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: 4J1QN

Calculation Name: 1A21-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1A21

Chain ID: A

ChEMBL ID:

UniProt ID: P24055

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2179969.068644
FMO2-HF: Nuclear repulsion 2097972.299871
FMO2-HF: Total energy -81996.768773
FMO2-MP2: Total energy -82237.197983


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:4:THR)


Summations of interaction energy for fragment #1(A:4: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.
-21.132-13.5952.98-4.304-6.2120.022
Interaction energy analysis for fragmet #1(A:4:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.008
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].
3A6ARG10.8390.9262.171-14.198-8.1782.623-3.734-4.9090.019
4A7ALA00.0590.0533.763-0.811-0.6100.0020.012-0.2140.000
5A8TYR0-0.093-0.0736.6620.5250.5250.0000.0000.0000.000
6A9ASN00.025-0.0128.772-0.139-0.1390.0000.0000.0000.000
7A10LEU0-0.030-0.00410.586-0.119-0.1190.0000.0000.0000.000
8A11THR0-0.013-0.01013.835-0.096-0.0960.0000.0000.0000.000
9A12TRP0-0.011-0.00917.566-0.020-0.0200.0000.0000.0000.000
10A13LYS10.8380.92219.520-0.552-0.5520.0000.0000.0000.000
11A14SER00.0280.00123.472-0.024-0.0240.0000.0000.0000.000
12A15THR0-0.021-0.01426.791-0.004-0.0040.0000.0000.0000.000
13A16ASN00.0540.02930.442-0.002-0.0020.0000.0000.0000.000
14A17PHE00.0220.00930.378-0.011-0.0110.0000.0000.0000.000
15A18LYS10.8630.95827.911-0.210-0.2100.0000.0000.0000.000
16A19THR0-0.026-0.02823.7050.0130.0130.0000.0000.0000.000
17A20ILE00.0300.01920.867-0.013-0.0130.0000.0000.0000.000
18A21LEU0-0.0340.00715.2730.0190.0190.0000.0000.0000.000
19A22GLU-1-0.766-0.87916.8550.4710.4710.0000.0000.0000.000
20A23TRP0-0.086-0.04410.7200.0470.0470.0000.0000.0000.000
21A24GLU-1-0.821-0.85710.9820.8830.8830.0000.0000.0000.000
22A25PRO00.0390.0187.3770.3590.3590.0000.0000.0000.000
23A26LYS10.8990.92810.432-0.427-0.4270.0000.0000.0000.000
24A27SER0-0.027-0.0119.276-0.038-0.0380.0000.0000.0000.000
25A28ILE00.0380.01912.158-0.037-0.0370.0000.0000.0000.000
26A29ASP-1-0.826-0.8998.650-0.602-0.6020.0000.0000.0000.000
27A30HIS0-0.054-0.0295.6630.4150.4150.0000.0000.0000.000
28A31VAL00.0110.02210.5580.1240.1240.0000.0000.0000.000
29A32TYR0-0.026-0.0438.1350.0660.0660.0000.0000.0000.000
30A33THR0-0.033-0.00912.241-0.122-0.1220.0000.0000.0000.000
31A34VAL0-0.013-0.00113.2890.1270.1270.0000.0000.0000.000
32A35GLN00.0190.00215.274-0.056-0.0560.0000.0000.0000.000
33A36ILE0-0.015-0.01317.4920.0660.0660.0000.0000.0000.000
34A37SER00.0000.00919.384-0.034-0.0340.0000.0000.0000.000
35A38THR00.0530.01721.9190.0160.0160.0000.0000.0000.000
36A39ARG10.9420.97224.436-0.200-0.2000.0000.0000.0000.000
37A40LEU0-0.005-0.00626.448-0.016-0.0160.0000.0000.0000.000
38A41GLU-1-0.924-0.95825.7300.1260.1260.0000.0000.0000.000
39A42ASN00.0160.00922.0560.0400.0400.0000.0000.0000.000
40A43TRP0-0.017-0.01016.5000.0180.0180.0000.0000.0000.000
41A44LYS10.9290.96119.822-0.205-0.2050.0000.0000.0000.000
42A45SER0-0.003-0.01117.7910.0540.0540.0000.0000.0000.000
43A46LYS10.7350.86619.537-0.244-0.2440.0000.0000.0000.000
44A47CYS0-0.045-0.02018.079-0.088-0.0880.0000.0000.0000.000
45A48PHE00.026-0.01017.7380.0360.0360.0000.0000.0000.000
46A49LEU0-0.0020.00414.085-0.013-0.0130.0000.0000.0000.000
47A50THR00.0440.03516.189-0.045-0.0450.0000.0000.0000.000
48A51ALA00.0750.03315.1080.0360.0360.0000.0000.0000.000
49A52GLU-1-0.866-0.91215.8600.3450.3450.0000.0000.0000.000
50A53THR0-0.029-0.02613.0000.0340.0340.0000.0000.0000.000
51A54GLU-1-0.907-0.96415.5020.4180.4180.0000.0000.0000.000
52A56ASP-1-0.757-0.84419.8590.2570.2570.0000.0000.0000.000
53A57LEU0-0.007-0.01419.487-0.019-0.0190.0000.0000.0000.000
54A58THR0-0.008-0.02724.010-0.016-0.0160.0000.0000.0000.000
55A59ASP-1-0.870-0.91527.5920.1760.1760.0000.0000.0000.000
56A60GLU-1-0.708-0.82124.7860.1700.1700.0000.0000.0000.000
57A61VAL00.0440.01825.294-0.009-0.0090.0000.0000.0000.000
58A62VAL0-0.039-0.02627.960-0.011-0.0110.0000.0000.0000.000
59A63LYS10.7940.90229.213-0.173-0.1730.0000.0000.0000.000
60A64ASP-1-0.754-0.87231.4500.1530.1530.0000.0000.0000.000
61A65VAL0-0.0320.00531.0940.0150.0150.0000.0000.0000.000
62A66GLY00.0280.00531.8020.0100.0100.0000.0000.0000.000
63A67GLN0-0.072-0.03028.8340.0100.0100.0000.0000.0000.000
64A68THR0-0.007-0.01424.3730.0030.0030.0000.0000.0000.000
65A69TYR0-0.054-0.04523.208-0.005-0.0050.0000.0000.0000.000
66A70MET0-0.0120.00817.3770.0480.0480.0000.0000.0000.000
67A71ALA00.0250.00317.450-0.048-0.0480.0000.0000.0000.000
68A72ARG10.8550.93112.298-0.448-0.4480.0000.0000.0000.000
69A73VAL00.0060.00910.216-0.159-0.1590.0000.0000.0000.000
70A74LEU0-0.035-0.0108.9280.3840.3840.0000.0000.0000.000
71A75SER00.018-0.0066.045-0.035-0.0350.0000.0000.0000.000
72A76TYR00.0220.0017.645-0.382-0.3820.0000.0000.0000.000
73A77PRO00.009-0.0037.6500.1620.1620.0000.0000.0000.000
74A78ALA00.0040.0099.9870.1170.1170.0000.0000.0000.000
75A79ARG10.8590.91512.3550.4420.4420.0000.0000.0000.000
76A80ASN0-0.001-0.02512.534-0.093-0.0930.0000.0000.0000.000
77A81GLY00.0100.01712.527-0.072-0.0720.0000.0000.0000.000
78A82ASN0-0.025-0.00413.0940.1650.1650.0000.0000.0000.000
79A83THR00.0130.00310.2100.0100.0100.0000.0000.0000.000
80A84THR0-0.0100.00212.3280.0630.0630.0000.0000.0000.000
81A85GLY00.0160.01214.7250.0410.0410.0000.0000.0000.000
82A86PHE0-0.041-0.02814.0900.0960.0960.0000.0000.0000.000
83A87PRO0-0.025-0.00111.794-0.180-0.1800.0000.0000.0000.000
84A88GLU-1-0.931-0.9696.122-3.851-3.8510.0000.0000.0000.000
85A89GLU-1-0.917-0.9548.149-0.229-0.2290.0000.0000.0000.000
86A90PRO0-0.033-0.0076.431-0.478-0.4780.0000.0000.0000.000
87A91PRO00.0030.0002.781-0.1631.1240.356-0.577-1.0660.003
88A92PHE00.006-0.0094.7690.1040.133-0.001-0.005-0.0230.000
89A93ARG10.8540.9216.045-2.314-2.3140.0000.0000.0000.000
90A94ASN00.0400.0049.304-0.200-0.2000.0000.0000.0000.000
91A95SER0-0.0030.00312.7830.0940.0940.0000.0000.0000.000
92A96PRO0-0.004-0.00615.232-0.034-0.0340.0000.0000.0000.000
93A97GLU-1-0.893-0.94817.9580.3770.3770.0000.0000.0000.000
94A98PHE0-0.017-0.01421.252-0.003-0.0030.0000.0000.0000.000
95A99THR00.0380.01823.903-0.011-0.0110.0000.0000.0000.000
96A100PRO0-0.025-0.00127.060-0.010-0.0100.0000.0000.0000.000
97A101TYR00.0370.00729.186-0.003-0.0030.0000.0000.0000.000
98A102LEU0-0.0270.00330.414-0.010-0.0100.0000.0000.0000.000
99A103ASP-1-0.809-0.90026.4240.3210.3210.0000.0000.0000.000
100A104THR0-0.036-0.00128.1710.0090.0090.0000.0000.0000.000
101A105ASN00.0180.00728.097-0.011-0.0110.0000.0000.0000.000
102A106LEU00.0290.01731.217-0.005-0.0050.0000.0000.0000.000
103A107GLY00.012-0.01134.6240.0060.0060.0000.0000.0000.000
104A108GLN0-0.093-0.05035.592-0.005-0.0050.0000.0000.0000.000
105A109PRO0-0.0070.00938.305-0.003-0.0030.0000.0000.0000.000
106A110THR0-0.015-0.02341.6550.0010.0010.0000.0000.0000.000
107A111ILE0-0.0120.01244.294-0.001-0.0010.0000.0000.0000.000
108A112GLN0-0.023-0.01047.871-0.002-0.0020.0000.0000.0000.000
109A113SER00.0130.00049.410-0.004-0.0040.0000.0000.0000.000
110A114PHE00.007-0.00552.7380.0030.0030.0000.0000.0000.000
111A115GLU-1-0.887-0.93355.4080.0590.0590.0000.0000.0000.000
112A116GLN00.007-0.00759.1370.0030.0030.0000.0000.0000.000
113A117VAL00.0540.02761.776-0.002-0.0020.0000.0000.0000.000
114A118GLY0-0.065-0.05264.933-0.001-0.0010.0000.0000.0000.000
115A119THR0-0.043-0.03865.8350.0000.0000.0000.0000.0000.000
116A120LYS10.8470.89662.920-0.060-0.0600.0000.0000.0000.000
117A121LEU0-0.0040.03356.2020.0000.0000.0000.0000.0000.000
118A122ASN0-0.039-0.03256.5180.0000.0000.0000.0000.0000.000
119A123VAL0-0.023-0.00751.1460.0010.0010.0000.0000.0000.000
120A124THR00.009-0.00550.9950.0000.0000.0000.0000.0000.000
121A125VAL0-0.061-0.03445.3080.0020.0020.0000.0000.0000.000
122A126GLN00.0440.02043.206-0.006-0.0060.0000.0000.0000.000
123A127ASP-1-0.879-0.95344.0460.1160.1160.0000.0000.0000.000
124A128ALA0-0.0090.00739.1340.0020.0020.0000.0000.0000.000
125A129ARG10.9210.95639.022-0.112-0.1120.0000.0000.0000.000
126A130THR0-0.0020.00033.1670.0060.0060.0000.0000.0000.000
127A131LEU00.0400.01834.094-0.008-0.0080.0000.0000.0000.000
128A132VAL0-0.016-0.01331.9080.0130.0130.0000.0000.0000.000
129A133ARG10.8840.96631.447-0.141-0.1410.0000.0000.0000.000
130A134ARG10.9290.94628.134-0.169-0.1690.0000.0000.0000.000
131A135ASN0-0.045-0.04032.0380.0030.0030.0000.0000.0000.000
132A136GLY00.025-0.00335.393-0.002-0.0020.0000.0000.0000.000
133A137THR00.0080.03336.603-0.002-0.0020.0000.0000.0000.000
134A138PHE00.0230.00136.5820.0070.0070.0000.0000.0000.000
135A139LEU00.004-0.00434.435-0.004-0.0040.0000.0000.0000.000
136A140SER0-0.030-0.02037.5760.0050.0050.0000.0000.0000.000
137A141LEU00.0510.02336.9700.0040.0040.0000.0000.0000.000
138A142ARG10.8890.93739.563-0.108-0.1080.0000.0000.0000.000
139A143ALA0-0.043-0.02641.153-0.002-0.0020.0000.0000.0000.000
140A144VAL0-0.0210.00536.152-0.001-0.0010.0000.0000.0000.000
141A145PHE00.013-0.00335.0270.0010.0010.0000.0000.0000.000
142A146GLY00.0220.02640.786-0.004-0.0040.0000.0000.0000.000
143A147LYS10.9440.93844.545-0.092-0.0920.0000.0000.0000.000
144A148ASP-1-0.845-0.89141.1750.1340.1340.0000.0000.0000.000
145A149LEU0-0.059-0.01040.3560.0060.0060.0000.0000.0000.000
146A150ASN0-0.050-0.02142.979-0.006-0.0060.0000.0000.0000.000
147A151TYR00.0420.01742.3040.0070.0070.0000.0000.0000.000
148A152THR0-0.041-0.02145.661-0.003-0.0030.0000.0000.0000.000
149A153LEU00.0020.00747.0720.0030.0030.0000.0000.0000.000
150A154TYR0-0.031-0.03143.985-0.003-0.0030.0000.0000.0000.000
151A155TYR00.0080.00450.047-0.002-0.0020.0000.0000.0000.000
152A156TRP00.0120.00349.0630.0010.0010.0000.0000.0000.000
153A157ARG10.8100.89855.538-0.065-0.0650.0000.0000.0000.000
154A158ALA00.0690.04957.6610.0020.0020.0000.0000.0000.000
155A159SER0-0.068-0.03758.593-0.003-0.0030.0000.0000.0000.000
156A160SER00.0260.00359.6820.0020.0020.0000.0000.0000.000
157A161THR0-0.049-0.05257.241-0.001-0.0010.0000.0000.0000.000
158A162GLY00.0320.02755.4470.0010.0010.0000.0000.0000.000
159A163LYS10.8290.92246.704-0.114-0.1140.0000.0000.0000.000
160A164LYS10.9500.99553.060-0.073-0.0730.0000.0000.0000.000
161A165THR0-0.013-0.02148.9300.0020.0020.0000.0000.0000.000
162A166ALA0-0.0120.01151.802-0.002-0.0020.0000.0000.0000.000
163A167THR0-0.010-0.02148.7990.0060.0060.0000.0000.0000.000
164A168THR00.0160.01849.344-0.005-0.0050.0000.0000.0000.000
165A169ASN00.007-0.01248.4000.0070.0070.0000.0000.0000.000
166A170THR0-0.013-0.00148.7200.0020.0020.0000.0000.0000.000
167A171ASN00.0210.00546.1820.0060.0060.0000.0000.0000.000
168A172GLU-1-0.834-0.89149.3790.0830.0830.0000.0000.0000.000
169A173PHE0-0.010-0.01148.5630.0010.0010.0000.0000.0000.000
170A174LEU0-0.008-0.01254.159-0.002-0.0020.0000.0000.0000.000
171A175ILE0-0.0290.00356.4120.0000.0000.0000.0000.0000.000
172A176ASP-1-0.824-0.89559.0670.0610.0610.0000.0000.0000.000
173A177VAL0-0.0220.00259.9800.0020.0020.0000.0000.0000.000
174A178ASP-1-0.758-0.83762.8930.0600.0600.0000.0000.0000.000
175A179LYS10.9970.99365.303-0.048-0.0480.0000.0000.0000.000
176A180GLY0-0.060-0.02066.859-0.001-0.0010.0000.0000.0000.000
177A181GLU-1-0.798-0.87863.0380.0630.0630.0000.0000.0000.000
178A182ASN0-0.0140.01759.4150.0030.0030.0000.0000.0000.000
179A183TYR0-0.004-0.04056.9790.0020.0020.0000.0000.0000.000
180A184CYS0-0.053-0.01751.4820.0000.0000.0000.0000.0000.000
181A185PHE00.052-0.01051.1570.0000.0000.0000.0000.0000.000
182A186SER00.030-0.01445.943-0.001-0.0010.0000.0000.0000.000
183A187VAL00.0100.00845.096-0.001-0.0010.0000.0000.0000.000
184A188GLN00.0060.00940.1200.0000.0000.0000.0000.0000.000
185A189ALA00.0380.02339.557-0.006-0.0060.0000.0000.0000.000
186A190VAL0-0.040-0.04140.2080.0070.0070.0000.0000.0000.000
187A191ILE00.0290.02837.154-0.005-0.0050.0000.0000.0000.000
188A192PRO00.005-0.01139.2190.0090.0090.0000.0000.0000.000
189A193SER0-0.020-0.00539.8710.0040.0040.0000.0000.0000.000
190A194ARG10.7750.89732.517-0.205-0.2050.0000.0000.0000.000
191A195LYS10.9800.97833.922-0.196-0.1960.0000.0000.0000.000
192A196ARG10.9010.94327.362-0.285-0.2850.0000.0000.0000.000
193A197LYS10.8730.91426.820-0.308-0.3080.0000.0000.0000.000
194A198GLN00.0170.00533.190-0.006-0.0060.0000.0000.0000.000
195A199ARG10.9020.95536.587-0.147-0.1470.0000.0000.0000.000
196A200SER00.0220.03835.9580.0090.0090.0000.0000.0000.000
197A201PRO00.000-0.00935.167-0.005-0.0050.0000.0000.0000.000
198A202GLU-1-0.830-0.89537.9660.1190.1190.0000.0000.0000.000
199A203SER00.0110.00340.9970.0040.0040.0000.0000.0000.000
200A204LEU0-0.0050.00141.9630.0000.0000.0000.0000.0000.000
201A205THR0-0.035-0.02844.792-0.001-0.0010.0000.0000.0000.000
202A206GLU-1-0.882-0.92248.2120.0890.0890.0000.0000.0000.000
203A208THR0-0.047-0.03155.038-0.003-0.0030.0000.0000.0000.000