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: R5218

Calculation Name: 1WDJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WDJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SI60

Base Structure: X-ray

Registration Date: 2023-06-20

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2014505.19151
FMO2-HF: Nuclear repulsion 1943625.602031
FMO2-HF: Total energy -70879.589479
FMO2-MP2: Total energy -71092.02689


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:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-14.918-4.5164.117-4.964-9.552-0.026
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.004
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].
3A4VAL00.0010.0003.568-0.7081.0350.027-0.761-1.0090.001
4A5LEU0-0.033-0.0165.0050.4710.548-0.001-0.007-0.0690.000
5A6ASP-1-0.817-0.9037.958-0.857-0.8570.0000.0000.0000.000
6A7LEU0-0.012-0.00210.7380.1110.1110.0000.0000.0000.000
7A8ALA0-0.056-0.02013.650-0.006-0.0060.0000.0000.0000.000
8A9ARG10.8430.88815.6900.2980.2980.0000.0000.0000.000
9A10PRO00.0130.01213.862-0.029-0.0290.0000.0000.0000.000
10A11VAL00.0010.02610.0870.0580.0580.0000.0000.0000.000
11A12SER00.013-0.03213.4450.0110.0110.0000.0000.0000.000
12A13GLU-1-0.712-0.85614.636-0.242-0.2420.0000.0000.0000.000
13A14GLU-1-0.840-0.88216.149-0.077-0.0770.0000.0000.0000.000
14A15GLU-1-0.829-0.86914.247-0.250-0.2500.0000.0000.0000.000
15A16LEU00.0380.0229.5600.0140.0140.0000.0000.0000.000
16A17ARG10.8100.88712.7870.0970.0970.0000.0000.0000.000
17A18ARG10.9740.98315.6980.1140.1140.0000.0000.0000.000
18A19LEU0-0.040-0.02110.7450.0230.0230.0000.0000.0000.000
19A20SER00.0350.00712.0300.0470.0470.0000.0000.0000.000
20A21GLU-1-0.894-0.93513.1090.0170.0170.0000.0000.0000.000
21A22LEU0-0.083-0.04215.8340.0170.0170.0000.0000.0000.000
22A23ASN0-0.111-0.04612.2050.0240.0240.0000.0000.0000.000
23A24PRO00.0640.01912.5740.0450.0450.0000.0000.0000.000
24A25GLY0-0.015-0.00412.7300.0130.0130.0000.0000.0000.000
25A26TYR0-0.058-0.0277.3780.2000.2000.0000.0000.0000.000
26A27GLN00.0310.0364.994-0.129-0.008-0.001-0.002-0.1170.000
27A28TRP00.017-0.0095.903-0.016-0.0160.0000.0000.0000.000
28A29GLU-1-0.780-0.8754.119-1.375-1.1050.000-0.039-0.2300.000
29A30ARG10.7000.8346.8090.3340.3340.0000.0000.0000.000
30A31SER00.013-0.0066.9400.0670.0670.0000.0000.0000.000
31A32PRO0-0.015-0.0188.1390.1240.1240.0000.0000.0000.000
32A33GLU-1-0.862-0.9109.576-0.937-0.9370.0000.0000.0000.000
33A34GLY0-0.0020.00011.4570.0650.0650.0000.0000.0000.000
34A35ARG10.8100.8878.1091.0001.0000.0000.0000.0000.000
35A36LEU00.0310.0167.0120.0160.0160.0000.0000.0000.000
36A37TRP0-0.020-0.0102.397-2.206-0.7261.057-0.666-1.8710.000
37A38VAL00.0230.0192.483-0.1910.5090.660-0.299-1.060-0.003
38A39SER00.0300.0042.690-2.5560.4201.632-2.009-2.598-0.023
39A40PRO0-0.0320.0104.023-0.722-0.6210.002-0.025-0.0790.000
40A41THR00.009-0.0057.2820.2690.2690.0000.0000.0000.000
41A42GLY00.0140.0109.834-0.187-0.1870.0000.0000.0000.000
42A43GLY00.0360.00212.126-0.008-0.0080.0000.0000.0000.000
43A44GLU-1-0.779-0.87914.6430.5260.5260.0000.0000.0000.000
44A45SER00.0260.0239.667-0.039-0.0390.0000.0000.0000.000
45A46GLY00.0600.04212.446-0.081-0.0810.0000.0000.0000.000
46A47ARG10.8080.89014.672-0.477-0.4770.0000.0000.0000.000
47A48ARG10.7140.84313.988-0.647-0.6470.0000.0000.0000.000
48A49SER00.0490.02012.255-0.070-0.0700.0000.0000.0000.000
49A50LEU00.0180.02614.702-0.058-0.0580.0000.0000.0000.000
50A51GLN00.0160.00318.121-0.056-0.0560.0000.0000.0000.000
51A52LEU00.006-0.00614.834-0.028-0.0280.0000.0000.0000.000
52A53ALA00.0640.02817.350-0.034-0.0340.0000.0000.0000.000
53A54TYR0-0.0190.00419.004-0.029-0.0290.0000.0000.0000.000
54A55GLN0-0.070-0.04021.672-0.035-0.0350.0000.0000.0000.000
55A56LEU00.0200.01418.703-0.016-0.0160.0000.0000.0000.000
56A57ALA00.0150.00622.251-0.018-0.0180.0000.0000.0000.000
57A58ARG10.9540.97124.212-0.128-0.1280.0000.0000.0000.000
58A59TRP0-0.040-0.02824.726-0.008-0.0080.0000.0000.0000.000
59A60ASN00.003-0.02825.473-0.015-0.0150.0000.0000.0000.000
60A61GLU-1-0.975-0.97427.4150.0660.0660.0000.0000.0000.000
61A62GLU-1-0.901-0.92830.0740.0570.0570.0000.0000.0000.000
62A63ARG10.7740.86629.900-0.052-0.0520.0000.0000.0000.000
63A64GLY0-0.0060.02130.718-0.006-0.0060.0000.0000.0000.000
64A65LEU00.0370.00828.254-0.006-0.0060.0000.0000.0000.000
65A66GLY0-0.021-0.03326.156-0.009-0.0090.0000.0000.0000.000
66A67VAL0-0.0280.02223.1960.0070.0070.0000.0000.0000.000
67A68VAL0-0.023-0.01920.326-0.006-0.0060.0000.0000.0000.000
68A69PHE0-0.0050.00517.571-0.003-0.0030.0000.0000.0000.000
69A70ASP-1-0.819-0.89216.0390.1640.1640.0000.0000.0000.000
70A71SER00.0220.00411.297-0.048-0.0480.0000.0000.0000.000
71A72SER0-0.112-0.05711.064-0.007-0.0070.0000.0000.0000.000
72A73THR0-0.005-0.00113.147-0.045-0.0450.0000.0000.0000.000
73A74GLY00.0170.00111.625-0.022-0.0220.0000.0000.0000.000
74A75PHE00.018-0.00112.4240.0130.0130.0000.0000.0000.000
75A76LYS10.8730.90612.5380.1330.1330.0000.0000.0000.000
76A77PHE0-0.008-0.00511.5990.0440.0440.0000.0000.0000.000
77A78PRO00.003-0.00915.171-0.012-0.0120.0000.0000.0000.000
78A79ASP-1-0.793-0.86013.164-0.475-0.4750.0000.0000.0000.000
79A80GLY00.0230.02015.020-0.027-0.0270.0000.0000.0000.000
80A81SER0-0.037-0.0359.464-0.002-0.0020.0000.0000.0000.000
81A82ILE0-0.066-0.0349.6670.0900.0900.0000.0000.0000.000
82A83LEU0-0.018-0.0026.085-0.135-0.1350.0000.0000.0000.000
83A84SER0-0.004-0.0087.8430.0770.0770.0000.0000.0000.000
84A85PRO0-0.0190.0099.1520.0940.0940.0000.0000.0000.000
85A86ASP-1-0.834-0.9349.4310.7240.7240.0000.0000.0000.000
86A87ALA0-0.027-0.01911.730-0.001-0.0010.0000.0000.0000.000
87A88ALA00.0050.00714.638-0.025-0.0250.0000.0000.0000.000
88A89PHE0-0.004-0.00816.8000.0120.0120.0000.0000.0000.000
89A90VAL00.0360.02019.927-0.018-0.0180.0000.0000.0000.000
90A91GLU-1-0.810-0.89422.250-0.008-0.0080.0000.0000.0000.000
91A92ARG10.9040.93125.926-0.019-0.0190.0000.0000.0000.000
92A93GLY0-0.0170.00028.533-0.002-0.0020.0000.0000.0000.000
93A94ALA0-0.008-0.00423.998-0.004-0.0040.0000.0000.0000.000
94A95TRP00.0240.00421.190-0.007-0.0070.0000.0000.0000.000
95A96GLU-1-0.852-0.93125.367-0.017-0.0170.0000.0000.0000.000
96A97ALA0-0.060-0.01727.032-0.001-0.0010.0000.0000.0000.000
97A98LEU0-0.0220.01622.176-0.006-0.0060.0000.0000.0000.000
98A99SER0-0.040-0.05626.4400.0100.0100.0000.0000.0000.000
99A100GLU-1-0.924-0.97926.606-0.025-0.0250.0000.0000.0000.000
100A101ALA00.021-0.00225.9120.0010.0010.0000.0000.0000.000
101A102GLU-1-0.886-0.90822.762-0.091-0.0910.0000.0000.0000.000
102A103ARG10.7450.85721.8400.0230.0230.0000.0000.0000.000
103A104GLU-1-0.916-0.95021.943-0.003-0.0030.0000.0000.0000.000
104A105GLY0-0.042-0.00919.8730.0020.0020.0000.0000.0000.000
105A106PHE0-0.039-0.03812.9310.0000.0000.0000.0000.0000.000
106A107PRO00.0450.03716.643-0.017-0.0170.0000.0000.0000.000
107A108PRO0-0.055-0.00817.385-0.023-0.0230.0000.0000.0000.000
108A109LEU0-0.033-0.02318.0520.0090.0090.0000.0000.0000.000
109A110ALA00.0290.01816.351-0.008-0.0080.0000.0000.0000.000
110A111PRO0-0.038-0.01215.2950.0180.0180.0000.0000.0000.000
111A112LYS10.7760.88018.1880.0020.0020.0000.0000.0000.000
112A113ALA0-0.036-0.02918.2830.0000.0000.0000.0000.0000.000
113A114VAL00.0070.01512.7880.0050.0050.0000.0000.0000.000
114A115PHE0-0.015-0.02513.4510.0010.0010.0000.0000.0000.000
115A116GLU-1-0.742-0.8476.7980.0540.0540.0000.0000.0000.000
116A117VAL0-0.050-0.0399.478-0.055-0.0550.0000.0000.0000.000
117A118ARG10.8430.9137.617-1.055-1.0550.0000.0000.0000.000
118A119SER00.0210.0056.906-0.127-0.1270.0000.0000.0000.000
119A120ALA0-0.022-0.0248.7140.1480.1480.0000.0000.0000.000
120A121SER0-0.046-0.0195.422-0.731-0.7310.0000.0000.0000.000
121A122GLN00.0650.0343.089-2.652-0.5190.729-0.843-2.0190.001
122A123ASP-1-0.796-0.8925.313-0.859-0.8590.0000.0000.0000.000
123A124PRO0-0.024-0.0306.2400.0140.0140.0000.0000.0000.000
124A125GLU-1-0.802-0.8658.478-0.172-0.1720.0000.0000.0000.000
125A126GLU-1-0.933-0.9623.499-3.124-2.4590.013-0.307-0.371-0.002
126A127LEU0-0.0060.0094.889-0.308-0.3080.0000.0000.0000.000
127A128ARG10.7300.8086.005-0.086-0.0860.0000.0000.0000.000
128A129ALA0-0.010-0.0027.422-0.005-0.0050.0000.0000.0000.000
129A130LYS10.8100.8894.4870.4700.606-0.001-0.006-0.1290.000
130A131MET0-0.0230.0007.6200.0900.0900.0000.0000.0000.000
131A132GLY00.0060.00711.0310.0340.0340.0000.0000.0000.000
132A133ILE0-0.042-0.0207.6140.0370.0370.0000.0000.0000.000
133A134TYR00.045-0.0088.5510.0090.0090.0000.0000.0000.000
134A135LEU0-0.012-0.01212.4990.0340.0340.0000.0000.0000.000
135A136ARG10.7690.89113.0460.5140.5140.0000.0000.0000.000
136A137ASN0-0.051-0.04013.0640.0350.0350.0000.0000.0000.000
137A138GLY00.0050.00516.4230.0170.0170.0000.0000.0000.000
138A139VAL0-0.038-0.00214.4720.0220.0220.0000.0000.0000.000
139A140LEU0-0.020-0.02017.6030.0030.0030.0000.0000.0000.000
140A141LEU0-0.032-0.02618.8100.0100.0100.0000.0000.0000.000
141A142GLY00.0570.03614.947-0.009-0.0090.0000.0000.0000.000
142A143VAL0-0.052-0.02714.4550.0090.0090.0000.0000.0000.000
143A144LEU00.0500.0309.4110.0160.0160.0000.0000.0000.000
144A145VAL0-0.001-0.00612.468-0.027-0.0270.0000.0000.0000.000
145A146ASP-1-0.742-0.86311.9710.8190.8190.0000.0000.0000.000
146A147PRO0-0.027-0.02012.592-0.092-0.0920.0000.0000.0000.000
147A148TYR0-0.077-0.04211.733-0.016-0.0160.0000.0000.0000.000
148A149ALA0-0.015-0.01415.501-0.059-0.0590.0000.0000.0000.000
149A150ARG10.8830.95817.369-0.358-0.3580.0000.0000.0000.000
150A151ALA00.0240.01616.833-0.050-0.0500.0000.0000.0000.000
151A152VAL0-0.016-0.01316.0530.0440.0440.0000.0000.0000.000
152A153GLU-1-0.835-0.90314.5280.0500.0500.0000.0000.0000.000
153A154VAL0-0.0050.00115.6800.0050.0050.0000.0000.0000.000
154A155PHE00.0340.01113.065-0.022-0.0220.0000.0000.0000.000
155A156ARG10.9010.93217.438-0.016-0.0160.0000.0000.0000.000
156A157PRO00.0400.02519.638-0.004-0.0040.0000.0000.0000.000
157A158GLY0-0.019-0.00921.3710.0120.0120.0000.0000.0000.000
158A159LYS10.8530.93522.4140.0360.0360.0000.0000.0000.000
159A160PRO00.004-0.00221.371-0.009-0.0090.0000.0000.0000.000
160A161PRO0-0.0060.02317.0620.0060.0060.0000.0000.0000.000
161A162LEU0-0.025-0.02219.0280.0080.0080.0000.0000.0000.000
162A163ARG10.8340.90116.501-0.178-0.1780.0000.0000.0000.000
163A164LEU0-0.025-0.01519.500-0.014-0.0140.0000.0000.0000.000
164A165GLU-1-0.784-0.89020.1070.2120.2120.0000.0000.0000.000
165A166GLY0-0.024-0.00822.140-0.019-0.0190.0000.0000.0000.000
166A167VAL0-0.0210.00023.056-0.009-0.0090.0000.0000.0000.000
167A168GLU-1-0.841-0.91124.0270.1360.1360.0000.0000.0000.000
168A169ARG10.8350.88224.454-0.097-0.0970.0000.0000.0000.000
169A170VAL00.0160.01620.377-0.003-0.0030.0000.0000.0000.000
170A171SER0-0.066-0.03923.8920.0000.0000.0000.0000.0000.000
171A172LEU00.028-0.00120.214-0.001-0.0010.0000.0000.0000.000
172A173ASP-1-0.817-0.84824.0130.0350.0350.0000.0000.0000.000
173A174PRO0-0.022-0.03326.8270.0000.0000.0000.0000.0000.000
174A175GLU-1-0.794-0.89523.222-0.004-0.0040.0000.0000.0000.000
175A176LEU0-0.0040.00720.958-0.003-0.0030.0000.0000.0000.000
176A177PRO0-0.012-0.00925.5520.0080.0080.0000.0000.0000.000
177A178GLY00.0390.02029.3400.0010.0010.0000.0000.0000.000
178A179PHE0-0.0360.00020.7160.0090.0090.0000.0000.0000.000
179A180ALA0-0.002-0.01525.493-0.001-0.0010.0000.0000.0000.000
180A181LEU0-0.0030.02418.2720.0060.0060.0000.0000.0000.000
181A182SER0-0.011-0.02022.9520.0020.0020.0000.0000.0000.000
182A183LEU00.0590.02218.9530.0160.0160.0000.0000.0000.000
183A184PRO00.0070.00720.6450.0310.0310.0000.0000.0000.000
184A185PRO0-0.014-0.01421.9920.0220.0220.0000.0000.0000.000
185A186LEU00.0110.01316.4090.0230.0230.0000.0000.0000.000
186A187TRP0-0.0010.02117.2800.1020.1020.0000.0000.0000.000