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: N184Q

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2232038.452006
FMO2-HF: Nuclear repulsion 2148338.601024
FMO2-HF: Total energy -83699.850981
FMO2-MP2: Total energy -83940.029041


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.
-24.898-24.06618.089-8.973-9.9470.031
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 : 0.081 / q_NPA : 0.052
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-1-0.880-0.9392.446-3.690-0.5171.017-1.779-2.4100.008
4A3THR0-0.012-0.0151.847-17.973-21.43817.042-6.789-6.7880.022
5A4LEU0-0.031-0.0163.871-2.386-1.5360.026-0.339-0.5370.001
6A5CYS0-0.035-0.0136.081-0.161-0.1610.0000.0000.0000.000
7A6GLN00.0060.0005.361-0.002-0.0020.0000.0000.0000.000
8A7ARG10.9390.9596.960-0.447-0.4470.0000.0000.0000.000
9A8LEU0-0.0160.0049.558-0.065-0.0650.0000.0000.0000.000
10A9ASN00.0250.02211.715-0.033-0.0330.0000.0000.0000.000
11A10VAL00.0650.04012.908-0.017-0.0170.0000.0000.0000.000
12A11CYS0-0.068-0.01813.540-0.015-0.0150.0000.0000.0000.000
13A12GLN0-0.008-0.02015.392-0.009-0.0090.0000.0000.0000.000
14A13ASP-1-0.867-0.92517.1280.0300.0300.0000.0000.0000.000
15A14LYS10.7780.88718.371-0.066-0.0660.0000.0000.0000.000
16A15ILE0-0.015-0.01418.067-0.004-0.0040.0000.0000.0000.000
17A16LEU0-0.019-0.00321.499-0.003-0.0030.0000.0000.0000.000
18A17THR00.001-0.01922.853-0.002-0.0020.0000.0000.0000.000
19A18HIS0-0.068-0.04922.957-0.004-0.0040.0000.0000.0000.000
20A19TYR0-0.024-0.02223.964-0.002-0.0020.0000.0000.0000.000
21A20GLU-1-0.968-0.98327.313-0.001-0.0010.0000.0000.0000.000
22A21ASN0-0.053-0.02328.178-0.002-0.0020.0000.0000.0000.000
23A22ASP-1-0.918-0.95830.6760.0080.0080.0000.0000.0000.000
24A23SER0-0.026-0.02831.018-0.001-0.0010.0000.0000.0000.000
25A24THR00.005-0.01632.726-0.001-0.0010.0000.0000.0000.000
26A25ASP-1-0.847-0.91632.4870.0280.0280.0000.0000.0000.000
27A26LEU00.0450.01631.3270.0010.0010.0000.0000.0000.000
28A27ARG10.8640.93327.975-0.044-0.0440.0000.0000.0000.000
29A28ASP-1-0.832-0.89327.1620.0330.0330.0000.0000.0000.000
30A29HIS00.0160.00226.2640.0030.0030.0000.0000.0000.000
31A30ILE0-0.033-0.00525.1100.0010.0010.0000.0000.0000.000
32A31ASP-1-0.805-0.87222.0950.0610.0610.0000.0000.0000.000
33A32TYR00.0520.02621.6630.0040.0040.0000.0000.0000.000
34A33TRP00.0250.00821.599-0.001-0.0010.0000.0000.0000.000
35A34LYS10.8170.90419.299-0.072-0.0720.0000.0000.0000.000
36A35HIS0-0.070-0.05017.0860.0150.0150.0000.0000.0000.000
37A36MET00.0520.03716.946-0.006-0.0060.0000.0000.0000.000
38A37ARG10.9070.94816.830-0.075-0.0750.0000.0000.0000.000
39A38LEU0-0.055-0.02111.124-0.005-0.0050.0000.0000.0000.000
40A39GLU-1-0.818-0.91812.631-0.044-0.0440.0000.0000.0000.000
41A40CYS0-0.065-0.03113.327-0.037-0.0370.0000.0000.0000.000
42A41ALA00.001-0.00311.842-0.022-0.0220.0000.0000.0000.000
43A42ILE0-0.023-0.0108.442-0.073-0.0730.0000.0000.0000.000
44A43TYR00.013-0.0069.332-0.132-0.1320.0000.0000.0000.000
45A44TYR0-0.095-0.06311.794-0.028-0.0280.0000.0000.0000.000
46A45LYS10.8650.9196.233-0.010-0.0100.0000.0000.0000.000
47A46ALA00.0270.0077.825-0.109-0.1090.0000.0000.0000.000
48A47ARG10.8810.9498.7440.1450.1450.0000.0000.0000.000
49A48GLU-1-0.829-0.8989.8450.0220.0220.0000.0000.0000.000
50A49MET0-0.117-0.0414.022-0.0690.2050.004-0.066-0.2120.000
51A50GLY00.0120.0168.423-0.018-0.0180.0000.0000.0000.000
52A51PHE0-0.038-0.0166.2960.0010.0010.0000.0000.0000.000
53A52LYS10.9550.94911.1260.1720.1720.0000.0000.0000.000
54A53HIS0-0.0080.00913.1970.0320.0320.0000.0000.0000.000
55A54ILE00.0410.0138.881-0.074-0.0740.0000.0000.0000.000
56A55ASN0-0.017-0.01310.6240.0190.0190.0000.0000.0000.000
57A56HIS0-0.001-0.00912.9230.0070.0070.0000.0000.0000.000
58A57GLN00.0380.03715.4070.0040.0040.0000.0000.0000.000
59A58VAL00.011-0.00315.483-0.023-0.0230.0000.0000.0000.000
60A59VAL0-0.0060.01212.2450.0090.0090.0000.0000.0000.000
61A60PRO00.0020.00315.4200.0060.0060.0000.0000.0000.000
62A61THR0-0.005-0.01316.380-0.016-0.0160.0000.0000.0000.000
63A62LEU00.0520.01913.7870.0020.0020.0000.0000.0000.000
64A63ALA00.0180.00516.9710.0070.0070.0000.0000.0000.000
65A64VAL00.0310.02320.0640.0060.0060.0000.0000.0000.000
66A65SER00.0340.01015.1490.0100.0100.0000.0000.0000.000
67A66LYS10.9860.99417.369-0.012-0.0120.0000.0000.0000.000
68A67ASN0-0.019-0.00318.3480.0120.0120.0000.0000.0000.000
69A68LYS10.9970.99619.3180.0390.0390.0000.0000.0000.000
70A69ALA00.0200.00916.7840.0060.0060.0000.0000.0000.000
71A70LEU0-0.036-0.01918.7980.0090.0090.0000.0000.0000.000
72A71GLN00.0680.03121.8740.0010.0010.0000.0000.0000.000
73A72ALA00.0360.02120.1490.0030.0030.0000.0000.0000.000
74A73ILE0-0.096-0.05318.6190.0070.0070.0000.0000.0000.000
75A74GLU-1-0.851-0.89522.3830.0240.0240.0000.0000.0000.000
76A75LEU00.0320.03225.5380.0010.0010.0000.0000.0000.000
77A76GLN0-0.022-0.02121.2250.0030.0030.0000.0000.0000.000
78A77LEU0-0.019-0.01124.4060.0020.0020.0000.0000.0000.000
79A78THR00.0200.02226.9970.0000.0000.0000.0000.0000.000
80A79LEU00.0200.00727.748-0.001-0.0010.0000.0000.0000.000
81A80GLU-1-0.802-0.89924.8930.0600.0600.0000.0000.0000.000
82A81THR0-0.023-0.00729.4190.0010.0010.0000.0000.0000.000
83A82ILE00.0200.01432.411-0.001-0.0010.0000.0000.0000.000
84A83TYR0-0.008-0.00931.8050.0000.0000.0000.0000.0000.000
85A84ASN0-0.112-0.05131.4610.0010.0010.0000.0000.0000.000
86A85SER00.014-0.00235.240-0.001-0.0010.0000.0000.0000.000
87A86GLN00.008-0.00238.3820.0000.0000.0000.0000.0000.000
88A87TYR00.0270.00438.781-0.001-0.0010.0000.0000.0000.000
89A88SER0-0.032-0.00236.376-0.001-0.0010.0000.0000.0000.000
90A89ASN0-0.042-0.02736.8650.0010.0010.0000.0000.0000.000
91A90GLU-1-0.832-0.86839.4670.0150.0150.0000.0000.0000.000
92A91LYS10.9480.97938.466-0.008-0.0080.0000.0000.0000.000
93A92TRP00.005-0.00734.226-0.001-0.0010.0000.0000.0000.000
94A93THR0-0.029-0.03534.4310.0000.0000.0000.0000.0000.000
95A94LEU00.0430.01128.0820.0010.0010.0000.0000.0000.000
96A95GLN0-0.044-0.02431.2030.0000.0000.0000.0000.0000.000
97A96ASP-1-0.827-0.87633.8230.0100.0100.0000.0000.0000.000
98A97VAL0-0.0130.00129.4810.0010.0010.0000.0000.0000.000
99A98SER00.0000.00229.5100.0000.0000.0000.0000.0000.000
100A99LEU0-0.006-0.02325.7570.0000.0000.0000.0000.0000.000
101A100GLU-1-0.899-0.93829.365-0.002-0.0020.0000.0000.0000.000
102A101VAL00.0310.03132.4020.0000.0000.0000.0000.0000.000
103A102TYR0-0.076-0.05830.2170.0000.0000.0000.0000.0000.000
104A103LEU0-0.035-0.03129.1810.0000.0000.0000.0000.0000.000
105A104THR0-0.009-0.00333.455-0.001-0.0010.0000.0000.0000.000
106A105ALA0-0.0250.00036.9460.0010.0010.0000.0000.0000.000
107A106PRO00.0210.00339.8810.0000.0000.0000.0000.0000.000
108A107THR00.006-0.00534.7460.0010.0010.0000.0000.0000.000
109A108GLY00.0050.00732.9030.0010.0010.0000.0000.0000.000
110A109CYS0-0.0060.01133.9870.0020.0020.0000.0000.0000.000
111A110ILE00.0150.01431.304-0.002-0.0020.0000.0000.0000.000
112A111LYS10.7700.88635.265-0.009-0.0090.0000.0000.0000.000
113A112LYS10.8290.90937.594-0.015-0.0150.0000.0000.0000.000
114A113HIS0-0.055-0.04840.1970.0000.0000.0000.0000.0000.000
115A114GLY00.0480.02842.1460.0000.0000.0000.0000.0000.000
116A115TYR0-0.053-0.02843.308-0.001-0.0010.0000.0000.0000.000
117A116THR00.001-0.00546.4300.0000.0000.0000.0000.0000.000
118A117VAL0-0.036-0.00847.8980.0000.0000.0000.0000.0000.000
119A118GLU-1-0.875-0.92649.524-0.001-0.0010.0000.0000.0000.000
120A119VAL0-0.003-0.01152.0170.0010.0010.0000.0000.0000.000
121A120GLN0-0.0070.01553.6930.0000.0000.0000.0000.0000.000
122A121PHE00.011-0.01751.9530.0000.0000.0000.0000.0000.000
123A122ASP-1-0.819-0.90757.483-0.001-0.0010.0000.0000.0000.000
124A123GLY00.0010.02060.7590.0000.0000.0000.0000.0000.000
125A124ASP-1-0.861-0.91158.850-0.003-0.0030.0000.0000.0000.000
126A125ILE00.0360.00957.4460.0000.0000.0000.0000.0000.000
127A126CYS0-0.066-0.02655.4770.0000.0000.0000.0000.0000.000
128A127ASN0-0.067-0.04354.2910.0000.0000.0000.0000.0000.000
129A128THR00.013-0.01152.8890.0010.0010.0000.0000.0000.000
130A129MET0-0.0210.02245.800-0.001-0.0010.0000.0000.0000.000
131A130HIS0-0.058-0.04947.0380.0000.0000.0000.0000.0000.000
132A131TYR0-0.058-0.07045.2370.0000.0000.0000.0000.0000.000
133A132THR0-0.014-0.01041.9970.0000.0000.0000.0000.0000.000
134A133ASN0-0.021-0.01344.2850.0010.0010.0000.0000.0000.000
135A134TRP00.0450.00038.7230.0000.0000.0000.0000.0000.000
136A135THR00.017-0.00844.6400.0000.0000.0000.0000.0000.000
137A136HIS00.0050.04542.5520.0000.0000.0000.0000.0000.000
138A137ILE0-0.0030.00840.4330.0000.0000.0000.0000.0000.000
139A138TYR0-0.046-0.07437.5160.0000.0000.0000.0000.0000.000
140A139ILE00.0190.02637.5340.0000.0000.0000.0000.0000.000
141A140CYS0-0.057-0.02834.1430.0000.0000.0000.0000.0000.000
142A141GLU-1-0.851-0.91135.7550.0210.0210.0000.0000.0000.000
143A142GLU-1-0.852-0.93134.0640.0320.0320.0000.0000.0000.000
144A143ALA0-0.104-0.05233.2310.0020.0020.0000.0000.0000.000
145A144SER0-0.039-0.01235.110-0.001-0.0010.0000.0000.0000.000
146A145VAL00.005-0.03236.4170.0000.0000.0000.0000.0000.000
147A146THR0-0.0180.00339.1350.0000.0000.0000.0000.0000.000
148A147VAL0-0.040-0.01041.7780.0000.0000.0000.0000.0000.000
149A148VAL0-0.029-0.01743.2180.0000.0000.0000.0000.0000.000
150A149GLU-1-0.881-0.92845.0530.0080.0080.0000.0000.0000.000
151A150GLY00.000-0.00146.4990.0000.0000.0000.0000.0000.000
152A151GLN0-0.094-0.05047.218-0.001-0.0010.0000.0000.0000.000
153A152VAL00.0400.01150.1340.0000.0000.0000.0000.0000.000
154A153ASP-1-0.784-0.88352.7350.0060.0060.0000.0000.0000.000
155A154TYR00.0240.00855.1860.0000.0000.0000.0000.0000.000
156A155TYR00.006-0.00554.7460.0000.0000.0000.0000.0000.000
157A156GLY00.0330.00151.0050.0000.0000.0000.0000.0000.000
158A157LEU0-0.0090.01546.3580.0000.0000.0000.0000.0000.000
159A158TYR0-0.009-0.02447.5500.0000.0000.0000.0000.0000.000
160A159TYR00.0610.04142.3380.0000.0000.0000.0000.0000.000
161A160VAL0-0.027-0.02747.6320.0000.0000.0000.0000.0000.000
162A161HIS00.005-0.01342.530-0.001-0.0010.0000.0000.0000.000
163A162GLU-1-0.920-0.95545.8900.0190.0190.0000.0000.0000.000
164A163GLY0-0.046-0.01448.7480.0000.0000.0000.0000.0000.000
165A164ILE0-0.026-0.01147.114-0.001-0.0010.0000.0000.0000.000
166A165ARG10.8510.93748.909-0.008-0.0080.0000.0000.0000.000
167A166THR00.001-0.00444.0010.0000.0000.0000.0000.0000.000
168A167TYR0-0.072-0.05546.8450.0000.0000.0000.0000.0000.000
169A168PHE0-0.055-0.02642.7170.0010.0010.0000.0000.0000.000
170A169VAL0-0.0060.00243.851-0.001-0.0010.0000.0000.0000.000
171A170GLN00.0110.00746.5550.0000.0000.0000.0000.0000.000
172A171PHE00.0160.01049.4850.0000.0000.0000.0000.0000.000
173A172LYS10.7710.86650.555-0.004-0.0040.0000.0000.0000.000
174A173ASP-1-0.840-0.91148.2710.0030.0030.0000.0000.0000.000
175A174ASP-1-0.747-0.84447.864-0.001-0.0010.0000.0000.0000.000
176A175ALA00.0090.01450.423-0.001-0.0010.0000.0000.0000.000
177A176GLU-1-0.854-0.92152.5380.0020.0020.0000.0000.0000.000
178A177LYS10.8030.91445.5450.0020.0020.0000.0000.0000.000
179A178TYR0-0.031-0.02847.385-0.001-0.0010.0000.0000.0000.000
180A179SER0-0.0160.00153.4650.0000.0000.0000.0000.0000.000
181A180LYS10.7850.88557.0170.0020.0020.0000.0000.0000.000
182A181ASN0-0.067-0.04159.8980.0000.0000.0000.0000.0000.000
183A182LYS10.8500.91056.406-0.003-0.0030.0000.0000.0000.000
184A183VAL00.0140.00159.4900.0000.0000.0000.0000.0000.000
185A184TRP0-0.026-0.00856.080-0.001-0.0010.0000.0000.0000.000
186A185GLU-1-0.882-0.92458.5370.0010.0010.0000.0000.0000.000
187A186VAL0-0.023-0.01153.8860.0000.0000.0000.0000.0000.000
188A187HIS00.004-0.01255.4120.0000.0000.0000.0000.0000.000
189A188ALA00.020-0.00353.3620.0000.0000.0000.0000.0000.000
190A189GLY00.0290.01253.6110.0000.0000.0000.0000.0000.000
191A190GLY0-0.044-0.01655.4640.0000.0000.0000.0000.0000.000
192A191GLN0-0.047-0.02358.5320.0000.0000.0000.0000.0000.000
193A192VAL00.0100.01358.5000.0000.0000.0000.0000.0000.000
194A193ILE0-0.031-0.00456.6350.0000.0000.0000.0000.0000.000
195A194LEU00.0380.01659.8170.0000.0000.0000.0000.0000.000
196A195CYS0-0.012-0.01562.1740.0000.0000.0000.0000.0000.000
197A196PRO0-0.0230.00961.4990.0000.0000.0000.0000.0000.000
198A197THR0-0.018-0.01664.3810.0000.0000.0000.0000.0000.000
199A198SER0-0.012-0.01466.4410.0000.0000.0000.0000.0000.000
200A199VAL00.0290.01965.9750.0000.0000.0000.0000.0000.000
201A200PHE0-0.0080.00468.3020.0000.0000.0000.0000.0000.000