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: QVR2Y

Calculation Name: 3DO9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DO9

Chain ID: A

ChEMBL ID:

UniProt ID: Q81SV3

Base Structure: X-ray

Registration Date: 2023-09-24

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1983726.877099
FMO2-HF: Nuclear repulsion 1907857.514626
FMO2-HF: Total energy -75869.362473
FMO2-MP2: Total energy -76089.657188


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:4:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-2.815-1.026-0.024-0.812-0.9520.004
Interaction energy analysis for fragmet #1(A:4:PRO)
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 : -0.015
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].
3A6SER0-0.026-0.0073.677-0.4301.298-0.023-0.810-0.8950.004
4A7VAL00.038-0.0056.664-0.300-0.3000.0000.0000.0000.000
5A8ASN0-0.013-0.0289.897-0.146-0.1460.0000.0000.0000.000
6A9GLU-1-0.848-0.9176.840-0.352-0.3520.0000.0000.0000.000
7A10LYS10.9040.9656.492-0.502-0.5020.0000.0000.0000.000
8A11LYS10.8740.93211.204-0.283-0.2830.0000.0000.0000.000
9A12ASP-1-0.908-0.95914.1810.0360.0360.0000.0000.0000.000
10A13PHE00.0260.03613.011-0.031-0.0310.0000.0000.0000.000
11A14VAL0-0.005-0.00514.894-0.015-0.0150.0000.0000.0000.000
12A15LYS10.9730.98317.177-0.079-0.0790.0000.0000.0000.000
13A16TRP0-0.0060.01317.408-0.010-0.0100.0000.0000.0000.000
14A17PHE00.003-0.00318.170-0.005-0.0050.0000.0000.0000.000
15A18LEU0-0.001-0.02220.059-0.003-0.0030.0000.0000.0000.000
16A19ASN0-0.092-0.04122.7950.0010.0010.0000.0000.0000.000
17A20ASN0-0.072-0.02922.572-0.005-0.0050.0000.0000.0000.000
18A21TYR0-0.052-0.02320.927-0.005-0.0050.0000.0000.0000.000
19A22GLN00.0150.02025.1480.0070.0070.0000.0000.0000.000
20A23LEU0-0.001-0.00822.632-0.005-0.0050.0000.0000.0000.000
21A24LYS10.8360.92226.7540.0270.0270.0000.0000.0000.000
22A25GLN00.0080.00228.2770.0020.0020.0000.0000.0000.000
23A26ARG11.0070.99728.048-0.011-0.0110.0000.0000.0000.000
24A27GLU-1-0.842-0.93828.5130.0160.0160.0000.0000.0000.000
25A28CYS0-0.0220.00424.0360.0050.0050.0000.0000.0000.000
26A29VAL00.0320.02423.2950.0030.0030.0000.0000.0000.000
27A30TRP0-0.011-0.01424.0460.0060.0060.0000.0000.0000.000
28A31ILE00.0160.02420.9360.0080.0080.0000.0000.0000.000
29A32LEU00.0220.00017.9920.0110.0110.0000.0000.0000.000
30A33ASN00.022-0.00119.7740.0140.0140.0000.0000.0000.000
31A34TYR0-0.0170.00321.3730.0090.0090.0000.0000.0000.000
32A35LEU0-0.001-0.00416.7930.0120.0120.0000.0000.0000.000
33A36MET0-0.025-0.00217.2480.0210.0210.0000.0000.0000.000
34A37SER0-0.063-0.01118.3660.0190.0190.0000.0000.0000.000
35A38HIS0-0.054-0.02919.1070.0030.0030.0000.0000.0000.000
36A39ASP-1-0.817-0.93515.5730.2200.2200.0000.0000.0000.000
37A40GLN00.0060.01014.1030.0620.0620.0000.0000.0000.000
38A41LEU0-0.072-0.04115.299-0.011-0.0110.0000.0000.0000.000
39A42MET0-0.004-0.01512.198-0.001-0.0010.0000.0000.0000.000
40A43HIS0-0.016-0.0039.479-0.022-0.0220.0000.0000.0000.000
41A44LYS10.9490.9809.322-0.174-0.1740.0000.0000.0000.000
42A45VAL0-0.0290.01511.594-0.042-0.0420.0000.0000.0000.000
43A46HIS10.8020.8977.147-0.136-0.1360.0000.0000.0000.000
44A47PHE00.0260.0099.418-0.004-0.0040.0000.0000.0000.000
45A48VAL00.0210.0159.694-0.051-0.0510.0000.0000.0000.000
46A49GLU-1-0.806-0.91512.109-0.154-0.1540.0000.0000.0000.000
47A50HIS0-0.035-0.02414.8390.0120.0120.0000.0000.0000.000
48A51ALA00.0610.01216.388-0.001-0.0010.0000.0000.0000.000
49A52LYS10.9270.96217.4060.0690.0690.0000.0000.0000.000
50A53TYR0-0.054-0.02618.1420.0080.0080.0000.0000.0000.000
51A54CYS0-0.0700.00015.310-0.001-0.0010.0000.0000.0000.000
52A55PRO00.0600.03516.9450.0050.0050.0000.0000.0000.000
53A56ARG10.8820.93718.042-0.059-0.0590.0000.0000.0000.000
54A57GLY00.0120.02917.7680.0060.0060.0000.0000.0000.000
55A58LEU0-0.028-0.01318.1900.0040.0040.0000.0000.0000.000
56A59VAL00.0120.00818.767-0.009-0.0090.0000.0000.0000.000
57A60MET0-0.014-0.00519.9110.0090.0090.0000.0000.0000.000
58A61SER00.0100.00421.761-0.011-0.0110.0000.0000.0000.000
59A62ALA00.0070.00324.1710.0070.0070.0000.0000.0000.000
60A63ASN0-0.044-0.04325.732-0.005-0.0050.0000.0000.0000.000
61A64CYS0-0.0360.02726.397-0.002-0.0020.0000.0000.0000.000
62A65VAL00.0440.01624.5780.0010.0010.0000.0000.0000.000
63A66LYS10.9010.93427.8610.0290.0290.0000.0000.0000.000
64A67ASP-1-0.829-0.90124.894-0.050-0.0500.0000.0000.0000.000
65A68THR0-0.004-0.01327.4940.0030.0030.0000.0000.0000.000
66A69PRO0-0.024-0.00926.501-0.002-0.0020.0000.0000.0000.000
67A70PHE00.025-0.00423.6370.0010.0010.0000.0000.0000.000
68A71HIS00.0110.02224.547-0.003-0.0030.0000.0000.0000.000
69A72PHE0-0.0060.00020.8890.0020.0020.0000.0000.0000.000
70A73PHE00.003-0.01721.592-0.002-0.0020.0000.0000.0000.000
71A74LYS10.9250.97221.861-0.031-0.0310.0000.0000.0000.000
72A75GLN00.024-0.00322.244-0.002-0.0020.0000.0000.0000.000
73A76ASN00.0010.01124.576-0.005-0.0050.0000.0000.0000.000
74A77VAL0-0.021-0.00227.385-0.001-0.0010.0000.0000.0000.000
75A78MET00.0050.00526.775-0.001-0.0010.0000.0000.0000.000
76A79THR0-0.0150.00827.539-0.001-0.0010.0000.0000.0000.000
77A80THR00.0480.00027.868-0.002-0.0020.0000.0000.0000.000
78A81ASP-1-0.880-0.93330.0160.0110.0110.0000.0000.0000.000
79A82ALA00.0480.01927.7170.0020.0020.0000.0000.0000.000
80A83GLU-1-0.898-0.95028.0320.0210.0210.0000.0000.0000.000
81A84LYS10.9280.97330.266-0.014-0.0140.0000.0000.0000.000
82A85SER00.024-0.00425.3480.0020.0020.0000.0000.0000.000
83A86PHE0-0.030-0.01724.1490.0060.0060.0000.0000.0000.000
84A87HIS0-0.004-0.01226.3130.0080.0080.0000.0000.0000.000
85A88ASP-1-0.860-0.92626.6220.0320.0320.0000.0000.0000.000
86A89ILE0-0.114-0.06021.1580.0060.0060.0000.0000.0000.000
87A90ARG10.9050.96222.543-0.043-0.0430.0000.0000.0000.000
88A91LEU00.006-0.00524.9350.0080.0080.0000.0000.0000.000
89A92ASN0-0.042-0.02222.769-0.001-0.0010.0000.0000.0000.000
90A93ARG10.8900.96520.462-0.098-0.0980.0000.0000.0000.000
91A94ASP-1-0.903-0.93518.5300.1010.1010.0000.0000.0000.000
92A95GLU-1-0.871-0.95017.3750.0770.0770.0000.0000.0000.000
93A96ASP-1-0.911-0.95711.8350.1620.1620.0000.0000.0000.000
94A97ILE0-0.097-0.04913.985-0.024-0.0240.0000.0000.0000.000
95A98TYR00.0480.01211.0160.0160.0160.0000.0000.0000.000
96A99ILE0-0.007-0.00113.913-0.006-0.0060.0000.0000.0000.000
97A100GLN00.0230.01614.362-0.017-0.0170.0000.0000.0000.000
98A101LEU0-0.017-0.02316.0880.0150.0150.0000.0000.0000.000
99A102ASN00.0310.01918.641-0.021-0.0210.0000.0000.0000.000
100A103PHE00.024-0.00117.0770.0140.0140.0000.0000.0000.000
101A104LYS10.9490.95722.1170.0380.0380.0000.0000.0000.000
102A105SER00.0240.01421.2720.0020.0020.0000.0000.0000.000
103A106SER00.0320.01018.481-0.011-0.0110.0000.0000.0000.000
104A107PHE0-0.0120.00514.059-0.007-0.0070.0000.0000.0000.000
105A108GLN00.0400.01617.969-0.003-0.0030.0000.0000.0000.000
106A109ASN0-0.024-0.01517.1730.0030.0030.0000.0000.0000.000
107A110ALA00.0820.02913.558-0.012-0.0120.0000.0000.0000.000
108A111ASN00.0370.00911.894-0.069-0.0690.0000.0000.0000.000
109A112TYR0-0.002-0.00311.546-0.013-0.0130.0000.0000.0000.000
110A113VAL00.009-0.00711.219-0.008-0.0080.0000.0000.0000.000
111A114ALA0-0.026-0.0047.972-0.062-0.0620.0000.0000.0000.000
112A115VAL0-0.018-0.0036.840-0.159-0.1590.0000.0000.0000.000
113A116LEU0-0.057-0.0178.0360.0820.0820.0000.0000.0000.000
114A117GLU-1-0.837-0.9124.775-0.0370.024-0.001-0.002-0.0570.000
115A118GLU-1-0.897-0.9586.180-0.255-0.2550.0000.0000.0000.000
116A119ASN0-0.016-0.0148.1970.0740.0740.0000.0000.0000.000
117A120PRO00.0020.00910.678-0.007-0.0070.0000.0000.0000.000
118A121TYR00.0400.00413.0660.0190.0190.0000.0000.0000.000
119A122LEU0-0.049-0.02515.6170.0120.0120.0000.0000.0000.000
120A123PRO0-0.026-0.00317.502-0.003-0.0030.0000.0000.0000.000
121A124LYS11.0500.97820.5500.0710.0710.0000.0000.0000.000
122A125HIS0-0.0830.00520.525-0.001-0.0010.0000.0000.0000.000
123A126ILE00.0670.00816.043-0.003-0.0030.0000.0000.0000.000
124A127GLU-1-0.979-0.97918.827-0.100-0.1000.0000.0000.0000.000
125A128VAL00.0370.03517.1660.0010.0010.0000.0000.0000.000
126A129ASN0-0.085-0.06115.715-0.009-0.0090.0000.0000.0000.000
127A130GLU-1-0.828-0.92114.589-0.296-0.2960.0000.0000.0000.000
128A131LYS10.8810.94111.5120.2730.2730.0000.0000.0000.000
129A132ASP-1-0.941-0.9678.275-0.694-0.6940.0000.0000.0000.000
130A133ARG10.9650.97510.9610.2640.2640.0000.0000.0000.000
131A134LEU0-0.087-0.03113.8640.0220.0220.0000.0000.0000.000
132A135LEU00.0250.0189.7850.0330.0330.0000.0000.0000.000
133A136ALA0-0.001-0.01213.8300.0250.0250.0000.0000.0000.000
134A137GLU-1-0.888-0.94015.197-0.138-0.1380.0000.0000.0000.000
135A138ARG10.9770.98416.2630.1840.1840.0000.0000.0000.000
136A139PHE0-0.035-0.01015.5090.0100.0100.0000.0000.0000.000
137A140LEU0-0.0170.00117.6500.0190.0190.0000.0000.0000.000
138A141GLU-1-0.894-0.95119.965-0.096-0.0960.0000.0000.0000.000
139A142GLU-1-0.868-0.93720.606-0.080-0.0800.0000.0000.0000.000
140A143SER0-0.019-0.01119.3520.0150.0150.0000.0000.0000.000
141A144VAL0-0.053-0.02022.0550.0120.0120.0000.0000.0000.000
142A145PHE0-0.008-0.00425.0010.0110.0110.0000.0000.0000.000
143A146SER0-0.032-0.03623.9290.0090.0090.0000.0000.0000.000
144A147PHE00.0490.03825.7490.0090.0090.0000.0000.0000.000
145A148ARG10.9710.97927.4730.0780.0780.0000.0000.0000.000
146A149ARG10.9951.00828.2290.0570.0570.0000.0000.0000.000
147A150GLU-1-0.947-0.97527.976-0.040-0.0400.0000.0000.0000.000
148A151ARG10.8240.92431.1450.0440.0440.0000.0000.0000.000
149A152LEU00.047-0.00733.0550.0040.0040.0000.0000.0000.000
150A153LEU0-0.014-0.02533.0750.0030.0030.0000.0000.0000.000
151A154LYS10.9220.99234.2290.0310.0310.0000.0000.0000.000
152A155GLN0-0.027-0.02536.7000.0000.0000.0000.0000.0000.000
153A156ILE00.0040.00938.5770.0020.0020.0000.0000.0000.000
154A157ASP-1-0.867-0.93439.454-0.023-0.0230.0000.0000.0000.000
155A158GLU-1-0.944-0.98139.084-0.026-0.0260.0000.0000.0000.000
156A159ALA0-0.054-0.02542.9720.0010.0010.0000.0000.0000.000
157A160LEU0-0.064-0.04243.6590.0010.0010.0000.0000.0000.000
158A161ASP-1-0.960-0.96345.362-0.015-0.0150.0000.0000.0000.000
159A162LYS10.9070.95544.2490.0210.0210.0000.0000.0000.000
160A163GLN0-0.025-0.00849.3230.0000.0000.0000.0000.0000.000
161A164ASP-1-0.838-0.90747.833-0.021-0.0210.0000.0000.0000.000
162A165LYS10.9320.94348.4550.0170.0170.0000.0000.0000.000
163A166GLU-1-0.903-0.96849.400-0.024-0.0240.0000.0000.0000.000
164A167ALA00.0120.00944.622-0.001-0.0010.0000.0000.0000.000
165A168PHE00.0440.04244.489-0.002-0.0020.0000.0000.0000.000
166A169HIS0-0.022-0.00244.4630.0000.0000.0000.0000.0000.000
167A170ARG10.9200.98143.8330.0270.0270.0000.0000.0000.000
168A171LEU00.031-0.01039.742-0.002-0.0020.0000.0000.0000.000
169A172THR0-0.025-0.03640.000-0.002-0.0020.0000.0000.0000.000
170A173ALA0-0.066-0.04840.829-0.001-0.0010.0000.0000.0000.000
171A174GLU-1-0.936-0.95738.600-0.043-0.0430.0000.0000.0000.000
172A175LEU0-0.050-0.02435.521-0.003-0.0030.0000.0000.0000.000
173A176LYS10.9300.97436.1400.0290.0290.0000.0000.0000.000
174A177MET0-0.0240.00535.848-0.001-0.0010.0000.0000.0000.000
175A178LEU0-0.009-0.00931.120-0.003-0.0030.0000.0000.0000.000
176A179GLU-1-0.927-0.97631.873-0.051-0.0510.0000.0000.0000.000
177A180GLY0-0.035-0.00932.798-0.001-0.0010.0000.0000.0000.000
178A181HIS0-0.020-0.00731.5100.0000.0000.0000.0000.0000.000
179A182HIS10.8330.94826.0110.0740.0740.0000.0000.0000.000