FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YYG62

Calculation Name: 3MSQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MSQ

Chain ID: A

ChEMBL ID:

UniProt ID: B2J5W7

Base Structure: X-ray

Registration Date: 2023-06-19

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 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2617453.111055
FMO2-HF: Nuclear repulsion 2531800.119937
FMO2-HF: Total energy -85652.991118
FMO2-MP2: Total energy -85904.038703


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:6:THR)


Summations of interaction energy for fragment #1(A:6:THR)
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.
0.1451.591-0.01-0.7-0.7360.001
Interaction energy analysis for fragmet #1(A:6:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.007
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].
3A8ASN0-0.017-0.0093.9280.9482.394-0.010-0.700-0.7360.001
4A9ASN00.0940.0246.529-0.201-0.2010.0000.0000.0000.000
5A10ASP-1-0.883-0.9308.939-0.257-0.2570.0000.0000.0000.000
6A11LYS10.9350.96010.2470.8480.8480.0000.0000.0000.000
7A12GLY00.0440.03411.6040.0390.0390.0000.0000.0000.000
8A13LEU0-0.010-0.00613.3580.0640.0640.0000.0000.0000.000
9A14LEU0-0.010-0.01314.0790.0320.0320.0000.0000.0000.000
10A15ALA00.0330.02216.0350.0360.0360.0000.0000.0000.000
11A16TYR00.0190.00817.6920.0360.0360.0000.0000.0000.000
12A17ILE0-0.004-0.00418.6580.0280.0280.0000.0000.0000.000
13A18GLN00.0070.01420.583-0.001-0.0010.0000.0000.0000.000
14A19PHE0-0.0020.00121.8110.0220.0220.0000.0000.0000.000
15A20LEU0-0.018-0.00422.8870.0190.0190.0000.0000.0000.000
16A21ALA00.0240.01725.2380.0130.0130.0000.0000.0000.000
17A22SER0-0.027-0.01225.9940.0110.0110.0000.0000.0000.000
18A23SER0-0.048-0.04526.9790.0090.0090.0000.0000.0000.000
19A24ALA00.0030.02129.6500.0080.0080.0000.0000.0000.000
20A25GLN0-0.0250.00030.7660.0110.0110.0000.0000.0000.000
21A26LYS10.8780.92734.0490.0920.0920.0000.0000.0000.000
22A27ILE0-0.021-0.00731.644-0.006-0.0060.0000.0000.0000.000
23A28GLY00.001-0.00433.8380.0080.0080.0000.0000.0000.000
24A29ASP-1-0.912-0.93934.486-0.102-0.1020.0000.0000.0000.000
25A30GLY00.0390.03631.6560.0030.0030.0000.0000.0000.000
26A31ASN0-0.078-0.07129.803-0.007-0.0070.0000.0000.0000.000
27A32THR00.0160.00928.382-0.004-0.0040.0000.0000.0000.000
28A33ASP-1-0.838-0.93326.152-0.173-0.1730.0000.0000.0000.000
29A34ARG10.9120.94524.6610.1350.1350.0000.0000.0000.000
30A35VAL0-0.007-0.00322.752-0.020-0.0200.0000.0000.0000.000
31A36PHE00.003-0.00421.306-0.021-0.0210.0000.0000.0000.000
32A37ASP-1-0.831-0.91119.974-0.310-0.3100.0000.0000.0000.000
33A38PHE0-0.033-0.01717.364-0.047-0.0470.0000.0000.0000.000
34A39GLU-1-0.769-0.90216.901-0.310-0.3100.0000.0000.0000.000
35A40ASP-1-0.801-0.88315.482-0.433-0.4330.0000.0000.0000.000
36A41ALA0-0.0290.01014.034-0.116-0.1160.0000.0000.0000.000
37A42LEU00.0120.00212.442-0.119-0.1190.0000.0000.0000.000
38A43ASP-1-0.786-0.86010.808-0.713-0.7130.0000.0000.0000.000
39A44GLN0-0.075-0.0507.811-0.295-0.2950.0000.0000.0000.000
40A45THR0-0.064-0.0476.421-0.656-0.6560.0000.0000.0000.000
41A46GLN00.0420.0145.4560.0520.0520.0000.0000.0000.000
42A47MET0-0.022-0.0156.3880.0900.0900.0000.0000.0000.000
43A48ALA00.0060.0158.7910.0900.0900.0000.0000.0000.000
44A49GLN0-0.024-0.0296.163-0.109-0.1090.0000.0000.0000.000
45A50LEU00.0220.0158.2960.1490.1490.0000.0000.0000.000
46A51ALA00.0180.00810.2130.0590.0590.0000.0000.0000.000
47A52VAL0-0.0050.00011.3070.0490.0490.0000.0000.0000.000
48A53ASP-1-0.868-0.9329.257-0.050-0.0500.0000.0000.0000.000
49A54GLU-1-0.867-0.92712.8070.0860.0860.0000.0000.0000.000
50A55LEU0-0.036-0.01215.7650.0160.0160.0000.0000.0000.000
51A56LYS10.8690.91914.6940.0860.0860.0000.0000.0000.000
52A57LYS10.7920.89614.583-0.044-0.0440.0000.0000.0000.000
53A58ILE0-0.046-0.00919.1900.0080.0080.0000.0000.0000.000
54A59PRO00.006-0.00722.408-0.009-0.0090.0000.0000.0000.000
55A60GLU-1-0.860-0.94424.513-0.022-0.0220.0000.0000.0000.000
56A61VAL00.0010.00320.228-0.007-0.0070.0000.0000.0000.000
57A62ASN00.010-0.00619.339-0.017-0.0170.0000.0000.0000.000
58A63ALA00.0090.02821.4080.0010.0010.0000.0000.0000.000
59A64LEU00.0110.00723.074-0.002-0.0020.0000.0000.0000.000
60A65PHE0-0.035-0.02915.794-0.011-0.0110.0000.0000.0000.000
61A66SER0-0.089-0.04620.386-0.001-0.0010.0000.0000.0000.000
62A67GLU-1-0.847-0.90322.352-0.044-0.0440.0000.0000.0000.000
63A68ARG10.8200.91616.1060.1530.1530.0000.0000.0000.000
64A69TRP00.0160.02422.782-0.007-0.0070.0000.0000.0000.000
65A70LEU00.0060.00223.149-0.016-0.0160.0000.0000.0000.000
66A71PRO0-0.046-0.00826.8730.0080.0080.0000.0000.0000.000
67A72ALA00.0000.00130.331-0.004-0.0040.0000.0000.0000.000
68A73PRO0-0.035-0.01933.388-0.002-0.0020.0000.0000.0000.000
69A74PHE00.014-0.00133.1850.0060.0060.0000.0000.0000.000
70A75ASN0-0.001-0.00837.884-0.005-0.0050.0000.0000.0000.000
71A76LEU00.043-0.00138.0020.0030.0030.0000.0000.0000.000
72A77ASP-1-0.858-0.92141.326-0.048-0.0480.0000.0000.0000.000
73A78ASP-1-0.829-0.90043.615-0.042-0.0420.0000.0000.0000.000
74A79LEU0-0.0160.00638.1480.0020.0020.0000.0000.0000.000
75A80ALA00.008-0.00842.8530.0020.0020.0000.0000.0000.000
76A81LYS10.7920.89545.4610.0430.0430.0000.0000.0000.000
77A82LEU0-0.0130.02542.6750.0020.0020.0000.0000.0000.000
78A83PRO00.003-0.01046.6520.0000.0000.0000.0000.0000.000
79A84GLU-1-0.808-0.88046.904-0.036-0.0360.0000.0000.0000.000
80A85GLY00.0080.01045.854-0.001-0.0010.0000.0000.0000.000
81A86THR0-0.065-0.03042.999-0.001-0.0010.0000.0000.0000.000
82A87LEU00.0120.00035.274-0.001-0.0010.0000.0000.0000.000
83A88GLY00.007-0.00839.522-0.003-0.0030.0000.0000.0000.000
84A89HIS00.0090.01640.755-0.003-0.0030.0000.0000.0000.000
85A90VAL0-0.004-0.01040.205-0.001-0.0010.0000.0000.0000.000
86A91TYR0-0.065-0.05233.771-0.001-0.0010.0000.0000.0000.000
87A92ALA00.0310.01139.145-0.003-0.0030.0000.0000.0000.000
88A93ARG10.7910.86841.4270.0380.0380.0000.0000.0000.000
89A94GLU-1-0.843-0.91537.804-0.065-0.0650.0000.0000.0000.000
90A95MET0-0.0220.01635.128-0.003-0.0030.0000.0000.0000.000
91A96LYS10.8160.90439.8360.0510.0510.0000.0000.0000.000
92A97ALA0-0.0220.00443.1310.0010.0010.0000.0000.0000.000
93A98ARG10.8080.88133.7050.0840.0840.0000.0000.0000.000
94A99GLY00.0220.00837.8620.0020.0020.0000.0000.0000.000
95A100PHE0-0.052-0.04232.605-0.003-0.0030.0000.0000.0000.000
96A101ASP-1-0.814-0.88234.841-0.103-0.1030.0000.0000.0000.000
97A102PRO00.0210.01730.2700.0020.0020.0000.0000.0000.000
98A103TYR0-0.114-0.06731.279-0.004-0.0040.0000.0000.0000.000
99A104PHE0-0.015-0.02231.4680.0010.0010.0000.0000.0000.000
100A105TYR0-0.071-0.04725.095-0.003-0.0030.0000.0000.0000.000
101A106LYS10.8690.94220.9510.3010.3010.0000.0000.0000.000
102A107LYS10.9460.96123.8890.1260.1260.0000.0000.0000.000
103A108VAL00.017-0.00517.807-0.008-0.0080.0000.0000.0000.000
104A109PRO0-0.020-0.00718.8640.0180.0180.0000.0000.0000.000
105A110VAL00.005-0.00718.417-0.032-0.0320.0000.0000.0000.000
106A111VAL0-0.003-0.00613.9400.0320.0320.0000.0000.0000.000
107A112ASP-1-0.822-0.88011.504-0.534-0.5340.0000.0000.0000.000
108A113ASP-1-0.747-0.86312.866-0.133-0.1330.0000.0000.0000.000
109A114ILE00.0090.0118.4600.0480.0480.0000.0000.0000.000
110A115SER0-0.027-0.05113.0730.0720.0720.0000.0000.0000.000
111A116TYR0-0.061-0.04415.8680.0400.0400.0000.0000.0000.000
112A117LEU00.0260.01414.9150.0270.0270.0000.0000.0000.000
113A118LYS10.7620.86715.4040.5340.5340.0000.0000.0000.000
114A119MET00.0200.02318.4810.0270.0270.0000.0000.0000.000
115A120LEU00.0140.03120.9930.0200.0200.0000.0000.0000.000
116A121TRP0-0.0160.00620.7260.0280.0280.0000.0000.0000.000
117A122ARG10.7490.85619.6880.3030.3030.0000.0000.0000.000
118A123SER0-0.038-0.01924.4890.0140.0140.0000.0000.0000.000
119A124THR0-0.002-0.00925.5910.0140.0140.0000.0000.0000.000
120A125HIS10.9040.96724.9200.1470.1470.0000.0000.0000.000
121A126ASP-1-0.802-0.87727.343-0.088-0.0880.0000.0000.0000.000
122A127ILE00.0300.01730.6860.0070.0070.0000.0000.0000.000
123A128TYR0-0.017-0.02024.8850.0050.0050.0000.0000.0000.000
124A129HIS10.8500.91630.8950.0810.0810.0000.0000.0000.000
125A130VAL00.0330.03033.2010.0050.0050.0000.0000.0000.000
126A131VAL0-0.0060.01033.5770.0050.0050.0000.0000.0000.000
127A132ALA00.0080.00331.9370.0050.0050.0000.0000.0000.000
128A133GLY0-0.0370.00234.0770.0040.0040.0000.0000.0000.000
129A134PHE0-0.042-0.02233.5410.0020.0020.0000.0000.0000.000
130A135ASP-1-0.844-0.91935.750-0.054-0.0540.0000.0000.0000.000
131A136THR0-0.006-0.01534.988-0.004-0.0040.0000.0000.0000.000
132A137ASN0-0.039-0.00534.915-0.007-0.0070.0000.0000.0000.000
133A138VAL00.0700.01632.174-0.003-0.0030.0000.0000.0000.000
134A139PHE0-0.003-0.01232.315-0.003-0.0030.0000.0000.0000.000
135A140GLY00.0350.03533.2270.0010.0010.0000.0000.0000.000
136A141GLU-1-0.841-0.93528.171-0.115-0.1150.0000.0000.0000.000
137A142ILE0-0.036-0.02427.653-0.004-0.0040.0000.0000.0000.000
138A143GLY00.0170.00828.7910.0010.0010.0000.0000.0000.000
139A144LEU00.0040.00328.3930.0040.0040.0000.0000.0000.000
140A145GLN0-0.012-0.01123.769-0.009-0.0090.0000.0000.0000.000
141A146ALA0-0.0010.00924.974-0.001-0.0010.0000.0000.0000.000
142A147PHE00.0160.00726.7800.0050.0050.0000.0000.0000.000
143A148PHE00.008-0.01720.7010.0060.0060.0000.0000.0000.000
144A149LEU0-0.028-0.02020.221-0.002-0.0020.0000.0000.0000.000
145A150ALA0-0.023-0.00222.7610.0070.0070.0000.0000.0000.000
146A151GLN0-0.069-0.03125.0150.0010.0010.0000.0000.0000.000
147A152THR0-0.006-0.00920.5060.0120.0120.0000.0000.0000.000
148A153PRO00.0140.01717.974-0.019-0.0190.0000.0000.0000.000
149A154ILE00.0480.03015.923-0.015-0.0150.0000.0000.0000.000
150A155PRO00.015-0.00412.6240.0250.0250.0000.0000.0000.000
151A156ILE00.0300.00915.4990.0240.0240.0000.0000.0000.000
152A157SER00.0620.03918.5780.0160.0160.0000.0000.0000.000
153A158VAL00.0120.01217.2280.0180.0180.0000.0000.0000.000
154A159MET0-0.046-0.01216.7370.0110.0110.0000.0000.0000.000
155A160LEU00.017-0.00820.0300.0150.0150.0000.0000.0000.000
156A161LEU00.0030.00622.9780.0140.0140.0000.0000.0000.000
157A162SER0-0.055-0.03321.7630.0150.0150.0000.0000.0000.000
158A163PHE00.0210.00823.8150.0070.0070.0000.0000.0000.000
159A164GLY00.0450.02925.3930.0070.0070.0000.0000.0000.000
160A165MET0-0.017-0.01726.2870.0100.0100.0000.0000.0000.000
161A166VAL00.0120.02726.2810.0070.0070.0000.0000.0000.000
162A167MET00.0020.01028.3230.0030.0030.0000.0000.0000.000
163A168ILE0-0.039-0.00831.0130.0050.0050.0000.0000.0000.000
164A169SER0-0.061-0.05031.9010.0040.0040.0000.0000.0000.000
165A170LEU0-0.023-0.00930.2230.0040.0040.0000.0000.0000.000
166A171TYR00.001-0.01331.5770.0010.0010.0000.0000.0000.000
167A172GLN0-0.0090.00636.2650.0040.0040.0000.0000.0000.000
168A173PRO00.0730.03337.6450.0010.0010.0000.0000.0000.000
169A174THR0-0.049-0.02238.6140.0020.0020.0000.0000.0000.000
170A175ASN0-0.033-0.02238.4170.0050.0050.0000.0000.0000.000
171A176PHE00.0530.02832.309-0.001-0.0010.0000.0000.0000.000
172A177LYS10.9910.99336.4190.0270.0270.0000.0000.0000.000
173A178ALA00.0110.01638.2990.0010.0010.0000.0000.0000.000
174A179LEU00.0400.03131.086-0.001-0.0010.0000.0000.0000.000
175A180MET00.012-0.00330.831-0.003-0.0030.0000.0000.0000.000
176A181THR0-0.064-0.03134.5970.0040.0040.0000.0000.0000.000
177A182GLU-1-0.759-0.85334.121-0.048-0.0480.0000.0000.0000.000
178A183ILE0-0.007-0.00329.109-0.001-0.0010.0000.0000.0000.000
179A184SER0-0.050-0.03931.0610.0020.0020.0000.0000.0000.000
180A185ARG10.7300.83733.1940.0490.0490.0000.0000.0000.000
181A186GLY00.0530.01531.3200.0020.0020.0000.0000.0000.000
182A187TYR00.0120.01124.791-0.001-0.0010.0000.0000.0000.000
183A188ARG10.9450.98329.8210.0270.0270.0000.0000.0000.000
184A189VAL0-0.008-0.01132.8990.0030.0030.0000.0000.0000.000
185A190GLY00.0280.03829.3650.0010.0010.0000.0000.0000.000
186A191SER0-0.049-0.05428.8760.0020.0020.0000.0000.0000.000
187A192HIS0-0.060-0.01829.8700.0050.0050.0000.0000.0000.000
188A193THR0-0.0010.01430.9580.0000.0000.0000.0000.0000.000
189A194PRO0-0.042-0.01130.019-0.003-0.0030.0000.0000.0000.000
190A195GLY00.0330.01629.301-0.001-0.0010.0000.0000.0000.000
191A196LYS10.8720.93924.8190.0300.0300.0000.0000.0000.000
192A197LEU00.0330.01126.8660.0000.0000.0000.0000.0000.000
193A198ILE0-0.001-0.01321.2280.0010.0010.0000.0000.0000.000
194A199ALA00.0010.00024.736-0.004-0.0040.0000.0000.0000.000
195A200GLN0-0.038-0.01526.1880.0090.0090.0000.0000.0000.000
196A201LYS10.8430.92128.5220.0400.0400.0000.0000.0000.000
197A202TRP00.017-0.02328.2930.0070.0070.0000.0000.0000.000
198A203ASP-1-0.810-0.90232.399-0.062-0.0620.0000.0000.0000.000
199A204GLN0-0.029-0.01733.6140.0020.0020.0000.0000.0000.000
200A205LEU0-0.012-0.01533.8650.0040.0040.0000.0000.0000.000
201A206TRP00.0330.01234.6130.0010.0010.0000.0000.0000.000
202A207ASP-1-0.883-0.93739.126-0.036-0.0360.0000.0000.0000.000
203A208VAL0-0.0140.00339.6900.0030.0030.0000.0000.0000.000
204A209GLN0-0.002-0.00541.286-0.003-0.0030.0000.0000.0000.000
205A210VAL00.0670.02538.7400.0000.0000.0000.0000.0000.000
206A211SER0-0.019-0.01639.859-0.001-0.0010.0000.0000.0000.000
207A212GLU-1-0.770-0.85741.223-0.022-0.0220.0000.0000.0000.000
208A213ILE00.0010.00335.6120.0010.0010.0000.0000.0000.000
209A214ARG10.8170.88436.8610.0410.0410.0000.0000.0000.000
210A215GLU-1-0.950-0.96437.612-0.019-0.0190.0000.0000.0000.000
211A216ARG10.8100.88536.7430.0290.0290.0000.0000.0000.000
212A217LEU0-0.057-0.02331.5700.0010.0010.0000.0000.0000.000
213A218GLY00.0400.02233.8800.0010.0010.0000.0000.0000.000
214A219VAL0-0.018-0.02734.5760.0010.0010.0000.0000.0000.000
215A220ASN0-0.0250.01036.1110.0000.0000.0000.0000.0000.000
216A221SER0-0.035-0.02035.8860.0040.0040.0000.0000.0000.000