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: 827LY

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2227216.450919
FMO2-HF: Nuclear repulsion 2143516.953561
FMO2-HF: Total energy -83699.497358
FMO2-MP2: Total energy -83939.753083


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.
-15.134-9.5218.64-5.96-8.2940.014
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 : 0.058 / q_NPA : 0.032
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-1-0.861-0.9302.671-0.9632.3891.429-1.962-2.8190.012
4A3THR0-0.022-0.0082.098-15.269-13.9817.194-3.685-4.7980.001
5A4LEU0-0.029-0.0183.687-0.1280.5800.014-0.255-0.4660.001
6A5CYS0-0.033-0.0095.9290.3140.3140.0000.0000.0000.000
7A6GLN00.0150.0116.251-0.465-0.4650.0000.0000.0000.000
8A7ARG10.9250.9577.5061.2921.2920.0000.0000.0000.000
9A8LEU0-0.0010.0039.6690.0820.0820.0000.0000.0000.000
10A9ASN00.0160.00711.5950.0450.0450.0000.0000.0000.000
11A10VAL00.0500.04612.8080.0220.0220.0000.0000.0000.000
12A11CYS0-0.065-0.02713.6550.0230.0230.0000.0000.0000.000
13A12GLN0-0.020-0.02615.5200.0550.0550.0000.0000.0000.000
14A13ASP-1-0.871-0.91717.338-0.120-0.1200.0000.0000.0000.000
15A14LYS10.7700.87918.6570.2460.2460.0000.0000.0000.000
16A15ILE0-0.026-0.01718.3230.0160.0160.0000.0000.0000.000
17A16LEU00.0070.00621.6030.0150.0150.0000.0000.0000.000
18A17THR00.010-0.01022.8550.0160.0160.0000.0000.0000.000
19A18HIS0-0.064-0.05123.2400.0200.0200.0000.0000.0000.000
20A19TYR0-0.041-0.02624.0840.0010.0010.0000.0000.0000.000
21A20GLU-1-0.965-0.97927.536-0.078-0.0780.0000.0000.0000.000
22A21ASN0-0.069-0.03528.4040.0130.0130.0000.0000.0000.000
23A22ASP-1-0.965-0.96230.782-0.082-0.0820.0000.0000.0000.000
24A23SER0-0.024-0.03331.3950.0080.0080.0000.0000.0000.000
25A24THR0-0.016-0.03133.1020.0010.0010.0000.0000.0000.000
26A25ASP-1-0.873-0.92332.883-0.099-0.0990.0000.0000.0000.000
27A26LEU00.0640.02931.757-0.008-0.0080.0000.0000.0000.000
28A27ARG10.8830.93828.0040.1270.1270.0000.0000.0000.000
29A28ASP-1-0.844-0.90627.698-0.139-0.1390.0000.0000.0000.000
30A29HIS00.009-0.00326.772-0.022-0.0220.0000.0000.0000.000
31A30ILE0-0.034-0.00425.355-0.014-0.0140.0000.0000.0000.000
32A31ASP-1-0.813-0.88122.541-0.254-0.2540.0000.0000.0000.000
33A32TYR00.0520.03522.024-0.031-0.0310.0000.0000.0000.000
34A33TRP00.0320.00421.962-0.036-0.0360.0000.0000.0000.000
35A34LYS10.9260.97219.1390.2470.2470.0000.0000.0000.000
36A35HIS0-0.076-0.05616.916-0.075-0.0750.0000.0000.0000.000
37A36MET00.0460.03917.275-0.049-0.0490.0000.0000.0000.000
38A37ARG10.9110.95217.3710.2630.2630.0000.0000.0000.000
39A38LEU0-0.077-0.03511.318-0.063-0.0630.0000.0000.0000.000
40A39GLU-1-0.797-0.91413.044-0.448-0.4480.0000.0000.0000.000
41A40CYS0-0.061-0.02813.554-0.039-0.0390.0000.0000.0000.000
42A41ALA0-0.003-0.00312.023-0.017-0.0170.0000.0000.0000.000
43A42ILE0-0.020-0.0098.537-0.157-0.1570.0000.0000.0000.000
44A43TYR00.0220.0079.402-0.133-0.1330.0000.0000.0000.000
45A44TYR0-0.067-0.03011.8570.0610.0610.0000.0000.0000.000
46A45LYS10.8960.9376.0280.7710.7710.0000.0000.0000.000
47A46ALA00.0300.0067.622-0.036-0.0360.0000.0000.0000.000
48A47ARG10.8890.9418.5840.3830.3830.0000.0000.0000.000
49A48GLU-1-0.881-0.9419.661-0.392-0.3920.0000.0000.0000.000
50A49MET0-0.123-0.0453.770-0.0340.2310.003-0.058-0.2110.000
51A50GLY00.0040.0148.2760.1150.1150.0000.0000.0000.000
52A51PHE0-0.029-0.0105.8420.0490.0490.0000.0000.0000.000
53A52LYS10.9450.94510.5960.0420.0420.0000.0000.0000.000
54A53HIS0-0.0070.00412.697-0.021-0.0210.0000.0000.0000.000
55A54ILE00.0440.0138.695-0.029-0.0290.0000.0000.0000.000
56A55ASN00.003-0.00210.6730.1010.1010.0000.0000.0000.000
57A56HIS0-0.017-0.01613.020-0.022-0.0220.0000.0000.0000.000
58A57GLN00.0410.04515.198-0.014-0.0140.0000.0000.0000.000
59A58VAL00.013-0.00715.409-0.024-0.0240.0000.0000.0000.000
60A59VAL00.0080.02411.997-0.027-0.0270.0000.0000.0000.000
61A60PRO0-0.0050.00515.2610.0390.0390.0000.0000.0000.000
62A61THR0-0.010-0.01716.192-0.033-0.0330.0000.0000.0000.000
63A62LEU00.0730.02713.512-0.009-0.0090.0000.0000.0000.000
64A63ALA00.0030.00217.008-0.015-0.0150.0000.0000.0000.000
65A64VAL00.0160.01420.0170.0020.0020.0000.0000.0000.000
66A65SER00.0380.01015.4310.0130.0130.0000.0000.0000.000
67A66LYS10.9780.99117.6820.1960.1960.0000.0000.0000.000
68A67ASN0-0.0110.00118.6650.0110.0110.0000.0000.0000.000
69A68LYS11.0061.00419.7100.2210.2210.0000.0000.0000.000
70A69ALA00.0230.00517.3390.0000.0000.0000.0000.0000.000
71A70LEU0-0.038-0.02419.3540.0050.0050.0000.0000.0000.000
72A71GLN00.0480.02522.3480.0020.0020.0000.0000.0000.000
73A72ALA00.0470.02820.6730.0090.0090.0000.0000.0000.000
74A73ILE0-0.088-0.05018.9730.0000.0000.0000.0000.0000.000
75A74GLU-1-0.844-0.88722.830-0.127-0.1270.0000.0000.0000.000
76A75LEU00.0280.02426.0340.0100.0100.0000.0000.0000.000
77A76GLN0-0.047-0.03621.825-0.020-0.0200.0000.0000.0000.000
78A77LEU0-0.027-0.01424.9600.0070.0070.0000.0000.0000.000
79A78THR00.0270.01627.5600.0130.0130.0000.0000.0000.000
80A79LEU00.018-0.00228.4360.0090.0090.0000.0000.0000.000
81A80GLU-1-0.877-0.93825.573-0.184-0.1840.0000.0000.0000.000
82A81THR0-0.0220.00630.2710.0070.0070.0000.0000.0000.000
83A82ILE00.0270.01733.3000.0070.0070.0000.0000.0000.000
84A83TYR0-0.001-0.00232.2820.0040.0040.0000.0000.0000.000
85A84ASN0-0.104-0.05431.9870.0070.0070.0000.0000.0000.000
86A85SER0-0.008-0.01335.8210.0070.0070.0000.0000.0000.000
87A86GLN00.001-0.00838.9290.0000.0000.0000.0000.0000.000
88A87TYR00.011-0.00839.4790.0030.0030.0000.0000.0000.000
89A88SER0-0.0180.01636.4850.0000.0000.0000.0000.0000.000
90A89ASN0-0.020-0.01737.269-0.004-0.0040.0000.0000.0000.000
91A90GLU-1-0.851-0.89039.818-0.067-0.0670.0000.0000.0000.000
92A91LYS10.9530.98338.8000.0630.0630.0000.0000.0000.000
93A92TRP0-0.012-0.01134.718-0.001-0.0010.0000.0000.0000.000
94A93THR0-0.021-0.03834.819-0.003-0.0030.0000.0000.0000.000
95A94LEU00.0830.02928.189-0.004-0.0040.0000.0000.0000.000
96A95GLN0-0.027-0.01831.715-0.009-0.0090.0000.0000.0000.000
97A96ASP-1-0.811-0.87034.153-0.083-0.0830.0000.0000.0000.000
98A97VAL0-0.038-0.00729.847-0.001-0.0010.0000.0000.0000.000
99A98SER00.0140.00629.763-0.012-0.0120.0000.0000.0000.000
100A99LEU00.004-0.02126.2130.0020.0020.0000.0000.0000.000
101A100GLU-1-0.916-0.94629.748-0.083-0.0830.0000.0000.0000.000
102A101VAL00.0410.02932.6960.0060.0060.0000.0000.0000.000
103A102TYR0-0.079-0.05830.4890.0050.0050.0000.0000.0000.000
104A103LEU0-0.032-0.03529.5450.0020.0020.0000.0000.0000.000
105A104THR0-0.033-0.00633.9070.0060.0060.0000.0000.0000.000
106A105ALA0-0.044-0.00937.415-0.001-0.0010.0000.0000.0000.000
107A106PRO00.021-0.00340.1730.0020.0020.0000.0000.0000.000
108A107THR00.009-0.00534.620-0.005-0.0050.0000.0000.0000.000
109A108GLY00.0210.01433.2160.0020.0020.0000.0000.0000.000
110A109CYS00.0050.02234.2890.0010.0010.0000.0000.0000.000
111A110ILE00.0140.00831.708-0.001-0.0010.0000.0000.0000.000
112A111LYS10.7810.90035.6500.0890.0890.0000.0000.0000.000
113A112LYS10.8240.90438.2880.0750.0750.0000.0000.0000.000
114A113HIS0-0.062-0.04540.7740.0020.0020.0000.0000.0000.000
115A114GLY00.0540.02942.7100.0020.0020.0000.0000.0000.000
116A115TYR0-0.045-0.02043.8150.0020.0020.0000.0000.0000.000
117A116THR00.002-0.00546.846-0.002-0.0020.0000.0000.0000.000
118A117VAL0-0.033-0.00448.2980.0020.0020.0000.0000.0000.000
119A118GLU-1-0.878-0.92950.007-0.036-0.0360.0000.0000.0000.000
120A119VAL0-0.009-0.01152.2530.0010.0010.0000.0000.0000.000
121A120GLN00.0240.02353.9850.0000.0000.0000.0000.0000.000
122A121PHE00.009-0.02051.9310.0010.0010.0000.0000.0000.000
123A122ASP-1-0.861-0.93257.478-0.024-0.0240.0000.0000.0000.000
124A123GLY00.0020.02260.9260.0010.0010.0000.0000.0000.000
125A124ASP-1-0.911-0.94458.777-0.024-0.0240.0000.0000.0000.000
126A125ILE00.008-0.01157.168-0.001-0.0010.0000.0000.0000.000
127A126CYS0-0.053-0.01755.430-0.001-0.0010.0000.0000.0000.000
128A127ASN0-0.063-0.02454.089-0.002-0.0020.0000.0000.0000.000
129A128THR00.026-0.00552.7520.0000.0000.0000.0000.0000.000
130A129MET0-0.0470.00845.787-0.001-0.0010.0000.0000.0000.000
131A130HIS0-0.045-0.03747.296-0.001-0.0010.0000.0000.0000.000
132A131TYR0-0.061-0.07445.564-0.001-0.0010.0000.0000.0000.000
133A132THR0-0.004-0.00242.0520.0010.0010.0000.0000.0000.000
134A133ASN0-0.022-0.00744.612-0.003-0.0030.0000.0000.0000.000
135A134TRP00.040-0.00738.910-0.002-0.0020.0000.0000.0000.000
136A135THR00.025-0.01244.8820.0010.0010.0000.0000.0000.000
137A136HIS00.0050.05443.0250.0010.0010.0000.0000.0000.000
138A137ILE00.0000.00640.787-0.004-0.0040.0000.0000.0000.000
139A138TYR0-0.050-0.06137.8910.0030.0030.0000.0000.0000.000
140A139ILE00.0140.00938.187-0.004-0.0040.0000.0000.0000.000
141A140CYS0-0.063-0.02934.6020.0020.0020.0000.0000.0000.000
142A141GLU-1-0.818-0.88836.471-0.073-0.0730.0000.0000.0000.000
143A142GLU-1-0.928-0.96134.368-0.079-0.0790.0000.0000.0000.000
144A143ALA0-0.066-0.04034.251-0.006-0.0060.0000.0000.0000.000
145A144SER0-0.027-0.00635.6220.0020.0020.0000.0000.0000.000
146A145VAL00.019-0.02236.866-0.003-0.0030.0000.0000.0000.000
147A146THR0-0.0120.00639.5430.0040.0040.0000.0000.0000.000
148A147VAL0-0.040-0.00442.148-0.002-0.0020.0000.0000.0000.000
149A148VAL0-0.018-0.00943.7550.0030.0030.0000.0000.0000.000
150A149GLU-1-0.885-0.93445.511-0.047-0.0470.0000.0000.0000.000
151A150GLY0-0.010-0.00247.0950.0000.0000.0000.0000.0000.000
152A151GLN0-0.115-0.07047.7090.0030.0030.0000.0000.0000.000
153A152VAL00.0400.01050.648-0.001-0.0010.0000.0000.0000.000
154A153ASP-1-0.798-0.89453.060-0.037-0.0370.0000.0000.0000.000
155A154TYR00.0090.00155.2570.0000.0000.0000.0000.0000.000
156A155TYR0-0.009-0.01654.8220.0010.0010.0000.0000.0000.000
157A156GLY00.0580.02151.161-0.001-0.0010.0000.0000.0000.000
158A157LEU0-0.038-0.00346.6820.0010.0010.0000.0000.0000.000
159A158TYR00.009-0.01447.966-0.001-0.0010.0000.0000.0000.000
160A159TYR00.0700.04442.7110.0000.0000.0000.0000.0000.000
161A160VAL0-0.023-0.02548.0450.0010.0010.0000.0000.0000.000
162A161HIS0-0.005-0.01842.9870.0010.0010.0000.0000.0000.000
163A162GLU-1-0.910-0.95346.209-0.055-0.0550.0000.0000.0000.000
164A163GLY0-0.049-0.02249.1320.0010.0010.0000.0000.0000.000
165A164ILE0-0.027-0.00747.8890.0020.0020.0000.0000.0000.000
166A165ARG10.8420.93349.2460.0380.0380.0000.0000.0000.000
167A166THR00.0050.00044.3880.0020.0020.0000.0000.0000.000
168A167TYR0-0.050-0.03547.5050.0000.0000.0000.0000.0000.000
169A168PHE0-0.039-0.02342.982-0.002-0.0020.0000.0000.0000.000
170A169VAL0-0.0050.00544.187-0.002-0.0020.0000.0000.0000.000
171A170GLN00.0210.01546.8020.0040.0040.0000.0000.0000.000
172A171PHE00.0180.00849.7060.0000.0000.0000.0000.0000.000
173A172LYS10.7950.87850.9680.0400.0400.0000.0000.0000.000
174A173ASP-1-0.859-0.91748.211-0.043-0.0430.0000.0000.0000.000
175A174ASP-1-0.770-0.86347.897-0.045-0.0450.0000.0000.0000.000
176A175ALA0-0.0200.00350.4790.0010.0010.0000.0000.0000.000
177A176GLU-1-0.827-0.90652.517-0.034-0.0340.0000.0000.0000.000
178A177LYS10.8040.92045.5420.0460.0460.0000.0000.0000.000
179A178TYR0-0.010-0.02647.3340.0000.0000.0000.0000.0000.000
180A179SER0-0.0090.00953.4120.0020.0020.0000.0000.0000.000
181A180LYS10.8710.93557.0060.0240.0240.0000.0000.0000.000
182A181ASN0-0.060-0.04859.6110.0010.0010.0000.0000.0000.000
183A182LYS10.8420.91056.3630.0310.0310.0000.0000.0000.000
184A183VAL00.0190.00759.7230.0000.0000.0000.0000.0000.000
185A184TRP0-0.027-0.01456.3620.0000.0000.0000.0000.0000.000
186A185GLU-1-0.928-0.95858.584-0.026-0.0260.0000.0000.0000.000
187A186VAL0-0.030-0.01054.246-0.001-0.0010.0000.0000.0000.000
188A187HIS00.0350.01355.4790.0010.0010.0000.0000.0000.000
189A188ALA00.0260.00653.461-0.002-0.0020.0000.0000.0000.000
190A189GLY00.0310.01954.037-0.001-0.0010.0000.0000.0000.000
191A190GLY0-0.036-0.01355.7280.0000.0000.0000.0000.0000.000
192A191GLN0-0.046-0.03358.7940.0020.0020.0000.0000.0000.000
193A192VAL00.0210.02058.901-0.001-0.0010.0000.0000.0000.000
194A193ILE0-0.038-0.00956.8820.0010.0010.0000.0000.0000.000
195A194LEU00.0300.00960.3140.0000.0000.0000.0000.0000.000
196A195CYS0-0.010-0.00962.311-0.001-0.0010.0000.0000.0000.000
197A196PRO0-0.0050.00961.8010.0010.0010.0000.0000.0000.000
198A197THR0-0.019-0.00964.2390.0000.0000.0000.0000.0000.000
199A198SER0-0.027-0.02366.6130.0000.0000.0000.0000.0000.000
200A199VAL00.0120.00966.463-0.001-0.0010.0000.0000.0000.000
201A200PHE0-0.0010.00668.4800.0010.0010.0000.0000.0000.000