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: 5J1RZ

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 OptAll
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 -2188327.143567
FMO2-HF: Nuclear repulsion 2106329.742722
FMO2-HF: Total energy -81997.400845
FMO2-MP2: Total energy -82237.872564


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.
-18.21-12.4062.089-3.205-4.6880.016
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 : 0.024 / q_NPA : 0.001
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].
3A6ARG10.8490.9482.139-12.523-7.8021.914-2.825-3.8100.015
4A7ALA00.0660.0494.011-0.354-0.1490.000-0.022-0.1830.000
5A8TYR0-0.097-0.0816.8440.6520.6520.0000.0000.0000.000
6A9ASN00.026-0.0128.898-0.148-0.1480.0000.0000.0000.000
7A10LEU0-0.035-0.00310.657-0.130-0.1300.0000.0000.0000.000
8A11THR0-0.007-0.01313.856-0.073-0.0730.0000.0000.0000.000
9A12TRP0-0.028-0.02417.592-0.042-0.0420.0000.0000.0000.000
10A13LYS10.8090.90218.998-0.463-0.4630.0000.0000.0000.000
11A14SER00.026-0.00123.501-0.022-0.0220.0000.0000.0000.000
12A15THR0-0.037-0.02026.8790.0010.0010.0000.0000.0000.000
13A16ASN00.0500.03530.580-0.003-0.0030.0000.0000.0000.000
14A17PHE00.0480.02830.687-0.011-0.0110.0000.0000.0000.000
15A18LYS10.8330.94528.119-0.147-0.1470.0000.0000.0000.000
16A19THR0-0.019-0.02424.1020.0150.0150.0000.0000.0000.000
17A20ILE00.0360.02421.027-0.017-0.0170.0000.0000.0000.000
18A21LEU0-0.036-0.00515.4000.0210.0210.0000.0000.0000.000
19A22GLU-1-0.770-0.87417.1600.3730.3730.0000.0000.0000.000
20A23TRP0-0.094-0.04510.8180.0450.0450.0000.0000.0000.000
21A24GLU-1-0.803-0.83711.0810.8150.8150.0000.0000.0000.000
22A25PRO00.0520.0177.5110.2340.2340.0000.0000.0000.000
23A26LYS10.8660.92310.491-0.354-0.3540.0000.0000.0000.000
24A27SER0-0.019-0.0139.1940.0390.0390.0000.0000.0000.000
25A28ILE00.0310.01311.903-0.042-0.0420.0000.0000.0000.000
26A29ASP-1-0.818-0.8828.612-0.454-0.4540.0000.0000.0000.000
27A30HIS0-0.034-0.0135.1140.3270.3270.0000.0000.0000.000
28A31VAL00.0050.01510.0380.1590.1590.0000.0000.0000.000
29A32TYR0-0.017-0.0318.201-0.047-0.0470.0000.0000.0000.000
30A33THR0-0.026-0.00512.485-0.052-0.0520.0000.0000.0000.000
31A34VAL0-0.024-0.00313.4320.0800.0800.0000.0000.0000.000
32A35GLN00.0310.00115.275-0.049-0.0490.0000.0000.0000.000
33A36ILE0-0.022-0.01517.5840.0650.0650.0000.0000.0000.000
34A37SER00.0100.01719.348-0.032-0.0320.0000.0000.0000.000
35A38THR00.0410.00921.8520.0160.0160.0000.0000.0000.000
36A39ARG10.9550.97524.549-0.154-0.1540.0000.0000.0000.000
37A40LEU0-0.006-0.00426.567-0.012-0.0120.0000.0000.0000.000
38A41GLU-1-0.868-0.92426.0160.0570.0570.0000.0000.0000.000
39A42ASN0-0.031-0.01922.3070.0260.0260.0000.0000.0000.000
40A43TRP0-0.024-0.01716.8270.0180.0180.0000.0000.0000.000
41A44LYS10.9170.96019.697-0.121-0.1210.0000.0000.0000.000
42A45SER0-0.001-0.01218.1300.0430.0430.0000.0000.0000.000
43A46LYS10.7550.86819.482-0.138-0.1380.0000.0000.0000.000
44A47CYS0-0.022-0.01218.209-0.067-0.0670.0000.0000.0000.000
45A48PHE00.035-0.00217.6540.0200.0200.0000.0000.0000.000
46A49LEU00.0100.00514.2900.0010.0010.0000.0000.0000.000
47A50THR00.0340.03315.919-0.023-0.0230.0000.0000.0000.000
48A51ALA00.0610.02215.1450.0100.0100.0000.0000.0000.000
49A52GLU-1-0.850-0.91315.8410.2700.2700.0000.0000.0000.000
50A53THR0-0.013-0.02012.819-0.002-0.0020.0000.0000.0000.000
51A54GLU-1-0.914-0.96115.3800.3210.3210.0000.0000.0000.000
52A56ASP-1-0.757-0.84920.1510.1820.1820.0000.0000.0000.000
53A57LEU00.0190.00119.726-0.014-0.0140.0000.0000.0000.000
54A58THR0-0.024-0.02224.218-0.011-0.0110.0000.0000.0000.000
55A59ASP-1-0.862-0.89727.8580.1060.1060.0000.0000.0000.000
56A60GLU-1-0.729-0.83125.2730.0880.0880.0000.0000.0000.000
57A61VAL00.0310.00825.214-0.006-0.0060.0000.0000.0000.000
58A62VAL0-0.033-0.02128.024-0.003-0.0030.0000.0000.0000.000
59A63LYS10.8040.90129.630-0.105-0.1050.0000.0000.0000.000
60A64ASP-1-0.752-0.86531.5210.1140.1140.0000.0000.0000.000
61A65VAL0-0.0260.00931.2590.0120.0120.0000.0000.0000.000
62A66GLY00.0210.00431.8860.0110.0110.0000.0000.0000.000
63A67GLN0-0.063-0.03528.7540.0100.0100.0000.0000.0000.000
64A68THR0-0.006-0.00724.6010.0030.0030.0000.0000.0000.000
65A69TYR0-0.053-0.04323.318-0.013-0.0130.0000.0000.0000.000
66A70MET00.0100.01817.5120.0430.0430.0000.0000.0000.000
67A71ALA00.0230.00717.585-0.047-0.0470.0000.0000.0000.000
68A72ARG10.8410.93012.043-0.204-0.2040.0000.0000.0000.000
69A73VAL00.0100.01310.531-0.138-0.1380.0000.0000.0000.000
70A74LEU0-0.041-0.0158.9370.3000.3000.0000.0000.0000.000
71A75SER00.011-0.0296.1610.0880.0880.0000.0000.0000.000
72A76TYR00.0190.0037.956-0.420-0.4200.0000.0000.0000.000
73A77PRO00.007-0.0047.5750.1870.1870.0000.0000.0000.000
74A78ALA0-0.021-0.0029.7020.1340.1340.0000.0000.0000.000
75A79ARG10.8500.89011.6590.4220.4220.0000.0000.0000.000
76A80ASN0-0.004-0.01211.648-0.097-0.0970.0000.0000.0000.000
77A81GLY00.0300.02412.322-0.101-0.1010.0000.0000.0000.000
78A82ASN0-0.013-0.01213.1790.1510.1510.0000.0000.0000.000
79A83THR0-0.017-0.00810.3040.0450.0450.0000.0000.0000.000
80A84THR0-0.028-0.00312.3450.0310.0310.0000.0000.0000.000
81A85GLY00.0040.01014.8170.0330.0330.0000.0000.0000.000
82A86PHE0-0.027-0.02514.2360.0870.0870.0000.0000.0000.000
83A87PRO0-0.0140.00611.385-0.173-0.1730.0000.0000.0000.000
84A88GLU-1-0.927-0.9655.613-4.208-4.2080.0000.0000.0000.000
85A89GLU-1-0.901-0.9568.479-0.466-0.4660.0000.0000.0000.000
86A90PRO0-0.034-0.0056.763-0.537-0.5370.0000.0000.0000.000
87A91PRO00.0300.0132.6870.1711.0460.176-0.354-0.6970.001
88A92PHE00.0070.0004.8360.6710.674-0.001-0.0040.0020.000
89A93ARG10.8460.9176.033-2.071-2.0710.0000.0000.0000.000
90A94ASN00.038-0.0049.277-0.202-0.2020.0000.0000.0000.000
91A95SER0-0.022-0.02313.0300.1120.1120.0000.0000.0000.000
92A96PRO00.0330.01115.345-0.030-0.0300.0000.0000.0000.000
93A97GLU-1-0.916-0.93618.1890.3080.3080.0000.0000.0000.000
94A98PHE0-0.019-0.01321.4370.0020.0020.0000.0000.0000.000
95A99THR00.0510.02424.093-0.010-0.0100.0000.0000.0000.000
96A100PRO0-0.0140.00927.484-0.006-0.0060.0000.0000.0000.000
97A101TYR00.0370.00829.368-0.002-0.0020.0000.0000.0000.000
98A102LEU0-0.0120.00530.742-0.007-0.0070.0000.0000.0000.000
99A103ASP-1-0.783-0.88226.6770.2650.2650.0000.0000.0000.000
100A104THR0-0.033-0.00328.1190.0110.0110.0000.0000.0000.000
101A105ASN00.0300.00828.331-0.006-0.0060.0000.0000.0000.000
102A106LEU00.0250.02131.335-0.007-0.0070.0000.0000.0000.000
103A107GLY00.011-0.01834.7320.0040.0040.0000.0000.0000.000
104A108GLN0-0.067-0.04135.517-0.004-0.0040.0000.0000.0000.000
105A109PRO0-0.0150.00138.342-0.003-0.0030.0000.0000.0000.000
106A110THR0-0.019-0.01341.7010.0000.0000.0000.0000.0000.000
107A111ILE00.0070.01044.184-0.001-0.0010.0000.0000.0000.000
108A112GLN0-0.055-0.04147.444-0.001-0.0010.0000.0000.0000.000
109A113SER00.0240.00949.619-0.003-0.0030.0000.0000.0000.000
110A114PHE00.009-0.00652.4590.0030.0030.0000.0000.0000.000
111A115GLU-1-0.896-0.92755.4790.0480.0480.0000.0000.0000.000
112A116GLN00.012-0.01359.2350.0030.0030.0000.0000.0000.000
113A117VAL00.0610.04961.882-0.002-0.0020.0000.0000.0000.000
114A118GLY0-0.049-0.03164.775-0.001-0.0010.0000.0000.0000.000
115A119THR0-0.078-0.07265.978-0.001-0.0010.0000.0000.0000.000
116A120LYS10.8260.89762.422-0.050-0.0500.0000.0000.0000.000
117A121LEU0-0.0080.01156.068-0.001-0.0010.0000.0000.0000.000
118A122ASN0-0.035-0.02756.0290.0000.0000.0000.0000.0000.000
119A123VAL0-0.009-0.00751.0290.0010.0010.0000.0000.0000.000
120A124THR00.008-0.00851.0260.0000.0000.0000.0000.0000.000
121A125VAL0-0.040-0.02145.1320.0020.0020.0000.0000.0000.000
122A126GLN00.0370.01942.943-0.005-0.0050.0000.0000.0000.000
123A127ASP-1-0.821-0.89843.7020.0930.0930.0000.0000.0000.000
124A128ALA00.0110.01838.8460.0010.0010.0000.0000.0000.000
125A129ARG10.8870.94138.740-0.083-0.0830.0000.0000.0000.000
126A130THR0-0.012-0.02032.6000.0060.0060.0000.0000.0000.000
127A131LEU00.0390.01234.007-0.007-0.0070.0000.0000.0000.000
128A132VAL0-0.014-0.00931.8910.0080.0080.0000.0000.0000.000
129A133ARG10.8720.92831.099-0.085-0.0850.0000.0000.0000.000
130A134ARG10.8900.93527.824-0.108-0.1080.0000.0000.0000.000
131A135ASN0-0.028-0.03131.9080.0010.0010.0000.0000.0000.000
132A136GLY00.0390.02135.275-0.003-0.0030.0000.0000.0000.000
133A137THR00.0150.02036.7400.0000.0000.0000.0000.0000.000
134A138PHE00.0110.00136.3660.0050.0050.0000.0000.0000.000
135A139LEU00.0230.01734.667-0.004-0.0040.0000.0000.0000.000
136A140SER0-0.031-0.04637.8810.0020.0020.0000.0000.0000.000
137A141LEU00.0360.01336.7600.0020.0020.0000.0000.0000.000
138A142ARG10.8570.92239.349-0.085-0.0850.0000.0000.0000.000
139A143ALA0-0.035-0.02641.199-0.002-0.0020.0000.0000.0000.000
140A144VAL0-0.0310.00536.261-0.001-0.0010.0000.0000.0000.000
141A145PHE00.0140.00135.0920.0000.0000.0000.0000.0000.000
142A146GLY00.0360.02440.869-0.002-0.0020.0000.0000.0000.000
143A147LYS10.9010.94544.672-0.077-0.0770.0000.0000.0000.000
144A148ASP-1-0.808-0.87440.9810.1110.1110.0000.0000.0000.000
145A149LEU0-0.056-0.01240.6060.0040.0040.0000.0000.0000.000
146A150ASN0-0.058-0.03242.833-0.006-0.0060.0000.0000.0000.000
147A151TYR00.0290.01342.7300.0080.0080.0000.0000.0000.000
148A152THR0-0.031-0.00745.369-0.003-0.0030.0000.0000.0000.000
149A153LEU00.0330.01946.9800.0020.0020.0000.0000.0000.000
150A154TYR0-0.023-0.03843.880-0.003-0.0030.0000.0000.0000.000
151A155TYR00.006-0.01149.960-0.002-0.0020.0000.0000.0000.000
152A156TRP0-0.025-0.01448.8950.0010.0010.0000.0000.0000.000
153A157ARG10.8250.90555.402-0.058-0.0580.0000.0000.0000.000
154A158ALA00.0780.05257.4660.0020.0020.0000.0000.0000.000
155A159SER0-0.069-0.03658.401-0.002-0.0020.0000.0000.0000.000
156A160SER0-0.005-0.03159.5560.0020.0020.0000.0000.0000.000
157A161THR0-0.049-0.04657.410-0.001-0.0010.0000.0000.0000.000
158A162GLY00.0350.03055.2110.0010.0010.0000.0000.0000.000
159A163LYS10.7970.87846.471-0.101-0.1010.0000.0000.0000.000
160A164LYS10.9641.01852.573-0.064-0.0640.0000.0000.0000.000
161A165THR0-0.007-0.01049.1650.0030.0030.0000.0000.0000.000
162A166ALA0-0.0110.00351.649-0.003-0.0030.0000.0000.0000.000
163A167THR0-0.018-0.02248.7760.0050.0050.0000.0000.0000.000
164A168THR00.0140.01549.246-0.004-0.0040.0000.0000.0000.000
165A169ASN0-0.032-0.02447.7650.0020.0020.0000.0000.0000.000
166A170THR00.0240.01948.2800.0020.0020.0000.0000.0000.000
167A171ASN00.017-0.00345.8560.0060.0060.0000.0000.0000.000
168A172GLU-1-0.826-0.89249.0090.0680.0680.0000.0000.0000.000
169A173PHE0-0.010-0.01048.4960.0020.0020.0000.0000.0000.000
170A174LEU00.0180.00154.256-0.002-0.0020.0000.0000.0000.000
171A175ILE0-0.037-0.00356.4960.0000.0000.0000.0000.0000.000
172A176ASP-1-0.800-0.88159.3020.0510.0510.0000.0000.0000.000
173A177VAL0-0.0150.00060.2110.0020.0020.0000.0000.0000.000
174A178ASP-1-0.737-0.83863.1860.0520.0520.0000.0000.0000.000
175A179LYS10.9600.98365.363-0.041-0.0410.0000.0000.0000.000
176A180GLY0-0.055-0.02366.587-0.001-0.0010.0000.0000.0000.000
177A181GLU-1-0.766-0.84263.2820.0560.0560.0000.0000.0000.000
178A182ASN0-0.0230.00659.5020.0020.0020.0000.0000.0000.000
179A183TYR0-0.019-0.04057.2190.0030.0030.0000.0000.0000.000
180A184CYS0-0.055-0.02551.3800.0000.0000.0000.0000.0000.000
181A185PHE00.007-0.00951.1970.0010.0010.0000.0000.0000.000
182A186SER00.043-0.00445.953-0.001-0.0010.0000.0000.0000.000
183A187VAL0-0.0020.00445.197-0.001-0.0010.0000.0000.0000.000
184A188GLN0-0.0010.01239.871-0.001-0.0010.0000.0000.0000.000
185A189ALA00.0320.02439.601-0.004-0.0040.0000.0000.0000.000
186A190VAL0-0.041-0.04240.4340.0070.0070.0000.0000.0000.000
187A191ILE00.0350.02037.151-0.004-0.0040.0000.0000.0000.000
188A192PRO0-0.009-0.00339.0420.0080.0080.0000.0000.0000.000
189A193SER0-0.019-0.02539.8590.0040.0040.0000.0000.0000.000
190A194ARG10.7560.88432.743-0.169-0.1690.0000.0000.0000.000
191A195LYS10.9890.97834.215-0.167-0.1670.0000.0000.0000.000
192A196ARG10.8590.91527.456-0.243-0.2430.0000.0000.0000.000
193A197LYS10.8590.91626.778-0.264-0.2640.0000.0000.0000.000
194A198GLN00.0170.01633.192-0.006-0.0060.0000.0000.0000.000
195A199ARG10.8820.93336.412-0.128-0.1280.0000.0000.0000.000
196A200SER0-0.0030.01236.0430.0080.0080.0000.0000.0000.000
197A201PRO00.0240.00235.384-0.002-0.0020.0000.0000.0000.000
198A202GLU-1-0.787-0.84838.1980.1020.1020.0000.0000.0000.000
199A203SER0-0.025-0.01941.0900.0040.0040.0000.0000.0000.000
200A204LEU00.0320.01742.3160.0010.0010.0000.0000.0000.000
201A205THR0-0.039-0.01244.7830.0000.0000.0000.0000.0000.000
202A206GLU-1-0.880-0.93048.1280.0740.0740.0000.0000.0000.000
203A208THR0-0.043-0.02455.049-0.004-0.0040.0000.0000.0000.000