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: ZY82N

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2010913.704821
FMO2-HF: Nuclear repulsion 1940034.468296
FMO2-HF: Total energy -70879.236524
FMO2-MP2: Total energy -71091.747915


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.
-16.612-5.9545.866-6.163-10.359-0.031
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 : 0.013 / q_NPA : -0.002
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].
3A4VAL00.022-0.0043.141-1.9970.7400.106-1.383-1.4600.001
4A5LEU0-0.038-0.0155.3910.4420.515-0.001-0.005-0.0660.000
5A6ASP-1-0.823-0.9088.309-1.010-1.0100.0000.0000.0000.000
6A7LEU00.0020.01811.1130.1260.1260.0000.0000.0000.000
7A8ALA0-0.067-0.02614.067-0.024-0.0240.0000.0000.0000.000
8A9ARG10.8590.88515.7880.3050.3050.0000.0000.0000.000
9A10PRO00.0200.01913.909-0.026-0.0260.0000.0000.0000.000
10A11VAL00.0160.03010.3880.0610.0610.0000.0000.0000.000
11A12SER00.001-0.04413.6510.0130.0130.0000.0000.0000.000
12A13GLU-1-0.735-0.86514.812-0.214-0.2140.0000.0000.0000.000
13A14GLU-1-0.830-0.88916.238-0.055-0.0550.0000.0000.0000.000
14A15GLU-1-0.828-0.87514.387-0.239-0.2390.0000.0000.0000.000
15A16LEU00.0130.0159.9400.0180.0180.0000.0000.0000.000
16A17ARG10.8500.90612.9090.0850.0850.0000.0000.0000.000
17A18ARG10.9890.99515.6770.0960.0960.0000.0000.0000.000
18A19LEU0-0.039-0.01610.5780.0250.0250.0000.0000.0000.000
19A20SER00.0260.00012.2320.0630.0630.0000.0000.0000.000
20A21GLU-1-0.916-0.94213.1050.0510.0510.0000.0000.0000.000
21A22LEU0-0.094-0.05115.2430.0160.0160.0000.0000.0000.000
22A23ASN0-0.115-0.04811.6700.0260.0260.0000.0000.0000.000
23A24PRO00.0820.03612.4720.0580.0580.0000.0000.0000.000
24A25GLY0-0.022-0.01212.2600.0200.0200.0000.0000.0000.000
25A26TYR0-0.061-0.0367.4730.2320.2320.0000.0000.0000.000
26A27GLN00.0020.0205.779-0.005-0.0050.0000.0000.0000.000
27A28TRP00.010-0.0135.7030.0330.0330.0000.0000.0000.000
28A29GLU-1-0.768-0.8673.886-1.471-1.1340.001-0.076-0.2620.000
29A30ARG10.7350.8706.9500.2760.2760.0000.0000.0000.000
30A31SER00.013-0.0116.6460.0930.0930.0000.0000.0000.000
31A32PRO00.001-0.0158.0900.1460.1460.0000.0000.0000.000
32A33GLU-1-0.922-0.9409.553-0.984-0.9840.0000.0000.0000.000
33A34GLY0-0.010-0.00211.0750.0730.0730.0000.0000.0000.000
34A35ARG10.8380.9017.7861.0891.0890.0000.0000.0000.000
35A36LEU00.0210.0157.1610.0320.0320.0000.0000.0000.000
36A37TRP0-0.013-0.0022.459-2.462-0.7020.992-0.653-2.098-0.002
37A38VAL00.0310.0172.346-0.5590.3160.984-0.541-1.319-0.003
38A39SER00.0490.0262.222-0.9190.7013.424-1.980-3.064-0.014
39A40PRO0-0.0320.0063.749-0.975-0.8530.012-0.026-0.1070.000
40A41THR00.0080.0037.3480.2930.2930.0000.0000.0000.000
41A42GLY00.0060.0059.713-0.188-0.1880.0000.0000.0000.000
42A43GLY00.0330.00012.400-0.035-0.0350.0000.0000.0000.000
43A44GLU-1-0.797-0.88414.2200.5540.5540.0000.0000.0000.000
44A45SER00.0300.0009.751-0.075-0.0750.0000.0000.0000.000
45A46GLY00.0600.04312.667-0.068-0.0680.0000.0000.0000.000
46A47ARG10.8200.90114.598-0.520-0.5200.0000.0000.0000.000
47A48ARG10.7690.87014.318-0.712-0.7120.0000.0000.0000.000
48A49SER00.0830.04712.714-0.085-0.0850.0000.0000.0000.000
49A50LEU00.0210.03715.098-0.065-0.0650.0000.0000.0000.000
50A51GLN00.006-0.00618.324-0.063-0.0630.0000.0000.0000.000
51A52LEU0-0.009-0.01115.062-0.034-0.0340.0000.0000.0000.000
52A53ALA00.0610.02117.715-0.039-0.0390.0000.0000.0000.000
53A54TYR0-0.0200.00019.331-0.036-0.0360.0000.0000.0000.000
54A55GLN0-0.063-0.03322.030-0.040-0.0400.0000.0000.0000.000
55A56LEU00.0130.02119.042-0.020-0.0200.0000.0000.0000.000
56A57ALA00.0250.00422.590-0.020-0.0200.0000.0000.0000.000
57A58ARG10.9480.97924.653-0.153-0.1530.0000.0000.0000.000
58A59TRP0-0.038-0.02024.814-0.010-0.0100.0000.0000.0000.000
59A60ASN00.030-0.02325.604-0.017-0.0170.0000.0000.0000.000
60A61GLU-1-0.997-0.97427.6060.0800.0800.0000.0000.0000.000
61A62GLU-1-0.895-0.93930.2500.0680.0680.0000.0000.0000.000
62A63ARG10.7830.89830.096-0.066-0.0660.0000.0000.0000.000
63A64GLY0-0.0120.00030.674-0.006-0.0060.0000.0000.0000.000
64A65LEU00.003-0.00728.501-0.007-0.0070.0000.0000.0000.000
65A66GLY0-0.012-0.03526.082-0.010-0.0100.0000.0000.0000.000
66A67VAL0-0.0270.01423.1010.0060.0060.0000.0000.0000.000
67A68VAL0-0.019-0.01420.421-0.004-0.0040.0000.0000.0000.000
68A69PHE0-0.0030.00617.511-0.006-0.0060.0000.0000.0000.000
69A70ASP-1-0.845-0.91016.3280.2130.2130.0000.0000.0000.000
70A71SER00.003-0.01611.548-0.046-0.0460.0000.0000.0000.000
71A72SER0-0.114-0.05111.4270.0160.0160.0000.0000.0000.000
72A73THR0-0.0070.00513.203-0.047-0.0470.0000.0000.0000.000
73A74GLY00.0100.00711.665-0.002-0.0020.0000.0000.0000.000
74A75PHE0-0.013-0.03112.1820.0160.0160.0000.0000.0000.000
75A76LYS10.8530.90212.7360.1260.1260.0000.0000.0000.000
76A77PHE00.0140.00111.7600.0490.0490.0000.0000.0000.000
77A78PRO00.013-0.00415.418-0.013-0.0130.0000.0000.0000.000
78A79ASP-1-0.795-0.85513.420-0.502-0.5020.0000.0000.0000.000
79A80GLY00.0100.01015.140-0.031-0.0310.0000.0000.0000.000
80A81SER0-0.038-0.0309.592-0.002-0.0020.0000.0000.0000.000
81A82ILE0-0.078-0.0419.9210.0890.0890.0000.0000.0000.000
82A83LEU0-0.007-0.0076.293-0.109-0.1090.0000.0000.0000.000
83A84SER00.017-0.0047.6340.1050.1050.0000.0000.0000.000
84A85PRO0-0.0420.0058.5660.0840.0840.0000.0000.0000.000
85A86ASP-1-0.830-0.93910.1430.8290.8290.0000.0000.0000.000
86A87ALA0-0.037-0.02612.084-0.018-0.0180.0000.0000.0000.000
87A88ALA00.0200.01314.912-0.024-0.0240.0000.0000.0000.000
88A89PHE0-0.006-0.00116.9760.0090.0090.0000.0000.0000.000
89A90VAL00.0210.01119.847-0.019-0.0190.0000.0000.0000.000
90A91GLU-1-0.835-0.90622.1870.0010.0010.0000.0000.0000.000
91A92ARG10.9220.93925.867-0.031-0.0310.0000.0000.0000.000
92A93GLY0-0.0220.00128.332-0.003-0.0030.0000.0000.0000.000
93A94ALA00.006-0.00424.296-0.003-0.0030.0000.0000.0000.000
94A95TRP00.0440.01421.282-0.007-0.0070.0000.0000.0000.000
95A96GLU-1-0.860-0.93425.507-0.003-0.0030.0000.0000.0000.000
96A97ALA0-0.072-0.02427.508-0.001-0.0010.0000.0000.0000.000
97A98LEU0-0.0240.01422.340-0.007-0.0070.0000.0000.0000.000
98A99SER0-0.034-0.05226.6720.0100.0100.0000.0000.0000.000
99A100GLU-1-0.924-0.98026.536-0.012-0.0120.0000.0000.0000.000
100A101ALA00.013-0.00225.9870.0030.0030.0000.0000.0000.000
101A102GLU-1-0.876-0.91122.845-0.080-0.0800.0000.0000.0000.000
102A103ARG10.7280.85321.6150.0100.0100.0000.0000.0000.000
103A104GLU-1-0.922-0.95321.8530.0180.0180.0000.0000.0000.000
104A105GLY0-0.0330.00419.9160.0040.0040.0000.0000.0000.000
105A106PHE0-0.043-0.03213.474-0.002-0.0020.0000.0000.0000.000
106A107PRO00.0320.02116.930-0.020-0.0200.0000.0000.0000.000
107A108PRO0-0.035-0.00517.519-0.023-0.0230.0000.0000.0000.000
108A109LEU0-0.013-0.00918.0120.0130.0130.0000.0000.0000.000
109A110ALA00.0200.01216.719-0.010-0.0100.0000.0000.0000.000
110A111PRO0-0.039-0.00915.6240.0160.0160.0000.0000.0000.000
111A112LYS10.8480.91518.366-0.011-0.0110.0000.0000.0000.000
112A113ALA0-0.036-0.02818.526-0.005-0.0050.0000.0000.0000.000
113A114VAL00.0250.02412.8920.0080.0080.0000.0000.0000.000
114A115PHE0-0.015-0.02813.750-0.003-0.0030.0000.0000.0000.000
115A116GLU-1-0.740-0.8477.2960.2150.2150.0000.0000.0000.000
116A117VAL0-0.050-0.03210.012-0.054-0.0540.0000.0000.0000.000
117A118ARG10.8300.9048.121-1.109-1.1090.0000.0000.0000.000
118A119SER00.0240.0096.651-0.127-0.1270.0000.0000.0000.000
119A120ALA0-0.007-0.0218.8520.2120.2120.0000.0000.0000.000
120A121SER0-0.028-0.0155.016-0.670-0.6700.0000.0000.0000.000
121A122GLN00.0260.0243.006-0.9300.2990.225-0.448-1.006-0.004
122A123ASP-1-0.814-0.9015.252-0.837-0.8370.0000.0000.0000.000
123A124PRO0-0.018-0.0356.764-0.008-0.0080.0000.0000.0000.000
124A125GLU-1-0.788-0.8789.013-0.139-0.1390.0000.0000.0000.000
125A126GLU-1-0.933-0.9503.164-6.392-4.4870.123-1.051-0.977-0.009
126A127LEU0-0.007-0.0014.969-0.317-0.3170.0000.0000.0000.000
127A128ARG10.7480.8316.637-0.158-0.1580.0000.0000.0000.000
128A129ALA0-0.020-0.0037.444-0.020-0.0200.0000.0000.0000.000
129A130LYS10.8360.9044.8870.4520.4520.0000.0000.0000.000
130A131MET0-0.0130.0067.8410.0790.0790.0000.0000.0000.000
131A132GLY00.0040.00711.2930.0310.0310.0000.0000.0000.000
132A133ILE0-0.041-0.0178.0480.0320.0320.0000.0000.0000.000
133A134TYR00.042-0.0118.7320.0040.0040.0000.0000.0000.000
134A135LEU0-0.020-0.01413.1130.0320.0320.0000.0000.0000.000
135A136ARG10.7790.90612.9120.5670.5670.0000.0000.0000.000
136A137ASN0-0.072-0.06313.5350.0320.0320.0000.0000.0000.000
137A138GLY00.0060.00716.7450.0170.0170.0000.0000.0000.000
138A139VAL0-0.0430.00814.7680.0230.0230.0000.0000.0000.000
139A140LEU0-0.043-0.03917.985-0.001-0.0010.0000.0000.0000.000
140A141LEU0-0.043-0.03119.0450.0090.0090.0000.0000.0000.000
141A142GLY00.0550.04315.059-0.003-0.0030.0000.0000.0000.000
142A143VAL0-0.061-0.03214.8830.0040.0040.0000.0000.0000.000
143A144LEU00.0680.0399.8000.0280.0280.0000.0000.0000.000
144A145VAL0-0.005-0.01112.641-0.035-0.0350.0000.0000.0000.000
145A146ASP-1-0.743-0.86712.2970.8810.8810.0000.0000.0000.000
146A147PRO0-0.034-0.03212.756-0.097-0.0970.0000.0000.0000.000
147A148TYR0-0.055-0.03511.963-0.022-0.0220.0000.0000.0000.000
148A149ALA0-0.0140.00515.920-0.059-0.0590.0000.0000.0000.000
149A150ARG10.8790.94717.531-0.381-0.3810.0000.0000.0000.000
150A151ALA00.0050.00617.311-0.052-0.0520.0000.0000.0000.000
151A152VAL0-0.013-0.00716.4310.0510.0510.0000.0000.0000.000
152A153GLU-1-0.839-0.91414.9860.0820.0820.0000.0000.0000.000
153A154VAL0-0.031-0.02116.0300.0060.0060.0000.0000.0000.000
154A155PHE00.0390.01313.541-0.026-0.0260.0000.0000.0000.000
155A156ARG10.8670.91117.794-0.029-0.0290.0000.0000.0000.000
156A157PRO00.0650.03320.376-0.009-0.0090.0000.0000.0000.000
157A158GLY0-0.020-0.00721.5450.0120.0120.0000.0000.0000.000
158A159LYS10.8770.94322.3030.0290.0290.0000.0000.0000.000
159A160PRO00.0110.01221.422-0.009-0.0090.0000.0000.0000.000
160A161PRO0-0.0010.01817.5270.0080.0080.0000.0000.0000.000
161A162LEU0-0.007-0.01219.5480.0060.0060.0000.0000.0000.000
162A163ARG10.8610.93016.703-0.203-0.2030.0000.0000.0000.000
163A164LEU0-0.036-0.01520.029-0.013-0.0130.0000.0000.0000.000
164A165GLU-1-0.813-0.91220.6750.2220.2220.0000.0000.0000.000
165A166GLY0-0.0100.00222.435-0.018-0.0180.0000.0000.0000.000
166A167VAL0-0.0230.00223.026-0.015-0.0150.0000.0000.0000.000
167A168GLU-1-0.935-0.97324.2140.1600.1600.0000.0000.0000.000
168A169ARG10.9470.95225.242-0.104-0.1040.0000.0000.0000.000
169A170VAL00.0170.01420.920-0.005-0.0050.0000.0000.0000.000
170A171SER0-0.047-0.01824.1700.0010.0010.0000.0000.0000.000
171A172LEU00.011-0.00320.5520.0000.0000.0000.0000.0000.000
172A173ASP-1-0.817-0.85624.2650.0470.0470.0000.0000.0000.000
173A174PRO0-0.026-0.04026.8780.0000.0000.0000.0000.0000.000
174A175GLU-1-0.814-0.91023.3340.0100.0100.0000.0000.0000.000
175A176LEU0-0.0010.01521.146-0.003-0.0030.0000.0000.0000.000
176A177PRO0-0.022-0.01825.7660.0080.0080.0000.0000.0000.000
177A178GLY00.011-0.01129.4950.0030.0030.0000.0000.0000.000
178A179PHE0-0.0160.02221.3460.0090.0090.0000.0000.0000.000
179A180ALA0-0.024-0.03025.659-0.003-0.0030.0000.0000.0000.000
180A181LEU0-0.0130.01518.4300.0060.0060.0000.0000.0000.000
181A182SER0-0.023-0.02423.0530.0000.0000.0000.0000.0000.000
182A183LEU00.0770.01219.3950.0200.0200.0000.0000.0000.000
183A184PRO00.0380.03321.1360.0310.0310.0000.0000.0000.000
184A185PRO0-0.042-0.02122.6400.0240.0240.0000.0000.0000.000
185A186LEU00.003-0.00117.1940.0190.0190.0000.0000.0000.000
186A187TRP00.0060.03317.5360.1180.1180.0000.0000.0000.000