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: 85Z4Y

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2233784.956401
FMO2-HF: Nuclear repulsion 2155748.412984
FMO2-HF: Total energy -78036.543417
FMO2-MP2: Total energy -78262.114199


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.
-13.614-0.9826.804-5.566-13.869-0.029
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 : 0.010 / q_NPA : 0.005
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].
3A3VAL00.0330.0202.799-1.2841.0710.644-0.705-2.2930.001
4A4ILE0-0.0110.0074.279-0.1140.0060.000-0.019-0.1010.000
5A5THR00.009-0.0107.8260.0170.0170.0000.0000.0000.000
6A6GLY00.0110.00210.9260.0360.0360.0000.0000.0000.000
7A7ALA00.0110.00610.8890.0270.0270.0000.0000.0000.000
8A8SER0-0.009-0.00812.9230.0140.0140.0000.0000.0000.000
9A9SER00.006-0.01615.6220.0080.0080.0000.0000.0000.000
10A10GLY0-0.0130.00117.033-0.007-0.0070.0000.0000.0000.000
11A11LEU00.0590.02416.0440.0130.0130.0000.0000.0000.000
12A12GLY00.0780.04313.1810.0270.0270.0000.0000.0000.000
13A13ALA0-0.046-0.01912.3600.0300.0300.0000.0000.0000.000
14A14GLU-1-0.902-0.96413.5590.1990.1990.0000.0000.0000.000
15A15LEU0-0.0010.00311.7610.0380.0380.0000.0000.0000.000
16A16ALA0-0.007-0.0069.3060.0870.0870.0000.0000.0000.000
17A17LYS10.9350.9699.994-0.049-0.0490.0000.0000.0000.000
18A18LEU00.0060.01512.7190.0520.0520.0000.0000.0000.000
19A19TYR0-0.010-0.0147.4780.0190.0190.0000.0000.0000.000
20A20ASP-1-0.763-0.8668.5270.8780.8780.0000.0000.0000.000
21A21ALA00.0070.0109.4520.0690.0690.0000.0000.0000.000
22A22GLU-1-0.832-0.89310.4600.9370.9370.0000.0000.0000.000
23A23GLY0-0.025-0.0159.9520.0830.0830.0000.0000.0000.000
24A24LYS10.7660.8825.257-0.993-0.9930.0000.0000.0000.000
25A25ALA00.0620.0362.919-1.400-0.6090.319-0.326-0.7850.000
26A26THR00.007-0.0042.781-2.525-0.0681.018-1.697-1.778-0.020
27A27TYR00.0340.0222.472-1.750-0.1520.657-0.414-1.841-0.002
28A28LEU0-0.028-0.0164.068-0.060-0.0010.001-0.015-0.0440.000
29A29THR00.0250.0057.801-0.045-0.0450.0000.0000.0000.000
30A30GLY0-0.006-0.02110.1470.0420.0420.0000.0000.0000.000
31A31ARG11.0001.01213.9230.0550.0550.0000.0000.0000.000
32A32SER0-0.045-0.00817.2660.0010.0010.0000.0000.0000.000
33A33GLU-1-0.817-0.92215.730-0.121-0.1210.0000.0000.0000.000
34A34SER00.0070.00716.2310.0060.0060.0000.0000.0000.000
35A35LYS10.9710.96717.8650.0280.0280.0000.0000.0000.000
36A36LEU0-0.0050.00711.3250.0200.0200.0000.0000.0000.000
37A37SER00.0020.02013.2400.0260.0260.0000.0000.0000.000
38A38THR0-0.042-0.01815.0350.0200.0200.0000.0000.0000.000
39A39VAL0-0.032-0.03112.4160.0200.0200.0000.0000.0000.000
40A40THR0-0.014-0.0259.5450.0290.0290.0000.0000.0000.000
41A41ASN00.0090.02111.8870.0280.0280.0000.0000.0000.000
42A42CYS0-0.092-0.03514.6440.0040.0040.0000.0000.0000.000
43A43LEU0-0.081-0.0269.0060.0260.0260.0000.0000.0000.000
44A44SER0-0.027-0.02511.301-0.066-0.0660.0000.0000.0000.000
45A45ASN0-0.073-0.0377.374-0.021-0.0210.0000.0000.0000.000
46A46ASN0-0.056-0.0295.8820.1030.1030.0000.0000.0000.000
47A47VAL00.0060.0062.590-0.480-0.2821.071-0.216-1.053-0.001
48A48GLY00.0190.0135.395-0.288-0.251-0.0010.000-0.0350.000
49A49TYR00.008-0.0136.6010.0560.0560.0000.0000.0000.000
50A50ARG10.9530.9908.7840.3690.3690.0000.0000.0000.000
51A51ALA00.0160.02010.7740.0030.0030.0000.0000.0000.000
52A52ARG10.8000.88211.2880.2330.2330.0000.0000.0000.000
53A53ASP-1-0.862-0.91814.481-0.113-0.1130.0000.0000.0000.000
54A54LEU0-0.028-0.03912.349-0.011-0.0110.0000.0000.0000.000
55A55ALA00.0230.02716.276-0.008-0.0080.0000.0000.0000.000
56A56SER00.0210.02718.558-0.002-0.0020.0000.0000.0000.000
57A57HIS00.001-0.02117.335-0.032-0.0320.0000.0000.0000.000
58A58GLN00.0600.03016.732-0.026-0.0260.0000.0000.0000.000
59A59GLU-1-0.867-0.93315.279-0.217-0.2170.0000.0000.0000.000
60A60VAL0-0.004-0.00712.176-0.038-0.0380.0000.0000.0000.000
61A61GLU-1-0.926-0.96511.799-0.324-0.3240.0000.0000.0000.000
62A62GLN0-0.007-0.00712.189-0.051-0.0510.0000.0000.0000.000
63A63LEU0-0.055-0.0237.313-0.039-0.0390.0000.0000.0000.000
64A64PHE0-0.004-0.0266.034-0.065-0.0650.0000.0000.0000.000
65A65GLU-1-0.899-0.9147.856-0.616-0.6160.0000.0000.0000.000
66A66GLN0-0.063-0.0358.699-0.018-0.0180.0000.0000.0000.000
67A67LEU0-0.041-0.0142.521-0.703-0.2020.914-0.244-1.170-0.002
68A68ASP-1-0.868-0.9213.952-3.115-2.8340.001-0.077-0.2050.000
69A69SER0-0.051-0.0222.951-2.069-0.6420.234-0.660-1.001-0.006
70A70ILE0-0.046-0.0244.266-0.0830.1540.000-0.031-0.2070.000
71A71PRO00.0020.0152.150-1.963-0.6791.671-1.194-1.7620.004
72A72SER00.0440.0112.5210.2011.2510.2750.066-1.391-0.003
73A73THR0-0.088-0.0494.0221.0251.2620.000-0.034-0.2030.000
74A74VAL00.0150.0115.325-0.479-0.4790.0000.0000.0000.000
75A75VAL0-0.0070.0017.5060.1330.1330.0000.0000.0000.000
76A76HIS00.0540.0369.866-0.030-0.0300.0000.0000.0000.000
77A77SER0-0.041-0.04512.4350.0420.0420.0000.0000.0000.000
78A78ALA0-0.0260.00014.6510.0160.0160.0000.0000.0000.000
79A79GLY00.0260.01116.283-0.001-0.0010.0000.0000.0000.000
80A80SER0-0.062-0.04120.0470.0010.0010.0000.0000.0000.000
81A81GLY00.0270.02123.298-0.002-0.0020.0000.0000.0000.000
82A82TYR00.0280.01826.758-0.002-0.0020.0000.0000.0000.000
83A83PHE0-0.027-0.01128.2460.0000.0000.0000.0000.0000.000
84A84GLY00.0730.04533.3290.0000.0000.0000.0000.0000.000
85A85LEU0-0.015-0.01136.978-0.001-0.0010.0000.0000.0000.000
86A86LEU00.0040.00636.746-0.001-0.0010.0000.0000.0000.000
87A87GLN00.029-0.00239.149-0.003-0.0030.0000.0000.0000.000
88A88GLU-1-0.939-0.96740.440-0.013-0.0130.0000.0000.0000.000
89A89GLN0-0.116-0.03434.128-0.004-0.0040.0000.0000.0000.000
90A90ASP-1-0.795-0.90435.574-0.033-0.0330.0000.0000.0000.000
91A91PRO00.002-0.02034.832-0.002-0.0020.0000.0000.0000.000
92A92GLU-1-0.925-0.95733.294-0.046-0.0460.0000.0000.0000.000
93A93GLN0-0.011-0.01230.822-0.006-0.0060.0000.0000.0000.000
94A94ILE0-0.036-0.01230.032-0.002-0.0020.0000.0000.0000.000
95A95GLN0-0.010-0.01928.1280.0000.0000.0000.0000.0000.000
96A96THR00.0170.01825.575-0.007-0.0070.0000.0000.0000.000
97A97LEU0-0.082-0.03725.376-0.005-0.0050.0000.0000.0000.000
98A98ILE00.0190.00025.215-0.004-0.0040.0000.0000.0000.000
99A99GLU-1-0.858-0.90723.231-0.091-0.0910.0000.0000.0000.000
100A100ASN0-0.007-0.02520.859-0.019-0.0190.0000.0000.0000.000
101A101ASN0-0.114-0.04720.045-0.003-0.0030.0000.0000.0000.000
102A102LEU00.0330.02420.703-0.006-0.0060.0000.0000.0000.000
103A103SER00.0190.00521.083-0.009-0.0090.0000.0000.0000.000
104A104SER0-0.020-0.02116.890-0.019-0.0190.0000.0000.0000.000
105A105ALA0-0.0060.00516.348-0.025-0.0250.0000.0000.0000.000
106A106ILE00.012-0.00216.884-0.019-0.0190.0000.0000.0000.000
107A107ASN0-0.055-0.03716.344-0.019-0.0190.0000.0000.0000.000
108A108VAL00.0140.00511.037-0.032-0.0320.0000.0000.0000.000
109A109LEU00.0350.02012.636-0.046-0.0460.0000.0000.0000.000
110A110ARG10.9690.97214.7400.1990.1990.0000.0000.0000.000
111A111GLU-1-0.883-0.92511.330-0.392-0.3920.0000.0000.0000.000
112A112LEU0-0.001-0.0068.301-0.048-0.0480.0000.0000.0000.000
113A113VAL00.0220.01111.469-0.027-0.0270.0000.0000.0000.000
114A114LYS10.8700.93414.4770.2930.2930.0000.0000.0000.000
115A115ARG10.7720.8559.7060.5610.5610.0000.0000.0000.000
116A116TYR00.0340.0086.621-0.030-0.0300.0000.0000.0000.000
117A117LYS10.9470.98011.5040.2710.2710.0000.0000.0000.000
118A118ASP-1-0.938-0.97914.680-0.205-0.2050.0000.0000.0000.000
119A119GLN00.0290.0059.6550.0120.0120.0000.0000.0000.000
120A120PRO0-0.028-0.0038.9290.0140.0140.0000.0000.0000.000
121A121VAL00.0000.0107.1190.0450.0450.0000.0000.0000.000
122A122ASN0-0.049-0.0218.1500.1010.1010.0000.0000.0000.000
123A123VAL00.0400.0079.342-0.088-0.0880.0000.0000.0000.000
124A124VAL00.0160.00511.3410.0640.0640.0000.0000.0000.000
125A125MET0-0.018-0.00813.102-0.029-0.0290.0000.0000.0000.000
126A126ILE0-0.018-0.01014.3600.0280.0280.0000.0000.0000.000
127A127MET0-0.0200.00117.353-0.014-0.0140.0000.0000.0000.000
128A128SER00.017-0.00320.9030.0070.0070.0000.0000.0000.000
129A129THR00.0480.01923.984-0.007-0.0070.0000.0000.0000.000
130A130ALA0-0.031-0.02227.129-0.001-0.0010.0000.0000.0000.000
131A131ALA00.002-0.00924.956-0.004-0.0040.0000.0000.0000.000
132A132GLN0-0.039-0.01727.082-0.007-0.0070.0000.0000.0000.000
133A133GLN0-0.007-0.00129.5580.0040.0040.0000.0000.0000.000
134A134PRO00.0220.01532.184-0.002-0.0020.0000.0000.0000.000
135A135LYS10.9260.96329.662-0.005-0.0050.0000.0000.0000.000
136A136ALA00.0320.01035.291-0.003-0.0030.0000.0000.0000.000
137A137GLN0-0.030-0.01836.6420.0000.0000.0000.0000.0000.000
138A138GLU-1-0.813-0.91431.100-0.001-0.0010.0000.0000.0000.000
139A139SER0-0.0060.01332.353-0.003-0.0030.0000.0000.0000.000
140A140THR00.061-0.00131.495-0.002-0.0020.0000.0000.0000.000
141A141TYR00.0230.01824.601-0.007-0.0070.0000.0000.0000.000
142A142CYS0-0.018-0.01227.908-0.001-0.0010.0000.0000.0000.000
143A143ALA0-0.0140.00629.111-0.003-0.0030.0000.0000.0000.000
144A144VAL00.0040.00325.246-0.004-0.0040.0000.0000.0000.000
145A145LYS10.9350.97420.9220.0350.0350.0000.0000.0000.000
146A146TRP0-0.047-0.02925.043-0.003-0.0030.0000.0000.0000.000
147A147ALA0-0.0350.00625.837-0.003-0.0030.0000.0000.0000.000
148A148VAL0-0.009-0.00819.905-0.007-0.0070.0000.0000.0000.000
149A149LYS10.9830.99022.4030.0110.0110.0000.0000.0000.000
150A150GLY00.0050.00324.180-0.002-0.0020.0000.0000.0000.000
151A151LEU00.0100.00519.318-0.003-0.0030.0000.0000.0000.000
152A152ILE0-0.014-0.01518.771-0.010-0.0100.0000.0000.0000.000
153A153GLU-1-0.887-0.94921.152-0.040-0.0400.0000.0000.0000.000
154A154SER0-0.053-0.02724.2380.0040.0040.0000.0000.0000.000
155A155VAL00.0430.01318.138-0.003-0.0030.0000.0000.0000.000
156A156ARG10.7830.87219.0640.0300.0300.0000.0000.0000.000
157A157LEU0-0.064-0.02521.4570.0030.0030.0000.0000.0000.000
158A158GLU-1-0.974-0.98021.771-0.132-0.1320.0000.0000.0000.000
159A159LEU0-0.055-0.02416.556-0.013-0.0130.0000.0000.0000.000
160A160LYS10.9800.98319.9780.0610.0610.0000.0000.0000.000
161A161GLY0-0.078-0.03421.796-0.004-0.0040.0000.0000.0000.000
162A162LYS10.9070.97017.4840.1540.1540.0000.0000.0000.000
163A163PRO0-0.0060.00113.3990.0220.0220.0000.0000.0000.000
164A164MET0-0.0180.03212.4480.0010.0010.0000.0000.0000.000
165A165LYS10.9200.96512.8130.0570.0570.0000.0000.0000.000
166A166ILE00.0240.01713.512-0.033-0.0330.0000.0000.0000.000
167A167ILE0-0.028-0.00213.6730.0310.0310.0000.0000.0000.000
168A168ALA0-0.0130.00816.435-0.017-0.0170.0000.0000.0000.000
169A169VAL00.0470.01416.6690.0210.0210.0000.0000.0000.000
170A170TYR0-0.005-0.02219.616-0.017-0.0170.0000.0000.0000.000
171A171PRO00.0410.02920.1050.0090.0090.0000.0000.0000.000
172A172GLY00.005-0.01123.162-0.012-0.0120.0000.0000.0000.000
173A173GLY0-0.031-0.01025.262-0.001-0.0010.0000.0000.0000.000
174A174MET0-0.0030.00420.4620.0080.0080.0000.0000.0000.000
175A191PHE0-0.049-0.02628.4290.0000.0000.0000.0000.0000.000
176A192MET0-0.005-0.00224.2390.0060.0060.0000.0000.0000.000
177A193SER00.0310.02724.688-0.006-0.0060.0000.0000.0000.000
178A194ALA0-0.005-0.02119.6530.0030.0030.0000.0000.0000.000
179A195GLU-1-0.883-0.93319.7970.1660.1660.0000.0000.0000.000
180A196ASP-1-0.887-0.95220.6420.1340.1340.0000.0000.0000.000
181A197ALA0-0.029-0.02020.8100.0080.0080.0000.0000.0000.000
182A198ALA0-0.005-0.00916.2880.0060.0060.0000.0000.0000.000
183A199LEU00.0680.03217.0820.0310.0310.0000.0000.0000.000
184A200MET0-0.0170.00318.8430.0170.0170.0000.0000.0000.000
185A201ILE0-0.054-0.04615.6140.0000.0000.0000.0000.0000.000
186A202HIS0-0.081-0.06111.681-0.080-0.0800.0000.0000.0000.000
187A203GLY00.0240.01515.3360.0360.0360.0000.0000.0000.000
188A204ALA0-0.048-0.02018.094-0.003-0.0030.0000.0000.0000.000
189A205LEU0-0.058-0.02413.842-0.022-0.0220.0000.0000.0000.000
190A206ALA00.0570.02814.6980.0560.0560.0000.0000.0000.000
191A207ASN0-0.032-0.04112.356-0.121-0.1210.0000.0000.0000.000
192A208ILE00.0310.02514.9460.0520.0520.0000.0000.0000.000
193A209GLY00.0000.00017.759-0.032-0.0320.0000.0000.0000.000
194A210ASN0-0.035-0.02718.276-0.006-0.0060.0000.0000.0000.000
195A211GLY00.0060.01419.346-0.023-0.0230.0000.0000.0000.000
196A212TYR0-0.026-0.01815.8530.0180.0180.0000.0000.0000.000
197A213VAL00.0110.01717.277-0.021-0.0210.0000.0000.0000.000
198A214SER0-0.005-0.02517.3010.0010.0010.0000.0000.0000.000
199A215ASP-1-0.809-0.88319.309-0.018-0.0180.0000.0000.0000.000
200A216ILE0-0.0080.01518.9040.0120.0120.0000.0000.0000.000
201A217THR0-0.016-0.01722.208-0.015-0.0150.0000.0000.0000.000
202A218VAL00.0040.01521.5970.0060.0060.0000.0000.0000.000
203A219ASN00.017-0.01224.696-0.014-0.0140.0000.0000.0000.000
204A220ARG11.0141.02227.741-0.064-0.0640.0000.0000.0000.000