Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: YVMK2

Calculation Name: 2QS9-A-Xray372

Preferred Name: Putative hydrolase RBBP9

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2QS9

Chain ID: A

ChEMBL ID: CHEMBL1075121

UniProt ID: O75884

Base Structure: X-ray

Registration Date: 2023-09-23

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2279498.621104
FMO2-HF: Nuclear repulsion 2202723.354878
FMO2-HF: Total energy -76775.266226
FMO2-MP2: Total energy -76999.679619


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:3:SER)


Summations of interaction energy for fragment #1(A:3:SER)
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.
-20.052-15.3631.954-2.717-3.9260.017
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.003
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].
3A5SER0-0.043-0.0273.8270.5241.675-0.012-0.427-0.7130.001
4A6LYS10.8740.9365.8580.0970.0970.0000.0000.0000.000
5A7ALA00.0060.0198.958-0.362-0.3620.0000.0000.0000.000
6A8VAL00.001-0.01011.5830.1730.1730.0000.0000.0000.000
7A9ILE0-0.018-0.01314.568-0.066-0.0660.0000.0000.0000.000
8A10VAL0-0.0110.00717.3980.0530.0530.0000.0000.0000.000
9A11PRO00.009-0.00919.915-0.029-0.0290.0000.0000.0000.000
10A12GLY00.0460.02823.296-0.004-0.0040.0000.0000.0000.000
11A13ASN0-0.035-0.01326.0300.0120.0120.0000.0000.0000.000
12A14GLY00.035-0.00128.823-0.001-0.0010.0000.0000.0000.000
13A15GLY0-0.057-0.03930.4300.0010.0010.0000.0000.0000.000
14A16GLY0-0.0170.00831.3260.0080.0080.0000.0000.0000.000
15A17ASP-1-0.815-0.89628.491-0.055-0.0550.0000.0000.0000.000
16A18VAL00.0510.00222.905-0.009-0.0090.0000.0000.0000.000
17A19THR0-0.108-0.07224.292-0.014-0.0140.0000.0000.0000.000
18A20THR0-0.087-0.05225.939-0.001-0.0010.0000.0000.0000.000
19A21HIS00.0320.03928.1120.0090.0090.0000.0000.0000.000
20A22GLY0-0.0040.00427.021-0.012-0.0120.0000.0000.0000.000
21A23TRP00.0340.00619.732-0.006-0.0060.0000.0000.0000.000
22A24TYR0-0.037-0.04021.763-0.010-0.0100.0000.0000.0000.000
23A25GLY00.0660.02921.434-0.008-0.0080.0000.0000.0000.000
24A26TRP00.0200.01521.199-0.007-0.0070.0000.0000.0000.000
25A27VAL00.0270.00917.608-0.007-0.0070.0000.0000.0000.000
26A28LYS10.8570.92817.8470.0320.0320.0000.0000.0000.000
27A29LYS10.9590.97117.8490.0880.0880.0000.0000.0000.000
28A30GLU-1-0.858-0.91718.557-0.189-0.1890.0000.0000.0000.000
29A31LEU0-0.033-0.03613.292-0.029-0.0290.0000.0000.0000.000
30A32GLU-1-0.896-0.94513.898-0.036-0.0360.0000.0000.0000.000
31A33LYS10.8160.91215.9070.1890.1890.0000.0000.0000.000
32A34ILE0-0.096-0.03610.5190.0010.0010.0000.0000.0000.000
33A35PRO00.005-0.01412.3680.0460.0460.0000.0000.0000.000
34A36GLY0-0.0030.0029.877-0.026-0.0260.0000.0000.0000.000
35A37PHE0-0.0200.0087.4130.1020.1020.0000.0000.0000.000
36A38GLN00.0380.01410.0320.0350.0350.0000.0000.0000.000
37A39CYS00.0170.01611.801-0.173-0.1730.0000.0000.0000.000
38A40LEU0-0.059-0.01314.4830.0740.0740.0000.0000.0000.000
39A41ALA00.0470.01216.823-0.060-0.0600.0000.0000.0000.000
40A42LYS10.8830.94219.680-0.031-0.0310.0000.0000.0000.000
41A43ASN00.0260.02322.899-0.032-0.0320.0000.0000.0000.000
42A44MET00.0220.02421.6880.0120.0120.0000.0000.0000.000
43A45PRO00.0110.00625.0610.0050.0050.0000.0000.0000.000
44A46ASP-1-0.800-0.90827.945-0.079-0.0790.0000.0000.0000.000
45A47PRO0-0.001-0.00128.851-0.010-0.0100.0000.0000.0000.000
46A48ILE00.0080.01529.919-0.010-0.0100.0000.0000.0000.000
47A49THR00.0050.00532.233-0.003-0.0030.0000.0000.0000.000
48A50ALA0-0.0040.00426.778-0.008-0.0080.0000.0000.0000.000
49A51ARG10.9350.96427.4470.0510.0510.0000.0000.0000.000
50A52GLU-1-0.730-0.82224.205-0.146-0.1460.0000.0000.0000.000
51A53SER0-0.057-0.04724.911-0.001-0.0010.0000.0000.0000.000
52A54ILE0-0.040-0.01426.7670.0150.0150.0000.0000.0000.000
53A55TRP0-0.007-0.02522.8330.0010.0010.0000.0000.0000.000
54A56LEU00.0220.00720.042-0.005-0.0050.0000.0000.0000.000
55A57PRO00.0170.00919.9830.0040.0040.0000.0000.0000.000
56A58PHE00.0310.02521.0290.0240.0240.0000.0000.0000.000
57A59MET0-0.014-0.02516.6230.0160.0160.0000.0000.0000.000
58A60GLU-1-0.885-0.92716.3570.0110.0110.0000.0000.0000.000
59A61THR0-0.039-0.06016.7540.0400.0400.0000.0000.0000.000
60A62GLU-1-0.902-0.90719.3490.1320.1320.0000.0000.0000.000
61A63LEU0-0.088-0.05016.4450.0110.0110.0000.0000.0000.000
62A64HIS00.0070.00713.9640.0030.0030.0000.0000.0000.000
63A65CYS0-0.0390.00512.049-0.008-0.0080.0000.0000.0000.000
64A66ASP-1-0.770-0.8798.3640.3630.3630.0000.0000.0000.000
65A67GLU-1-0.923-0.9795.6270.2290.2290.0000.0000.0000.000
66A68LYS10.8240.9132.634-18.833-16.5851.898-1.785-2.3610.019
67A69THR0-0.001-0.0065.091-0.244-0.212-0.001-0.007-0.0230.000
68A70ILE0-0.015-0.0057.047-0.261-0.2610.0000.0000.0000.000
69A71ILE00.0220.0019.4770.2160.2160.0000.0000.0000.000
70A72ILE0-0.022-0.00512.911-0.053-0.0530.0000.0000.0000.000
71A73GLY00.0250.01715.8210.0650.0650.0000.0000.0000.000
72A74HIS0-0.0140.00218.804-0.013-0.0130.0000.0000.0000.000
73A75SER00.0750.02622.3220.0270.0270.0000.0000.0000.000
74A76SER00.0510.02724.087-0.010-0.0100.0000.0000.0000.000
75A77GLY00.0710.02221.6440.0000.0000.0000.0000.0000.000
76A78ALA0-0.075-0.03519.697-0.039-0.0390.0000.0000.0000.000
77A79ILE00.0150.03320.249-0.030-0.0300.0000.0000.0000.000
78A80ALA0-0.054-0.03920.882-0.004-0.0040.0000.0000.0000.000
79A81ALA0-0.025-0.01416.047-0.002-0.0020.0000.0000.0000.000
80A82MET0-0.023-0.00216.879-0.045-0.0450.0000.0000.0000.000
81A83ARG10.7960.87718.8450.1970.1970.0000.0000.0000.000
82A84TYR0-0.034-0.02013.4700.0220.0220.0000.0000.0000.000
83A85ALA00.0250.00814.7330.0140.0140.0000.0000.0000.000
84A86GLU-1-0.815-0.88515.682-0.243-0.2430.0000.0000.0000.000
85A87THR0-0.080-0.05117.9280.0110.0110.0000.0000.0000.000
86A88HIS10.8390.93313.5290.2080.2080.0000.0000.0000.000
87A89ARG10.9150.9708.1110.7880.7880.0000.0000.0000.000
88A90VAL00.0000.0018.6950.1150.1150.0000.0000.0000.000
89A91TYR0-0.022-0.0213.159-1.653-0.6400.063-0.422-0.654-0.003
90A92ALA00.002-0.0346.0910.0100.0100.0000.0000.0000.000
91A93ILE00.0270.0239.1710.1310.1310.0000.0000.0000.000
92A94VAL0-0.043-0.03012.782-0.011-0.0110.0000.0000.0000.000
93A95LEU0-0.017-0.01315.2400.0610.0610.0000.0000.0000.000
94A96VAL00.0060.00718.6910.0000.0000.0000.0000.0000.000
95A97SER00.0150.01421.7020.0170.0170.0000.0000.0000.000
96A98ALA0-0.0050.00221.9820.0110.0110.0000.0000.0000.000
97A99TYR0-0.067-0.07424.090-0.002-0.0020.0000.0000.0000.000
98A100THR0-0.054-0.06225.778-0.010-0.0100.0000.0000.0000.000
99A101SER00.008-0.01227.9950.0090.0090.0000.0000.0000.000
100A102ASP-1-0.850-0.93231.020-0.122-0.1220.0000.0000.0000.000
101A103LEU0-0.005-0.01531.5090.0060.0060.0000.0000.0000.000
102A104GLY0-0.042-0.01334.9200.0060.0060.0000.0000.0000.000
103A105ASP-1-0.862-0.93035.455-0.095-0.0950.0000.0000.0000.000
104A106GLU-1-0.801-0.90136.282-0.077-0.0770.0000.0000.0000.000
105A107ASN0-0.030-0.02833.2860.0090.0090.0000.0000.0000.000
106A108GLU-1-0.834-0.88730.469-0.152-0.1520.0000.0000.0000.000
107A109ARG10.8160.90432.0380.0760.0760.0000.0000.0000.000
108A110ALA0-0.085-0.04133.7040.0010.0010.0000.0000.0000.000
109A111SER0-0.001-0.00429.0130.0020.0020.0000.0000.0000.000
110A112GLY0-0.029-0.02329.5450.0010.0010.0000.0000.0000.000
111A113TYR00.008-0.00123.872-0.010-0.0100.0000.0000.0000.000
112A114PHE00.0250.00527.362-0.013-0.0130.0000.0000.0000.000
113A115THR0-0.042-0.00629.9700.0010.0010.0000.0000.0000.000
114A116ARG10.7890.87024.9540.1570.1570.0000.0000.0000.000
115A117PRO00.0220.01229.034-0.010-0.0100.0000.0000.0000.000
116A118TRP00.0210.01422.168-0.004-0.0040.0000.0000.0000.000
117A119GLN0-0.040-0.02722.1230.0120.0120.0000.0000.0000.000
118A120TRP00.051-0.00321.129-0.029-0.0290.0000.0000.0000.000
119A121GLU-1-0.819-0.91519.760-0.379-0.3790.0000.0000.0000.000
120A122LYS10.8610.93718.6240.1570.1570.0000.0000.0000.000
121A123ILE00.0110.01816.244-0.038-0.0380.0000.0000.0000.000
122A124LYS10.8550.94014.9210.3310.3310.0000.0000.0000.000
123A125ALA0-0.037-0.00714.454-0.081-0.0810.0000.0000.0000.000
124A126ASN0-0.077-0.05212.572-0.066-0.0660.0000.0000.0000.000
125A127CYS0-0.0320.01810.192-0.151-0.1510.0000.0000.0000.000
126A128PRO0-0.0450.0077.0890.0950.0950.0000.0000.0000.000
127A129TYR0-0.010-0.0276.3870.0430.0430.0000.0000.0000.000
128A130ILE00.0320.01510.890-0.010-0.0100.0000.0000.0000.000
129A131VAL0-0.052-0.02213.4160.0570.0570.0000.0000.0000.000
130A132GLN00.0350.01815.980-0.004-0.0040.0000.0000.0000.000
131A133PHE0-0.023-0.01617.5120.0030.0030.0000.0000.0000.000
132A134GLY00.0600.02522.0240.0080.0080.0000.0000.0000.000
133A135SER0-0.023-0.02525.689-0.006-0.0060.0000.0000.0000.000
134A136THR0-0.027-0.04029.0900.0040.0040.0000.0000.0000.000
135A137ASP-1-0.839-0.88732.305-0.168-0.1680.0000.0000.0000.000
136A138ASP-1-0.778-0.87529.624-0.189-0.1890.0000.0000.0000.000
137A139PRO0-0.043-0.02032.6610.0040.0040.0000.0000.0000.000
138A140PHE0-0.014-0.00331.9000.0090.0090.0000.0000.0000.000
139A141LEU0-0.032-0.00527.997-0.001-0.0010.0000.0000.0000.000
140A142PRO00.0350.04332.2050.0000.0000.0000.0000.0000.000
141A143TRP00.051-0.01126.889-0.008-0.0080.0000.0000.0000.000
142A144LYS10.9280.95030.3690.1560.1560.0000.0000.0000.000
143A145GLU-1-0.692-0.80529.228-0.186-0.1860.0000.0000.0000.000
144A146GLN00.0300.02326.431-0.040-0.0400.0000.0000.0000.000
145A147GLN0-0.090-0.05225.701-0.020-0.0200.0000.0000.0000.000
146A148GLU-1-0.853-0.90926.642-0.226-0.2260.0000.0000.0000.000
147A149VAL00.0120.00621.534-0.016-0.0160.0000.0000.0000.000
148A150ALA0-0.039-0.01822.145-0.032-0.0320.0000.0000.0000.000
149A151ASP-1-0.877-0.93822.531-0.300-0.3000.0000.0000.0000.000
150A152ARG10.8610.93123.7760.2430.2430.0000.0000.0000.000
151A153LEU0-0.019-0.02618.031-0.008-0.0080.0000.0000.0000.000
152A154GLU-1-0.754-0.85118.332-0.486-0.4860.0000.0000.0000.000
153A155THR0-0.037-0.01017.613-0.052-0.0520.0000.0000.0000.000
154A156LYS10.8600.94412.8940.9940.9940.0000.0000.0000.000
155A157LEU0-0.003-0.01718.496-0.014-0.0140.0000.0000.0000.000
156A158HIS10.8180.92817.4830.5220.5220.0000.0000.0000.000
157A159LYS10.9750.98522.4410.2410.2410.0000.0000.0000.000
158A160PHE00.0240.00223.487-0.006-0.0060.0000.0000.0000.000
159A161THR00.011-0.02228.4510.0010.0010.0000.0000.0000.000
160A162ASP-1-0.929-0.94631.331-0.177-0.1770.0000.0000.0000.000
161A163CYS0-0.0210.00227.993-0.001-0.0010.0000.0000.0000.000
162A164GLY00.0280.01929.8180.0000.0000.0000.0000.0000.000
163A165HIS0-0.067-0.04428.714-0.012-0.0120.0000.0000.0000.000
164A166PHE0-0.030-0.02224.716-0.012-0.0120.0000.0000.0000.000
165A167GLN00.002-0.00726.840-0.003-0.0030.0000.0000.0000.000
166A168ASN00.0210.01828.4020.0250.0250.0000.0000.0000.000
167A169THR00.0680.00227.735-0.006-0.0060.0000.0000.0000.000
168A170GLU-1-0.999-0.98124.976-0.153-0.1530.0000.0000.0000.000
169A171PHE00.016-0.00921.550-0.010-0.0100.0000.0000.0000.000
170A172HIS00.0760.03020.592-0.034-0.0340.0000.0000.0000.000
171A173GLU-1-0.881-0.95019.637-0.334-0.3340.0000.0000.0000.000
172A174LEU00.0000.01816.156-0.068-0.0680.0000.0000.0000.000
173A175ILE00.0250.00915.744-0.095-0.0950.0000.0000.0000.000
174A176THR0-0.055-0.02714.696-0.071-0.0710.0000.0000.0000.000
175A177VAL00.0040.00713.439-0.078-0.0780.0000.0000.0000.000
176A178VAL00.0530.04810.412-0.172-0.1720.0000.0000.0000.000
177A179LYS10.9740.9799.8230.1900.1900.0000.0000.0000.000
178A180SER0-0.145-0.07910.213-0.093-0.0930.0000.0000.0000.000
179A181LEU00.0700.0247.793-0.114-0.1140.0000.0000.0000.000
180A182LEU0-0.0220.0015.576-0.656-0.6560.0000.0000.0000.000
181A183LYS10.8500.9355.8040.7370.7370.0000.0000.0000.000
182A184VAL0-0.041-0.0053.708-0.287-0.0420.006-0.076-0.1750.000
183A185PRO0-0.044-0.0036.4760.3130.3130.0000.0000.0000.000
184A186ALA00.0330.0149.957-0.163-0.1630.0000.0000.0000.000
185A187LEU00.0060.0079.7790.0160.0160.0000.0000.0000.000
186A188GLU-1-0.839-0.92912.998-0.791-0.7910.0000.0000.0000.000
187A189HIS0-0.060-0.02716.533-0.030-0.0300.0000.0000.0000.000
188A190HIS00.0260.02616.0440.0570.0570.0000.0000.0000.000
189A191HIS10.7610.84319.4180.3900.3900.0000.0000.0000.000
190A192HIS00.0460.03915.3890.0450.0450.0000.0000.0000.000
191A193HIS0-0.085-0.04920.7840.0330.0330.0000.0000.0000.000
192A194HIS00.0290.01622.934-0.011-0.0110.0000.0000.0000.000