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: 14KLZ

Calculation Name: 2WVN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WVN

Chain ID: A

ChEMBL ID:

UniProt ID: Q03689

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2523926.596045
FMO2-HF: Nuclear repulsion 2440091.604286
FMO2-HF: Total energy -83834.991759
FMO2-MP2: Total energy -84080.591816


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:11:ALA)


Summations of interaction energy for fragment #1(A:11:ALA)
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.
-9.041-4.4310.694-2.741-2.564-0.015
Interaction energy analysis for fragmet #1(A:11:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.015
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].
3A13ASN0-0.0070.0063.617-2.024-0.3900.000-0.995-0.6400.003
4A14VAL00.0630.0176.2320.1800.1800.0000.0000.0000.000
5A15ALA00.0470.0338.0200.2540.2540.0000.0000.0000.000
6A16GLY00.0300.0177.8410.1860.1860.0000.0000.0000.000
7A17LEU0-0.033-0.0023.6480.1520.4010.003-0.050-0.2010.000
8A18PHE00.0420.0167.4560.2630.2630.0000.0000.0000.000
9A19ASN00.014-0.01011.2230.1780.1780.0000.0000.0000.000
10A20ASN00.0010.0008.4240.2300.2300.0000.0000.0000.000
11A21CYS00.0090.02910.2330.1160.1160.0000.0000.0000.000
12A22VAL0-0.019-0.00212.3450.0450.0450.0000.0000.0000.000
13A23ASP-1-0.778-0.89513.3660.0010.0010.0000.0000.0000.000
14A24CYS0-0.066-0.03012.4440.0560.0560.0000.0000.0000.000
15A25PHE0-0.023-0.02715.2570.0240.0240.0000.0000.0000.000
16A26GLU-1-0.848-0.89818.140-0.036-0.0360.0000.0000.0000.000
17A27TYR0-0.069-0.02816.4060.0190.0190.0000.0000.0000.000
18A28VAL0-0.065-0.02519.3640.0210.0210.0000.0000.0000.000
19A29GLN00.0370.02321.618-0.005-0.0050.0000.0000.0000.000
20A30LEU0-0.0030.00025.2550.0100.0100.0000.0000.0000.000
21A31GLY00.0670.02628.098-0.005-0.0050.0000.0000.0000.000
22A32ARG10.9800.99930.299-0.054-0.0540.0000.0000.0000.000
23A33PRO0-0.001-0.00732.192-0.006-0.0060.0000.0000.0000.000
24A34PHE0-0.020-0.00528.335-0.003-0.0030.0000.0000.0000.000
25A35GLY00.0090.00733.781-0.005-0.0050.0000.0000.0000.000
26A36ARG10.8190.88336.424-0.029-0.0290.0000.0000.0000.000
27A37ASP-1-0.848-0.90734.6620.0300.0300.0000.0000.0000.000
28A38TYR00.0620.03729.754-0.002-0.0020.0000.0000.0000.000
29A39GLU-1-0.765-0.87531.9970.0040.0040.0000.0000.0000.000
30A40ARG10.9810.98832.492-0.023-0.0230.0000.0000.0000.000
31A41CYS0-0.048-0.02729.457-0.001-0.0010.0000.0000.0000.000
32A42GLN0-0.029-0.02425.2450.0090.0090.0000.0000.0000.000
33A43LEU00.0360.02327.560-0.003-0.0030.0000.0000.0000.000
34A44ARG10.7790.86528.039-0.029-0.0290.0000.0000.0000.000
35A45LEU0-0.0200.00322.207-0.001-0.0010.0000.0000.0000.000
36A46ASP-1-0.752-0.86023.597-0.011-0.0110.0000.0000.0000.000
37A47ILE00.0130.00124.763-0.012-0.0120.0000.0000.0000.000
38A48ALA0-0.007-0.00122.332-0.011-0.0110.0000.0000.0000.000
39A49LYS10.7820.87819.7590.0280.0280.0000.0000.0000.000
40A50ALA00.021-0.00620.853-0.023-0.0230.0000.0000.0000.000
41A51ARG10.7830.87523.2260.0310.0310.0000.0000.0000.000
42A52LEU00.0080.00815.245-0.016-0.0160.0000.0000.0000.000
43A53SER0-0.054-0.04218.783-0.034-0.0340.0000.0000.0000.000
44A54ARG10.8010.85819.7800.0570.0570.0000.0000.0000.000
45A55TRP00.0150.02114.704-0.033-0.0330.0000.0000.0000.000
46A56GLY00.007-0.01117.553-0.024-0.0240.0000.0000.0000.000
47A57GLU-1-0.864-0.91918.242-0.199-0.1990.0000.0000.0000.000
48A58ALA0-0.001-0.00321.401-0.009-0.0090.0000.0000.0000.000
49A59VAL0-0.070-0.02617.015-0.001-0.0010.0000.0000.0000.000
50A60LYS10.9180.95219.0650.1900.1900.0000.0000.0000.000
51A61ILE00.0070.00512.616-0.047-0.0470.0000.0000.0000.000
52A62ASN0-0.002-0.01214.941-0.126-0.1260.0000.0000.0000.000
53A63ASP-1-0.923-0.97216.638-0.371-0.3710.0000.0000.0000.000
54A64ASP-1-0.784-0.86317.458-0.451-0.4510.0000.0000.0000.000
55A65PRO00.009-0.01115.672-0.075-0.0750.0000.0000.0000.000
56A66ARG10.7860.87013.9690.2710.2710.0000.0000.0000.000
57A67PHE00.0020.01111.455-0.107-0.1070.0000.0000.0000.000
58A68HIS0-0.068-0.04710.501-0.199-0.1990.0000.0000.0000.000
59A69SER0-0.032-0.0178.992-0.072-0.0720.0000.0000.0000.000
60A70ASP-1-0.868-0.9502.636-11.977-9.5530.665-1.596-1.493-0.019
61A71ALA00.0140.0135.2460.0130.0130.0000.0000.0000.000
62A72PRO0-0.0050.0157.5090.2090.2090.0000.0000.0000.000
63A73THR00.018-0.01210.7180.0980.0980.0000.0000.0000.000
64A74ASP-1-0.810-0.88813.976-0.275-0.2750.0000.0000.0000.000
65A75LYS11.0040.98314.4800.0940.0940.0000.0000.0000.000
66A76SER00.0330.02115.2420.0120.0120.0000.0000.0000.000
67A77VAL0-0.035-0.01511.0980.0060.0060.0000.0000.0000.000
68A78GLN0-0.051-0.02310.796-0.005-0.0050.0000.0000.0000.000
69A79LEU0-0.0040.01511.3290.0520.0520.0000.0000.0000.000
70A80ALA00.0080.01612.8910.0520.0520.0000.0000.0000.000
71A81LYS10.8610.9352.9693.6693.9720.026-0.100-0.2300.001
72A82SER00.0240.0068.7810.1330.1330.0000.0000.0000.000
73A83ILE00.006-0.01310.5580.0810.0810.0000.0000.0000.000
74A84VAL0-0.013-0.0029.1330.0560.0560.0000.0000.0000.000
75A85GLU-1-0.910-0.9735.2410.4800.4800.0000.0000.0000.000
76A86GLU-1-0.934-0.9739.0110.3670.3670.0000.0000.0000.000
77A87ILE00.0030.00212.6400.0120.0120.0000.0000.0000.000
78A88LEU0-0.004-0.0137.4590.0130.0130.0000.0000.0000.000
79A89LEU00.0150.01910.0390.0370.0370.0000.0000.0000.000
80A90LEU0-0.0230.01612.744-0.018-0.0180.0000.0000.0000.000
81A91PHE00.018-0.00113.713-0.006-0.0060.0000.0000.0000.000
82A92GLU-1-0.835-0.89811.3520.7470.7470.0000.0000.0000.000
83A93SER0-0.065-0.04614.543-0.012-0.0120.0000.0000.0000.000
84A94ALA0-0.0050.00417.708-0.024-0.0240.0000.0000.0000.000
85A95GLN00.0090.00815.2260.0290.0290.0000.0000.0000.000
86A96LYS10.7880.88114.326-0.545-0.5450.0000.0000.0000.000
87A97THR0-0.062-0.05320.165-0.014-0.0140.0000.0000.0000.000
88A98SER0-0.023-0.01022.304-0.012-0.0120.0000.0000.0000.000
89A99LYS10.9650.96618.065-0.308-0.3080.0000.0000.0000.000
90A100ARG10.8890.95122.525-0.220-0.2200.0000.0000.0000.000
91A101TYR0-0.0110.01026.263-0.008-0.0080.0000.0000.0000.000
92A102GLU-1-0.818-0.90225.4470.1340.1340.0000.0000.0000.000
93A103LEU0-0.070-0.03326.652-0.004-0.0040.0000.0000.0000.000
94A104VAL0-0.072-0.03229.843-0.004-0.0040.0000.0000.0000.000
95A105ALA0-0.0100.02732.064-0.007-0.0070.0000.0000.0000.000
96A106ASP-1-0.821-0.89333.7390.0650.0650.0000.0000.0000.000
97A107GLN00.024-0.02734.671-0.002-0.0020.0000.0000.0000.000
98A108GLN0-0.056-0.02635.184-0.005-0.0050.0000.0000.0000.000
99A109ASP-1-0.964-0.99333.8270.0650.0650.0000.0000.0000.000
100A110LEU0-0.033-0.02529.8250.0040.0040.0000.0000.0000.000
101A111VAL0-0.051-0.00731.0910.0000.0000.0000.0000.0000.000
102A112VAL0-0.012-0.01427.5040.0010.0010.0000.0000.0000.000
103A113PHE0-0.096-0.03730.801-0.005-0.0050.0000.0000.0000.000
104A114GLU-1-0.900-0.95829.3210.0320.0320.0000.0000.0000.000
105A115ASP-1-0.674-0.81031.014-0.007-0.0070.0000.0000.0000.000
106A116LYS10.8420.91532.840-0.028-0.0280.0000.0000.0000.000
107A117ASP-1-0.855-0.90935.0850.0240.0240.0000.0000.0000.000
108A118MET0-0.0680.00330.9640.0000.0000.0000.0000.0000.000
109A119LYS10.8830.91336.868-0.007-0.0070.0000.0000.0000.000
110A120PRO0-0.015-0.03038.326-0.001-0.0010.0000.0000.0000.000
111A121ILE00.0160.01638.485-0.001-0.0010.0000.0000.0000.000
112A122GLY00.0640.04135.823-0.003-0.0030.0000.0000.0000.000
113A123ARG10.8360.90233.8930.0000.0000.0000.0000.0000.000
114A124ALA0-0.032-0.02133.455-0.003-0.0030.0000.0000.0000.000
115A125LEU00.0400.02033.292-0.005-0.0050.0000.0000.0000.000
116A126HIS0-0.058-0.03926.773-0.004-0.0040.0000.0000.0000.000
117A127ARG10.8010.85528.8200.0110.0110.0000.0000.0000.000
118A128ARG10.9160.95829.5260.0440.0440.0000.0000.0000.000
119A129LEU0-0.001-0.00627.279-0.008-0.0080.0000.0000.0000.000
120A130ASN00.0650.02124.606-0.012-0.0120.0000.0000.0000.000
121A131ASP-1-0.934-0.94124.891-0.073-0.0730.0000.0000.0000.000
122A132LEU0-0.055-0.01326.210-0.014-0.0140.0000.0000.0000.000
123A133VAL00.0100.00121.328-0.015-0.0150.0000.0000.0000.000
124A134SER0-0.012-0.02821.764-0.021-0.0210.0000.0000.0000.000
125A135ARG10.9040.96522.4840.1040.1040.0000.0000.0000.000
126A136ARG10.7330.85021.0400.1250.1250.0000.0000.0000.000
127A137GLN0-0.064-0.02415.748-0.042-0.0420.0000.0000.0000.000
128A138LYS10.8710.94217.0000.4010.4010.0000.0000.0000.000
129A139GLN0-0.021-0.01910.387-0.031-0.0310.0000.0000.0000.000
130A140THR00.0730.05015.7930.0220.0220.0000.0000.0000.000
131A141SER0-0.044-0.01011.4480.0440.0440.0000.0000.0000.000
132A142LEU00.0040.00810.708-0.102-0.1020.0000.0000.0000.000
133A143ALA0-0.010-0.0158.0920.0360.0360.0000.0000.0000.000
134A144LYS10.9470.97110.080-0.117-0.1170.0000.0000.0000.000
135A145LYS10.7880.88111.1150.0340.0340.0000.0000.0000.000
136A146THR0-0.035-0.02514.737-0.020-0.0200.0000.0000.0000.000
137A147ALA00.0110.00818.1920.0130.0130.0000.0000.0000.000
138A148TRP0-0.020-0.00417.8310.0240.0240.0000.0000.0000.000
139A149ALA00.0850.05421.884-0.012-0.0120.0000.0000.0000.000
140A150LEU00.0120.02122.7280.0170.0170.0000.0000.0000.000
141A151TYR0-0.031-0.06625.595-0.016-0.0160.0000.0000.0000.000
142A152ASP-1-0.798-0.88928.3750.0950.0950.0000.0000.0000.000
143A153GLY00.0510.02428.6800.0020.0020.0000.0000.0000.000
144A154LYS10.8880.94129.294-0.075-0.0750.0000.0000.0000.000
145A155SER0-0.028-0.03524.4700.0070.0070.0000.0000.0000.000
146A156LEU0-0.0210.01224.0780.0080.0080.0000.0000.0000.000
147A157GLU-1-0.785-0.88025.0390.0380.0380.0000.0000.0000.000
148A158LYS10.9240.99121.878-0.175-0.1750.0000.0000.0000.000
149A159ILE00.0140.00119.6070.0010.0010.0000.0000.0000.000
150A160VAL00.0350.01821.640-0.009-0.0090.0000.0000.0000.000
151A161ASP-1-0.847-0.92423.7610.0340.0340.0000.0000.0000.000
152A162GLN0-0.025-0.03120.0310.0020.0020.0000.0000.0000.000
153A163VAL0-0.0020.00518.059-0.005-0.0050.0000.0000.0000.000
154A164ALA00.0010.00720.185-0.021-0.0210.0000.0000.0000.000
155A165ARG10.7580.85722.280-0.030-0.0300.0000.0000.0000.000
156A166PHE00.0130.00517.206-0.012-0.0120.0000.0000.0000.000
157A167VAL0-0.015-0.00918.834-0.028-0.0280.0000.0000.0000.000
158A168ASP-1-0.779-0.86720.187-0.035-0.0350.0000.0000.0000.000
159A169GLU-1-1.014-1.01318.3700.0030.0030.0000.0000.0000.000
160A170LEU00.007-0.00314.579-0.018-0.0180.0000.0000.0000.000
161A171GLU-1-0.801-0.89018.600-0.116-0.1160.0000.0000.0000.000
162A172LYS10.9390.98222.0420.0400.0400.0000.0000.0000.000
163A173ALA0-0.070-0.01618.394-0.003-0.0030.0000.0000.0000.000
164A174PHE0-0.050-0.04516.054-0.046-0.0460.0000.0000.0000.000
165A175PRO00.0300.03621.8790.0140.0140.0000.0000.0000.000
166A176ILE0-0.025-0.02621.498-0.009-0.0090.0000.0000.0000.000
167A177GLU-1-0.804-0.90525.786-0.098-0.0980.0000.0000.0000.000
168A178ALA0-0.034-0.01627.8390.0060.0060.0000.0000.0000.000
169A179VAL0-0.021-0.01826.1140.0040.0040.0000.0000.0000.000
170A180CYS0-0.037-0.03124.700-0.005-0.0050.0000.0000.0000.000
171A181HIS00.0110.01427.3320.0040.0040.0000.0000.0000.000
172A182LYS10.8810.94030.9780.0850.0850.0000.0000.0000.000
173A183LEU0-0.027-0.03325.0760.0030.0030.0000.0000.0000.000
174A184ALA00.0020.01729.1890.0020.0020.0000.0000.0000.000
175A185GLU-1-0.863-0.93030.489-0.062-0.0620.0000.0000.0000.000
176A186ILE0-0.031-0.01231.1000.0020.0020.0000.0000.0000.000
177A187GLU-1-0.803-0.87226.743-0.092-0.0920.0000.0000.0000.000
178A188ILE0-0.003-0.01931.0700.0060.0060.0000.0000.0000.000
179A189GLU-1-0.949-0.96534.479-0.074-0.0740.0000.0000.0000.000
180A190GLU-1-0.876-0.92235.414-0.062-0.0620.0000.0000.0000.000
181A191VAL0-0.103-0.04135.6760.0040.0040.0000.0000.0000.000
182A192GLU-1-0.816-0.90138.295-0.042-0.0420.0000.0000.0000.000
183A193ASP-1-0.876-0.91141.387-0.022-0.0220.0000.0000.0000.000
184A194GLU-1-0.807-0.92541.775-0.016-0.0160.0000.0000.0000.000
185A195ALA0-0.053-0.00742.2770.0010.0010.0000.0000.0000.000
186A196SER0-0.023-0.05238.0920.0020.0020.0000.0000.0000.000
187A197LEU00.0180.01737.7490.0000.0000.0000.0000.0000.000
188A198THR0-0.001-0.01338.1620.0000.0000.0000.0000.0000.000
189A199ILE0-0.053-0.02335.4720.0030.0030.0000.0000.0000.000
190A200LEU0-0.001-0.00132.1970.0030.0030.0000.0000.0000.000
191A201LYS10.9250.96334.1090.0110.0110.0000.0000.0000.000
192A202ASP-1-0.904-0.94235.668-0.003-0.0030.0000.0000.0000.000
193A203ALA0-0.061-0.03632.0800.0040.0040.0000.0000.0000.000
194A204ALA00.0530.03130.4440.0030.0030.0000.0000.0000.000
195A205GLY00.0440.03130.917-0.001-0.0010.0000.0000.0000.000
196A206GLY0-0.047-0.04131.5260.0050.0050.0000.0000.0000.000
197A207ILE0-0.081-0.04826.5930.0070.0070.0000.0000.0000.000
198A208ASP-1-0.730-0.85626.716-0.062-0.0620.0000.0000.0000.000
199A209ALA00.0050.01328.8250.0000.0000.0000.0000.0000.000
200A210ALA00.0620.03429.0110.0010.0010.0000.0000.0000.000
201A211MET0-0.003-0.00228.3150.0020.0020.0000.0000.0000.000
202A212SER0-0.056-0.02731.6980.0030.0030.0000.0000.0000.000
203A213ASP-1-0.863-0.92934.485-0.034-0.0340.0000.0000.0000.000
204A214ALA0-0.0250.00334.3340.0010.0010.0000.0000.0000.000
205A215ALA0-0.0030.00035.8040.0010.0010.0000.0000.0000.000
206A216ALA0-0.038-0.03237.4990.0020.0020.0000.0000.0000.000
207A217GLN0-0.019-0.01937.6670.0020.0020.0000.0000.0000.000
208A218LYS10.7920.88039.4040.0460.0460.0000.0000.0000.000
209A219ILE0-0.025-0.02241.3210.0010.0010.0000.0000.0000.000
210A220ASP-1-0.916-0.95943.676-0.022-0.0220.0000.0000.0000.000
211A221ALA0-0.078-0.03144.5960.0000.0000.0000.0000.0000.000
212A222ILE0-0.049-0.01645.0680.0000.0000.0000.0000.0000.000
213A223VAL0-0.099-0.02747.8040.0030.0030.0000.0000.0000.000