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: K98L3

Calculation Name: 3G67-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3G67

Chain ID: A

ChEMBL ID:

UniProt ID: Q7DFA3

Base Structure: X-ray

Registration Date: 2023-06-22

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1717095.022613
FMO2-HF: Nuclear repulsion 1631978.40117
FMO2-HF: Total energy -85116.621443
FMO2-MP2: Total energy -85363.303863


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:41:ARG)


Summations of interaction energy for fragment #1(A:41:ARG)
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.
-180.772-178.17621.097-12.053-11.639-0.137
Interaction energy analysis for fragmet #1(A:41:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.906
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].
3A43GLU-1-0.823-0.9212.679-28.799-26.2330.116-0.925-1.757-0.003
4A44GLU-1-0.777-0.8481.727-127.042-127.59120.964-11.034-9.380-0.134
5A45VAL0-0.041-0.0253.2522.3862.8840.018-0.094-0.4220.000
6A46LYS10.8730.9495.95627.73627.7360.0000.0000.0000.000
7A47GLU-1-0.905-0.9567.892-25.089-25.0890.0000.0000.0000.000
8A48ARG10.8230.9034.48347.46247.543-0.0010.000-0.0800.000
9A49PHE0-0.005-0.0139.6592.0382.0380.0000.0000.0000.000
10A50VAL00.0570.04912.1451.6981.6980.0000.0000.0000.000
11A51ASN0-0.0080.00113.6542.5762.5760.0000.0000.0000.000
12A52LEU0-0.015-0.01711.9941.0311.0310.0000.0000.0000.000
13A53ASN00.016-0.00115.8651.3571.3570.0000.0000.0000.000
14A54ARG10.8330.91117.84516.27516.2750.0000.0000.0000.000
15A55LEU0-0.027-0.01617.3930.6870.6870.0000.0000.0000.000
16A56PHE0-0.023-0.01119.7310.7010.7010.0000.0000.0000.000
17A57GLN0-0.004-0.02121.4421.2031.2030.0000.0000.0000.000
18A58GLU-1-0.879-0.92423.723-12.858-12.8580.0000.0000.0000.000
19A59LEU0-0.025-0.01022.9710.5270.5270.0000.0000.0000.000
20A60VAL00.0030.01225.2890.5570.5570.0000.0000.0000.000
21A61GLY00.0100.00227.7490.4770.4770.0000.0000.0000.000
22A62ASP-1-0.942-0.97229.215-9.657-9.6570.0000.0000.0000.000
23A63PHE0-0.021-0.01730.2300.4420.4420.0000.0000.0000.000
24A64GLN0-0.015-0.03131.1310.6110.6110.0000.0000.0000.000
25A65ALA00.0170.03033.8470.3450.3450.0000.0000.0000.000
26A66LYS10.9210.95635.0348.7728.7720.0000.0000.0000.000
27A67SER00.005-0.00635.6370.3810.3810.0000.0000.0000.000
28A68ASP-1-0.810-0.90937.460-7.988-7.9880.0000.0000.0000.000
29A69GLN0-0.061-0.02439.7220.1990.1990.0000.0000.0000.000
30A70LEU0-0.033-0.00838.5100.2230.2230.0000.0000.0000.000
31A71VAL00.0310.01541.1460.2130.2130.0000.0000.0000.000
32A72SER0-0.057-0.03143.5630.2160.2160.0000.0000.0000.000
33A73VAL00.0170.00345.4680.1770.1770.0000.0000.0000.000
34A74ILE0-0.039-0.01643.4220.1580.1580.0000.0000.0000.000
35A75GLN00.0250.00547.2770.1220.1220.0000.0000.0000.000
36A76ASP-1-0.952-0.96249.634-5.954-5.9540.0000.0000.0000.000
37A77MET00.006-0.00650.3550.2040.2040.0000.0000.0000.000
38A78GLU-1-0.803-0.89249.757-6.415-6.4150.0000.0000.0000.000
39A79LYS10.8400.93153.2485.6265.6260.0000.0000.0000.000
40A80ILE00.009-0.00355.2490.1510.1510.0000.0000.0000.000
41A81SER00.005-0.01055.0900.0960.0960.0000.0000.0000.000
42A82GLU-1-0.918-0.95357.142-5.405-5.4050.0000.0000.0000.000
43A83ASN00.0430.01559.4430.0890.0890.0000.0000.0000.000
44A84ILE00.0700.04158.2660.0960.0960.0000.0000.0000.000
45A85MET0-0.065-0.02358.5540.0900.0900.0000.0000.0000.000
46A86GLU-1-0.941-0.96462.672-4.938-4.9380.0000.0000.0000.000
47A87GLU-1-0.942-0.97263.826-4.993-4.9930.0000.0000.0000.000
48A88LEU0-0.067-0.03662.0700.0960.0960.0000.0000.0000.000
49A89LYS10.8790.92863.6565.1635.1630.0000.0000.0000.000
50A90LYS10.8990.96268.6054.4594.4590.0000.0000.0000.000
51A91SER0-0.010-0.02069.0090.0990.0990.0000.0000.0000.000
52A92GLY00.0000.00770.5810.0520.0520.0000.0000.0000.000
53A93THR00.0140.00871.9380.0690.0690.0000.0000.0000.000
54A94ASN0-0.002-0.00274.1800.0800.0800.0000.0000.0000.000
55A95VAL00.002-0.00573.1120.0660.0660.0000.0000.0000.000
56A96ASP-1-0.867-0.92775.692-4.270-4.2700.0000.0000.0000.000
57A97GLN0-0.065-0.04177.9630.0260.0260.0000.0000.0000.000
58A98ILE0-0.015-0.00677.2610.0680.0680.0000.0000.0000.000
59A99VAL0-0.0040.00778.3770.0520.0520.0000.0000.0000.000
60A100GLU-1-0.807-0.90181.198-3.824-3.8240.0000.0000.0000.000
61A101ARG10.8570.90383.7023.8053.8050.0000.0000.0000.000
62A102VAL00.0150.01682.8470.0510.0510.0000.0000.0000.000
63A103LYS10.8110.90684.7203.8813.8810.0000.0000.0000.000
64A104GLU-1-0.863-0.90187.677-3.609-3.6090.0000.0000.0000.000
65A105ALA00.010-0.00288.1960.0490.0490.0000.0000.0000.000
66A106SER0-0.014-0.02988.5100.0330.0330.0000.0000.0000.000
67A107SER0-0.011-0.00391.1090.0430.0430.0000.0000.0000.000
68A108GLN0-0.004-0.00692.1030.0100.0100.0000.0000.0000.000
69A109ILE00.0050.01792.3860.0460.0460.0000.0000.0000.000
70A110GLY00.0250.00795.3900.0380.0380.0000.0000.0000.000
71A111GLU-1-0.931-0.96397.270-3.253-3.2530.0000.0000.0000.000
72A112THR0-0.027-0.00398.2090.0510.0510.0000.0000.0000.000
73A113LEU00.000-0.00397.7080.0410.0410.0000.0000.0000.000
74A114GLU-1-0.997-0.984100.856-3.071-3.0710.0000.0000.0000.000
75A115ASN00.0500.008103.1560.0640.0640.0000.0000.0000.000
76A116ILE0-0.037-0.018102.3580.0400.0400.0000.0000.0000.000
77A117ARG10.9540.975101.7923.2043.2040.0000.0000.0000.000
78A118SER0-0.045-0.012106.7940.0490.0490.0000.0000.0000.000
79A119ILE00.008-0.009106.8460.0410.0410.0000.0000.0000.000
80A120GLU-1-0.881-0.937106.970-3.031-3.0310.0000.0000.0000.000
81A121LYS10.9200.971110.8182.8902.8900.0000.0000.0000.000
82A122LEU0-0.033-0.028112.3600.0410.0410.0000.0000.0000.000
83A123ILE00.0320.014112.3160.0350.0350.0000.0000.0000.000
84A124GLN0-0.013-0.011112.5940.0430.0430.0000.0000.0000.000
85A125ASN0-0.012-0.004116.8360.0500.0500.0000.0000.0000.000
86A126ILE00.0530.025116.6990.0310.0310.0000.0000.0000.000
87A127MET00.0110.008116.1620.0230.0230.0000.0000.0000.000
88A128ARG10.8110.894120.3042.6542.6540.0000.0000.0000.000
89A129ILE00.0230.014122.4130.0260.0260.0000.0000.0000.000
90A130ALA00.0360.030122.9160.0270.0270.0000.0000.0000.000
91A131ARG10.9140.957119.2932.7292.7290.0000.0000.0000.000
92A132GLU-1-0.879-0.935126.236-2.548-2.5480.0000.0000.0000.000
93A133THR0-0.001-0.008127.8100.0280.0280.0000.0000.0000.000
94A134ASN00.0210.014128.0830.0240.0240.0000.0000.0000.000
95A135ILE00.001-0.005130.0790.0200.0200.0000.0000.0000.000
96A136LEU0-0.0180.004132.3140.0260.0260.0000.0000.0000.000
97A137ALA00.0140.010132.6580.0220.0220.0000.0000.0000.000
98A138LEU0-0.007-0.006133.6950.0170.0170.0000.0000.0000.000
99A139ASN0-0.024-0.031135.6740.0240.0240.0000.0000.0000.000
100A140ALA00.0070.019137.7070.0220.0220.0000.0000.0000.000
101A141THR0-0.027-0.019136.9610.0210.0210.0000.0000.0000.000
102A142ILE0-0.0010.005139.1490.0220.0220.0000.0000.0000.000
103A143GLU-1-0.790-0.886142.128-2.238-2.2380.0000.0000.0000.000
104A144ALA0-0.040-0.006142.6310.0190.0190.0000.0000.0000.000
105A145ALA0-0.057-0.049143.4570.0180.0180.0000.0000.0000.000
106A146ARG10.7890.875145.3812.2602.2600.0000.0000.0000.000
107A147ALA0-0.0250.008147.7200.0180.0180.0000.0000.0000.000
108A148GLY00.0570.036148.8870.0190.0190.0000.0000.0000.000
109A149GLU-1-0.924-0.978148.648-2.177-2.1770.0000.0000.0000.000
110A150ALA00.0290.012148.589-0.016-0.0160.0000.0000.0000.000
111A151GLY00.0100.012146.075-0.012-0.0120.0000.0000.0000.000
112A152LYS10.8720.924144.1422.2222.2220.0000.0000.0000.000
113A153GLY00.0430.020142.336-0.017-0.0170.0000.0000.0000.000
114A154PHE0-0.004-0.015140.815-0.019-0.0190.0000.0000.0000.000
115A155MET0-0.0160.010139.483-0.016-0.0160.0000.0000.0000.000
116A156ILE00.0120.009136.873-0.020-0.0200.0000.0000.0000.000
117A157VAL00.0090.015135.433-0.021-0.0210.0000.0000.0000.000
118A158ALA00.0000.006134.656-0.022-0.0220.0000.0000.0000.000
119A159ASN0-0.012-0.022134.117-0.004-0.0040.0000.0000.0000.000
120A160GLU-1-0.834-0.905129.068-2.557-2.5570.0000.0000.0000.000
121A161VAL00.0050.003130.008-0.025-0.0250.0000.0000.0000.000
122A162GLN00.0010.016129.337-0.011-0.0110.0000.0000.0000.000
123A163ASN0-0.003-0.009127.688-0.025-0.0250.0000.0000.0000.000
124A164LEU00.0220.016125.788-0.028-0.0280.0000.0000.0000.000
125A165SER0-0.046-0.032124.597-0.026-0.0260.0000.0000.0000.000
126A166ASN0-0.081-0.046123.830-0.041-0.0410.0000.0000.0000.000
127A167GLU-1-0.855-0.920120.424-2.741-2.7410.0000.0000.0000.000
128A168THR0-0.044-0.025120.067-0.031-0.0310.0000.0000.0000.000
129A169ASN0-0.109-0.066118.906-0.040-0.0400.0000.0000.0000.000
130A170GLU-1-0.805-0.900115.904-2.867-2.8670.0000.0000.0000.000
131A171VAL00.0810.044114.956-0.033-0.0330.0000.0000.0000.000
132A172THR0-0.044-0.038114.045-0.034-0.0340.0000.0000.0000.000
133A173LYS10.8400.924113.3722.8072.8070.0000.0000.0000.000
134A174GLN0-0.047-0.024110.789-0.058-0.0580.0000.0000.0000.000
135A175ILE0-0.008-0.005109.308-0.035-0.0350.0000.0000.0000.000
136A176VAL0-0.017-0.005108.686-0.028-0.0280.0000.0000.0000.000
137A177GLU-1-0.806-0.879104.873-3.144-3.1440.0000.0000.0000.000
138A178LYS10.8510.908103.4443.1103.1100.0000.0000.0000.000
139A179ALA0-0.002-0.008103.842-0.036-0.0360.0000.0000.0000.000
140A180ARG10.8230.882100.9843.1593.1590.0000.0000.0000.000
141A181GLU-1-0.832-0.902100.654-3.243-3.2430.0000.0000.0000.000
142A182ILE00.0020.01199.169-0.045-0.0450.0000.0000.0000.000
143A183LEU0-0.0120.01898.537-0.047-0.0470.0000.0000.0000.000
144A184GLU-1-0.851-0.91596.565-3.385-3.3850.0000.0000.0000.000
145A185SER0-0.046-0.01894.880-0.062-0.0620.0000.0000.0000.000
146A186SER00.014-0.01893.856-0.043-0.0430.0000.0000.0000.000
147A187GLN0-0.062-0.03393.1670.0040.0040.0000.0000.0000.000
148A188ARG10.9440.96890.4263.4723.4720.0000.0000.0000.000
149A189SER0-0.082-0.05489.620-0.053-0.0530.0000.0000.0000.000
150A190LEU00.011-0.01089.009-0.043-0.0430.0000.0000.0000.000
151A191GLU-1-0.855-0.90687.749-3.650-3.6500.0000.0000.0000.000
152A192ASN0-0.060-0.02384.634-0.077-0.0770.0000.0000.0000.000
153A193LEU00.012-0.01884.237-0.059-0.0590.0000.0000.0000.000
154A194GLU-1-0.952-0.95584.205-3.863-3.8630.0000.0000.0000.000
155A195PHE00.015-0.00377.865-0.067-0.0670.0000.0000.0000.000
156A196MET0-0.0060.00679.970-0.049-0.0490.0000.0000.0000.000
157A197ALA0-0.012-0.00579.490-0.065-0.0650.0000.0000.0000.000
158A198ASN0-0.021-0.02978.521-0.074-0.0740.0000.0000.0000.000
159A199LEU00.0160.01575.420-0.076-0.0760.0000.0000.0000.000
160A200PHE0-0.017-0.01674.750-0.079-0.0790.0000.0000.0000.000
161A201GLU-1-0.774-0.85574.890-4.419-4.4190.0000.0000.0000.000
162A202THR0-0.053-0.01971.376-0.081-0.0810.0000.0000.0000.000
163A203VAL00.0040.00870.235-0.090-0.0900.0000.0000.0000.000
164A204GLY00.0670.03469.823-0.070-0.0700.0000.0000.0000.000
165A205LYS10.8080.87868.9364.3794.3790.0000.0000.0000.000
166A206THR0-0.047-0.03665.230-0.100-0.1000.0000.0000.0000.000
167A207LEU00.0180.01265.232-0.101-0.1010.0000.0000.0000.000
168A208GLN00.0690.03865.563-0.108-0.1080.0000.0000.0000.000
169A209ASN0-0.013-0.01162.857-0.077-0.0770.0000.0000.0000.000
170A210MET0-0.0100.00560.947-0.134-0.1340.0000.0000.0000.000
171A211VAL0-0.0230.00060.608-0.089-0.0890.0000.0000.0000.000
172A212ARG10.9000.94460.1845.0335.0330.0000.0000.0000.000
173A213PHE0-0.0020.00353.168-0.096-0.0960.0000.0000.0000.000
174A214MET00.0310.01755.956-0.129-0.1290.0000.0000.0000.000
175A215GLU-1-0.813-0.90856.313-5.334-5.3340.0000.0000.0000.000
176A216ASN0-0.115-0.07054.181-0.149-0.1490.0000.0000.0000.000
177A217ASN0-0.008-0.01351.509-0.206-0.2060.0000.0000.0000.000
178A218VAL00.0360.01851.382-0.137-0.1370.0000.0000.0000.000
179A219LYS10.9530.98351.5245.8505.8500.0000.0000.0000.000
180A220LEU00.0370.03145.719-0.132-0.1320.0000.0000.0000.000
181A221LEU0-0.003-0.00346.873-0.182-0.1820.0000.0000.0000.000
182A222GLN00.0030.00046.872-0.058-0.0580.0000.0000.0000.000
183A223GLU-1-1.017-1.00344.404-7.193-7.1930.0000.0000.0000.000
184A224VAL0-0.021-0.01941.661-0.215-0.2150.0000.0000.0000.000
185A225ARG10.8020.88841.9996.6236.6230.0000.0000.0000.000
186A226ASN00.0570.02042.412-0.130-0.1300.0000.0000.0000.000
187A227SER0-0.0240.00639.249-0.244-0.2440.0000.0000.0000.000
188A228LEU0-0.0110.00237.380-0.284-0.2840.0000.0000.0000.000
189A229ASP-1-0.898-0.96637.925-7.796-7.7960.0000.0000.0000.000
190A230THR00.024-0.00338.158-0.230-0.2300.0000.0000.0000.000
191A231SER0-0.041-0.03034.115-0.306-0.3060.0000.0000.0000.000
192A232LYS10.8490.94833.3177.8217.8210.0000.0000.0000.000
193A233GLU-1-0.909-0.94233.325-8.464-8.4640.0000.0000.0000.000
194A234SER0-0.042-0.02932.159-0.327-0.3270.0000.0000.0000.000
195A235LEU0-0.013-0.00127.388-0.387-0.3870.0000.0000.0000.000
196A236SER00.0230.02928.364-0.414-0.4140.0000.0000.0000.000
197A237GLU-1-0.927-0.96028.798-10.285-10.2850.0000.0000.0000.000
198A238LYS10.9360.96026.15310.15210.1520.0000.0000.0000.000
199A239SER0-0.051-0.04224.246-0.532-0.5320.0000.0000.0000.000
200A240ALA00.0520.02823.809-0.530-0.5300.0000.0000.0000.000
201A241GLU-1-0.960-0.96723.099-12.563-12.5630.0000.0000.0000.000
202A242ILE0-0.035-0.02719.396-0.556-0.5560.0000.0000.0000.000
203A243ASP-1-0.848-0.89819.378-14.628-14.6280.0000.0000.0000.000
204A244SER0-0.016-0.01620.246-0.280-0.2800.0000.0000.0000.000
205A245ALA0-0.013-0.01218.312-0.331-0.3310.0000.0000.0000.000
206A246THR0-0.050-0.03314.832-1.318-1.3180.0000.0000.0000.000
207A247LYS10.8530.92315.57214.09414.0940.0000.0000.0000.000
208A248VAL00.0150.00316.795-0.101-0.1010.0000.0000.0000.000
209A249LEU0-0.038-0.01612.304-0.547-0.5470.0000.0000.0000.000
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