
8A6GLN 00.0160.0148.6960.0950.0950.0000.0000.0000.000
9A7ARG 10.9200.9547.514-0.466-0.4660.0000.0000.0000.000
10A8LEU 00.0020.00310.7290.0200.0200.0000.0000.0000.000
11A9ASN 00.0340.01713.1170.0060.0060.0000.0000.0000.000
12A10VAL 00.0290.03414.3120.0100.0100.0000.0000.0000.000
13A11CYS 0-0.084-0.03114.4160.0140.0140.0000.0000.0000.000
14A12GLN 00.009-0.01116.383-0.015-0.0150.0000.0000.0000.000
15A13ASP -1-0.872-0.91718.705-0.009-0.0090.0000.0000.0000.000
16A14LYS 10.8010.88019.424-0.087-0.0870.0000.0000.0000.000
17A15ILE 0-0.032-0.01419.2360.0000.0000.0000.0000.0000.000
18A16LEU 00.0080.00422.633-0.003-0.0030.0000.0000.0000.000
19A17THR 00.0190.00524.307-0.002-0.0020.0000.0000.0000.000
20A18HIS 0-0.071-0.05423.730-0.005-0.0050.0000.0000.0000.000
21A19TYR 0-0.0410.00125.0840.0010.0010.0000.0000.0000.000
22A20GLU -1-0.967-0.97928.8020.0040.0040.0000.0000.0000.000
23A21ASN 0-0.070-0.03628.774-0.004-0.0040.0000.0000.0000.000
24A22ASP -1-0.967-0.96031.6280.0240.0240.0000.0000.0000.000
25A23SER 0-0.037-0.03131.744-0.001-0.0010.0000.0000.0000.000
26A24THR 0-0.020-0.03633.610-0.001-0.0010.0000.0000.0000.000
27A25ASP -1-0.867-0.92532.7990.0530.0530.0000.0000.0000.000
28A26LEU 00.0640.02931.7190.0030.0030.0000.0000.0000.000
29A27ARG 10.8780.93727.200-0.082-0.0820.0000.0000.0000.000
30A28ASP -1-0.845-0.91127.7950.0640.0640.0000.0000.0000.000
31A29HIS 00.013-0.00127.0110.0070.0070.0000.0000.0000.000
32A30ILE 0-0.0170.00324.9240.0060.0060.0000.0000.0000.000
33A31ASP -1-0.834-0.88622.4210.1170.1170.0000.0000.0000.000
34A32TYR 00.030-0.00222.1980.0120.0120.0000.0000.0000.000
35A33TRP 00.0380.00622.1850.0090.0090.0000.0000.0000.000
36A34LYS 10.9340.97518.299-0.175-0.1750.0000.0000.0000.000
37A35HIS 0-0.076-0.05417.2930.0350.0350.0000.0000.0000.000
38A36MET 00.0510.04017.5220.0050.0050.0000.0000.0000.000
39A37ARG 10.9070.95416.787-0.194-0.1940.0000.0000.0000.000
40A38LEU 0-0.080-0.04211.1680.0360.0360.0000.0000.0000.000
41A39GLU -1-0.817-0.92513.1560.0610.0610.0000.0000.0000.000
42A40CYS 0-0.037-0.01014.145-0.021-0.0210.0000.0000.0000.000
43A41ALA 0-0.007-0.00311.559-0.008-0.0080.0000.0000.0000.000
44A42ILE 0-0.031-0.0119.4190.0320.0320.0000.0000.0000.000
45A43TYR 00.0380.00810.246-0.063-0.0630.0000.0000.0000.000
46A44TYR 0-0.064-0.02311.892-0.053-0.0530.0000.0000.0000.000
47A45LYS 10.9730.9825.203-0.524-0.5240.0000.0000.0000.000
48A46ALA 00.020-0.0038.877-0.112-0.1120.0000.0000.0000.000
49A47ARG 10.8850.9459.8970.0170.0170.0000.0000.0000.000
50A48GLU -1-0.937-0.98210.2940.1550.1550.0000.0000.0000.000
51A49MET 0-0.122-0.0405.670-0.129-0.1030.000-0.009-0.0160.000
52A50GLY 00.0040.0169.687-0.082-0.0820.0000.0000.0000.000
53A51PHE 0-0.029-0.0118.720-0.009-0.0090.0000.0000.0000.000
54A52LYS 10.9360.94413.2900.1660.1660.0000.0000.0000.000
55A53HIS 0-0.0020.01215.5160.0370.0370.0000.0000.0000.000
56A54ILE 00.0320.00710.606-0.058-0.0580.0000.0000.0000.000
57A55ASN 00.0220.00314.1810.0000.0000.0000.0000.0000.000
58A56HIS 0-0.025-0.02216.3410.0290.0290.0000.0000.0000.000
59A57GLN 00.0140.02517.5760.0310.0310.0000.0000.0000.000
60A58VAL 00.012-0.00417.662-0.018-0.0180.0000.0000.0000.000
61A59VAL 00.0020.01813.8860.0130.0130.0000.0000.0000.000
62A60PRO 00.0000.00516.764-0.006-0.0060.0000.0000.0000.000
63A61THR 0-0.003-0.01217.307-0.003-0.0030.0000.0000.0000.000
64A62LEU 00.0720.02614.1640.0070.0070.0000.0000.0000.000
65A63ALA 00.0010.00217.5810.0170.0170.0000.0000.0000.000
66A64VAL 00.0080.01020.7140.0080.0080.0000.0000.0000.000
67A65SER 00.0420.01116.0820.0050.0050.0000.0000.0000.000
68A66LYS 10.9790.99317.930-0.085-0.0850.0000.0000.0000.000
69A67ASN 00.0020.00118.7380.0130.0130.0000.0000.0000.000
70A68LYS 10.9971.00320.195-0.019-0.0190.0000.0000.0000.000
71A69ALA 00.0330.00917.3440.0060.0060.0000.0000.0000.000
72A70LEU 0-0.050-0.03219.2870.0090.0090.0000.0000.0000.000
73A71GLN 00.0480.02622.049-0.001-0.0010.0000.0000.0000.000
74A72ALA 00.0390.02720.557-0.001-0.0010.0000.0000.0000.000
75A73ILE 0-0.080-0.04618.3620.0080.0080.0000.0000.0000.000
76A74GLU -1-0.839-0.88322.3130.0690.0690.0000.0000.0000.000
77A75LEU 00.0240.01425.751-0.003-0.0030.0000.0000.0000.000
78A76GLN 0-0.038-0.02921.2530.0100.0100.0000.0000.0000.000
79A77LEU 0-0.039-0.02223.9070.0000.0000.0000.0000.0000.000
80A78THR 00.0320.01826.796-0.005-0.0050.0000.0000.0000.000
81A79LEU 00.005-0.01028.163-0.004-0.0040.0000.0000.0000.000
82A80GLU -1-0.896-0.94724.8560.1240.1240.0000.0000.0000.000
83A81THR 0-0.0200.00029.489-0.002-0.0020.0000.0000.0000.000
84A82ILE 00.0190.01232.446-0.004-0.0040.0000.0000.0000.000
85A83TYR 0-0.014-0.00131.675-0.002-0.0020.0000.0000.0000.000
86A84ASN 0-0.058-0.03231.346-0.004-0.0040.0000.0000.0000.000
87A85SER 0-0.012-0.01134.976-0.004-0.0040.0000.0000.0000.000
88A86GLN 0-0.015-0.02238.1170.0000.0000.0000.0000.0000.000
89A87TYR 00.0180.00038.906-0.002-0.0020.0000.0000.0000.000
90A88SER 0-0.0290.01135.956-0.002-0.0020.0000.0000.0000.000
91A89ASN 0-0.020-0.01737.0640.0010.0010.0000.0000.0000.000
92A90GLU -1-0.859-0.90139.6320.0340.0340.0000.0000.0000.000
93A91LYS 10.9490.97638.819-0.023-0.0230.0000.0000.0000.000
94A92TRP 0-0.004-0.01334.7220.0000.0000.0000.0000.0000.000
95A93THR 0-0.010-0.00335.2410.0010.0010.0000.0000.0000.000
96A94LEU 00.0970.02728.4640.0020.0020.0000.0000.0000.000
97A95GLN 00.0010.00132.0270.0020.0020.0000.0000.0000.000
98A96ASP -1-0.827-0.90834.5320.0330.0330.0000.0000.0000.000
99A97VAL 0-0.043-0.01029.8390.0020.0020.0000.0000.0000.000
100A98SER 00.0040.00329.9830.0040.0040.0000.0000.0000.000
101A99LEU 00.011-0.01526.7320.0010.0010.0000.0000.0000.000
102A100GLU -1-0.941-0.96330.0140.0170.0170.0000.0000.0000.000
103A101VAL 00.0310.02533.129-0.001-0.0010.0000.0000.0000.000
104A102TYR 0-0.079-0.06030.396-0.001-0.0010.0000.0000.0000.000
105A103LEU 0-0.030-0.03429.8550.0010.0010.0000.0000.0000.000
106A104THR 0-0.046-0.01434.061-0.003-0.0030.0000.0000.0000.000
107A105ALA 0-0.034-0.00537.6460.0020.0020.0000.0000.0000.000
108A106PRO 00.0250.00140.240-0.001-0.0010.0000.0000.0000.000
109A107THR 00.007-0.00234.5770.0020.0020.0000.0000.0000.000
110A108GLY 00.0260.01532.9960.0010.0010.0000.0000.0000.000
111A109CYS 00.0120.03034.0570.0020.0020.0000.0000.0000.000
112A110ILE 00.0140.00631.549-0.002-0.0020.0000.0000.0000.000
113A111LYS 10.7710.89435.459-0.036-0.0360.0000.0000.0000.000
114A112LYS 10.8560.93638.312-0.036-0.0360.0000.0000.0000.000
115A113HIS 0-0.058-0.03440.786-0.001-0.0010.0000.0000.0000.000
116A114GLY 00.0530.02542.9420.0000.0000.0000.0000.0000.000
117A115TYR 0-0.044-0.02344.048-0.001-0.0010.0000.0000.0000.000
118A116THR 00.0170.00947.1670.0010.0010.0000.0000.0000.000
119A117VAL 0-0.039-0.01048.7290.0000.0000.0000.0000.0000.000
120A118GLU -1-0.913-0.95550.4460.0080.0080.0000.0000.0000.000
121A119VAL 0-0.030-0.02352.5820.0000.0000.0000.0000.0000.000
122A120GLN 00.0300.02654.5270.0000.0000.0000.0000.0000.000
123A121PHE 0-0.011-0.03352.6310.0000.0000.0000.0000.0000.000
124A122ASP -1-0.957-1.00258.0220.0050.0050.0000.0000.0000.000
125A123GLY 00.0160.03561.5220.0000.0000.0000.0000.0000.000
126A124ASP -1-0.917-0.94959.6690.0030.0030.0000.0000.0000.000
127A125ILE 0-0.006-0.02258.0820.0000.0000.0000.0000.0000.000
128A126CYS 0-0.090-0.03656.3240.0000.0000.0000.0000.0000.000
129A127ASN 0-0.016-0.00154.9050.0000.0000.0000.0000.0000.000
130A128THR 00.014-0.00853.3000.0010.0010.0000.0000.0000.000
131A129MET 0-0.078-0.01646.469-0.001-0.0010.0000.0000.0000.000
132A130HIS 00.0230.00747.7930.0010.0010.0000.0000.0000.000
133A131TYR 0-0.070-0.07245.9960.0000.0000.0000.0000.0000.000
134A132THR 0-0.007-0.00842.407-0.001-0.0010.0000.0000.0000.000
135A133ASN 00.0170.01744.8230.0020.0020.0000.0000.0000.000
136A134TRP 00.020-0.01839.2930.0000.0000.0000.0000.0000.000
137A135THR 00.004-0.03144.9270.0000.0000.0000.0000.0000.000
138A136HIS 00.0060.05442.7920.0000.0000.0000.0000.0000.000
139A137ILE 00.0060.00940.5050.0010.0010.0000.0000.0000.000
140A138TYR 0-0.041-0.05337.471-0.001-0.0010.0000.0000.0000.000
141A139ILE 00.0090.00237.7560.0020.0020.0000.0000.0000.000
142A140CYS 0-0.040-0.01234.2940.0010.0010.0000.0000.0000.000
143A141GLU -1-0.845-0.91235.7500.0460.0460.0000.0000.0000.000
144A142GLU -1-0.947-0.97533.3670.0600.0600.0000.0000.0000.000
145A143ALA 0-0.041-0.01933.2590.0040.0040.0000.0000.0000.000
146A144SER 0-0.039-0.01234.539-0.003-0.0030.0000.0000.0000.000
147A145VAL 00.018-0.01736.2370.0010.0010.0000.0000.0000.000
148A146THR 00.0010.01038.771-0.002-0.0020.0000.0000.0000.000
149A147VAL 0-0.063-0.01041.5760.0000.0000.0000.0000.0000.000
150A148VAL 0-0.021-0.01743.257-0.002-0.0020.0000.0000.0000.000
151A149GLU -1-0.935-0.96745.2080.0220.0220.0000.0000.0000.000
152A150GLY 0-0.020-0.00847.0160.0000.0000.0000.0000.0000.000
153A151GLN 0-0.056-0.03447.585-0.002-0.0020.0000.0000.0000.000
154A152VAL 00.0190.00050.6050.0000.0000.0000.0000.0000.000
155A153ASP -1-0.778-0.88053.0780.0160.0160.0000.0000.0000.000
156A154TYR 00.006-0.00155.3510.0000.0000.0000.0000.0000.000
157A155TYR 0-0.034-0.02254.765-0.001-0.0010.0000.0000.0000.000
158A156GLY 00.0660.02151.2160.0000.0000.0000.0000.0000.000
159A157LEU 0-0.0380.00146.8070.0000.0000.0000.0000.0000.000
160A158TYR 0-0.017-0.01947.8040.0010.0010.0000.0000.0000.000
161A159TYR 00.0780.04642.2960.0000.0000.0000.0000.0000.000
162A160VAL 0-0.048-0.03847.7480.0000.0000.0000.0000.0000.000
163A161HIS 00.0270.00842.280-0.002-0.0020.0000.0000.0000.000
164A162GLU -1-0.907-0.95344.7470.0380.0380.0000.0000.0000.000
165A163GLY 0-0.051-0.02148.375-0.001-0.0010.0000.0000.0000.000
166A164ILE 0-0.014-0.00147.267-0.002-0.0020.0000.0000.0000.000
167A165ARG 10.8810.95148.726-0.019-0.0190.0000.0000.0000.000
168A166THR 00.0060.00544.0760.0000.0000.0000.0000.0000.000
169A167TYR 0-0.094-0.06947.2510.0000.0000.0000.0000.0000.000
170A168PHE 0-0.031-0.02342.9110.0010.0010.0000.0000.0000.000
171A169VAL 00.0020.01044.2390.0000.0000.0000.0000.0000.000
172A170GLN 00.0250.00746.902-0.001-0.0010.0000.0000.0000.000
173A171PHE 00.0270.01650.0020.0000.0000.0000.0000.0000.000
174A172LYS 10.9410.96052.120-0.015-0.0150.0000.0000.0000.000
175A173ASP -1-0.885-0.92948.0010.0150.0150.0000.0000.0000.000
176A174ASP -1-0.838-0.91148.2310.0110.0110.0000.0000.0000.000
177A175ALA 0-0.035-0.01250.907-0.001-0.0010.0000.0000.0000.000
178A176GLU -1-1.000-0.99752.7110.0100.0100.0000.0000.0000.000
179A177LYS 10.8820.96645.165-0.010-0.0100.0000.0000.0000.000
180A178TYR 0-0.029-0.02547.697-0.001-0.0010.0000.0000.0000.000
181A179SER 00.0020.01654.043-0.001-0.0010.0000.0000.0000.000
182A180LYS 10.9300.96657.588-0.003-0.0030.0000.0000.0000.000
183A181ASN 00.0250.02760.1730.0000.0000.0000.0000.0000.000
184A182LYS 10.9210.94957.205-0.011-0.0110.0000.0000.0000.000
185A183VAL 00.007-0.01160.0390.0010.0010.0000.0000.0000.000
186A184TRP 0-0.014-0.00356.438-0.001-0.0010.0000.0000.0000.000
187A185GLU -1-0.954-0.96859.0310.0080.0080.0000.0000.0000.000
188A186VAL 0-0.022-0.00854.5960.0000.0000.0000.0000.0000.000
189A187HIS 00.0450.01955.8670.0000.0000.0000.0000.0000.000
190A188ALA 00.0200.00253.6790.0000.0000.0000.0000.0000.000
191A189GLY 00.0240.01654.2870.0010.0010.0000.0000.0000.000
192A190GLY 0-0.033-0.01356.0550.0000.0000.0000.0000.0000.000
193A191GLN 0-0.058-0.03559.073-0.001-0.0010.0000.0000.0000.000
194A192VAL 00.0300.02259.1970.0000.0000.0000.0000.0000.000
195A193ILE 0-0.028-0.00557.0000.0000.0000.0000.0000.0000.000
196A194LEU 00.0360.00960.5770.0000.0000.0000.0000.0000.000
197A195CYS 0-0.012-0.01162.4820.0010.0010.0000.0000.0000.000
198A196PRO 0-0.0050.01061.8310.0000.0000.0000.0000.0000.000
199A197THR 0-0.030-0.01963.9060.0000.0000.0000.0000.0000.000
200A198SER 0-0.030-0.01966.6670.0000.0000.0000.0000.0000.000
201A199VAL 00.0230.01566.6520.0000.0000.0000.0000.0000.000
202A200PHE 0-0.037-0.02768.7350.0000.0000.0000.0000.0000.000
203A201NME 00.0290.02868.9970.0000.0000.0000.0000.0000.000