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: 53V9Z

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 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 -2615116.640805
FMO2-HF: Nuclear repulsion 2529464.577432
FMO2-HF: Total energy -85652.063373
FMO2-MP2: Total energy -85903.039387


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.
0.0440000000000011.472-0.01-0.693-0.7260.002
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 : 0.020 / q_NPA : -0.006
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].
3A8ASN0-0.007-0.0033.9281.0142.442-0.010-0.693-0.7260.002
4A9ASN00.0780.0146.567-0.207-0.2070.0000.0000.0000.000
5A10ASP-1-0.877-0.9278.988-0.187-0.1870.0000.0000.0000.000
6A11LYS10.8990.94410.3610.7980.7980.0000.0000.0000.000
7A12GLY00.0530.03811.6590.0300.0300.0000.0000.0000.000
8A13LEU0-0.004-0.00213.4040.0580.0580.0000.0000.0000.000
9A14LEU0-0.010-0.01714.1010.0280.0280.0000.0000.0000.000
10A15ALA00.0350.02516.0760.0330.0330.0000.0000.0000.000
11A16TYR00.0050.00517.7350.0350.0350.0000.0000.0000.000
12A17ILE00.006-0.00218.7840.0270.0270.0000.0000.0000.000
13A18GLN00.0100.01520.487-0.005-0.0050.0000.0000.0000.000
14A19PHE00.0060.00521.7900.0220.0220.0000.0000.0000.000
15A20LEU0-0.027-0.00622.9640.0190.0190.0000.0000.0000.000
16A21ALA00.0190.01225.2810.0120.0120.0000.0000.0000.000
17A22SER0-0.042-0.02525.9780.0100.0100.0000.0000.0000.000
18A23SER0-0.074-0.07226.9460.0090.0090.0000.0000.0000.000
19A24ALA00.0110.02029.6270.0080.0080.0000.0000.0000.000
20A25GLN0-0.0060.01430.7760.0120.0120.0000.0000.0000.000
21A26LYS10.8720.92434.0890.0920.0920.0000.0000.0000.000
22A27ILE0-0.018-0.00731.659-0.007-0.0070.0000.0000.0000.000
23A28GLY0-0.006-0.00833.7380.0080.0080.0000.0000.0000.000
24A29ASP-1-0.897-0.93434.564-0.101-0.1010.0000.0000.0000.000
25A30GLY00.0330.03531.6760.0020.0020.0000.0000.0000.000
26A31ASN0-0.062-0.06129.797-0.006-0.0060.0000.0000.0000.000
27A32THR00.003-0.00528.369-0.008-0.0080.0000.0000.0000.000
28A33ASP-1-0.862-0.93826.154-0.178-0.1780.0000.0000.0000.000
29A34ARG10.9640.99224.6590.1300.1300.0000.0000.0000.000
30A35VAL0-0.015-0.01122.728-0.018-0.0180.0000.0000.0000.000
31A36PHE00.009-0.00221.295-0.021-0.0210.0000.0000.0000.000
32A37ASP-1-0.869-0.93119.973-0.301-0.3010.0000.0000.0000.000
33A38PHE0-0.028-0.02117.290-0.045-0.0450.0000.0000.0000.000
34A39GLU-1-0.850-0.97416.888-0.326-0.3260.0000.0000.0000.000
35A40ASP-1-0.825-0.89515.473-0.443-0.4430.0000.0000.0000.000
36A41ALA0-0.0400.00414.037-0.118-0.1180.0000.0000.0000.000
37A42LEU0-0.0010.00112.414-0.114-0.1140.0000.0000.0000.000
38A43ASP-1-0.779-0.84910.790-0.707-0.7070.0000.0000.0000.000
39A44GLN0-0.067-0.0457.829-0.332-0.3320.0000.0000.0000.000
40A45THR0-0.080-0.0686.413-0.632-0.6320.0000.0000.0000.000
41A46GLN00.0380.0144.9370.0170.0170.0000.0000.0000.000
42A47MET0-0.019-0.0136.3380.0800.0800.0000.0000.0000.000
43A48ALA00.0140.0188.7020.0900.0900.0000.0000.0000.000
44A49GLN00.004-0.0055.975-0.108-0.1080.0000.0000.0000.000
45A50LEU00.0230.0048.2730.1620.1620.0000.0000.0000.000
46A51ALA00.0100.01510.1720.0570.0570.0000.0000.0000.000
47A52VAL0-0.015-0.00611.3130.0480.0480.0000.0000.0000.000
48A53ASP-1-0.903-0.9559.312-0.015-0.0150.0000.0000.0000.000
49A54GLU-1-0.923-0.97812.7870.0910.0910.0000.0000.0000.000
50A55LEU0-0.032-0.01415.7300.0150.0150.0000.0000.0000.000
51A56LYS10.9020.94414.8100.0840.0840.0000.0000.0000.000
52A57LYS10.8660.95914.901-0.070-0.0700.0000.0000.0000.000
53A58ILE0-0.037-0.00319.1660.0080.0080.0000.0000.0000.000
54A59PRO00.009-0.00822.410-0.010-0.0100.0000.0000.0000.000
55A60GLU-1-0.870-0.95224.524-0.020-0.0200.0000.0000.0000.000
56A61VAL0-0.0050.00720.094-0.008-0.0080.0000.0000.0000.000
57A62ASN00.0270.00319.341-0.013-0.0130.0000.0000.0000.000
58A63ALA0-0.0090.02221.4000.0000.0000.0000.0000.0000.000
59A64LEU00.0220.01123.077-0.002-0.0020.0000.0000.0000.000
60A65PHE0-0.041-0.03115.861-0.010-0.0100.0000.0000.0000.000
61A66SER0-0.099-0.05420.397-0.002-0.0020.0000.0000.0000.000
62A67GLU-1-0.865-0.92222.361-0.049-0.0490.0000.0000.0000.000
63A68ARG10.8660.95416.3940.1640.1640.0000.0000.0000.000
64A69TRP00.0070.02422.795-0.007-0.0070.0000.0000.0000.000
65A70LEU00.000-0.01523.240-0.016-0.0160.0000.0000.0000.000
66A71PRO0-0.049-0.00726.8800.0080.0080.0000.0000.0000.000
67A72ALA00.002-0.00430.335-0.004-0.0040.0000.0000.0000.000
68A73PRO0-0.046-0.02333.397-0.002-0.0020.0000.0000.0000.000
69A74PHE00.0170.00233.1880.0060.0060.0000.0000.0000.000
70A75ASN00.002-0.00337.889-0.006-0.0060.0000.0000.0000.000
71A76LEU00.0470.00138.2470.0030.0030.0000.0000.0000.000
72A77ASP-1-0.914-0.96341.326-0.050-0.0500.0000.0000.0000.000
73A78ASP-1-0.896-0.95243.472-0.044-0.0440.0000.0000.0000.000
74A79LEU0-0.033-0.00138.1620.0020.0020.0000.0000.0000.000
75A80ALA00.004-0.01342.8500.0020.0020.0000.0000.0000.000
76A81LYS10.8770.94645.4540.0430.0430.0000.0000.0000.000
77A82LEU0-0.0130.02942.5490.0020.0020.0000.0000.0000.000
78A83PRO0-0.001-0.01546.5870.0000.0000.0000.0000.0000.000
79A84GLU-1-0.788-0.87146.891-0.036-0.0360.0000.0000.0000.000
80A85GLY0-0.003-0.00445.818-0.001-0.0010.0000.0000.0000.000
81A86THR0-0.053-0.02143.031-0.001-0.0010.0000.0000.0000.000
82A87LEU00.0250.00535.301-0.001-0.0010.0000.0000.0000.000
83A88GLY00.002-0.01339.509-0.003-0.0030.0000.0000.0000.000
84A89HIS0-0.0180.00640.745-0.003-0.0030.0000.0000.0000.000
85A90VAL0-0.008-0.01340.544-0.001-0.0010.0000.0000.0000.000
86A91TYR0-0.033-0.01033.520-0.001-0.0010.0000.0000.0000.000
87A92ALA00.0290.00539.131-0.003-0.0030.0000.0000.0000.000
88A93ARG10.7970.88141.4180.0390.0390.0000.0000.0000.000
89A94GLU-1-0.867-0.92738.152-0.062-0.0620.0000.0000.0000.000
90A95MET0-0.043-0.00434.983-0.003-0.0030.0000.0000.0000.000
91A96LYS10.8670.94639.8220.0510.0510.0000.0000.0000.000
92A97ALA0-0.0170.00543.1580.0010.0010.0000.0000.0000.000
93A98ARG10.8750.94533.4100.0870.0870.0000.0000.0000.000
94A99GLY0-0.015-0.02538.4360.0010.0010.0000.0000.0000.000
95A100PHE0-0.067-0.04432.491-0.003-0.0030.0000.0000.0000.000
96A101ASP-1-0.800-0.88234.569-0.107-0.1070.0000.0000.0000.000
97A102PRO00.0060.01530.3800.0020.0020.0000.0000.0000.000
98A103TYR0-0.103-0.06231.287-0.005-0.0050.0000.0000.0000.000
99A104PHE0-0.007-0.01631.5160.0000.0000.0000.0000.0000.000
100A105TYR0-0.036-0.01825.427-0.006-0.0060.0000.0000.0000.000
101A106LYS10.9530.99322.0790.2760.2760.0000.0000.0000.000
102A107LYS10.9550.97623.9780.1330.1330.0000.0000.0000.000
103A108VAL00.018-0.00117.965-0.010-0.0100.0000.0000.0000.000
104A109PRO0-0.016-0.00619.0890.0190.0190.0000.0000.0000.000
105A110VAL0-0.010-0.01318.498-0.033-0.0330.0000.0000.0000.000
106A111VAL0-0.002-0.00613.8900.0350.0350.0000.0000.0000.000
107A112ASP-1-0.871-0.91410.918-0.621-0.6210.0000.0000.0000.000
108A113ASP-1-0.817-0.92712.816-0.154-0.1540.0000.0000.0000.000
109A114ILE00.0360.0268.6390.0550.0550.0000.0000.0000.000
110A115SER0-0.013-0.03213.0790.0770.0770.0000.0000.0000.000
111A116TYR0-0.054-0.03415.9150.0430.0430.0000.0000.0000.000
112A117LEU00.0240.01215.1110.0290.0290.0000.0000.0000.000
113A118LYS10.7860.88015.6040.5190.5190.0000.0000.0000.000
114A119MET00.0070.01818.4800.0310.0310.0000.0000.0000.000
115A120LEU00.0330.04921.0810.0180.0180.0000.0000.0000.000
116A121TRP00.0060.02120.7110.0290.0290.0000.0000.0000.000
117A122ARG10.7870.89319.8390.3050.3050.0000.0000.0000.000
118A123SER0-0.080-0.06724.4840.0130.0130.0000.0000.0000.000
119A124THR0-0.019-0.03325.5770.0150.0150.0000.0000.0000.000
120A125HIS10.9340.97825.1590.1490.1490.0000.0000.0000.000
121A126ASP-1-0.840-0.93127.327-0.090-0.0900.0000.0000.0000.000
122A127ILE00.0130.01330.6700.0070.0070.0000.0000.0000.000
123A128TYR00.0110.00324.8930.0040.0040.0000.0000.0000.000
124A129HIS10.8650.92630.8720.0830.0830.0000.0000.0000.000
125A130VAL00.0390.02933.1750.0050.0050.0000.0000.0000.000
126A131VAL0-0.0130.00033.5860.0050.0050.0000.0000.0000.000
127A132ALA0-0.005-0.00831.9210.0050.0050.0000.0000.0000.000
128A133GLY0-0.054-0.00634.0460.0040.0040.0000.0000.0000.000
129A134PHE0-0.042-0.01332.7080.0020.0020.0000.0000.0000.000
130A135ASP-1-0.850-0.92635.717-0.053-0.0530.0000.0000.0000.000
131A136THR00.004-0.01134.952-0.004-0.0040.0000.0000.0000.000
132A137ASN0-0.039-0.00734.890-0.006-0.0060.0000.0000.0000.000
133A138VAL00.0670.01232.195-0.002-0.0020.0000.0000.0000.000
134A139PHE00.008-0.00932.282-0.003-0.0030.0000.0000.0000.000
135A140GLY00.0410.04133.1890.0010.0010.0000.0000.0000.000
136A141GLU-1-0.892-0.95628.741-0.107-0.1070.0000.0000.0000.000
137A142ILE0-0.055-0.03327.635-0.004-0.0040.0000.0000.0000.000
138A143GLY00.0220.01228.7500.0020.0020.0000.0000.0000.000
139A144LEU00.0030.00228.1830.0040.0040.0000.0000.0000.000
140A145GLN00.0190.00723.635-0.007-0.0070.0000.0000.0000.000
141A146ALA0-0.0050.01024.934-0.001-0.0010.0000.0000.0000.000
142A147PHE00.0150.00526.7350.0050.0050.0000.0000.0000.000
143A148PHE0-0.012-0.02520.7140.0060.0060.0000.0000.0000.000
144A149LEU0-0.013-0.01320.140-0.001-0.0010.0000.0000.0000.000
145A150ALA0-0.033-0.00622.7140.0080.0080.0000.0000.0000.000
146A151GLN0-0.050-0.00924.9750.0010.0010.0000.0000.0000.000
147A152THR0-0.019-0.02320.5400.0120.0120.0000.0000.0000.000
148A153PRO00.0270.01917.780-0.019-0.0190.0000.0000.0000.000
149A154ILE00.0400.03215.887-0.014-0.0140.0000.0000.0000.000
150A155PRO00.0260.00112.5160.0270.0270.0000.0000.0000.000
151A156ILE00.0340.01615.4620.0260.0260.0000.0000.0000.000
152A157SER00.0660.03018.5480.0170.0170.0000.0000.0000.000
153A158VAL0-0.0030.00417.0930.0180.0180.0000.0000.0000.000
154A159MET0-0.050-0.01816.7230.0120.0120.0000.0000.0000.000
155A160LEU00.013-0.01219.9950.0140.0140.0000.0000.0000.000
156A161LEU00.0210.01422.9380.0130.0130.0000.0000.0000.000
157A162SER0-0.045-0.02121.8770.0140.0140.0000.0000.0000.000
158A163PHE00.0150.00723.7760.0070.0070.0000.0000.0000.000
159A164GLY00.0420.02525.3540.0070.0070.0000.0000.0000.000
160A165MET0-0.023-0.01826.1020.0090.0090.0000.0000.0000.000
161A166VAL00.0110.03426.1060.0070.0070.0000.0000.0000.000
162A167MET00.0040.00928.1710.0030.0030.0000.0000.0000.000
163A168ILE0-0.039-0.00730.9800.0040.0040.0000.0000.0000.000
164A169SER0-0.062-0.05731.9160.0040.0040.0000.0000.0000.000
165A170LEU0-0.021-0.01130.3590.0040.0040.0000.0000.0000.000
166A171TYR00.001-0.00931.7870.0040.0040.0000.0000.0000.000
167A172GLN0-0.0210.00236.2130.0050.0050.0000.0000.0000.000
168A173PRO00.0630.03137.6030.0010.0010.0000.0000.0000.000
169A174THR0-0.033-0.01738.5700.0020.0020.0000.0000.0000.000
170A175ASN0-0.046-0.02038.4330.0050.0050.0000.0000.0000.000
171A176PHE00.0590.02532.319-0.001-0.0010.0000.0000.0000.000
172A177LYS10.9800.98536.3710.0250.0250.0000.0000.0000.000
173A178ALA00.0130.00438.2510.0010.0010.0000.0000.0000.000
174A179LEU00.0320.03131.180-0.001-0.0010.0000.0000.0000.000
175A180MET00.009-0.00530.747-0.003-0.0030.0000.0000.0000.000
176A181THR0-0.055-0.02334.5440.0040.0040.0000.0000.0000.000
177A182GLU-1-0.792-0.90933.970-0.046-0.0460.0000.0000.0000.000
178A183ILE0-0.011-0.00728.991-0.001-0.0010.0000.0000.0000.000
179A184SER0-0.044-0.02231.0130.0020.0020.0000.0000.0000.000
180A185ARG10.7930.89833.1440.0460.0460.0000.0000.0000.000
181A186GLY00.0530.01631.2880.0020.0020.0000.0000.0000.000
182A187TYR00.0130.01024.729-0.001-0.0010.0000.0000.0000.000
183A188ARG10.9390.97429.7730.0250.0250.0000.0000.0000.000
184A189VAL0-0.006-0.01132.8500.0030.0030.0000.0000.0000.000
185A190GLY00.0240.03729.3230.0010.0010.0000.0000.0000.000
186A191SER0-0.031-0.03928.8310.0020.0020.0000.0000.0000.000
187A192HIS0-0.081-0.02529.8230.0060.0060.0000.0000.0000.000
188A193THR0-0.0010.01131.1380.0000.0000.0000.0000.0000.000
189A194PRO0-0.041-0.01129.981-0.002-0.0020.0000.0000.0000.000
190A195GLY00.0280.01329.267-0.001-0.0010.0000.0000.0000.000
191A196LYS10.8990.94924.5230.0270.0270.0000.0000.0000.000
192A197LEU00.0170.00726.725-0.001-0.0010.0000.0000.0000.000
193A198ILE0-0.010-0.01521.1360.0010.0010.0000.0000.0000.000
194A199ALA00.0120.00024.716-0.004-0.0040.0000.0000.0000.000
195A200GLN0-0.050-0.02026.1710.0090.0090.0000.0000.0000.000
196A201LYS10.8570.93528.6750.0410.0410.0000.0000.0000.000
197A202TRP00.025-0.01928.1400.0070.0070.0000.0000.0000.000
198A203ASP-1-0.808-0.89532.390-0.063-0.0630.0000.0000.0000.000
199A204GLN0-0.001-0.00633.6880.0010.0010.0000.0000.0000.000
200A205LEU0-0.023-0.02033.8300.0040.0040.0000.0000.0000.000
201A206TRP00.0390.01734.6780.0020.0020.0000.0000.0000.000
202A207ASP-1-0.891-0.94039.118-0.036-0.0360.0000.0000.0000.000
203A208VAL0-0.0140.00439.6970.0030.0030.0000.0000.0000.000
204A209GLN0-0.001-0.00141.270-0.003-0.0030.0000.0000.0000.000
205A210VAL00.0640.02338.6810.0000.0000.0000.0000.0000.000
206A211SER0-0.025-0.01939.834-0.001-0.0010.0000.0000.0000.000
207A212GLU-1-0.838-0.91241.458-0.021-0.0210.0000.0000.0000.000
208A213ILE0-0.006-0.00135.5800.0010.0010.0000.0000.0000.000
209A214ARG10.8600.91436.8290.0410.0410.0000.0000.0000.000
210A215GLU-1-0.938-0.96237.581-0.018-0.0180.0000.0000.0000.000
211A216ARG10.8790.94736.6850.0300.0300.0000.0000.0000.000
212A217LEU0-0.066-0.02731.5380.0010.0010.0000.0000.0000.000
213A218GLY00.0410.02433.8480.0020.0020.0000.0000.0000.000
214A219VAL0-0.024-0.03834.4520.0010.0010.0000.0000.0000.000
215A220ASN0-0.055-0.00736.0740.0000.0000.0000.0000.0000.000
216A221SER0-0.0020.00335.8250.0030.0030.0000.0000.0000.000