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: 7M7GK

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 OptAll
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 -729683.789595
FMO2-HF: Nuclear repulsion 691253.991041
FMO2-HF: Total energy -38429.798555
FMO2-MP2: Total energy -38542.932166


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.
-7.328-4.488.724-5.7-5.874-0.04
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 : 0.181 / q_NPA : 0.019
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].
4A19ALA0-0.0820.1094.7540.2120.412-0.001-0.089-0.1100.000
5A20VAL00.084-0.1163.856-0.5740.588-0.012-0.627-0.5230.002
6A20VAL0-0.1210.0956.423-0.023-0.0230.0000.0000.0000.000
7A21LEU00.102-0.0856.7510.2560.2560.0000.0000.0000.000
8A21LEU0-0.1220.0957.912-0.007-0.0070.0000.0000.0000.000
9A22MET00.061-0.1258.9850.0030.0030.0000.0000.0000.000
10A22MET0-0.1080.07613.0220.0140.0140.0000.0000.0000.000
11A23ALA00.120-0.07111.416-0.053-0.0530.0000.0000.0000.000
12A23ALA0-0.0670.09112.317-0.014-0.0140.0000.0000.0000.000
13A24VAL0-0.037-0.12213.5740.0400.0400.0000.0000.0000.000
14A24VAL0-0.0560.10715.9250.0050.0050.0000.0000.0000.000
15A25HIS00.060-0.11116.694-0.036-0.0360.0000.0000.0000.000
16A25HIS0-0.0430.09818.128-0.008-0.0080.0000.0000.0000.000
17A26ALA00.139-0.08119.4590.0200.0200.0000.0000.0000.000
18A26ALA0-0.0500.11520.7010.0010.0010.0000.0000.0000.000
19A27ALA00.123-0.07421.877-0.020-0.0200.0000.0000.0000.000
20A27ALA0-0.1120.09926.0700.0020.0020.0000.0000.0000.000
21A28VAL00.082-0.12321.4520.0180.0180.0000.0000.0000.000
22A28VAL0-0.1010.09519.432-0.002-0.0020.0000.0000.0000.000
23A29ARG00.100-0.10822.894-0.009-0.0090.0000.0000.0000.000
24A29ARG10.7451.04226.8550.0660.0660.0000.0000.0000.000
25A30PRO0-0.004-0.10224.2790.0070.0070.0000.0000.0000.000
26A31LEU00.059-0.01425.6260.0010.0010.0000.0000.0000.000
27A31LEU0-0.0860.12527.1880.0010.0010.0000.0000.0000.000
28A32GLY00.001-0.11527.3910.0050.0050.0000.0000.0000.000
29A33ALA00.077-0.00128.9300.0030.0030.0000.0000.0000.000
30A33ALA0-0.0760.11828.537-0.002-0.0020.0000.0000.0000.000
31A34GLY0-0.004-0.09430.3050.0010.0010.0000.0000.0000.000
32A35PRO0-0.034-0.04632.366-0.002-0.0020.0000.0000.0000.000
33A36ASP00.0610.00133.738-0.002-0.0020.0000.0000.0000.000
34A36ASP-1-0.914-0.82935.729-0.052-0.0520.0000.0000.0000.000
35A37ALA00.100-0.10130.325-0.003-0.0030.0000.0000.0000.000
36A37ALA0-0.0960.11729.334-0.001-0.0010.0000.0000.0000.000
37A38GLU00.039-0.10329.7980.0060.0060.0000.0000.0000.000
38A38GLU-1-0.911-0.81327.671-0.115-0.1150.0000.0000.0000.000
39A39ALA00.114-0.10826.698-0.006-0.0060.0000.0000.0000.000
40A39ALA0-0.1120.08227.1970.0020.0020.0000.0000.0000.000
41A40GLN00.059-0.12124.0800.0070.0070.0000.0000.0000.000
42A40GLN0-0.0930.10023.063-0.018-0.0180.0000.0000.0000.000
43A41LEU00.112-0.08323.2500.0010.0010.0000.0000.0000.000
44A41LEU0-0.1040.10022.2490.0020.0020.0000.0000.0000.000
45A42ARG0-0.012-0.13519.422-0.013-0.0130.0000.0000.0000.000
46A42ARG10.7651.00617.5510.2200.2200.0000.0000.0000.000
47A43ARG00.169-0.05015.5870.0340.0340.0000.0000.0000.000
48A43ARG10.7901.03112.2560.3770.3770.0000.0000.0000.000
49A44LEU00.046-0.12113.811-0.041-0.0410.0000.0000.0000.000
50A44LEU0-0.0610.11414.3680.0100.0100.0000.0000.0000.000
51A45GLN00.040-0.07910.6850.0480.0480.0000.0000.0000.000
52A45GLN0-0.0860.0538.2410.1230.1230.0000.0000.0000.000
53A46LEU00.156-0.0899.265-0.053-0.0530.0000.0000.0000.000
54A46LEU0-0.1260.1009.7820.0180.0180.0000.0000.0000.000
55A47SER00.033-0.0964.8860.2430.260-0.002-0.005-0.0100.000
56A47SER0-0.0380.0524.139-0.167-0.0530.001-0.052-0.0630.000
57A48ALA00.166-0.0693.229-0.911-0.9140.0060.289-0.2920.000
58A48ALA0-0.1040.0992.431-0.0630.4750.707-0.692-0.5530.004
59A49ASP00.063-0.1191.989-4.921-5.7806.803-3.387-2.558-0.044
60A49ASP-1-0.877-0.7635.8780.2010.2010.0000.0000.0000.000
61A50PRO0-0.049-0.1312.480-0.7400.3410.324-0.440-0.9660.001
62A51GLU00.091-0.0153.8820.0940.1610.005-0.058-0.0130.000
63A51GLU-1-0.994-0.8267.290-0.110-0.1100.0000.0000.0000.000
64A52ARG0-0.031-0.1127.119-0.015-0.0150.0000.0000.0000.000
65A52ARG10.6320.9188.525-0.217-0.2170.0000.0000.0000.000
66A53PRO00.095-0.0917.2620.0810.0810.0000.0000.0000.000
67A54GLY0-0.022-0.0127.724-0.195-0.1950.0000.0000.0000.000
68A55ARG00.0690.0388.282-0.078-0.0780.0000.0000.0000.000
69A55ARG10.8051.0059.306-0.312-0.3120.0000.0000.0000.000
70A56PHE00.050-0.1026.5520.1830.1830.0000.0000.0000.000
71A56PHE0-0.0590.1116.7600.0270.0270.0000.0000.0000.000
72A57ARG00.109-0.0856.7900.0130.0130.0000.0000.0000.000
73A57ARG10.7591.0102.7790.6371.1680.893-0.639-0.786-0.003
74A58LEU00.114-0.1008.218-0.033-0.0330.0000.0000.0000.000
75A58LEU0-0.1390.08111.9450.0100.0100.0000.0000.0000.000
76A59GLU00.078-0.1279.3170.0320.0320.0000.0000.0000.000
77A59GLU-1-0.858-0.7405.672-1.166-1.1660.0000.0000.0000.000
78A60LEU00.086-0.10210.4090.0310.0310.0000.0000.0000.000
79A60LEU0-0.1150.09614.7790.0110.0110.0000.0000.0000.000
80A61LEU00.098-0.08913.247-0.011-0.0110.0000.0000.0000.000
81A61LEU0-0.0940.09910.4390.0060.0060.0000.0000.0000.000
82A62GLY00.079-0.05813.9970.0590.0590.0000.0000.0000.000
83A63ALA00.055-0.03716.8380.0000.0000.0000.0000.0000.000
84A63ALA0-0.0580.12021.4940.0040.0040.0000.0000.0000.000
85A64GLY0-0.019-0.10319.4280.0250.0250.0000.0000.0000.000
86A65PRO0-0.028-0.01518.002-0.031-0.0310.0000.0000.0000.000
87A66GLY00.0300.00517.2620.0250.0250.0000.0000.0000.000
88A67ALA00.0990.02718.304-0.002-0.0020.0000.0000.0000.000
89A67ALA0-0.1030.08118.5070.0070.0070.0000.0000.0000.000
90A68VAL00.042-0.12515.288-0.053-0.0530.0000.0000.0000.000
91A68VAL0-0.0650.11414.8570.0050.0050.0000.0000.0000.000
92A69ASN00.079-0.07011.8780.0600.0600.0000.0000.0000.000
93A69ASN0-0.0430.07710.9460.0540.0540.0000.0000.0000.000
94A70LEU00.015-0.12012.872-0.022-0.0220.0000.0000.0000.000
95A70LEU0-0.0690.10514.4210.0120.0120.0000.0000.0000.000
96A71GLU00.061-0.1379.317-0.030-0.0300.0000.0000.0000.000
97A71GLU-1-0.837-0.7716.829-0.715-0.7150.0000.0000.0000.000
98A72TRP0-0.025-0.12410.5570.0170.0170.0000.0000.0000.000
99A72TRP0-0.0130.11413.0770.0000.0000.0000.0000.0000.000
100A73PRO00.076-0.07310.1780.0050.0050.0000.0000.0000.000
101A74LEU00.1360.03510.781-0.029-0.0290.0000.0000.0000.000
102A74LEU0-0.1410.10311.1110.0000.0000.0000.0000.0000.000
103A75GLU00.060-0.12812.598-0.029-0.0290.0000.0000.0000.000
104A75GLU-1-0.817-0.76112.9240.2130.2130.0000.0000.0000.000
105A76SER0-0.015-0.09514.7860.0050.0050.0000.0000.0000.000
106A76SER0-0.0240.05214.982-0.007-0.0070.0000.0000.0000.000
107A77VAL00.006-0.11016.482-0.017-0.0170.0000.0000.0000.000
108A77VAL0-0.1020.09814.995-0.006-0.0060.0000.0000.0000.000
109A78SER00.098-0.06517.6600.0180.0180.0000.0000.0000.000
110A78SER0-0.0590.08021.8110.0020.0020.0000.0000.0000.000
111A79TYR00.082-0.09619.455-0.016-0.0160.0000.0000.0000.000
112A79TYR0-0.0930.07317.655-0.005-0.0050.0000.0000.0000.000
113A80THR0-0.089-0.12120.8220.0140.0140.0000.0000.0000.000
114A80THR0-0.0180.08124.489-0.001-0.0010.0000.0000.0000.000
115A81ILE00.144-0.08123.829-0.010-0.0100.0000.0000.0000.000
116A81ILE0-0.0960.10123.4510.0020.0020.0000.0000.0000.000
117A82ARG00.047-0.12525.7870.0060.0060.0000.0000.0000.000
118A82ARG10.7751.00327.2740.0150.0150.0000.0000.0000.000
119A83GLY00.001-0.10128.2570.0010.0010.0000.0000.0000.000
120A84PRO0-0.003-0.01728.024-0.001-0.0010.0000.0000.0000.000
121A85THR00.0190.02326.9680.0040.0040.0000.0000.0000.000
122A85THR0-0.0170.08428.2690.0010.0010.0000.0000.0000.000
123A86GLN00.171-0.06126.154-0.009-0.0090.0000.0000.0000.000
124A86GLN0-0.0640.10427.040-0.002-0.0020.0000.0000.0000.000
125A87HIS00.003-0.09622.6870.0120.0120.0000.0000.0000.000
126A87HIS0-0.0310.11221.260-0.007-0.0070.0000.0000.0000.000
127A88GLU00.145-0.09223.572-0.010-0.0100.0000.0000.0000.000
128A88GLU-1-0.920-0.76524.875-0.027-0.0270.0000.0000.0000.000
129A89LEU00.075-0.09119.8060.0160.0160.0000.0000.0000.000
130A89LEU0-0.0920.09416.448-0.002-0.0020.0000.0000.0000.000
131A90GLN00.134-0.09420.921-0.014-0.0140.0000.0000.0000.000
132A90GLN0-0.1090.11022.9060.0020.0020.0000.0000.0000.000
133A91PRO0-0.017-0.10317.6930.0110.0110.0000.0000.0000.000
134A92PRO00.0290.00616.8920.0070.0070.0000.0000.0000.000
135A93PRO0-0.011-0.00119.980-0.012-0.0120.0000.0000.0000.000
136A94GLY00.0050.00221.728-0.002-0.0020.0000.0000.0000.000
137A95GLY00.0010.01719.624-0.015-0.0150.0000.0000.0000.000
138A96PRO0-0.040-0.03018.9650.0070.0070.0000.0000.0000.000
139A97GLY00.0310.01021.8930.0060.0060.0000.0000.0000.000
140A98THR00.0240.01422.405-0.009-0.0090.0000.0000.0000.000
141A98THR0-0.0300.06824.4360.0000.0000.0000.0000.0000.000
142A99LEU00.046-0.10422.0230.0010.0010.0000.0000.0000.000
143A99LEU0-0.0360.11119.359-0.004-0.0040.0000.0000.0000.000
144A100SER00.058-0.06023.4300.0070.0070.0000.0000.0000.000
145A100SER0-0.0280.06426.8020.0000.0000.0000.0000.0000.000
146A101MET00.048-0.09622.099-0.010-0.0100.0000.0000.0000.000
147A101MET0-0.0960.08618.485-0.009-0.0090.0000.0000.0000.000
148A102HIS00.102-0.08323.5520.0110.0110.0000.0000.0000.000
149A102HIS0-0.0900.08426.6930.0040.0040.0000.0000.0000.000
150A103PHE00.096-0.09023.993-0.014-0.0140.0000.0000.0000.000
151A103PHE0-0.1140.08419.5850.0020.0020.0000.0000.0000.000
152A104LEU00.120-0.09924.6180.0070.0070.0000.0000.0000.000
153A104LEU0-0.0680.11923.4960.0000.0000.0000.0000.0000.000
154A105ASN00.026-0.08626.0300.0030.0030.0000.0000.0000.000
155A105ASN0-0.1000.04525.3940.0090.0090.0000.0000.0000.000
156A106PRO00.074-0.08526.004-0.001-0.0010.0000.0000.0000.000
157A107GLN00.1340.03925.7590.0050.0050.0000.0000.0000.000
158A107GLN0-0.0920.09224.7650.0040.0040.0000.0000.0000.000
159A108GLU00.029-0.14521.9140.0160.0160.0000.0000.0000.000
160A108GLU-1-0.949-0.80821.301-0.050-0.0500.0000.0000.0000.000
161A109ALA00.148-0.07721.1940.0030.0030.0000.0000.0000.000
162A109ALA0-0.0650.11724.448-0.001-0.0010.0000.0000.0000.000
163A110GLN00.079-0.11722.0600.0040.0040.0000.0000.0000.000
164A110GLN0-0.0930.10924.479-0.005-0.0050.0000.0000.0000.000
165A111ARG00.084-0.08720.7420.0140.0140.0000.0000.0000.000
166A111ARG10.8371.05518.704-0.023-0.0230.0000.0000.0000.000
167A112TRP00.107-0.08117.2800.0280.0280.0000.0000.0000.000
168A112TRP0-0.0970.08812.7550.0050.0050.0000.0000.0000.000
169A113ALA00.141-0.09317.4240.0110.0110.0000.0000.0000.000
170A113ALA0-0.1000.08521.505-0.001-0.0010.0000.0000.0000.000
171A114VAL0-0.027-0.12619.4420.0070.0070.0000.0000.0000.000
172A114VAL0-0.0950.08319.2460.0000.0000.0000.0000.0000.000
173A115LEU00.108-0.09215.3550.0240.0240.0000.0000.0000.000
174A115LEU0-0.0810.11412.418-0.005-0.0050.0000.0000.0000.000
175A116VAL00.152-0.07914.5320.0450.0450.0000.0000.0000.000
176A116VAL0-0.0970.11214.657-0.004-0.0040.0000.0000.0000.000
177A117ARG00.084-0.09315.5900.0170.0170.0000.0000.0000.000
178A117ARG10.8231.05019.573-0.094-0.0940.0000.0000.0000.000
179A118GLY0-0.056-0.12016.2280.0040.0040.0000.0000.0000.000
180A119ALA00.0840.01612.0600.0520.0520.0000.0000.0000.000
181A119ALA0-0.0510.09711.101-0.003-0.0030.0000.0000.0000.000
182A120THR0-0.007-0.10712.4250.0300.0300.0000.0000.0000.000
183A120THR0-0.0400.05315.649-0.015-0.0150.0000.0000.0000.000
184A121VAL0-0.118-0.13314.804-0.020-0.0200.0000.0000.0000.000
185A121VAL00.0530.03813.2970.0070.0070.0000.0000.0000.000