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: KGY43

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1985933.14249
FMO2-HF: Nuclear repulsion 1910062.0688
FMO2-HF: Total energy -75871.07369
FMO2-MP2: Total energy -76091.432161


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.
-2.367-0.63-0.026-0.84-0.8730.003
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 : -0.030 / q_NPA : -0.030
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].
3A6SER0-0.061-0.0373.8080.1971.893-0.025-0.835-0.8370.003
4A7VAL00.046-0.0016.865-0.230-0.2300.0000.0000.0000.000
5A8ASN0-0.014-0.02710.225-0.091-0.0910.0000.0000.0000.000
6A9GLU-1-0.798-0.8786.421-0.992-0.9920.0000.0000.0000.000
7A10LYS10.8560.9236.887-0.459-0.4590.0000.0000.0000.000
8A11LYS10.8270.88811.529-0.185-0.1850.0000.0000.0000.000
9A12ASP-1-0.824-0.90714.185-0.065-0.0650.0000.0000.0000.000
10A13PHE00.0230.03113.044-0.019-0.0190.0000.0000.0000.000
11A14VAL00.005-0.00314.9600.0000.0000.0000.0000.0000.000
12A15LYS10.8820.92917.4250.0180.0180.0000.0000.0000.000
13A16TRP0-0.0060.01417.463-0.006-0.0060.0000.0000.0000.000
14A17PHE0-0.004-0.00418.0340.0040.0040.0000.0000.0000.000
15A18LEU00.002-0.01919.9920.0030.0030.0000.0000.0000.000
16A19ASN0-0.089-0.04422.8110.0060.0060.0000.0000.0000.000
17A20ASN0-0.081-0.03222.317-0.003-0.0030.0000.0000.0000.000
18A21TYR0-0.049-0.02220.766-0.002-0.0020.0000.0000.0000.000
19A22GLN00.0270.02525.0710.0070.0070.0000.0000.0000.000
20A23LEU00.001-0.00722.654-0.003-0.0030.0000.0000.0000.000
21A24LYS10.7440.86026.7030.0350.0350.0000.0000.0000.000
22A25GLN00.0040.00328.2450.0010.0010.0000.0000.0000.000
23A26ARG10.9350.95828.118-0.008-0.0080.0000.0000.0000.000
24A27GLU-1-0.779-0.90628.8080.0110.0110.0000.0000.0000.000
25A28CYS0-0.0180.00624.2030.0070.0070.0000.0000.0000.000
26A29VAL00.0450.02823.5840.0020.0020.0000.0000.0000.000
27A30TRP0-0.013-0.01424.3570.0050.0050.0000.0000.0000.000
28A31ILE00.0060.01721.2500.0080.0080.0000.0000.0000.000
29A32LEU00.0260.00618.3460.0130.0130.0000.0000.0000.000
30A33ASN00.0320.00020.0950.0070.0070.0000.0000.0000.000
31A34TYR0-0.0210.00121.7840.0070.0070.0000.0000.0000.000
32A35LEU00.005-0.00917.2000.0130.0130.0000.0000.0000.000
33A36MET0-0.0280.00217.5730.0170.0170.0000.0000.0000.000
34A37SER0-0.047-0.01018.7000.0070.0070.0000.0000.0000.000
35A38HIS0-0.040-0.01219.4020.0070.0070.0000.0000.0000.000
36A39ASP-1-0.750-0.87915.9010.1990.1990.0000.0000.0000.000
37A40GLN0-0.013-0.00414.4070.0520.0520.0000.0000.0000.000
38A41LEU0-0.063-0.03315.5620.0050.0050.0000.0000.0000.000
39A42MET00.001-0.01112.5410.0080.0080.0000.0000.0000.000
40A43HIS0-0.0190.0019.948-0.030-0.0300.0000.0000.0000.000
41A44LYS10.9360.9839.576-0.233-0.2330.0000.0000.0000.000
42A45VAL0-0.0190.01712.044-0.041-0.0410.0000.0000.0000.000
43A46HIS10.7720.8677.345-0.351-0.3510.0000.0000.0000.000
44A47PHE00.0130.0089.417-0.012-0.0120.0000.0000.0000.000
45A48VAL00.0280.0159.654-0.041-0.0410.0000.0000.0000.000
46A49GLU-1-0.756-0.84812.071-0.168-0.1680.0000.0000.0000.000
47A50HIS0-0.033-0.02214.7780.0180.0180.0000.0000.0000.000
48A51ALA00.0640.01016.3870.0070.0070.0000.0000.0000.000
49A52LYS10.9050.95817.3960.0480.0480.0000.0000.0000.000
50A53TYR0-0.043-0.03318.1490.0050.0050.0000.0000.0000.000
51A54CYS0-0.0650.00315.4810.0030.0030.0000.0000.0000.000
52A55PRO00.0400.02916.918-0.004-0.0040.0000.0000.0000.000
53A56ARG10.8080.88418.105-0.130-0.1300.0000.0000.0000.000
54A57GLY00.0040.02517.9420.0080.0080.0000.0000.0000.000
55A58LEU0-0.038-0.01718.216-0.002-0.0020.0000.0000.0000.000
56A59VAL00.0190.00718.758-0.010-0.0100.0000.0000.0000.000
57A60MET0-0.015-0.00220.3080.0090.0090.0000.0000.0000.000
58A61SER00.0190.00321.711-0.013-0.0130.0000.0000.0000.000
59A62ALA00.0080.00324.0390.0060.0060.0000.0000.0000.000
60A63ASN0-0.026-0.04325.664-0.004-0.0040.0000.0000.0000.000
61A64CYS0-0.0300.02826.317-0.002-0.0020.0000.0000.0000.000
62A65VAL00.0690.03324.3490.0020.0020.0000.0000.0000.000
63A66LYS10.9310.96627.7700.0340.0340.0000.0000.0000.000
64A67ASP-1-0.809-0.89724.984-0.050-0.0500.0000.0000.0000.000
65A68THR00.016-0.01127.5240.0000.0000.0000.0000.0000.000
66A69PRO0-0.031-0.00326.458-0.002-0.0020.0000.0000.0000.000
67A70PHE00.022-0.00423.8040.0000.0000.0000.0000.0000.000
68A71HIS00.0090.03224.399-0.005-0.0050.0000.0000.0000.000
69A72PHE0-0.010-0.00421.2730.0020.0020.0000.0000.0000.000
70A73PHE0-0.002-0.02321.640-0.004-0.0040.0000.0000.0000.000
71A74LYS10.8890.93821.997-0.058-0.0580.0000.0000.0000.000
72A75GLN00.0270.00422.2610.0010.0010.0000.0000.0000.000
73A76ASN0-0.027-0.00424.669-0.001-0.0010.0000.0000.0000.000
74A77VAL0-0.015-0.00327.526-0.004-0.0040.0000.0000.0000.000
75A78MET00.0220.01426.9010.0000.0000.0000.0000.0000.000
76A79THR00.0020.01327.677-0.005-0.0050.0000.0000.0000.000
77A80THR00.0510.00827.924-0.002-0.0020.0000.0000.0000.000
78A81ASP-1-0.840-0.89430.0370.0200.0200.0000.0000.0000.000
79A82ALA00.0660.03127.9520.0040.0040.0000.0000.0000.000
80A83GLU-1-0.906-0.95528.2900.0250.0250.0000.0000.0000.000
81A84LYS10.8580.91630.528-0.022-0.0220.0000.0000.0000.000
82A85SER00.027-0.00925.5880.0050.0050.0000.0000.0000.000
83A86PHE0-0.021-0.01424.8770.0080.0080.0000.0000.0000.000
84A87HIS0-0.014-0.01726.5830.0070.0070.0000.0000.0000.000
85A88ASP-1-0.828-0.89926.0850.0590.0590.0000.0000.0000.000
86A89ILE0-0.044-0.02521.5590.0090.0090.0000.0000.0000.000
87A90ARG10.8650.94622.802-0.047-0.0470.0000.0000.0000.000
88A91LEU00.009-0.00225.2000.0080.0080.0000.0000.0000.000
89A92ASN0-0.0190.00623.3530.0020.0020.0000.0000.0000.000
90A93ARG10.8760.94320.777-0.115-0.1150.0000.0000.0000.000
91A94ASP-1-0.920-0.94518.7050.1660.1660.0000.0000.0000.000
92A95GLU-1-0.820-0.91317.5070.1280.1280.0000.0000.0000.000
93A96ASP-1-0.863-0.92311.9560.3340.3340.0000.0000.0000.000
94A97ILE0-0.090-0.03914.216-0.036-0.0360.0000.0000.0000.000
95A98TYR00.0550.01711.4430.0160.0160.0000.0000.0000.000
96A99ILE0-0.0060.00114.007-0.014-0.0140.0000.0000.0000.000
97A100GLN00.0310.01514.338-0.015-0.0150.0000.0000.0000.000
98A101LEU0-0.020-0.01615.7520.0140.0140.0000.0000.0000.000
99A102ASN00.0230.01418.582-0.021-0.0210.0000.0000.0000.000
100A103PHE00.0230.00117.2480.0140.0140.0000.0000.0000.000
101A104LYS10.9220.95322.0120.0520.0520.0000.0000.0000.000
102A105SER00.0440.02321.2640.0040.0040.0000.0000.0000.000
103A106SER00.018-0.00818.287-0.013-0.0130.0000.0000.0000.000
104A107PHE00.0040.00614.133-0.016-0.0160.0000.0000.0000.000
105A108GLN00.0370.01917.830-0.003-0.0030.0000.0000.0000.000
106A109ASN0-0.035-0.01417.3520.0040.0040.0000.0000.0000.000
107A110ALA00.0840.02713.587-0.012-0.0120.0000.0000.0000.000
108A111ASN00.0270.00011.900-0.070-0.0700.0000.0000.0000.000
109A112TYR0-0.005-0.00111.558-0.027-0.0270.0000.0000.0000.000
110A113VAL00.019-0.00111.0560.0010.0010.0000.0000.0000.000
111A114ALA0-0.025-0.0018.016-0.048-0.0480.0000.0000.0000.000
112A115VAL0-0.028-0.0126.842-0.191-0.1910.0000.0000.0000.000
113A116LEU0-0.048-0.0107.9740.1190.1190.0000.0000.0000.000
114A117GLU-1-0.770-0.8724.6710.1930.234-0.001-0.005-0.0360.000
115A118GLU-1-0.850-0.9186.147-0.180-0.1800.0000.0000.0000.000
116A119ASN0-0.026-0.0208.1690.1080.1080.0000.0000.0000.000
117A120PRO0-0.014-0.00210.760-0.023-0.0230.0000.0000.0000.000
118A121TYR00.031-0.00613.0940.0110.0110.0000.0000.0000.000
119A122LEU0-0.040-0.01815.134-0.002-0.0020.0000.0000.0000.000
120A123PRO0-0.026-0.00617.4910.0010.0010.0000.0000.0000.000
121A124LYS11.0180.96720.5470.0350.0350.0000.0000.0000.000
122A125HIS0-0.0810.00420.6060.0030.0030.0000.0000.0000.000
123A126ILE00.043-0.00416.061-0.008-0.0080.0000.0000.0000.000
124A127GLU-1-0.895-0.93518.775-0.073-0.0730.0000.0000.0000.000
125A128VAL00.0300.02816.887-0.004-0.0040.0000.0000.0000.000
126A129ASN0-0.069-0.04515.3440.0010.0010.0000.0000.0000.000
127A130GLU-1-0.794-0.89514.040-0.268-0.2680.0000.0000.0000.000
128A131LYS10.8670.91611.6130.2030.2030.0000.0000.0000.000
129A132ASP-1-0.940-0.9677.878-0.651-0.6510.0000.0000.0000.000
130A133ARG10.8760.92510.8110.2480.2480.0000.0000.0000.000
131A134LEU0-0.076-0.02913.4930.0140.0140.0000.0000.0000.000
132A135LEU00.0340.0269.9790.0310.0310.0000.0000.0000.000
133A136ALA00.002-0.01413.7960.0190.0190.0000.0000.0000.000
134A137GLU-1-0.907-0.94615.243-0.149-0.1490.0000.0000.0000.000
135A138ARG10.9030.90715.8760.1890.1890.0000.0000.0000.000
136A139PHE0-0.035-0.00415.5450.0050.0050.0000.0000.0000.000
137A140LEU0-0.0100.00717.6690.0160.0160.0000.0000.0000.000
138A141GLU-1-0.862-0.90319.994-0.106-0.1060.0000.0000.0000.000
139A142GLU-1-0.792-0.90320.540-0.102-0.1020.0000.0000.0000.000
140A143SER0-0.032-0.00619.4080.0120.0120.0000.0000.0000.000
141A144VAL0-0.062-0.02722.0740.0120.0120.0000.0000.0000.000
142A145PHE00.0060.00625.0180.0120.0120.0000.0000.0000.000
143A146SER0-0.016-0.03823.9830.0090.0090.0000.0000.0000.000
144A147PHE00.0250.02325.7170.0100.0100.0000.0000.0000.000
145A148ARG10.9810.98427.4800.1050.1050.0000.0000.0000.000
146A149ARG10.8780.93429.2710.0830.0830.0000.0000.0000.000
147A150GLU-1-0.850-0.91128.089-0.072-0.0720.0000.0000.0000.000
148A151ARG10.8370.93131.1520.0700.0700.0000.0000.0000.000
149A152LEU00.022-0.01233.0550.0050.0050.0000.0000.0000.000
150A153LEU0-0.013-0.01833.0770.0040.0040.0000.0000.0000.000
151A154LYS10.8540.93934.5520.0580.0580.0000.0000.0000.000
152A155GLN0-0.011-0.01736.6990.0000.0000.0000.0000.0000.000
153A156ILE0-0.0040.00338.6240.0030.0030.0000.0000.0000.000
154A157ASP-1-0.853-0.92639.818-0.041-0.0410.0000.0000.0000.000
155A158GLU-1-0.886-0.93739.024-0.049-0.0490.0000.0000.0000.000
156A159ALA0-0.010-0.00142.9660.0020.0020.0000.0000.0000.000
157A160LEU0-0.050-0.03143.7210.0020.0020.0000.0000.0000.000
158A161ASP-1-0.892-0.92145.355-0.032-0.0320.0000.0000.0000.000
159A162LYS10.7820.87744.1840.0390.0390.0000.0000.0000.000
160A163GLN0-0.037-0.01549.3150.0010.0010.0000.0000.0000.000
161A164ASP-1-0.836-0.89547.878-0.035-0.0350.0000.0000.0000.000
162A165LYS10.9080.91548.4610.0270.0270.0000.0000.0000.000
163A166GLU-1-0.864-0.92649.638-0.036-0.0360.0000.0000.0000.000
164A167ALA00.0310.00944.703-0.001-0.0010.0000.0000.0000.000
165A168PHE00.0270.03344.467-0.002-0.0020.0000.0000.0000.000
166A169HIS00.0120.01444.4830.0000.0000.0000.0000.0000.000
167A170ARG10.8820.94344.4200.0400.0400.0000.0000.0000.000
168A171LEU00.038-0.00539.702-0.002-0.0020.0000.0000.0000.000
169A172THR0-0.019-0.02340.023-0.002-0.0020.0000.0000.0000.000
170A173ALA0-0.063-0.04340.823-0.001-0.0010.0000.0000.0000.000
171A174GLU-1-0.931-0.95538.611-0.058-0.0580.0000.0000.0000.000
172A175LEU0-0.055-0.03235.580-0.003-0.0030.0000.0000.0000.000
173A176LYS10.9370.97536.0640.0390.0390.0000.0000.0000.000
174A177MET0-0.0170.00736.6690.0000.0000.0000.0000.0000.000
175A178LEU0-0.024-0.01231.753-0.003-0.0030.0000.0000.0000.000
176A179GLU-1-0.915-0.97131.723-0.066-0.0660.0000.0000.0000.000
177A180GLY0-0.040-0.01432.6590.0000.0000.0000.0000.0000.000
178A181HIS0-0.057-0.02131.4940.0010.0010.0000.0000.0000.000
179A182HIS10.7500.87625.1920.0950.0950.0000.0000.0000.000