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: ZNV7N

Calculation Name: 1YQ1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQ1

Chain ID: A

ChEMBL ID:

UniProt ID: Q93698

Base Structure: X-ray

Registration Date: 2023-09-27

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2412214.481555
FMO2-HF: Nuclear repulsion 2331264.178495
FMO2-HF: Total energy -80950.30306
FMO2-MP2: Total energy -81191.995906


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-4.299-2.739-0.014-0.811-0.7360.004
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.006
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].
3A3SER00.0140.0073.882-0.4211.176-0.013-0.801-0.7840.004
4A4TYR0-0.008-0.0226.7700.6420.6420.0000.0000.0000.000
5A5LYS10.8970.9589.8171.1281.1280.0000.0000.0000.000
6A6LEU00.0070.01413.0540.1060.1060.0000.0000.0000.000
7A7THR0-0.0010.01616.572-0.013-0.0130.0000.0000.0000.000
8A8TYR00.0500.00619.3920.0570.0570.0000.0000.0000.000
9A9PHE00.0080.03322.833-0.017-0.0170.0000.0000.0000.000
10A10PHE00.0290.00725.220-0.004-0.0040.0000.0000.0000.000
11A11PHE0-0.0100.01226.6470.0070.0070.0000.0000.0000.000
12A12ARG10.8860.90226.7790.1160.1160.0000.0000.0000.000
13A13GLY0-0.026-0.01826.786-0.008-0.0080.0000.0000.0000.000
14A14LEU0-0.001-0.01926.6630.0100.0100.0000.0000.0000.000
15A15GLY00.0570.02923.3130.0030.0030.0000.0000.0000.000
16A16GLU-1-0.743-0.82122.487-0.211-0.2110.0000.0000.0000.000
17A17PRO0-0.003-0.00223.307-0.001-0.0010.0000.0000.0000.000
18A18ILE00.0240.01018.1200.0130.0130.0000.0000.0000.000
19A19ARG10.7490.84918.9310.2750.2750.0000.0000.0000.000
20A20LEU0-0.031-0.02419.4100.0010.0010.0000.0000.0000.000
21A21LEU00.0200.01218.0960.0190.0190.0000.0000.0000.000
22A22PHE00.0490.01312.1850.0150.0150.0000.0000.0000.000
23A23HIS0-0.075-0.03015.645-0.013-0.0130.0000.0000.0000.000
24A24LEU0-0.061-0.01718.1650.0220.0220.0000.0000.0000.000
25A25ALA0-0.035-0.01015.8680.0290.0290.0000.0000.0000.000
26A26GLY00.0210.01715.3170.0470.0470.0000.0000.0000.000
27A27VAL0-0.074-0.0279.7900.0050.0050.0000.0000.0000.000
28A28GLN0-0.025-0.0208.831-0.240-0.2400.0000.0000.0000.000
29A29PHE0-0.017-0.0209.491-0.144-0.1440.0000.0000.0000.000
30A30GLU-1-0.893-0.94710.700-1.248-1.2480.0000.0000.0000.000
31A31GLU-1-0.827-0.92013.300-0.348-0.3480.0000.0000.0000.000
32A32VAL0-0.017-0.01616.049-0.003-0.0030.0000.0000.0000.000
33A33ARG10.9200.95718.6410.4240.4240.0000.0000.0000.000
34A34MET00.0200.00321.2100.0040.0040.0000.0000.0000.000
35A35ASN00.0500.00024.5820.0280.0280.0000.0000.0000.000
36A36PRO0-0.031-0.00728.145-0.002-0.0020.0000.0000.0000.000
37A37ASP-1-0.908-0.95030.560-0.157-0.1570.0000.0000.0000.000
38A38GLN0-0.027-0.02429.4710.0090.0090.0000.0000.0000.000
39A39THR0-0.070-0.03427.544-0.015-0.0150.0000.0000.0000.000
40A40TRP00.0270.02228.5560.0200.0200.0000.0000.0000.000
41A41LEU00.0220.01729.106-0.012-0.0120.0000.0000.0000.000
42A42ASP-1-0.841-0.93828.935-0.193-0.1930.0000.0000.0000.000
43A43ILE0-0.045-0.02523.810-0.013-0.0130.0000.0000.0000.000
44A44LYS10.8800.93425.0730.1690.1690.0000.0000.0000.000
45A45ASP-1-0.844-0.92226.725-0.180-0.1800.0000.0000.0000.000
46A46SER00.0010.00823.1660.0010.0010.0000.0000.0000.000
47A47THR0-0.0150.01422.205-0.037-0.0370.0000.0000.0000.000
48A48PRO00.0320.02019.6600.0420.0420.0000.0000.0000.000
49A49MET0-0.040-0.02022.6840.0260.0260.0000.0000.0000.000
50A50LYS10.7940.88425.9050.1940.1940.0000.0000.0000.000
51A51GLN0-0.011-0.01725.6410.0040.0040.0000.0000.0000.000
52A52LEU0-0.0050.04822.721-0.018-0.0180.0000.0000.0000.000
53A53PRO0-0.061-0.05020.9530.0290.0290.0000.0000.0000.000
54A54VAL0-0.001-0.01217.5420.0280.0280.0000.0000.0000.000
55A55LEU0-0.0190.00813.292-0.042-0.0420.0000.0000.0000.000
56A56ASN0-0.024-0.02112.4180.0140.0140.0000.0000.0000.000
57A57ILE0-0.002-0.0017.995-0.019-0.0190.0000.0000.0000.000
58A58ASP-1-0.809-0.9114.980-4.807-4.844-0.001-0.0100.0480.000
59A59GLY0-0.0180.0098.4030.2690.2690.0000.0000.0000.000
60A60PHE0-0.0050.01811.4330.2120.2120.0000.0000.0000.000
61A61GLU-1-0.869-0.96513.095-0.598-0.5980.0000.0000.0000.000
62A62LEU0-0.038-0.01516.1950.0780.0780.0000.0000.0000.000
63A63PRO00.0420.00718.506-0.017-0.0170.0000.0000.0000.000
64A64GLN00.0390.02121.9760.0190.0190.0000.0000.0000.000
65A65SER00.0370.03822.6950.0030.0030.0000.0000.0000.000
66A66GLY00.0660.03223.2100.0030.0030.0000.0000.0000.000
67A67ALA0-0.019-0.01122.2910.0160.0160.0000.0000.0000.000
68A68ILE0-0.031-0.02917.7860.0170.0170.0000.0000.0000.000
69A69LEU0-0.0020.00119.0020.0070.0070.0000.0000.0000.000
70A70ARG10.8810.91920.2100.0370.0370.0000.0000.0000.000
71A71TYR0-0.002-0.00113.3740.0340.0340.0000.0000.0000.000
72A72LEU0-0.0040.00013.8650.0410.0410.0000.0000.0000.000
73A73ALA00.0390.02316.6690.0510.0510.0000.0000.0000.000
74A74ARG10.7880.86219.446-0.052-0.0520.0000.0000.0000.000
75A75LYS10.8590.93511.305-0.064-0.0640.0000.0000.0000.000
76A76PHE0-0.075-0.05912.1900.0450.0450.0000.0000.0000.000
77A77GLY00.0300.04516.3230.0090.0090.0000.0000.0000.000
78A78PHE0-0.009-0.01618.470-0.012-0.0120.0000.0000.0000.000
79A79ALA00.005-0.00822.179-0.026-0.0260.0000.0000.0000.000
80A80GLY00.0490.02723.821-0.011-0.0110.0000.0000.0000.000
81A81LYS10.8430.92025.520-0.076-0.0760.0000.0000.0000.000
82A82THR0-0.007-0.01427.0470.0090.0090.0000.0000.0000.000
83A83PRO00.0580.01928.909-0.007-0.0070.0000.0000.0000.000
84A84GLU-1-0.852-0.91429.9000.0690.0690.0000.0000.0000.000
85A85GLU-1-0.826-0.91729.4430.0560.0560.0000.0000.0000.000
86A86GLU-1-0.751-0.84624.5190.0800.0800.0000.0000.0000.000
87A87ALA00.0030.00828.684-0.013-0.0130.0000.0000.0000.000
88A88TRP0-0.008-0.00731.378-0.013-0.0130.0000.0000.0000.000
89A89VAL0-0.0060.01226.659-0.011-0.0110.0000.0000.0000.000
90A90ASP-1-0.815-0.89827.412-0.011-0.0110.0000.0000.0000.000
91A91ALA00.0010.00929.911-0.010-0.0100.0000.0000.0000.000
92A92VAL0-0.021-0.01531.699-0.007-0.0070.0000.0000.0000.000
93A93HIS0-0.014-0.00227.449-0.014-0.0140.0000.0000.0000.000
94A94ASP-1-0.836-0.93231.066-0.050-0.0500.0000.0000.0000.000
95A95LEU00.0160.03133.349-0.005-0.0050.0000.0000.0000.000
96A96PHE00.0080.00129.806-0.008-0.0080.0000.0000.0000.000
97A97LYS10.8010.89929.9310.0590.0590.0000.0000.0000.000
98A98ASP-1-0.867-0.92733.969-0.046-0.0460.0000.0000.0000.000
99A99PHE0-0.015-0.01937.046-0.002-0.0020.0000.0000.0000.000
100A100LEU0-0.054-0.02332.248-0.006-0.0060.0000.0000.0000.000
101A101ALA0-0.024-0.02736.343-0.004-0.0040.0000.0000.0000.000
102A102GLU-1-0.767-0.88738.192-0.051-0.0510.0000.0000.0000.000
103A103PHE0-0.034-0.00836.526-0.002-0.0020.0000.0000.0000.000
104A104LYS10.8940.95633.3020.1040.1040.0000.0000.0000.000
105A105LYS10.8180.89539.5650.0540.0540.0000.0000.0000.000
106A106PHE00.0170.02742.5650.0020.0020.0000.0000.0000.000
107A107ALA00.004-0.01740.6620.0000.0000.0000.0000.0000.000
108A108ALA0-0.048-0.02642.285-0.001-0.0010.0000.0000.0000.000
109A109GLU-1-0.806-0.92643.696-0.053-0.0530.0000.0000.0000.000
110A110ARG10.7940.91344.3750.0680.0680.0000.0000.0000.000
111A111ARG10.8800.93440.1990.0920.0920.0000.0000.0000.000
112A112SER0-0.025-0.00247.500-0.003-0.0030.0000.0000.0000.000
113A113GLY00.0350.05249.1090.0020.0020.0000.0000.0000.000
114A114LYS10.8150.87351.7330.0550.0550.0000.0000.0000.000
115A115SER0-0.027-0.04954.608-0.001-0.0010.0000.0000.0000.000
116A116ALA0-0.016-0.00457.405-0.001-0.0010.0000.0000.0000.000
117A117GLU-1-0.862-0.90859.828-0.041-0.0410.0000.0000.0000.000
118A118GLU-1-0.848-0.88653.939-0.052-0.0520.0000.0000.0000.000
119A119VAL0-0.007-0.01055.209-0.003-0.0030.0000.0000.0000.000
120A120GLU-1-0.838-0.91453.007-0.040-0.0400.0000.0000.0000.000
121A121LYS10.8000.86351.9960.0370.0370.0000.0000.0000.000
122A122PHE00.0470.03353.2550.0010.0010.0000.0000.0000.000
123A123ARG10.9170.98445.3780.0530.0530.0000.0000.0000.000
124A124SER0-0.010-0.04049.325-0.002-0.0020.0000.0000.0000.000
125A125GLU-1-0.899-0.93050.408-0.035-0.0350.0000.0000.0000.000
126A126PHE00.016-0.00547.7930.0010.0010.0000.0000.0000.000
127A127PHE00.007-0.00442.1090.0000.0000.0000.0000.0000.000
128A128LEU00.0610.03846.0130.0000.0000.0000.0000.0000.000
129A129PRO00.0020.02047.4210.0010.0010.0000.0000.0000.000
130A130ALA00.0250.03144.0300.0020.0020.0000.0000.0000.000
131A131ARG10.7440.87742.8240.0400.0400.0000.0000.0000.000
132A132ASN00.021-0.01543.382-0.001-0.0010.0000.0000.0000.000
133A133THR00.0110.01344.3210.0030.0030.0000.0000.0000.000
134A134TYR00.0330.00735.8240.0040.0040.0000.0000.0000.000
135A135PHE00.029-0.00239.3130.0020.0020.0000.0000.0000.000
136A136ASN0-0.0120.01242.0760.0030.0030.0000.0000.0000.000
137A137ILE0-0.0110.01639.0150.0030.0030.0000.0000.0000.000
138A138LEU00.015-0.00635.5720.0030.0030.0000.0000.0000.000
139A139ASN0-0.043-0.04839.2510.0040.0040.0000.0000.0000.000
140A140GLY00.0170.01241.9310.0030.0030.0000.0000.0000.000
141A141LEU0-0.084-0.03936.0340.0040.0040.0000.0000.0000.000
142A142LEU00.019-0.00136.6690.0030.0030.0000.0000.0000.000
143A143GLU-1-0.881-0.90539.1720.0000.0000.0000.0000.0000.000
144A144LYS10.8530.93640.415-0.011-0.0110.0000.0000.0000.000
145A145SER0-0.004-0.00835.6540.0070.0070.0000.0000.0000.000
146A146ASN0-0.018-0.01436.2470.0010.0010.0000.0000.0000.000
147A147SER00.010-0.02532.108-0.001-0.0010.0000.0000.0000.000
148A148GLY0-0.034-0.00934.472-0.002-0.0020.0000.0000.0000.000
149A149PHE0-0.007-0.01129.839-0.008-0.0080.0000.0000.0000.000
150A150LEU00.0050.01131.9310.0040.0040.0000.0000.0000.000
151A151ILE0-0.043-0.03230.1310.0020.0020.0000.0000.0000.000
152A152GLY00.0880.05730.6660.0010.0010.0000.0000.0000.000
153A153SER0-0.027-0.02530.006-0.002-0.0020.0000.0000.0000.000
154A154ASP-1-0.882-0.90326.0110.0540.0540.0000.0000.0000.000
155A155ILE0-0.0270.01024.698-0.007-0.0070.0000.0000.0000.000
156A156THR00.015-0.01025.4030.0100.0100.0000.0000.0000.000
157A157PHE0-0.005-0.02622.871-0.017-0.0170.0000.0000.0000.000
158A158ALA00.0280.01724.741-0.016-0.0160.0000.0000.0000.000
159A159ASP-1-0.753-0.87928.403-0.015-0.0150.0000.0000.0000.000
160A160LEU0-0.037-0.00222.721-0.009-0.0090.0000.0000.0000.000
161A161VAL0-0.030-0.02426.886-0.011-0.0110.0000.0000.0000.000
162A162VAL00.0010.01428.619-0.005-0.0050.0000.0000.0000.000
163A163VAL00.0170.00229.611-0.002-0.0020.0000.0000.0000.000
164A164ASP-1-0.742-0.84728.535-0.129-0.1290.0000.0000.0000.000
165A165ASN00.000-0.01330.6920.0030.0030.0000.0000.0000.000
166A166LEU00.0550.02933.5000.0000.0000.0000.0000.0000.000
167A167LEU0-0.038-0.00331.4540.0020.0020.0000.0000.0000.000
168A168THR0-0.049-0.02133.563-0.003-0.0030.0000.0000.0000.000
169A169LEU0-0.039-0.01535.6220.0010.0010.0000.0000.0000.000
170A170LYS10.8540.93038.1240.0570.0570.0000.0000.0000.000
171A171ASN0-0.0010.01635.6090.0060.0060.0000.0000.0000.000
172A172TYR0-0.044-0.01837.7750.0000.0000.0000.0000.0000.000
173A173GLY0-0.008-0.01841.6910.0030.0030.0000.0000.0000.000
174A174LEU0-0.078-0.02941.9830.0040.0040.0000.0000.0000.000
175A175PHE0-0.004-0.02539.0400.0020.0020.0000.0000.0000.000
176A176ASP-1-0.800-0.90742.901-0.043-0.0430.0000.0000.0000.000
177A177GLU-1-0.812-0.89538.827-0.049-0.0490.0000.0000.0000.000
178A178SER00.0090.00442.6020.0040.0040.0000.0000.0000.000
179A179GLU-1-0.864-0.92446.009-0.031-0.0310.0000.0000.0000.000
180A180PHE0-0.045-0.02742.9740.0030.0030.0000.0000.0000.000
181A181THR00.0490.01042.779-0.001-0.0010.0000.0000.0000.000
182A182LYS10.8550.92641.5810.0100.0100.0000.0000.0000.000
183A183LEU00.0370.01138.2660.0000.0000.0000.0000.0000.000
184A184ALA0-0.0020.01437.574-0.003-0.0030.0000.0000.0000.000
185A185ALA00.0120.00437.590-0.002-0.0020.0000.0000.0000.000
186A186LEU0-0.024-0.00332.6940.0000.0000.0000.0000.0000.000
187A187ARG10.8920.90933.3480.0620.0620.0000.0000.0000.000
188A188GLU-1-0.897-0.92832.851-0.045-0.0450.0000.0000.0000.000
189A189LYS10.8870.95332.165-0.012-0.0120.0000.0000.0000.000
190A190VAL00.0050.00627.3140.0020.0020.0000.0000.0000.000
191A191ASN0-0.077-0.05727.792-0.014-0.0140.0000.0000.0000.000
192A192SER0-0.058-0.03328.359-0.005-0.0050.0000.0000.0000.000
193A193TYR0-0.003-0.01424.0720.0050.0050.0000.0000.0000.000
194A194PRO00.0020.00523.882-0.014-0.0140.0000.0000.0000.000
195A195GLY00.0460.02621.2670.0090.0090.0000.0000.0000.000
196A196ILE0-0.058-0.03421.890-0.031-0.0310.0000.0000.0000.000
197A197LYS10.9470.98923.9170.0340.0340.0000.0000.0000.000
198A198GLU-1-0.867-0.94922.720-0.074-0.0740.0000.0000.0000.000
199A199TYR0-0.043-0.04021.148-0.018-0.0180.0000.0000.0000.000
200A200ILE0-0.048-0.03823.066-0.014-0.0140.0000.0000.0000.000
201A201ALA0-0.027-0.00726.4540.0000.0000.0000.0000.0000.000
202A202LYS10.8940.94720.6240.2300.2300.0000.0000.0000.000
203A203ARG10.8470.94725.0900.1240.1240.0000.0000.0000.000
204A204PRO00.000-0.00226.3310.0140.0140.0000.0000.0000.000
205A205VAL0-0.027-0.01129.3290.0110.0110.0000.0000.0000.000