Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 5J1LZ

Calculation Name: 1T33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T33

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZQN9

Base Structure: X-ray

Registration Date: 2023-09-24

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2506013.590476
FMO2-HF: Nuclear repulsion 2419547.619896
FMO2-HF: Total energy -86465.97058
FMO2-MP2: Total energy -86718.090908


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.
-3.85-5.58324.672-7.098-15.841-0.007
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 : 0.077 / q_NPA : 0.031
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].
3A3ILE00.0230.0183.706-2.578-0.657-0.012-1.029-0.8810.001
4A4PRO0-0.017-0.0145.599-0.508-0.5080.0000.0000.0000.000
5A5THR0-0.0090.0066.6160.1620.1620.0000.0000.0000.000
6A6THR00.0180.0108.4090.0360.0360.0000.0000.0000.000
7A7THR0-0.006-0.00111.8620.0510.0510.0000.0000.0000.000
8A8THR00.0940.03211.690-0.049-0.0490.0000.0000.0000.000
9A9LYS10.9510.96512.1820.1660.1660.0000.0000.0000.000
10A10GLY00.0350.02210.7970.0140.0140.0000.0000.0000.000
11A11GLU-1-0.909-0.9657.349-0.364-0.3640.0000.0000.0000.000
12A12GLN00.0480.0337.5840.0360.0360.0000.0000.0000.000
13A13ALA0-0.019-0.0119.2950.0310.0310.0000.0000.0000.000
14A14LYS10.8790.9572.9352.2633.1770.145-0.255-0.8040.002
15A15SER00.0370.0115.3200.0380.0380.0000.0000.0000.000
16A16GLN0-0.013-0.0096.2720.0610.0610.0000.0000.0000.000
17A17LEU0-0.019-0.0177.3430.0360.0360.0000.0000.0000.000
18A18ILE00.0240.0202.0924.817-3.75012.277-0.837-2.874-0.002
19A19ALA00.0040.0175.9050.0740.0740.0000.0000.0000.000
20A20ALA00.002-0.0029.1310.0150.0150.0000.0000.0000.000
21A21ALA00.0130.0007.3390.0230.0230.0000.0000.0000.000
22A22LEU00.0180.0087.3810.0230.0230.0000.0000.0000.000
23A23ALA0-0.049-0.0089.8470.0170.0170.0000.0000.0000.000
24A24GLN0-0.007-0.01912.8460.0080.0080.0000.0000.0000.000
25A25PHE0-0.009-0.0088.4400.0110.0110.0000.0000.0000.000
26A26GLY00.0010.00212.8890.0150.0150.0000.0000.0000.000
27A27GLU-1-0.895-0.94314.3880.0180.0180.0000.0000.0000.000
28A28TYR0-0.015-0.01516.5800.0010.0010.0000.0000.0000.000
29A29GLY0-0.0060.00515.2370.0040.0040.0000.0000.0000.000
30A30LEU00.031-0.00712.144-0.016-0.0160.0000.0000.0000.000
31A31HIS0-0.020-0.00715.728-0.003-0.0030.0000.0000.0000.000
32A32ALA00.0040.02914.480-0.004-0.0040.0000.0000.0000.000
33A33THR0-0.009-0.01015.909-0.006-0.0060.0000.0000.0000.000
34A34THR00.0870.02212.684-0.003-0.0030.0000.0000.0000.000
35A35ARG10.9430.97014.6560.0310.0310.0000.0000.0000.000
36A36ASP-1-0.867-0.93716.969-0.049-0.0490.0000.0000.0000.000
37A37ILE00.0080.00410.282-0.003-0.0030.0000.0000.0000.000
38A38ALA0-0.024-0.01413.195-0.011-0.0110.0000.0000.0000.000
39A39ALA0-0.026-0.01914.2380.0000.0000.0000.0000.0000.000
40A40LEU0-0.041-0.01114.1600.0020.0020.0000.0000.0000.000
41A41ALA0-0.0140.00111.4880.0040.0040.0000.0000.0000.000
42A42GLY0-0.0130.00813.483-0.009-0.0090.0000.0000.0000.000
43A43GLN0-0.046-0.02011.370-0.020-0.0200.0000.0000.0000.000
44A44ASN00.0270.00714.7560.0140.0140.0000.0000.0000.000
45A45ILE00.0440.00614.564-0.022-0.0220.0000.0000.0000.000
46A46ALA0-0.017-0.01114.699-0.008-0.0080.0000.0000.0000.000
47A47ALA0-0.014-0.00611.727-0.011-0.0110.0000.0000.0000.000
48A48ILE00.0150.0079.617-0.063-0.0630.0000.0000.0000.000
49A49THR0-0.004-0.0019.872-0.031-0.0310.0000.0000.0000.000
50A50TYR0-0.047-0.01611.1160.0350.0350.0000.0000.0000.000
51A51TYR0-0.015-0.0126.4560.0300.0300.0000.0000.0000.000
52A52PHE0-0.023-0.0272.693-1.015-0.3890.260-0.138-0.7490.001
53A53GLY00.0480.0507.3180.1840.1840.0000.0000.0000.000
54A54SER0-0.038-0.0359.2910.0060.0060.0000.0000.0000.000
55A55LYS10.8960.9539.444-0.045-0.0450.0000.0000.0000.000
56A56GLU-1-0.868-0.9519.864-0.014-0.0140.0000.0000.0000.000
57A57ASP-1-0.856-0.9105.7180.3780.3780.0000.0000.0000.000
58A58LEU0-0.070-0.0314.878-0.427-0.330-0.001-0.003-0.0930.000
59A59TYR0-0.041-0.0515.636-0.111-0.1110.0000.0000.0000.000
60A60LEU00.0440.0154.420-0.0810.051-0.001-0.010-0.1200.000
61A61ALA0-0.034-0.0102.077-1.233-1.0393.538-1.204-2.5280.008
62A62CYS0-0.051-0.0143.072-0.3431.3010.424-0.593-1.476-0.010
63A63ALA00.0340.0245.0400.2180.295-0.001-0.006-0.0700.000
64A64GLN0-0.070-0.0481.852-0.871-2.0337.565-2.335-4.068-0.003
65A65TRP00.0310.0043.389-2.077-0.2180.442-0.627-1.673-0.003
66A66ILE0-0.031-0.0154.235-0.596-0.6260.0330.114-0.1160.000
67A67ALA0-0.0110.0037.087-0.117-0.1170.0000.0000.0000.000
68A68ASP-1-0.852-0.9354.045-1.863-1.3610.004-0.173-0.332-0.001
69A69PHE0-0.026-0.0157.555-0.111-0.1110.0000.0000.0000.000
70A70LEU0-0.009-0.0259.428-0.083-0.0830.0000.0000.0000.000
71A71GLY00.0400.01911.030-0.028-0.0280.0000.0000.0000.000
72A72GLU-1-0.955-0.98810.988-0.093-0.0930.0000.0000.0000.000
73A73LYS10.9100.96012.845-0.063-0.0630.0000.0000.0000.000
74A74PHE0-0.024-0.01015.484-0.007-0.0070.0000.0000.0000.000
75A75ARG10.9431.01114.5120.0690.0690.0000.0000.0000.000
76A76PRO0-0.014-0.02616.8400.0010.0010.0000.0000.0000.000
77A77HIS0-0.022-0.01520.2300.0030.0030.0000.0000.0000.000
78A78ALA00.0780.04618.8640.0020.0020.0000.0000.0000.000
79A79GLU-1-0.914-0.96319.195-0.049-0.0490.0000.0000.0000.000
80A80LYS10.8200.91322.0760.0120.0120.0000.0000.0000.000
81A81ALA00.0560.02324.0660.0010.0010.0000.0000.0000.000
82A82GLU-1-0.859-0.93222.3900.0100.0100.0000.0000.0000.000
83A83ARG10.8810.93524.3950.0200.0200.0000.0000.0000.000
84A84LEU0-0.062-0.01327.7760.0000.0000.0000.0000.0000.000
85A85PHE00.031-0.00126.6040.0010.0010.0000.0000.0000.000
86A86SER0-0.096-0.03029.6530.0010.0010.0000.0000.0000.000
87A87GLN00.021-0.00631.4950.0000.0000.0000.0000.0000.000
88A88PRO0-0.025-0.01635.0160.0010.0010.0000.0000.0000.000
89A89ALA0-0.004-0.00937.7120.0010.0010.0000.0000.0000.000
90A90PRO0-0.026-0.00433.602-0.001-0.0010.0000.0000.0000.000
91A91ASP-1-0.864-0.93035.5610.0020.0020.0000.0000.0000.000
92A92ARG10.9150.94835.533-0.009-0.0090.0000.0000.0000.000
93A93ASP-1-0.884-0.94736.4720.0050.0050.0000.0000.0000.000
94A94ALA00.0450.02532.8790.0000.0000.0000.0000.0000.000
95A95ILE0-0.048-0.02131.6160.0000.0000.0000.0000.0000.000
96A96ARG10.8600.92331.311-0.006-0.0060.0000.0000.0000.000
97A97GLU-1-0.941-0.97731.5140.0030.0030.0000.0000.0000.000
98A98LEU0-0.040-0.01225.8520.0000.0000.0000.0000.0000.000
99A99ILE00.0150.00527.0180.0020.0020.0000.0000.0000.000
100A100LEU00.0280.01527.5760.0020.0020.0000.0000.0000.000
101A101LEU0-0.021-0.00724.7140.0000.0000.0000.0000.0000.000
102A102ALA00.0050.01923.1710.0010.0010.0000.0000.0000.000
103A103CYS00.0170.00423.2660.0040.0040.0000.0000.0000.000
104A104LYS10.9910.99825.062-0.001-0.0010.0000.0000.0000.000
105A105ASN0-0.076-0.06220.573-0.001-0.0010.0000.0000.0000.000
106A106MET00.0030.01120.4020.0060.0060.0000.0000.0000.000
107A107ILE00.0230.01621.4250.0040.0040.0000.0000.0000.000
108A108MET0-0.030-0.00721.659-0.001-0.0010.0000.0000.0000.000
109A109LEU0-0.0020.00115.5970.0020.0020.0000.0000.0000.000
110A110LEU0-0.055-0.04118.9920.0050.0050.0000.0000.0000.000
111A111THR0-0.043-0.01521.116-0.004-0.0040.0000.0000.0000.000
112A112GLN0-0.0120.00917.8030.0050.0050.0000.0000.0000.000
113A113GLU-1-0.878-0.97719.4230.0220.0220.0000.0000.0000.000
114A114ASP-1-0.932-0.95415.4560.0490.0490.0000.0000.0000.000
115A115THR00.0360.01614.3930.0180.0180.0000.0000.0000.000
116A116VAL0-0.025-0.00815.5510.0070.0070.0000.0000.0000.000
117A117ASN00.034-0.00912.807-0.003-0.0030.0000.0000.0000.000
118A118LEU00.0310.03811.376-0.001-0.0010.0000.0000.0000.000
119A119SER00.0140.00112.800-0.002-0.0020.0000.0000.0000.000
120A120LYS10.8350.94215.398-0.019-0.0190.0000.0000.0000.000
121A121PHE00.014-0.0029.4920.0020.0020.0000.0000.0000.000
122A122ILE00.0120.00412.4870.0010.0010.0000.0000.0000.000
123A123SER0-0.002-0.01215.081-0.005-0.0050.0000.0000.0000.000
124A124ARG10.8930.95915.562-0.044-0.0440.0000.0000.0000.000
125A125GLU-1-0.742-0.85613.0950.1040.1040.0000.0000.0000.000
126A126GLN0-0.026-0.00116.5040.0050.0050.0000.0000.0000.000
127A127LEU0-0.043-0.02219.092-0.003-0.0030.0000.0000.0000.000
128A128SER0-0.079-0.02919.081-0.002-0.0020.0000.0000.0000.000
129A129PRO00.0030.01516.3420.0020.0020.0000.0000.0000.000
130A130THR0-0.027-0.03512.5200.0070.0070.0000.0000.0000.000
131A131SER00.021-0.0019.299-0.009-0.0090.0000.0000.0000.000
132A132ALA0-0.035-0.0218.7880.0170.0170.0000.0000.0000.000
133A133TYR00.007-0.0129.8560.0060.0060.0000.0000.0000.000
134A134GLN0-0.045-0.01111.987-0.013-0.0130.0000.0000.0000.000
135A135LEU00.0130.0194.534-0.0440.016-0.001-0.002-0.0570.000
136A136VAL0-0.003-0.0129.184-0.031-0.0310.0000.0000.0000.000
137A137HIS00.003-0.00710.576-0.021-0.0210.0000.0000.0000.000
138A138GLU-1-0.864-0.94611.7320.2100.2100.0000.0000.0000.000
139A139GLN0-0.0160.0126.957-0.026-0.0260.0000.0000.0000.000
140A140VAL0-0.026-0.01311.179-0.022-0.0220.0000.0000.0000.000
141A141ILE0-0.0340.01713.908-0.008-0.0080.0000.0000.0000.000
142A142ASP-1-0.890-0.94616.0620.0660.0660.0000.0000.0000.000
143A143PRO0-0.0110.02015.380-0.009-0.0090.0000.0000.0000.000
144A144LEU00.0350.01617.968-0.006-0.0060.0000.0000.0000.000
145A145HIS00.0360.02719.806-0.004-0.0040.0000.0000.0000.000
146A146THR0-0.019-0.02621.206-0.004-0.0040.0000.0000.0000.000
147A147HIS00.003-0.00221.426-0.005-0.0050.0000.0000.0000.000
148A148LEU00.0100.00823.013-0.003-0.0030.0000.0000.0000.000
149A149THR0-0.032-0.01925.761-0.002-0.0020.0000.0000.0000.000
150A150ARG10.8680.93226.547-0.034-0.0340.0000.0000.0000.000
151A151LEU0-0.024-0.00526.740-0.002-0.0020.0000.0000.0000.000
152A152VAL00.0190.00129.913-0.002-0.0020.0000.0000.0000.000
153A153ALA0-0.050-0.01431.551-0.001-0.0010.0000.0000.0000.000
154A154ALA00.0140.00432.646-0.001-0.0010.0000.0000.0000.000
155A155TYR0-0.049-0.02034.140-0.001-0.0010.0000.0000.0000.000
156A156THR0-0.059-0.02535.957-0.001-0.0010.0000.0000.0000.000
157A157GLY00.0180.02437.266-0.001-0.0010.0000.0000.0000.000
158A158CYS0-0.050-0.03236.0930.0000.0000.0000.0000.0000.000
159A159ASP-1-0.853-0.93934.0510.0270.0270.0000.0000.0000.000
160A160ALA00.012-0.01329.7340.0010.0010.0000.0000.0000.000
161A161ASN0-0.027-0.01829.2020.0050.0050.0000.0000.0000.000
162A162ASP-1-0.804-0.87231.0440.0300.0300.0000.0000.0000.000
163A163THR00.0710.01931.1050.0010.0010.0000.0000.0000.000
164A164ARG10.8620.90831.731-0.025-0.0250.0000.0000.0000.000
165A165MET00.0250.03631.973-0.001-0.0010.0000.0000.0000.000
166A166ILE00.0200.01026.5550.0000.0000.0000.0000.0000.000
167A167LEU0-0.043-0.03028.6560.0010.0010.0000.0000.0000.000
168A168HIS0-0.014-0.00830.878-0.001-0.0010.0000.0000.0000.000
169A169THR00.0180.00626.809-0.002-0.0020.0000.0000.0000.000
170A170HIS0-0.023-0.01623.503-0.001-0.0010.0000.0000.0000.000
171A171ALA0-0.015-0.00527.5420.0000.0000.0000.0000.0000.000
172A172LEU00.001-0.00228.651-0.001-0.0010.0000.0000.0000.000
173A173LEU0-0.0130.00023.493-0.001-0.0010.0000.0000.0000.000
174A174GLY00.0070.00326.0140.0020.0020.0000.0000.0000.000
175A175GLU-1-0.867-0.91627.6870.0190.0190.0000.0000.0000.000
176A176VAL0-0.019-0.00824.063-0.001-0.0010.0000.0000.0000.000
177A177LEU0-0.005-0.02321.6710.0000.0000.0000.0000.0000.000
178A178ALA00.0210.03024.6320.0010.0010.0000.0000.0000.000
179A179PHE00.0090.00026.739-0.001-0.0010.0000.0000.0000.000
180A180ARG10.8400.93618.159-0.049-0.0490.0000.0000.0000.000
181A181LEU0-0.012-0.02420.961-0.001-0.0010.0000.0000.0000.000
182A182GLY0-0.0040.00824.193-0.001-0.0010.0000.0000.0000.000
183A183LYS10.9100.96522.722-0.022-0.0220.0000.0000.0000.000
184A184GLU-1-0.867-0.93826.8620.0090.0090.0000.0000.0000.000
185A185THR0-0.041-0.01729.006-0.002-0.0020.0000.0000.0000.000
186A186ILE00.0340.01229.405-0.002-0.0020.0000.0000.0000.000
187A187LEU0-0.0090.01327.604-0.001-0.0010.0000.0000.0000.000
188A188LEU00.0040.00531.846-0.002-0.0020.0000.0000.0000.000
189A189ARG10.8660.93334.564-0.011-0.0110.0000.0000.0000.000
190A190THR0-0.046-0.03633.978-0.001-0.0010.0000.0000.0000.000
191A191GLY0-0.0130.00835.908-0.001-0.0010.0000.0000.0000.000
192A192TRP0-0.040-0.02431.604-0.001-0.0010.0000.0000.0000.000
193A193PRO00.0100.00532.1010.0010.0010.0000.0000.0000.000
194A194GLN00.010-0.00527.2000.0000.0000.0000.0000.0000.000
195A195PHE0-0.005-0.01325.181-0.001-0.0010.0000.0000.0000.000
196A196ASP-1-0.789-0.88127.5080.0030.0030.0000.0000.0000.000
197A197GLU-1-0.904-0.96627.2250.0030.0030.0000.0000.0000.000
198A198GLU-1-0.864-0.92929.1040.0000.0000.0000.0000.0000.000
199A199LYS10.7710.87830.547-0.003-0.0030.0000.0000.0000.000
200A200ALA0-0.007-0.00127.3380.0020.0020.0000.0000.0000.000
201A201GLU-1-0.942-0.97129.1650.0020.0020.0000.0000.0000.000
202A202LEU0-0.013-0.00732.0310.0000.0000.0000.0000.0000.000
203A203ILE0-0.0160.00428.3820.0010.0010.0000.0000.0000.000
204A204TYR00.0160.00428.9960.0010.0010.0000.0000.0000.000
205A205GLN0-0.0140.00530.9980.0000.0000.0000.0000.0000.000
206A206THR0-0.045-0.02833.6180.0000.0000.0000.0000.0000.000
207A207VAL00.0380.01029.2960.0000.0000.0000.0000.0000.000
208A208THR0-0.031-0.01932.4150.0000.0000.0000.0000.0000.000
209A209CYS0-0.058-0.01733.8210.0000.0000.0000.0000.0000.000
210A210HIS0-0.046-0.05734.617-0.001-0.0010.0000.0000.0000.000
211A211ILE00.0270.00829.9900.0010.0010.0000.0000.0000.000
212A212ASP-1-0.797-0.88134.4990.0090.0090.0000.0000.0000.000
213A213LEU0-0.060-0.03037.4660.0000.0000.0000.0000.0000.000
214A214ILE0-0.007-0.00335.1580.0000.0000.0000.0000.0000.000
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