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: ZY5JN

Calculation Name: 1R8I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R8I

Chain ID: A

ChEMBL ID:

UniProt ID: Q9L6G5

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1873102.919081
FMO2-HF: Nuclear repulsion 1797063.336486
FMO2-HF: Total energy -76039.582595
FMO2-MP2: Total energy -76252.937479


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:32:THR)


Summations of interaction energy for fragment #1(A:32:THR)
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.
-3.6630.7150.096-1.977-2.4970.008
Interaction energy analysis for fragmet #1(A:32:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.016
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].
3A34LEU0-0.0180.0033.197-3.5790.4690.098-1.932-2.2150.008
4A35ILE00.0220.0014.067-1.042-0.848-0.001-0.019-0.1740.000
5A36LYS10.8360.9314.9331.3131.449-0.001-0.026-0.1080.000
6A37GLN00.008-0.0086.3660.2450.2450.0000.0000.0000.000
7A38GLY0-0.006-0.0029.1070.0740.0740.0000.0000.0000.000
8A39GLU-1-0.840-0.9039.809-0.945-0.9450.0000.0000.0000.000
9A40GLN00.0300.00411.1550.2220.2220.0000.0000.0000.000
10A41LEU0-0.006-0.00312.9930.0850.0850.0000.0000.0000.000
11A42GLU-1-0.859-0.93214.494-0.167-0.1670.0000.0000.0000.000
12A43GLN0-0.029-0.02413.9980.0720.0720.0000.0000.0000.000
13A44MET0-0.047-0.01015.1550.0520.0520.0000.0000.0000.000
14A45ALA00.0490.02119.2450.0270.0270.0000.0000.0000.000
15A46GLN0-0.039-0.00819.012-0.004-0.0040.0000.0000.0000.000
16A47GLN00.0720.03620.2390.0360.0360.0000.0000.0000.000
17A48LEU0-0.0130.01723.2280.0190.0190.0000.0000.0000.000
18A49GLU-1-0.900-0.95325.394-0.095-0.0950.0000.0000.0000.000
19A50GLN0-0.031-0.01225.5150.0000.0000.0000.0000.0000.000
20A51LEU0-0.031-0.02126.3140.0110.0110.0000.0000.0000.000
21A52LYS10.8870.94129.4120.1010.1010.0000.0000.0000.000
22A53SER00.0170.01331.0300.0090.0090.0000.0000.0000.000
23A54GLN00.007-0.00129.7380.0130.0130.0000.0000.0000.000
24A55LEU00.0190.02433.6920.0070.0070.0000.0000.0000.000
25A56GLU-1-0.849-0.91835.532-0.061-0.0610.0000.0000.0000.000
26A57THR0-0.030-0.00937.0650.0060.0060.0000.0000.0000.000
27A58GLN0-0.055-0.05535.3300.0060.0060.0000.0000.0000.000
28A59LYS10.9210.98139.3680.0650.0650.0000.0000.0000.000
29A60ASN00.0190.00441.3160.0070.0070.0000.0000.0000.000
30A61MET0-0.038-0.03140.1940.0040.0040.0000.0000.0000.000
31A62TYR0-0.005-0.04443.3750.0040.0040.0000.0000.0000.000
32A63GLU-1-0.867-0.96445.089-0.043-0.0430.0000.0000.0000.000
33A64SER0-0.087-0.03647.0470.0040.0040.0000.0000.0000.000
34A65MET00.0220.02445.1590.0030.0030.0000.0000.0000.000
35A66ALA0-0.0200.00449.3900.0020.0020.0000.0000.0000.000
36A67LYS10.8210.93148.9990.0450.0450.0000.0000.0000.000
37A68THR0-0.058-0.04752.5590.0010.0010.0000.0000.0000.000
38A69THR00.0010.03053.1730.0010.0010.0000.0000.0000.000
39A70ASN0-0.0100.00355.2600.0010.0010.0000.0000.0000.000
40A71LEU0-0.005-0.01154.7070.0010.0010.0000.0000.0000.000
41A72GLY0-0.012-0.00158.0790.0010.0010.0000.0000.0000.000
42A73ASP-1-1.007-0.99860.290-0.026-0.0260.0000.0000.0000.000
43A74LEU0-0.058-0.05159.1530.0000.0000.0000.0000.0000.000
44A75LEU00.0010.01258.2960.0000.0000.0000.0000.0000.000
45A76GLY00.0120.01962.4000.0010.0010.0000.0000.0000.000
46A77THR00.031-0.01066.1820.0000.0000.0000.0000.0000.000
47A78SER0-0.055-0.04068.7200.0000.0000.0000.0000.0000.000
48A79THR0-0.069-0.01464.7850.0000.0000.0000.0000.0000.000
49A80ASN00.020-0.00564.8930.0000.0000.0000.0000.0000.000
50A81THR0-0.0060.02264.9800.0000.0000.0000.0000.0000.000
51A82LEU00.005-0.01565.631-0.001-0.0010.0000.0000.0000.000
52A83ALA00.0630.03562.029-0.001-0.0010.0000.0000.0000.000
53A84ASN0-0.038-0.02460.8360.0000.0000.0000.0000.0000.000
54A85ASN00.069-0.00657.934-0.001-0.0010.0000.0000.0000.000
55A86LEU0-0.059-0.02953.8950.0000.0000.0000.0000.0000.000
56A87PRO0-0.0070.03752.326-0.002-0.0020.0000.0000.0000.000
57A88ASP-1-0.838-0.94349.580-0.045-0.0450.0000.0000.0000.000
58A89ASN00.0640.00547.5680.0010.0010.0000.0000.0000.000
59A90TRP00.0150.03442.9650.0000.0000.0000.0000.0000.000
60A91LYS10.8830.97445.7620.0380.0380.0000.0000.0000.000
61A92GLU-1-0.868-0.94142.867-0.055-0.0550.0000.0000.0000.000
62A93VAL0-0.0300.02242.448-0.002-0.0020.0000.0000.0000.000
63A94TYR0-0.107-0.09842.827-0.003-0.0030.0000.0000.0000.000
64A95SER0-0.029-0.04541.9440.0000.0000.0000.0000.0000.000
65A96ASP-1-0.865-0.94138.280-0.072-0.0720.0000.0000.0000.000
66A97ALA0-0.050-0.05138.929-0.002-0.0020.0000.0000.0000.000
67A98MET0-0.072-0.02040.6490.0000.0000.0000.0000.0000.000
68A99ASN0-0.0100.00737.2800.0030.0030.0000.0000.0000.000
69A100SER0-0.064-0.02535.627-0.004-0.0040.0000.0000.0000.000
70A101SER00.0000.00831.5840.0030.0030.0000.0000.0000.000
71A102SER0-0.057-0.03632.9810.0020.0020.0000.0000.0000.000
72A103SER0-0.002-0.01434.9510.0000.0000.0000.0000.0000.000
73A104VAL0-0.0280.00735.0260.0000.0000.0000.0000.0000.000
74A105THR0-0.009-0.02337.3510.0050.0050.0000.0000.0000.000
75A106PRO0-0.028-0.00740.704-0.002-0.0020.0000.0000.0000.000
76A107SER00.0910.06139.9510.0010.0010.0000.0000.0000.000
77A108VAL00.1060.03341.5780.0030.0030.0000.0000.0000.000
78A109ASN00.0190.00341.1260.0040.0040.0000.0000.0000.000
79A110SER0-0.057-0.01943.3610.0030.0030.0000.0000.0000.000
80A111MET0-0.098-0.03245.4390.0020.0020.0000.0000.0000.000
81A112MET0-0.009-0.01147.5100.0030.0030.0000.0000.0000.000
82A113GLY0-0.060-0.02948.9220.0000.0000.0000.0000.0000.000
83A114GLN0-0.007-0.02447.135-0.001-0.0010.0000.0000.0000.000
84A115PHE00.0830.03244.0950.0000.0000.0000.0000.0000.000
85A116ASN0-0.055-0.04646.127-0.002-0.0020.0000.0000.0000.000
86A117ALA0-0.0180.00348.4010.0010.0010.0000.0000.0000.000
87A118GLU-1-0.837-0.93950.127-0.036-0.0360.0000.0000.0000.000
88A119VAL0-0.081-0.03646.4020.0000.0000.0000.0000.0000.000
89A120ASP-1-0.843-0.89949.856-0.036-0.0360.0000.0000.0000.000
90A121ASP-1-0.975-0.98852.629-0.027-0.0270.0000.0000.0000.000
91A122MET0-0.0360.02654.3020.0000.0000.0000.0000.0000.000
92A123THR00.0590.04755.324-0.001-0.0010.0000.0000.0000.000
93A124PRO00.0310.00355.1640.0000.0000.0000.0000.0000.000
94A125SER0-0.043-0.03256.4950.0010.0010.0000.0000.0000.000
95A126GLU-1-0.933-0.97658.509-0.026-0.0260.0000.0000.0000.000
96A127ALA00.002-0.00553.5330.0000.0000.0000.0000.0000.000
97A128ILE0-0.0220.00153.310-0.001-0.0010.0000.0000.0000.000
98A129ALA00.0550.03355.394-0.001-0.0010.0000.0000.0000.000
99A130TYR00.0000.00652.0150.0000.0000.0000.0000.0000.000
100A131MET0-0.033-0.04049.725-0.001-0.0010.0000.0000.0000.000
101A132ASN00.0420.01552.495-0.002-0.0020.0000.0000.0000.000
102A133LYS10.9570.99454.7330.0280.0280.0000.0000.0000.000
103A134LYS10.9300.96951.7650.0340.0340.0000.0000.0000.000
104A135LEU00.0200.00448.5490.0000.0000.0000.0000.0000.000
105A136ALA0-0.028-0.01351.5460.0000.0000.0000.0000.0000.000
106A137GLU-1-0.984-0.99254.583-0.028-0.0280.0000.0000.0000.000
107A138LYS10.8640.93549.7700.0350.0350.0000.0000.0000.000
108A139GLY00.0370.01749.819-0.002-0.0020.0000.0000.0000.000
109A140ALA00.0140.02748.058-0.001-0.0010.0000.0000.0000.000
110A141TYR0-0.0040.00748.439-0.002-0.0020.0000.0000.0000.000
111A142ASP-1-0.866-0.91350.139-0.035-0.0350.0000.0000.0000.000
112A143ARG10.9690.95448.1660.0380.0380.0000.0000.0000.000
113A144VAL00.0020.04447.427-0.001-0.0010.0000.0000.0000.000
114A145MET0-0.040-0.04846.809-0.002-0.0020.0000.0000.0000.000
115A146ALA00.0050.02544.440-0.002-0.0020.0000.0000.0000.000
116A147GLU-1-0.888-0.96542.910-0.046-0.0460.0000.0000.0000.000
117A148LYS10.8900.96442.3560.0360.0360.0000.0000.0000.000
118A149ALA0-0.013-0.00340.071-0.002-0.0020.0000.0000.0000.000
119A150TYR0-0.001-0.09038.387-0.003-0.0030.0000.0000.0000.000
120A151ASN0-0.017-0.01737.762-0.006-0.0060.0000.0000.0000.000
121A152ASN0-0.076-0.03536.288-0.005-0.0050.0000.0000.0000.000
122A153GLN00.0860.03731.305-0.008-0.0080.0000.0000.0000.000
123A154MET00.0130.01032.964-0.007-0.0070.0000.0000.0000.000
124A155GLN0-0.061-0.03133.264-0.003-0.0030.0000.0000.0000.000
125A156GLU-1-0.835-0.91729.676-0.077-0.0770.0000.0000.0000.000
126A157LEU0-0.022-0.01628.026-0.006-0.0060.0000.0000.0000.000
127A158SER0-0.044-0.02628.235-0.006-0.0060.0000.0000.0000.000
128A159ASP-1-0.894-0.94128.883-0.064-0.0640.0000.0000.0000.000
129A160MET0-0.061-0.03324.826-0.005-0.0050.0000.0000.0000.000
130A161GLN0-0.0180.00024.056-0.003-0.0030.0000.0000.0000.000
131A162ALA00.0590.03124.049-0.003-0.0030.0000.0000.0000.000
132A163LEU0-0.055-0.02722.4270.0050.0050.0000.0000.0000.000
133A164THR00.017-0.02419.043-0.002-0.0020.0000.0000.0000.000
134A165GLU-1-0.995-0.99019.551-0.081-0.0810.0000.0000.0000.000
135A166GLN0-0.010-0.00620.1670.0050.0050.0000.0000.0000.000
136A167ILE00.0130.00616.2320.0130.0130.0000.0000.0000.000
137A168LYS10.9841.00115.6620.1920.1920.0000.0000.0000.000
138A169SER0-0.084-0.05316.6290.0030.0030.0000.0000.0000.000
139A170THR0-0.194-0.09117.3410.0220.0220.0000.0000.0000.000
140A171PRO0-0.032-0.01212.946-0.013-0.0130.0000.0000.0000.000
141A172ASP-1-0.783-0.89213.9920.0340.0340.0000.0000.0000.000
142A173LEU00.013-0.0078.899-0.041-0.0410.0000.0000.0000.000
143A174LYS10.9590.99612.912-0.004-0.0040.0000.0000.0000.000
144A175SER0-0.009-0.01716.469-0.016-0.0160.0000.0000.0000.000
145A176ILE0-0.023-0.00912.101-0.010-0.0100.0000.0000.0000.000
146A177ALA00.0180.01915.172-0.024-0.0240.0000.0000.0000.000
147A178ASP-1-0.903-0.95316.456-0.099-0.0990.0000.0000.0000.000
148A179LEU0-0.041-0.01418.9690.0000.0000.0000.0000.0000.000
149A180GLN00.0420.02716.5080.0130.0130.0000.0000.0000.000
150A181ALA00.0390.01219.1460.0040.0040.0000.0000.0000.000
151A182ARG10.8720.93521.7060.1010.1010.0000.0000.0000.000
152A183ILE00.0500.00820.6710.0080.0080.0000.0000.0000.000
153A184GLN0-0.040-0.01821.587-0.010-0.0100.0000.0000.0000.000
154A185THR0-0.032-0.01424.1690.0110.0110.0000.0000.0000.000
155A186SER0-0.004-0.00727.2460.0060.0060.0000.0000.0000.000
156A187GLN0-0.040-0.00823.3810.0120.0120.0000.0000.0000.000
157A188GLY00.0180.00727.9200.0070.0070.0000.0000.0000.000
158A189ALA0-0.0140.00630.1830.0070.0070.0000.0000.0000.000
159A190ILE00.0440.02130.2980.0070.0070.0000.0000.0000.000
160A191GLN00.0010.00428.259-0.005-0.0050.0000.0000.0000.000
161A192GLY00.0260.00432.9020.0050.0050.0000.0000.0000.000
162A193GLU-1-0.737-0.80035.390-0.060-0.0600.0000.0000.0000.000
163A194GLN00.006-0.01835.6470.0090.0090.0000.0000.0000.000
164A195ALA00.0190.04537.5980.0040.0040.0000.0000.0000.000
165A196LYS10.8470.90739.3340.0590.0590.0000.0000.0000.000
166A197LEU00.0000.01739.1730.0040.0040.0000.0000.0000.000
167A198ASN00.0460.02738.9890.0040.0040.0000.0000.0000.000
168A199LEU00.0280.01843.1190.0030.0030.0000.0000.0000.000
169A200MET0-0.016-0.02145.1900.0030.0030.0000.0000.0000.000
170A201ASN0-0.043-0.03145.8960.0020.0020.0000.0000.0000.000
171A202MET0-0.017-0.01347.1550.0020.0020.0000.0000.0000.000
172A203LEU0-0.035-0.03448.7820.0030.0030.0000.0000.0000.000
173A204GLN00.0930.03750.3100.0020.0020.0000.0000.0000.000
174A205GLN00.0360.02250.6870.0030.0030.0000.0000.0000.000
175A206SER0-0.042-0.04753.1420.0020.0020.0000.0000.0000.000
176A207GLN00.0340.03353.5710.0020.0020.0000.0000.0000.000
177A208ASP-1-0.870-0.93555.961-0.035-0.0350.0000.0000.0000.000
178A209LYS10.8060.92055.0480.0400.0400.0000.0000.0000.000
179A210LEU00.0420.03059.2450.0010.0010.0000.0000.0000.000
180A211LEU00.0310.03260.8070.0010.0010.0000.0000.0000.000
181A212ARG10.8550.90359.4110.0330.0330.0000.0000.0000.000
182A213ALA0-0.017-0.00963.7910.0010.0010.0000.0000.0000.000
183A214GLN00.0640.05464.9170.0010.0010.0000.0000.0000.000
184A215LYS10.8270.93365.0990.0270.0270.0000.0000.0000.000
185A216ASP-1-0.923-0.94668.902-0.022-0.0220.0000.0000.0000.000
186A217ARG10.9310.94770.6390.0210.0210.0000.0000.0000.000
187A218ALA0-0.0290.00072.8240.0010.0010.0000.0000.0000.000