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: YZLR2

Calculation Name: 1W30-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1W30

Chain ID: A

ChEMBL ID:

UniProt ID: P9WHK3

Base Structure: X-ray

Registration Date: 2023-09-20

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 174
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1696689.983535
FMO2-HF: Nuclear repulsion 1632132.610813
FMO2-HF: Total energy -64557.372722
FMO2-MP2: Total energy -64750.06742


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:12:GLU)


Summations of interaction energy for fragment #1(A:12:GLU)
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.
-172.687-187.82246.44-17.568-13.7370.124
Interaction energy analysis for fragmet #1(A:12:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.845 / q_NPA : -0.906
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].
3A14ARG10.9490.9653.813-26.237-24.249-0.023-1.065-0.9000.006
4A15GLU-1-0.937-0.9676.78918.56118.5610.0000.0000.0000.000
5A16LEU00.0100.0069.647-0.454-0.4540.0000.0000.0000.000
6A17MET0-0.042-0.01212.547-1.226-1.2260.0000.0000.0000.000
7A18SER00.1260.06015.671-0.072-0.0720.0000.0000.0000.000
8A19ALA00.052-0.00317.277-0.413-0.4130.0000.0000.0000.000
9A20ALA00.0150.00919.667-0.500-0.5000.0000.0000.0000.000
10A21ASN00.0240.02718.7750.2340.2340.0000.0000.0000.000
11A22VAL0-0.0060.02818.639-0.382-0.3820.0000.0000.0000.000
12A23GLY00.0670.02721.431-0.382-0.3820.0000.0000.0000.000
13A24ARG10.9470.98524.583-10.890-10.8900.0000.0000.0000.000
14A25THR0-0.041-0.02221.957-0.252-0.2520.0000.0000.0000.000
15A26ILE00.007-0.00823.623-0.167-0.1670.0000.0000.0000.000
16A27SER00.0320.02326.518-0.364-0.3640.0000.0000.0000.000
17A28ARG10.8050.91024.111-11.980-11.9800.0000.0000.0000.000
18A29ILE0-0.007-0.01524.567-0.183-0.1830.0000.0000.0000.000
19A30ALA00.0270.00929.077-0.226-0.2260.0000.0000.0000.000
20A31HIS0-0.027-0.01632.178-0.427-0.4270.0000.0000.0000.000
21A32GLN00.0440.03129.1430.2320.2320.0000.0000.0000.000
22A33ILE0-0.022-0.01430.906-0.123-0.1230.0000.0000.0000.000
23A34ILE00.0090.03134.449-0.148-0.1480.0000.0000.0000.000
24A35GLU-1-0.904-0.95135.2098.5308.5300.0000.0000.0000.000
25A36LYS10.8020.89233.137-9.327-9.3270.0000.0000.0000.000
26A37THR0-0.121-0.09736.718-0.140-0.1400.0000.0000.0000.000
27A38ALA00.0530.02939.547-0.123-0.1230.0000.0000.0000.000
28A39LEU0-0.064-0.03238.568-0.138-0.1380.0000.0000.0000.000
29A40ASP-1-0.890-0.93341.6277.4747.4740.0000.0000.0000.000
30A41ASP-1-0.978-0.97844.1696.7276.7270.0000.0000.0000.000
31A42PRO0-0.062-0.04546.9350.0060.0060.0000.0000.0000.000
32A43VAL00.0340.00948.168-0.007-0.0070.0000.0000.0000.000
33A44GLY0-0.003-0.00849.615-0.156-0.1560.0000.0000.0000.000
34A45PRO0-0.029-0.01049.3230.1120.1120.0000.0000.0000.000
35A46ASP-1-0.899-0.95046.9396.6416.6410.0000.0000.0000.000
36A47ALA0-0.0130.02045.1270.1330.1330.0000.0000.0000.000
37A48PRO0-0.041-0.00441.830-0.098-0.0980.0000.0000.0000.000
38A49ARG10.8830.92743.115-6.955-6.9550.0000.0000.0000.000
39A50VAL00.0490.01937.4260.0970.0970.0000.0000.0000.000
40A51VAL0-0.037-0.02136.966-0.035-0.0350.0000.0000.0000.000
41A52LEU0-0.0060.00432.3360.1950.1950.0000.0000.0000.000
42A53LEU0-0.022-0.00632.699-0.088-0.0880.0000.0000.0000.000
43A54GLY00.0160.01128.6540.2750.2750.0000.0000.0000.000
44A55ILE00.0310.01225.138-0.342-0.3420.0000.0000.0000.000
45A56PRO0-0.0410.01225.1840.4820.4820.0000.0000.0000.000
46A57THR0-0.014-0.01822.0560.1850.1850.0000.0000.0000.000
47A58ARG10.7910.82917.030-15.931-15.9310.0000.0000.0000.000
48A59GLY00.1110.06522.470-0.117-0.1170.0000.0000.0000.000
49A60VAL0-0.0190.00124.821-0.326-0.3260.0000.0000.0000.000
50A61THR0-0.0150.01524.590-0.197-0.1970.0000.0000.0000.000
51A62LEU00.0180.01423.113-0.159-0.1590.0000.0000.0000.000
52A63ALA00.0610.02726.238-0.213-0.2130.0000.0000.0000.000
53A64ASN00.000-0.00329.585-0.395-0.3950.0000.0000.0000.000
54A65ARG10.6740.78023.103-11.943-11.9430.0000.0000.0000.000
55A66LEU00.0200.00727.857-0.107-0.1070.0000.0000.0000.000
56A67ALA00.0190.02130.973-0.213-0.2130.0000.0000.0000.000
57A68GLY00.0020.00533.112-0.244-0.2440.0000.0000.0000.000
58A69ASN0-0.060-0.05230.0700.1650.1650.0000.0000.0000.000
59A70ILE00.0210.00833.563-0.126-0.1260.0000.0000.0000.000
60A71THR0-0.027-0.02836.045-0.228-0.2280.0000.0000.0000.000
61A72GLU-1-0.903-0.92633.9108.7028.7020.0000.0000.0000.000
62A73TYR0-0.124-0.06232.4460.1250.1250.0000.0000.0000.000
63A74SER00.026-0.00338.286-0.133-0.1330.0000.0000.0000.000
64A75GLY0-0.006-0.00341.099-0.198-0.1980.0000.0000.0000.000
65A76ILE00.0050.01140.787-0.125-0.1250.0000.0000.0000.000
66A77HIS0-0.0180.00940.2300.3020.3020.0000.0000.0000.000
67A78VAL00.0100.02036.682-0.117-0.1170.0000.0000.0000.000
68A79GLY00.0190.00838.5260.0740.0740.0000.0000.0000.000
69A80HIS0-0.030-0.04033.5450.0360.0360.0000.0000.0000.000
70A81GLY00.0350.01634.030-0.209-0.2090.0000.0000.0000.000
71A82ALA0-0.086-0.03430.9900.3560.3560.0000.0000.0000.000
72A83LEU00.0230.00830.899-0.300-0.3000.0000.0000.0000.000
73A84ASP-1-0.818-0.89729.66410.31410.3140.0000.0000.0000.000
74A85ILE0-0.007-0.00525.596-0.170-0.1700.0000.0000.0000.000
75A86THR0-0.109-0.08628.5650.2830.2830.0000.0000.0000.000
76A87LEU0-0.009-0.00729.5610.0920.0920.0000.0000.0000.000
77A88TYR0-0.058-0.05331.243-0.040-0.0400.0000.0000.0000.000
78A89ARG10.9030.98523.671-11.510-11.5100.0000.0000.0000.000
79A90ASP-1-0.868-0.92426.84911.28011.2800.0000.0000.0000.000
80A99PRO00.002-0.03224.3860.0150.0150.0000.0000.0000.000
81A100LEU0-0.060-0.01223.839-0.031-0.0310.0000.0000.0000.000
82A101ALA00.0220.01627.533-0.306-0.3060.0000.0000.0000.000
83A102SER00.0660.03829.9630.0700.0700.0000.0000.0000.000
84A103THR0-0.010-0.01033.0870.2040.2040.0000.0000.0000.000
85A104SER0-0.056-0.02034.692-0.293-0.2930.0000.0000.0000.000
86A105ILE00.0440.02036.1700.1880.1880.0000.0000.0000.000
87A106PRO00.0320.02437.892-0.135-0.1350.0000.0000.0000.000
88A107ALA00.0370.01040.698-0.089-0.0890.0000.0000.0000.000
89A108GLY00.0140.00644.4550.0090.0090.0000.0000.0000.000
90A109GLY00.0070.01442.624-0.058-0.0580.0000.0000.0000.000
91A110ILE0-0.027-0.03138.7860.0700.0700.0000.0000.0000.000
92A111ASP-1-0.805-0.88242.1796.9026.9020.0000.0000.0000.000
93A112ASP-1-0.838-0.90245.2936.6276.6270.0000.0000.0000.000
94A113ALA0-0.050-0.00441.463-0.014-0.0140.0000.0000.0000.000
95A114LEU0-0.0010.00536.9780.0460.0460.0000.0000.0000.000
96A115VAL00.008-0.00434.7860.0600.0600.0000.0000.0000.000
97A116ILE0-0.0020.00631.2390.1420.1420.0000.0000.0000.000
98A117LEU00.0300.01929.6710.0680.0680.0000.0000.0000.000
99A118VAL0-0.009-0.01226.2990.2360.2360.0000.0000.0000.000
100A119ASP-1-0.830-0.94422.91112.84312.8430.0000.0000.0000.000
101A120ASP-1-0.882-0.96018.60515.39815.3980.0000.0000.0000.000
102A121VAL0-0.018-0.01815.8090.4720.4720.0000.0000.0000.000
103A122LEU0-0.0200.00719.087-0.471-0.4710.0000.0000.0000.000
104A123TYR00.0450.01014.5200.6240.6240.0000.0000.0000.000
105A124SER00.0730.04019.187-0.454-0.4540.0000.0000.0000.000
106A125GLY00.0420.01521.783-0.483-0.4830.0000.0000.0000.000
107A126ARG10.8570.90823.601-12.650-12.6500.0000.0000.0000.000
108A127SER00.0370.01822.314-0.389-0.3890.0000.0000.0000.000
109A128VAL00.0340.01925.301-0.345-0.3450.0000.0000.0000.000
110A129ARG10.8610.91727.696-9.898-9.8980.0000.0000.0000.000
111A130SER0-0.006-0.02728.212-0.204-0.2040.0000.0000.0000.000
112A131ALA00.0070.00529.230-0.293-0.2930.0000.0000.0000.000
113A132LEU0-0.015-0.01931.004-0.310-0.3100.0000.0000.0000.000
114A133ASP-1-0.809-0.87033.3658.6938.6930.0000.0000.0000.000
115A134ALA00.0510.02333.144-0.240-0.2400.0000.0000.0000.000
116A135LEU0-0.003-0.01634.645-0.197-0.1970.0000.0000.0000.000
117A136ARG10.8170.91036.768-8.394-8.3940.0000.0000.0000.000
118A137ASP-1-0.844-0.87938.7117.6697.6690.0000.0000.0000.000
119A138VAL0-0.110-0.04437.703-0.131-0.1310.0000.0000.0000.000
120A139GLY00.0430.01140.749-0.202-0.2020.0000.0000.0000.000
121A140ARG10.8570.91741.748-6.935-6.9350.0000.0000.0000.000
122A141PRO0-0.0150.00838.913-0.147-0.1470.0000.0000.0000.000
123A142ARG10.8090.87042.004-6.817-6.8170.0000.0000.0000.000
124A143ALA0-0.051-0.02839.0320.0180.0180.0000.0000.0000.000
125A144VAL00.0080.00033.7390.0160.0160.0000.0000.0000.000
126A145GLN00.0040.02332.9760.1770.1770.0000.0000.0000.000
127A146LEU0-0.017-0.00326.0030.0830.0830.0000.0000.0000.000
128A147ALA00.0170.00927.5350.0530.0530.0000.0000.0000.000
129A148VAL00.016-0.00122.2270.0840.0840.0000.0000.0000.000
130A149LEU0-0.0070.00319.041-0.045-0.0450.0000.0000.0000.000
131A150VAL0-0.031-0.02415.1890.3310.3310.0000.0000.0000.000
132A151ASP-1-0.745-0.82218.64414.28614.2860.0000.0000.0000.000
133A152ARG10.8160.88411.676-22.402-22.4020.0000.0000.0000.000
134A153GLY00.0120.00815.8560.9900.9900.0000.0000.0000.000
135A154HIS0-0.066-0.07214.492-0.785-0.7850.0000.0000.0000.000
136A155ARG10.7530.85719.328-14.251-14.2510.0000.0000.0000.000
137A156GLU-1-0.851-0.92121.29714.31114.3110.0000.0000.0000.000
138A157LEU0-0.0090.00224.860-0.549-0.5490.0000.0000.0000.000
139A158PRO00.0130.01727.1150.3990.3990.0000.0000.0000.000
140A159LEU0-0.014-0.00927.163-0.307-0.3070.0000.0000.0000.000
141A160ARG10.8630.88626.483-9.506-9.5060.0000.0000.0000.000
142A161ALA00.0020.01625.316-0.355-0.3550.0000.0000.0000.000
143A162ASP-1-0.811-0.87627.2519.5259.5250.0000.0000.0000.000
144A163TYR00.005-0.00328.081-0.057-0.0570.0000.0000.0000.000
145A164VAL00.0500.02321.9700.2780.2780.0000.0000.0000.000
146A165GLY0-0.011-0.00522.066-0.254-0.2540.0000.0000.0000.000
147A166LYS10.8610.91215.461-17.888-17.8880.0000.0000.0000.000
148A167ASN00.0400.02318.8470.2230.2230.0000.0000.0000.000
149A168VAL0-0.040-0.03412.3460.2880.2880.0000.0000.0000.000
150A169PRO00.0420.01914.1980.1960.1960.0000.0000.0000.000
151A170THR0-0.0110.01210.9751.4441.4440.0000.0000.0000.000
152A171SER00.008-0.0068.584-1.919-1.9190.0000.0000.0000.000
153A172ARG10.9060.92211.017-17.155-17.1550.0000.0000.0000.000
154A173SER0-0.040-0.0027.8020.9470.9470.0000.0000.0000.000
155A174GLU-1-0.809-0.8616.02040.45040.4500.0000.0000.0000.000
156A175SER0-0.0180.0027.734-4.814-4.8140.0000.0000.0000.000
157A176VAL00.004-0.0038.6981.8931.8930.0000.0000.0000.000
158A177HIS0-0.042-0.0187.730-2.416-2.4160.0000.0000.0000.000
159A178VAL00.0370.02512.4110.2290.2290.0000.0000.0000.000
160A179ARG10.8030.91413.007-18.827-18.8270.0000.0000.0000.000
161A180LEU00.0590.01516.691-0.285-0.2850.0000.0000.0000.000
162A181ARG10.9270.94820.316-11.609-11.6090.0000.0000.0000.000
163A182GLU-1-0.777-0.86021.96711.75511.7550.0000.0000.0000.000
164A183HIS10.8390.90620.551-12.406-12.4060.0000.0000.0000.000
165A184ASP-1-0.724-0.83616.50015.98415.9840.0000.0000.0000.000
166A185GLY00.0150.03117.5400.5470.5470.0000.0000.0000.000
167A186ARG10.9070.93316.265-15.391-15.3910.0000.0000.0000.000
168A187ASP-1-0.748-0.83317.71913.21313.2130.0000.0000.0000.000
169A188GLY00.0290.00815.4800.1960.1960.0000.0000.0000.000
170A189VAL0-0.022-0.00412.783-0.204-0.2040.0000.0000.0000.000
171A190VAL0-0.021-0.0037.4910.3780.3780.0000.0000.0000.000
172A191ILE00.0340.0195.599-1.659-1.6590.0000.0000.0000.000
173A192SER0-0.054-0.0364.3130.2110.363-0.001-0.071-0.0800.000
174A193ARG10.9310.9641.708-125.735-143.01046.464-16.432-12.7570.118