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: 4JQQN

Calculation Name: 1TWD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TWD

Chain ID: A

ChEMBL ID:

UniProt ID: P67825

Base Structure: X-ray

Registration Date: 2023-09-22

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2757220.74458
FMO2-HF: Nuclear repulsion 2666501.80258
FMO2-HF: Total energy -90718.942
FMO2-MP2: Total energy -90976.14669


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:2:ALA)


Summations of interaction energy for fragment #1(A:2: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.
-4.8162.1577.163-5.512-8.625-0.026
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.022
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].
3A4LEU00.011-0.0073.771-0.7031.562-0.005-1.192-1.0680.007
4A5GLU-1-0.777-0.8775.993-0.272-0.2720.0000.0000.0000.000
5A6ILE0-0.011-0.0198.8350.1300.1300.0000.0000.0000.000
6A7CYS0-0.058-0.02511.8880.0380.0380.0000.0000.0000.000
7A8CYS0-0.057-0.01814.7960.0120.0120.0000.0000.0000.000
8A9TYR00.0450.00417.9670.0200.0200.0000.0000.0000.000
9A10SER00.0180.00421.3710.0150.0150.0000.0000.0000.000
10A11MET00.0310.02321.666-0.026-0.0260.0000.0000.0000.000
11A12GLU-1-0.911-0.96222.359-0.189-0.1890.0000.0000.0000.000
12A13CYS0-0.058-0.01019.515-0.010-0.0100.0000.0000.0000.000
13A14ALA00.0640.02517.790-0.034-0.0340.0000.0000.0000.000
14A15LEU0-0.027-0.01017.779-0.045-0.0450.0000.0000.0000.000
15A16THR00.001-0.00618.465-0.017-0.0170.0000.0000.0000.000
16A17ALA00.0340.01614.081-0.024-0.0240.0000.0000.0000.000
17A18GLN00.0710.04814.333-0.076-0.0760.0000.0000.0000.000
18A19GLN0-0.074-0.04715.162-0.038-0.0380.0000.0000.0000.000
19A20ASN0-0.072-0.04314.8150.0430.0430.0000.0000.0000.000
20A21GLY00.0580.03411.278-0.027-0.0270.0000.0000.0000.000
21A22ALA0-0.0200.0049.809-0.266-0.2660.0000.0000.0000.000
22A23ASP-1-0.807-0.8936.672-2.736-2.7360.0000.0000.0000.000
23A24ARG10.7010.8128.2180.9450.9450.0000.0000.0000.000
24A25VAL0-0.017-0.01111.471-0.012-0.0120.0000.0000.0000.000
25A26GLU-1-0.798-0.87913.635-0.215-0.2150.0000.0000.0000.000
26A27LEU0-0.054-0.03915.1390.0140.0140.0000.0000.0000.000
27A28CYS00.0000.00618.1710.0230.0230.0000.0000.0000.000
28A29ALA00.0250.01221.091-0.003-0.0030.0000.0000.0000.000
29A30ALA00.017-0.00123.9790.0020.0020.0000.0000.0000.000
30A31PRO00.0810.03322.5620.0060.0060.0000.0000.0000.000
31A32LYS10.8650.93123.8190.0790.0790.0000.0000.0000.000
32A33GLU-1-0.853-0.92025.950-0.057-0.0570.0000.0000.0000.000
33A34GLY0-0.0260.00022.0070.0060.0060.0000.0000.0000.000
34A35GLY0-0.0100.00620.841-0.009-0.0090.0000.0000.0000.000
35A36LEU0-0.049-0.00822.1220.0090.0090.0000.0000.0000.000
36A37THR00.0570.01823.943-0.016-0.0160.0000.0000.0000.000
37A38PRO0-0.048-0.00523.0490.0080.0080.0000.0000.0000.000
38A39SER00.0430.01825.9660.0020.0020.0000.0000.0000.000
39A40LEU00.1040.04128.307-0.010-0.0100.0000.0000.0000.000
40A41GLY0-0.016-0.00429.605-0.007-0.0070.0000.0000.0000.000
41A42VAL0-0.007-0.00724.821-0.007-0.0070.0000.0000.0000.000
42A43LEU00.0300.02123.924-0.017-0.0170.0000.0000.0000.000
43A44LYS10.9940.98125.7030.1090.1090.0000.0000.0000.000
44A45SER0-0.029-0.00927.181-0.009-0.0090.0000.0000.0000.000
45A46VAL00.0280.00020.976-0.008-0.0080.0000.0000.0000.000
46A47ARG10.8710.94422.6960.2070.2070.0000.0000.0000.000
47A48GLN0-0.057-0.02824.6990.0050.0050.0000.0000.0000.000
48A49ARG10.8930.94924.7590.2040.2040.0000.0000.0000.000
49A50VAL0-0.039-0.01718.419-0.010-0.0100.0000.0000.0000.000
50A51THR0-0.057-0.03318.8630.0130.0130.0000.0000.0000.000
51A52ILE0-0.0010.01913.4310.0100.0100.0000.0000.0000.000
52A53PRO00.016-0.00612.7310.0690.0690.0000.0000.0000.000
53A54VAL00.0240.00814.693-0.039-0.0390.0000.0000.0000.000
54A55HIS0-0.039-0.01213.7850.0090.0090.0000.0000.0000.000
55A56PRO0-0.003-0.00116.932-0.003-0.0030.0000.0000.0000.000
56A57ILE00.0050.01818.7790.0080.0080.0000.0000.0000.000
57A58ILE0-0.033-0.02120.2710.0060.0060.0000.0000.0000.000
58A59ARG10.8570.92222.5870.0890.0890.0000.0000.0000.000
59A60PRO00.0220.01425.011-0.005-0.0050.0000.0000.0000.000
60A61ARG10.7840.88027.9380.0420.0420.0000.0000.0000.000
61A62GLY00.0470.02126.447-0.003-0.0030.0000.0000.0000.000
62A63GLY0-0.048-0.02327.0450.0040.0040.0000.0000.0000.000
63A64ASP-1-0.813-0.89226.343-0.031-0.0310.0000.0000.0000.000
64A65PHE00.025-0.00321.863-0.007-0.0070.0000.0000.0000.000
65A66CYS0-0.048-0.01426.8550.0010.0010.0000.0000.0000.000
66A67TYR0-0.005-0.00724.756-0.001-0.0010.0000.0000.0000.000
67A68SER00.027-0.02131.4140.0030.0030.0000.0000.0000.000
68A69ASP-1-0.853-0.95234.055-0.031-0.0310.0000.0000.0000.000
69A70GLY0-0.039-0.01435.859-0.003-0.0030.0000.0000.0000.000
70A71GLU-1-0.790-0.87231.645-0.048-0.0480.0000.0000.0000.000
71A72PHE00.0040.00028.712-0.005-0.0050.0000.0000.0000.000
72A73ALA00.0050.00531.636-0.004-0.0040.0000.0000.0000.000
73A74ALA0-0.015-0.00532.274-0.003-0.0030.0000.0000.0000.000
74A75ILE00.0450.02626.537-0.006-0.0060.0000.0000.0000.000
75A76LEU0-0.003-0.00528.208-0.008-0.0080.0000.0000.0000.000
76A77GLU-1-0.818-0.87129.927-0.078-0.0780.0000.0000.0000.000
77A78ASP-1-0.882-0.94226.926-0.107-0.1070.0000.0000.0000.000
78A79VAL0-0.057-0.02624.509-0.013-0.0130.0000.0000.0000.000
79A80ARG10.8400.88726.4240.0630.0630.0000.0000.0000.000
80A81THR0-0.021-0.00928.702-0.004-0.0040.0000.0000.0000.000
81A82VAL0-0.043-0.02922.206-0.010-0.0100.0000.0000.0000.000
82A83ARG10.9100.96224.7650.0850.0850.0000.0000.0000.000
83A84GLU-1-0.930-0.96925.767-0.112-0.1120.0000.0000.0000.000
84A85LEU0-0.098-0.04426.312-0.002-0.0020.0000.0000.0000.000
85A86GLY00.0070.01324.730-0.011-0.0110.0000.0000.0000.000
86A87PHE0-0.079-0.03620.205-0.019-0.0190.0000.0000.0000.000
87A88PRO00.0010.00116.6980.0120.0120.0000.0000.0000.000
88A89GLY00.0710.02116.9800.0040.0040.0000.0000.0000.000
89A90LEU0-0.041-0.01417.7700.0010.0010.0000.0000.0000.000
90A91VAL0-0.0080.00415.1570.0020.0020.0000.0000.0000.000
91A92THR0-0.014-0.02717.9410.0140.0140.0000.0000.0000.000
92A93GLY00.0310.01119.5790.0030.0030.0000.0000.0000.000
93A94VAL0-0.032-0.01822.013-0.002-0.0020.0000.0000.0000.000
94A95LEU0-0.022-0.00422.8670.0040.0040.0000.0000.0000.000
95A96ASP-1-0.786-0.87926.7180.0040.0040.0000.0000.0000.000
96A97VAL0-0.016-0.03829.5780.0000.0000.0000.0000.0000.000
97A98ASP-1-0.958-0.96731.2740.0150.0150.0000.0000.0000.000
98A99GLY0-0.0230.00827.0330.0060.0060.0000.0000.0000.000
99A100ASN0-0.048-0.03525.8990.0140.0140.0000.0000.0000.000
100A101VAL00.0330.00722.205-0.007-0.0070.0000.0000.0000.000
101A102ASP-1-0.808-0.88525.263-0.018-0.0180.0000.0000.0000.000
102A103MET00.0340.01325.371-0.007-0.0070.0000.0000.0000.000
103A104PRO00.004-0.00128.125-0.005-0.0050.0000.0000.0000.000
104A105ARG10.7670.86729.6770.0240.0240.0000.0000.0000.000
105A106MET00.0140.01121.994-0.009-0.0090.0000.0000.0000.000
106A107GLU-1-0.858-0.92525.926-0.040-0.0400.0000.0000.0000.000
107A108LYS10.9000.94827.9880.0260.0260.0000.0000.0000.000
108A109ILE0-0.009-0.00623.823-0.006-0.0060.0000.0000.0000.000
109A110MET00.0160.01620.683-0.015-0.0150.0000.0000.0000.000
110A111ALA00.0040.01025.080-0.007-0.0070.0000.0000.0000.000
111A112ALA0-0.064-0.03628.018-0.004-0.0040.0000.0000.0000.000
112A113ALA00.0280.00322.803-0.008-0.0080.0000.0000.0000.000
113A114GLY0-0.023-0.01024.258-0.012-0.0120.0000.0000.0000.000
114A115PRO0-0.031-0.02122.3500.0030.0030.0000.0000.0000.000
115A116LEU0-0.069-0.00620.032-0.018-0.0180.0000.0000.0000.000
116A117ALA00.0090.00414.9690.0170.0170.0000.0000.0000.000
117A118VAL00.003-0.00116.841-0.025-0.0250.0000.0000.0000.000
118A119THR0-0.004-0.01013.0350.0060.0060.0000.0000.0000.000
119A120PHE00.0500.01915.3570.0040.0040.0000.0000.0000.000
120A121HIS00.0750.02215.2700.0070.0070.0000.0000.0000.000
121A122ARG10.9150.93215.2090.0300.0300.0000.0000.0000.000
122A123ALA00.0170.02917.3510.0150.0150.0000.0000.0000.000
123A124PHE00.0480.00316.2380.0110.0110.0000.0000.0000.000
124A125ASP-1-0.794-0.87816.3420.0610.0610.0000.0000.0000.000
125A126MET0-0.066-0.02119.1380.0050.0050.0000.0000.0000.000
126A127CYS0-0.051-0.00621.569-0.004-0.0040.0000.0000.0000.000
127A128ALA00.0380.03523.2290.0100.0100.0000.0000.0000.000
128A129ASN0-0.0020.00423.8010.0170.0170.0000.0000.0000.000
129A130PRO00.0460.02918.522-0.004-0.0040.0000.0000.0000.000
130A131LEU00.0670.02618.648-0.001-0.0010.0000.0000.0000.000
131A132TYR0-0.029-0.02720.708-0.002-0.0020.0000.0000.0000.000
132A133THR0-0.007-0.01319.642-0.013-0.0130.0000.0000.0000.000
133A134LEU00.0070.00415.002-0.014-0.0140.0000.0000.0000.000
134A135ASN00.0260.02518.7530.0010.0010.0000.0000.0000.000
135A136ASN00.0030.00021.639-0.008-0.0080.0000.0000.0000.000
136A137LEU0-0.022-0.01517.014-0.012-0.0120.0000.0000.0000.000
137A138ALA00.0170.00719.007-0.015-0.0150.0000.0000.0000.000
138A139GLU-1-0.990-0.98619.9880.0110.0110.0000.0000.0000.000
139A140LEU0-0.056-0.02522.033-0.008-0.0080.0000.0000.0000.000
140A141GLY00.0290.02720.482-0.011-0.0110.0000.0000.0000.000
141A142ILE0-0.098-0.05115.962-0.022-0.0220.0000.0000.0000.000
142A143ALA00.0030.00813.8770.0130.0130.0000.0000.0000.000
143A144ARG10.8150.8678.9110.4630.4630.0000.0000.0000.000
144A145VAL00.0100.00111.585-0.011-0.0110.0000.0000.0000.000
145A146LEU0-0.0400.00710.6610.0200.0200.0000.0000.0000.000
146A147THR0-0.028-0.03411.2720.0290.0290.0000.0000.0000.000
147A148SER0-0.003-0.03511.6370.0160.0160.0000.0000.0000.000
148A149GLY00.011-0.00513.9500.0200.0200.0000.0000.0000.000
149A150GLN0-0.097-0.05815.1980.0090.0090.0000.0000.0000.000
150A151LYS10.9150.98417.413-0.119-0.1190.0000.0000.0000.000
151A152SER0-0.0030.01118.200-0.010-0.0100.0000.0000.0000.000
152A153ASP-1-0.867-0.93515.8640.0760.0760.0000.0000.0000.000
153A154ALA00.0470.00410.9470.0210.0210.0000.0000.0000.000
154A155LEU0-0.022-0.00112.5080.0450.0450.0000.0000.0000.000
155A156GLN0-0.074-0.04913.8750.0280.0280.0000.0000.0000.000
156A157GLY0-0.028-0.00615.4830.0030.0030.0000.0000.0000.000
157A158LEU00.0330.0169.2700.0110.0110.0000.0000.0000.000
158A159SER0-0.009-0.00612.9040.0440.0440.0000.0000.0000.000
159A160LYS10.8620.91215.464-0.176-0.1760.0000.0000.0000.000
160A161ILE00.013-0.0049.347-0.002-0.0020.0000.0000.0000.000
161A162MET0-0.027-0.00710.6770.0410.0410.0000.0000.0000.000
162A163GLU-1-0.866-0.90212.4010.2200.2200.0000.0000.0000.000
163A164LEU0-0.041-0.03213.548-0.017-0.0170.0000.0000.0000.000
164A165ILE0-0.007-0.0048.149-0.028-0.0280.0000.0000.0000.000
165A166ALA0-0.033-0.00112.2840.0140.0140.0000.0000.0000.000
166A167HIS0-0.075-0.03615.125-0.018-0.0180.0000.0000.0000.000
167A168ARG10.8430.90315.983-0.131-0.1310.0000.0000.0000.000
168A169ASP-1-0.870-0.92517.1100.1070.1070.0000.0000.0000.000
169A170ALA00.0280.01815.397-0.024-0.0240.0000.0000.0000.000
170A171PRO0-0.0320.00413.8970.0070.0070.0000.0000.0000.000
171A172ILE00.006-0.0077.5940.0480.0480.0000.0000.0000.000
172A173ILE00.0180.0069.001-0.067-0.0670.0000.0000.0000.000
173A174MET0-0.068-0.0086.5440.0130.0130.0000.0000.0000.000
174A175ALA00.0280.0236.437-0.001-0.0010.0000.0000.0000.000
175A176GLY00.0540.0088.012-0.116-0.1160.0000.0000.0000.000
176A177ALA0-0.021-0.00710.7340.0380.0380.0000.0000.0000.000
177A178GLY00.0180.00013.8030.0350.0350.0000.0000.0000.000
178A179VAL0-0.0250.0177.5000.0220.0220.0000.0000.0000.000
179A180ARG10.8820.93110.838-0.071-0.0710.0000.0000.0000.000
180A181ALA00.0710.02610.2800.0440.0440.0000.0000.0000.000
181A182GLU-1-0.901-0.94211.2980.0730.0730.0000.0000.0000.000
182A183ASN0-0.002-0.01511.2440.0220.0220.0000.0000.0000.000
183A184LEU00.0540.0324.2080.0350.106-0.001-0.008-0.0630.000
184A185HIS00.0470.0156.8180.1960.1960.0000.0000.0000.000
185A186HIS00.0230.0248.5330.2040.2040.0000.0000.0000.000
186A187PHE0-0.029-0.0215.9920.0240.0240.0000.0000.0000.000
187A188LEU0-0.007-0.0022.600-0.441-0.3811.630-0.432-1.2590.000
188A189ASP-1-0.880-0.9314.8381.2981.319-0.001-0.003-0.0160.000
189A190ALA0-0.072-0.0377.874-0.057-0.0570.0000.0000.0000.000
190A191GLY00.0040.0125.889-0.172-0.1720.0000.0000.0000.000
191A192VAL0-0.084-0.0414.478-0.190-0.080-0.001-0.028-0.0810.000
192A193LEU00.0430.0202.706-0.9680.7320.754-0.918-1.536-0.009
193A194GLU-1-0.699-0.8042.447-3.830-2.4133.332-2.318-2.432-0.023
194A195VAL0-0.0110.0003.1900.0990.5640.0800.067-0.6110.000
195A196HIS0-0.020-0.0224.944-0.242-0.281-0.001-0.0020.0420.000
196A197SER0-0.005-0.0288.5640.1190.1190.0000.0000.0000.000
197A198SER00.0300.01211.029-0.036-0.0360.0000.0000.0000.000
198A199ALA00.0020.01812.9410.0380.0380.0000.0000.0000.000
199A200GLY00.0740.02714.831-0.025-0.0250.0000.0000.0000.000
200A201ALA0-0.0130.00718.5540.0230.0230.0000.0000.0000.000
201A202TRP0-0.016-0.00122.029-0.007-0.0070.0000.0000.0000.000
202A203GLN00.0430.02625.5000.0120.0120.0000.0000.0000.000
203A204ALA00.057-0.00127.5490.0040.0040.0000.0000.0000.000
204A205SER00.010-0.00631.310-0.006-0.0060.0000.0000.0000.000
205A206PRO00.0140.00832.9860.0030.0030.0000.0000.0000.000
206A207MET0-0.037-0.01935.5660.0020.0020.0000.0000.0000.000
207A208ARG10.9700.98338.7860.0610.0610.0000.0000.0000.000
208A209TYR0-0.009-0.00941.7200.0030.0030.0000.0000.0000.000
209A210ARG10.9630.97139.2590.0440.0440.0000.0000.0000.000
210A211ASN00.0620.06044.1210.0030.0030.0000.0000.0000.000
211A225TYR00.0030.00228.8570.0020.0020.0000.0000.0000.000
212A226SER0-0.089-0.04030.1330.0040.0040.0000.0000.0000.000
213A227ARG10.9280.95227.4400.1100.1100.0000.0000.0000.000
214A228TYR0-0.027-0.00817.9660.0180.0180.0000.0000.0000.000
215A229ILE0-0.042-0.03122.153-0.006-0.0060.0000.0000.0000.000
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