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: LN3J9

Calculation Name: 1XWT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XWT

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RJN8

Base Structure: X-ray

Registration Date: 2023-09-23

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 402
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7634931.509737
FMO2-HF: Nuclear repulsion 7474419.700371
FMO2-HF: Total energy -160511.809366
FMO2-MP2: Total energy -160982.257533


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:ALA)


Summations of interaction energy for fragment #1(A:1: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.
-5.659-4.46.697-3.571-4.384-0.029
Interaction energy analysis for fragmet #1(A:1:ALA)
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 : 0.010
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].
3A3ASN00.0390.0203.870-0.2641.604-0.008-0.922-0.9380.005
4A4ASN0-0.045-0.0206.1170.2920.2920.0000.0000.0000.000
5A5ASN0-0.012-0.0158.0440.2990.2990.0000.0000.0000.000
6A6PRO00.0030.01810.641-0.007-0.0070.0000.0000.0000.000
7A7SER00.0410.00912.2070.1430.1430.0000.0000.0000.000
8A8SER00.0150.01514.6750.0000.0000.0000.0000.0000.000
9A9VAL0-0.033-0.01517.5980.0480.0480.0000.0000.0000.000
10A10GLY00.0540.03717.562-0.058-0.0580.0000.0000.0000.000
11A11ALA00.0370.01716.0140.0280.0280.0000.0000.0000.000
12A12TYR0-0.109-0.07817.7610.0410.0410.0000.0000.0000.000
13A13SER0-0.025-0.01721.4120.0240.0240.0000.0000.0000.000
14A14SER00.000-0.01317.9500.0060.0060.0000.0000.0000.000
15A15GLY00.0080.01918.9360.0010.0010.0000.0000.0000.000
16A16THR0-0.059-0.02613.065-0.013-0.0130.0000.0000.0000.000
17A17TYR00.005-0.00414.175-0.039-0.0390.0000.0000.0000.000
18A18ARG10.7640.8537.4861.8721.8720.0000.0000.0000.000
19A19ASN00.012-0.0088.7920.2290.2290.0000.0000.0000.000
20A20LEU00.0540.0287.136-0.369-0.3690.0000.0000.0000.000
21A21ALA00.0410.0116.694-0.345-0.3450.0000.0000.0000.000
22A22GLN00.0180.0105.7700.1050.1050.0000.0000.0000.000
23A23GLU-1-0.791-0.8552.776-4.013-3.0250.177-0.407-0.7580.001
24A24MET0-0.054-0.0042.010-5.301-7.1136.529-2.206-2.511-0.035
25A25GLY00.0340.0203.6321.1501.3360.000-0.034-0.1520.000
26A26LYS10.7840.9014.9100.4320.461-0.001-0.002-0.0250.000
27A27THR00.0320.0018.432-0.045-0.0450.0000.0000.0000.000
28A28ASN0-0.014-0.02111.232-0.045-0.0450.0000.0000.0000.000
29A29ILE00.0130.0188.7080.0000.0000.0000.0000.0000.000
30A30GLN00.0640.02613.3340.0230.0230.0000.0000.0000.000
31A31GLN00.0560.03316.366-0.019-0.0190.0000.0000.0000.000
32A32LYS10.9150.99515.8020.1980.1980.0000.0000.0000.000
33A33VAL0-0.0240.00215.9750.0020.0020.0000.0000.0000.000
34A34ASN00.0280.00618.637-0.001-0.0010.0000.0000.0000.000
35A35SER00.014-0.00820.8370.0090.0090.0000.0000.0000.000
36A36THR0-0.022-0.02820.1380.0070.0070.0000.0000.0000.000
37A37PHE00.0360.00522.7060.0070.0070.0000.0000.0000.000
38A38ASP-1-0.834-0.92524.933-0.104-0.1040.0000.0000.0000.000
39A39ASN0-0.053-0.02324.8900.0190.0190.0000.0000.0000.000
40A40MET0-0.0170.00726.7280.0000.0000.0000.0000.0000.000
41A41PHE00.023-0.02427.8470.0040.0040.0000.0000.0000.000
42A42GLY00.0540.05130.6340.0060.0060.0000.0000.0000.000
43A43TYR0-0.036-0.01932.498-0.002-0.0020.0000.0000.0000.000
44A44ASN00.0480.01330.5230.0060.0060.0000.0000.0000.000
45A45ASN00.0040.00934.4190.0000.0000.0000.0000.0000.000
46A46THR0-0.029-0.00730.9180.0030.0030.0000.0000.0000.000
47A47GLN00.035-0.01026.7510.0010.0010.0000.0000.0000.000
48A48GLN0-0.073-0.01129.712-0.004-0.0040.0000.0000.0000.000
49A49LEU0-0.030-0.01228.9550.0010.0010.0000.0000.0000.000
50A50TYR00.0120.03432.3240.0000.0000.0000.0000.0000.000
51A51TYR0-0.007-0.02034.0130.0040.0040.0000.0000.0000.000
52A52PRO0-0.0010.00837.768-0.003-0.0030.0000.0000.0000.000
53A53TYR0-0.034-0.04240.7170.0020.0020.0000.0000.0000.000
54A54THR00.005-0.00743.8540.0000.0000.0000.0000.0000.000
55A55GLU-1-0.781-0.83147.384-0.051-0.0510.0000.0000.0000.000
56A56ASN00.004-0.01250.9230.0010.0010.0000.0000.0000.000
57A57GLY00.0260.02350.7510.0020.0020.0000.0000.0000.000
58A58VAL0-0.021-0.00450.133-0.001-0.0010.0000.0000.0000.000
59A59TYR0-0.014-0.03240.470-0.001-0.0010.0000.0000.0000.000
60A60LYS10.8360.92045.5460.0510.0510.0000.0000.0000.000
61A61ALA00.0320.01941.432-0.002-0.0020.0000.0000.0000.000
62A62HIS00.0360.03037.1130.0030.0030.0000.0000.0000.000
63A63TYR0-0.013-0.01737.282-0.003-0.0030.0000.0000.0000.000
64A64ILE0-0.012-0.00231.6600.0010.0010.0000.0000.0000.000
65A65LYS10.8630.92234.6870.0630.0630.0000.0000.0000.000
66A66ALA0-0.032-0.02234.719-0.005-0.0050.0000.0000.0000.000
67A67ILE0-0.033-0.02033.9210.0050.0050.0000.0000.0000.000
68A68ASN0-0.077-0.04736.186-0.002-0.0020.0000.0000.0000.000
69A69PRO00.0160.01937.8440.0030.0030.0000.0000.0000.000
70A70ASP-1-0.850-0.90239.355-0.054-0.0540.0000.0000.0000.000
71A71GLU-1-0.811-0.90140.921-0.068-0.0680.0000.0000.0000.000
72A72GLY00.0040.00843.0240.0020.0020.0000.0000.0000.000
73A73ASP-1-0.807-0.90840.053-0.064-0.0640.0000.0000.0000.000
74A74ASP-1-0.770-0.84639.490-0.076-0.0760.0000.0000.0000.000
75A75ILE0-0.0040.01438.321-0.003-0.0030.0000.0000.0000.000
76A76ARG10.8490.89635.6980.0890.0890.0000.0000.0000.000
77A77THR00.0120.01135.980-0.005-0.0050.0000.0000.0000.000
78A78GLU-1-0.803-0.85831.937-0.141-0.1410.0000.0000.0000.000
79A79GLY00.0640.04231.226-0.009-0.0090.0000.0000.0000.000
80A80GLN00.003-0.00731.504-0.006-0.0060.0000.0000.0000.000
81A81SER0-0.011-0.02031.836-0.007-0.0070.0000.0000.0000.000
82A82TRP0-0.014-0.00927.384-0.011-0.0110.0000.0000.0000.000
83A83GLY00.0180.01827.536-0.011-0.0110.0000.0000.0000.000
84A84MET0-0.0190.00629.007-0.003-0.0030.0000.0000.0000.000
85A85THR0-0.010-0.03324.989-0.009-0.0090.0000.0000.0000.000
86A86ALA0-0.039-0.03024.361-0.018-0.0180.0000.0000.0000.000
87A87ALA00.0120.00625.011-0.008-0.0080.0000.0000.0000.000
88A88VAL00.0110.01126.637-0.001-0.0010.0000.0000.0000.000
89A89MET0-0.0600.01321.755-0.015-0.0150.0000.0000.0000.000
90A90LEU0-0.027-0.01020.710-0.013-0.0130.0000.0000.0000.000
91A91ASN0-0.033-0.01524.2720.0070.0070.0000.0000.0000.000
92A92LYS10.8140.91626.7900.1320.1320.0000.0000.0000.000
93A93GLN00.0340.01529.574-0.001-0.0010.0000.0000.0000.000
94A94GLU-1-0.849-0.91432.900-0.075-0.0750.0000.0000.0000.000
95A95GLU-1-0.846-0.93430.685-0.108-0.1080.0000.0000.0000.000
96A96PHE0-0.007-0.01230.634-0.002-0.0020.0000.0000.0000.000
97A97ASP-1-0.752-0.85933.262-0.099-0.0990.0000.0000.0000.000
98A98ASN0-0.007-0.00636.9050.0070.0070.0000.0000.0000.000
99A99LEU0-0.047-0.00232.4450.0030.0030.0000.0000.0000.000
100A100TRP0-0.010-0.03036.3040.0000.0000.0000.0000.0000.000
101A101ARG10.7700.83937.7960.0760.0760.0000.0000.0000.000
102A102PHE00.0110.00339.7000.0040.0040.0000.0000.0000.000
103A103ALA00.0100.00238.1150.0020.0020.0000.0000.0000.000
104A104LYS10.8000.88440.2750.0860.0860.0000.0000.0000.000
105A105ALA0-0.0150.00742.6940.0030.0030.0000.0000.0000.000
106A106TYR0-0.029-0.03344.0990.0020.0020.0000.0000.0000.000
107A107GLN00.0300.00837.945-0.002-0.0020.0000.0000.0000.000
108A108LYS10.8370.92343.0640.0760.0760.0000.0000.0000.000
109A109ASN0-0.024-0.01144.5220.0070.0070.0000.0000.0000.000
110A110PRO00.0190.01047.584-0.002-0.0020.0000.0000.0000.000
111A111ASP-1-0.773-0.89448.010-0.072-0.0720.0000.0000.0000.000
112A112ASN0-0.012-0.00750.523-0.001-0.0010.0000.0000.0000.000
113A113HIS0-0.029-0.02551.0310.0030.0030.0000.0000.0000.000
114A114PRO00.0280.01053.587-0.001-0.0010.0000.0000.0000.000
115A115ASP-1-0.770-0.86051.519-0.062-0.0620.0000.0000.0000.000
116A116ALA00.0390.00351.768-0.002-0.0020.0000.0000.0000.000
117A117LYS10.9010.95748.0330.0630.0630.0000.0000.0000.000
118A118LYS10.8530.92847.0740.0570.0570.0000.0000.0000.000
119A119GLN0-0.070-0.03047.491-0.004-0.0040.0000.0000.0000.000
120A120GLY00.0400.02346.261-0.002-0.0020.0000.0000.0000.000
121A121VAL0-0.032-0.00142.847-0.005-0.0050.0000.0000.0000.000
122A122TYR0-0.032-0.04139.9140.0040.0040.0000.0000.0000.000
123A123ALA00.0070.01041.114-0.003-0.0030.0000.0000.0000.000
124A124TRP0-0.064-0.04538.708-0.003-0.0030.0000.0000.0000.000
125A125LYS10.7840.89239.4450.0690.0690.0000.0000.0000.000
126A126LEU0-0.007-0.00341.8010.0040.0040.0000.0000.0000.000
127A127LYS10.8580.92642.7410.0550.0550.0000.0000.0000.000
128A128LEU0-0.0040.01144.2170.0000.0000.0000.0000.0000.000
129A129ASN00.0370.01347.0130.0020.0020.0000.0000.0000.000
130A130GLN00.0290.00350.525-0.001-0.0010.0000.0000.0000.000
131A131ASN0-0.042-0.01852.8530.0030.0030.0000.0000.0000.000
132A132GLY00.0080.01249.2480.0000.0000.0000.0000.0000.000
133A133PHE0-0.007-0.00648.521-0.002-0.0020.0000.0000.0000.000
134A134VAL0-0.007-0.00844.6500.0000.0000.0000.0000.0000.000
135A135TYR0-0.043-0.01947.4080.0020.0020.0000.0000.0000.000
136A136LYS10.8270.89745.9450.0650.0650.0000.0000.0000.000
137A137VAL0-0.043-0.02145.4500.0030.0030.0000.0000.0000.000
138A138ASP-1-0.800-0.89544.824-0.068-0.0680.0000.0000.0000.000
139A139GLU-1-0.803-0.87945.400-0.061-0.0610.0000.0000.0000.000
140A140GLY0-0.0150.00644.849-0.002-0.0020.0000.0000.0000.000
141A141PRO00.0120.00540.580-0.001-0.0010.0000.0000.0000.000
142A142ALA00.0350.01136.5200.0020.0020.0000.0000.0000.000
143A143PRO0-0.0110.00136.306-0.007-0.0070.0000.0000.0000.000
144A144ASH00.024-0.01931.059-0.008-0.0080.0000.0000.0000.000
145A145GLY0-0.0070.00032.328-0.009-0.0090.0000.0000.0000.000
146A146GLU-1-0.782-0.90934.185-0.109-0.1090.0000.0000.0000.000
147A147GLU-1-0.810-0.89731.999-0.158-0.1580.0000.0000.0000.000
148A148TYR00.006-0.01325.388-0.017-0.0170.0000.0000.0000.000
149A149PHE00.0120.00230.844-0.004-0.0040.0000.0000.0000.000
150A150ALA00.0090.00633.5840.0000.0000.0000.0000.0000.000
151A151PHE0-0.014-0.00524.522-0.002-0.0020.0000.0000.0000.000
152A152ALA00.0020.01329.411-0.004-0.0040.0000.0000.0000.000
153A153LEU00.0030.00230.4120.0010.0010.0000.0000.0000.000
154A154LEU0-0.021-0.00731.6170.0040.0040.0000.0000.0000.000
155A155ASN0-0.007-0.01626.764-0.010-0.0100.0000.0000.0000.000
156A156ALA00.0350.02529.6820.0000.0000.0000.0000.0000.000
157A157SER0-0.025-0.02032.0730.0090.0090.0000.0000.0000.000
158A158ALA0-0.047-0.01929.9890.0050.0050.0000.0000.0000.000
159A159ARG10.7940.90724.0310.1950.1950.0000.0000.0000.000
160A160TRP0-0.004-0.00929.6940.0020.0020.0000.0000.0000.000
161A161GLY00.0070.02834.1600.0080.0080.0000.0000.0000.000
162A162ASN0-0.050-0.05736.946-0.003-0.0030.0000.0000.0000.000
163A163SER00.003-0.00940.0190.0030.0030.0000.0000.0000.000
164A164GLY00.0430.04040.9700.0030.0030.0000.0000.0000.000
165A165GLU-1-0.807-0.87041.316-0.073-0.0730.0000.0000.0000.000
166A166PHE0-0.025-0.01439.1100.0010.0010.0000.0000.0000.000
167A167ASN00.0190.01140.619-0.005-0.0050.0000.0000.0000.000
168A168TYR00.011-0.04135.9100.0000.0000.0000.0000.0000.000
169A169TYR0-0.009-0.01236.269-0.002-0.0020.0000.0000.0000.000
170A170ASN00.009-0.01138.288-0.003-0.0030.0000.0000.0000.000
171A171ASP-1-0.758-0.84139.322-0.089-0.0890.0000.0000.0000.000
172A172ALA00.0180.01335.874-0.001-0.0010.0000.0000.0000.000
173A173ILE0-0.006-0.00837.714-0.002-0.0020.0000.0000.0000.000
174A174THR0-0.049-0.02540.1560.0040.0040.0000.0000.0000.000
175A175MET0-0.0150.01436.8100.0020.0020.0000.0000.0000.000
176A176LEU0-0.008-0.01234.861-0.001-0.0010.0000.0000.0000.000
177A177ASN0-0.046-0.03638.8360.0030.0030.0000.0000.0000.000
178A178THR00.0040.00941.2850.0040.0040.0000.0000.0000.000
179A179ILE00.004-0.00935.8210.0010.0010.0000.0000.0000.000
180A180LYS10.8100.88439.9510.0970.0970.0000.0000.0000.000
181A181ASN0-0.054-0.03041.6830.0030.0030.0000.0000.0000.000
182A182LYS10.8110.92443.6990.0760.0760.0000.0000.0000.000
183A183LEU0-0.0250.00039.1800.0010.0010.0000.0000.0000.000
184A184MET0-0.0100.01935.995-0.006-0.0060.0000.0000.0000.000
185A185GLU-1-0.777-0.87940.805-0.081-0.0810.0000.0000.0000.000
186A186ASN0-0.046-0.03140.910-0.004-0.0040.0000.0000.0000.000
187A187GLN0-0.031-0.01138.189-0.002-0.0020.0000.0000.0000.000
188A188ILE00.0050.00035.044-0.010-0.0100.0000.0000.0000.000
189A189ILE00.0290.02333.5360.0090.0090.0000.0000.0000.000
190A190ARG10.8070.90036.9010.0850.0850.0000.0000.0000.000
191A191PHE00.0170.00537.666-0.004-0.0040.0000.0000.0000.000
192A192SER00.0740.02239.1410.0020.0020.0000.0000.0000.000
193A193PRO00.002-0.00442.6020.0010.0010.0000.0000.0000.000
194A194TYR0-0.096-0.08845.2520.0020.0020.0000.0000.0000.000
195A195ILE0-0.020-0.00244.1080.0030.0030.0000.0000.0000.000
196A196ASP-1-0.806-0.87144.390-0.078-0.0780.0000.0000.0000.000
197A197ASN0-0.022-0.03642.263-0.004-0.0040.0000.0000.0000.000
198A198LEU0-0.0080.00439.6860.0000.0000.0000.0000.0000.000
199A199THR00.002-0.00635.033-0.004-0.0040.0000.0000.0000.000
200A200ASP-1-0.681-0.79832.680-0.134-0.1340.0000.0000.0000.000
201A201PRO0-0.024-0.02130.138-0.008-0.0080.0000.0000.0000.000
202A202SER0-0.078-0.06228.450-0.016-0.0160.0000.0000.0000.000
203A203TYR0-0.016-0.01328.794-0.009-0.0090.0000.0000.0000.000
204A204HIS0-0.0080.02029.186-0.011-0.0110.0000.0000.0000.000
205A205ILE00.0240.01624.799-0.022-0.0220.0000.0000.0000.000
206A206PRO0-0.033-0.01825.5500.0040.0040.0000.0000.0000.000
207A207ALA00.0240.00623.8100.0110.0110.0000.0000.0000.000
208A208PHE00.0060.00424.8570.0010.0010.0000.0000.0000.000
209A209TYR0-0.033-0.03228.2580.0070.0070.0000.0000.0000.000
210A210ASP-1-0.725-0.85327.412-0.206-0.2060.0000.0000.0000.000
211A211TYR0-0.006-0.01427.1360.0080.0080.0000.0000.0000.000
212A212PHE00.0150.00329.0840.0110.0110.0000.0000.0000.000
213A213ALA0-0.017-0.00232.3030.0100.0100.0000.0000.0000.000
214A214ASN0-0.0020.00028.4060.0190.0190.0000.0000.0000.000
215A215ASN00.0320.01129.9800.0120.0120.0000.0000.0000.000
216A216VAL00.0020.03333.9290.0090.0090.0000.0000.0000.000
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