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: JLZ79

Calculation Name: 3GUY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GUY

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2241862.20087
FMO2-HF: Nuclear repulsion 2163824.126316
FMO2-HF: Total energy -78038.074553
FMO2-MP2: Total energy -78263.710437


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:1:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-14.9830.0899999999999997.541-7.599-15.014-0.037
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.043
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].
3A3VAL00.0250.0102.444-2.2201.0801.030-1.454-2.8760.001
4A4ILE0-0.0090.0024.403-0.145-0.052-0.001-0.019-0.0730.000
5A5THR00.0250.0088.1720.0620.0620.0000.0000.0000.000
6A6GLY00.0380.01511.3360.0030.0030.0000.0000.0000.000
7A7ALA0-0.013-0.00210.3900.0190.0190.0000.0000.0000.000
8A8SER0-0.007-0.00112.3850.0180.0180.0000.0000.0000.000
9A9SER00.023-0.01115.1180.0220.0220.0000.0000.0000.000
10A10GLY00.0140.02417.558-0.006-0.0060.0000.0000.0000.000
11A11LEU00.0520.01816.207-0.001-0.0010.0000.0000.0000.000
12A12GLY00.0810.04713.194-0.012-0.0120.0000.0000.0000.000
13A13ALA0-0.026-0.01212.042-0.018-0.0180.0000.0000.0000.000
14A14GLU-1-0.835-0.90513.384-0.062-0.0620.0000.0000.0000.000
15A15LEU00.010-0.00411.8420.0070.0070.0000.0000.0000.000
16A16ALA0-0.020-0.0069.103-0.027-0.0270.0000.0000.0000.000
17A17LYS10.8520.9079.7980.0870.0870.0000.0000.0000.000
18A18LEU0-0.0070.00912.4390.0340.0340.0000.0000.0000.000
19A19TYR0-0.001-0.0137.409-0.030-0.0300.0000.0000.0000.000
20A20ASP-1-0.711-0.8608.1760.3210.3210.0000.0000.0000.000
21A21ALA00.0140.0119.2430.0810.0810.0000.0000.0000.000
22A22GLU-1-0.838-0.9029.660-0.203-0.2030.0000.0000.0000.000
23A23GLY0-0.0080.0049.7460.0330.0330.0000.0000.0000.000
24A24LYS10.7470.8704.9200.5210.5210.0000.0000.0000.000
25A25ALA00.0520.0292.538-1.193-0.2290.498-0.507-0.955-0.001
26A26THR00.0050.0022.586-4.459-1.6851.885-2.360-2.299-0.031
27A27TYR00.0280.0192.333-1.147-0.0310.919-0.355-1.680-0.002
28A28LEU0-0.023-0.0103.837-0.071-0.0300.0030.012-0.0560.000
29A29THR00.031-0.0107.5410.0200.0200.0000.0000.0000.000
30A30GLY00.003-0.01610.474-0.001-0.0010.0000.0000.0000.000
31A31ARG10.8760.93214.2420.1280.1280.0000.0000.0000.000
32A32SER0-0.029-0.00716.5470.0130.0130.0000.0000.0000.000
33A33GLU-1-0.757-0.87914.675-0.118-0.1180.0000.0000.0000.000
34A34SER00.0330.01515.9570.0010.0010.0000.0000.0000.000
35A35LYS10.9230.96817.2060.0860.0860.0000.0000.0000.000
36A36LEU00.0060.01710.9440.0050.0050.0000.0000.0000.000
37A37SER00.0110.02212.8490.0120.0120.0000.0000.0000.000
38A38THR0-0.057-0.03114.8550.0170.0170.0000.0000.0000.000
39A39VAL0-0.014-0.01312.0340.0110.0110.0000.0000.0000.000
40A40THR0-0.007-0.0279.3150.0120.0120.0000.0000.0000.000
41A41ASN0-0.053-0.03411.8440.0390.0390.0000.0000.0000.000
42A42CYS0-0.108-0.03814.6380.0090.0090.0000.0000.0000.000
43A43LEU0-0.077-0.0199.027-0.006-0.0060.0000.0000.0000.000
44A44SER0-0.057-0.04911.000-0.011-0.0110.0000.0000.0000.000
45A45ASN0-0.056-0.0297.5840.1120.1120.0000.0000.0000.000
46A46ASN0-0.080-0.0435.8020.2220.2220.0000.0000.0000.000
47A47VAL00.0160.0102.564-0.503-0.1180.798-0.198-0.985-0.001
48A48GLY00.0130.0085.638-0.161-0.1610.0000.0000.0000.000
49A49TYR00.0040.0006.494-0.018-0.0180.0000.0000.0000.000
50A50ARG10.8990.9558.6640.2130.2130.0000.0000.0000.000
51A51ALA0-0.0090.00411.346-0.020-0.0200.0000.0000.0000.000
52A52ARG10.7200.84211.4370.1740.1740.0000.0000.0000.000
53A53ASP-1-0.777-0.87214.760-0.126-0.1260.0000.0000.0000.000
54A54LEU0-0.052-0.05012.973-0.018-0.0180.0000.0000.0000.000
55A55ALA00.0060.01516.820-0.005-0.0050.0000.0000.0000.000
56A56SER00.0080.00419.1500.0030.0030.0000.0000.0000.000
57A57HIS00.0530.02017.808-0.023-0.0230.0000.0000.0000.000
58A58GLN00.0800.03016.767-0.020-0.0200.0000.0000.0000.000
59A59GLU-1-0.843-0.90315.840-0.150-0.1500.0000.0000.0000.000
60A60VAL00.0300.01412.386-0.021-0.0210.0000.0000.0000.000
61A61GLU-1-0.908-0.93811.878-0.188-0.1880.0000.0000.0000.000
62A62GLN0-0.036-0.03012.353-0.018-0.0180.0000.0000.0000.000
63A63LEU0-0.033-0.0027.505-0.003-0.0030.0000.0000.0000.000
64A64PHE00.005-0.0256.511-0.046-0.0460.0000.0000.0000.000
65A65GLU-1-0.848-0.8778.378-0.253-0.2530.0000.0000.0000.000
66A66GLN0-0.0210.0028.5680.0200.0200.0000.0000.0000.000
67A67LEU0-0.046-0.0152.696-0.791-0.0660.276-0.171-0.8300.000
68A68ASP-1-0.859-0.9063.588-2.020-1.4810.010-0.214-0.335-0.001
69A69SER0-0.067-0.0482.763-1.2100.0240.595-0.675-1.153-0.006
70A70ILE0-0.024-0.0153.704-0.793-0.3370.009-0.160-0.305-0.001
71A71PRO0-0.0090.0092.236-1.655-0.2681.237-0.945-1.6790.003
72A72SER0-0.026-0.0292.588-0.7831.0370.284-0.488-1.6170.002
73A73THR0-0.025-0.0224.2220.6910.966-0.001-0.049-0.2250.000
74A74VAL0-0.004-0.0025.025-0.202-0.238-0.001-0.0160.0540.000
75A75VAL00.0100.0147.2380.1100.1100.0000.0000.0000.000
76A76HIS00.0470.0309.8930.0120.0120.0000.0000.0000.000
77A77SER0-0.031-0.04012.4980.0300.0300.0000.0000.0000.000
78A78ALA0-0.040-0.01414.5520.0290.0290.0000.0000.0000.000
79A79GLY00.0420.01816.322-0.001-0.0010.0000.0000.0000.000
80A80SER0-0.044-0.02320.1190.0030.0030.0000.0000.0000.000
81A81GLY00.0490.02223.550-0.004-0.0040.0000.0000.0000.000
82A82TYR00.0250.01926.9610.0030.0030.0000.0000.0000.000
83A83PHE0-0.024-0.01428.293-0.002-0.0020.0000.0000.0000.000
84A84GLY00.0680.04033.6510.0020.0020.0000.0000.0000.000
85A85LEU0-0.023-0.01637.442-0.002-0.0020.0000.0000.0000.000
86A86LEU00.0010.00336.8930.0000.0000.0000.0000.0000.000
87A87GLN0-0.030-0.03639.459-0.002-0.0020.0000.0000.0000.000
88A88GLU-1-0.871-0.91940.368-0.037-0.0370.0000.0000.0000.000
89A89GLN0-0.087-0.01834.192-0.004-0.0040.0000.0000.0000.000
90A90ASP-1-0.763-0.89035.261-0.053-0.0530.0000.0000.0000.000
91A91PRO00.009-0.01135.082-0.004-0.0040.0000.0000.0000.000
92A92GLU-1-0.912-0.94533.273-0.056-0.0560.0000.0000.0000.000
93A93GLN0-0.0140.00130.656-0.009-0.0090.0000.0000.0000.000
94A94ILE0-0.039-0.01830.250-0.006-0.0060.0000.0000.0000.000
95A95GLN0-0.039-0.02828.462-0.004-0.0040.0000.0000.0000.000
96A96THR00.010-0.00326.432-0.007-0.0070.0000.0000.0000.000
97A97LEU0-0.058-0.01625.664-0.010-0.0100.0000.0000.0000.000
98A98ILE00.0360.00925.240-0.010-0.0100.0000.0000.0000.000
99A99GLU-1-0.860-0.91523.795-0.099-0.0990.0000.0000.0000.000
100A100ASN0-0.015-0.03021.194-0.018-0.0180.0000.0000.0000.000
101A101ASN0-0.095-0.03720.282-0.021-0.0210.0000.0000.0000.000
102A102LEU00.0160.01620.842-0.010-0.0100.0000.0000.0000.000
103A103SER00.0290.01021.318-0.008-0.0080.0000.0000.0000.000
104A104SER0-0.028-0.01917.286-0.012-0.0120.0000.0000.0000.000
105A105ALA00.0160.01316.706-0.019-0.0190.0000.0000.0000.000
106A106ILE00.0220.00117.229-0.016-0.0160.0000.0000.0000.000
107A107ASN0-0.047-0.03616.773-0.005-0.0050.0000.0000.0000.000
108A108VAL00.0030.00111.609-0.014-0.0140.0000.0000.0000.000
109A109LEU00.0240.00813.181-0.030-0.0300.0000.0000.0000.000
110A110ARG10.9340.97115.1380.1510.1510.0000.0000.0000.000
111A111GLU-1-0.763-0.87011.799-0.223-0.2230.0000.0000.0000.000
112A112LEU00.005-0.0048.498-0.021-0.0210.0000.0000.0000.000
113A113VAL00.0220.00511.627-0.008-0.0080.0000.0000.0000.000
114A114LYS10.7330.85114.6200.2050.2050.0000.0000.0000.000
115A115ARG10.7360.8269.9130.2950.2950.0000.0000.0000.000
116A116TYR00.0290.0056.767-0.007-0.0070.0000.0000.0000.000
117A117LYS10.8920.94811.4150.1650.1650.0000.0000.0000.000
118A118ASP-1-0.853-0.91414.564-0.147-0.1470.0000.0000.0000.000
119A119GLN0-0.002-0.0119.8080.0450.0450.0000.0000.0000.000
120A120PRO00.0010.0058.499-0.017-0.0170.0000.0000.0000.000
121A121VAL0-0.0140.0057.299-0.067-0.0670.0000.0000.0000.000
122A122ASN0-0.007-0.0078.1060.3020.3020.0000.0000.0000.000
123A123VAL00.0300.0089.655-0.114-0.1140.0000.0000.0000.000
124A124VAL00.0140.00610.9820.0800.0800.0000.0000.0000.000
125A125MET00.0080.01312.898-0.006-0.0060.0000.0000.0000.000
126A126ILE0-0.031-0.01814.4600.0300.0300.0000.0000.0000.000
127A127MET0-0.037-0.01217.2700.0130.0130.0000.0000.0000.000
128A128SER0-0.023-0.02820.8750.0080.0080.0000.0000.0000.000
129A129THR00.0190.00023.9750.0010.0010.0000.0000.0000.000
130A130ALA0-0.011-0.01527.2250.0040.0040.0000.0000.0000.000
131A131ALA0-0.015-0.00724.7540.0020.0020.0000.0000.0000.000
132A132GLN0-0.012-0.00426.643-0.003-0.0030.0000.0000.0000.000
133A133GLN00.0080.00729.3540.0030.0030.0000.0000.0000.000
134A134PRO00.0200.02732.119-0.003-0.0030.0000.0000.0000.000
135A135LYS10.8530.89429.8290.0780.0780.0000.0000.0000.000
136A136ALA00.0220.01535.5010.0000.0000.0000.0000.0000.000
137A137GLN00.002-0.00836.520-0.001-0.0010.0000.0000.0000.000
138A138GLU-1-0.761-0.87130.571-0.075-0.0750.0000.0000.0000.000
139A139SER00.0130.01632.058-0.005-0.0050.0000.0000.0000.000
140A140THR00.038-0.00131.679-0.003-0.0030.0000.0000.0000.000
141A141TYR00.0320.01424.335-0.009-0.0090.0000.0000.0000.000
142A142CYS0-0.035-0.02327.662-0.006-0.0060.0000.0000.0000.000
143A143ALA00.0010.00928.790-0.005-0.0050.0000.0000.0000.000
144A144VAL00.0020.00825.324-0.004-0.0040.0000.0000.0000.000
145A145LYS10.8810.94720.6230.1330.1330.0000.0000.0000.000
146A146TRP0-0.024-0.01924.764-0.007-0.0070.0000.0000.0000.000
147A147ALA0-0.0220.00826.372-0.003-0.0030.0000.0000.0000.000
148A148VAL0-0.026-0.01319.823-0.005-0.0050.0000.0000.0000.000
149A149LYS10.9110.96022.1100.1070.1070.0000.0000.0000.000
150A150GLY00.004-0.00224.073-0.002-0.0020.0000.0000.0000.000
151A151LEU0-0.0070.01419.4550.0010.0010.0000.0000.0000.000
152A152ILE0-0.008-0.01218.548-0.005-0.0050.0000.0000.0000.000
153A153GLU-1-0.836-0.92620.967-0.138-0.1380.0000.0000.0000.000
154A154SER0-0.042-0.02624.0710.0090.0090.0000.0000.0000.000
155A155VAL00.001-0.00618.5040.0010.0010.0000.0000.0000.000
156A156ARG10.7420.83319.4740.1730.1730.0000.0000.0000.000
157A157LEU0-0.053-0.01921.8490.0060.0060.0000.0000.0000.000
158A158GLU-1-0.931-0.96721.783-0.132-0.1320.0000.0000.0000.000
159A159LEU0-0.049-0.02016.8660.0010.0010.0000.0000.0000.000
160A160LYS10.9400.96420.3140.0860.0860.0000.0000.0000.000
161A161GLY0-0.028-0.00321.8460.0080.0080.0000.0000.0000.000
162A162LYS10.8430.91617.3720.1460.1460.0000.0000.0000.000
163A163PRO0-0.018-0.00113.3580.0000.0000.0000.0000.0000.000
164A164MET0-0.0200.03312.512-0.031-0.0310.0000.0000.0000.000
165A165LYS10.8510.91812.6520.3740.3740.0000.0000.0000.000
166A166ILE00.0170.01613.746-0.055-0.0550.0000.0000.0000.000
167A167ILE0-0.022-0.00613.6850.0370.0370.0000.0000.0000.000
168A168ALA0-0.0170.00516.196-0.012-0.0120.0000.0000.0000.000
169A169VAL00.0360.00516.3910.0110.0110.0000.0000.0000.000
170A170TYR0-0.018-0.02119.4300.0030.0030.0000.0000.0000.000
171A171PRO00.0320.02420.6750.0120.0120.0000.0000.0000.000
172A172GLY00.0420.01923.3950.0040.0040.0000.0000.0000.000
173A173GLY0-0.019-0.00425.523-0.005-0.0050.0000.0000.0000.000
174A174MET0-0.0050.00721.045-0.001-0.0010.0000.0000.0000.000
175A191PHE0-0.018-0.01228.5130.0000.0000.0000.0000.0000.000
176A192MET0-0.040-0.01124.2210.0040.0040.0000.0000.0000.000
177A193SER00.007-0.01824.211-0.001-0.0010.0000.0000.0000.000
178A194ALA00.001-0.03119.585-0.006-0.0060.0000.0000.0000.000
179A195GLU-1-0.870-0.92919.478-0.059-0.0590.0000.0000.0000.000
180A196ASP-1-0.819-0.86920.588-0.061-0.0610.0000.0000.0000.000
181A197ALA0-0.001-0.00720.954-0.004-0.0040.0000.0000.0000.000
182A198ALA00.013-0.00116.139-0.013-0.0130.0000.0000.0000.000
183A199LEU00.0430.02517.064-0.019-0.0190.0000.0000.0000.000
184A200MET0-0.018-0.00718.610-0.002-0.0020.0000.0000.0000.000
185A201ILE0-0.038-0.03115.652-0.006-0.0060.0000.0000.0000.000
186A202HIS0-0.049-0.03511.3270.0010.0010.0000.0000.0000.000
187A203GLY00.0110.00914.635-0.013-0.0130.0000.0000.0000.000
188A204ALA0-0.022-0.00517.0360.0160.0160.0000.0000.0000.000
189A205LEU0-0.031-0.00813.7100.0050.0050.0000.0000.0000.000
190A206ALA00.0130.01113.398-0.042-0.0420.0000.0000.0000.000
191A207ASN0-0.002-0.02112.493-0.008-0.0080.0000.0000.0000.000
192A208ILE00.0100.00414.5310.0160.0160.0000.0000.0000.000
193A209GLY00.0200.01617.2130.0040.0040.0000.0000.0000.000
194A210ASN0-0.037-0.02018.050-0.006-0.0060.0000.0000.0000.000
195A211GLY00.0120.00719.2380.0000.0000.0000.0000.0000.000
196A212TYR0-0.019-0.01515.821-0.015-0.0150.0000.0000.0000.000
197A213VAL00.0150.02217.1010.0170.0170.0000.0000.0000.000
198A214SER00.006-0.01517.232-0.026-0.0260.0000.0000.0000.000
199A215ASP-1-0.783-0.85819.217-0.173-0.1730.0000.0000.0000.000
200A216ILE00.0140.01818.3850.0140.0140.0000.0000.0000.000
201A217THR0-0.015-0.00922.127-0.005-0.0050.0000.0000.0000.000
202A218VAL0-0.0020.01021.5340.0070.0070.0000.0000.0000.000
203A219ASN00.025-0.01124.763-0.001-0.0010.0000.0000.0000.000
204A220ARG10.8880.95027.7090.0540.0540.0000.0000.0000.000