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: 4J21N

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1988233.867369
FMO2-HF: Nuclear repulsion 1912361.989406
FMO2-HF: Total energy -75871.877963
FMO2-MP2: Total energy -76092.203911


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.
-1.665-0.172-0.018-0.734-0.7410.002
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 : -0.035 / q_NPA : -0.033
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].
3A6SER0-0.068-0.0543.8971.0192.435-0.017-0.723-0.6760.002
4A7VAL00.028-0.0056.848-0.224-0.2240.0000.0000.0000.000
5A8ASN0-0.005-0.01210.530-0.061-0.0610.0000.0000.0000.000
6A9GLU-1-0.792-0.8666.662-1.023-1.0230.0000.0000.0000.000
7A10LYS10.8500.9096.557-0.856-0.8560.0000.0000.0000.000
8A11LYS10.8110.89511.128-0.205-0.2050.0000.0000.0000.000
9A12ASP-1-0.803-0.88914.179-0.077-0.0770.0000.0000.0000.000
10A13PHE00.0050.02112.728-0.019-0.0190.0000.0000.0000.000
11A14VAL00.0170.00614.6730.0000.0000.0000.0000.0000.000
12A15LYS10.8560.90116.9650.0410.0410.0000.0000.0000.000
13A16TRP0-0.0140.00617.210-0.007-0.0070.0000.0000.0000.000
14A17PHE00.0170.01317.9420.0050.0050.0000.0000.0000.000
15A18LEU0-0.013-0.02519.8620.0020.0020.0000.0000.0000.000
16A19ASN0-0.090-0.04522.5320.0060.0060.0000.0000.0000.000
17A20ASN0-0.087-0.04122.286-0.010-0.0100.0000.0000.0000.000
18A21TYR0-0.045-0.02920.707-0.003-0.0030.0000.0000.0000.000
19A22GLN00.0210.02724.8020.0090.0090.0000.0000.0000.000
20A23LEU00.006-0.00222.290-0.003-0.0030.0000.0000.0000.000
21A24LYS10.7300.84826.3250.0150.0150.0000.0000.0000.000
22A25GLN00.0160.00828.0760.0000.0000.0000.0000.0000.000
23A26ARG10.9170.94927.689-0.022-0.0220.0000.0000.0000.000
24A27GLU-1-0.766-0.88428.0110.0300.0300.0000.0000.0000.000
25A28CYS0-0.032-0.00323.8130.0100.0100.0000.0000.0000.000
26A29VAL00.0490.02623.1660.0060.0060.0000.0000.0000.000
27A30TRP0-0.016-0.00923.9160.0060.0060.0000.0000.0000.000
28A31ILE00.0080.01520.7400.0100.0100.0000.0000.0000.000
29A32LEU00.0280.01017.8970.0170.0170.0000.0000.0000.000
30A33ASN00.0340.00419.7220.0090.0090.0000.0000.0000.000
31A34TYR0-0.027-0.00621.5090.0070.0070.0000.0000.0000.000
32A35LEU00.0230.01116.8160.0140.0140.0000.0000.0000.000
33A36MET0-0.0100.00817.3430.0210.0210.0000.0000.0000.000
34A37SER0-0.060-0.02618.5140.0040.0040.0000.0000.0000.000
35A38HIS0-0.022-0.00219.089-0.003-0.0030.0000.0000.0000.000
36A39ASP-1-0.782-0.88315.7090.2490.2490.0000.0000.0000.000
37A40GLN00.0230.00714.4430.0690.0690.0000.0000.0000.000
38A41LEU0-0.036-0.01315.9570.0080.0080.0000.0000.0000.000
39A42MET00.007-0.00112.4870.0260.0260.0000.0000.0000.000
40A43HIS0-0.029-0.0169.987-0.008-0.0080.0000.0000.0000.000
41A44LYS10.8570.9489.987-0.286-0.2860.0000.0000.0000.000
42A45VAL0-0.0110.01211.642-0.049-0.0490.0000.0000.0000.000
43A46HIS10.7790.8807.286-0.609-0.6090.0000.0000.0000.000
44A47PHE00.0110.0098.943-0.046-0.0460.0000.0000.0000.000
45A48VAL00.0300.0129.542-0.032-0.0320.0000.0000.0000.000
46A49GLU-1-0.765-0.84611.994-0.130-0.1300.0000.0000.0000.000
47A50HIS00.0160.00014.9580.0240.0240.0000.0000.0000.000
48A51ALA00.0700.02415.9290.0120.0120.0000.0000.0000.000
49A52LYS10.8190.92017.0340.0160.0160.0000.0000.0000.000
50A53TYR0-0.022-0.03218.226-0.002-0.0020.0000.0000.0000.000
51A54CYS0-0.0610.00115.4400.0050.0050.0000.0000.0000.000
52A55PRO00.0170.01516.674-0.010-0.0100.0000.0000.0000.000
53A56ARG10.7390.82317.900-0.219-0.2190.0000.0000.0000.000
54A57GLY00.0150.02917.5100.0180.0180.0000.0000.0000.000
55A58LEU0-0.044-0.02517.949-0.008-0.0080.0000.0000.0000.000
56A59VAL00.0190.00518.379-0.007-0.0070.0000.0000.0000.000
57A60MET0-0.0010.00619.4510.0050.0050.0000.0000.0000.000
58A61SER00.016-0.00221.617-0.012-0.0120.0000.0000.0000.000
59A62ALA00.0260.01123.8210.0050.0050.0000.0000.0000.000
60A63ASN0-0.009-0.03225.486-0.004-0.0040.0000.0000.0000.000
61A64CYS0-0.0250.01826.482-0.002-0.0020.0000.0000.0000.000
62A65VAL00.0590.03824.610-0.003-0.0030.0000.0000.0000.000
63A66LYS10.9330.96128.0870.0210.0210.0000.0000.0000.000
64A67ASP-1-0.836-0.91124.896-0.025-0.0250.0000.0000.0000.000
65A68THR00.030-0.00127.200-0.001-0.0010.0000.0000.0000.000
66A69PRO0-0.0190.00126.365-0.001-0.0010.0000.0000.0000.000
67A70PHE00.0280.00223.3500.0010.0010.0000.0000.0000.000
68A71HIS0-0.0200.01824.044-0.008-0.0080.0000.0000.0000.000
69A72PHE0-0.015-0.00221.1150.0050.0050.0000.0000.0000.000
70A73PHE00.017-0.00721.345-0.012-0.0120.0000.0000.0000.000
71A74LYS10.8920.93021.694-0.100-0.1000.0000.0000.0000.000
72A75GLN00.015-0.00321.934-0.001-0.0010.0000.0000.0000.000
73A76ASN0-0.039-0.00624.4660.0000.0000.0000.0000.0000.000
74A77VAL0-0.012-0.00726.985-0.007-0.0070.0000.0000.0000.000
75A78MET00.0120.03026.5170.0040.0040.0000.0000.0000.000
76A79THR00.011-0.00127.028-0.007-0.0070.0000.0000.0000.000
77A80THR00.0410.00227.386-0.001-0.0010.0000.0000.0000.000
78A81ASP-1-0.831-0.88429.4980.0430.0430.0000.0000.0000.000
79A82ALA00.0490.03127.3480.0070.0070.0000.0000.0000.000
80A83GLU-1-0.920-0.95527.8790.0450.0450.0000.0000.0000.000
81A84LYS10.8540.89830.021-0.043-0.0430.0000.0000.0000.000
82A85SER00.010-0.01025.1430.0070.0070.0000.0000.0000.000
83A86PHE00.003-0.00824.9370.0100.0100.0000.0000.0000.000
84A87HIS00.0000.00126.4710.0050.0050.0000.0000.0000.000
85A88ASP-1-0.795-0.88326.4670.1040.1040.0000.0000.0000.000
86A89ILE0-0.0030.00721.4430.0090.0090.0000.0000.0000.000
87A90ARG10.8420.93422.987-0.073-0.0730.0000.0000.0000.000
88A91LEU0-0.004-0.00425.4220.0080.0080.0000.0000.0000.000
89A92ASN0-0.035-0.02523.1630.0060.0060.0000.0000.0000.000
90A93ARG10.8630.92321.447-0.150-0.1500.0000.0000.0000.000
91A94ASP-1-0.895-0.93418.9100.2350.2350.0000.0000.0000.000
92A95GLU-1-0.790-0.88617.8090.2040.2040.0000.0000.0000.000
93A96ASP-1-0.777-0.85512.4770.5210.5210.0000.0000.0000.000
94A97ILE0-0.059-0.02613.865-0.057-0.0570.0000.0000.0000.000
95A98TYR0-0.002-0.02411.2750.0200.0200.0000.0000.0000.000
96A99ILE0-0.003-0.01213.413-0.028-0.0280.0000.0000.0000.000
97A100GLN00.0150.01013.983-0.008-0.0080.0000.0000.0000.000
98A101LEU0-0.004-0.00515.5600.0120.0120.0000.0000.0000.000
99A102ASN00.0370.02418.479-0.022-0.0220.0000.0000.0000.000
100A103PHE00.014-0.01517.3010.0110.0110.0000.0000.0000.000
101A104LYS10.9270.95921.8850.0380.0380.0000.0000.0000.000
102A105SER00.0270.02221.0400.0050.0050.0000.0000.0000.000
103A106SER0-0.013-0.02418.061-0.010-0.0100.0000.0000.0000.000
104A107PHE00.0450.01613.873-0.017-0.0170.0000.0000.0000.000
105A108GLN00.0320.02117.589-0.010-0.0100.0000.0000.0000.000
106A109ASN0-0.0180.00217.1590.0050.0050.0000.0000.0000.000
107A110ALA00.0690.02614.117-0.013-0.0130.0000.0000.0000.000
108A111ASN00.015-0.00112.173-0.070-0.0700.0000.0000.0000.000
109A112TYR0-0.030-0.01511.568-0.025-0.0250.0000.0000.0000.000
110A113VAL00.018-0.00710.933-0.008-0.0080.0000.0000.0000.000
111A114ALA0-0.0180.0028.011-0.037-0.0370.0000.0000.0000.000
112A115VAL0-0.023-0.0086.602-0.223-0.2230.0000.0000.0000.000
113A116LEU0-0.038-0.0117.6460.1770.1770.0000.0000.0000.000
114A117GLU-1-0.756-0.8594.3070.5360.613-0.001-0.011-0.0650.000
115A118GLU-1-0.805-0.8976.448-0.128-0.1280.0000.0000.0000.000
116A119ASN0-0.029-0.0278.5650.1180.1180.0000.0000.0000.000
117A120PRO0-0.024-0.01210.489-0.032-0.0320.0000.0000.0000.000
118A121TYR00.023-0.00913.054-0.009-0.0090.0000.0000.0000.000
119A122LEU0-0.035-0.01214.687-0.013-0.0130.0000.0000.0000.000
120A123PRO0-0.015-0.00417.758-0.002-0.0020.0000.0000.0000.000
121A124LYS10.9840.95320.6670.0040.0040.0000.0000.0000.000
122A125HIS0-0.0440.01620.6750.0050.0050.0000.0000.0000.000
123A126ILE0-0.001-0.00415.850-0.009-0.0090.0000.0000.0000.000
124A127GLU-1-0.901-0.94918.419-0.045-0.0450.0000.0000.0000.000
125A128VAL00.0330.02917.007-0.003-0.0030.0000.0000.0000.000
126A129ASN0-0.024-0.01915.5030.0000.0000.0000.0000.0000.000
127A130GLU-1-0.810-0.89014.189-0.231-0.2310.0000.0000.0000.000
128A131LYS10.8500.89411.7300.1140.1140.0000.0000.0000.000
129A132ASP-1-0.913-0.9597.794-0.614-0.6140.0000.0000.0000.000
130A133ARG10.8880.93110.4980.2420.2420.0000.0000.0000.000
131A134LEU0-0.069-0.02012.9080.0090.0090.0000.0000.0000.000
132A135LEU00.0250.0149.3040.0340.0340.0000.0000.0000.000
133A136ALA0-0.002-0.01513.2240.0160.0160.0000.0000.0000.000
134A137GLU-1-0.935-0.95614.578-0.132-0.1320.0000.0000.0000.000
135A138ARG10.9140.90815.8480.1540.1540.0000.0000.0000.000
136A139PHE0-0.044-0.00115.0550.0030.0030.0000.0000.0000.000
137A140LEU0-0.0020.01117.1780.0140.0140.0000.0000.0000.000
138A141GLU-1-0.842-0.88419.853-0.091-0.0910.0000.0000.0000.000
139A142GLU-1-0.782-0.88720.255-0.093-0.0930.0000.0000.0000.000
140A143SER0-0.033-0.00219.1760.0100.0100.0000.0000.0000.000
141A144VAL0-0.053-0.02421.9120.0110.0110.0000.0000.0000.000
142A145PHE00.0090.00224.9760.0120.0120.0000.0000.0000.000
143A146SER0-0.021-0.03823.7870.0080.0080.0000.0000.0000.000
144A147PHE00.0060.01225.6660.0090.0090.0000.0000.0000.000
145A148ARG10.9460.97127.3900.1020.1020.0000.0000.0000.000
146A149ARG10.8820.92328.4750.0800.0800.0000.0000.0000.000
147A150GLU-1-0.827-0.89028.205-0.072-0.0720.0000.0000.0000.000
148A151ARG10.7910.90331.2900.0700.0700.0000.0000.0000.000
149A152LEU00.020-0.00533.3570.0040.0040.0000.0000.0000.000
150A153LEU0-0.005-0.00233.0160.0040.0040.0000.0000.0000.000
151A154LYS10.8720.93234.6490.0610.0610.0000.0000.0000.000
152A155GLN0-0.019-0.02136.8640.0000.0000.0000.0000.0000.000
153A156ILE0-0.017-0.00338.5640.0030.0030.0000.0000.0000.000
154A157ASP-1-0.868-0.93139.466-0.039-0.0390.0000.0000.0000.000
155A158GLU-1-0.814-0.89738.987-0.053-0.0530.0000.0000.0000.000
156A159ALA00.0130.01742.6890.0020.0020.0000.0000.0000.000
157A160LEU0-0.035-0.02343.6590.0020.0020.0000.0000.0000.000
158A161ASP-1-0.894-0.92545.249-0.034-0.0340.0000.0000.0000.000
159A162LYS10.7710.86444.6230.0410.0410.0000.0000.0000.000
160A163GLN0-0.031-0.01249.3540.0020.0020.0000.0000.0000.000
161A164ASP-1-0.812-0.89047.746-0.035-0.0350.0000.0000.0000.000
162A165LYS10.8940.90548.2210.0250.0250.0000.0000.0000.000
163A166GLU-1-0.879-0.91549.245-0.036-0.0360.0000.0000.0000.000
164A167ALA00.0390.00544.853-0.001-0.0010.0000.0000.0000.000
165A168PHE00.0200.01644.309-0.002-0.0020.0000.0000.0000.000
166A169HIS0-0.0100.01344.3860.0000.0000.0000.0000.0000.000
167A170ARG10.8870.94044.1550.0400.0400.0000.0000.0000.000
168A171LEU00.0310.01039.599-0.002-0.0020.0000.0000.0000.000
169A172THR0-0.017-0.02439.857-0.002-0.0020.0000.0000.0000.000
170A173ALA0-0.066-0.03640.9520.0000.0000.0000.0000.0000.000
171A174GLU-1-0.931-0.97038.226-0.055-0.0550.0000.0000.0000.000
172A175LEU0-0.040-0.02334.657-0.003-0.0030.0000.0000.0000.000
173A176LYS10.9380.97435.5360.0350.0350.0000.0000.0000.000
174A177MET0-0.0210.00436.0820.0010.0010.0000.0000.0000.000
175A178LEU0-0.048-0.02231.511-0.004-0.0040.0000.0000.0000.000
176A179GLU-1-0.890-0.97131.339-0.060-0.0600.0000.0000.0000.000
177A180GLY0-0.051-0.01532.0500.0000.0000.0000.0000.0000.000
178A181HIS0-0.044-0.01431.1720.0020.0020.0000.0000.0000.000
179A182HIS10.7250.84024.6750.0880.0880.0000.0000.0000.000