Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: XQVRY

Calculation Name: 4WFV-A-Xray23

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4WFV

Chain ID: A

ChEMBL ID:

UniProt ID: Q28133

Base Structure: X-ray

Registration Date: 2018-06-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 210
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1752938.748954
FMO2-HF: Nuclear repulsion 1686472.750984
FMO2-HF: Total energy -66465.99797
FMO2-MP2: Total energy -66656.875339


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:3:ACE)


Summations of interaction energy for fragment #1(A:3: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.
0.8483.4290.097-1.158-1.519-0.004
Interaction energy analysis for fragmet #1(A:3:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.070 / q_NPA : 0.023
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].
3A5ALA0-0.005-0.0093.6090.5011.2760.007-0.301-0.4800.001
4A6GLU-1-0.948-0.9693.105-0.8160.8330.091-0.822-0.918-0.005
5A7ILE0-0.0440.0034.7140.6640.821-0.001-0.035-0.1210.000
6A8ASP-1-0.768-0.8326.563-0.308-0.3080.0000.0000.0000.000
7A9PRO00.029-0.00210.2160.1070.1070.0000.0000.0000.000
8A10SER0-0.035-0.03012.2550.1230.1230.0000.0000.0000.000
9A11LYS10.8360.92711.7250.4730.4730.0000.0000.0000.000
10A12ILE00.0210.02211.4770.0350.0350.0000.0000.0000.000
11A13PRO0-0.0180.01015.1740.0430.0430.0000.0000.0000.000
12A14GLY00.0210.00618.962-0.005-0.0050.0000.0000.0000.000
13A15GLU-1-0.934-0.98521.360-0.116-0.1160.0000.0000.0000.000
14A16TRP0-0.108-0.04015.7530.0220.0220.0000.0000.0000.000
15A17ARG10.8870.93921.5180.0880.0880.0000.0000.0000.000
16A18ILE00.0070.01520.227-0.009-0.0090.0000.0000.0000.000
17A19ILE0-0.074-0.04120.5940.0100.0100.0000.0000.0000.000
18A20TYR0-0.022-0.02319.2610.0150.0150.0000.0000.0000.000
19A21ALA00.0610.04419.404-0.014-0.0140.0000.0000.0000.000
20A22ALA00.0180.01718.2130.0090.0090.0000.0000.0000.000
21A23ALA00.0520.01619.126-0.005-0.0050.0000.0000.0000.000
22A24ASP-1-0.751-0.86820.8190.0640.0640.0000.0000.0000.000
23A25ASN0-0.041-0.02322.2480.0030.0030.0000.0000.0000.000
24A26LYS10.9690.98425.258-0.034-0.0340.0000.0000.0000.000
25A27ASP-1-0.774-0.85226.3660.0080.0080.0000.0000.0000.000
26A28LYS10.8130.87524.849-0.001-0.0010.0000.0000.0000.000
27A29ILE00.0010.01522.266-0.006-0.0060.0000.0000.0000.000
28A30VAL0-0.0130.01725.722-0.002-0.0020.0000.0000.0000.000
29A31GLU-1-0.829-0.89228.930-0.015-0.0150.0000.0000.0000.000
30A32GLY0-0.026-0.00131.2770.0020.0020.0000.0000.0000.000
31A33GLY00.0220.02629.0960.0000.0000.0000.0000.0000.000
32A34PRO0-0.017-0.00327.605-0.004-0.0040.0000.0000.0000.000
33A35LEU00.004-0.00222.372-0.006-0.0060.0000.0000.0000.000
34A36ARG10.7560.86523.4960.0120.0120.0000.0000.0000.000
35A37ASN00.0280.01122.7910.0060.0060.0000.0000.0000.000
36A38TYR0-0.021-0.02823.791-0.003-0.0030.0000.0000.0000.000
37A39TYR0-0.041-0.04418.550-0.009-0.0090.0000.0000.0000.000
38A40ARG10.7220.83623.6460.0730.0730.0000.0000.0000.000
39A41ARG10.8680.92123.2540.1260.1260.0000.0000.0000.000
40A42ILE00.0070.01917.2980.0040.0040.0000.0000.0000.000
41A43GLU-1-0.835-0.88120.924-0.181-0.1810.0000.0000.0000.000
42A48CYS0-0.064-0.03015.270-0.058-0.0580.0000.0000.0000.000
43A45ILE0-0.009-0.00619.9420.0220.0220.0000.0000.0000.000
44A46ASN0-0.055-0.04720.779-0.009-0.0090.0000.0000.0000.000
45A47ASP-1-0.831-0.90218.231-0.262-0.2620.0000.0000.0000.000
46A49GLU-1-0.811-0.87716.351-0.274-0.2740.0000.0000.0000.000
47A50SER0-0.036-0.04318.5320.0290.0290.0000.0000.0000.000
48A51LEU0-0.0020.01115.074-0.017-0.0170.0000.0000.0000.000
49A52SER0-0.0130.00219.6270.0250.0250.0000.0000.0000.000
50A53ILE00.0400.01218.591-0.012-0.0120.0000.0000.0000.000
51A54THR00.001-0.00922.6180.0110.0110.0000.0000.0000.000
52A55PHE0-0.014-0.01524.340-0.004-0.0040.0000.0000.0000.000
53A56TYR00.0330.00826.4260.0060.0060.0000.0000.0000.000
54A57LEU00.0220.03128.1280.0000.0000.0000.0000.0000.000
55A58LYS10.8310.89030.2290.0270.0270.0000.0000.0000.000
56A59ASP-1-0.864-0.89433.232-0.022-0.0220.0000.0000.0000.000
57A60GLN00.017-0.00436.0180.0010.0010.0000.0000.0000.000
58A61GLY0-0.034-0.01036.9330.0010.0010.0000.0000.0000.000
59A62THR0-0.035-0.01337.890-0.001-0.0010.0000.0000.0000.000
60A154CYS0-0.054-0.00631.3430.0020.0020.0000.0000.0000.000
61A64LEU00.004-0.00133.433-0.001-0.0010.0000.0000.0000.000
62A65LEU0-0.018-0.00529.902-0.002-0.0020.0000.0000.0000.000
63A66LEU0-0.005-0.00228.6910.0020.0020.0000.0000.0000.000
64A67THR00.002-0.00626.278-0.007-0.0070.0000.0000.0000.000
65A68GLU-1-0.858-0.89124.083-0.071-0.0710.0000.0000.0000.000
66A69VAL0-0.045-0.02923.236-0.014-0.0140.0000.0000.0000.000
67A70ALA0-0.0080.01318.7860.0090.0090.0000.0000.0000.000
68A71LYS10.8710.93519.9930.1540.1540.0000.0000.0000.000
69A72ARG10.8650.93312.8590.4430.4430.0000.0000.0000.000
70A73GLN0-0.103-0.05915.1140.0320.0320.0000.0000.0000.000
71A74GLU-1-0.889-0.96612.911-0.180-0.1800.0000.0000.0000.000
72A75GLY0-0.0170.0099.814-0.028-0.0280.0000.0000.0000.000
73A76TYR0-0.077-0.0607.3460.1900.1900.0000.0000.0000.000
74A77VAL00.0270.01710.1780.0480.0480.0000.0000.0000.000
75A78TYR0-0.061-0.04212.333-0.023-0.0230.0000.0000.0000.000
76A79VAL00.0320.01715.8920.0240.0240.0000.0000.0000.000
77A80LEU0-0.004-0.01419.166-0.011-0.0110.0000.0000.0000.000
78A81GLU-1-0.825-0.84522.081-0.040-0.0400.0000.0000.0000.000
79A82PHE00.0100.01724.294-0.003-0.0030.0000.0000.0000.000
80A83TYR00.0040.00225.4220.0060.0060.0000.0000.0000.000
81A84GLY00.0510.03726.5460.0060.0060.0000.0000.0000.000
82A85THR0-0.038-0.07122.354-0.005-0.0050.0000.0000.0000.000
83A86ASN0-0.053-0.02619.6000.0170.0170.0000.0000.0000.000
84A87THR00.0230.02015.286-0.005-0.0050.0000.0000.0000.000
85A88LEU0-0.002-0.00313.8150.0170.0170.0000.0000.0000.000
86A89GLU-1-0.779-0.8787.212-0.237-0.2370.0000.0000.0000.000
87A90VAL0-0.009-0.0019.1220.0690.0690.0000.0000.0000.000
88A91ILE0-0.031-0.0186.319-0.250-0.2500.0000.0000.0000.000
89A92HIS00.0110.0015.8860.0300.0300.0000.0000.0000.000
90A93VAL00.0020.0068.0260.0800.0800.0000.0000.0000.000
91A94SER0-0.0080.0089.854-0.070-0.0700.0000.0000.0000.000
92A95GLU-1-0.820-0.93212.464-0.246-0.2460.0000.0000.0000.000
93A96ASN0-0.014-0.01315.8340.0140.0140.0000.0000.0000.000
94A97MET0-0.045-0.00513.1710.0240.0240.0000.0000.0000.000
95A98LEU00.0150.01112.571-0.062-0.0620.0000.0000.0000.000
96A99VAL0-0.026-0.00810.5440.0620.0620.0000.0000.0000.000
97A100THR0-0.017-0.01410.811-0.070-0.0700.0000.0000.0000.000
98A101TYR0-0.041-0.05910.9120.0740.0740.0000.0000.0000.000
99A102VAL00.0200.00112.752-0.038-0.0380.0000.0000.0000.000
100A103GLU-1-0.849-0.87515.3460.0960.0960.0000.0000.0000.000
101A104ASN00.017-0.00117.863-0.007-0.0070.0000.0000.0000.000
102A105TYR0-0.034-0.02221.4840.0120.0120.0000.0000.0000.000
103A106ASP-1-0.729-0.83624.320-0.005-0.0050.0000.0000.0000.000
104A107GLY00.0040.00427.826-0.001-0.0010.0000.0000.0000.000
105A108GLU-1-1.011-0.97729.4850.0140.0140.0000.0000.0000.000
106A109ARG10.7720.83826.550-0.011-0.0110.0000.0000.0000.000
107A110ILE00.0200.00620.729-0.007-0.0070.0000.0000.0000.000
108A111THR0-0.036-0.01421.2960.0100.0100.0000.0000.0000.000
109A112LYS10.8360.93115.429-0.144-0.1440.0000.0000.0000.000
110A113MET0-0.011-0.01617.1870.0080.0080.0000.0000.0000.000
111A114THR0-0.021-0.03113.312-0.010-0.0100.0000.0000.0000.000
112A115GLU-1-0.795-0.87615.223-0.087-0.0870.0000.0000.0000.000
113A116GLY00.0200.00515.110-0.019-0.0190.0000.0000.0000.000
114A117LEU0-0.003-0.00116.1330.0150.0150.0000.0000.0000.000
115A118ALA00.025-0.00617.082-0.009-0.0090.0000.0000.0000.000
116A119LYS10.9671.01818.6570.1930.1930.0000.0000.0000.000
117A120GLY0-0.0200.00221.5650.0090.0090.0000.0000.0000.000
118A121THR00.031-0.00424.0540.0000.0000.0000.0000.0000.000
119A122SER0-0.019-0.02023.6590.0070.0070.0000.0000.0000.000
120A123PHE00.0400.03716.562-0.008-0.0080.0000.0000.0000.000
121A124THR00.0020.00619.3760.0150.0150.0000.0000.0000.000
122A125PRO00.026-0.01120.0350.0040.0040.0000.0000.0000.000
123A126GLU-1-0.882-0.92915.6480.0200.0200.0000.0000.0000.000
124A127GLU-1-0.782-0.88415.513-0.052-0.0520.0000.0000.0000.000
125A128LEU0-0.012-0.01215.6130.0070.0070.0000.0000.0000.000
126A129GLU-1-0.928-0.94414.7870.2110.2110.0000.0000.0000.000
127A130LYS10.9620.98111.3870.0220.0220.0000.0000.0000.000
128A131TYR0-0.037-0.02212.0900.0400.0400.0000.0000.0000.000
129A132GLN00.003-0.00713.8380.0020.0020.0000.0000.0000.000
130A133GLN00.0000.01311.081-0.050-0.0500.0000.0000.0000.000
131A134LEU0-0.011-0.0107.3620.0430.0430.0000.0000.0000.000
132A135ASN00.0220.03010.7330.0050.0050.0000.0000.0000.000
133A136SER0-0.017-0.02013.948-0.007-0.0070.0000.0000.0000.000
134A137GLU-1-0.908-0.9498.1040.8230.8230.0000.0000.0000.000
135A138ARG10.8270.9125.922-0.457-0.4570.0000.0000.0000.000
136A139GLY0-0.0130.00312.808-0.044-0.0440.0000.0000.0000.000
137A140VAL0-0.0200.00015.377-0.028-0.0280.0000.0000.0000.000
138A141PRO0-0.0170.00817.4180.0140.0140.0000.0000.0000.000
139A142ASN00.0640.00317.009-0.027-0.0270.0000.0000.0000.000
140A143GLU-1-0.918-0.96120.5450.0830.0830.0000.0000.0000.000
141A144ASN0-0.079-0.03522.779-0.011-0.0110.0000.0000.0000.000
142A145ILE0-0.0300.00319.260-0.008-0.0080.0000.0000.0000.000
143A146GLU-1-0.818-0.88522.6110.0050.0050.0000.0000.0000.000
144A147ASN0-0.035-0.03623.479-0.010-0.0100.0000.0000.0000.000
145A148LEU00.0700.02922.9890.0010.0010.0000.0000.0000.000
146A149ILE00.0140.01725.346-0.001-0.0010.0000.0000.0000.000
147A150LYS10.8790.94026.9780.0100.0100.0000.0000.0000.000
148A151THR0-0.0170.02529.3850.0020.0020.0000.0000.0000.000
149A152ASP-1-0.762-0.85127.891-0.053-0.0530.0000.0000.0000.000
150A153ASN0-0.029-0.01330.414-0.003-0.0030.0000.0000.0000.000
151A155PRO0-0.0030.00632.929-0.001-0.0010.0000.0000.0000.000
152A156PRO-1-0.890-0.93430.439-0.072-0.0720.0000.0000.0000.000
153A201HOH00.0180.02032.6840.0010.0010.0000.0000.0000.000
154A202HOH0-0.023-0.00830.5890.0000.0000.0000.0000.0000.000
155A203HOH0-0.028-0.02927.132-0.002-0.0020.0000.0000.0000.000
156A204HOH0-0.006-0.00131.8830.0000.0000.0000.0000.0000.000
157A205HOH0-0.044-0.04029.1950.0010.0010.0000.0000.0000.000
158A206HOH0-0.055-0.04112.4350.0220.0220.0000.0000.0000.000
159A207HOH00.004-0.00421.695-0.011-0.0110.0000.0000.0000.000
160A208HOH0-0.099-0.08433.6490.0000.0000.0000.0000.0000.000
161A209HOH0-0.069-0.04521.5350.0060.0060.0000.0000.0000.000
162A210HOH0-0.023-0.0167.0980.2100.2100.0000.0000.0000.000
163A211HOH0-0.031-0.02518.258-0.008-0.0080.0000.0000.0000.000
164A212HOH0-0.053-0.04914.824-0.006-0.0060.0000.0000.0000.000
165A213HOH0-0.023-0.02416.3510.0090.0090.0000.0000.0000.000
166A214HOH0-0.028-0.02929.243-0.002-0.0020.0000.0000.0000.000
167A215HOH0-0.043-0.0308.1580.1000.1000.0000.0000.0000.000
168A216HOH0-0.005-0.0067.779-0.037-0.0370.0000.0000.0000.000
169A217HOH0-0.044-0.03516.769-0.002-0.0020.0000.0000.0000.000
170A218HOH00.0210.02416.152-0.004-0.0040.0000.0000.0000.000
171A219HOH00.0280.02716.521-0.004-0.0040.0000.0000.0000.000
172A220HOH0-0.011-0.00830.177-0.001-0.0010.0000.0000.0000.000
173A221HOH0-0.031-0.02222.4600.0020.0020.0000.0000.0000.000
174A222HOH0-0.039-0.02736.347-0.001-0.0010.0000.0000.0000.000
175A223HOH0-0.032-0.04630.2240.0000.0000.0000.0000.0000.000
176A224HOH00.0460.03029.594-0.001-0.0010.0000.0000.0000.000
177A225HOH0-0.026-0.01828.0810.0020.0020.0000.0000.0000.000
178A226HOH0-0.041-0.02516.403-0.006-0.0060.0000.0000.0000.000
179A227HOH00.0290.00517.540-0.001-0.0010.0000.0000.0000.000
180A228HOH00.0270.01923.718-0.001-0.0010.0000.0000.0000.000
181A229HOH00.0110.00630.5290.0000.0000.0000.0000.0000.000
182A230HOH0-0.049-0.04929.906-0.001-0.0010.0000.0000.0000.000
183A231HOH00.0240.00925.5600.0030.0030.0000.0000.0000.000
184A232HOH00.0280.01824.883-0.005-0.0050.0000.0000.0000.000
185A237HOH0-0.011-0.00625.8810.0020.0020.0000.0000.0000.000
186A238HOH0-0.0080.00024.9240.0020.0020.0000.0000.0000.000
187A240HOH0-0.015-0.01213.0120.0010.0010.0000.0000.0000.000
188A241HOH0-0.037-0.02625.415-0.003-0.0030.0000.0000.0000.000
189A242HOH0-0.009-0.01029.0180.0000.0000.0000.0000.0000.000
190A243HOH0-0.023-0.01621.5630.0020.0020.0000.0000.0000.000
191A244HOH0-0.047-0.03415.8660.0140.0140.0000.0000.0000.000
192A245HOH0-0.002-0.00710.730-0.004-0.0040.0000.0000.0000.000
193A246HOH00.003-0.00229.9000.0010.0010.0000.0000.0000.000
194A247HOH00.0210.01525.129-0.003-0.0030.0000.0000.0000.000
195A248HOH0-0.0030.0038.4740.0470.0470.0000.0000.0000.000
196A249HOH0-0.004-0.00419.6180.0000.0000.0000.0000.0000.000
197A250HOH0-0.086-0.07221.5370.0020.0020.0000.0000.0000.000
198A252HOH0-0.061-0.04617.7790.0090.0090.0000.0000.0000.000
199A253HOH0-0.113-0.10426.587-0.001-0.0010.0000.0000.0000.000
200A255HOH0-0.050-0.03815.1570.0020.0020.0000.0000.0000.000
201A256HOH0-0.014-0.01333.227-0.002-0.0020.0000.0000.0000.000
202A257HOH0-0.0020.00928.340-0.002-0.0020.0000.0000.0000.000
203A258HOH0-0.009-0.00328.738-0.001-0.0010.0000.0000.0000.000
204A259HOH00.0070.01027.9650.0000.0000.0000.0000.0000.000
205A260HOH0-0.035-0.0225.977-0.257-0.2570.0000.0000.0000.000
206A261HOH0-0.005-0.0046.909-0.005-0.0050.0000.0000.0000.000
207A262HOH00.0070.00225.072-0.002-0.0020.0000.0000.0000.000
208A264HOH00.0230.01526.535-0.003-0.0030.0000.0000.0000.000
209A265HOH0-0.041-0.03728.6860.0010.0010.0000.0000.0000.000
210A267HOH00.0300.01413.399-0.011-0.0110.0000.0000.0000.000