Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: LN459

Calculation Name: 4J8S-A-Xray372

Preferred Name: CCR4-NOT transcription complex subunit 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4J8S

Chain ID: A

ChEMBL ID: CHEMBL4105919

UniProt ID: A5YKK6

Base Structure: X-ray

Registration Date: 2023-09-23

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2109889.841711
FMO2-HF: Nuclear repulsion 2033953.629349
FMO2-HF: Total energy -75936.212362
FMO2-MP2: Total energy -76156.035472


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:815:GLN)


Summations of interaction energy for fragment #1(A:815:GLN)
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.
-13.206-9.4240.733-1.885-2.6290.014
Interaction energy analysis for fragmet #1(A:815:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.013
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].
3A817THR0-0.019-0.0113.861-2.724-0.859-0.005-0.900-0.9600.003
4A818ASP-1-0.826-0.8815.7620.0460.0460.0000.0000.0000.000
5A819LEU0-0.026-0.0228.923-0.018-0.0180.0000.0000.0000.000
6A820SER0-0.003-0.03012.1560.0770.0770.0000.0000.0000.000
7A821GLN0-0.068-0.04011.5040.0760.0760.0000.0000.0000.000
8A822VAL0-0.044-0.01515.4760.0170.0170.0000.0000.0000.000
9A823TRP0-0.025-0.01014.3400.0220.0220.0000.0000.0000.000
10A824PRO0-0.010-0.00217.5050.0130.0130.0000.0000.0000.000
11A825GLU-1-0.784-0.90415.3740.1390.1390.0000.0000.0000.000
12A826ALA0-0.0240.01818.960-0.008-0.0080.0000.0000.0000.000
13A827ASN0-0.011-0.02221.758-0.009-0.0090.0000.0000.0000.000
14A828GLN00.0560.00520.8590.0070.0070.0000.0000.0000.000
15A829HIS0-0.081-0.03124.0040.0040.0040.0000.0000.0000.000
16A830PHE0-0.025-0.01925.9900.0010.0010.0000.0000.0000.000
17A831SER00.0250.02420.7350.0040.0040.0000.0000.0000.000
18A832LYS10.8870.93422.010-0.126-0.1260.0000.0000.0000.000
19A833GLU-1-0.829-0.91523.0120.1350.1350.0000.0000.0000.000
20A834ILE0-0.034-0.01722.0020.0070.0070.0000.0000.0000.000
21A835ASP-1-0.813-0.90619.1290.2380.2380.0000.0000.0000.000
22A836ASP-1-0.881-0.93121.0950.2360.2360.0000.0000.0000.000
23A837GLU-1-0.887-0.93623.7020.1390.1390.0000.0000.0000.000
24A838ALA00.010-0.00520.8670.0060.0060.0000.0000.0000.000
25A839ASN00.0000.00220.4270.0500.0500.0000.0000.0000.000
26A840SER00.0090.02021.5550.0030.0030.0000.0000.0000.000
27A841TYR0-0.009-0.02224.473-0.015-0.0150.0000.0000.0000.000
28A842PHE00.0160.01118.6770.0010.0010.0000.0000.0000.000
29A843GLN0-0.015-0.00622.3070.0000.0000.0000.0000.0000.000
30A844ARG10.8540.91123.991-0.198-0.1980.0000.0000.0000.000
31A845ILE0-0.0080.01222.546-0.016-0.0160.0000.0000.0000.000
32A846TYR0-0.027-0.04018.874-0.001-0.0010.0000.0000.0000.000
33A847ASN0-0.046-0.02224.0200.0120.0120.0000.0000.0000.000
34A848HIS0-0.057-0.04427.1100.0090.0090.0000.0000.0000.000
35A849PRO00.0600.03730.259-0.003-0.0030.0000.0000.0000.000
36A850PRO0-0.026-0.01333.7630.0030.0030.0000.0000.0000.000
37A851HIS0-0.0030.00829.890-0.012-0.0120.0000.0000.0000.000
38A852PRO00.0170.00131.4740.0010.0010.0000.0000.0000.000
39A853THR00.0070.00729.4600.0140.0140.0000.0000.0000.000
40A854MET0-0.042-0.01628.953-0.011-0.0110.0000.0000.0000.000
41A855SER0-0.032-0.04628.9920.0160.0160.0000.0000.0000.000
42A856VAL00.044-0.00225.7870.0020.0020.0000.0000.0000.000
43A857ASP-1-0.797-0.87927.9980.1580.1580.0000.0000.0000.000
44A858GLU-1-0.820-0.85930.6960.1390.1390.0000.0000.0000.000
45A859VAL00.0090.00524.748-0.005-0.0050.0000.0000.0000.000
46A860LEU0-0.029-0.00924.860-0.003-0.0030.0000.0000.0000.000
47A861GLU-1-0.871-0.91628.0540.0990.0990.0000.0000.0000.000
48A862MET00.0230.01626.409-0.008-0.0080.0000.0000.0000.000
49A863LEU0-0.024-0.02023.291-0.008-0.0080.0000.0000.0000.000
50A864GLN0-0.035-0.02727.040-0.008-0.0080.0000.0000.0000.000
51A865ARG10.8190.91629.244-0.116-0.1160.0000.0000.0000.000
52A866PHE0-0.030-0.04026.858-0.007-0.0070.0000.0000.0000.000
53A867LYS10.8060.90924.732-0.081-0.0810.0000.0000.0000.000
54A868ASP-1-0.833-0.90726.7880.0580.0580.0000.0000.0000.000
55A869SER0-0.009-0.00529.641-0.010-0.0100.0000.0000.0000.000
56A870THR00.0140.00031.348-0.002-0.0020.0000.0000.0000.000
57A871ILE0-0.014-0.00132.474-0.006-0.0060.0000.0000.0000.000
58A872LYS10.8200.88326.996-0.043-0.0430.0000.0000.0000.000
59A873ARG10.8820.93827.548-0.103-0.1030.0000.0000.0000.000
60A874GLU-1-0.820-0.88527.5500.0990.0990.0000.0000.0000.000
61A875ARG10.8920.94026.159-0.038-0.0380.0000.0000.0000.000
62A876GLU-1-0.764-0.87023.7320.0670.0670.0000.0000.0000.000
63A877VAL00.0090.01122.6700.0150.0150.0000.0000.0000.000
64A878PHE00.0280.01022.2240.0280.0280.0000.0000.0000.000
65A879ASN0-0.035-0.02820.0670.0230.0230.0000.0000.0000.000
66A880CYS0-0.054-0.02218.4280.0280.0280.0000.0000.0000.000
67A881MET0-0.0180.00417.8040.0400.0400.0000.0000.0000.000
68A882LEU00.001-0.00518.0260.0600.0600.0000.0000.0000.000
69A883ARG10.8380.92213.746-0.092-0.0920.0000.0000.0000.000
70A884ASN00.014-0.00513.2980.1240.1240.0000.0000.0000.000
71A885LEU0-0.028-0.00713.0950.1370.1370.0000.0000.0000.000
72A886PHE0-0.012-0.02012.2070.0520.0520.0000.0000.0000.000
73A887GLU-1-0.840-0.9269.0280.1650.1650.0000.0000.0000.000
74A888GLU-1-0.818-0.8888.4332.1222.1220.0000.0000.0000.000
75A889TYR0-0.063-0.0329.1360.2010.2010.0000.0000.0000.000
76A890ARG10.8800.9372.567-13.234-11.3170.738-0.985-1.6690.011
77A891PHE0-0.034-0.0215.2590.7530.7530.0000.0000.0000.000
78A892PHE00.0270.0349.413-0.331-0.3310.0000.0000.0000.000
79A893PRO0-0.021-0.03210.791-0.158-0.1580.0000.0000.0000.000
80A894GLN0-0.040-0.0238.212-0.268-0.2680.0000.0000.0000.000
81A895TYR0-0.047-0.03412.565-0.163-0.1630.0000.0000.0000.000
82A896PRO00.0320.01515.955-0.054-0.0540.0000.0000.0000.000
83A897ASP-1-0.822-0.91819.6630.4050.4050.0000.0000.0000.000
84A898LYS10.8450.94121.475-0.306-0.3060.0000.0000.0000.000
85A899GLU-1-0.755-0.88919.2600.3430.3430.0000.0000.0000.000
86A900LEU0-0.0160.02216.2290.0040.0040.0000.0000.0000.000
87A901HIS00.0500.01619.247-0.002-0.0020.0000.0000.0000.000
88A902ILE0-0.010-0.00122.705-0.023-0.0230.0000.0000.0000.000
89A903THR00.011-0.00516.745-0.011-0.0110.0000.0000.0000.000
90A904ALA0-0.0230.00120.204-0.012-0.0120.0000.0000.0000.000
91A905CYS0-0.025-0.01421.277-0.036-0.0360.0000.0000.0000.000
92A906LEU0-0.004-0.00120.759-0.027-0.0270.0000.0000.0000.000
93A907PHE0-0.015-0.00415.142-0.024-0.0240.0000.0000.0000.000
94A908GLY00.0260.00220.377-0.024-0.0240.0000.0000.0000.000
95A909GLY0-0.006-0.00822.856-0.023-0.0230.0000.0000.0000.000
96A910ILE00.0130.00319.899-0.019-0.0190.0000.0000.0000.000
97A911ILE0-0.030-0.00519.330-0.020-0.0200.0000.0000.0000.000
98A912GLU-1-0.776-0.86123.0690.0940.0940.0000.0000.0000.000
99A913LYS10.8140.89226.642-0.129-0.1290.0000.0000.0000.000
100A914GLY00.0090.02425.453-0.007-0.0070.0000.0000.0000.000
101A915LEU0-0.032-0.01723.427-0.008-0.0080.0000.0000.0000.000
102A916VAL0-0.0160.00118.480-0.001-0.0010.0000.0000.0000.000
103A917THR00.019-0.00421.331-0.004-0.0040.0000.0000.0000.000
104A918TYR00.0380.00220.516-0.006-0.0060.0000.0000.0000.000
105A919MET00.0170.01912.3250.0260.0260.0000.0000.0000.000
106A920ALA00.0730.04115.9710.0050.0050.0000.0000.0000.000
107A921LEU00.0040.01816.9760.0280.0280.0000.0000.0000.000
108A922GLY00.0140.00617.5500.0170.0170.0000.0000.0000.000
109A923LEU0-0.028-0.01210.2970.0090.0090.0000.0000.0000.000
110A924ALA00.0350.01614.1270.0450.0450.0000.0000.0000.000
111A925LEU00.0170.01016.4540.0310.0310.0000.0000.0000.000
112A926ARG10.8770.9378.230-0.102-0.1020.0000.0000.0000.000
113A927TYR0-0.016-0.0129.082-0.028-0.0280.0000.0000.0000.000
114A928VAL00.0280.02713.8570.0490.0490.0000.0000.0000.000
115A929LEU0-0.0020.00616.9410.0030.0030.0000.0000.0000.000
116A930GLU-1-0.851-0.92810.7970.2940.2940.0000.0000.0000.000
117A931ALA0-0.049-0.00114.8440.0330.0330.0000.0000.0000.000
118A932LEU00.0080.00816.341-0.009-0.0090.0000.0000.0000.000
119A933ARG10.8870.94916.731-0.174-0.1740.0000.0000.0000.000
120A934LYS10.8530.93412.342-0.493-0.4930.0000.0000.0000.000
121A935PRO00.0410.01118.061-0.021-0.0210.0000.0000.0000.000
122A936PHE00.0690.04721.1930.0230.0230.0000.0000.0000.000
123A937GLY0-0.0040.00924.356-0.004-0.0040.0000.0000.0000.000
124A938SER0-0.048-0.03719.0940.0280.0280.0000.0000.0000.000
125A939LYS10.8630.91216.842-0.516-0.5160.0000.0000.0000.000
126A940MET00.0080.01113.8430.0160.0160.0000.0000.0000.000
127A941TYR00.0020.02118.069-0.016-0.0160.0000.0000.0000.000
128A942TYR00.014-0.00420.979-0.021-0.0210.0000.0000.0000.000
129A943PHE00.0130.01016.830-0.011-0.0110.0000.0000.0000.000
130A944GLY00.0420.00819.840-0.016-0.0160.0000.0000.0000.000
131A945ILE0-0.016-0.01620.524-0.024-0.0240.0000.0000.0000.000
132A946ALA0-0.019-0.00923.639-0.018-0.0180.0000.0000.0000.000
133A947ALA0-0.003-0.00220.781-0.013-0.0130.0000.0000.0000.000
134A948LEU0-0.004-0.01222.751-0.020-0.0200.0000.0000.0000.000
135A949ASP-1-0.810-0.90124.3420.1220.1220.0000.0000.0000.000
136A950ARG10.7490.85425.564-0.191-0.1910.0000.0000.0000.000
137A951PHE00.0280.02321.990-0.009-0.0090.0000.0000.0000.000
138A952LYS10.8320.92127.170-0.137-0.1370.0000.0000.0000.000
139A953ASN0-0.050-0.05129.025-0.003-0.0030.0000.0000.0000.000
140A954ARG10.8510.92626.597-0.101-0.1010.0000.0000.0000.000
141A955LEU0-0.031-0.00425.396-0.004-0.0040.0000.0000.0000.000
142A956LYS10.8600.92028.253-0.070-0.0700.0000.0000.0000.000
143A957ASP-1-0.886-0.94228.0500.0680.0680.0000.0000.0000.000
144A958TYR0-0.043-0.02424.460-0.002-0.0020.0000.0000.0000.000
145A959PRO00.0770.04826.2180.0060.0060.0000.0000.0000.000
146A960GLN00.003-0.02224.7450.0030.0030.0000.0000.0000.000
147A961TYR0-0.057-0.04418.9250.0010.0010.0000.0000.0000.000
148A962CYS0-0.0130.02023.3540.0120.0120.0000.0000.0000.000
149A963GLN00.0260.02026.1470.0020.0020.0000.0000.0000.000
150A964HIS0-0.001-0.00320.5120.0100.0100.0000.0000.0000.000
151A965LEU0-0.017-0.00521.5750.0110.0110.0000.0000.0000.000
152A966ALA00.0440.01723.7160.0050.0050.0000.0000.0000.000
153A967SER0-0.100-0.05123.247-0.002-0.0020.0000.0000.0000.000
154A968ILE0-0.049-0.00921.0550.0020.0020.0000.0000.0000.000
155A969SER00.0220.00023.664-0.003-0.0030.0000.0000.0000.000
156A970HIS0-0.0080.00021.489-0.023-0.0230.0000.0000.0000.000
157A971PHE0-0.0060.00726.4020.0070.0070.0000.0000.0000.000
158A972MET00.0140.00227.415-0.001-0.0010.0000.0000.0000.000
159A973GLN0-0.044-0.01728.523-0.002-0.0020.0000.0000.0000.000
160A974PHE00.0130.00823.5140.0120.0120.0000.0000.0000.000
161A975PRO00.0000.00228.848-0.010-0.0100.0000.0000.0000.000
162A976HIS00.0210.00331.7760.0010.0010.0000.0000.0000.000
163A977HIS00.010-0.00931.857-0.007-0.0070.0000.0000.0000.000
164A978LEU0-0.015-0.01327.503-0.002-0.0020.0000.0000.0000.000
165A979GLN0-0.007-0.00530.173-0.006-0.0060.0000.0000.0000.000
166A980GLU-1-0.833-0.90831.7030.0670.0670.0000.0000.0000.000
167A981TYR0-0.042-0.06430.706-0.005-0.0050.0000.0000.0000.000
168A982ILE0-0.0120.00726.263-0.001-0.0010.0000.0000.0000.000
169A983GLU-1-0.887-0.94829.7320.0660.0660.0000.0000.0000.000
170A984TYR0-0.050-0.04332.541-0.008-0.0080.0000.0000.0000.000
171A985GLY00.0770.03230.453-0.004-0.0040.0000.0000.0000.000
172A986GLN0-0.026-0.03029.058-0.001-0.0010.0000.0000.0000.000
173A987GLN0-0.098-0.03831.063-0.008-0.0080.0000.0000.0000.000
174A988SER0-0.026-0.01132.801-0.004-0.0040.0000.0000.0000.000
175A989ARG10.8920.95433.777-0.050-0.0500.0000.0000.0000.000
176A990ASP-1-0.775-0.87734.7600.0700.0700.0000.0000.0000.000
177A991PRO00.0300.01534.771-0.004-0.0040.0000.0000.0000.000
178A992PRO0-0.033-0.01537.498-0.002-0.0020.0000.0000.0000.000
179A993VAL0-0.0060.00339.773-0.002-0.0020.0000.0000.0000.000
180A994LYS10.8860.96036.460-0.061-0.0610.0000.0000.0000.000