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: VQ611

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2280898.538443
FMO2-HF: Nuclear repulsion 2204122.702147
FMO2-HF: Total energy -76775.836297
FMO2-MP2: Total energy -77000.266338


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.
-15.637-12.6333.89-2.762-4.1320.025
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 : 0.008 / q_NPA : -0.002
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].
3A5SER0-0.050-0.0313.827-1.412-0.151-0.015-0.494-0.7520.002
4A6LYS10.8480.9295.920-0.955-0.9550.0000.0000.0000.000
5A7ALA00.0000.0108.9580.1090.1090.0000.0000.0000.000
6A8VAL00.003-0.00611.583-0.031-0.0310.0000.0000.0000.000
7A9ILE0-0.017-0.01714.6250.0150.0150.0000.0000.0000.000
8A10VAL0-0.0050.00517.884-0.005-0.0050.0000.0000.0000.000
9A11PRO00.012-0.00720.340-0.001-0.0010.0000.0000.0000.000
10A12GLY00.0380.02623.6100.0140.0140.0000.0000.0000.000
11A13ASN0-0.043-0.02726.465-0.006-0.0060.0000.0000.0000.000
12A14GLY00.016-0.00629.387-0.009-0.0090.0000.0000.0000.000
13A15GLY0-0.051-0.03730.7400.0050.0050.0000.0000.0000.000
14A16GLY0-0.0260.00431.351-0.004-0.0040.0000.0000.0000.000
15A17ASP-1-0.788-0.85728.5050.0850.0850.0000.0000.0000.000
16A18VAL00.0450.00023.034-0.007-0.0070.0000.0000.0000.000
17A19THR0-0.110-0.08024.350-0.009-0.0090.0000.0000.0000.000
18A20THR0-0.088-0.05725.929-0.012-0.0120.0000.0000.0000.000
19A21HIS00.0150.03628.102-0.010-0.0100.0000.0000.0000.000
20A22GLY00.0040.00827.0190.0060.0060.0000.0000.0000.000
21A23TRP00.0340.00119.651-0.007-0.0070.0000.0000.0000.000
22A24TYR0-0.033-0.04021.765-0.006-0.0060.0000.0000.0000.000
23A25GLY00.0690.03321.440-0.004-0.0040.0000.0000.0000.000
24A26TRP0-0.032-0.01421.145-0.011-0.0110.0000.0000.0000.000
25A27VAL00.0250.00517.638-0.019-0.0190.0000.0000.0000.000
26A28LYS10.8330.90117.790-0.076-0.0760.0000.0000.0000.000
27A29LYS10.9650.97517.803-0.023-0.0230.0000.0000.0000.000
28A30GLU-1-0.829-0.89618.607-0.126-0.1260.0000.0000.0000.000
29A31LEU0-0.034-0.03713.147-0.044-0.0440.0000.0000.0000.000
30A32GLU-1-0.861-0.91913.830-0.039-0.0390.0000.0000.0000.000
31A33LYS10.7920.89515.8620.0930.0930.0000.0000.0000.000
32A34ILE0-0.104-0.04310.471-0.036-0.0360.0000.0000.0000.000
33A35PRO00.014-0.00812.2680.0120.0120.0000.0000.0000.000
34A36GLY0-0.0070.0029.866-0.122-0.1220.0000.0000.0000.000
35A37PHE0-0.0120.0167.1620.0030.0030.0000.0000.0000.000
36A38GLN0-0.001-0.00710.0100.1070.1070.0000.0000.0000.000
37A39CYS00.0190.01511.7940.0170.0170.0000.0000.0000.000
38A40LEU0-0.0390.00614.481-0.025-0.0250.0000.0000.0000.000
39A41ALA00.0460.01016.8380.0140.0140.0000.0000.0000.000
40A42LYS10.8680.92620.016-0.239-0.2390.0000.0000.0000.000
41A43ASN00.012-0.00422.8990.0090.0090.0000.0000.0000.000
42A44MET00.0160.02922.2640.0110.0110.0000.0000.0000.000
43A45PRO00.0190.01025.417-0.016-0.0160.0000.0000.0000.000
44A46ASP-1-0.793-0.90228.5420.1400.1400.0000.0000.0000.000
45A47PRO00.0110.00329.3870.0040.0040.0000.0000.0000.000
46A48ILE00.0000.01230.438-0.001-0.0010.0000.0000.0000.000
47A49THR00.0050.00633.073-0.002-0.0020.0000.0000.0000.000
48A50ALA0-0.0030.00827.6240.0050.0050.0000.0000.0000.000
49A51ARG10.9150.95728.298-0.115-0.1150.0000.0000.0000.000
50A52GLU-1-0.724-0.81824.9950.2550.2550.0000.0000.0000.000
51A53SER0-0.053-0.04525.5810.0170.0170.0000.0000.0000.000
52A54ILE0-0.050-0.02227.2960.0010.0010.0000.0000.0000.000
53A55TRP0-0.002-0.02023.5830.0170.0170.0000.0000.0000.000
54A56LEU00.0270.01220.7250.0230.0230.0000.0000.0000.000
55A57PRO00.0220.01120.4490.0320.0320.0000.0000.0000.000
56A58PHE00.0300.02221.2730.0140.0140.0000.0000.0000.000
57A59MET0-0.005-0.02017.4190.0010.0010.0000.0000.0000.000
58A60GLU-1-0.876-0.90516.6230.4810.4810.0000.0000.0000.000
59A61THR0-0.022-0.03416.8050.0380.0380.0000.0000.0000.000
60A62GLU-1-0.910-0.92619.2980.2310.2310.0000.0000.0000.000
61A63LEU0-0.079-0.03916.825-0.025-0.0250.0000.0000.0000.000
62A64HIS00.0000.01113.7650.0710.0710.0000.0000.0000.000
63A65CYS0-0.053-0.00512.4540.1030.1030.0000.0000.0000.000
64A66ASP-1-0.749-0.8508.4601.3781.3780.0000.0000.0000.000
65A67GLU-1-0.905-0.9715.5821.9441.9440.0000.0000.0000.000
66A68LYS10.8240.9162.174-13.739-13.0733.860-1.892-2.6350.024
67A69THR00.001-0.0265.355-0.957-0.931-0.001-0.008-0.0170.000
68A70ILE0-0.019-0.0036.9320.1610.1610.0000.0000.0000.000
69A71ILE00.0210.0009.788-0.126-0.1260.0000.0000.0000.000
70A72ILE0-0.023-0.00713.490-0.013-0.0130.0000.0000.0000.000
71A73GLY00.0310.02215.986-0.012-0.0120.0000.0000.0000.000
72A74HIS0-0.028-0.00619.265-0.008-0.0080.0000.0000.0000.000
73A75SER00.0760.03222.5980.0020.0020.0000.0000.0000.000
74A76SER00.0820.04424.7880.0140.0140.0000.0000.0000.000
75A77GLY00.0300.01422.2720.0180.0180.0000.0000.0000.000
76A78ALA0-0.081-0.04120.4260.0390.0390.0000.0000.0000.000
77A79ILE0-0.025-0.00721.2140.0350.0350.0000.0000.0000.000
78A80ALA00.0460.02121.8490.0180.0180.0000.0000.0000.000
79A81ALA0-0.016-0.00817.0010.0340.0340.0000.0000.0000.000
80A82MET0-0.0310.00017.8690.0580.0580.0000.0000.0000.000
81A83ARG10.7780.86219.840-0.214-0.2140.0000.0000.0000.000
82A84TYR0-0.042-0.03413.999-0.011-0.0110.0000.0000.0000.000
83A85ALA00.0270.00815.7390.0400.0400.0000.0000.0000.000
84A86GLU-1-0.812-0.87616.6770.3020.3020.0000.0000.0000.000
85A87THR0-0.081-0.05318.634-0.005-0.0050.0000.0000.0000.000
86A88HIS10.8180.91314.166-0.526-0.5260.0000.0000.0000.000
87A89ARG10.9160.9669.406-1.215-1.2150.0000.0000.0000.000
88A90VAL0-0.010-0.0089.5040.0300.0300.0000.0000.0000.000
89A91TYR0-0.007-0.0133.759-0.972-0.2090.037-0.275-0.5250.000
90A92ALA00.000-0.0297.097-0.243-0.2430.0000.0000.0000.000
91A93ILE00.0260.0189.956-0.058-0.0580.0000.0000.0000.000
92A94VAL0-0.050-0.03112.879-0.049-0.0490.0000.0000.0000.000
93A95LEU0-0.020-0.01415.397-0.013-0.0130.0000.0000.0000.000
94A96VAL00.0130.00919.038-0.026-0.0260.0000.0000.0000.000
95A97SER00.006-0.00121.7770.0020.0020.0000.0000.0000.000
96A98ALA0-0.0110.00122.5660.0060.0060.0000.0000.0000.000
97A99TYR0-0.077-0.07924.673-0.011-0.0110.0000.0000.0000.000
98A100THR0-0.039-0.06026.7530.0140.0140.0000.0000.0000.000
99A101SER0-0.013-0.01828.9910.0040.0040.0000.0000.0000.000
100A102ASP-1-0.849-0.93932.0050.1150.1150.0000.0000.0000.000
101A103LEU0-0.019-0.01632.108-0.007-0.0070.0000.0000.0000.000
102A104GLY0-0.036-0.00735.836-0.007-0.0070.0000.0000.0000.000
103A105ASP-1-0.858-0.93036.3830.0870.0870.0000.0000.0000.000
104A106GLU-1-0.811-0.88337.2430.1000.1000.0000.0000.0000.000
105A107ASN0-0.034-0.02933.9740.0040.0040.0000.0000.0000.000
106A108GLU-1-0.799-0.87431.1060.1440.1440.0000.0000.0000.000
107A109ARG10.8080.88932.997-0.092-0.0920.0000.0000.0000.000
108A110ALA0-0.082-0.03834.6680.0060.0060.0000.0000.0000.000
109A111SER00.001-0.00829.9040.0080.0080.0000.0000.0000.000
110A112GLY0-0.032-0.02430.4090.0120.0120.0000.0000.0000.000
111A113TYR0-0.013-0.01824.7960.0200.0200.0000.0000.0000.000
112A114PHE00.0150.00528.3610.0130.0130.0000.0000.0000.000
113A115THR0-0.0260.00030.973-0.005-0.0050.0000.0000.0000.000
114A116ARG10.7840.86425.728-0.229-0.2290.0000.0000.0000.000
115A117PRO00.0260.01429.9400.0060.0060.0000.0000.0000.000
116A118TRP00.0290.01423.3660.0180.0180.0000.0000.0000.000
117A119GLN0-0.045-0.03223.195-0.016-0.0160.0000.0000.0000.000
118A120TRP00.044-0.00122.1170.0370.0370.0000.0000.0000.000
119A121GLU-1-0.792-0.90120.7300.2850.2850.0000.0000.0000.000
120A122LYS10.8760.93719.545-0.262-0.2620.0000.0000.0000.000
121A123ILE00.0140.01717.2560.0570.0570.0000.0000.0000.000
122A124LYS10.8190.91215.906-0.184-0.1840.0000.0000.0000.000
123A125ALA0-0.027-0.00615.3600.0470.0470.0000.0000.0000.000
124A126ASN0-0.070-0.04213.4760.1340.1340.0000.0000.0000.000
125A127CYS0-0.0270.01611.1840.2280.2280.0000.0000.0000.000
126A128PRO0-0.0400.0088.078-0.148-0.1480.0000.0000.0000.000
127A129TYR0-0.019-0.0326.587-0.215-0.2150.0000.0000.0000.000
128A130ILE00.0370.01711.4870.0430.0430.0000.0000.0000.000
129A131VAL0-0.054-0.02413.318-0.075-0.0750.0000.0000.0000.000
130A132GLN00.0370.02316.0330.0310.0310.0000.0000.0000.000
131A133PHE0-0.021-0.01617.535-0.027-0.0270.0000.0000.0000.000
132A134GLY00.0520.02221.9980.0140.0140.0000.0000.0000.000
133A135SER0-0.014-0.02625.661-0.012-0.0120.0000.0000.0000.000
134A136THR0-0.033-0.04029.0650.0040.0040.0000.0000.0000.000
135A137ASP-1-0.826-0.87532.2770.0500.0500.0000.0000.0000.000
136A138ASP-1-0.758-0.87229.6350.0910.0910.0000.0000.0000.000
137A139PRO0-0.041-0.01832.6610.0010.0010.0000.0000.0000.000
138A140PHE0-0.019-0.00532.224-0.001-0.0010.0000.0000.0000.000
139A141LEU0-0.0280.00328.3340.0050.0050.0000.0000.0000.000
140A142PRO00.0410.04132.728-0.007-0.0070.0000.0000.0000.000
141A143TRP00.037-0.02326.7240.0050.0050.0000.0000.0000.000
142A144LYS10.9230.95030.802-0.078-0.0780.0000.0000.0000.000
143A145GLU-1-0.690-0.80630.0200.1280.1280.0000.0000.0000.000
144A146GLN00.0270.02226.9270.0160.0160.0000.0000.0000.000
145A147GLN0-0.097-0.06026.2130.0020.0020.0000.0000.0000.000
146A148GLU-1-0.850-0.90527.2730.1570.1570.0000.0000.0000.000
147A149VAL00.0180.00722.1860.0140.0140.0000.0000.0000.000
148A150ALA0-0.040-0.01622.6890.0200.0200.0000.0000.0000.000
149A151ASP-1-0.871-0.93223.1640.1300.1300.0000.0000.0000.000
150A152ARG10.8650.93224.715-0.169-0.1690.0000.0000.0000.000
151A153LEU0-0.013-0.01618.9770.0200.0200.0000.0000.0000.000
152A154GLU-1-0.784-0.86019.2330.2400.2400.0000.0000.0000.000
153A155THR0-0.030-0.01318.0940.0080.0080.0000.0000.0000.000
154A156LYS10.8150.90113.200-0.225-0.2250.0000.0000.0000.000
155A157LEU0-0.015-0.02118.4600.0000.0000.0000.0000.0000.000
156A158HIS10.8340.93517.315-0.091-0.0910.0000.0000.0000.000
157A159LYS10.9540.98122.417-0.062-0.0620.0000.0000.0000.000
158A160PHE00.007-0.00323.528-0.010-0.0100.0000.0000.0000.000
159A161THR00.004-0.02028.4300.0050.0050.0000.0000.0000.000
160A162ASP-1-0.913-0.94131.1870.0220.0220.0000.0000.0000.000
161A163CYS0-0.0210.00027.933-0.004-0.0040.0000.0000.0000.000
162A164GLY00.0360.02329.8020.0040.0040.0000.0000.0000.000
163A165HIS0-0.068-0.04829.1510.0100.0100.0000.0000.0000.000
164A166PHE0-0.023-0.01524.5520.0080.0080.0000.0000.0000.000
165A167GLN00.000-0.00926.8270.0020.0020.0000.0000.0000.000
166A168ASN00.0270.02728.416-0.006-0.0060.0000.0000.0000.000
167A169THR00.0600.00027.7330.0060.0060.0000.0000.0000.000
168A170GLU-1-0.955-0.96224.996-0.024-0.0240.0000.0000.0000.000
169A171PHE00.019-0.00821.5500.0080.0080.0000.0000.0000.000
170A172HIS00.0690.02920.6770.0000.0000.0000.0000.0000.000
171A173GLU-1-0.868-0.94519.644-0.019-0.0190.0000.0000.0000.000
172A174LEU0-0.0020.01516.2300.0000.0000.0000.0000.0000.000
173A175ILE00.0130.00115.743-0.007-0.0070.0000.0000.0000.000
174A176THR0-0.051-0.02414.705-0.051-0.0510.0000.0000.0000.000
175A177VAL00.0030.00713.616-0.036-0.0360.0000.0000.0000.000
176A178VAL00.0530.03910.3990.0000.0000.0000.0000.0000.000
177A179LYS10.9640.9819.8290.1350.1350.0000.0000.0000.000
178A180SER0-0.132-0.06410.228-0.116-0.1160.0000.0000.0000.000
179A181LEU00.0710.0257.837-0.059-0.0590.0000.0000.0000.000
180A182LEU0-0.0230.0035.5970.0360.0360.0000.0000.0000.000
181A183LYS10.8480.9305.8320.0440.0440.0000.0000.0000.000
182A184VAL0-0.041-0.0053.625-0.446-0.1580.009-0.093-0.203-0.001
183A185PRO0-0.0220.0096.463-0.057-0.0570.0000.0000.0000.000
184A186ALA00.0210.0119.9280.1130.1130.0000.0000.0000.000
185A187LEU00.0020.0059.8960.0330.0330.0000.0000.0000.000
186A188GLU-1-0.804-0.88513.1510.1340.1340.0000.0000.0000.000
187A189HIS0-0.045-0.02516.7150.0400.0400.0000.0000.0000.000
188A190HIS00.0160.01717.469-0.024-0.0240.0000.0000.0000.000
189A191HIS10.7680.84919.833-0.172-0.1720.0000.0000.0000.000
190A192HIS00.0530.04316.267-0.029-0.0290.0000.0000.0000.000
191A193HIS0-0.092-0.05221.380-0.035-0.0350.0000.0000.0000.000
192A194HIS00.0380.02323.7080.0330.0330.0000.0000.0000.000