FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: LQL69

Calculation Name: 2D5R-B-Xray540

Preferred Name: CCR4-NOT transcription complex subunit 7

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2D5R

Chain ID: B

ChEMBL ID: CHEMBL3616361

UniProt ID: Q9UIV1

Base Structure: X-ray

Registration Date: 2025-07-11

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1016232.475768
FMO2-HF: Nuclear repulsion 969555.328346
FMO2-HF: Total energy -46677.147423
FMO2-MP2: Total energy -46815.538218


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(B:24:HIS)


Summations of interaction energy for fragment #1(B:24:HIS)
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.
-5.231-1.9630.32-1.591-1.9970.011
Interaction energy analysis for fragmet #1(B:24:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.182 / q_NPA : 0.068
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].
4B25MET0-0.0870.1063.9920.2330.485-0.001-0.077-0.1740.000
5B26GLN00.107-0.0953.005-3.362-1.2240.120-1.073-1.1850.008
6B26GLN0-0.1350.0922.8300.8411.5070.203-0.403-0.4670.003
7B27LEU00.137-0.1083.777-0.342-0.1600.000-0.031-0.1510.000
8B27LEU0-0.0810.1275.000-0.001-0.0010.0000.0000.0000.000
9B28GLU00.061-0.1425.7950.3520.3520.0000.0000.0000.000
10B28GLU-1-0.828-0.7595.542-2.536-2.543-0.001-0.0030.0120.000
11B29ILE00.075-0.0967.419-0.014-0.0140.0000.0000.0000.000
12B29ILE0-0.0800.0907.9760.0180.0180.0000.0000.0000.000
13B30GLN00.107-0.0908.408-0.040-0.0400.0000.0000.0000.000
14B30GLN0-0.0710.1027.7210.1150.1150.0000.0000.0000.000
15B31VAL00.023-0.0969.9980.0230.0230.0000.0000.0000.000
16B31VAL0-0.0420.10510.019-0.013-0.0130.0000.0000.0000.000
17B32ALA00.099-0.10811.9380.0110.0110.0000.0000.0000.000
18B32ALA0-0.0680.11212.855-0.010-0.0100.0000.0000.0000.000
19B33LEU00.028-0.15412.958-0.037-0.0370.0000.0000.0000.000
20B33LEU0-0.1260.14212.1920.0060.0060.0000.0000.0000.000
21B34ASN00.167-0.06714.056-0.009-0.0090.0000.0000.0000.000
22B34ASN0-0.1180.07613.4570.0250.0250.0000.0000.0000.000
23B35PHE00.079-0.09315.9480.0030.0030.0000.0000.0000.000
24B35PHE0-0.0690.09817.181-0.008-0.0080.0000.0000.0000.000
25B36ILE00.093-0.06417.718-0.008-0.0080.0000.0000.0000.000
26B36ILE0-0.0650.09517.351-0.001-0.0010.0000.0000.0000.000
27B37ILE00.054-0.11318.518-0.017-0.0170.0000.0000.0000.000
28B37ILE0-0.0570.11317.7750.0010.0010.0000.0000.0000.000
29B38SER0-0.019-0.11219.9930.0060.0060.0000.0000.0000.000
30B38SER0-0.0660.03720.497-0.008-0.0080.0000.0000.0000.000
31B39TYR0-0.042-0.15621.832-0.001-0.0010.0000.0000.0000.000
32B39TYR0-0.0560.11722.347-0.005-0.0050.0000.0000.0000.000
33B40LEU00.095-0.07923.603-0.010-0.0100.0000.0000.0000.000
34B40LEU0-0.0770.10722.4840.0040.0040.0000.0000.0000.000
35B41TYR00.136-0.09324.158-0.001-0.0010.0000.0000.0000.000
36B41TYR0-0.1190.06320.1680.0010.0010.0000.0000.0000.000
37B42ASN0-0.057-0.11325.583-0.008-0.0080.0000.0000.0000.000
38B42ASN0-0.0650.07727.3140.0050.0050.0000.0000.0000.000
39B43LYS00.022-0.13528.489-0.006-0.0060.0000.0000.0000.000
40B43LYS10.9461.12328.655-0.046-0.0460.0000.0000.0000.000
41B44LEU00.025-0.11728.420-0.007-0.0070.0000.0000.0000.000
42B44LEU00.0080.15226.7280.0030.0030.0000.0000.0000.000
43B45PRO0-0.002-0.11628.4010.0080.0080.0000.0000.0000.000
44B46ARG00.1620.02925.9240.0070.0070.0000.0000.0000.000
45B46ARG10.8301.05824.032-0.135-0.1350.0000.0000.0000.000
46B47ARG00.060-0.09624.4100.0150.0150.0000.0000.0000.000
47B47ARG10.8791.06025.044-0.182-0.1820.0000.0000.0000.000
48B48ARG00.151-0.07523.9840.0240.0240.0000.0000.0000.000
49B48ARG10.8191.05326.610-0.110-0.1100.0000.0000.0000.000
50B49VAL00.117-0.07823.1740.0090.0090.0000.0000.0000.000
51B49VAL0-0.0670.11321.626-0.001-0.0010.0000.0000.0000.000
52B50ASN00.096-0.05020.0070.0100.0100.0000.0000.0000.000
53B50ASN0-0.0790.06720.557-0.003-0.0030.0000.0000.0000.000
54B51ILE00.085-0.05219.0870.0430.0430.0000.0000.0000.000
55B51ILE0-0.0780.07821.584-0.005-0.0050.0000.0000.0000.000
56B52PHE00.114-0.06519.4660.0320.0320.0000.0000.0000.000
57B52PHE0-0.0950.08720.177-0.002-0.0020.0000.0000.0000.000
58B53GLY0-0.047-0.12217.2290.0010.0010.0000.0000.0000.000
59B54GLU00.127-0.03814.9810.0420.0420.0000.0000.0000.000
60B54GLU-1-1.052-0.84015.2550.4680.4680.0000.0000.0000.000
61B55GLU00.075-0.13215.0890.0880.0880.0000.0000.0000.000
62B55GLU-1-0.853-0.74218.6880.2760.2760.0000.0000.0000.000
63B56LEU00.097-0.11316.2430.0070.0070.0000.0000.0000.000
64B56LEU0-0.0780.11015.620-0.008-0.0080.0000.0000.0000.000
65B57GLU00.102-0.11912.048-0.085-0.0850.0000.0000.0000.000
66B57GLU-1-0.880-0.7929.1671.3931.3930.0000.0000.0000.000
67B58ARG00.049-0.10911.5550.0970.0970.0000.0000.0000.000
68B58ARG10.7220.98113.915-0.345-0.3450.0000.0000.0000.000
69B59LEU00.034-0.14613.1330.0110.0110.0000.0000.0000.000
70B59LEU0-0.0960.12716.374-0.010-0.0100.0000.0000.0000.000
71B60LEU00.068-0.11612.538-0.072-0.0720.0000.0000.0000.000
72B60LEU0-0.0790.11011.836-0.009-0.0090.0000.0000.0000.000
73B61LYS00.101-0.0928.880-0.232-0.2320.0000.0000.0000.000
74B61LYS10.7641.0066.436-2.307-2.3070.0000.0000.0000.000
75B62LYS00.106-0.0669.696-0.121-0.1210.0000.0000.0000.000
76B62LYS10.8281.04613.678-0.170-0.1700.0000.0000.0000.000
77B63LYS00.075-0.09712.319-0.075-0.0750.0000.0000.0000.000
78B63LYS10.8671.08313.6810.1000.1000.0000.0000.0000.000
79B64TYR0-0.038-0.1689.570-0.029-0.0290.0000.0000.0000.000
80B64TYR0-0.0230.1118.947-0.023-0.0230.0000.0000.0000.000
81B65GLU00.113-0.1148.572-0.317-0.3170.0000.0000.0000.000
82B65GLU-1-1.007-0.8129.4510.0640.0640.0000.0000.0000.000
83B66GLY0-0.032-0.1149.2690.0870.0870.0000.0000.0000.000
84B67HIS0-0.086-0.05310.3510.0350.0350.0000.0000.0000.000
85B67HIS10.8141.04311.9540.3610.3610.0000.0000.0000.000
86B68TRP00.216-0.0767.3570.1960.1960.0000.0000.0000.000
87B68TRP0-0.0840.1455.1190.1870.224-0.001-0.004-0.0320.000
88B69TYR00.019-0.1048.486-0.168-0.1680.0000.0000.0000.000
89B69TYR0-0.1170.05611.6030.0790.0790.0000.0000.0000.000
90B70PRO00.092-0.0816.7560.1260.1260.0000.0000.0000.000
91B71GLU00.2040.0488.9960.0830.0830.0000.0000.0000.000
92B71GLU-1-1.046-0.86012.232-0.629-0.6290.0000.0000.0000.000
93B72LYS0-0.024-0.12112.4020.0960.0960.0000.0000.0000.000
94B72LYS10.8011.02414.7510.4000.4000.0000.0000.0000.000
95B73PRO00.145-0.04311.6220.0240.0240.0000.0000.0000.000
96B74TYR00.2250.05512.9350.0000.0000.0000.0000.0000.000
97B74TYR0-0.0490.10517.6510.0030.0030.0000.0000.0000.000
98B75LYS00.067-0.12315.3000.0690.0690.0000.0000.0000.000
99B75LYS10.8091.08414.3820.4280.4280.0000.0000.0000.000
100B76GLY0-0.035-0.11913.914-0.077-0.0770.0000.0000.0000.000
101B77SER00.0680.00515.207-0.001-0.0010.0000.0000.0000.000
102B77SER0-0.0020.10116.2300.0020.0020.0000.0000.0000.000
103B78GLY0-0.021-0.09116.2990.0260.0260.0000.0000.0000.000
104B79PHE00.1220.02917.1330.0310.0310.0000.0000.0000.000
105B79PHE0-0.1610.04513.9460.0010.0010.0000.0000.0000.000
106B80ARG00.016-0.14313.8510.0600.0600.0000.0000.0000.000
107B80ARG10.6670.94610.9210.6380.6380.0000.0000.0000.000
108B81CYS00.133-0.08415.1380.0140.0140.0000.0000.0000.000
109B81CYS0-0.1510.11518.8470.0110.0110.0000.0000.0000.000
110B82ILE00.081-0.09117.8350.0110.0110.0000.0000.0000.000
111B82ILE0-0.0950.08815.0510.0110.0110.0000.0000.0000.000
112B83HIS00.092-0.08419.004-0.002-0.0020.0000.0000.0000.000
113B83HIS0-0.1220.08223.1510.0050.0050.0000.0000.0000.000
114B84ILE00.034-0.12922.6980.0100.0100.0000.0000.0000.000
115B84ILE0-0.0700.09421.7650.0040.0040.0000.0000.0000.000
116B85GLY00.110-0.04525.119-0.001-0.0010.0000.0000.0000.000
117B86GLU00.0820.00728.7120.0090.0090.0000.0000.0000.000
118B86GLU-1-1.000-0.85932.207-0.012-0.0120.0000.0000.0000.000
119B87LYS00.133-0.07129.3720.0080.0080.0000.0000.0000.000
120B87LYS10.8231.04725.0760.0410.0410.0000.0000.0000.000
121B88VAL00.011-0.14126.035-0.011-0.0110.0000.0000.0000.000
122B88VAL0-0.0310.14124.7480.0020.0020.0000.0000.0000.000
123B89ASP00.004-0.12721.776-0.001-0.0010.0000.0000.0000.000
124B89ASP-1-0.939-0.83420.180-0.057-0.0570.0000.0000.0000.000
125B90PRO00.071-0.08321.7620.0150.0150.0000.0000.0000.000
126B91VAL00.048-0.03618.7550.0160.0160.0000.0000.0000.000
127B91VAL0-0.0430.12717.093-0.001-0.0010.0000.0000.0000.000
128B92ILE00.065-0.09520.1910.0340.0340.0000.0000.0000.000
129B92ILE0-0.0330.11019.4990.0000.0000.0000.0000.0000.000
130B93GLU00.118-0.10521.8640.0180.0180.0000.0000.0000.000
131B93GLU-1-0.997-0.82725.1480.0190.0190.0000.0000.0000.000
132B94GLN00.028-0.11622.4230.0040.0040.0000.0000.0000.000
133B94GLN0-0.0810.08220.7450.0180.0180.0000.0000.0000.000
134B95ALA00.128-0.08520.3640.0100.0100.0000.0000.0000.000
135B95ALA0-0.0490.11919.5070.0020.0020.0000.0000.0000.000
136B96SER00.042-0.09521.4780.0200.0200.0000.0000.0000.000
137B96SER0-0.0250.07724.655-0.005-0.0050.0000.0000.0000.000
138B97LYS00.056-0.11024.6800.0020.0020.0000.0000.0000.000
139B97LYS10.8461.08226.306-0.092-0.0920.0000.0000.0000.000
140B98GLU0-0.009-0.14223.561-0.009-0.0090.0000.0000.0000.000
141B98GLU-1-1.020-0.84022.7680.1360.1360.0000.0000.0000.000
142B99SER0-0.061-0.14024.0600.0180.0180.0000.0000.0000.000
143B99SER0-0.0090.09423.073-0.001-0.0010.0000.0000.0000.000
144B100GLY0-0.070-0.14125.127-0.002-0.0020.0000.0000.0000.000
145B101LEU00.013-0.03427.232-0.006-0.0060.0000.0000.0000.000
146B101LEU0-0.0470.11724.6870.0000.0000.0000.0000.0000.000
147B102ASP00.151-0.09628.4820.0020.0020.0000.0000.0000.000
148B102ASP-1-0.931-0.79432.1970.0470.0470.0000.0000.0000.000
149B103ILE00.137-0.10928.3340.0030.0030.0000.0000.0000.000
150B103ILE0-0.0590.10927.5710.0000.0000.0000.0000.0000.000
151B104ASP00.104-0.13229.347-0.003-0.0030.0000.0000.0000.000
152B104ASP-1-0.983-0.81033.3320.0250.0250.0000.0000.0000.000
153B105ASP00.104-0.11031.008-0.007-0.0070.0000.0000.0000.000
154B105ASP-1-1.044-0.86430.4100.0560.0560.0000.0000.0000.000
155B106VAL0-0.016-0.11526.4160.0000.0000.0000.0000.0000.000
156B106VAL0-0.0660.09324.3570.0010.0010.0000.0000.0000.000
157B107ARG00.070-0.12027.067-0.001-0.0010.0000.0000.0000.000
158B107ARG10.8181.05528.865-0.008-0.0080.0000.0000.0000.000
159B108GLY0-0.050-0.10628.575-0.006-0.0060.0000.0000.0000.000
160B109ASN00.0310.02228.782-0.006-0.0060.0000.0000.0000.000
161B109ASN0-0.1290.02628.0640.0010.0010.0000.0000.0000.000
162B110LEU00.032-0.12625.8560.0050.0050.0000.0000.0000.000
163B110LEU0-0.0790.10923.118-0.001-0.0010.0000.0000.0000.000
164B111PRO0-0.050-0.11225.116-0.004-0.0040.0000.0000.0000.000
165B112GLN00.1680.02027.5450.0000.0000.0000.0000.0000.000
166B112GLN0-0.1140.09131.525-0.004-0.0040.0000.0000.0000.000
167B113ASP00.094-0.10327.893-0.003-0.0030.0000.0000.0000.000
168B113ASP-1-1.013-0.86928.567-0.037-0.0370.0000.0000.0000.000
169B114LEU00.145-0.09124.274-0.012-0.0120.0000.0000.0000.000
170B114LEU0-0.1170.10421.5430.0020.0020.0000.0000.0000.000
171B115SER0-0.053-0.11121.9530.0100.0100.0000.0000.0000.000
172B115SER00.0060.10621.9080.0010.0010.0000.0000.0000.000
173B116VAL00.105-0.09017.907-0.007-0.0070.0000.0000.0000.000
174B116VAL0-0.0940.09315.7730.0060.0060.0000.0000.0000.000
175B117TRP00.065-0.11916.1690.0130.0130.0000.0000.0000.000
176B117TRP0-0.0880.12716.0910.0070.0070.0000.0000.0000.000
177B118ILE00.155-0.08411.992-0.001-0.0010.0000.0000.0000.000
178B118ILE0-0.1230.1049.8570.0020.0020.0000.0000.0000.000
179B119ASP00.072-0.14011.084-0.078-0.0780.0000.0000.0000.000
180B119ASP-1-0.867-0.75712.463-0.493-0.4930.0000.0000.0000.000
181B120PRO0-0.101-0.1427.591-0.067-0.0670.0000.0000.0000.000
182B121PHE00.1120.0197.6060.2030.2030.0000.0000.0000.000
183B121PHE0-0.0910.0836.161-0.088-0.0880.0000.0000.0000.000
184B122GLU00.137-0.1249.2590.1360.1360.0000.0000.0000.000
185B122GLU-1-1.049-0.84713.168-0.383-0.3830.0000.0000.0000.000
186B123VAL00.090-0.09112.233-0.045-0.0450.0000.0000.0000.000
187B123VAL0-0.1250.09410.9780.0090.0090.0000.0000.0000.000
188B124SER00.022-0.10213.5940.0450.0450.0000.0000.0000.000
189B124SER00.0010.10616.8210.0070.0070.0000.0000.0000.000
190B125TYR00.050-0.08417.368-0.007-0.0070.0000.0000.0000.000
191B125TYR0-0.0660.07319.3500.0120.0120.0000.0000.0000.000
192B126GLN00.123-0.14720.277-0.004-0.0040.0000.0000.0000.000
193B126GLN0-0.1230.12023.638-0.007-0.0070.0000.0000.0000.000
194B127ILE00.069-0.09123.9440.0030.0030.0000.0000.0000.000
195B127ILE0-0.1180.09325.0720.0010.0010.0000.0000.0000.000
196B128GLY00.048-0.07326.6730.0020.0020.0000.0000.0000.000
197B129GLU00.1860.00628.287-0.010-0.0100.0000.0000.0000.000
198B129GLU-1-0.999-0.84130.454-0.058-0.0580.0000.0000.0000.000
199B130LYS0-0.019-0.13529.751-0.009-0.0090.0000.0000.0000.000
200B130LYS10.8431.06032.9980.0480.0480.0000.0000.0000.000
201B131GLY0-0.024-0.08628.9010.0000.0000.0000.0000.0000.000
202B132PRO0-0.019-0.01827.303-0.008-0.0080.0000.0000.0000.000
203B133VAL00.145-0.00523.1440.0120.0120.0000.0000.0000.000
204B133VAL0-0.0550.12521.212-0.001-0.0010.0000.0000.0000.000
205B134LYS00.025-0.10422.393-0.008-0.0080.0000.0000.0000.000
206B134LYS10.8471.05922.6290.0700.0700.0000.0000.0000.000
207B135VAL00.100-0.12218.434-0.004-0.0040.0000.0000.0000.000
208B135VAL0-0.0420.14516.6730.0020.0020.0000.0000.0000.000
209B136LEU0-0.011-0.13516.4410.0230.0230.0000.0000.0000.000
210B136LEU0-0.0910.09715.8290.0040.0040.0000.0000.0000.000
211B137TYR00.094-0.12112.8310.0510.0510.0000.0000.0000.000
212B137TYR0-0.1020.0969.050-0.035-0.0350.0000.0000.0000.000
213B138VAL00.056-0.10013.134-0.049-0.0490.0000.0000.0000.000
214B138VAL0-0.0450.11114.4420.0080.0080.0000.0000.0000.000
215B139ASP0-0.119-0.12311.2690.0560.0560.0000.0000.0000.000
216B139ASP-1-0.863-0.93510.723-0.556-0.5560.0000.0000.0000.000