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: 53L5Z

Calculation Name: 1WNH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WNH

Chain ID: A

ChEMBL ID:

UniProt ID: P70202

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptAll
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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2742428.957398
FMO2-HF: Nuclear repulsion 2652900.861499
FMO2-HF: Total energy -89528.095898
FMO2-MP2: Total energy -89786.841896


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:ALA)


Summations of interaction energy for fragment #1(A:-2: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.
-14.638-15.97511.823-5.993-4.494-0.055
Interaction energy analysis for fragmet #1(A:-2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.007
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].
3A0THR0-0.0080.0012.974-1.0011.3070.033-1.166-1.1750.003
4A1MET0-0.0070.0005.4560.5910.5910.0000.0000.0000.000
5A2GLU-1-0.796-0.8579.234-1.023-1.0230.0000.0000.0000.000
6A3ILE0-0.045-0.02411.2650.0810.0810.0000.0000.0000.000
7A4PRO00.009-0.00714.3310.0350.0350.0000.0000.0000.000
8A5PRO00.0380.02116.558-0.005-0.0050.0000.0000.0000.000
9A6THR00.0180.01017.7790.0090.0090.0000.0000.0000.000
10A7HIS00.0100.01917.6460.0240.0240.0000.0000.0000.000
11A8TYR00.0580.02019.591-0.001-0.0010.0000.0000.0000.000
12A9ALA00.0080.00615.9460.0230.0230.0000.0000.0000.000
13A10ALA00.0300.01715.403-0.001-0.0010.0000.0000.0000.000
14A11SER0-0.022-0.01716.3560.0420.0420.0000.0000.0000.000
15A12ARG10.8540.93318.9900.2790.2790.0000.0000.0000.000
16A13ALA00.0390.02414.3960.0330.0330.0000.0000.0000.000
17A14ALA00.0340.00616.5480.0400.0400.0000.0000.0000.000
18A15SER0-0.029-0.02617.8890.0420.0420.0000.0000.0000.000
19A16VAL0-0.017-0.00517.7470.0290.0290.0000.0000.0000.000
20A17ALA00.0300.01016.4050.0340.0340.0000.0000.0000.000
21A18GLU-1-0.795-0.87818.477-0.078-0.0780.0000.0000.0000.000
22A19ASN0-0.030-0.01021.9230.0280.0280.0000.0000.0000.000
23A20CYS0-0.0480.00019.8890.0250.0250.0000.0000.0000.000
24A21ILE00.0200.00818.9230.0180.0180.0000.0000.0000.000
25A22ASN0-0.042-0.04222.6060.0190.0190.0000.0000.0000.000
26A23TYR0-0.0130.00625.2140.0060.0060.0000.0000.0000.000
27A24GLN0-0.025-0.02720.1790.0190.0190.0000.0000.0000.000
28A25GLN0-0.014-0.00224.5870.0060.0060.0000.0000.0000.000
29A26GLY00.0280.02527.021-0.001-0.0010.0000.0000.0000.000
30A27THR0-0.077-0.07929.7500.0040.0040.0000.0000.0000.000
31A28PRO0-0.027-0.01533.529-0.005-0.0050.0000.0000.0000.000
32A29HIS10.7910.87935.940-0.005-0.0050.0000.0000.0000.000
33A30LYS10.8410.93528.594-0.031-0.0310.0000.0000.0000.000
34A31LEU0-0.0140.00029.8740.0010.0010.0000.0000.0000.000
35A32PHE0-0.001-0.00325.4940.0020.0020.0000.0000.0000.000
36A33LEU0-0.0150.01326.483-0.004-0.0040.0000.0000.0000.000
37A34VAL00.000-0.01621.0680.0040.0040.0000.0000.0000.000
38A35GLN0-0.0280.00223.634-0.009-0.0090.0000.0000.0000.000
39A36THR0-0.033-0.03521.830-0.007-0.0070.0000.0000.0000.000
40A37VAL0-0.0160.00316.7940.0070.0070.0000.0000.0000.000
41A38GLN0-0.087-0.05517.385-0.004-0.0040.0000.0000.0000.000
42A39GLN0-0.051-0.0649.6440.1190.1190.0000.0000.0000.000
43A40ALA0-0.0130.00012.1190.0490.0490.0000.0000.0000.000
44A41SER0-0.001-0.0297.579-0.015-0.0150.0000.0000.0000.000
45A42LYS10.8070.9089.2660.9080.9080.0000.0000.0000.000
46A43GLU-1-0.806-0.9081.814-14.777-18.50911.791-4.821-3.238-0.058
47A44ASP-1-0.904-0.9596.510-0.205-0.2050.0000.0000.0000.000
48A45ILE0-0.0040.0155.852-0.295-0.2950.0000.0000.0000.000
49A46PRO00.0470.0127.3510.2070.2070.0000.0000.0000.000
50A47GLY0-0.030-0.01010.3300.1050.1050.0000.0000.0000.000
51A48ARG10.7530.84010.293-0.017-0.0170.0000.0000.0000.000
52A49GLY00.0170.00311.2920.0560.0560.0000.0000.0000.000
53A50HIS0-0.051-0.0339.947-0.172-0.1720.0000.0000.0000.000
54A51LYS10.8460.9154.2050.5020.589-0.001-0.006-0.0810.000
55A52TYR0-0.048-0.0598.449-0.308-0.3080.0000.0000.0000.000
56A53HIS0-0.005-0.0036.6420.2160.2160.0000.0000.0000.000
57A54LEU00.005-0.0038.784-0.059-0.0590.0000.0000.0000.000
58A55LYS10.8760.92910.4310.2470.2470.0000.0000.0000.000
59A56PHE00.0410.01114.765-0.036-0.0360.0000.0000.0000.000
60A57SER00.0260.02318.4730.0220.0220.0000.0000.0000.000
61A58VAL0-0.033-0.02221.555-0.013-0.0130.0000.0000.0000.000
62A59GLU-1-0.867-0.92224.065-0.052-0.0520.0000.0000.0000.000
63A60GLU-1-0.740-0.87127.797-0.016-0.0160.0000.0000.0000.000
64A61ILE0-0.013-0.01130.045-0.001-0.0010.0000.0000.0000.000
65A62ILE0-0.105-0.03932.745-0.001-0.0010.0000.0000.0000.000
66A63GLN00.006-0.01934.944-0.003-0.0030.0000.0000.0000.000
67A64LYS10.8210.91433.7190.0240.0240.0000.0000.0000.000
68A65GLN0-0.059-0.03334.1930.0000.0000.0000.0000.0000.000
69A66VAL0-0.0030.00828.1320.0020.0020.0000.0000.0000.000
70A67THR0-0.017-0.01726.157-0.007-0.0070.0000.0000.0000.000
71A68VAL0-0.0050.00823.2250.0060.0060.0000.0000.0000.000
72A69ASN00.0310.01419.212-0.032-0.0320.0000.0000.0000.000
73A70CYS0-0.0320.00217.9000.0370.0370.0000.0000.0000.000
74A71THR0-0.010-0.00311.438-0.050-0.0500.0000.0000.0000.000
75A72ALA0-0.014-0.01412.8660.0620.0620.0000.0000.0000.000
76A73GLU-1-0.824-0.8886.4930.2040.2040.0000.0000.0000.000
77A74VAL0-0.006-0.00310.8480.0960.0960.0000.0000.0000.000
78A75LEU0-0.025-0.0039.597-0.158-0.1580.0000.0000.0000.000
79A76TYR00.0310.00911.5950.0910.0910.0000.0000.0000.000
80A77PRO0-0.002-0.00413.572-0.058-0.0580.0000.0000.0000.000
81A78GLN00.0220.01815.490-0.011-0.0110.0000.0000.0000.000
82A79MET00.0240.01116.9770.0430.0430.0000.0000.0000.000
83A80GLY0-0.002-0.00319.7080.0050.0050.0000.0000.0000.000
84A81GLN0-0.053-0.02519.2930.0340.0340.0000.0000.0000.000
85A82GLY0-0.017-0.00821.956-0.009-0.0090.0000.0000.0000.000
86A83SER0-0.057-0.02219.1970.0120.0120.0000.0000.0000.000
87A84ALA00.0540.02219.782-0.021-0.0210.0000.0000.0000.000
88A85PRO0-0.017-0.00316.2240.0110.0110.0000.0000.0000.000
89A86GLU-1-0.801-0.84613.5800.1440.1440.0000.0000.0000.000
90A87VAL0-0.030-0.02213.806-0.049-0.0490.0000.0000.0000.000
91A88ASN0-0.022-0.00712.6450.0700.0700.0000.0000.0000.000
92A89PHE00.008-0.01014.083-0.055-0.0550.0000.0000.0000.000
93A90THR0-0.0070.00014.9720.0530.0530.0000.0000.0000.000
94A91PHE00.0360.00917.036-0.030-0.0300.0000.0000.0000.000
95A92GLU-1-0.915-0.94719.1330.0160.0160.0000.0000.0000.000
96A93GLY0-0.004-0.00820.0010.0120.0120.0000.0000.0000.000
97A94GLU-1-0.968-0.98123.7110.0780.0780.0000.0000.0000.000
98A95ILE00.0160.00924.510-0.012-0.0120.0000.0000.0000.000
99A96GLY00.0190.01227.753-0.008-0.0080.0000.0000.0000.000
100A97LYS10.9130.94631.383-0.026-0.0260.0000.0000.0000.000
101A98ASN00.0790.05831.779-0.007-0.0070.0000.0000.0000.000
102A99PRO00.0170.01434.2720.0000.0000.0000.0000.0000.000
103A100ASP-1-0.866-0.94636.5640.0330.0330.0000.0000.0000.000
104A101GLU-1-0.926-0.95638.9020.0170.0170.0000.0000.0000.000
105A102GLU-1-0.830-0.90540.590-0.001-0.0010.0000.0000.0000.000
106A103ASP-1-0.763-0.85436.8220.0090.0090.0000.0000.0000.000
107A104ASN0-0.019-0.03640.4580.0000.0000.0000.0000.0000.000
108A105THR0-0.029-0.01843.038-0.001-0.0010.0000.0000.0000.000
109A106PHE0-0.024-0.02340.192-0.001-0.0010.0000.0000.0000.000
110A107TYR0-0.023-0.03242.109-0.001-0.0010.0000.0000.0000.000
111A108GLN00.0450.01744.001-0.001-0.0010.0000.0000.0000.000
112A109SER0-0.028-0.00147.419-0.001-0.0010.0000.0000.0000.000
113A110LEU0-0.038-0.03043.471-0.001-0.0010.0000.0000.0000.000
114A111MET0-0.0060.01246.4370.0000.0000.0000.0000.0000.000
115A112SER0-0.044-0.02248.8670.0000.0000.0000.0000.0000.000
116A113LEU0-0.074-0.02448.511-0.001-0.0010.0000.0000.0000.000
117A114LYS10.9290.95652.334-0.003-0.0030.0000.0000.0000.000
118A115ARG10.9270.96154.2010.0030.0030.0000.0000.0000.000
119A116PRO00.0360.02449.4830.0000.0000.0000.0000.0000.000
120A117LEU00.0180.01544.957-0.002-0.0020.0000.0000.0000.000
121A118GLU-1-0.871-0.93047.672-0.009-0.0090.0000.0000.0000.000
122A119ALA0-0.049-0.01446.0790.0000.0000.0000.0000.0000.000
123A120GLN00.014-0.00145.4640.0010.0010.0000.0000.0000.000
124A121ASP-1-0.901-0.92844.088-0.031-0.0310.0000.0000.0000.000
125A122ILE0-0.0040.02940.9390.0010.0010.0000.0000.0000.000
126A123PRO00.007-0.02238.9940.0000.0000.0000.0000.0000.000
127A124ASP-1-0.733-0.84842.014-0.035-0.0350.0000.0000.0000.000
128A125ASN0-0.072-0.04643.581-0.004-0.0040.0000.0000.0000.000
129A126PHE0-0.056-0.02744.953-0.002-0.0020.0000.0000.0000.000
130A127GLY00.0350.03141.995-0.002-0.0020.0000.0000.0000.000
131A128ASN0-0.113-0.06442.7380.0020.0020.0000.0000.0000.000
132A129VAL00.017-0.00941.1160.0000.0000.0000.0000.0000.000
133A130SER0-0.0090.00344.5190.0000.0000.0000.0000.0000.000
134A131PRO00.044-0.00445.3550.0000.0000.0000.0000.0000.000
135A132GLN00.0430.02045.0600.0000.0000.0000.0000.0000.000
136A133MET00.0240.01744.2430.0020.0020.0000.0000.0000.000
137A134LYS10.8770.95738.5040.0260.0260.0000.0000.0000.000
138A135PRO00.0420.02539.391-0.002-0.0020.0000.0000.0000.000
139A136VAL00.0150.01538.8520.0010.0010.0000.0000.0000.000
140A137GLN00.0530.04137.0770.0020.0020.0000.0000.0000.000
141A138HIS0-0.007-0.01035.132-0.002-0.0020.0000.0000.0000.000
142A139LEU00.0460.02434.1540.0000.0000.0000.0000.0000.000
143A140ALA00.0090.01034.3060.0010.0010.0000.0000.0000.000
144A141TRP00.030-0.01031.1430.0000.0000.0000.0000.0000.000
145A142VAL0-0.0060.01629.893-0.004-0.0040.0000.0000.0000.000
146A143ALA0-0.023-0.01329.3070.0010.0010.0000.0000.0000.000
147A144CYS0-0.046-0.03529.957-0.003-0.0030.0000.0000.0000.000
148A145GLY00.0660.04626.662-0.008-0.0080.0000.0000.0000.000
149A146TYR0-0.039-0.02724.851-0.006-0.0060.0000.0000.0000.000
150A147VAL0-0.023-0.00525.652-0.004-0.0040.0000.0000.0000.000
151A148MET00.0090.01325.707-0.009-0.0090.0000.0000.0000.000
152A149TRP00.0050.01318.788-0.008-0.0080.0000.0000.0000.000
153A150GLN0-0.026-0.02021.729-0.003-0.0030.0000.0000.0000.000
154A151ASN0-0.023-0.02423.5180.0000.0000.0000.0000.0000.000
155A152SER0-0.049-0.03320.574-0.014-0.0140.0000.0000.0000.000
156A153THR00.004-0.01019.304-0.005-0.0050.0000.0000.0000.000
157A154GLU-1-0.728-0.82514.521-0.536-0.5360.0000.0000.0000.000
158A155ASP-1-0.904-0.94818.485-0.259-0.2590.0000.0000.0000.000
159A156THR0-0.063-0.01222.1810.0130.0130.0000.0000.0000.000
160A157TRP00.002-0.03822.482-0.027-0.0270.0000.0000.0000.000
161A158TYR0-0.015-0.00524.6600.0140.0140.0000.0000.0000.000
162A159LYS10.9140.95325.7600.1090.1090.0000.0000.0000.000
163A160MET00.0430.02929.0190.0030.0030.0000.0000.0000.000
164A161LEU0-0.040-0.00231.985-0.001-0.0010.0000.0000.0000.000
165A162LYS10.8380.88735.1840.0410.0410.0000.0000.0000.000
166A163ILE0-0.0030.00237.9540.0000.0000.0000.0000.0000.000
167A164GLN0-0.021-0.00839.843-0.002-0.0020.0000.0000.0000.000
168A165THR00.034-0.00942.2030.0010.0010.0000.0000.0000.000
169A166VAL0-0.037-0.01341.6650.0000.0000.0000.0000.0000.000
170A167LYS10.8720.92543.3020.0110.0110.0000.0000.0000.000
171A168GLN00.0220.01644.185-0.001-0.0010.0000.0000.0000.000
172A169VAL0-0.040-0.02643.859-0.001-0.0010.0000.0000.0000.000
173A170GLN0-0.051-0.04246.3590.0020.0020.0000.0000.0000.000
174A171ARG10.8210.89740.581-0.021-0.0210.0000.0000.0000.000
175A172ASN0-0.017-0.00347.165-0.001-0.0010.0000.0000.0000.000
176A173ASP-1-0.823-0.90143.5020.0270.0270.0000.0000.0000.000
177A174ASP-1-0.866-0.93343.8460.0270.0270.0000.0000.0000.000
178A175PHE0-0.069-0.01236.9690.0000.0000.0000.0000.0000.000
179A176ILE00.0260.01840.931-0.003-0.0030.0000.0000.0000.000
180A177GLU-1-0.744-0.85540.2620.0150.0150.0000.0000.0000.000
181A178LEU0-0.031-0.01039.754-0.001-0.0010.0000.0000.0000.000
182A179ASP-1-0.838-0.90239.718-0.011-0.0110.0000.0000.0000.000
183A180TYR0-0.009-0.02837.495-0.001-0.0010.0000.0000.0000.000
184A181THR00.0040.00438.420-0.001-0.0010.0000.0000.0000.000
185A182ILE0-0.023-0.02333.3760.0000.0000.0000.0000.0000.000
186A183LEU0-0.022-0.00636.441-0.001-0.0010.0000.0000.0000.000
187A184LEU00.0450.02029.478-0.001-0.0010.0000.0000.0000.000
188A185HIS0-0.026-0.03231.7560.0050.0050.0000.0000.0000.000
189A186ASP-1-0.763-0.86826.871-0.145-0.1450.0000.0000.0000.000
190A187ILE0-0.016-0.01726.8520.0010.0010.0000.0000.0000.000
191A188ALA0-0.054-0.02725.222-0.008-0.0080.0000.0000.0000.000
192A189SER0-0.047-0.04327.286-0.004-0.0040.0000.0000.0000.000
193A190GLN0-0.049-0.02229.8840.0150.0150.0000.0000.0000.000
194A191GLU-1-0.894-0.90431.550-0.090-0.0900.0000.0000.0000.000
195A192ILE00.0290.00533.1750.0000.0000.0000.0000.0000.000
196A193ILE0-0.065-0.03631.1280.0010.0010.0000.0000.0000.000
197A194PRO00.0260.01534.5570.0020.0020.0000.0000.0000.000
198A195TRP0-0.012-0.01329.502-0.005-0.0050.0000.0000.0000.000
199A196GLN0-0.049-0.03635.6970.0020.0020.0000.0000.0000.000
200A197MET0-0.022-0.01633.5860.0000.0000.0000.0000.0000.000
201A198GLN00.0000.01935.905-0.002-0.0020.0000.0000.0000.000
202A199VAL0-0.016-0.01934.5960.0020.0020.0000.0000.0000.000
203A200LEU0-0.006-0.00635.8230.0000.0000.0000.0000.0000.000
204A201TRP00.008-0.02335.182-0.001-0.0010.0000.0000.0000.000
205A202HIS00.0770.03837.0400.0010.0010.0000.0000.0000.000
206A203PRO0-0.017-0.00236.9450.0030.0030.0000.0000.0000.000
207A204GLN0-0.0160.00436.3160.0010.0010.0000.0000.0000.000
208A205TYR0-0.048-0.02233.5080.0050.0050.0000.0000.0000.000
209A206GLY00.0450.04232.2710.0040.0040.0000.0000.0000.000
210A207THR0-0.008-0.02731.345-0.004-0.0040.0000.0000.0000.000
211A208LYS10.9040.95130.732-0.032-0.0320.0000.0000.0000.000
212A209VAL00.0410.03130.397-0.003-0.0030.0000.0000.0000.000
213A210LYS10.7660.89231.959-0.008-0.0080.0000.0000.0000.000
214A211HIS0-0.012-0.02734.0890.0030.0030.0000.0000.0000.000
215A212ASN00.0300.01429.811-0.007-0.0070.0000.0000.0000.000
216A213SER00.0120.01633.4790.0030.0030.0000.0000.0000.000
217A214ARG10.9821.00429.9360.0720.0720.0000.0000.0000.000
218A215LEU0-0.026-0.00834.3620.0040.0040.0000.0000.0000.000
219A216PRO0-0.001-0.01137.638-0.005-0.0050.0000.0000.0000.000
220A217LYS10.9090.96236.3630.0680.0680.0000.0000.0000.000