FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: QN1LY

Calculation Name: 3DHU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DHU

Chain ID: A

ChEMBL ID:

UniProt ID: F9USZ1

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptH
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 422
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8020820.792063
FMO2-HF: Nuclear repulsion 7853242.441882
FMO2-HF: Total energy -167578.350181
FMO2-MP2: Total energy -168072.098927


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:6:GLN)


Summations of interaction energy for fragment #1(A:6:GLN)
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.
-41.817-34.09815.154-8.074-14.799-0.032
Interaction energy analysis for fragmet #1(A:6:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / 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].
3A8GLN0-0.001-0.0103.039-4.696-1.7940.017-1.310-1.6080.004
4A9LEU00.1080.0692.829-1.138-0.0590.198-0.318-0.9600.000
5A10ARG10.7650.8845.2852.0082.0080.0000.0000.0000.000
6A11ASN0-0.109-0.0627.8570.7590.7590.0000.0000.0000.000
7A12GLU-1-0.937-0.9617.410-1.964-1.9640.0000.0000.0000.000
8A13MET0-0.073-0.03910.515-0.043-0.0430.0000.0000.0000.000
9A14ILE0-0.0010.0059.9340.0230.0230.0000.0000.0000.000
10A15TYR00.003-0.02513.9160.1280.1280.0000.0000.0000.000
11A16SER0-0.048-0.00317.4210.0160.0160.0000.0000.0000.000
12A17VAL00.002-0.01518.8430.0870.0870.0000.0000.0000.000
13A18PHE00.0250.01322.137-0.024-0.0240.0000.0000.0000.000
14A19VAL0-0.015-0.01524.4970.0400.0400.0000.0000.0000.000
15A20ARG10.7750.89326.8280.4460.4460.0000.0000.0000.000
16A21ASN00.0380.01228.6850.0600.0600.0000.0000.0000.000
17A22TYR0-0.040-0.01625.2110.0030.0030.0000.0000.0000.000
18A23SER0-0.015-0.01428.7670.0260.0260.0000.0000.0000.000
19A24GLU-1-0.885-0.96432.096-0.289-0.2890.0000.0000.0000.000
20A25ALA0-0.062-0.02634.6730.0050.0050.0000.0000.0000.000
21A26GLY0-0.0040.01531.4360.0050.0050.0000.0000.0000.000
22A27ASN00.0290.01330.978-0.019-0.0190.0000.0000.0000.000
23A28PHE00.0900.01125.217-0.021-0.0210.0000.0000.0000.000
24A29ALA0-0.0090.01028.275-0.013-0.0130.0000.0000.0000.000
25A30GLY00.0010.00530.5860.0060.0060.0000.0000.0000.000
26A31VAL00.0130.00523.944-0.007-0.0070.0000.0000.0000.000
27A32THR00.002-0.02626.213-0.009-0.0090.0000.0000.0000.000
28A33ALA0-0.071-0.03027.2300.0100.0100.0000.0000.0000.000
29A34ASP-1-0.814-0.87227.452-0.381-0.3810.0000.0000.0000.000
30A35LEU0-0.014-0.00221.849-0.024-0.0240.0000.0000.0000.000
31A36GLN0-0.058-0.02523.322-0.009-0.0090.0000.0000.0000.000
32A37ARG10.8270.88924.5740.4810.4810.0000.0000.0000.000
33A38ILE00.0230.01219.844-0.021-0.0210.0000.0000.0000.000
34A39LYS10.9290.96717.2190.4540.4540.0000.0000.0000.000
35A40ASP-1-0.865-0.94420.249-0.358-0.3580.0000.0000.0000.000
36A41LEU0-0.085-0.02420.7930.0210.0210.0000.0000.0000.000
37A42GLY0-0.024-0.02818.361-0.007-0.0070.0000.0000.0000.000
38A43THR0-0.061-0.03116.061-0.098-0.0980.0000.0000.0000.000
39A44ASP-1-0.819-0.89711.387-1.010-1.0100.0000.0000.0000.000
40A45ILE0-0.024-0.0208.5670.0280.0280.0000.0000.0000.000
41A46LEU00.015-0.00313.1810.0070.0070.0000.0000.0000.000
42A47TRP0-0.022-0.02114.501-0.083-0.0830.0000.0000.0000.000
43A48LEU0-0.051-0.02316.4480.0890.0890.0000.0000.0000.000
44A49LEU00.020-0.00519.263-0.051-0.0510.0000.0000.0000.000
45A50PRO0-0.0280.00621.0420.0350.0350.0000.0000.0000.000
46A51ILE00.012-0.00122.6750.0440.0440.0000.0000.0000.000
47A52ASN0-0.030-0.00124.1590.0080.0080.0000.0000.0000.000
48A53PRO0-0.020-0.01427.160-0.006-0.0060.0000.0000.0000.000
49A54ILE00.0070.03028.880-0.012-0.0120.0000.0000.0000.000
50A55GLY0-0.0080.00731.0000.0250.0250.0000.0000.0000.000
51A56GLU-1-0.967-0.98833.026-0.244-0.2440.0000.0000.0000.000
52A57VAL0-0.027-0.02636.6790.0070.0070.0000.0000.0000.000
53A58ASN0-0.053-0.03835.093-0.017-0.0170.0000.0000.0000.000
54A59ARG10.8730.94734.1470.2880.2880.0000.0000.0000.000
55A60LYS10.9080.96530.0500.4180.4180.0000.0000.0000.000
56A61GLY00.0060.00233.982-0.015-0.0150.0000.0000.0000.000
57A62THR0-0.094-0.09436.3420.0080.0080.0000.0000.0000.000
58A63LEU0-0.053-0.03333.4860.0140.0140.0000.0000.0000.000
59A64GLY00.0480.03632.500-0.004-0.0040.0000.0000.0000.000
60A65SER00.0270.01926.581-0.024-0.0240.0000.0000.0000.000
61A66PRO00.007-0.00924.6790.0150.0150.0000.0000.0000.000
62A67TYR0-0.049-0.05719.5570.0000.0000.0000.0000.0000.000
63A68ALA00.0030.01524.6980.0010.0010.0000.0000.0000.000
64A69ILE00.0030.00223.3700.0300.0300.0000.0000.0000.000
65A70LYS10.9200.96827.6250.2600.2600.0000.0000.0000.000
66A71ASP-1-0.843-0.94529.224-0.275-0.2750.0000.0000.0000.000
67A72TYR00.0240.00123.254-0.001-0.0010.0000.0000.0000.000
68A73ARG10.8640.92824.9820.2400.2400.0000.0000.0000.000
69A74GLY00.0330.04127.1680.0200.0200.0000.0000.0000.000
70A75ILE0-0.031-0.02626.679-0.035-0.0350.0000.0000.0000.000
71A76ASN0-0.001-0.01428.7320.0550.0550.0000.0000.0000.000
72A77PRO00.0360.01430.590-0.001-0.0010.0000.0000.0000.000
73A78GLU-1-0.833-0.91632.006-0.368-0.3680.0000.0000.0000.000
74A79TYR0-0.048-0.02326.2330.0030.0030.0000.0000.0000.000
75A80GLY00.0210.02530.9870.0000.0000.0000.0000.0000.000
76A81THR0-0.034-0.03032.4800.0050.0050.0000.0000.0000.000
77A82LEU00.0570.01727.205-0.016-0.0160.0000.0000.0000.000
78A83ALA0-0.0050.00328.744-0.013-0.0130.0000.0000.0000.000
79A84ASP-1-0.843-0.92429.774-0.272-0.2720.0000.0000.0000.000
80A85PHE00.0000.00121.190-0.014-0.0140.0000.0000.0000.000
81A86LYS10.9260.96025.0510.2340.2340.0000.0000.0000.000
82A87ALA00.0080.00525.567-0.001-0.0010.0000.0000.0000.000
83A88LEU0-0.0090.00822.039-0.004-0.0040.0000.0000.0000.000
84A89THR00.021-0.00320.577-0.017-0.0170.0000.0000.0000.000
85A90ASP-1-0.910-0.94621.228-0.286-0.2860.0000.0000.0000.000
86A91ARG10.9320.97723.2660.3080.3080.0000.0000.0000.000
87A92ALA00.021-0.00419.1070.0050.0050.0000.0000.0000.000
88A93HIS10.8180.89516.8550.5070.5070.0000.0000.0000.000
89A94GLU-1-0.963-0.95719.552-0.184-0.1840.0000.0000.0000.000
90A95LEU0-0.076-0.04121.1570.0270.0270.0000.0000.0000.000
91A96GLY0-0.040-0.02417.176-0.010-0.0100.0000.0000.0000.000
92A97MET0-0.086-0.02415.288-0.063-0.0630.0000.0000.0000.000
93A98LYS10.8800.9379.0231.0631.0630.0000.0000.0000.000
94A99VAL00.008-0.00314.117-0.051-0.0510.0000.0000.0000.000
95A100MET0-0.0200.0109.654-0.025-0.0250.0000.0000.0000.000
96A101LEU00.0130.00014.8240.0930.0930.0000.0000.0000.000
97A102ASP-1-0.710-0.85215.960-1.226-1.2260.0000.0000.0000.000
98A103ILE0-0.025-0.01215.9660.1170.1170.0000.0000.0000.000
99A104VAL00.0140.00717.605-0.079-0.0790.0000.0000.0000.000
100A105TYR0-0.001-0.01518.0920.0640.0640.0000.0000.0000.000
101A106ASN00.0340.04620.4150.0570.0570.0000.0000.0000.000
102A107HIS00.0580.04821.7570.0600.0600.0000.0000.0000.000
103A108THR00.0120.02624.796-0.022-0.0220.0000.0000.0000.000
104A109SER0-0.016-0.01127.5960.0010.0010.0000.0000.0000.000
105A110PRO00.0040.00430.7860.0080.0080.0000.0000.0000.000
106A111ASP-1-0.786-0.87833.854-0.265-0.2650.0000.0000.0000.000
107A112SER0-0.029-0.03230.3520.0160.0160.0000.0000.0000.000
108A113VAL00.0320.01031.1440.0150.0150.0000.0000.0000.000
109A114LEU00.011-0.00526.4700.0180.0180.0000.0000.0000.000
110A115ALA00.0270.03631.0370.0160.0160.0000.0000.0000.000
111A116THR0-0.111-0.04633.1840.0210.0210.0000.0000.0000.000
112A117GLU-1-0.987-1.00533.974-0.167-0.1670.0000.0000.0000.000
113A118HIS10.8300.92031.3330.1910.1910.0000.0000.0000.000
114A119PRO00.0680.04632.181-0.014-0.0140.0000.0000.0000.000
115A120GLU-1-0.881-0.95632.718-0.164-0.1640.0000.0000.0000.000
116A121TRP0-0.023-0.01328.134-0.008-0.0080.0000.0000.0000.000
117A122PHE0-0.0120.00828.355-0.028-0.0280.0000.0000.0000.000
118A123TYR0-0.026-0.00125.5550.0080.0080.0000.0000.0000.000
119A124HIS0-0.035-0.03230.990-0.004-0.0040.0000.0000.0000.000
120A125ASP-1-0.902-0.95734.723-0.196-0.1960.0000.0000.0000.000
121A126ALA0-0.036-0.02536.5760.0100.0100.0000.0000.0000.000
122A127ASP-1-0.973-0.98340.187-0.143-0.1430.0000.0000.0000.000
123A128GLY0-0.048-0.02138.8230.0060.0060.0000.0000.0000.000
124A129GLN0-0.057-0.01638.208-0.008-0.0080.0000.0000.0000.000
125A130LEU00.0490.03132.936-0.006-0.0060.0000.0000.0000.000
126A131THR0-0.012-0.01631.505-0.005-0.0050.0000.0000.0000.000
127A132ASN0-0.001-0.00329.3350.0020.0020.0000.0000.0000.000
128A133LYS10.9040.97222.7990.4900.4900.0000.0000.0000.000
129A134VAL0-0.0210.00724.9720.0040.0040.0000.0000.0000.000
130A135GLY00.0200.00828.3540.0100.0100.0000.0000.0000.000
131A136ASP-1-0.905-0.97129.339-0.383-0.3830.0000.0000.0000.000
132A137TRP0-0.040-0.00922.1320.0000.0000.0000.0000.0000.000
133A138SER00.002-0.00929.5330.0010.0010.0000.0000.0000.000
134A139ASP-1-0.872-0.94329.921-0.405-0.4050.0000.0000.0000.000
135A140VAL0-0.056-0.02726.7070.0020.0020.0000.0000.0000.000
136A141LYS10.8560.91929.3040.3070.3070.0000.0000.0000.000
137A142ASP-1-0.794-0.91726.371-0.434-0.4340.0000.0000.0000.000
138A143LEU0-0.044-0.02223.7790.0320.0320.0000.0000.0000.000
139A144ASP-1-0.835-0.93325.113-0.261-0.2610.0000.0000.0000.000
140A145TYR0-0.081-0.09320.5190.0140.0140.0000.0000.0000.000
141A146GLY00.0170.01423.4900.0210.0210.0000.0000.0000.000
142A147HIS0-0.044-0.01025.9010.0440.0440.0000.0000.0000.000
143A148HIS00.002-0.01122.229-0.003-0.0030.0000.0000.0000.000
144A149GLU-1-0.928-0.97025.007-0.109-0.1090.0000.0000.0000.000
145A150LEU0-0.0130.01223.635-0.007-0.0070.0000.0000.0000.000
146A151TRP0-0.014-0.02219.318-0.030-0.0300.0000.0000.0000.000
147A152GLN0-0.007-0.02121.859-0.010-0.0100.0000.0000.0000.000
148A153TYR00.0380.02623.8300.0080.0080.0000.0000.0000.000
149A154GLN00.0220.00220.4310.0050.0050.0000.0000.0000.000
150A155ILE00.001-0.00318.141-0.057-0.0570.0000.0000.0000.000
151A156ASP-1-0.872-0.93520.237-0.163-0.1630.0000.0000.0000.000
152A157THR0-0.044-0.01222.1260.0160.0160.0000.0000.0000.000
153A158LEU0-0.0160.00616.191-0.013-0.0130.0000.0000.0000.000
154A159LEU0-0.0150.00018.446-0.003-0.0030.0000.0000.0000.000
155A160TYR0-0.024-0.00120.3100.0270.0270.0000.0000.0000.000
156A161TRP00.0310.00419.7870.0160.0160.0000.0000.0000.000
157A162SER00.0320.02515.813-0.042-0.0420.0000.0000.0000.000
158A163GLN0-0.129-0.04718.2520.0530.0530.0000.0000.0000.000
159A164PHE0-0.081-0.04320.4280.0360.0360.0000.0000.0000.000
160A165VAL0-0.057-0.03516.211-0.014-0.0140.0000.0000.0000.000
161A166ASP-1-0.748-0.85612.335-0.663-0.6630.0000.0000.0000.000
162A167GLY00.0140.00111.322-0.163-0.1630.0000.0000.0000.000
163A168TYR0-0.043-0.03511.4130.1750.1750.0000.0000.0000.000
164A169ARG10.8040.89111.3060.8950.8950.0000.0000.0000.000
165A170CYS0-0.082-0.02212.3430.2480.2480.0000.0000.0000.000
166A171ASP-1-0.793-0.91614.115-1.033-1.0330.0000.0000.0000.000
167A172VAL00.002-0.00516.9140.0570.0570.0000.0000.0000.000
168A173ALA00.0200.01312.8310.0810.0810.0000.0000.0000.000
169A174PRO0-0.055-0.02214.0060.0910.0910.0000.0000.0000.000
170A175LEU0-0.0050.00715.4820.1150.1150.0000.0000.0000.000
171A176VAL0-0.0200.01216.7010.0950.0950.0000.0000.0000.000
172A177PRO00.0260.00916.139-0.078-0.0780.0000.0000.0000.000
173A178LEU00.0280.00710.601-0.025-0.0250.0000.0000.0000.000
174A179ASP-1-0.888-0.96113.866-0.201-0.2010.0000.0000.0000.000
175A180PHE00.0230.03216.3010.0470.0470.0000.0000.0000.000
176A181TRP00.044-0.00811.550-0.040-0.0400.0000.0000.0000.000
177A182LEU0-0.040-0.02110.1040.0300.0300.0000.0000.0000.000
178A183GLU-1-0.883-0.91512.6660.2250.2250.0000.0000.0000.000
179A184ALA00.017-0.00114.2660.0460.0460.0000.0000.0000.000
180A185ARG10.8610.9355.6570.9200.9200.0000.0000.0000.000
181A186LYS10.9110.96512.316-0.204-0.2040.0000.0000.0000.000
182A187GLN0-0.081-0.05914.0440.0450.0450.0000.0000.0000.000
183A188VAL00.0530.01613.9170.0390.0390.0000.0000.0000.000
184A189ASN00.0280.0239.203-0.102-0.1020.0000.0000.0000.000
185A190ALA0-0.054-0.01613.0870.1350.1350.0000.0000.0000.000
186A191LYS10.8300.93015.741-0.018-0.0180.0000.0000.0000.000
187A192TYR00.0170.00014.5780.0260.0260.0000.0000.0000.000
188A193PRO00.0140.00910.874-0.095-0.0950.0000.0000.0000.000
189A194GLU-1-0.922-0.9638.685-0.690-0.6900.0000.0000.0000.000
190A195THR0-0.0180.0098.538-0.272-0.2720.0000.0000.0000.000
191A196LEU0-0.015-0.0055.379-0.200-0.2000.0000.0000.0000.000
192A197TRP0-0.031-0.0166.7540.4640.4640.0000.0000.0000.000
193A198LEU0-0.029-0.0176.429-1.459-1.4590.0000.0000.0000.000
194A199ALA00.0430.0198.2040.6680.6680.0000.0000.0000.000
195A200GLU-1-0.896-0.95710.183-1.406-1.4060.0000.0000.0000.000
196A201SER00.0170.00210.9930.0800.0800.0000.0000.0000.000
197A202ALA00.0150.01012.9580.1030.1030.0000.0000.0000.000
198A203GLY00.0460.02615.777-0.061-0.0610.0000.0000.0000.000
199A204SER00.017-0.01518.4040.0260.0260.0000.0000.0000.000
200A205GLY00.0100.00719.9480.0490.0490.0000.0000.0000.000
201A206PHE00.0410.01319.8000.0370.0370.0000.0000.0000.000
202A207ILE00.0120.00915.9290.0360.0360.0000.0000.0000.000
203A208GLU-1-0.944-0.97720.297-0.361-0.3610.0000.0000.0000.000
204A209GLU-1-0.944-0.96023.443-0.314-0.3140.0000.0000.0000.000
205A210LEU0-0.008-0.01320.5990.0300.0300.0000.0000.0000.000
206A211ARG10.8610.91516.8730.5620.5620.0000.0000.0000.000
207A212SER0-0.093-0.03423.9100.0460.0460.0000.0000.0000.000
208A213GLN0-0.033-0.01227.0870.0480.0480.0000.0000.0000.000
209A214GLY0-0.048-0.01726.8750.0140.0140.0000.0000.0000.000
210A215TYR0-0.018-0.00524.1540.0020.0020.0000.0000.0000.000
211A216THR0-0.016-0.00818.4560.0210.0210.0000.0000.0000.000
212A217GLY00.0690.02418.655-0.030-0.0300.0000.0000.0000.000
213A218LEU0-0.099-0.02213.0280.0190.0190.0000.0000.0000.000
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