FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: VQGY1

Calculation Name: 2GZ4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GZ4

Chain ID: A

ChEMBL ID:

UniProt ID: Q7D028

Base Structure: X-ray

Registration Date: 2023-09-23

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2246789.824079
FMO2-HF: Nuclear repulsion 2168413.511523
FMO2-HF: Total energy -78376.312556
FMO2-MP2: Total energy -78603.085118


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:6:SER)


Summations of interaction energy for fragment #1(A:6:SER)
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.
0.9292.274-0.007-0.598-0.740.002
Interaction energy analysis for fragmet #1(A:6:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.010
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].
3A8ARG10.9110.9423.766-0.1441.201-0.007-0.598-0.7400.002
4A9ALA00.0540.0266.2640.6330.6330.0000.0000.0000.000
5A10TRP00.0250.0047.7670.2550.2550.0000.0000.0000.000
6A11GLN0-0.016-0.00810.603-0.264-0.2640.0000.0000.0000.000
7A12ARG10.8680.92311.9390.8410.8410.0000.0000.0000.000
8A13MET0-0.0020.01714.2100.0100.0100.0000.0000.0000.000
9A14LEU00.013-0.00917.976-0.017-0.0170.0000.0000.0000.000
10A15SER0-0.051-0.05220.1780.0000.0000.0000.0000.0000.000
11A16GLY00.0160.01918.2770.0250.0250.0000.0000.0000.000
12A17ARG10.8960.95717.4100.2580.2580.0000.0000.0000.000
13A18ARG10.9170.94312.0720.5530.5530.0000.0000.0000.000
14A19LEU00.0500.05015.4310.0520.0520.0000.0000.0000.000
15A20ASP-1-0.884-0.95712.038-0.654-0.6540.0000.0000.0000.000
16A21LEU0-0.011-0.01010.8490.0550.0550.0000.0000.0000.000
17A22LEU0-0.019-0.01111.7860.0810.0810.0000.0000.0000.000
18A23ASP-1-0.889-0.91414.806-0.075-0.0750.0000.0000.0000.000
19A24PRO0-0.0160.01616.676-0.011-0.0110.0000.0000.0000.000
20A25SER00.018-0.01618.2030.0530.0530.0000.0000.0000.000
21A26PRO00.040-0.00420.518-0.020-0.0200.0000.0000.0000.000
22A27LEU0-0.018-0.00722.907-0.002-0.0020.0000.0000.0000.000
23A28ASP-1-0.911-0.92218.813-0.330-0.3300.0000.0000.0000.000
24A29VAL0-0.074-0.03021.085-0.031-0.0310.0000.0000.0000.000
25A30GLU-1-0.815-0.90223.323-0.185-0.1850.0000.0000.0000.000
26A31ILE00.0330.02525.340-0.018-0.0180.0000.0000.0000.000
27A32ALA00.0130.01226.699-0.003-0.0030.0000.0000.0000.000
28A33ASP-1-0.774-0.85421.780-0.351-0.3510.0000.0000.0000.000
29A34ILE00.0060.00223.652-0.013-0.0130.0000.0000.0000.000
30A35ALA00.0180.01325.2090.0010.0010.0000.0000.0000.000
31A36HIS0-0.008-0.00323.3530.0180.0180.0000.0000.0000.000
32A37GLY00.0240.02123.146-0.001-0.0010.0000.0000.0000.000
33A38LEU00.0340.00523.9250.0060.0060.0000.0000.0000.000
34A39ALA0-0.0180.00526.7840.0150.0150.0000.0000.0000.000
35A40ARG10.8060.88024.9850.2580.2580.0000.0000.0000.000
36A41VAL0-0.0260.01522.8850.0000.0000.0000.0000.0000.000
37A42ALA00.0160.01225.5720.0170.0170.0000.0000.0000.000
38A43ARG10.8890.93527.4800.1160.1160.0000.0000.0000.000
39A44TRP0-0.051-0.04830.1620.0050.0050.0000.0000.0000.000
40A45ASN0-0.025-0.01827.401-0.001-0.0010.0000.0000.0000.000
41A46GLY00.0230.01828.5550.0000.0000.0000.0000.0000.000
42A47GLN0-0.048-0.00230.2210.0020.0020.0000.0000.0000.000
43A48THR0-0.016-0.03033.3030.0040.0040.0000.0000.0000.000
44A49ARG10.8150.89935.6990.0650.0650.0000.0000.0000.000
45A50GLY00.0390.00338.237-0.001-0.0010.0000.0000.0000.000
46A51ASP-1-0.935-0.95436.538-0.103-0.1030.0000.0000.0000.000
47A52HIS0-0.048-0.01933.688-0.016-0.0160.0000.0000.0000.000
48A53ALA00.0360.00930.1800.0060.0060.0000.0000.0000.000
49A54PHE00.0370.02032.090-0.002-0.0020.0000.0000.0000.000
50A55THR00.0020.00029.899-0.003-0.0030.0000.0000.0000.000
51A56VAL00.0430.01127.0310.0120.0120.0000.0000.0000.000
52A57ALA0-0.0020.01030.0310.0090.0090.0000.0000.0000.000
53A58GLN00.0330.00331.4750.0030.0030.0000.0000.0000.000
54A59HIS10.7910.89932.3140.1240.1240.0000.0000.0000.000
55A60CYS0-0.049-0.02131.4480.0060.0060.0000.0000.0000.000
56A61LEU00.0090.01334.3040.0070.0070.0000.0000.0000.000
57A62ILE0-0.0110.01037.2850.0080.0080.0000.0000.0000.000
58A63VAL0-0.002-0.00635.9220.0070.0070.0000.0000.0000.000
59A64GLU-1-0.773-0.85237.637-0.083-0.0830.0000.0000.0000.000
60A65THR00.0210.00839.4260.0060.0060.0000.0000.0000.000
61A66ILE0-0.028-0.01841.4040.0060.0060.0000.0000.0000.000
62A67PHE0-0.004-0.01840.5010.0050.0050.0000.0000.0000.000
63A68CYS0-0.010-0.00442.6260.0050.0050.0000.0000.0000.000
64A69ARG10.9090.96445.0770.0610.0610.0000.0000.0000.000
65A70MET0-0.062-0.04044.8660.0030.0030.0000.0000.0000.000
66A71CYS0-0.079-0.02444.6140.0040.0040.0000.0000.0000.000
67A72PRO00.0490.02346.967-0.002-0.0020.0000.0000.0000.000
68A73GLY0-0.032-0.01049.2020.0000.0000.0000.0000.0000.000
69A74ALA0-0.039-0.00243.6080.0000.0000.0000.0000.0000.000
70A75THR0-0.053-0.06843.080-0.001-0.0010.0000.0000.0000.000
71A76PRO00.031-0.00642.285-0.002-0.0020.0000.0000.0000.000
72A77ASP-1-0.760-0.86938.509-0.088-0.0880.0000.0000.0000.000
73A78GLU-1-0.787-0.85537.794-0.066-0.0660.0000.0000.0000.000
74A79MET0-0.028-0.00238.554-0.004-0.0040.0000.0000.0000.000
75A80GLN0-0.007-0.01634.370-0.007-0.0070.0000.0000.0000.000
76A81MET0-0.025-0.01633.868-0.006-0.0060.0000.0000.0000.000
77A82ALA0-0.032-0.01534.006-0.004-0.0040.0000.0000.0000.000
78A83LEU0-0.035-0.00433.783-0.004-0.0040.0000.0000.0000.000
79A84LEU0-0.020-0.02029.839-0.012-0.0120.0000.0000.0000.000
80A85HIS0-0.0100.01129.715-0.002-0.0020.0000.0000.0000.000
81A86ASP-1-0.851-0.94028.482-0.137-0.1370.0000.0000.0000.000
82A87ALA00.0280.01026.756-0.018-0.0180.0000.0000.0000.000
83A88PRO00.020-0.00123.163-0.029-0.0290.0000.0000.0000.000
84A89GLH0-0.053-0.06321.963-0.027-0.0270.0000.0000.0000.000
85A90TYR0-0.048-0.01921.231-0.024-0.0240.0000.0000.0000.000
86A91VAL0-0.032-0.01216.418-0.047-0.0470.0000.0000.0000.000
87A92ILE0-0.051-0.01517.494-0.044-0.0440.0000.0000.0000.000
88A93GLY00.0020.01019.5000.0070.0070.0000.0000.0000.000
89A94ASP-1-0.864-0.90621.481-0.138-0.1380.0000.0000.0000.000
90A95MET0-0.028-0.01023.5040.0030.0030.0000.0000.0000.000
91A96ILE00.0430.02625.4770.0090.0090.0000.0000.0000.000
92A97SER00.031-0.01228.5250.0010.0010.0000.0000.0000.000
93A98PRO00.0130.00730.5490.0040.0040.0000.0000.0000.000
94A99PHE00.0540.02425.8110.0090.0090.0000.0000.0000.000
95A100LYS10.8980.93825.3520.1340.1340.0000.0000.0000.000
96A101SER0-0.049-0.02727.3490.0010.0010.0000.0000.0000.000
97A102VAL0-0.0100.00225.1990.0100.0100.0000.0000.0000.000
98A103VAL0-0.0260.01421.3040.0100.0100.0000.0000.0000.000
99A104GLY00.0520.03521.6380.0020.0020.0000.0000.0000.000
100A105GLY00.003-0.02223.069-0.017-0.0170.0000.0000.0000.000
101A106GLY00.0340.02219.349-0.007-0.0070.0000.0000.0000.000
102A107TYR00.0560.02919.443-0.014-0.0140.0000.0000.0000.000
103A108LYS10.9070.94420.7150.0450.0450.0000.0000.0000.000
104A109THR0-0.052-0.03221.114-0.001-0.0010.0000.0000.0000.000
105A110VAL00.0370.02217.018-0.002-0.0020.0000.0000.0000.000
106A111GLU-1-0.797-0.89720.029-0.145-0.1450.0000.0000.0000.000
107A112LYS10.9350.97023.0060.0690.0690.0000.0000.0000.000
108A113ARG10.8090.86918.1810.1410.1410.0000.0000.0000.000
109A114LEU00.0330.01618.707-0.005-0.0050.0000.0000.0000.000
110A115GLU-1-0.833-0.89322.419-0.104-0.1040.0000.0000.0000.000
111A116ALA0-0.0040.00725.1310.0030.0030.0000.0000.0000.000
112A117ALA00.0020.00322.2540.0040.0040.0000.0000.0000.000
113A118VAL00.020-0.00524.2620.0000.0000.0000.0000.0000.000
114A119HIS0-0.057-0.04426.2770.0040.0040.0000.0000.0000.000
115A120LEU00.006-0.00426.6460.0070.0070.0000.0000.0000.000
116A121ARG10.7890.89926.1750.1850.1850.0000.0000.0000.000
117A122PHE0-0.008-0.01228.2050.0010.0010.0000.0000.0000.000
118A123GLY00.0340.02831.5670.0080.0080.0000.0000.0000.000
119A124LEU0-0.053-0.01232.3570.0080.0080.0000.0000.0000.000
120A125PRO00.007-0.01232.699-0.001-0.0010.0000.0000.0000.000
121A126PRO00.0330.02229.429-0.005-0.0050.0000.0000.0000.000
122A127HIS0-0.082-0.05727.146-0.003-0.0030.0000.0000.0000.000
123A128ALA00.0670.04131.8730.0060.0060.0000.0000.0000.000
124A129SER00.0300.01835.0060.0030.0030.0000.0000.0000.000
125A130ARG10.9820.97037.0610.0340.0340.0000.0000.0000.000
126A131GLU-1-0.835-0.89438.523-0.051-0.0510.0000.0000.0000.000
127A132LEU00.0660.04937.3110.0000.0000.0000.0000.0000.000
128A133LYS10.8540.91630.6940.0910.0910.0000.0000.0000.000
129A134ASP-1-0.863-0.90737.005-0.049-0.0490.0000.0000.0000.000
130A135ARG10.7810.84239.8400.0560.0560.0000.0000.0000.000
131A136ILE00.0230.01735.192-0.001-0.0010.0000.0000.0000.000
132A137LYS10.8660.93134.0390.0760.0760.0000.0000.0000.000
133A138LYS10.8230.89137.6400.0460.0460.0000.0000.0000.000
134A139ALA00.0450.02739.7390.0010.0010.0000.0000.0000.000
135A140ASP-1-0.843-0.92034.732-0.096-0.0960.0000.0000.0000.000
136A141THR0-0.061-0.04137.654-0.001-0.0010.0000.0000.0000.000
137A142VAL00.0160.00639.3590.0020.0020.0000.0000.0000.000
138A143ALA00.0300.01638.1540.0010.0010.0000.0000.0000.000
139A144ALA0-0.022-0.01136.868-0.001-0.0010.0000.0000.0000.000
140A145PHE00.0170.00838.3950.0020.0020.0000.0000.0000.000
141A146PHE00.0460.00641.9100.0020.0020.0000.0000.0000.000
142A147GLU-1-0.714-0.81735.576-0.105-0.1050.0000.0000.0000.000
143A148ALA0-0.0030.00138.6390.0000.0000.0000.0000.0000.000
144A149THR0-0.024-0.02039.5780.0020.0020.0000.0000.0000.000
145A150GLU-1-0.886-0.93942.216-0.064-0.0640.0000.0000.0000.000
146A151LEU0-0.055-0.01637.2900.0000.0000.0000.0000.0000.000
147A152ALA0-0.0020.00136.168-0.001-0.0010.0000.0000.0000.000
148A153GLY0-0.034-0.00237.8680.0020.0020.0000.0000.0000.000
149A154PHE0-0.039-0.00136.2670.0040.0040.0000.0000.0000.000
150A155SER0-0.006-0.04541.8570.0000.0000.0000.0000.0000.000
151A156THR00.047-0.00244.989-0.001-0.0010.0000.0000.0000.000
152A157ALA00.0000.00847.1450.0000.0000.0000.0000.0000.000
153A158GLU-1-0.809-0.86941.960-0.043-0.0430.0000.0000.0000.000
154A159ALA00.0250.01642.2800.0000.0000.0000.0000.0000.000
155A160GLN0-0.027-0.01943.352-0.001-0.0010.0000.0000.0000.000
156A161LYS10.9030.95543.8980.0260.0260.0000.0000.0000.000
157A162PHE0-0.043-0.02239.1720.0020.0020.0000.0000.0000.000
158A163PHE0-0.031-0.02236.925-0.002-0.0020.0000.0000.0000.000
159A164GLY00.0140.02841.7750.0000.0000.0000.0000.0000.000
160A165LEU0-0.029-0.02045.410-0.002-0.0020.0000.0000.0000.000
161A166PRO00.0090.01545.4120.0010.0010.0000.0000.0000.000
162A167ARG10.9660.97547.8660.0390.0390.0000.0000.0000.000
163A168GLY0-0.022-0.01950.398-0.001-0.0010.0000.0000.0000.000
164A169ILE0-0.0090.00445.769-0.001-0.0010.0000.0000.0000.000
165A170THR0-0.024-0.05349.2340.0020.0020.0000.0000.0000.000
166A171ARG10.9400.96545.9180.0690.0690.0000.0000.0000.000
167A172ASP-1-0.884-0.91247.212-0.059-0.0590.0000.0000.0000.000
168A173MET0-0.082-0.01947.257-0.001-0.0010.0000.0000.0000.000
169A174PHE00.0070.00142.616-0.003-0.0030.0000.0000.0000.000
170A175ASP-1-0.884-0.93241.836-0.083-0.0830.0000.0000.0000.000
171A176ILE0-0.036-0.02939.485-0.006-0.0060.0000.0000.0000.000
172A177ILE00.004-0.00339.642-0.003-0.0030.0000.0000.0000.000
173A178PRO0-0.0040.01035.505-0.002-0.0020.0000.0000.0000.000
174A179LEU0-0.0110.00236.3770.0010.0010.0000.0000.0000.000
175A180PRO00.0340.01634.165-0.008-0.0080.0000.0000.0000.000
176A181SER00.015-0.00929.517-0.001-0.0010.0000.0000.0000.000
177A182THR0-0.022-0.02231.574-0.003-0.0030.0000.0000.0000.000
178A183GLU-1-0.740-0.82833.066-0.120-0.1200.0000.0000.0000.000
179A184ALA00.0050.00632.6520.0030.0030.0000.0000.0000.000
180A185GLN00.0370.01428.0070.0000.0000.0000.0000.0000.000
181A186ARG10.8080.87232.1590.1200.1200.0000.0000.0000.000
182A187LEU00.0000.00135.2770.0040.0040.0000.0000.0000.000
183A188PHE00.0190.00430.0350.0030.0030.0000.0000.0000.000
184A189ILE0-0.015-0.01330.6890.0000.0000.0000.0000.0000.000
185A190ALA00.0450.03334.1760.0050.0050.0000.0000.0000.000
186A191ARG10.8070.87437.3450.0990.0990.0000.0000.0000.000
187A192PHE00.0520.01432.5400.0040.0040.0000.0000.0000.000
188A193GLU-1-0.883-0.95435.713-0.129-0.1290.0000.0000.0000.000
189A194ALA0-0.029-0.01137.7650.0070.0070.0000.0000.0000.000
190A195ILE0-0.031-0.02437.8520.0070.0070.0000.0000.0000.000
191A196GLU-1-0.796-0.87735.746-0.109-0.1090.0000.0000.0000.000
192A197THR0-0.023-0.00838.9620.0050.0050.0000.0000.0000.000
193A198LEU0-0.038-0.01842.4240.0060.0060.0000.0000.0000.000
194A199ARG10.7800.85135.2800.1050.1050.0000.0000.0000.000
195A200VAL00.0020.02140.9900.0040.0040.0000.0000.0000.000
196A201THR0-0.058-0.03343.3430.0050.0050.0000.0000.0000.000
197A202ARG10.8930.94644.8020.0610.0610.0000.0000.0000.000
198A203THR0-0.043-0.02342.5670.0030.0030.0000.0000.0000.000
199A204GLY0-0.0080.01745.2550.0040.0040.0000.0000.0000.000
200A205GLY0-0.026-0.01746.066-0.003-0.0030.0000.0000.0000.000