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: 43MYN

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2745234.447928
FMO2-HF: Nuclear repulsion 2655706.785826
FMO2-HF: Total energy -89527.662102
FMO2-MP2: Total energy -89786.528531


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.
-12.323-10.8657.186-4.531-4.113-0.037
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 : 0.012 / q_NPA : 0.011
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].
3A0THR0-0.0050.0013.003-1.7110.6770.058-1.195-1.2510.004
4A1MET0-0.0020.0035.4910.6600.6600.0000.0000.0000.000
5A2GLU-1-0.792-0.8669.230-1.009-1.0090.0000.0000.0000.000
6A3ILE0-0.045-0.02411.2080.0870.0870.0000.0000.0000.000
7A4PRO00.002-0.01214.1610.0320.0320.0000.0000.0000.000
8A5PRO00.0600.03616.575-0.008-0.0080.0000.0000.0000.000
9A6THR00.0040.00017.6560.0080.0080.0000.0000.0000.000
10A7HIS00.0100.02017.5100.0220.0220.0000.0000.0000.000
11A8TYR00.0560.00519.296-0.007-0.0070.0000.0000.0000.000
12A9ALA00.0060.00316.0210.0190.0190.0000.0000.0000.000
13A10ALA00.0330.02215.557-0.013-0.0130.0000.0000.0000.000
14A11SER0-0.035-0.01516.4880.0400.0400.0000.0000.0000.000
15A12ARG10.8900.93519.2190.2850.2850.0000.0000.0000.000
16A13ALA00.0220.02114.7070.0280.0280.0000.0000.0000.000
17A14ALA00.0610.02016.8430.0320.0320.0000.0000.0000.000
18A15SER0-0.015-0.00318.0950.0400.0400.0000.0000.0000.000
19A16VAL0-0.028-0.00318.1260.0290.0290.0000.0000.0000.000
20A17ALA00.0270.00416.5540.0300.0300.0000.0000.0000.000
21A18GLU-1-0.820-0.90918.565-0.098-0.0980.0000.0000.0000.000
22A19ASN0-0.041-0.01822.0260.0290.0290.0000.0000.0000.000
23A20CYS0-0.035-0.00219.2930.0260.0260.0000.0000.0000.000
24A21ILE00.0270.02219.2930.0190.0190.0000.0000.0000.000
25A22ASN0-0.033-0.02722.7770.0230.0230.0000.0000.0000.000
26A23TYR0-0.0180.00325.3350.0100.0100.0000.0000.0000.000
27A24GLN0-0.029-0.02420.6730.0180.0180.0000.0000.0000.000
28A25GLN0-0.020-0.01524.6460.0070.0070.0000.0000.0000.000
29A26GLY00.0100.01427.2390.0000.0000.0000.0000.0000.000
30A27THR0-0.077-0.08029.8640.0040.0040.0000.0000.0000.000
31A28PRO0-0.024-0.00933.565-0.005-0.0050.0000.0000.0000.000
32A29HIS10.7970.88236.1760.0120.0120.0000.0000.0000.000
33A30LYS10.8560.94128.8020.0040.0040.0000.0000.0000.000
34A31LEU0-0.006-0.00530.0650.0000.0000.0000.0000.0000.000
35A32PHE0-0.015-0.00925.6020.0020.0020.0000.0000.0000.000
36A33LEU0-0.0220.00826.590-0.004-0.0040.0000.0000.0000.000
37A34VAL0-0.001-0.01121.3340.0030.0030.0000.0000.0000.000
38A35GLN0-0.054-0.02323.887-0.002-0.0020.0000.0000.0000.000
39A36THR0-0.038-0.03621.942-0.004-0.0040.0000.0000.0000.000
40A37VAL00.0050.00816.9740.0040.0040.0000.0000.0000.000
41A38GLN0-0.072-0.05617.428-0.010-0.0100.0000.0000.0000.000
42A39GLN0-0.067-0.0669.7870.1070.1070.0000.0000.0000.000
43A40ALA00.0120.00712.1420.0390.0390.0000.0000.0000.000
44A41SER00.017-0.0087.412-0.013-0.0130.0000.0000.0000.000
45A42LYS10.7990.9209.0790.8560.8560.0000.0000.0000.000
46A43GLU-1-0.856-0.9281.963-11.590-12.5777.129-3.335-2.807-0.041
47A44ASP-1-0.915-0.9506.292-0.358-0.3580.0000.0000.0000.000
48A45ILE00.0070.0055.478-0.258-0.2580.0000.0000.0000.000
49A46PRO00.0410.0057.2900.2400.2400.0000.0000.0000.000
50A47GLY0-0.032-0.01310.3010.0930.0930.0000.0000.0000.000
51A48ARG10.7830.85910.1010.0830.0830.0000.0000.0000.000
52A49GLY00.0160.01411.2690.0570.0570.0000.0000.0000.000
53A50HIS0-0.088-0.0589.773-0.167-0.1670.0000.0000.0000.000
54A51LYS10.8560.9164.7880.8310.888-0.001-0.001-0.0550.000
55A52TYR0-0.053-0.0628.288-0.354-0.3540.0000.0000.0000.000
56A53HIS0-0.066-0.0366.9820.2310.2310.0000.0000.0000.000
57A54LEU00.001-0.0139.101-0.024-0.0240.0000.0000.0000.000
58A55LYS10.9340.97611.4860.2490.2490.0000.0000.0000.000
59A56PHE00.0440.01214.978-0.026-0.0260.0000.0000.0000.000
60A57SER00.0410.04118.5900.0170.0170.0000.0000.0000.000
61A58VAL0-0.034-0.01821.709-0.012-0.0120.0000.0000.0000.000
62A59GLU-1-0.865-0.92924.270-0.069-0.0690.0000.0000.0000.000
63A60GLU-1-0.752-0.87127.989-0.038-0.0380.0000.0000.0000.000
64A61ILE0-0.001-0.02130.1800.0020.0020.0000.0000.0000.000
65A62ILE0-0.090-0.02232.8630.0010.0010.0000.0000.0000.000
66A63GLN0-0.003-0.02434.974-0.001-0.0010.0000.0000.0000.000
67A64LYS10.8120.91134.0710.0380.0380.0000.0000.0000.000
68A65GLN0-0.056-0.03234.3130.0010.0010.0000.0000.0000.000
69A66VAL0-0.0100.00928.3030.0010.0010.0000.0000.0000.000
70A67THR00.0040.00126.256-0.005-0.0050.0000.0000.0000.000
71A68VAL0-0.0100.00023.5630.0060.0060.0000.0000.0000.000
72A69ASN00.012-0.00219.483-0.030-0.0300.0000.0000.0000.000
73A70CYS0-0.029-0.00118.3530.0340.0340.0000.0000.0000.000
74A71THR0-0.030-0.00812.045-0.036-0.0360.0000.0000.0000.000
75A72ALA0-0.009-0.01113.1070.0630.0630.0000.0000.0000.000
76A73GLU-1-0.815-0.8876.866-0.165-0.1650.0000.0000.0000.000
77A74VAL0-0.011-0.00311.0330.1060.1060.0000.0000.0000.000
78A75LEU0-0.030-0.0069.649-0.151-0.1510.0000.0000.0000.000
79A76TYR00.0390.01811.9750.0950.0950.0000.0000.0000.000
80A77PRO00.0190.01013.642-0.060-0.0600.0000.0000.0000.000
81A78GLN00.0240.01415.592-0.002-0.0020.0000.0000.0000.000
82A79MET00.0290.01116.7400.0400.0400.0000.0000.0000.000
83A80GLY0-0.001-0.00519.6620.0100.0100.0000.0000.0000.000
84A81GLN0-0.060-0.01919.0330.0370.0370.0000.0000.0000.000
85A82GLY0-0.023-0.01021.687-0.010-0.0100.0000.0000.0000.000
86A83SER0-0.047-0.01819.2220.0110.0110.0000.0000.0000.000
87A84ALA00.0520.02920.190-0.019-0.0190.0000.0000.0000.000
88A85PRO0-0.005-0.00516.3560.0030.0030.0000.0000.0000.000
89A86GLU-1-0.847-0.87413.7740.0520.0520.0000.0000.0000.000
90A87VAL0-0.013-0.02414.251-0.055-0.0550.0000.0000.0000.000
91A88ASN0-0.0210.00212.5680.0670.0670.0000.0000.0000.000
92A89PHE00.015-0.01414.265-0.054-0.0540.0000.0000.0000.000
93A90THR00.0080.01115.4330.0440.0440.0000.0000.0000.000
94A91PHE00.014-0.00617.485-0.032-0.0320.0000.0000.0000.000
95A92GLU-1-0.916-0.94419.441-0.015-0.0150.0000.0000.0000.000
96A93GLY00.0150.00020.3860.0140.0140.0000.0000.0000.000
97A94GLU-1-0.952-0.97624.1090.0470.0470.0000.0000.0000.000
98A95ILE0-0.0060.00124.734-0.009-0.0090.0000.0000.0000.000
99A96GLY00.0340.00928.060-0.006-0.0060.0000.0000.0000.000
100A97LYS10.9060.94431.691-0.010-0.0100.0000.0000.0000.000
101A98ASN00.0910.06131.620-0.008-0.0080.0000.0000.0000.000
102A99PRO00.0180.02734.4910.0020.0020.0000.0000.0000.000
103A100ASP-1-0.856-0.94736.9830.0110.0110.0000.0000.0000.000
104A101GLU-1-0.941-0.95739.3160.0020.0020.0000.0000.0000.000
105A102GLU-1-0.852-0.92540.443-0.016-0.0160.0000.0000.0000.000
106A103ASP-1-0.750-0.84936.792-0.011-0.0110.0000.0000.0000.000
107A104ASN0-0.015-0.02840.4330.0010.0010.0000.0000.0000.000
108A105THR0-0.037-0.01743.2590.0000.0000.0000.0000.0000.000
109A106PHE0-0.027-0.02240.110-0.001-0.0010.0000.0000.0000.000
110A107TYR0-0.014-0.02342.2500.0000.0000.0000.0000.0000.000
111A108GLN00.0320.00244.094-0.001-0.0010.0000.0000.0000.000
112A109SER0-0.0190.00647.2890.0000.0000.0000.0000.0000.000
113A110LEU0-0.038-0.02943.438-0.001-0.0010.0000.0000.0000.000
114A111MET0-0.0120.00846.5670.0000.0000.0000.0000.0000.000
115A112SER0-0.042-0.02748.9680.0010.0010.0000.0000.0000.000
116A113LEU0-0.094-0.02448.738-0.001-0.0010.0000.0000.0000.000
117A114LYS10.9390.97252.4820.0070.0070.0000.0000.0000.000
118A115ARG10.9340.96054.6390.0130.0130.0000.0000.0000.000
119A116PRO00.0380.01749.9020.0000.0000.0000.0000.0000.000
120A117LEU00.0230.01645.202-0.001-0.0010.0000.0000.0000.000
121A118GLU-1-0.868-0.92648.029-0.019-0.0190.0000.0000.0000.000
122A119ALA0-0.061-0.02446.1190.0000.0000.0000.0000.0000.000
123A120GLN00.013-0.00945.5010.0010.0010.0000.0000.0000.000
124A121ASP-1-0.898-0.92544.083-0.040-0.0400.0000.0000.0000.000
125A122ILE0-0.0120.03340.9190.0010.0010.0000.0000.0000.000
126A123PRO00.027-0.02239.076-0.002-0.0020.0000.0000.0000.000
127A124ASP-1-0.759-0.86342.235-0.042-0.0420.0000.0000.0000.000
128A125ASN0-0.054-0.03843.873-0.004-0.0040.0000.0000.0000.000
129A126PHE0-0.052-0.03444.623-0.002-0.0020.0000.0000.0000.000
130A127GLY00.0240.02942.096-0.001-0.0010.0000.0000.0000.000
131A128ASN0-0.096-0.05542.7180.0010.0010.0000.0000.0000.000
132A129VAL00.011-0.00841.0630.0000.0000.0000.0000.0000.000
133A130SER0-0.019-0.00144.5670.0000.0000.0000.0000.0000.000
134A131PRO00.0580.00745.3440.0000.0000.0000.0000.0000.000
135A132GLN00.0370.01045.164-0.001-0.0010.0000.0000.0000.000
136A133MET00.0170.01644.1470.0020.0020.0000.0000.0000.000
137A134LYS10.8950.96238.9160.0400.0400.0000.0000.0000.000
138A135PRO00.0420.02939.419-0.002-0.0020.0000.0000.0000.000
139A136VAL00.0250.02039.0190.0000.0000.0000.0000.0000.000
140A137GLN00.0380.02837.0930.0010.0010.0000.0000.0000.000
141A138HIS00.001-0.01535.328-0.002-0.0020.0000.0000.0000.000
142A139LEU00.0470.03434.235-0.002-0.0020.0000.0000.0000.000
143A140ALA00.0120.00834.4620.0000.0000.0000.0000.0000.000
144A141TRP00.027-0.00731.226-0.001-0.0010.0000.0000.0000.000
145A142VAL00.0030.01730.053-0.005-0.0050.0000.0000.0000.000
146A143ALA0-0.021-0.01329.491-0.001-0.0010.0000.0000.0000.000
147A144CYS0-0.053-0.03430.106-0.004-0.0040.0000.0000.0000.000
148A145GLY00.0690.05226.812-0.009-0.0090.0000.0000.0000.000
149A146TYR0-0.046-0.02925.126-0.007-0.0070.0000.0000.0000.000
150A147VAL0-0.013-0.00925.907-0.005-0.0050.0000.0000.0000.000
151A148MET00.0040.00225.873-0.009-0.0090.0000.0000.0000.000
152A149TRP0-0.028-0.00519.061-0.005-0.0050.0000.0000.0000.000
153A150GLN0-0.024-0.01921.845-0.005-0.0050.0000.0000.0000.000
154A151ASN0-0.029-0.02723.369-0.001-0.0010.0000.0000.0000.000
155A152SER0-0.027-0.02220.976-0.009-0.0090.0000.0000.0000.000
156A153THR00.000-0.00619.572-0.010-0.0100.0000.0000.0000.000
157A154GLU-1-0.750-0.83714.847-0.542-0.5420.0000.0000.0000.000
158A155ASP-1-0.902-0.94318.928-0.258-0.2580.0000.0000.0000.000
159A156THR0-0.069-0.01122.2610.0210.0210.0000.0000.0000.000
160A157TRP0-0.024-0.04422.636-0.029-0.0290.0000.0000.0000.000
161A158TYR0-0.030-0.01124.8140.0170.0170.0000.0000.0000.000
162A159LYS10.9380.97725.7100.1330.1330.0000.0000.0000.000
163A160MET00.0270.02829.3800.0030.0030.0000.0000.0000.000
164A161LEU0-0.035-0.00832.1980.0000.0000.0000.0000.0000.000
165A162LYS10.8030.86835.3960.0520.0520.0000.0000.0000.000
166A163ILE00.0100.01237.944-0.001-0.0010.0000.0000.0000.000
167A164GLN00.003-0.00239.939-0.001-0.0010.0000.0000.0000.000
168A165THR00.034-0.00442.3640.0020.0020.0000.0000.0000.000
169A166VAL0-0.041-0.01141.973-0.001-0.0010.0000.0000.0000.000
170A167LYS10.8820.92943.7300.0230.0230.0000.0000.0000.000
171A168GLN00.0210.01544.957-0.001-0.0010.0000.0000.0000.000
172A169VAL0-0.017-0.01644.4480.0000.0000.0000.0000.0000.000
173A170GLN0-0.057-0.04046.8410.0020.0020.0000.0000.0000.000
174A171ARG10.8130.90340.853-0.004-0.0040.0000.0000.0000.000
175A172ASN0-0.009-0.00447.470-0.001-0.0010.0000.0000.0000.000
176A173ASP-1-0.818-0.90344.0020.0090.0090.0000.0000.0000.000
177A174ASP-1-0.860-0.91844.2820.0110.0110.0000.0000.0000.000
178A175PHE0-0.075-0.03337.459-0.001-0.0010.0000.0000.0000.000
179A176ILE00.0080.01641.209-0.002-0.0020.0000.0000.0000.000
180A177GLU-1-0.748-0.86740.724-0.005-0.0050.0000.0000.0000.000
181A178LEU0-0.039-0.02039.844-0.001-0.0010.0000.0000.0000.000
182A179ASP-1-0.871-0.90539.905-0.025-0.0250.0000.0000.0000.000
183A180TYR00.000-0.03337.8780.0000.0000.0000.0000.0000.000
184A181THR0-0.0020.00439.076-0.001-0.0010.0000.0000.0000.000
185A182ILE0-0.026-0.02833.4880.0010.0010.0000.0000.0000.000
186A183LEU0-0.028-0.00436.6190.0000.0000.0000.0000.0000.000
187A184LEU00.0230.01429.898-0.001-0.0010.0000.0000.0000.000
188A185HIS0-0.022-0.03431.9050.0040.0040.0000.0000.0000.000
189A186ASP-1-0.740-0.87427.337-0.163-0.1630.0000.0000.0000.000
190A187ILE0-0.015-0.02227.0980.0020.0020.0000.0000.0000.000
191A188ALA0-0.059-0.01825.388-0.005-0.0050.0000.0000.0000.000
192A189SER0-0.037-0.04627.425-0.003-0.0030.0000.0000.0000.000
193A190GLN0-0.064-0.02030.1420.0170.0170.0000.0000.0000.000
194A191GLU-1-0.877-0.90031.565-0.104-0.1040.0000.0000.0000.000
195A192ILE00.013-0.00633.289-0.001-0.0010.0000.0000.0000.000
196A193ILE0-0.035-0.01531.1170.0030.0030.0000.0000.0000.000
197A194PRO00.0130.00834.6270.0010.0010.0000.0000.0000.000
198A195TRP0-0.003-0.01429.819-0.004-0.0040.0000.0000.0000.000
199A196GLN0-0.031-0.02235.8560.0010.0010.0000.0000.0000.000
200A197MET0-0.026-0.00933.901-0.002-0.0020.0000.0000.0000.000
201A198GLN0-0.0090.01736.070-0.001-0.0010.0000.0000.0000.000
202A199VAL0-0.008-0.02734.9760.0010.0010.0000.0000.0000.000
203A200LEU0-0.020-0.00436.1300.0010.0010.0000.0000.0000.000
204A201TRP00.015-0.02035.223-0.001-0.0010.0000.0000.0000.000
205A202HIS00.0810.03737.1410.0020.0020.0000.0000.0000.000
206A203PRO0-0.0150.00037.0220.0010.0010.0000.0000.0000.000
207A204GLN0-0.0310.00036.7510.0020.0020.0000.0000.0000.000
208A205TYR0-0.045-0.02934.1510.0030.0030.0000.0000.0000.000
209A206GLY00.0520.04632.6350.0020.0020.0000.0000.0000.000
210A207THR0-0.012-0.02431.497-0.001-0.0010.0000.0000.0000.000
211A208LYS10.9660.98531.276-0.007-0.0070.0000.0000.0000.000
212A209VAL00.0160.01630.728-0.001-0.0010.0000.0000.0000.000
213A210LYS10.7570.88332.1570.0060.0060.0000.0000.0000.000
214A211HIS0-0.002-0.01834.2410.0040.0040.0000.0000.0000.000
215A212ASN00.0400.01630.323-0.007-0.0070.0000.0000.0000.000
216A213SER00.0040.01633.4150.0020.0020.0000.0000.0000.000
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