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: 1N3GZ

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 OptAll
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 -2285738.640229
FMO2-HF: Nuclear repulsion 2208962.515927
FMO2-HF: Total energy -76776.124302
FMO2-MP2: Total energy -77000.566518


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.
-19.31-17.5666.84-3.871-4.7120.029
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 : 0.025 / q_NPA : 0.007
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].
3A5SER0-0.077-0.0483.307-2.279-0.5740.033-0.905-0.833-0.001
4A6LYS10.8400.9265.731-0.429-0.4290.0000.0000.0000.000
5A7ALA00.0010.0039.3500.0220.0220.0000.0000.0000.000
6A8VAL0-0.002-0.00912.0050.0120.0120.0000.0000.0000.000
7A9ILE0-0.026-0.00914.9930.0070.0070.0000.0000.0000.000
8A10VAL0-0.013-0.00418.0730.0030.0030.0000.0000.0000.000
9A11PRO00.0130.00420.600-0.001-0.0010.0000.0000.0000.000
10A12GLY00.0500.02023.9760.0080.0080.0000.0000.0000.000
11A13ASN0-0.074-0.04227.004-0.003-0.0030.0000.0000.0000.000
12A14GLY00.0210.00529.977-0.005-0.0050.0000.0000.0000.000
13A15GLY0-0.045-0.02831.4140.0030.0030.0000.0000.0000.000
14A16GLY0-0.027-0.00331.534-0.003-0.0030.0000.0000.0000.000
15A17ASP-1-0.764-0.85028.5190.0570.0570.0000.0000.0000.000
16A18VAL00.0340.00823.142-0.005-0.0050.0000.0000.0000.000
17A19THR0-0.101-0.07624.187-0.004-0.0040.0000.0000.0000.000
18A20THR0-0.104-0.07225.628-0.008-0.0080.0000.0000.0000.000
19A21HIS00.0140.02628.430-0.007-0.0070.0000.0000.0000.000
20A22GLY00.0270.01027.0210.0030.0030.0000.0000.0000.000
21A23TRP00.0310.01019.916-0.004-0.0040.0000.0000.0000.000
22A24TYR0-0.053-0.03322.071-0.005-0.0050.0000.0000.0000.000
23A25GLY00.0880.04021.824-0.003-0.0030.0000.0000.0000.000
24A26TRP0-0.074-0.03521.210-0.007-0.0070.0000.0000.0000.000
25A27VAL00.017-0.01017.657-0.012-0.0120.0000.0000.0000.000
26A28LYS10.8430.88917.826-0.059-0.0590.0000.0000.0000.000
27A29LYS10.9270.95817.679-0.023-0.0230.0000.0000.0000.000
28A30GLU-1-0.800-0.88618.837-0.074-0.0740.0000.0000.0000.000
29A31LEU0-0.025-0.02113.146-0.032-0.0320.0000.0000.0000.000
30A32GLU-1-0.790-0.88413.998-0.019-0.0190.0000.0000.0000.000
31A33LYS10.7930.89115.7670.0600.0600.0000.0000.0000.000
32A34ILE0-0.074-0.02110.715-0.013-0.0130.0000.0000.0000.000
33A35PRO0-0.003-0.01812.6220.0080.0080.0000.0000.0000.000
34A36GLY00.0090.0139.866-0.083-0.0830.0000.0000.0000.000
35A37PHE0-0.0140.0117.4680.0300.0300.0000.0000.0000.000
36A38GLN0-0.008-0.01310.1110.1030.1030.0000.0000.0000.000
37A39CYS0-0.0260.00411.886-0.017-0.0170.0000.0000.0000.000
38A40LEU0-0.0030.02014.271-0.001-0.0010.0000.0000.0000.000
39A41ALA00.0370.00816.5380.0010.0010.0000.0000.0000.000
40A42LYS10.8080.90820.014-0.160-0.1600.0000.0000.0000.000
41A43ASN00.007-0.01223.0170.0030.0030.0000.0000.0000.000
42A44MET00.0140.03122.4040.0060.0060.0000.0000.0000.000
43A45PRO00.0100.00825.963-0.009-0.0090.0000.0000.0000.000
44A46ASP-1-0.751-0.89028.7410.0860.0860.0000.0000.0000.000
45A47PRO00.0060.01229.5810.0030.0030.0000.0000.0000.000
46A48ILE0-0.027-0.00230.630-0.002-0.0020.0000.0000.0000.000
47A49THR0-0.006-0.01333.206-0.002-0.0020.0000.0000.0000.000
48A50ALA0-0.0040.00327.7480.0030.0030.0000.0000.0000.000
49A51ARG10.9070.96028.110-0.069-0.0690.0000.0000.0000.000
50A52GLU-1-0.728-0.82925.0730.1460.1460.0000.0000.0000.000
51A53SER0-0.055-0.04225.6270.0110.0110.0000.0000.0000.000
52A54ILE0-0.039-0.01427.5100.0000.0000.0000.0000.0000.000
53A55TRP0-0.007-0.01823.8330.0110.0110.0000.0000.0000.000
54A56LEU00.0180.01120.8670.0130.0130.0000.0000.0000.000
55A57PRO00.0260.00720.6510.0200.0200.0000.0000.0000.000
56A58PHE00.0270.01621.6570.0110.0110.0000.0000.0000.000
57A59MET00.003-0.01517.2860.0020.0020.0000.0000.0000.000
58A60GLU-1-0.881-0.90717.1090.2810.2810.0000.0000.0000.000
59A61THR0-0.027-0.03517.4830.0220.0220.0000.0000.0000.000
60A62GLU-1-0.899-0.92720.0980.1620.1620.0000.0000.0000.000
61A63LEU0-0.024-0.02617.002-0.013-0.0130.0000.0000.0000.000
62A64HIS00.0090.01714.0360.0480.0480.0000.0000.0000.000
63A65CYS0-0.0510.00212.7440.0610.0610.0000.0000.0000.000
64A66ASP-1-0.712-0.8288.7520.7950.7950.0000.0000.0000.000
65A67GLU-1-0.930-0.9816.1550.8640.8640.0000.0000.0000.000
66A68LYS10.8490.9241.974-15.541-17.0326.628-2.368-2.7690.030
67A69THR0-0.003-0.0245.690-0.552-0.5520.0000.0000.0000.000
68A70ILE0-0.027-0.0147.2720.1280.1280.0000.0000.0000.000
69A71ILE00.0330.00610.300-0.068-0.0680.0000.0000.0000.000
70A72ILE0-0.028-0.00913.8940.0000.0000.0000.0000.0000.000
71A73GLY00.0330.03016.278-0.008-0.0080.0000.0000.0000.000
72A74HIS0-0.012-0.00119.427-0.003-0.0030.0000.0000.0000.000
73A75SER00.0500.02122.8290.0020.0020.0000.0000.0000.000
74A76SER00.0710.03025.1860.0090.0090.0000.0000.0000.000
75A77GLY00.0350.02022.7080.0090.0090.0000.0000.0000.000
76A78ALA0-0.074-0.03920.8300.0220.0220.0000.0000.0000.000
77A79ILE0-0.019-0.01321.5570.0180.0180.0000.0000.0000.000
78A80ALA00.0410.02521.8300.0110.0110.0000.0000.0000.000
79A81ALA0-0.028-0.01417.3130.0190.0190.0000.0000.0000.000
80A82MET0-0.0240.00017.7430.0350.0350.0000.0000.0000.000
81A83ARG10.7720.84819.668-0.121-0.1210.0000.0000.0000.000
82A84TYR0-0.030-0.04014.176-0.011-0.0110.0000.0000.0000.000
83A85ALA00.0470.02515.6040.0200.0200.0000.0000.0000.000
84A86GLU-1-0.810-0.87516.6380.1650.1650.0000.0000.0000.000
85A87THR0-0.091-0.04818.473-0.008-0.0080.0000.0000.0000.000
86A88HIS10.8170.91214.389-0.299-0.2990.0000.0000.0000.000
87A89ARG10.8960.9529.415-0.613-0.6130.0000.0000.0000.000
88A90VAL0-0.002-0.0089.460-0.022-0.0220.0000.0000.0000.000
89A91TYR0-0.033-0.0193.433-1.409-0.3300.131-0.443-0.7660.001
90A92ALA00.014-0.0217.0920.0100.0100.0000.0000.0000.000
91A93ILE00.0030.00910.172-0.081-0.0810.0000.0000.0000.000
92A94VAL0-0.039-0.02913.151-0.014-0.0140.0000.0000.0000.000
93A95LEU0-0.012-0.00215.818-0.019-0.0190.0000.0000.0000.000
94A96VAL00.0230.00619.458-0.013-0.0130.0000.0000.0000.000
95A97SER0-0.007-0.01722.1840.0020.0020.0000.0000.0000.000
96A98ALA00.0060.00523.0700.0030.0030.0000.0000.0000.000
97A99TYR0-0.083-0.07525.210-0.006-0.0060.0000.0000.0000.000
98A100THR0-0.049-0.05226.9860.0080.0080.0000.0000.0000.000
99A101SER0-0.026-0.03229.2040.0010.0010.0000.0000.0000.000
100A102ASP-1-0.841-0.93432.0630.0690.0690.0000.0000.0000.000
101A103LEU0-0.037-0.02932.700-0.003-0.0030.0000.0000.0000.000
102A104GLY0-0.021-0.00136.155-0.004-0.0040.0000.0000.0000.000
103A105ASP-1-0.858-0.92736.6550.0540.0540.0000.0000.0000.000
104A106GLU-1-0.829-0.88937.4520.0600.0600.0000.0000.0000.000
105A107ASN0-0.033-0.02134.1320.0020.0020.0000.0000.0000.000
106A108GLU-1-0.757-0.86031.1250.0870.0870.0000.0000.0000.000
107A109ARG10.8230.90332.922-0.055-0.0550.0000.0000.0000.000
108A110ALA0-0.075-0.03734.5520.0040.0040.0000.0000.0000.000
109A111SER0-0.005-0.01229.9500.0050.0050.0000.0000.0000.000
110A112GLY0-0.009-0.00430.2920.0070.0070.0000.0000.0000.000
111A113TYR00.0180.00124.7690.0080.0080.0000.0000.0000.000
112A114PHE00.0280.01928.2940.0060.0060.0000.0000.0000.000
113A115THR0-0.066-0.03731.079-0.003-0.0030.0000.0000.0000.000
114A116ARG10.7690.86525.294-0.135-0.1350.0000.0000.0000.000
115A117PRO00.0250.01029.7450.0040.0040.0000.0000.0000.000
116A118TRP00.0250.02223.6210.0110.0110.0000.0000.0000.000
117A119GLN0-0.029-0.02522.915-0.008-0.0080.0000.0000.0000.000
118A120TRP00.029-0.00621.8760.0210.0210.0000.0000.0000.000
119A121GLU-1-0.772-0.89620.3470.1710.1710.0000.0000.0000.000
120A122LYS10.8720.93619.037-0.145-0.1450.0000.0000.0000.000
121A123ILE00.0270.02217.0150.0340.0340.0000.0000.0000.000
122A124LYS10.8120.90315.529-0.103-0.1030.0000.0000.0000.000
123A125ALA00.0060.01815.2370.0290.0290.0000.0000.0000.000
124A126ASN0-0.071-0.04713.0150.0690.0690.0000.0000.0000.000
125A127CYS0-0.0190.01910.9870.1310.1310.0000.0000.0000.000
126A128PRO0-0.0410.0077.884-0.103-0.1030.0000.0000.0000.000
127A129TYR0-0.025-0.0416.273-0.124-0.1240.0000.0000.0000.000
128A130ILE00.0270.01411.323-0.026-0.0260.0000.0000.0000.000
129A131VAL0-0.042-0.02413.318-0.046-0.0460.0000.0000.0000.000
130A132GLN00.0200.01816.1600.0120.0120.0000.0000.0000.000
131A133PHE0-0.022-0.02117.735-0.015-0.0150.0000.0000.0000.000
132A134GLY00.0510.02022.2400.0070.0070.0000.0000.0000.000
133A135SER0-0.007-0.03325.962-0.007-0.0070.0000.0000.0000.000
134A136THR0-0.051-0.03629.4270.0020.0020.0000.0000.0000.000
135A137ASP-1-0.790-0.86332.6210.0310.0310.0000.0000.0000.000
136A138ASP-1-0.755-0.86329.8140.0560.0560.0000.0000.0000.000
137A139PRO0-0.033-0.01132.7910.0010.0010.0000.0000.0000.000
138A140PHE0-0.025-0.00832.629-0.001-0.0010.0000.0000.0000.000
139A141LEU0-0.0290.00728.7290.0030.0030.0000.0000.0000.000
140A142PRO00.0610.04132.876-0.003-0.0030.0000.0000.0000.000
141A143TRP00.026-0.01926.8730.0030.0030.0000.0000.0000.000
142A144LYS10.9120.94531.210-0.052-0.0520.0000.0000.0000.000
143A145GLU-1-0.722-0.81930.2890.0750.0750.0000.0000.0000.000
144A146GLN00.0230.01227.3350.0090.0090.0000.0000.0000.000
145A147GLN0-0.088-0.04926.5220.0010.0010.0000.0000.0000.000
146A148GLU-1-0.806-0.89327.3370.0950.0950.0000.0000.0000.000
147A149VAL00.0270.00022.2810.0090.0090.0000.0000.0000.000
148A150ALA0-0.029-0.00522.8880.0140.0140.0000.0000.0000.000
149A151ASP-1-0.876-0.94023.3690.0810.0810.0000.0000.0000.000
150A152ARG10.8310.92224.640-0.100-0.1000.0000.0000.0000.000
151A153LEU0-0.017-0.01118.9810.0110.0110.0000.0000.0000.000
152A154GLU-1-0.772-0.85719.1210.1520.1520.0000.0000.0000.000
153A155THR0-0.032-0.01418.4250.0070.0070.0000.0000.0000.000
154A156LYS10.8380.90013.161-0.240-0.2400.0000.0000.0000.000
155A157LEU0-0.037-0.02318.229-0.005-0.0050.0000.0000.0000.000
156A158HIS10.8260.92617.511-0.075-0.0750.0000.0000.0000.000
157A159LYS10.9290.98122.572-0.043-0.0430.0000.0000.0000.000
158A160PHE0-0.008-0.01023.791-0.006-0.0060.0000.0000.0000.000
159A161THR0-0.010-0.02328.7630.0030.0030.0000.0000.0000.000
160A162ASP-1-0.870-0.92031.1450.0150.0150.0000.0000.0000.000
161A163CYS0-0.028-0.00628.307-0.002-0.0020.0000.0000.0000.000
162A164GLY00.0250.00930.0980.0020.0020.0000.0000.0000.000
163A165HIS0-0.068-0.04429.5900.0060.0060.0000.0000.0000.000
164A166PHE0-0.013-0.00324.9470.0050.0050.0000.0000.0000.000
165A167GLN00.003-0.00926.9310.0000.0000.0000.0000.0000.000
166A168ASN00.0180.02228.257-0.002-0.0020.0000.0000.0000.000
167A169THR00.0440.00127.6610.0040.0040.0000.0000.0000.000
168A170GLU-1-0.933-0.95525.169-0.013-0.0130.0000.0000.0000.000
169A171PHE00.017-0.00321.8970.0050.0050.0000.0000.0000.000
170A172HIS00.0700.03320.3950.0000.0000.0000.0000.0000.000
171A173GLU-1-0.834-0.92719.634-0.008-0.0080.0000.0000.0000.000
172A174LEU00.0090.02516.3450.0010.0010.0000.0000.0000.000
173A175ILE00.0040.00215.867-0.007-0.0070.0000.0000.0000.000
174A176THR0-0.059-0.03614.987-0.036-0.0360.0000.0000.0000.000
175A177VAL00.0100.00913.965-0.018-0.0180.0000.0000.0000.000
176A178VAL00.0330.03210.6510.0080.0080.0000.0000.0000.000
177A179LYS10.9070.95310.0820.0760.0760.0000.0000.0000.000
178A180SER0-0.123-0.05911.045-0.062-0.0620.0000.0000.0000.000
179A181LEU00.0570.0218.154-0.031-0.0310.0000.0000.0000.000
180A182LEU0-0.018-0.0095.6400.1840.1840.0000.0000.0000.000
181A183LYS10.8380.9175.462-0.069-0.0690.0000.0000.0000.000
182A184VAL0-0.0170.0093.231-0.582-0.1310.048-0.155-0.344-0.001
183A185PRO0-0.0180.0156.032-0.170-0.1700.0000.0000.0000.000
184A186ALA00.0230.0089.8600.1320.1320.0000.0000.0000.000
185A187LEU00.0080.0159.6180.0340.0340.0000.0000.0000.000
186A188GLU-1-0.816-0.89412.9760.1260.1260.0000.0000.0000.000
187A189HIS0-0.030-0.01716.7510.0250.0250.0000.0000.0000.000
188A190HIS00.0090.01217.462-0.018-0.0180.0000.0000.0000.000
189A191HIS10.7800.86119.566-0.105-0.1050.0000.0000.0000.000
190A192HIS00.0240.02115.888-0.033-0.0330.0000.0000.0000.000
191A193HIS0-0.093-0.04821.076-0.025-0.0250.0000.0000.0000.000
192A194HIS00.0250.01623.6320.0180.0180.0000.0000.0000.000