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: N3RGQ

Calculation Name: 1WDJ-A-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 187
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2017430.978015
FMO2-HF: Nuclear repulsion 1946401.428726
FMO2-HF: Total energy -71029.54929
FMO2-MP2: Total energy -71242.57574


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:ACE )


Summations of interaction energy for fragment #1(A:1:ACE )
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.
5.917-9.9737.453-14.135-7.431-0.053
Interaction energy analysis for fragmet #1(A:1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : -0.034
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].
3A3LEU 00.0010.0013.7510.4620.824-0.001-0.222-0.1390.001
4A4VAL 00.003-0.0126.7390.2470.2470.0000.0000.0000.000
5A5LEU 0-0.039-0.0209.0030.2130.2130.0000.0000.0000.000
6A6ASP -1-0.900-0.97112.656-0.419-0.4190.0000.0000.0000.000
7A7LEU 00.0050.01915.0120.0470.0470.0000.0000.0000.000
8A8ALA 0-0.060-0.01718.3040.0040.0040.0000.0000.0000.000
9A9ARG 10.8800.90420.1190.2520.2520.0000.0000.0000.000
10A10PRO 00.0160.01618.374-0.026-0.0260.0000.0000.0000.000
11A11VAL 00.0120.02615.3950.0290.0290.0000.0000.0000.000
12A12SER 0-0.013-0.04118.5770.0220.0220.0000.0000.0000.000
13A13GLU -1-0.805-0.92120.010-0.175-0.1750.0000.0000.0000.000
14A14GLU -1-0.871-0.93021.237-0.148-0.1480.0000.0000.0000.000
15A15GLU -1-0.846-0.91220.002-0.247-0.2470.0000.0000.0000.000
16A16LEU 00.0100.01215.157-0.017-0.0170.0000.0000.0000.000
17A17ARG 10.9650.99218.3470.1290.1290.0000.0000.0000.000
18A18ARG 10.9820.99021.0120.1750.1750.0000.0000.0000.000
19A19LEU 0-0.041-0.01716.1900.0080.0080.0000.0000.0000.000
20A20SER 00.0270.00917.297-0.012-0.0120.0000.0000.0000.000
21A21GLU -1-0.984-0.98318.273-0.125-0.1250.0000.0000.0000.000
22A22LEU 0-0.089-0.05120.6400.0160.0160.0000.0000.0000.000
23A23ASN 0-0.128-0.05216.2540.0000.0000.0000.0000.0000.000
24A24PRO 00.0880.03916.751-0.016-0.0160.0000.0000.0000.000
25A25GLY 0-0.018-0.01015.598-0.003-0.0030.0000.0000.0000.000
26A26TYR 0-0.063-0.03811.247-0.012-0.0120.0000.0000.0000.000
27A27GLN 00.0310.0349.670-0.020-0.0200.0000.0000.0000.000
28A28TRP 0-0.010-0.02410.698-0.223-0.2230.0000.0000.0000.000
29A29GLU -1-0.779-0.8578.499-0.544-0.5440.0000.0000.0000.000
30A30ARG 10.7840.89711.9300.1810.1810.0000.0000.0000.000
31A31SER 00.0390.02710.6140.0580.0580.0000.0000.0000.000
32A32PRO 00.003-0.01811.7480.0570.0570.0000.0000.0000.000
33A33GLU -1-0.935-0.96713.052-0.336-0.3360.0000.0000.0000.000
34A34GLY 0-0.019-0.00314.9810.0230.0230.0000.0000.0000.000
35A35ARG 10.9000.94711.8650.4870.4870.0000.0000.0000.000
36A36LEU 00.0270.01712.2650.0100.0100.0000.0000.0000.000
37A37TRP 0-0.028-0.0027.332-0.179-0.1790.0000.0000.0000.000
38A38VAL 00.0480.0228.0150.2830.2830.0000.0000.0000.000
39A39SER 00.0270.0125.612-0.461-0.4610.0000.0000.0000.000
40A40PRO 0-0.0040.0147.0070.2240.2240.0000.0000.0000.000
41A41THR 00.0180.0109.0340.1210.1210.0000.0000.0000.000
42A42GLY 0-0.0020.00011.397-0.005-0.0050.0000.0000.0000.000
43A43GLY 00.028-0.00313.4120.0150.0150.0000.0000.0000.000
44A44GLU -1-0.826-0.91613.5260.2130.2130.0000.0000.0000.000
45A45SER 00.0270.0019.6550.0310.0310.0000.0000.0000.000
46A46GLY 00.0310.02712.557-0.009-0.0090.0000.0000.0000.000
47A47ARG 10.7830.89115.551-0.204-0.2040.0000.0000.0000.000
48A48ARG 10.8120.88512.938-0.356-0.3560.0000.0000.0000.000
49A49SER 00.0590.03213.771-0.018-0.0180.0000.0000.0000.000
50A50LEU 00.0290.04115.741-0.016-0.0160.0000.0000.0000.000
51A51GLN 00.0130.00819.319-0.009-0.0090.0000.0000.0000.000
52A52LEU 00.004-0.00815.679-0.006-0.0060.0000.0000.0000.000
53A53ALA 00.0560.01619.115-0.011-0.0110.0000.0000.0000.000
54A54TYR 0-0.024-0.00120.575-0.010-0.0100.0000.0000.0000.000
55A55GLN 0-0.064-0.04122.413-0.009-0.0090.0000.0000.0000.000
56A56LEU 00.0090.02220.801-0.006-0.0060.0000.0000.0000.000
57A57ALA 00.0230.00023.879-0.009-0.0090.0000.0000.0000.000
58A58ARG 10.9350.97226.172-0.077-0.0770.0000.0000.0000.000
59A59TRP 0-0.036-0.01926.689-0.004-0.0040.0000.0000.0000.000
60A60ASN 00.017-0.02527.361-0.004-0.0040.0000.0000.0000.000
61A61GLU -1-1.006-0.97929.3010.0200.0200.0000.0000.0000.000
62A62GLU -1-0.989-0.98731.8040.0470.0470.0000.0000.0000.000
63A63ARG 10.8920.95131.704-0.046-0.0460.0000.0000.0000.000
64A64GLY 0-0.012-0.00532.544-0.003-0.0030.0000.0000.0000.000
65A65LEU 0-0.004-0.01630.473-0.004-0.0040.0000.0000.0000.000
66A66GLY 0-0.013-0.03628.537-0.003-0.0030.0000.0000.0000.000
67A67VAL 0-0.0240.01426.0080.0010.0010.0000.0000.0000.000
68A68VAL 0-0.021-0.01322.3420.0030.0030.0000.0000.0000.000
69A69PHE 0-0.011-0.00120.447-0.006-0.0060.0000.0000.0000.000
70A70ASP -1-0.857-0.94119.339-0.018-0.0180.0000.0000.0000.000
71A71SER 00.004-0.01513.929-0.021-0.0210.0000.0000.0000.000
72A72SER 0-0.087-0.01114.679-0.033-0.0330.0000.0000.0000.000
73A73THR 0-0.0070.00516.886-0.026-0.0260.0000.0000.0000.000
74A74GLY 00.0080.00715.870-0.010-0.0100.0000.0000.0000.000
75A75PHE 00.001-0.02316.3340.0240.0240.0000.0000.0000.000
76A76LYS 10.8650.92717.0100.1030.1030.0000.0000.0000.000
77A77PHE 00.002-0.00915.5200.0380.0380.0000.0000.0000.000
78A78PRO 00.009-0.00619.207-0.012-0.0120.0000.0000.0000.000
79A79ASP -1-0.786-0.85016.470-0.181-0.1810.0000.0000.0000.000
80A80GLY 00.0060.00918.912-0.017-0.0170.0000.0000.0000.000
81A81SER 0-0.042-0.01413.561-0.021-0.0210.0000.0000.0000.000
82A82ILE 0-0.048-0.03014.4660.0450.0450.0000.0000.0000.000
83A83LEU 0-0.018-0.01710.435-0.080-0.0800.0000.0000.0000.000
84A84SER 0-0.012-0.02411.6250.0520.0520.0000.0000.0000.000
85A85PRO 0-0.0210.01511.6630.0040.0040.0000.0000.0000.000
86A86ASP -1-0.814-0.91711.0420.2240.2240.0000.0000.0000.000
87A87ALA 0-0.035-0.02513.801-0.011-0.0110.0000.0000.0000.000
88A88ALA 00.0160.01216.9030.0090.0090.0000.0000.0000.000
89A89PHE 00.0040.00319.271-0.002-0.0020.0000.0000.0000.000
90A90VAL 00.0180.00922.751-0.002-0.0020.0000.0000.0000.000
91A91GLU -1-0.904-0.95724.9430.0160.0160.0000.0000.0000.000
92A92ARG 10.9340.95428.486-0.011-0.0110.0000.0000.0000.000
93A93GLY 0-0.0150.00731.297-0.004-0.0040.0000.0000.0000.000
94A94ALA 00.007-0.00227.433-0.003-0.0030.0000.0000.0000.000
95A95TRP 00.0390.01024.951-0.006-0.0060.0000.0000.0000.000
96A96GLU -1-0.890-0.96729.045-0.024-0.0240.0000.0000.0000.000
97A97ALA 0-0.075-0.03031.169-0.002-0.0020.0000.0000.0000.000
98A98LEU 0-0.0080.02026.153-0.004-0.0040.0000.0000.0000.000
99A99SER 0-0.034-0.02030.7900.0030.0030.0000.0000.0000.000
100A100GLU -1-0.903-0.97230.938-0.048-0.0480.0000.0000.0000.000
101A101ALA 00.0110.00130.686-0.003-0.0030.0000.0000.0000.000
102A102GLU -1-0.899-0.94527.461-0.070-0.0700.0000.0000.0000.000
103A103ARG 10.7540.87526.0770.0300.0300.0000.0000.0000.000
104A104GLU -1-0.937-0.95926.155-0.066-0.0660.0000.0000.0000.000
105A105GLY 0-0.0240.01024.643-0.009-0.0090.0000.0000.0000.000
106A106PHE 0-0.044-0.03218.635-0.004-0.0040.0000.0000.0000.000
107A107PRO 00.0240.01821.1300.0020.0020.0000.0000.0000.000
108A108PRO 0-0.048-0.00821.715-0.010-0.0100.0000.0000.0000.000
109A109LEU 0-0.018-0.01321.9600.0130.0130.0000.0000.0000.000
110A110ALA 00.0260.01819.888-0.009-0.0090.0000.0000.0000.000
111A111PRO 0-0.039-0.00918.5540.0130.0130.0000.0000.0000.000
112A112LYS 10.9230.97420.684-0.027-0.0270.0000.0000.0000.000
113A113ALA 0-0.039-0.02920.0490.0100.0100.0000.0000.0000.000
114A114VAL 00.0140.01814.518-0.013-0.0130.0000.0000.0000.000
115A115PHE 0-0.020-0.02815.1470.0310.0310.0000.0000.0000.000
116A116GLU -1-0.744-0.8429.5220.0640.0640.0000.0000.0000.000
117A117VAL 0-0.043-0.03210.5600.0530.0530.0000.0000.0000.000
118A118ARG 10.8250.9176.322-1.742-1.7420.0000.0000.0000.000
119A119SER 00.0230.0086.067-0.023-0.0230.0000.0000.0000.000
120A120ALA 0-0.003-0.0186.4680.3880.3880.0000.0000.0000.000
121A121SER 0-0.030-0.0145.1670.0550.0550.0000.0000.0000.000
122A122GLN 00.0400.0571.9996.644-2.01420.902-8.518-3.726-0.014
123A123ASP -1-0.832-0.9142.5020.251-1.8200.6411.751-0.321-0.003
124A124PRO 0-0.022-0.0384.4930.0940.2670.000-0.021-0.1520.000
125A125GLU -1-0.793-0.8927.3470.3870.3870.0000.0000.0000.000
126A126GLU -1-0.930-0.9312.0990.795-4.88215.911-7.114-3.119-0.037
127A127LEU 00.0090.0084.960-0.598-0.6140.000-0.0110.0260.000
128A128ARG 10.8110.8836.136-0.875-0.8750.0000.0000.0000.000
129A129ALA 0-0.021-0.0017.706-0.167-0.1670.0000.0000.0000.000
130A130LYS 10.8270.8906.7840.1510.1510.0000.0000.0000.000
131A131MET 0-0.0200.0008.859-0.066-0.0660.0000.0000.0000.000
132A132GLY 00.0140.01211.914-0.041-0.0410.0000.0000.0000.000
133A133ILE 0-0.037-0.0169.911-0.030-0.0300.0000.0000.0000.000
134A134TYR 00.023-0.02110.928-0.037-0.0370.0000.0000.0000.000
135A135LEU 0-0.019-0.01414.934-0.007-0.0070.0000.0000.0000.000
136A136ARG 10.7900.90514.4990.1350.1350.0000.0000.0000.000
137A137ASN 0-0.079-0.07015.872-0.009-0.0090.0000.0000.0000.000
138A138GLY 0-0.0040.00319.165-0.005-0.0050.0000.0000.0000.000
139A139VAL 0-0.0420.01016.9240.0070.0070.0000.0000.0000.000
140A140LEU 0-0.034-0.03719.8730.0100.0100.0000.0000.0000.000
141A141LEU 0-0.036-0.02619.9710.0110.0110.0000.0000.0000.000
142A142GLY 00.0470.03915.932-0.013-0.0130.0000.0000.0000.000
143A143VAL 0-0.057-0.02615.8920.0200.0200.0000.0000.0000.000
144A144LEU 00.0620.0359.2100.0040.0040.0000.0000.0000.000
145A145VAL 00.013-0.00512.579-0.017-0.0170.0000.0000.0000.000
146A146ASP -1-0.776-0.89010.8660.9850.9850.0000.0000.0000.000
147A147PRO 0-0.016-0.03011.118-0.076-0.0760.0000.0000.0000.000
148A148TYR 0-0.060-0.03610.102-0.067-0.0670.0000.0000.0000.000
149A149ALA 0-0.029-0.00713.641-0.052-0.0520.0000.0000.0000.000
150A150ARG 10.8920.95615.311-0.314-0.3140.0000.0000.0000.000
151A151ALA 00.0000.00215.612-0.046-0.0460.0000.0000.0000.000
152A152VAL 0-0.008-0.00315.4520.0380.0380.0000.0000.0000.000
153A153GLU -1-0.853-0.93113.9940.3940.3940.0000.0000.0000.000
154A154VAL 0-0.034-0.02016.000-0.002-0.0020.0000.0000.0000.000
155A155PHE 00.0200.00213.243-0.015-0.0150.0000.0000.0000.000
156A156ARG 10.8860.92717.975-0.123-0.1230.0000.0000.0000.000
157A157PRO 00.0550.02921.1010.0040.0040.0000.0000.0000.000
158A158GLY 0-0.032-0.01222.223-0.002-0.0020.0000.0000.0000.000
159A159LYS 10.8960.94722.611-0.075-0.0750.0000.0000.0000.000
160A160PRO 00.0020.00621.4480.0070.0070.0000.0000.0000.000
161A161PRO 0-0.0110.01317.150-0.006-0.0060.0000.0000.0000.000
162A162LEU 00.010-0.00319.1370.0000.0000.0000.0000.0000.000
163A163ARG 10.8910.94314.670-0.403-0.4030.0000.0000.0000.000
164A164LEU 0-0.043-0.03019.119-0.026-0.0260.0000.0000.0000.000
165A165GLU -1-0.824-0.90819.0580.3240.3240.0000.0000.0000.000
166A166GLY 0-0.0080.00520.734-0.025-0.0250.0000.0000.0000.000
167A167VAL 0-0.0280.00221.881-0.022-0.0220.0000.0000.0000.000
168A168GLU -1-0.927-0.96423.0900.1310.1310.0000.0000.0000.000
169A169ARG 10.9500.95124.574-0.095-0.0950.0000.0000.0000.000
170A170VAL 00.0100.01520.9530.0030.0030.0000.0000.0000.000
171A171SER 0-0.0210.00024.304-0.005-0.0050.0000.0000.0000.000
172A172LEU 00.014-0.00221.2210.0090.0090.0000.0000.0000.000
173A173ASP -1-0.832-0.87424.9850.0590.0590.0000.0000.0000.000
174A174PRO 0-0.042-0.04427.4910.0060.0060.0000.0000.0000.000
175A175GLU -1-0.820-0.91824.0690.0700.0700.0000.0000.0000.000
176A176LEU 0-0.0130.00022.495-0.008-0.0080.0000.0000.0000.000
177A177PRO 0-0.026-0.01927.0640.0050.0050.0000.0000.0000.000
178A178GLY 00.001-0.01530.707-0.003-0.0030.0000.0000.0000.000
179A179PHE 0-0.0080.02022.4160.0020.0020.0000.0000.0000.000
180A180ALA 0-0.026-0.02826.0970.0060.0060.0000.0000.0000.000
181A181LEU 0-0.0150.01618.533-0.004-0.0040.0000.0000.0000.000
182A182SER 0-0.027-0.03623.3010.0100.0100.0000.0000.0000.000
183A183LEU 00.0760.00018.6800.0070.0070.0000.0000.0000.000
184A184PRO 00.0370.02820.2580.0140.0140.0000.0000.0000.000
185A185PRO 0-0.064-0.02721.5820.0060.0060.0000.0000.0000.000
186A186LEU 0-0.041-0.01816.710-0.007-0.0070.0000.0000.0000.000
187A187TRP -1-0.797-0.84216.0760.3040.3040.0000.0000.0000.000