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: GNR11

Calculation Name: 2NNU-A-Xray372

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: 2023-03-13

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2226516.994537
FMO2-HF: Nuclear repulsion 2142818.629076
FMO2-HF: Total energy -83698.365461
FMO2-MP2: Total energy -83938.654263


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-16.211-9.5925.328-4.767-7.1810.03
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.083 / q_NPA : 0.035
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].
3A2GLU-1-0.894-0.9502.363-4.446-1.0401.480-2.069-2.8180.008
4A3THR0-0.0020.0062.199-9.729-7.4303.833-2.410-3.7220.021
5A4LEU0-0.032-0.0243.740-1.609-0.9220.013-0.240-0.4610.001
6A5CYS0-0.024-0.0055.8640.0200.0200.0000.0000.0000.000
7A6GLN00.0150.0136.4820.0930.0930.0000.0000.0000.000
8A7ARG10.9210.9557.511-0.134-0.1340.0000.0000.0000.000
9A8LEU00.0050.0049.789-0.006-0.0060.0000.0000.0000.000
10A9ASN00.0330.01611.6740.0090.0090.0000.0000.0000.000
11A10VAL00.0270.03313.1140.0040.0040.0000.0000.0000.000
12A11CYS0-0.081-0.03013.6890.0130.0130.0000.0000.0000.000
13A12GLN00.008-0.01215.617-0.005-0.0050.0000.0000.0000.000
14A13ASP-1-0.874-0.91817.510-0.089-0.0890.0000.0000.0000.000
15A14LYS10.7980.87918.9080.0160.0160.0000.0000.0000.000
16A15ILE0-0.026-0.01218.3080.0060.0060.0000.0000.0000.000
17A16LEU00.0060.00321.6860.0040.0040.0000.0000.0000.000
18A17THR00.0190.00523.3560.0020.0020.0000.0000.0000.000
19A18HIS0-0.071-0.05323.1980.0020.0020.0000.0000.0000.000
20A19TYR0-0.0410.00123.9530.0050.0050.0000.0000.0000.000
21A20GLU-1-0.968-0.98027.677-0.048-0.0480.0000.0000.0000.000
22A21ASN0-0.070-0.03628.418-0.001-0.0010.0000.0000.0000.000
23A22ASP-1-0.967-0.96030.867-0.013-0.0130.0000.0000.0000.000
24A23SER0-0.038-0.03131.3690.0020.0020.0000.0000.0000.000
25A24THR0-0.020-0.03633.1750.0010.0010.0000.0000.0000.000
26A25ASP-1-0.867-0.92532.7800.0070.0070.0000.0000.0000.000
27A26LEU00.0630.02931.6850.0000.0000.0000.0000.0000.000
28A27ARG10.8790.93628.002-0.020-0.0200.0000.0000.0000.000
29A28ASP-1-0.845-0.91127.782-0.002-0.0020.0000.0000.0000.000
30A29HIS00.014-0.00126.766-0.001-0.0010.0000.0000.0000.000
31A30ILE0-0.0180.00225.1870.0020.0020.0000.0000.0000.000
32A31ASP-1-0.832-0.88622.6210.0080.0080.0000.0000.0000.000
33A32TYR00.030-0.00221.9680.0010.0010.0000.0000.0000.000
34A33TRP00.0390.00621.757-0.001-0.0010.0000.0000.0000.000
35A34LYS10.9330.97518.817-0.054-0.0540.0000.0000.0000.000
36A35HIS0-0.078-0.05416.9710.0050.0050.0000.0000.0000.000
37A36MET00.0590.04217.006-0.008-0.0080.0000.0000.0000.000
38A37ARG10.9010.95317.052-0.086-0.0860.0000.0000.0000.000
39A38LEU0-0.082-0.04211.1670.0110.0110.0000.0000.0000.000
40A39GLU-1-0.816-0.92412.761-0.072-0.0720.0000.0000.0000.000
41A40CYS0-0.040-0.01213.284-0.023-0.0230.0000.0000.0000.000
42A41ALA0-0.003-0.00211.8140.0030.0030.0000.0000.0000.000
43A42ILE0-0.029-0.0108.301-0.009-0.0090.0000.0000.0000.000
44A43TYR00.0370.0089.220-0.077-0.0770.0000.0000.0000.000
45A44TYR0-0.058-0.02111.765-0.014-0.0140.0000.0000.0000.000
46A45LYS10.9670.9806.018-0.792-0.7920.0000.0000.0000.000
47A46ALA00.019-0.0037.5950.0270.0270.0000.0000.0000.000
48A47ARG10.8880.9468.5350.0750.0750.0000.0000.0000.000
49A48GLU-1-0.932-0.98110.0390.3900.3900.0000.0000.0000.000
50A49MET0-0.130-0.0434.2280.2560.4830.002-0.048-0.1800.000
51A50GLY00.0060.0168.269-0.018-0.0180.0000.0000.0000.000
52A51PHE0-0.031-0.0115.541-0.099-0.0990.0000.0000.0000.000
53A52LYS10.9380.94510.5760.0570.0570.0000.0000.0000.000
54A53HIS0-0.0020.01212.5120.0250.0250.0000.0000.0000.000
55A54ILE00.0290.0078.590-0.062-0.0620.0000.0000.0000.000
56A55ASN00.0240.00411.1010.0010.0010.0000.0000.0000.000
57A56HIS0-0.025-0.02313.0940.0320.0320.0000.0000.0000.000
58A57GLN00.0140.02515.1960.0350.0350.0000.0000.0000.000
59A58VAL00.011-0.00415.409-0.017-0.0170.0000.0000.0000.000
60A59VAL00.0030.01912.0210.0030.0030.0000.0000.0000.000
61A60PRO0-0.0010.00415.1240.0170.0170.0000.0000.0000.000
62A61THR0-0.002-0.01216.1420.0030.0030.0000.0000.0000.000
63A62LEU00.0730.02613.667-0.010-0.0100.0000.0000.0000.000
64A63ALA0-0.0020.00017.0390.0030.0030.0000.0000.0000.000
65A64VAL00.0080.01019.9340.0000.0000.0000.0000.0000.000
66A65SER00.0470.01315.216-0.003-0.0030.0000.0000.0000.000
67A66LYS10.9770.99217.576-0.109-0.1090.0000.0000.0000.000
68A67ASN0-0.0010.00018.6140.0080.0080.0000.0000.0000.000
69A68LYS10.9971.00319.5950.0170.0170.0000.0000.0000.000
70A69ALA00.0320.01017.243-0.001-0.0010.0000.0000.0000.000
71A70LEU0-0.049-0.03319.1990.0060.0060.0000.0000.0000.000
72A71GLN00.0480.02622.233-0.004-0.0040.0000.0000.0000.000
73A72ALA00.0430.02820.462-0.001-0.0010.0000.0000.0000.000
74A73ILE0-0.083-0.04718.8650.0030.0030.0000.0000.0000.000
75A74GLU-1-0.840-0.88422.6460.0420.0420.0000.0000.0000.000
76A75LEU00.0250.01425.845-0.001-0.0010.0000.0000.0000.000
77A76GLN0-0.036-0.02721.6530.0010.0010.0000.0000.0000.000
78A77LEU0-0.041-0.02424.7410.0000.0000.0000.0000.0000.000
79A78THR00.0260.01627.352-0.001-0.0010.0000.0000.0000.000
80A79LEU00.013-0.00828.139-0.002-0.0020.0000.0000.0000.000
81A80GLU-1-0.897-0.94725.4650.0500.0500.0000.0000.0000.000
82A81THR0-0.022-0.00130.0130.0000.0000.0000.0000.0000.000
83A82ILE00.0190.01333.072-0.002-0.0020.0000.0000.0000.000
84A83TYR0-0.010-0.00132.144-0.002-0.0020.0000.0000.0000.000
85A84ASN0-0.060-0.03332.195-0.003-0.0030.0000.0000.0000.000
86A85SER0-0.015-0.01135.6510.0000.0000.0000.0000.0000.000
87A86GLN0-0.012-0.02138.704-0.001-0.0010.0000.0000.0000.000
88A87TYR00.0190.00139.180-0.001-0.0010.0000.0000.0000.000
89A88SER0-0.0300.00936.277-0.002-0.0020.0000.0000.0000.000
90A89ASN0-0.019-0.01637.196-0.002-0.0020.0000.0000.0000.000
91A90GLU-1-0.858-0.90139.7840.0080.0080.0000.0000.0000.000
92A91LYS10.9470.97538.7210.0030.0030.0000.0000.0000.000
93A92TRP0-0.004-0.01234.5070.0010.0010.0000.0000.0000.000
94A93THR0-0.009-0.00334.701-0.002-0.0020.0000.0000.0000.000
95A94LEU00.0970.02727.8430.0020.0020.0000.0000.0000.000
96A95GLN0-0.0010.00031.4050.0000.0000.0000.0000.0000.000
97A96ASP-1-0.829-0.90933.8310.0030.0030.0000.0000.0000.000
98A97VAL0-0.041-0.00929.4200.0030.0030.0000.0000.0000.000
99A98SER00.0040.00229.4580.0020.0020.0000.0000.0000.000
100A99LEU00.013-0.01426.1450.0020.0020.0000.0000.0000.000
101A100GLU-1-0.942-0.96429.495-0.003-0.0030.0000.0000.0000.000
102A101VAL00.0290.02432.4400.0010.0010.0000.0000.0000.000
103A102TYR0-0.076-0.05930.4420.0010.0010.0000.0000.0000.000
104A103LEU0-0.030-0.03529.4450.0030.0030.0000.0000.0000.000
105A104THR0-0.045-0.01333.7120.0000.0000.0000.0000.0000.000
106A105ALA0-0.036-0.00537.2060.0020.0020.0000.0000.0000.000
107A106PRO00.0250.00239.987-0.002-0.0020.0000.0000.0000.000
108A107THR00.006-0.00434.4060.0000.0000.0000.0000.0000.000
109A108GLY00.0250.01433.0450.0020.0020.0000.0000.0000.000
110A109CYS00.0120.03134.1190.0020.0020.0000.0000.0000.000
111A110ILE00.0150.00631.505-0.002-0.0020.0000.0000.0000.000
112A111LYS10.7730.89435.398-0.013-0.0130.0000.0000.0000.000
113A112LYS10.8570.93737.999-0.009-0.0090.0000.0000.0000.000
114A113HIS0-0.057-0.03440.475-0.001-0.0010.0000.0000.0000.000
115A114GLY00.0510.02542.4160.0010.0010.0000.0000.0000.000
116A115TYR0-0.043-0.02343.524-0.001-0.0010.0000.0000.0000.000
117A116THR00.0150.00846.4210.0010.0010.0000.0000.0000.000
118A117VAL0-0.038-0.00948.0260.0000.0000.0000.0000.0000.000
119A118GLU-1-0.912-0.95549.7710.0000.0000.0000.0000.0000.000
120A119VAL0-0.019-0.01951.9920.0000.0000.0000.0000.0000.000
121A120GLN00.0200.02353.7800.0000.0000.0000.0000.0000.000
122A121PHE0-0.009-0.03251.9400.0010.0010.0000.0000.0000.000
123A122ASP-1-0.958-1.00357.3020.0030.0030.0000.0000.0000.000
124A123GLY00.0150.03460.7640.0000.0000.0000.0000.0000.000
125A124ASP-1-0.917-0.94958.7620.0010.0010.0000.0000.0000.000
126A125ILE0-0.004-0.02156.9770.0000.0000.0000.0000.0000.000
127A126CYS0-0.092-0.03755.2270.0000.0000.0000.0000.0000.000
128A127ASN0-0.016-0.00153.8950.0000.0000.0000.0000.0000.000
129A128THR00.016-0.00852.4250.0010.0010.0000.0000.0000.000
130A129MET0-0.080-0.01745.723-0.001-0.0010.0000.0000.0000.000
131A130HIS00.0240.00746.9070.0000.0000.0000.0000.0000.000
132A131TYR0-0.071-0.07245.3480.0000.0000.0000.0000.0000.000
133A132THR0-0.008-0.00941.818-0.001-0.0010.0000.0000.0000.000
134A133ASN00.0160.01744.3800.0020.0020.0000.0000.0000.000
135A134TRP00.021-0.01738.749-0.001-0.0010.0000.0000.0000.000
136A135THR00.009-0.03044.6180.0000.0000.0000.0000.0000.000
137A136HIS00.0040.05342.7430.0000.0000.0000.0000.0000.000
138A137ILE00.0020.00940.5160.0000.0000.0000.0000.0000.000
139A138TYR0-0.040-0.05237.5960.0000.0000.0000.0000.0000.000
140A139ILE00.0110.00337.9710.0010.0010.0000.0000.0000.000
141A140CYS0-0.044-0.01434.8470.0000.0000.0000.0000.0000.000
142A141GLU-1-0.843-0.91136.3160.0310.0310.0000.0000.0000.000
143A142GLU-1-0.947-0.97534.3230.0380.0380.0000.0000.0000.000
144A143ALA0-0.040-0.01834.0960.0010.0010.0000.0000.0000.000
145A144SER0-0.039-0.01335.458-0.003-0.0030.0000.0000.0000.000
146A145VAL00.022-0.01636.7810.0000.0000.0000.0000.0000.000
147A146THR0-0.0060.00839.333-0.001-0.0010.0000.0000.0000.000
148A147VAL0-0.060-0.00941.9290.0000.0000.0000.0000.0000.000
149A148VAL0-0.022-0.01743.5150.0000.0000.0000.0000.0000.000
150A149GLU-1-0.937-0.96845.2700.0080.0080.0000.0000.0000.000
151A150GLY0-0.016-0.00646.8620.0010.0010.0000.0000.0000.000
152A151GLN0-0.058-0.03547.479-0.001-0.0010.0000.0000.0000.000
153A152VAL00.0190.00050.4370.0000.0000.0000.0000.0000.000
154A153ASP-1-0.777-0.87952.8450.0100.0100.0000.0000.0000.000
155A154TYR00.0060.00055.0630.0000.0000.0000.0000.0000.000
156A155TYR0-0.034-0.02354.6250.0000.0000.0000.0000.0000.000
157A156GLY00.0650.02150.9950.0000.0000.0000.0000.0000.000
158A157LEU0-0.0320.00346.428-0.001-0.0010.0000.0000.0000.000
159A158TYR0-0.015-0.01947.7850.0010.0010.0000.0000.0000.000
160A159TYR00.0700.04442.538-0.001-0.0010.0000.0000.0000.000
161A160VAL0-0.046-0.03847.8560.0010.0010.0000.0000.0000.000
162A161HIS00.0270.00942.899-0.002-0.0020.0000.0000.0000.000
163A162GLU-1-0.906-0.95345.5110.0270.0270.0000.0000.0000.000
164A163GLY0-0.051-0.02148.9840.0000.0000.0000.0000.0000.000
165A164ILE0-0.015-0.00147.882-0.001-0.0010.0000.0000.0000.000
166A165ARG10.8810.95149.101-0.013-0.0130.0000.0000.0000.000
167A166THR00.0040.00544.3010.0010.0010.0000.0000.0000.000
168A167TYR0-0.091-0.06847.3470.0000.0000.0000.0000.0000.000
169A168PHE0-0.032-0.02442.7870.0010.0010.0000.0000.0000.000
170A169VAL00.0030.01144.0310.0000.0000.0000.0000.0000.000
171A170GLN00.0230.00746.641-0.001-0.0010.0000.0000.0000.000
172A171PHE00.0260.01649.6280.0000.0000.0000.0000.0000.000
173A172LYS10.9440.96151.723-0.014-0.0140.0000.0000.0000.000
174A173ASP-1-0.888-0.93047.7410.0130.0130.0000.0000.0000.000
175A174ASP-1-0.835-0.90947.6320.0070.0070.0000.0000.0000.000
176A175ALA0-0.035-0.01250.344-0.001-0.0010.0000.0000.0000.000
177A176GLU-1-1.001-0.99852.2650.0110.0110.0000.0000.0000.000
178A177LYS10.8830.96644.487-0.008-0.0080.0000.0000.0000.000
179A178TYR0-0.027-0.02446.902-0.001-0.0010.0000.0000.0000.000
180A179SER00.0000.01653.283-0.001-0.0010.0000.0000.0000.000
181A180LYS10.9310.96656.876-0.003-0.0030.0000.0000.0000.000
182A181ASN00.0200.02459.5410.0010.0010.0000.0000.0000.000
183A182LYS10.9190.94956.915-0.010-0.0100.0000.0000.0000.000
184A183VAL00.009-0.01159.5950.0000.0000.0000.0000.0000.000
185A184TRP0-0.017-0.00356.1110.0000.0000.0000.0000.0000.000
186A185GLU-1-0.953-0.96758.4010.0030.0030.0000.0000.0000.000
187A186VAL0-0.018-0.00754.0920.0000.0000.0000.0000.0000.000
188A187HIS00.0420.01955.2470.0000.0000.0000.0000.0000.000
189A188ALA00.0180.00053.2140.0000.0000.0000.0000.0000.000
190A189GLY00.0260.01653.7650.0000.0000.0000.0000.0000.000
191A190GLY0-0.034-0.01355.4450.0000.0000.0000.0000.0000.000
192A191GLN0-0.056-0.03558.5180.0000.0000.0000.0000.0000.000
193A192VAL00.0270.02258.6450.0000.0000.0000.0000.0000.000
194A193ILE0-0.026-0.00456.6490.0000.0000.0000.0000.0000.000
195A194LEU00.0360.01060.1060.0000.0000.0000.0000.0000.000
196A195CYS0-0.012-0.01162.1380.0010.0010.0000.0000.0000.000
197A196PRO0-0.0020.01061.6310.0000.0000.0000.0000.0000.000
198A197THR0-0.032-0.02063.7300.0000.0000.0000.0000.0000.000
199A198SER0-0.033-0.02066.4660.0000.0000.0000.0000.0000.000
200A199VAL00.0280.01766.2640.0000.0000.0000.0000.0000.000
201A200PHE0-0.0080.00268.3570.0000.0000.0000.0000.0000.000