FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 2LQ2R

Calculation Name: 4EMO-A-Xray540

Preferred Name: Sharpin/RBCK1/RNF31

Target Type: PROTEIN COMPLEX

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4EMO

Chain ID: A

ChEMBL ID: CHEMBL4296109

UniProt ID: Q9H0F6

Base Structure: X-ray

Registration Date: 2025-07-09

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 185
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -729855.196425
FMO2-HF: Nuclear repulsion 691426.785968
FMO2-HF: Total energy -38428.410456
FMO2-MP2: Total energy -38541.668271


3D Structure Molmil
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:18:ALA)


Summations of interaction energy for fragment #1(A:18:ALA)
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.
-4.060.4843.11-3.883-3.771-0.01
Interaction energy analysis for fragmet #1(A:18:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.161 / q_NPA : 0.011
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].
4A19ALA0-0.0790.0974.5280.2610.419-0.001-0.064-0.0930.000
5A20VAL00.115-0.1213.753-0.2090.866-0.015-0.558-0.5020.003
6A20VAL0-0.1000.1016.580-0.017-0.0170.0000.0000.0000.000
7A21LEU00.103-0.0756.8070.2000.2000.0000.0000.0000.000
8A21LEU0-0.1390.0998.4590.0090.0090.0000.0000.0000.000
9A22MET00.073-0.1439.3690.0070.0070.0000.0000.0000.000
10A22MET0-0.1160.09113.4050.0260.0260.0000.0000.0000.000
11A23ALA00.106-0.04211.863-0.021-0.0210.0000.0000.0000.000
12A23ALA0-0.0350.06512.330-0.013-0.0130.0000.0000.0000.000
13A24VAL0-0.090-0.12413.6330.0300.0300.0000.0000.0000.000
14A24VAL0-0.0270.10316.4640.0060.0060.0000.0000.0000.000
15A25HIS00.093-0.10416.935-0.030-0.0300.0000.0000.0000.000
16A25HIS0-0.0610.09118.0120.0040.0040.0000.0000.0000.000
17A26ALA00.112-0.08619.5220.0170.0170.0000.0000.0000.000
18A26ALA0-0.0630.12120.8550.0030.0030.0000.0000.0000.000
19A27ALA00.124-0.08521.794-0.020-0.0200.0000.0000.0000.000
20A27ALA0-0.1080.11025.9270.0020.0020.0000.0000.0000.000
21A28VAL00.096-0.12621.8080.0160.0160.0000.0000.0000.000
22A28VAL0-0.1240.10519.798-0.001-0.0010.0000.0000.0000.000
23A29ARG00.087-0.12523.236-0.008-0.0080.0000.0000.0000.000
24A29ARG10.8481.09227.4720.0570.0570.0000.0000.0000.000
25A30PRO00.025-0.09524.7120.0060.0060.0000.0000.0000.000
26A31LEU00.030-0.08925.9210.0000.0000.0000.0000.0000.000
27A31LEU0-0.0720.16227.0560.0010.0010.0000.0000.0000.000
28A32GLY0-0.011-0.09627.7260.0050.0050.0000.0000.0000.000
29A33ALA00.042-0.02429.2990.0050.0050.0000.0000.0000.000
30A33ALA0-0.0410.12429.325-0.002-0.0020.0000.0000.0000.000
31A34GLY00.011-0.08231.016-0.001-0.0010.0000.0000.0000.000
32A35PRO0-0.071-0.05832.854-0.003-0.0030.0000.0000.0000.000
33A36ASP00.038-0.00234.428-0.002-0.0020.0000.0000.0000.000
34A36ASP-1-0.988-0.84836.028-0.046-0.0460.0000.0000.0000.000
35A37ALA00.164-0.07330.277-0.003-0.0030.0000.0000.0000.000
36A37ALA0-0.0860.09729.3200.0000.0000.0000.0000.0000.000
37A38GLU00.034-0.11930.0370.0050.0050.0000.0000.0000.000
38A38GLU-1-0.979-0.84128.248-0.107-0.1070.0000.0000.0000.000
39A39ALA00.080-0.11726.747-0.004-0.0040.0000.0000.0000.000
40A39ALA0-0.1080.07626.9720.0010.0010.0000.0000.0000.000
41A40GLN00.045-0.16324.3690.0050.0050.0000.0000.0000.000
42A40GLN0-0.0330.15023.586-0.009-0.0090.0000.0000.0000.000
43A41LEU00.081-0.04823.1740.0020.0020.0000.0000.0000.000
44A41LEU0-0.0760.09022.1510.0020.0020.0000.0000.0000.000
45A42ARG0-0.030-0.12219.125-0.013-0.0130.0000.0000.0000.000
46A42ARG10.8521.02117.5800.1940.1940.0000.0000.0000.000
47A43ARG00.131-0.02615.4500.0350.0350.0000.0000.0000.000
48A43ARG10.8451.03213.1010.4240.4240.0000.0000.0000.000
49A44LEU00.103-0.14313.923-0.032-0.0320.0000.0000.0000.000
50A44LEU0-0.0570.13714.8550.0110.0110.0000.0000.0000.000
51A45GLN00.012-0.09810.6940.0330.0330.0000.0000.0000.000
52A45GLN0-0.0840.0788.3440.0560.0560.0000.0000.0000.000
53A46LEU00.124-0.1049.731-0.004-0.0040.0000.0000.0000.000
54A46LEU0-0.1390.11610.0720.0130.0130.0000.0000.0000.000
55A47SER00.075-0.0965.0670.0370.045-0.002-0.004-0.0030.000
56A47SER0-0.0300.0844.1280.0070.1180.000-0.063-0.0480.000
57A48ALA00.171-0.0653.326-0.418-0.4890.0020.229-0.1600.000
58A48ALA0-0.0910.1022.4380.3450.7000.499-0.418-0.4350.001
59A49ASP00.063-0.1112.910-3.033-1.0180.171-1.391-0.795-0.014
60A49ASP-1-0.902-0.7886.4090.5760.5760.0000.0000.0000.000
61A50PRO0-0.079-0.1282.512-0.5870.2690.334-0.371-0.8190.001
62A51GLU00.054-0.0354.2130.0030.0400.001-0.0420.0040.000
63A51GLU-1-0.981-0.8217.4800.3080.3080.0000.0000.0000.000
64A52ARG0-0.015-0.1207.056-0.136-0.1360.0000.0000.0000.000
65A52ARG10.7150.9768.895-0.440-0.4400.0000.0000.0000.000
66A53PRO00.080-0.0767.6700.0670.0670.0000.0000.0000.000
67A54GLY0-0.011-0.0117.979-0.206-0.2060.0000.0000.0000.000
68A55ARG00.0950.0508.850-0.105-0.1050.0000.0000.0000.000
69A55ARG10.8531.0409.670-0.379-0.3790.0000.0000.0000.000
70A56PHE00.012-0.1107.2390.1940.1940.0000.0000.0000.000
71A56PHE0-0.0470.1097.2410.0150.0150.0000.0000.0000.000
72A57ARG00.073-0.0967.216-0.001-0.0010.0000.0000.0000.000
73A57ARG10.8671.0632.514-0.351-0.3512.121-1.201-0.920-0.001
74A58LEU00.186-0.1128.739-0.076-0.0760.0000.0000.0000.000
75A58LEU0-0.1580.10412.5790.0060.0060.0000.0000.0000.000
76A59GLU00.070-0.1629.5420.0780.0780.0000.0000.0000.000
77A59GLU-1-0.879-0.7405.884-0.950-0.9500.0000.0000.0000.000
78A60LEU00.087-0.08810.663-0.015-0.0150.0000.0000.0000.000
79A60LEU0-0.1390.07315.1400.0100.0100.0000.0000.0000.000
80A61LEU00.106-0.11313.2670.0070.0070.0000.0000.0000.000
81A61LEU0-0.0980.10810.4050.0000.0000.0000.0000.0000.000
82A62GLY00.017-0.08013.9810.0550.0550.0000.0000.0000.000
83A63ALA00.060-0.03416.901-0.020-0.0200.0000.0000.0000.000
84A63ALA0-0.0480.11521.5010.0050.0050.0000.0000.0000.000
85A64GLY0-0.027-0.09019.6300.0160.0160.0000.0000.0000.000
86A65PRO0-0.012-0.00817.636-0.022-0.0220.0000.0000.0000.000
87A66GLY00.008-0.00816.9540.0280.0280.0000.0000.0000.000
88A67ALA00.0670.02017.8230.0120.0120.0000.0000.0000.000
89A67ALA0-0.0730.08517.8970.0060.0060.0000.0000.0000.000
90A68VAL00.040-0.11314.822-0.056-0.0560.0000.0000.0000.000
91A68VAL0-0.0510.09814.5990.0050.0050.0000.0000.0000.000
92A69ASN00.061-0.05711.7190.0350.0350.0000.0000.0000.000
93A69ASN0-0.0340.08210.5200.0410.0410.0000.0000.0000.000
94A70LEU00.042-0.12612.6250.0040.0040.0000.0000.0000.000
95A70LEU0-0.0450.10814.8080.0070.0070.0000.0000.0000.000
96A71GLU00.059-0.1269.663-0.052-0.0520.0000.0000.0000.000
97A71GLU-1-0.954-0.8247.445-0.235-0.2350.0000.0000.0000.000
98A72TRP0-0.028-0.15610.9820.0250.0250.0000.0000.0000.000
99A72TRP0-0.0370.13013.886-0.009-0.0090.0000.0000.0000.000
100A73PRO00.048-0.07610.7960.0090.0090.0000.0000.0000.000
101A74LEU00.155-0.03311.514-0.041-0.0410.0000.0000.0000.000
102A74LEU0-0.1130.15411.871-0.005-0.0050.0000.0000.0000.000
103A75GLU00.063-0.09513.350-0.029-0.0290.0000.0000.0000.000
104A75GLU-1-0.930-0.86113.5250.2490.2490.0000.0000.0000.000
105A76SER00.011-0.11515.317-0.008-0.0080.0000.0000.0000.000
106A76SER0-0.0490.06315.7710.0050.0050.0000.0000.0000.000
107A77VAL00.023-0.06817.097-0.015-0.0150.0000.0000.0000.000
108A77VAL0-0.1180.09515.852-0.005-0.0050.0000.0000.0000.000
109A78SER00.040-0.08018.4270.0140.0140.0000.0000.0000.000
110A78SER0-0.0180.07522.3570.0010.0010.0000.0000.0000.000
111A79TYR00.075-0.07720.019-0.015-0.0150.0000.0000.0000.000
112A79TYR0-0.1170.03718.663-0.006-0.0060.0000.0000.0000.000
113A80THR0-0.061-0.11321.2680.0120.0120.0000.0000.0000.000
114A80THR0-0.0090.08224.934-0.001-0.0010.0000.0000.0000.000
115A81ILE00.174-0.07724.646-0.011-0.0110.0000.0000.0000.000
116A81ILE0-0.1050.10323.2990.0010.0010.0000.0000.0000.000
117A82ARG00.052-0.15726.2330.0070.0070.0000.0000.0000.000
118A82ARG10.8921.11228.0780.0080.0080.0000.0000.0000.000
119A83GLY0-0.030-0.09128.6560.0010.0010.0000.0000.0000.000
120A84PRO0-0.002-0.01328.432-0.001-0.0010.0000.0000.0000.000
121A85THR00.0190.00327.2000.0000.0000.0000.0000.0000.000
122A85THR0-0.0340.09428.1490.0020.0020.0000.0000.0000.000
123A86GLN00.184-0.05626.823-0.010-0.0100.0000.0000.0000.000
124A86GLN0-0.0960.09427.9230.0000.0000.0000.0000.0000.000
125A87HIS00.021-0.11023.4040.0110.0110.0000.0000.0000.000
126A87HIS0-0.0060.14822.248-0.004-0.0040.0000.0000.0000.000
127A88GLU00.141-0.09624.166-0.010-0.0100.0000.0000.0000.000
128A88GLU-1-1.055-0.85025.342-0.016-0.0160.0000.0000.0000.000
129A89LEU00.119-0.08920.1800.0140.0140.0000.0000.0000.000
130A89LEU0-0.0790.08516.738-0.003-0.0030.0000.0000.0000.000
131A90GLN00.064-0.09921.391-0.013-0.0130.0000.0000.0000.000
132A90GLN0-0.0940.09923.3610.0020.0020.0000.0000.0000.000
133A91PRO0-0.020-0.09118.3510.0120.0120.0000.0000.0000.000
134A92PRO00.0270.01117.7660.0040.0040.0000.0000.0000.000
135A93PRO0-0.011-0.02220.785-0.012-0.0120.0000.0000.0000.000
136A94GLY00.0030.00821.9900.0020.0020.0000.0000.0000.000
137A95GLY0-0.0070.01320.077-0.009-0.0090.0000.0000.0000.000
138A96PRO0-0.039-0.02519.1560.0000.0000.0000.0000.0000.000
139A97GLY00.0450.02222.0900.0010.0010.0000.0000.0000.000
140A98THR00.0460.01622.822-0.007-0.0070.0000.0000.0000.000
141A98THR0-0.0370.07525.0780.0010.0010.0000.0000.0000.000
142A99LEU00.060-0.09122.247-0.001-0.0010.0000.0000.0000.000
143A99LEU0-0.0700.09019.655-0.005-0.0050.0000.0000.0000.000
144A100SER00.069-0.05723.6720.0080.0080.0000.0000.0000.000
145A100SER00.0000.06326.825-0.001-0.0010.0000.0000.0000.000
146A101MET00.052-0.07122.309-0.009-0.0090.0000.0000.0000.000
147A101MET0-0.1040.08218.614-0.007-0.0070.0000.0000.0000.000
148A102HIS00.112-0.11623.7180.0100.0100.0000.0000.0000.000
149A102HIS0-0.0930.10327.1800.0020.0020.0000.0000.0000.000
150A103PHE00.054-0.07724.288-0.013-0.0130.0000.0000.0000.000
151A103PHE0-0.1000.08120.1300.0010.0010.0000.0000.0000.000
152A104LEU00.168-0.12024.9330.0080.0080.0000.0000.0000.000
153A104LEU0-0.0640.14024.221-0.001-0.0010.0000.0000.0000.000
154A105ASN0-0.008-0.07826.3210.0040.0040.0000.0000.0000.000
155A105ASN0-0.0850.03525.9430.0070.0070.0000.0000.0000.000
156A106PRO00.069-0.08326.379-0.003-0.0030.0000.0000.0000.000
157A107GLN00.1460.02826.4320.0060.0060.0000.0000.0000.000
158A107GLN0-0.0810.09425.3680.0030.0030.0000.0000.0000.000
159A108GLU0-0.031-0.14022.4280.0120.0120.0000.0000.0000.000
160A108GLU-1-0.903-0.81021.985-0.106-0.1060.0000.0000.0000.000
161A109ALA00.153-0.09221.674-0.003-0.0030.0000.0000.0000.000
162A109ALA0-0.0710.13124.7210.0000.0000.0000.0000.0000.000
163A110GLN00.061-0.13422.6330.0050.0050.0000.0000.0000.000
164A110GLN0-0.0780.11724.792-0.003-0.0030.0000.0000.0000.000
165A111ARG00.079-0.09221.2630.0170.0170.0000.0000.0000.000
166A111ARG10.8931.07319.2440.0460.0460.0000.0000.0000.000
167A112TRP00.067-0.07117.9760.0200.0200.0000.0000.0000.000
168A112TRP0-0.0630.08413.312-0.001-0.0010.0000.0000.0000.000
169A113ALA00.120-0.08318.2010.0120.0120.0000.0000.0000.000
170A113ALA0-0.0930.07822.2090.0000.0000.0000.0000.0000.000
171A114VAL0-0.052-0.11519.8390.0150.0150.0000.0000.0000.000
172A114VAL0-0.0850.08220.0970.0000.0000.0000.0000.0000.000
173A115LEU00.129-0.10116.0840.0310.0310.0000.0000.0000.000
174A115LEU0-0.0600.11913.076-0.008-0.0080.0000.0000.0000.000
175A116VAL00.108-0.09215.2700.0400.0400.0000.0000.0000.000
176A116VAL0-0.1010.10815.437-0.002-0.0020.0000.0000.0000.000
177A117ARG00.114-0.10616.2750.0260.0260.0000.0000.0000.000
178A117ARG10.8131.05620.183-0.075-0.0750.0000.0000.0000.000
179A118GLY0-0.077-0.12116.9600.0110.0110.0000.0000.0000.000
180A119ALA00.1090.00812.7980.0450.0450.0000.0000.0000.000
181A119ALA0-0.0810.08911.905-0.006-0.0060.0000.0000.0000.000
182A120THR0-0.006-0.06913.2020.0510.0510.0000.0000.0000.000
183A120THR0-0.0730.05316.030-0.011-0.0110.0000.0000.0000.000
184A121VAL0-0.101-0.14415.713-0.022-0.0220.0000.0000.0000.000
185A121VAL00.0220.02114.0400.0100.0100.0000.0000.0000.000