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: 9M832

Calculation Name: 3B02-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B02

Chain ID: A

ChEMBL ID:

UniProt ID: Q53W63

Base Structure: X-ray

Registration Date: 2023-09-27

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 OptHSide
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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2206906.348144
FMO2-HF: Nuclear repulsion 2129990.405833
FMO2-HF: Total energy -76915.942311
FMO2-MP2: Total energy -77143.208986


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-17.293-13.07724.072-10.663-17.624-0.058
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.004
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].
3A3ARG10.8440.9153.806-0.7942.192-0.029-1.506-1.4510.005
4A4PHE00.0120.0005.541-0.285-0.2850.0000.0000.0000.000
5A5ALA00.0610.0409.0440.1630.1630.0000.0000.0000.000
6A6ARG10.7280.81912.243-0.018-0.0180.0000.0000.0000.000
7A7LYS10.7430.83314.956-0.058-0.0580.0000.0000.0000.000
8A8GLU-1-0.860-0.89611.693-0.482-0.4820.0000.0000.0000.000
9A9THR0-0.010-0.01814.2150.0690.0690.0000.0000.0000.000
10A10ILE0-0.090-0.0468.844-0.063-0.0630.0000.0000.0000.000
11A11TYR0-0.0260.00011.463-0.057-0.0570.0000.0000.0000.000
12A12LEU00.0030.00414.1050.0510.0510.0000.0000.0000.000
13A13ARG10.8780.93617.901-0.004-0.0040.0000.0000.0000.000
14A14GLY0-0.037-0.02620.770-0.013-0.0130.0000.0000.0000.000
15A15GLU-1-0.880-0.93416.765-0.199-0.1990.0000.0000.0000.000
16A16GLU-1-0.824-0.89116.678-0.107-0.1070.0000.0000.0000.000
17A17ALA0-0.0130.00015.123-0.026-0.0260.0000.0000.0000.000
18A18ARG10.7810.85112.8930.2190.2190.0000.0000.0000.000
19A19THR0-0.036-0.0157.4830.0380.0380.0000.0000.0000.000
20A20LEU00.0350.04710.1650.0010.0010.0000.0000.0000.000
21A21TYR00.025-0.0036.298-0.049-0.0490.0000.0000.0000.000
22A22ARG10.8030.8774.002-1.323-1.223-0.001-0.014-0.0850.000
23A23LEU0-0.0260.0006.0070.8090.973-0.001-0.008-0.1550.000
24A24GLU-1-0.796-0.8662.364-2.729-2.0844.568-2.093-3.120-0.018
25A25GLU-1-0.812-0.9045.696-0.060-0.0600.0000.0000.0000.000
26A26GLY00.0320.0128.1690.0390.0390.0000.0000.0000.000
27A27LEU0-0.003-0.01111.2110.0380.0380.0000.0000.0000.000
28A28VAL00.0170.01610.947-0.059-0.0590.0000.0000.0000.000
29A29ARG10.7560.85314.027-0.066-0.0660.0000.0000.0000.000
30A30VAL00.0060.00516.265-0.016-0.0160.0000.0000.0000.000
31A31VAL0-0.017-0.01518.445-0.004-0.0040.0000.0000.0000.000
32A32GLU-1-0.755-0.85621.5200.0230.0230.0000.0000.0000.000
33A33LEU0-0.0050.00724.4380.0010.0010.0000.0000.0000.000
34A34LEU0-0.026-0.03126.739-0.001-0.0010.0000.0000.0000.000
35A35PRO00.019-0.00830.252-0.005-0.0050.0000.0000.0000.000
36A36ASP-1-0.834-0.88133.2900.0090.0090.0000.0000.0000.000
37A37GLY00.0120.01231.398-0.002-0.0020.0000.0000.0000.000
38A38ARG10.8250.88430.308-0.023-0.0230.0000.0000.0000.000
39A39LEU0-0.0010.02122.933-0.001-0.0010.0000.0000.0000.000
40A40ILE0-0.006-0.00226.0630.0030.0030.0000.0000.0000.000
41A41THR00.0230.00721.5100.0000.0000.0000.0000.0000.000
42A42LEU0-0.0100.01121.9840.0000.0000.0000.0000.0000.000
43A43ARG10.7840.84516.193-0.267-0.2670.0000.0000.0000.000
44A44HIS00.0210.03218.047-0.015-0.0150.0000.0000.0000.000
45A45VAL0-0.025-0.01412.123-0.001-0.0010.0000.0000.0000.000
46A46LEU00.035-0.00313.6330.0130.0130.0000.0000.0000.000
47A47PRO00.0060.0019.6300.0660.0660.0000.0000.0000.000
48A48GLY0-0.021-0.0138.819-0.162-0.1620.0000.0000.0000.000
49A49ASP-1-0.811-0.8589.8980.3810.3810.0000.0000.0000.000
50A50TYR0-0.008-0.0189.9730.1990.1990.0000.0000.0000.000
51A51PHE00.017-0.0048.793-0.112-0.1120.0000.0000.0000.000
52A52GLY00.0900.04612.0370.0280.0280.0000.0000.0000.000
53A53GLU-1-0.796-0.89013.6930.2310.2310.0000.0000.0000.000
54A54GLU-1-0.696-0.85216.1600.1070.1070.0000.0000.0000.000
55A55ALA0-0.0070.01713.823-0.017-0.0170.0000.0000.0000.000
56A56LEU0-0.116-0.06715.5020.0030.0030.0000.0000.0000.000
57A57GLU-1-0.963-0.99017.6120.0780.0780.0000.0000.0000.000
58A58GLY00.0140.03320.087-0.014-0.0140.0000.0000.0000.000
59A59LYS10.8440.89519.921-0.037-0.0370.0000.0000.0000.000
60A60ALA00.0170.01319.045-0.020-0.0200.0000.0000.0000.000
61A61TYR0-0.0250.00312.109-0.004-0.0040.0000.0000.0000.000
62A62ARG10.7960.86418.728-0.056-0.0560.0000.0000.0000.000
63A63TYR0-0.021-0.02119.443-0.010-0.0100.0000.0000.0000.000
64A64THR00.0360.02217.695-0.014-0.0140.0000.0000.0000.000
65A65ALA0-0.0060.02313.5960.0320.0320.0000.0000.0000.000
66A66GLU-1-0.760-0.86214.598-0.021-0.0210.0000.0000.0000.000
67A67ALA00.0390.02911.7040.0730.0730.0000.0000.0000.000
68A68MET0-0.0130.00813.581-0.057-0.0570.0000.0000.0000.000
69A69THR0-0.005-0.01512.236-0.025-0.0250.0000.0000.0000.000
70A70GLU-1-0.873-0.92910.255-0.122-0.1220.0000.0000.0000.000
71A71ALA0-0.014-0.0108.5450.1130.1130.0000.0000.0000.000
72A72VAL0-0.0080.0092.3470.043-1.9145.534-1.122-2.4540.001
73A73VAL00.0110.0074.1470.1860.9540.018-0.240-0.5460.000
74A74GLN00.0850.0272.109-11.865-10.12713.891-6.310-9.320-0.047
75A75GLY0-0.0060.0062.905-0.807-1.1470.0930.633-0.3860.001
76A76LEU0-0.050-0.0354.9050.3060.418-0.001-0.003-0.1070.000
77A77GLU-1-0.877-0.9407.668-0.080-0.0800.0000.0000.0000.000
78A78PRO00.003-0.01210.6890.0520.0520.0000.0000.0000.000
79A79ARG10.9350.94113.763-0.065-0.0650.0000.0000.0000.000
80A80ALA00.0070.02412.306-0.019-0.0190.0000.0000.0000.000
81A81MET0-0.060-0.00512.6820.0750.0750.0000.0000.0000.000
82A82ASP-1-0.764-0.88514.8690.2840.2840.0000.0000.0000.000
83A83HIS00.0250.00517.0240.0110.0110.0000.0000.0000.000
84A84GLU-1-0.839-0.90314.2110.3200.3200.0000.0000.0000.000
85A85ALA0-0.060-0.02912.9650.0190.0190.0000.0000.0000.000
86A86LEU00.0580.02514.1240.0190.0190.0000.0000.0000.000
87A87HIS00.0100.01317.013-0.006-0.0060.0000.0000.0000.000
88A88ARG10.7790.86211.513-0.412-0.4120.0000.0000.0000.000
89A89VAL00.0110.01413.1710.0090.0090.0000.0000.0000.000
90A90ALA00.0370.02415.177-0.014-0.0140.0000.0000.0000.000
91A91ARG10.9390.96417.444-0.229-0.2290.0000.0000.0000.000
92A92ASN0-0.035-0.03114.102-0.008-0.0080.0000.0000.0000.000
93A93LEU00.0660.03616.300-0.007-0.0070.0000.0000.0000.000
94A94ALA00.0140.01618.339-0.022-0.0220.0000.0000.0000.000
95A95ARG10.8990.94116.348-0.288-0.2880.0000.0000.0000.000
96A96GLN00.002-0.01514.933-0.036-0.0360.0000.0000.0000.000
97A97MET00.0090.02119.539-0.019-0.0190.0000.0000.0000.000
98A98ARG10.8620.89421.993-0.190-0.1900.0000.0000.0000.000
99A99ARG10.8110.86716.102-0.338-0.3380.0000.0000.0000.000
100A100VAL0-0.020-0.00522.392-0.010-0.0100.0000.0000.0000.000
101A101GLN00.0480.03124.080-0.009-0.0090.0000.0000.0000.000
102A102ALA00.0030.00626.222-0.011-0.0110.0000.0000.0000.000
103A103TYR0-0.065-0.05524.769-0.008-0.0080.0000.0000.0000.000
104A104GLU-1-0.885-0.95826.8830.0850.0850.0000.0000.0000.000
105A105ALA00.0000.01129.397-0.009-0.0090.0000.0000.0000.000
106A106HIS0-0.032-0.00128.281-0.009-0.0090.0000.0000.0000.000
107A107LEU0-0.056-0.02828.206-0.008-0.0080.0000.0000.0000.000
108A108GLN0-0.082-0.04231.931-0.011-0.0110.0000.0000.0000.000
109A109THR0-0.013-0.00134.572-0.004-0.0040.0000.0000.0000.000
110A110GLY00.0200.00535.7620.0020.0020.0000.0000.0000.000
111A111GLU-1-0.874-0.93937.8710.0360.0360.0000.0000.0000.000
112A112LEU0-0.016-0.01334.1360.0030.0030.0000.0000.0000.000
113A113ARG10.7210.79735.367-0.032-0.0320.0000.0000.0000.000
114A114ALA00.0570.03935.6950.0030.0030.0000.0000.0000.000
115A115ARG10.8240.91732.417-0.046-0.0460.0000.0000.0000.000
116A116ILE00.011-0.01131.1480.0070.0070.0000.0000.0000.000
117A117ALA00.0050.01230.6950.0050.0050.0000.0000.0000.000
118A118ARG10.8190.90229.643-0.070-0.0700.0000.0000.0000.000
119A119TYR0-0.020-0.02822.4300.0040.0040.0000.0000.0000.000
120A120LEU0-0.026-0.01926.0270.0100.0100.0000.0000.0000.000
121A121LEU00.0110.00026.3870.0070.0070.0000.0000.0000.000
122A122PHE0-0.0200.00720.4380.0110.0110.0000.0000.0000.000
123A123LEU0-0.006-0.00821.0220.0170.0170.0000.0000.0000.000
124A124ALA0-0.031-0.01621.7070.0130.0130.0000.0000.0000.000
125A125ASP-1-0.927-0.93821.6220.1460.1460.0000.0000.0000.000
126A126THR0-0.057-0.04117.6340.0350.0350.0000.0000.0000.000
127A127PRO0-0.041-0.03113.473-0.027-0.0270.0000.0000.0000.000
128A128LEU0-0.0250.00416.144-0.019-0.0190.0000.0000.0000.000
129A129SER0-0.054-0.01918.783-0.038-0.0380.0000.0000.0000.000
130A130ALA00.0140.00719.9820.0090.0090.0000.0000.0000.000
131A131ARG10.9610.97222.268-0.078-0.0780.0000.0000.0000.000
132A132ASP-1-0.789-0.88025.2620.0320.0320.0000.0000.0000.000
133A133ARG10.9420.96328.001-0.020-0.0200.0000.0000.0000.000
134A134GLN0-0.054-0.01531.2910.0010.0010.0000.0000.0000.000
135A135GLY00.0510.03030.6010.0010.0010.0000.0000.0000.000
136A136ILE0-0.009-0.01225.6940.0000.0000.0000.0000.0000.000
137A137TYR0-0.010-0.00722.310-0.010-0.0100.0000.0000.0000.000
138A138VAL00.0570.03423.1570.0110.0110.0000.0000.0000.000
139A139THR0-0.044-0.02320.516-0.022-0.0220.0000.0000.0000.000
140A140VAL00.0150.00821.3810.0110.0110.0000.0000.0000.000
141A141SER0-0.044-0.04423.706-0.012-0.0120.0000.0000.0000.000
142A142HIS00.004-0.03626.0710.0070.0070.0000.0000.0000.000
143A143GLU-1-0.799-0.88326.6870.0110.0110.0000.0000.0000.000
144A144GLU-1-0.715-0.79121.0260.0570.0570.0000.0000.0000.000
145A145ILE00.0260.01425.2610.0090.0090.0000.0000.0000.000
146A146ALA0-0.0250.00827.7810.0040.0040.0000.0000.0000.000
147A147ASP-1-0.785-0.89025.5110.0400.0400.0000.0000.0000.000
148A148ALA0-0.036-0.00524.8780.0060.0060.0000.0000.0000.000
149A149THR0-0.027-0.03326.9470.0020.0020.0000.0000.0000.000
150A150ALA00.0330.02930.385-0.005-0.0050.0000.0000.0000.000
151A151SER0-0.040-0.02032.184-0.005-0.0050.0000.0000.0000.000
152A152ILE00.0650.03532.7760.0000.0000.0000.0000.0000.000
153A153ARG10.8740.88931.3170.0000.0000.0000.0000.0000.000
154A154GLU-1-0.843-0.90333.2900.0070.0070.0000.0000.0000.000
155A155SER00.005-0.00636.7150.0000.0000.0000.0000.0000.000
156A156VAL00.0330.02531.2310.0010.0010.0000.0000.0000.000
157A157SER0-0.044-0.03034.6630.0000.0000.0000.0000.0000.000
158A158LYS10.8550.92235.684-0.021-0.0210.0000.0000.0000.000
159A159VAL00.0530.03036.4920.0000.0000.0000.0000.0000.000
160A160LEU00.0300.01731.5600.0010.0010.0000.0000.0000.000
161A161ALA0-0.095-0.03535.925-0.001-0.0010.0000.0000.0000.000
162A162ASP-1-0.770-0.86739.0130.0210.0210.0000.0000.0000.000
163A163LEU00.0630.02435.1260.0000.0000.0000.0000.0000.000
164A164ARG10.8510.91834.541-0.020-0.0200.0000.0000.0000.000
165A165ARG10.8040.90038.594-0.019-0.0190.0000.0000.0000.000
166A166GLU-1-0.834-0.89441.3030.0290.0290.0000.0000.0000.000
167A167GLY00.0080.02039.9340.0010.0010.0000.0000.0000.000
168A168LEU00.0060.01036.5140.0020.0020.0000.0000.0000.000
169A169ILE0-0.024-0.01232.9120.0040.0040.0000.0000.0000.000
170A170ALA00.0340.02133.260-0.005-0.0050.0000.0000.0000.000
171A171THR0-0.0060.01031.2310.0040.0040.0000.0000.0000.000
172A172ALA00.005-0.00530.103-0.005-0.0050.0000.0000.0000.000
173A173TYR00.0110.00126.9740.0030.0030.0000.0000.0000.000
174A174ARG10.9380.96321.5890.0210.0210.0000.0000.0000.000
175A175ARG10.8980.97823.944-0.024-0.0240.0000.0000.0000.000
176A176VAL00.0120.00126.571-0.008-0.0080.0000.0000.0000.000
177A177TYR0-0.066-0.05828.0420.0060.0060.0000.0000.0000.000
178A178LEU0-0.012-0.01427.706-0.004-0.0040.0000.0000.0000.000
179A179LEU0-0.028-0.01831.4180.0010.0010.0000.0000.0000.000
180A180ASP-1-0.846-0.91234.7280.0440.0440.0000.0000.0000.000
181A181LEU00.003-0.01130.5040.0010.0010.0000.0000.0000.000
182A182ALA00.0900.05133.9980.0020.0020.0000.0000.0000.000
183A183ALA0-0.059-0.04336.8770.0000.0000.0000.0000.0000.000
184A184LEU00.008-0.00532.0600.0000.0000.0000.0000.0000.000
185A185GLU-1-0.912-0.96232.7200.0750.0750.0000.0000.0000.000
186A186ARG10.8900.95434.900-0.045-0.0450.0000.0000.0000.000
187A187GLU-1-0.859-0.89636.5990.0400.0400.0000.0000.0000.000
188A188ALA0-0.029-0.00733.0160.0000.0000.0000.0000.0000.000
189A189GLY00.0040.01535.0420.0010.0010.0000.0000.0000.000
190A190SER0-0.029-0.00833.1930.0000.0000.0000.0000.0000.000
191A191ALA00.019-0.00329.0450.0000.0000.0000.0000.0000.000
192A192LEU0-0.009-0.00325.309-0.002-0.0020.0000.0000.0000.000
193A193GLU-1-0.871-0.92624.0660.1500.1500.0000.0000.0000.000
194A194ALA00.0710.03321.8080.0100.0100.0000.0000.0000.000
195A195ALA0-0.0350.00919.3540.0070.0070.0000.0000.0000.000