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: R5GZ8

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 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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1872143.810496
FMO2-HF: Nuclear repulsion 1796102.367437
FMO2-HF: Total energy -76041.44306
FMO2-MP2: Total energy -76254.5581


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.
-2.9091.2370.093-1.916-2.3230.007
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 : 0.003 / q_NPA : -0.018
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].
3A34LEU0-0.0210.0033.109-3.2120.7310.094-1.895-2.1420.007
4A35ILE00.0200.0013.994-0.949-0.746-0.001-0.021-0.1810.000
5A36LYS10.8270.9134.9091.6901.6900.0000.0000.0000.000
6A37GLN00.013-0.0046.3670.3210.3210.0000.0000.0000.000
7A38GLY0-0.0020.0009.0260.0990.0990.0000.0000.0000.000
8A39GLU-1-0.825-0.8849.847-1.115-1.1150.0000.0000.0000.000
9A40GLN00.0230.00210.7950.2310.2310.0000.0000.0000.000
10A41LEU0-0.003-0.00112.9140.0960.0960.0000.0000.0000.000
11A42GLU-1-0.796-0.88214.420-0.188-0.1880.0000.0000.0000.000
12A43GLN0-0.018-0.02313.4930.0730.0730.0000.0000.0000.000
13A44MET0-0.051-0.01015.1440.0590.0590.0000.0000.0000.000
14A45ALA00.0440.02019.1710.0320.0320.0000.0000.0000.000
15A46GLN0-0.060-0.02019.197-0.003-0.0030.0000.0000.0000.000
16A47GLN00.0640.03119.5240.0400.0400.0000.0000.0000.000
17A48LEU0-0.0050.01123.1280.0210.0210.0000.0000.0000.000
18A49GLU-1-0.809-0.87025.325-0.107-0.1070.0000.0000.0000.000
19A50GLN0-0.040-0.01625.5290.0020.0020.0000.0000.0000.000
20A51LEU0-0.028-0.02126.3140.0130.0130.0000.0000.0000.000
21A52LYS10.7950.86329.2170.1200.1200.0000.0000.0000.000
22A53SER0-0.0100.00330.9700.0100.0100.0000.0000.0000.000
23A54GLN00.016-0.00129.7400.0140.0140.0000.0000.0000.000
24A55LEU00.0340.03333.6800.0080.0080.0000.0000.0000.000
25A56GLU-1-0.747-0.84435.459-0.067-0.0670.0000.0000.0000.000
26A57THR0-0.040-0.01736.7560.0060.0060.0000.0000.0000.000
27A58GLN0-0.060-0.04735.6190.0050.0050.0000.0000.0000.000
28A59LYS10.8450.92739.3580.0740.0740.0000.0000.0000.000
29A60ASN0-0.042-0.03641.0850.0070.0070.0000.0000.0000.000
30A61MET0-0.002-0.01240.3600.0050.0050.0000.0000.0000.000
31A62TYR0-0.013-0.04443.3240.0040.0040.0000.0000.0000.000
32A63GLU-1-0.734-0.85145.050-0.046-0.0460.0000.0000.0000.000
33A64SER0-0.038-0.01446.9990.0030.0030.0000.0000.0000.000
34A65MET0-0.0400.01445.0780.0030.0030.0000.0000.0000.000
35A66ALA0-0.0090.00949.3720.0020.0020.0000.0000.0000.000
36A67LYS10.7960.89849.2250.0500.0500.0000.0000.0000.000
37A68THR0-0.061-0.04652.4660.0010.0010.0000.0000.0000.000
38A69THR0-0.0010.02253.0420.0010.0010.0000.0000.0000.000
39A70ASN0-0.0020.00355.2140.0010.0010.0000.0000.0000.000
40A71LEU00.0030.00654.5630.0010.0010.0000.0000.0000.000
41A72GLY0-0.0060.00058.0400.0010.0010.0000.0000.0000.000
42A73ASP-1-1.002-0.99960.264-0.029-0.0290.0000.0000.0000.000
43A74LEU0-0.060-0.04859.2180.0000.0000.0000.0000.0000.000
44A75LEU0-0.0050.00258.1820.0000.0000.0000.0000.0000.000
45A76GLY00.0110.01962.3730.0010.0010.0000.0000.0000.000
46A77THR00.032-0.00766.1560.0000.0000.0000.0000.0000.000
47A78SER0-0.068-0.03668.6920.0000.0000.0000.0000.0000.000
48A79THR00.0030.01064.1630.0000.0000.0000.0000.0000.000
49A80ASN0-0.028-0.01964.8590.0000.0000.0000.0000.0000.000
50A81THR0-0.0080.01564.9370.0000.0000.0000.0000.0000.000
51A82LEU00.014-0.00465.580-0.001-0.0010.0000.0000.0000.000
52A83ALA00.0480.03762.016-0.001-0.0010.0000.0000.0000.000
53A84ASN0-0.019-0.01761.0150.0000.0000.0000.0000.0000.000
54A85ASN00.056-0.00558.153-0.001-0.0010.0000.0000.0000.000
55A86LEU0-0.030-0.01953.6010.0000.0000.0000.0000.0000.000
56A87PRO0-0.0260.02852.262-0.002-0.0020.0000.0000.0000.000
57A88ASP-1-0.852-0.94649.527-0.050-0.0500.0000.0000.0000.000
58A89ASN00.0590.01647.4980.0010.0010.0000.0000.0000.000
59A90TRP00.0170.02542.8430.0000.0000.0000.0000.0000.000
60A91LYS10.9160.98645.6910.0410.0410.0000.0000.0000.000
61A92GLU-1-0.877-0.95242.903-0.059-0.0590.0000.0000.0000.000
62A93VAL0-0.036-0.01042.376-0.002-0.0020.0000.0000.0000.000
63A94TYR0-0.097-0.08942.776-0.003-0.0030.0000.0000.0000.000
64A95SER0-0.015-0.02041.9800.0000.0000.0000.0000.0000.000
65A96ASP-1-0.874-0.93838.240-0.080-0.0800.0000.0000.0000.000
66A97ALA0-0.060-0.05338.893-0.003-0.0030.0000.0000.0000.000
67A98MET0-0.068-0.02540.6230.0000.0000.0000.0000.0000.000
68A99ASN0-0.020-0.00137.2570.0030.0030.0000.0000.0000.000
69A100SER0-0.056-0.02135.600-0.004-0.0040.0000.0000.0000.000
70A101SER00.0120.01332.1990.0020.0020.0000.0000.0000.000
71A102SER0-0.073-0.04632.8810.0010.0010.0000.0000.0000.000
72A103SER0-0.014-0.01934.9180.0000.0000.0000.0000.0000.000
73A104VAL0-0.028-0.00434.962-0.001-0.0010.0000.0000.0000.000
74A105THR0-0.022-0.02737.3410.0060.0060.0000.0000.0000.000
75A106PRO00.001-0.00540.687-0.002-0.0020.0000.0000.0000.000
76A107SER00.0470.03839.8390.0000.0000.0000.0000.0000.000
77A108VAL00.0880.01641.5490.0030.0030.0000.0000.0000.000
78A109ASN00.0310.01140.6270.0050.0050.0000.0000.0000.000
79A110SER0-0.0050.02243.3160.0020.0020.0000.0000.0000.000
80A111MET0-0.063-0.01645.4050.0030.0030.0000.0000.0000.000
81A112MET0-0.0010.00147.4710.0030.0030.0000.0000.0000.000
82A113GLY0-0.059-0.03448.8770.0000.0000.0000.0000.0000.000
83A114GLN00.020-0.00446.997-0.001-0.0010.0000.0000.0000.000
84A115PHE00.0600.03344.0610.0000.0000.0000.0000.0000.000
85A116ASN0-0.056-0.04546.108-0.002-0.0020.0000.0000.0000.000
86A117ALA0-0.0100.00448.3760.0020.0020.0000.0000.0000.000
87A118GLU-1-0.819-0.92050.147-0.040-0.0400.0000.0000.0000.000
88A119VAL0-0.109-0.04146.3660.0000.0000.0000.0000.0000.000
89A120ASP-1-0.840-0.90549.814-0.039-0.0390.0000.0000.0000.000
90A121ASP-1-0.966-0.98252.592-0.030-0.0300.0000.0000.0000.000
91A122MET0-0.0300.01654.4090.0000.0000.0000.0000.0000.000
92A123THR00.0670.04955.279-0.001-0.0010.0000.0000.0000.000
93A124PRO00.0330.00555.038-0.001-0.0010.0000.0000.0000.000
94A125SER0-0.042-0.03856.4380.0010.0010.0000.0000.0000.000
95A126GLU-1-0.955-0.98158.454-0.029-0.0290.0000.0000.0000.000
96A127ALA00.000-0.00353.5010.0000.0000.0000.0000.0000.000
97A128ILE0-0.0130.00352.734-0.001-0.0010.0000.0000.0000.000
98A129ALA00.0470.03155.347-0.001-0.0010.0000.0000.0000.000
99A130TYR00.0280.00451.8400.0000.0000.0000.0000.0000.000
100A131MET0-0.046-0.04649.0280.0000.0000.0000.0000.0000.000
101A132ASN00.0260.01552.468-0.003-0.0030.0000.0000.0000.000
102A133LYS10.8270.90654.7010.0310.0310.0000.0000.0000.000
103A134LYS10.9090.96851.7410.0370.0370.0000.0000.0000.000
104A135LEU00.0400.00748.2150.0000.0000.0000.0000.0000.000
105A136ALA0-0.036-0.01451.5120.0000.0000.0000.0000.0000.000
106A137GLU-1-0.854-0.91154.556-0.031-0.0310.0000.0000.0000.000
107A138LYS10.7980.90349.2880.0400.0400.0000.0000.0000.000
108A139GLY00.0410.01949.803-0.002-0.0020.0000.0000.0000.000
109A140ALA00.0090.02448.044-0.002-0.0020.0000.0000.0000.000
110A141TYR00.0090.00448.422-0.002-0.0020.0000.0000.0000.000
111A142ASP-1-0.865-0.92450.147-0.038-0.0380.0000.0000.0000.000
112A143ARG10.7830.82348.1710.0440.0440.0000.0000.0000.000
113A144VAL00.0080.04247.435-0.002-0.0020.0000.0000.0000.000
114A145MET0-0.032-0.03446.816-0.002-0.0020.0000.0000.0000.000
115A146ALA00.0130.02844.431-0.002-0.0020.0000.0000.0000.000
116A147GLU-1-0.799-0.90742.917-0.050-0.0500.0000.0000.0000.000
117A148LYS10.8920.96542.3750.0400.0400.0000.0000.0000.000
118A149ALA0-0.0020.00540.137-0.002-0.0020.0000.0000.0000.000
119A150TYR00.008-0.04738.509-0.003-0.0030.0000.0000.0000.000
120A151ASN0-0.037-0.02637.779-0.006-0.0060.0000.0000.0000.000
121A152ASN0-0.051-0.02436.751-0.005-0.0050.0000.0000.0000.000
122A153GLN00.0690.04731.415-0.009-0.0090.0000.0000.0000.000
123A154MET00.0250.01232.987-0.009-0.0090.0000.0000.0000.000
124A155GLN0-0.105-0.05433.299-0.001-0.0010.0000.0000.0000.000
125A156GLU-1-0.795-0.88529.825-0.091-0.0910.0000.0000.0000.000
126A157LEU0-0.016-0.00928.216-0.007-0.0070.0000.0000.0000.000
127A158SER0-0.012-0.01928.276-0.007-0.0070.0000.0000.0000.000
128A159ASP-1-0.856-0.91628.799-0.072-0.0720.0000.0000.0000.000
129A160MET0-0.046-0.01924.832-0.006-0.0060.0000.0000.0000.000
130A161GLN0-0.017-0.00124.110-0.005-0.0050.0000.0000.0000.000
131A162ALA00.0580.03023.965-0.005-0.0050.0000.0000.0000.000
132A163LEU0-0.053-0.02722.0850.0040.0040.0000.0000.0000.000
133A164THR00.014-0.01819.069-0.005-0.0050.0000.0000.0000.000
134A165GLU-1-0.973-0.98419.465-0.103-0.1030.0000.0000.0000.000
135A166GLN0-0.010-0.00820.0830.0040.0040.0000.0000.0000.000
136A167ILE00.0040.00116.3300.0130.0130.0000.0000.0000.000
137A168LYS10.9230.95215.4470.2230.2230.0000.0000.0000.000
138A169SER0-0.063-0.04816.5450.0060.0060.0000.0000.0000.000
139A170THR0-0.211-0.09817.4440.0270.0270.0000.0000.0000.000
140A171PRO0-0.0080.00612.902-0.015-0.0150.0000.0000.0000.000
141A172ASP-1-0.722-0.84314.0960.0160.0160.0000.0000.0000.000
142A173LEU0-0.030-0.0208.939-0.049-0.0490.0000.0000.0000.000
143A174LYS10.9190.97512.9930.0070.0070.0000.0000.0000.000
144A175SER0-0.028-0.04716.539-0.018-0.0180.0000.0000.0000.000
145A176ILE0-0.012-0.00312.269-0.011-0.0110.0000.0000.0000.000
146A177ALA00.0090.01215.099-0.026-0.0260.0000.0000.0000.000
147A178ASP-1-0.892-0.95416.484-0.104-0.1040.0000.0000.0000.000
148A179LEU0-0.028-0.00818.996-0.001-0.0010.0000.0000.0000.000
149A180GLN00.0160.01516.494-0.005-0.0050.0000.0000.0000.000
150A181ALA00.0240.00719.1540.0050.0050.0000.0000.0000.000
151A182ARG10.8210.89521.7030.1130.1130.0000.0000.0000.000
152A183ILE00.0490.00620.6770.0100.0100.0000.0000.0000.000
153A184GLN0-0.028-0.01021.440-0.010-0.0100.0000.0000.0000.000
154A185THR0-0.039-0.02424.1470.0120.0120.0000.0000.0000.000
155A186SER0-0.009-0.01927.2220.0080.0080.0000.0000.0000.000
156A187GLN0-0.041-0.00923.2600.0120.0120.0000.0000.0000.000
157A188GLY00.0350.01827.8930.0080.0080.0000.0000.0000.000
158A189ALA0-0.0160.00430.1450.0080.0080.0000.0000.0000.000
159A190ILE00.0540.02330.6470.0070.0070.0000.0000.0000.000
160A191GLN0-0.016-0.00528.204-0.004-0.0040.0000.0000.0000.000
161A192GLY00.0290.00632.8620.0060.0060.0000.0000.0000.000
162A193GLU-1-0.755-0.83235.362-0.066-0.0660.0000.0000.0000.000
163A194GLN00.020-0.00235.1590.0100.0100.0000.0000.0000.000
164A195ALA00.0150.03837.5430.0040.0040.0000.0000.0000.000
165A196LYS10.8600.91139.2870.0640.0640.0000.0000.0000.000
166A197LEU0-0.0010.00539.4730.0050.0050.0000.0000.0000.000
167A198ASN00.0410.02339.0740.0040.0040.0000.0000.0000.000
168A199LEU00.0270.02043.0580.0040.0040.0000.0000.0000.000
169A200MET0-0.021-0.02445.1430.0030.0030.0000.0000.0000.000
170A201ASN0-0.044-0.04645.7940.0030.0030.0000.0000.0000.000
171A202MET0-0.031-0.01847.0080.0020.0020.0000.0000.0000.000
172A203LEU0-0.022-0.02748.7170.0030.0030.0000.0000.0000.000
173A204GLN00.0780.03350.0850.0030.0030.0000.0000.0000.000
174A205GLN00.0280.02650.4870.0040.0040.0000.0000.0000.000
175A206SER0-0.018-0.02053.0740.0020.0020.0000.0000.0000.000
176A207GLN00.0120.00453.1760.0020.0020.0000.0000.0000.000
177A208ASP-1-0.799-0.88356.142-0.036-0.0360.0000.0000.0000.000
178A209LYS10.7890.90354.8720.0430.0430.0000.0000.0000.000
179A210LEU00.0460.02359.1810.0010.0010.0000.0000.0000.000
180A211LEU00.0240.02660.7600.0020.0020.0000.0000.0000.000
181A212ARG10.7710.85059.2060.0370.0370.0000.0000.0000.000
182A213ALA0-0.015-0.00763.7210.0010.0010.0000.0000.0000.000
183A214GLN00.0650.04464.9730.0020.0020.0000.0000.0000.000
184A215LYS10.8210.92865.1340.0300.0300.0000.0000.0000.000
185A216ASP-1-0.915-0.94668.903-0.025-0.0250.0000.0000.0000.000
186A217ARG10.9220.94370.5680.0230.0230.0000.0000.0000.000
187A218ALA0-0.0290.00372.7240.0010.0010.0000.0000.0000.000