Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 1488Z

Calculation Name: 1WYZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WYZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A031

Base Structure: X-ray

Registration Date: 2023-06-19

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 OptH
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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2612187.838778
FMO2-HF: Nuclear repulsion 2523530.736886
FMO2-HF: Total energy -88657.101892
FMO2-MP2: Total energy -88917.260712


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:GLU)


Summations of interaction energy for fragment #1(A:2:GLU)
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.
-18.268-15.0438.872-6.783-5.314-0.007
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.961 / q_NPA : -0.983
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].
3A4ALA0-0.038-0.0473.804-5.341-3.7420.000-0.666-0.9320.003
4A5LEU00.0280.0155.5961.1871.1870.0000.0000.0000.000
5A6TYR00.0400.0071.612-7.906-8.5468.816-5.194-2.981-0.011
6A7LEU0-0.046-0.0318.139-1.810-1.8100.0000.0000.0000.000
7A8LEU0-0.007-0.0239.0520.4490.4490.0000.0000.0000.000
8A9PRO0-0.0210.01112.815-1.273-1.2730.0000.0000.0000.000
9A10VAL00.0320.02015.9530.7430.7430.0000.0000.0000.000
10A11THR0-0.036-0.03218.5530.0120.0120.0000.0000.0000.000
11A12LEU0-0.021-0.01821.771-0.243-0.2430.0000.0000.0000.000
12A13GLY00.020-0.00924.905-0.500-0.5000.0000.0000.0000.000
13A14ASP-1-1.004-0.97925.58311.57311.5730.0000.0000.0000.000
14A15THR00.0000.01024.649-0.204-0.2040.0000.0000.0000.000
15A16PRO0-0.009-0.00423.8440.4110.4110.0000.0000.0000.000
16A17LEU00.0650.01716.9840.2000.2000.0000.0000.0000.000
17A18GLU-1-0.909-0.95719.11515.59415.5940.0000.0000.0000.000
18A19GLN0-0.086-0.04620.140-0.163-0.1630.0000.0000.0000.000
19A20VAL0-0.052-0.04020.431-0.272-0.2720.0000.0000.0000.000
20A21LEU0-0.0100.00015.6280.4740.4740.0000.0000.0000.000
21A22PRO0-0.0090.00413.480-0.162-0.1620.0000.0000.0000.000
22A23SER00.0610.01713.6070.6980.6980.0000.0000.0000.000
23A24TYR0-0.0040.0095.3580.2550.2550.0000.0000.0000.000
24A25ASN00.035-0.0058.7005.3315.3310.0000.0000.0000.000
25A26THR00.0180.0069.2851.5981.5980.0000.0000.0000.000
26A27GLU-1-0.985-0.9896.93636.01936.0190.0000.0000.0000.000
27A28ILE00.0300.0234.2512.5102.9840.000-0.074-0.4000.000
28A29ILE0-0.040-0.0205.1490.6270.644-0.001-0.001-0.0150.000
29A30ARG10.8580.9057.747-28.250-28.2500.0000.0000.0000.000
30A31GLY0-0.0240.0124.399-1.709-1.520-0.001-0.018-0.1700.000
31A32ILE0-0.091-0.0345.443-3.359-3.3590.0000.0000.0000.000
32A33ARG10.9670.9827.189-30.379-30.3790.0000.0000.0000.000
33A34HIS00.0220.02010.278-1.211-1.2110.0000.0000.0000.000
34A35PHE00.0470.00910.4701.5041.5040.0000.0000.0000.000
35A36ILE0-0.0250.00313.559-1.510-1.5100.0000.0000.0000.000
36A37VAL0-0.008-0.02016.3110.4130.4130.0000.0000.0000.000
37A38GLU-1-0.805-0.90318.70913.69213.6920.0000.0000.0000.000
38A39ASP-1-0.809-0.93121.38611.75111.7510.0000.0000.0000.000
39A40VAL00.0060.01320.3080.4370.4370.0000.0000.0000.000
40A41ARG10.8990.96121.501-11.166-11.1660.0000.0000.0000.000
41A42SER00.0030.00322.6670.4160.4160.0000.0000.0000.000
42A43ALA00.0900.05617.7130.3870.3870.0000.0000.0000.000
43A44ARG10.9110.96218.037-14.004-14.0040.0000.0000.0000.000
44A45ARG10.8690.92219.158-12.022-12.0220.0000.0000.0000.000
45A46PHE00.0710.03514.235-0.016-0.0160.0000.0000.0000.000
46A47LEU00.0370.01312.7620.2750.2750.0000.0000.0000.000
47A48LYS10.8070.92516.036-16.470-16.4700.0000.0000.0000.000
48A49LYN0-0.0040.01218.788-0.102-0.1020.0000.0000.0000.000
49A50VAL0-0.0250.00812.6940.1210.1210.0000.0000.0000.000
50A51ASP-1-0.808-0.89713.33722.71622.7160.0000.0000.0000.000
51A52ARG10.8940.92515.686-15.586-15.5860.0000.0000.0000.000
52A53GLU-1-0.911-0.95815.06215.98515.9850.0000.0000.0000.000
53A54ILE0-0.044-0.00811.2470.3650.3650.0000.0000.0000.000
54A55ASP-1-0.826-0.92014.72115.32315.3230.0000.0000.0000.000
55A56ILE0-0.077-0.04116.3490.3660.3660.0000.0000.0000.000
56A57ASP-1-0.934-0.95818.04813.75913.7590.0000.0000.0000.000
57A58SER0-0.0170.00514.247-0.037-0.0370.0000.0000.0000.000
58A59LEU0-0.080-0.05915.9960.7260.7260.0000.0000.0000.000
59A60THR0-0.014-0.00514.966-0.277-0.2770.0000.0000.0000.000
60A61PHE0-0.030-0.01516.4460.3510.3510.0000.0000.0000.000
61A62TYR00.0190.00915.237-0.800-0.8000.0000.0000.0000.000
62A63PRO0-0.025-0.02419.3910.3400.3400.0000.0000.0000.000
63A64LEU00.0010.01619.878-0.204-0.2040.0000.0000.0000.000
64A65ASN00.0300.00622.604-0.296-0.2960.0000.0000.0000.000
65A66LYS10.9820.98224.730-10.239-10.2390.0000.0000.0000.000
66A67HIS0-0.025-0.03026.752-0.381-0.3810.0000.0000.0000.000
67A68THR0-0.0370.00523.106-0.202-0.2020.0000.0000.0000.000
68A69SER00.0610.03525.7900.0380.0380.0000.0000.0000.000
69A70PRO00.014-0.04723.2960.5220.5220.0000.0000.0000.000
70A71GLU-1-0.917-0.97422.70612.56512.5650.0000.0000.0000.000
71A72ASP-1-0.835-0.93223.18612.15612.1560.0000.0000.0000.000
72A73ILE0-0.029-0.00418.7130.6560.6560.0000.0000.0000.000
73A74SER00.0170.01218.7281.2421.2420.0000.0000.0000.000
74A75GLY0-0.030-0.02918.3270.6610.6610.0000.0000.0000.000
75A76TYR0-0.029-0.01317.4710.5190.5190.0000.0000.0000.000
76A77LEU00.0200.00214.0771.2351.2350.0000.0000.0000.000
77A78LYS10.9390.98913.593-13.127-13.1270.0000.0000.0000.000
78A79PRO00.0200.00311.8610.3680.3680.0000.0000.0000.000
79A80LEU00.0360.0328.0571.1091.1090.0000.0000.0000.000
80A81ALA0-0.082-0.04110.1421.0051.0050.0000.0000.0000.000
81A82GLY0-0.033-0.01212.223-0.526-0.5260.0000.0000.0000.000
82A83GLY0-0.0190.0008.363-0.273-0.2730.0000.0000.0000.000
83A84ALA0-0.056-0.0246.5693.6843.6840.0000.0000.0000.000
84A85SER00.006-0.0152.996-4.451-3.0520.060-0.819-0.6410.001
85A86MET0-0.038-0.0035.726-2.694-2.6940.0000.0000.0000.000
86A87GLY00.0230.0188.6842.1372.1370.0000.0000.0000.000
87A88VAL0-0.046-0.02010.548-1.995-1.9950.0000.0000.0000.000
88A89ILE0-0.004-0.00613.6560.7550.7550.0000.0000.0000.000
89A90SER0-0.003-0.01116.294-0.392-0.3920.0000.0000.0000.000
90A91GLU-1-0.974-0.98119.87313.26713.2670.0000.0000.0000.000
91A99ASP-1-0.873-0.94722.47512.37312.3730.0000.0000.0000.000
92A100PRO0-0.027-0.00622.1130.1190.1190.0000.0000.0000.000
93A101GLY00.0630.02518.3280.3460.3460.0000.0000.0000.000
94A102ALA0-0.034-0.02517.5050.7780.7780.0000.0000.0000.000
95A103ASP-1-0.907-0.95919.10012.84912.8490.0000.0000.0000.000
96A104VAL0-0.007-0.00515.0890.0780.0780.0000.0000.0000.000
97A105VAL00.0070.01013.7120.6470.6470.0000.0000.0000.000
98A106ALA0-0.0080.00615.4920.1650.1650.0000.0000.0000.000
99A107ILE0-0.0460.02418.062-0.300-0.3000.0000.0000.0000.000
100A108ALA00.0390.00512.705-0.032-0.0320.0000.0000.0000.000
101A109GLN00.002-0.00412.8700.2590.2590.0000.0000.0000.000
102A110ARG10.9070.97515.199-12.631-12.6310.0000.0000.0000.000
103A111GLN0-0.068-0.03115.6110.1110.1110.0000.0000.0000.000
104A112LYS10.9170.96312.419-18.726-18.7260.0000.0000.0000.000
105A113LEU00.0200.01110.5291.0871.0870.0000.0000.0000.000
106A114LYS10.9300.9714.337-34.679-34.580-0.001-0.005-0.0930.000
107A115VAL00.0370.0217.7221.2201.2200.0000.0000.0000.000
108A116ILE0-0.051-0.0284.343-0.840-0.752-0.001-0.006-0.0820.000
109A117PRO00.0020.0137.6091.1211.1210.0000.0000.0000.000
110A118LEU00.0240.0167.4980.6670.6670.0000.0000.0000.000
111A119VAL0-0.011-0.01511.350-1.617-1.6170.0000.0000.0000.000
112A120GLY00.0690.02214.7570.8120.8120.0000.0000.0000.000
113A121PRO0-0.0250.02017.522-0.603-0.6030.0000.0000.0000.000
114A122SER00.0800.03121.078-0.176-0.1760.0000.0000.0000.000
115A123SER00.0490.01322.734-0.255-0.2550.0000.0000.0000.000
116A124ILE00.0230.01224.669-0.490-0.4900.0000.0000.0000.000
117A125ILE00.041-0.00221.409-0.422-0.4220.0000.0000.0000.000
118A126LEU00.0170.01424.239-0.303-0.3030.0000.0000.0000.000
119A127SER0-0.003-0.00326.838-0.509-0.5090.0000.0000.0000.000
120A128VAL0-0.027-0.00728.180-0.366-0.3660.0000.0000.0000.000
121A129MET0-0.042-0.02325.510-0.164-0.1640.0000.0000.0000.000
122A130ALA00.0350.02829.776-0.247-0.2470.0000.0000.0000.000
123A131SER0-0.055-0.02232.609-0.379-0.3790.0000.0000.0000.000
124A132GLY00.0250.01733.715-0.322-0.3220.0000.0000.0000.000
125A133PHE0-0.065-0.05034.138-0.328-0.3280.0000.0000.0000.000
126A134ASN0-0.018-0.00632.5940.4280.4280.0000.0000.0000.000
127A135GLY00.1110.03929.4760.1000.1000.0000.0000.0000.000
128A136GLN0-0.069-0.02527.9980.6400.6400.0000.0000.0000.000
129A137SER00.0230.00629.6450.0600.0600.0000.0000.0000.000
130A138PHE0-0.008-0.01624.903-0.355-0.3550.0000.0000.0000.000
131A139ALA00.0220.02129.3370.2320.2320.0000.0000.0000.000
132A140PHE00.0320.02527.088-0.277-0.2770.0000.0000.0000.000
133A141HIS0-0.051-0.04929.5940.0240.0240.0000.0000.0000.000
134A142GLY00.0390.02630.432-0.090-0.0900.0000.0000.0000.000
135A143TYR00.0220.02530.999-0.285-0.2850.0000.0000.0000.000
136A144LEU0-0.027-0.02134.382-0.089-0.0890.0000.0000.0000.000
137A145PRO0-0.012-0.01837.6140.0040.0040.0000.0000.0000.000
138A146ILE00.0500.01739.451-0.123-0.1230.0000.0000.0000.000
139A147GLU-1-0.954-0.96042.1846.6166.6160.0000.0000.0000.000
140A148PRO00.0610.00045.5380.0550.0550.0000.0000.0000.000
141A149GLY00.0350.03847.698-0.046-0.0460.0000.0000.0000.000
142A150GLU-1-0.850-0.93643.3226.9386.9380.0000.0000.0000.000
143A151ARG10.7730.87441.495-7.316-7.3160.0000.0000.0000.000
144A152ALA0-0.0030.00643.5770.0910.0910.0000.0000.0000.000
145A153LYS10.9500.98345.003-6.602-6.6020.0000.0000.0000.000
146A154LYS10.8850.97035.830-8.273-8.2730.0000.0000.0000.000
147A155LEU00.0120.00940.6320.0980.0980.0000.0000.0000.000
148A156LYS10.9480.98242.293-6.351-6.3510.0000.0000.0000.000
149A157THR0-0.014-0.00840.543-0.045-0.0450.0000.0000.0000.000
150A158LEU00.012-0.00336.5830.0790.0790.0000.0000.0000.000
151A159GLU-1-0.718-0.80939.5386.8826.8820.0000.0000.0000.000
152A160GLN0-0.048-0.03942.0460.0330.0330.0000.0000.0000.000
153A161ARG11.0141.00435.092-8.340-8.3400.0000.0000.0000.000
154A162VAL0-0.0420.01738.5060.0920.0920.0000.0000.0000.000
155A163TYR0-0.116-0.08639.5730.0360.0360.0000.0000.0000.000
156A164ALA0-0.041-0.00941.035-0.065-0.0650.0000.0000.0000.000
157A165GLU-1-0.901-0.95535.5418.3018.3010.0000.0000.0000.000
158A166SER0-0.080-0.03136.5810.1190.1190.0000.0000.0000.000
159A167GLN00.0220.02532.1030.1320.1320.0000.0000.0000.000
160A168THR0-0.031-0.01132.444-0.315-0.3150.0000.0000.0000.000
161A169GLN0-0.051-0.03733.1820.2430.2430.0000.0000.0000.000
162A170LEU00.005-0.00529.091-0.135-0.1350.0000.0000.0000.000
163A171PHE0-0.007-0.00832.4900.0370.0370.0000.0000.0000.000
164A172ILE00.0300.00729.862-0.033-0.0330.0000.0000.0000.000
165A173GLU-1-0.774-0.91633.5017.9757.9750.0000.0000.0000.000
166A174THR0-0.0410.00535.4730.2030.2030.0000.0000.0000.000
167A175PRO00.0510.00535.038-0.236-0.2360.0000.0000.0000.000
168A176TYR00.0320.00337.679-0.160-0.1600.0000.0000.0000.000
169A177ARG10.9010.95840.176-7.486-7.4860.0000.0000.0000.000
170A178ASN0-0.0010.00437.366-0.100-0.1000.0000.0000.0000.000
171A179HIS00.0790.03241.120-0.171-0.1710.0000.0000.0000.000
172A180LYS10.8930.95644.564-6.779-6.7790.0000.0000.0000.000
173A181MET0-0.023-0.00639.665-0.069-0.0690.0000.0000.0000.000
174A182ILE00.0250.02542.399-0.060-0.0600.0000.0000.0000.000
175A183GLU-1-0.869-0.94244.2546.1876.1870.0000.0000.0000.000
176A184ASP-1-0.821-0.91444.7966.7476.7470.0000.0000.0000.000
177A185ILE0-0.039-0.00740.950-0.082-0.0820.0000.0000.0000.000
178A186LEU0-0.040-0.03244.889-0.095-0.0950.0000.0000.0000.000
179A187GLN0-0.0320.00748.027-0.198-0.1980.0000.0000.0000.000
180A188ASN0-0.077-0.06546.784-0.200-0.2000.0000.0000.0000.000
181A189CYS0-0.078-0.02643.4750.0050.0050.0000.0000.0000.000
182A190ARG10.8680.93445.367-6.791-6.7910.0000.0000.0000.000
183A191PRO0-0.005-0.01747.9670.0940.0940.0000.0000.0000.000
184A192GLN00.042-0.00648.4680.1580.1580.0000.0000.0000.000
185A193THR0-0.062-0.04642.7860.0610.0610.0000.0000.0000.000
186A194LYS10.9200.96541.248-7.456-7.4560.0000.0000.0000.000
187A195LEU00.0300.01539.2930.1230.1230.0000.0000.0000.000
188A196CYS0-0.0580.00536.060-0.016-0.0160.0000.0000.0000.000
189A197ILE00.0050.00737.1440.1210.1210.0000.0000.0000.000
190A198ALA00.0660.02232.882-0.015-0.0150.0000.0000.0000.000
191A199ALA0-0.014-0.03433.8330.1700.1700.0000.0000.0000.000
192A200ASN00.0280.02032.1980.1580.1580.0000.0000.0000.000
193A201ILE00.0290.02127.9820.0760.0760.0000.0000.0000.000
194A202THR0-0.046-0.02525.3700.5680.5680.0000.0000.0000.000
195A203CYS0-0.004-0.00228.3250.2060.2060.0000.0000.0000.000
196A204GLU-1-0.876-0.93830.3199.9519.9510.0000.0000.0000.000
197A205GLY0-0.0340.01932.983-0.307-0.3070.0000.0000.0000.000
198A206GLU-1-0.955-1.01331.3469.9709.9700.0000.0000.0000.000
199A207PHE0-0.027-0.00434.715-0.341-0.3410.0000.0000.0000.000
200A208ILE00.0230.00531.9840.1180.1180.0000.0000.0000.000
201A209GLN00.0050.02136.328-0.145-0.1450.0000.0000.0000.000
202A210THR0-0.013-0.03237.7920.0310.0310.0000.0000.0000.000
203A211ARG10.8840.94340.187-7.179-7.1790.0000.0000.0000.000
204A212THR00.0090.03143.5870.0960.0960.0000.0000.0000.000
205A213VAL00.0770.04345.126-0.030-0.0300.0000.0000.0000.000
206A214LYS10.9150.94247.021-5.924-5.9240.0000.0000.0000.000
207A215ASP-1-0.910-0.98048.1436.2636.2630.0000.0000.0000.000
208A216TRP0-0.047-0.03041.416-0.037-0.0370.0000.0000.0000.000
209A217LYS10.8620.95747.665-6.185-6.1850.0000.0000.0000.000
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211A219HIS0-0.016-0.02148.4330.1910.1910.0000.0000.0000.000
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