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

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FMODB ID: XYN12

Calculation Name: 1WHI-A-Xray31

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WHI

Chain ID: A

ChEMBL ID:

UniProt ID: P04450

Base Structure: X-ray

Registration Date: 2018-09-06

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 184
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1147758.124723
FMO2-HF: Nuclear repulsion 1096664.851216
FMO2-HF: Total energy -51093.273507
FMO2-MP2: Total energy -51241.616914


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-5.992-0.04800000000000111.187-5.294-11.835-0.014
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.020
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].
3A3GLN0-0.006-0.0122.6910.3583.0610.097-1.055-1.7450.001
4A4GLN00.0410.0145.4990.4280.4280.0000.0000.0000.000
5A5GLU-1-0.865-0.9518.437-0.916-0.9160.0000.0000.0000.000
6A6SER0-0.0150.0255.579-0.415-0.4150.0000.0000.0000.000
7A7ARG10.9640.9847.8530.4710.4710.0000.0000.0000.000
8A8LEU0-0.039-0.0097.8390.0390.0390.0000.0000.0000.000
9A9LYS11.0261.02011.249-0.054-0.0540.0000.0000.0000.000
10A10VAL0-0.0010.00013.873-0.042-0.0420.0000.0000.0000.000
11A11ALA0-0.0140.00416.1330.0360.0360.0000.0000.0000.000
12A12ASP-1-0.684-0.81017.866-0.149-0.1490.0000.0000.0000.000
13A13ASN00.0100.00321.179-0.007-0.0070.0000.0000.0000.000
14A14SER0-0.023-0.04021.584-0.002-0.0020.0000.0000.0000.000
15A15GLY00.0300.01723.706-0.001-0.0010.0000.0000.0000.000
16A16ALA0-0.047-0.01219.7260.0020.0020.0000.0000.0000.000
17A17ARG10.8760.93919.8670.0930.0930.0000.0000.0000.000
18A18GLU-1-0.900-0.95814.474-0.142-0.1420.0000.0000.0000.000
19A19VAL0-0.0150.00213.2280.0050.0050.0000.0000.0000.000
20A20LEU0-0.021-0.00211.676-0.034-0.0340.0000.0000.0000.000
21A21VAL00.0050.0008.5440.0810.0810.0000.0000.0000.000
22A22ILE00.0290.04111.459-0.040-0.0400.0000.0000.0000.000
23A23LYS11.0040.98111.1100.4710.4710.0000.0000.0000.000
24A24VAL00.0050.0206.7950.0270.0270.0000.0000.0000.000
25A25LEU0-0.029-0.01210.2730.1000.1000.0000.0000.0000.000
26A26GLY00.039-0.00311.861-0.072-0.0720.0000.0000.0000.000
27A27GLY00.0180.02513.6600.0330.0330.0000.0000.0000.000
28A28SER0-0.005-0.00913.101-0.094-0.0940.0000.0000.0000.000
29A29GLY00.0700.03411.7050.0310.0310.0000.0000.0000.000
30A30ARG10.7750.9046.2900.9810.9810.0000.0000.0000.000
31A31ARG10.9610.9826.4160.7200.7200.0000.0000.0000.000
32A32TYR00.0160.0072.330-2.8210.0572.945-1.349-4.474-0.008
33A33ALA0-0.0010.0134.0970.3540.590-0.001-0.017-0.2170.000
34A34ASN00.0100.0044.709-0.497-0.360-0.001-0.009-0.1260.000
35A35ILE00.0590.0116.767-0.024-0.0240.0000.0000.0000.000
36A36GLY00.0030.01710.304-0.012-0.0120.0000.0000.0000.000
37A37ASP-1-0.781-0.8667.676-0.997-0.9970.0000.0000.0000.000
38A38VAL00.004-0.00411.0250.0390.0390.0000.0000.0000.000
39A39VAL0-0.027-0.0129.218-0.114-0.1140.0000.0000.0000.000
40A40VAL00.0070.00512.2770.1230.1230.0000.0000.0000.000
41A41ALA00.013-0.00613.599-0.108-0.1080.0000.0000.0000.000
42A42THR00.0690.05115.2910.0540.0540.0000.0000.0000.000
43A43VAL0-0.017-0.01517.085-0.027-0.0270.0000.0000.0000.000
44A44LYS10.9110.96515.3740.2260.2260.0000.0000.0000.000
45A45ASP-1-0.845-0.93318.762-0.077-0.0770.0000.0000.0000.000
46A46ALA00.0290.00220.984-0.014-0.0140.0000.0000.0000.000
47A47THR0-0.019-0.00423.7160.0070.0070.0000.0000.0000.000
48A48PRO00.0300.01626.893-0.010-0.0100.0000.0000.0000.000
49A49GLY00.0060.00929.9210.0060.0060.0000.0000.0000.000
50A50GLY00.0130.03528.9840.0040.0040.0000.0000.0000.000
51A51VAL0-0.003-0.00327.251-0.005-0.0050.0000.0000.0000.000
52A52VAL0-0.0250.00022.488-0.012-0.0120.0000.0000.0000.000
53A53LYS10.9850.98225.6270.1250.1250.0000.0000.0000.000
54A54LYS10.9420.97422.8760.1030.1030.0000.0000.0000.000
55A55GLY00.0200.00822.0000.0140.0140.0000.0000.0000.000
56A56GLN00.0550.05122.999-0.016-0.0160.0000.0000.0000.000
57A57VAL00.0070.00118.698-0.026-0.0260.0000.0000.0000.000
58A58VAL0-0.051-0.01617.7010.0340.0340.0000.0000.0000.000
59A59LYS10.9580.97516.8220.2840.2840.0000.0000.0000.000
60A60ALA00.013-0.00414.4860.0520.0520.0000.0000.0000.000
61A61VAL00.0090.02313.826-0.094-0.0940.0000.0000.0000.000
62A62VAL0-0.011-0.0128.0320.0470.0470.0000.0000.0000.000
63A63VAL00.010-0.00811.4020.0340.0340.0000.0000.0000.000
64A64ARG10.7930.90411.115-0.043-0.0430.0000.0000.0000.000
65A65THR0-0.014-0.0145.620-0.019-0.0190.0000.0000.0000.000
66A66LYS10.9600.9875.988-1.273-1.2730.0000.0000.0000.000
67A67ARG10.9190.9541.801-2.115-3.6777.361-1.691-4.1080.003
68A68GLY00.0440.0185.600-0.173-0.1730.0000.0000.0000.000
69A69VAL0-0.041-0.0097.370-0.038-0.0380.0000.0000.0000.000
70A70ARG10.9190.9469.711-0.242-0.2420.0000.0000.0000.000
71A71ARG10.7240.82111.559-0.213-0.2130.0000.0000.0000.000
72A72PRO00.0330.00514.8430.0210.0210.0000.0000.0000.000
73A73ASP-1-0.824-0.89817.4690.1590.1590.0000.0000.0000.000
74A74GLY0-0.0210.00017.4860.0030.0030.0000.0000.0000.000
75A75SER0-0.054-0.02417.2590.0410.0410.0000.0000.0000.000
76A76TYR00.033-0.00111.2730.0210.0210.0000.0000.0000.000
77A77ILE00.0210.02712.9910.0040.0040.0000.0000.0000.000
78A78ARG10.9020.9399.672-0.941-0.9410.0000.0000.0000.000
79A79PHE00.0380.01610.200-0.103-0.1030.0000.0000.0000.000
80A80ASP-1-0.819-0.89310.5710.6220.6220.0000.0000.0000.000
81A81GLU-1-0.861-0.92610.3990.1940.1940.0000.0000.0000.000
82A82ASN0-0.006-0.0225.3050.1500.1500.0000.0000.0000.000
83A83ALA0-0.0050.0058.723-0.098-0.0980.0000.0000.0000.000
84A84CYS0-0.057-0.02611.426-0.076-0.0760.0000.0000.0000.000
85A85VAL00.0540.03813.5330.0560.0560.0000.0000.0000.000
86A86ILE00.0030.00017.165-0.047-0.0470.0000.0000.0000.000
87A87ILE0-0.019-0.00117.8660.0320.0320.0000.0000.0000.000
88A88ARG10.9250.96020.8520.1110.1110.0000.0000.0000.000
89A89ASP-1-0.904-0.96922.234-0.249-0.2490.0000.0000.0000.000
90A90ASP-1-0.851-0.92323.253-0.156-0.1560.0000.0000.0000.000
91A91LYS10.8950.95218.1640.2500.2500.0000.0000.0000.000
92A92SER0-0.0130.01421.9090.0080.0080.0000.0000.0000.000
93A93PRO0-0.021-0.00622.044-0.018-0.0180.0000.0000.0000.000
94A94ARG10.8550.91122.9030.1920.1920.0000.0000.0000.000
95A95GLY0-0.0010.01223.7640.0110.0110.0000.0000.0000.000
96A96THR0-0.036-0.04225.3150.0030.0030.0000.0000.0000.000
97A97ARG10.8880.94525.5540.0410.0410.0000.0000.0000.000
98A98ILE0-0.0070.00119.613-0.016-0.0160.0000.0000.0000.000
99A99PHE0-0.016-0.01520.3710.0130.0130.0000.0000.0000.000
100A100GLY00.0520.01718.800-0.001-0.0010.0000.0000.0000.000
101A101PRO00.0350.02517.056-0.024-0.0240.0000.0000.0000.000
102A102VAL0-0.0110.00015.9910.0010.0010.0000.0000.0000.000
103A103ALA00.0310.01813.9760.0180.0180.0000.0000.0000.000
104A104ARG10.9550.95615.958-0.105-0.1050.0000.0000.0000.000
105A105GLU-1-0.738-0.85212.9220.0670.0670.0000.0000.0000.000
106A106LEU0-0.050-0.02414.496-0.048-0.0480.0000.0000.0000.000
107A107ARG10.9470.96716.9880.0370.0370.0000.0000.0000.000
108A108ASP-1-0.829-0.88816.913-0.069-0.0690.0000.0000.0000.000
109A109LYS10.8380.93012.7520.2530.2530.0000.0000.0000.000
110A110ASP-1-0.858-0.94217.756-0.152-0.1520.0000.0000.0000.000
111A111PHE0-0.0190.00515.944-0.012-0.0120.0000.0000.0000.000
112A112MET00.0450.00620.7820.0170.0170.0000.0000.0000.000
113A113LYS10.9710.99524.1390.0800.0800.0000.0000.0000.000
114A114ILE00.0380.00918.6310.0120.0120.0000.0000.0000.000
115A115ILE0-0.0110.00119.7720.0160.0160.0000.0000.0000.000
116A116SER0-0.080-0.04222.5760.0140.0140.0000.0000.0000.000
117A117LEU0-0.024-0.02124.1670.0070.0070.0000.0000.0000.000
118A118ALA0-0.0180.00221.1890.0050.0050.0000.0000.0000.000
119A119PRO0-0.034-0.01021.7280.0040.0040.0000.0000.0000.000
120A120GLU-1-0.807-0.89222.3320.1090.1090.0000.0000.0000.000
121A121VAL0-0.044-0.01420.046-0.006-0.0060.0000.0000.0000.000
122A122ILE-1-0.720-0.83717.7570.1270.1270.0000.0000.0000.000
123A200HOH0-0.026-0.02021.9160.0030.0030.0000.0000.0000.000
124A201HOH0-0.002-0.01027.2350.0000.0000.0000.0000.0000.000
125A202HOH0-0.051-0.05021.2760.0090.0090.0000.0000.0000.000
126A203HOH0-0.017-0.0056.7220.2060.2060.0000.0000.0000.000
127A204HOH00.0020.00210.4200.0690.0690.0000.0000.0000.000
128A205HOH00.0230.01010.1980.0860.0860.0000.0000.0000.000
129A206HOH0-0.031-0.03622.2230.0050.0050.0000.0000.0000.000
130A207HOH00.0180.01124.2130.0010.0010.0000.0000.0000.000
131A208HOH00.0150.01723.4430.0000.0000.0000.0000.0000.000
132A209HOH0-0.014-0.0082.751-1.678-0.4820.737-1.025-0.908-0.010
133A210HOH00.003-0.0062.845-0.582-0.3040.049-0.132-0.1950.000
134A212HOH00.0140.00213.3540.0420.0420.0000.0000.0000.000
135A213HOH0-0.045-0.02314.9580.0210.0210.0000.0000.0000.000
136A214HOH0-0.009-0.01211.0470.0560.0560.0000.0000.0000.000
137A215HOH0-0.006-0.0193.6710.6450.7230.000-0.016-0.0620.000
138A217HOH00.0160.0127.198-0.018-0.0180.0000.0000.0000.000
139A219HOH0-0.019-0.01419.2470.0040.0040.0000.0000.0000.000
140A220HOH00.0250.01929.368-0.001-0.0010.0000.0000.0000.000
141A221HOH00.0320.01127.403-0.003-0.0030.0000.0000.0000.000
142A222HOH0-0.037-0.02018.0920.0110.0110.0000.0000.0000.000
143A224HOH0-0.034-0.01711.879-0.019-0.0190.0000.0000.0000.000
144A225HOH0-0.038-0.02113.4520.0440.0440.0000.0000.0000.000
145A227HOH0-0.036-0.02612.9720.0380.0380.0000.0000.0000.000
146A229HOH0-0.023-0.00911.1840.0320.0320.0000.0000.0000.000
147A230HOH00.0400.02216.580-0.022-0.0220.0000.0000.0000.000
148A231HOH00.0270.01613.942-0.010-0.0100.0000.0000.0000.000
149A232HOH0-0.019-0.0217.089-0.009-0.0090.0000.0000.0000.000
150A235HOH0-0.037-0.03613.6350.0250.0250.0000.0000.0000.000
151A236HOH0-0.034-0.02210.5720.0370.0370.0000.0000.0000.000
152A237HOH0-0.035-0.0227.1870.0020.0020.0000.0000.0000.000
153A238HOH0-0.009-0.01815.9360.0220.0220.0000.0000.0000.000
154A241HOH0-0.035-0.02526.5900.0000.0000.0000.0000.0000.000
155A242HOH0-0.036-0.03227.8550.0010.0010.0000.0000.0000.000
156A243HOH0-0.002-0.00530.087-0.001-0.0010.0000.0000.0000.000
157A247HOH0-0.026-0.01626.9430.0050.0050.0000.0000.0000.000
158A248HOH0-0.001-0.01923.9730.0040.0040.0000.0000.0000.000
159A249HOH00.0350.02024.507-0.002-0.0020.0000.0000.0000.000
160A252HOH00.0280.03416.7640.0150.0150.0000.0000.0000.000
161A253HOH0-0.023-0.01413.1430.0040.0040.0000.0000.0000.000
162A254HOH0-0.028-0.01420.478-0.001-0.0010.0000.0000.0000.000
163A255HOH0-0.015-0.00813.035-0.024-0.0240.0000.0000.0000.000
164A256HOH0-0.048-0.03517.418-0.012-0.0120.0000.0000.0000.000
165A257HOH00.005-0.01514.4110.0010.0010.0000.0000.0000.000
166A258HOH0-0.0110.0069.357-0.002-0.0020.0000.0000.0000.000
167A259HOH0-0.052-0.02915.375-0.010-0.0100.0000.0000.0000.000
168A261HOH00.0200.01421.131-0.005-0.0050.0000.0000.0000.000
169A262HOH0-0.039-0.02328.9950.0000.0000.0000.0000.0000.000
170A263HOH00.0090.00625.8770.0000.0000.0000.0000.0000.000
171A265HOH0-0.015-0.00625.7340.0050.0050.0000.0000.0000.000
172A266HOH00.0360.01526.762-0.002-0.0020.0000.0000.0000.000
173A269HOH00.0090.02226.6450.0020.0020.0000.0000.0000.000
174A272HOH00.0280.02229.0710.0010.0010.0000.0000.0000.000
175A274HOH00.0420.02123.3830.0000.0000.0000.0000.0000.000
176A276HOH0-0.014-0.02313.413-0.005-0.0050.0000.0000.0000.000
177A277HOH00.0340.02724.1630.0030.0030.0000.0000.0000.000
178A278HOH0-0.064-0.05415.166-0.014-0.0140.0000.0000.0000.000
179A283HOH0-0.033-0.01326.8760.0020.0020.0000.0000.0000.000
180A284HOH00.0140.00525.674-0.004-0.0040.0000.0000.0000.000
181A285HOH0-0.056-0.03822.7850.0020.0020.0000.0000.0000.000
182A286HOH0-0.074-0.04622.9710.0020.0020.0000.0000.0000.000
183A299HOH0-0.0020.00127.7570.0010.0010.0000.0000.0000.000
184A301HOH00.000-0.0048.2130.0040.0040.0000.0000.0000.000