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: 76VKK

Calculation Name: 2GS5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GS5

Chain ID: A

ChEMBL ID:

UniProt ID: Q6NEA9

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2009165.420348
FMO2-HF: Nuclear repulsion 1935264.952837
FMO2-HF: Total energy -73900.467511
FMO2-MP2: Total energy -74113.281115


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-11.672-7.1116.183-5.809-14.936-0.006
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.022
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].
3A3ALA00.0570.0403.049-1.4151.4740.009-1.356-1.541-0.001
4A4ASP-1-0.776-0.8794.9681.3441.514-0.001-0.007-0.1610.000
5A5ARG10.9370.9575.8070.2320.2320.0000.0000.0000.000
6A6LEU0-0.057-0.0132.959-0.295-0.5083.254-0.606-2.4360.001
7A7PHE00.0270.0106.9190.0500.0500.0000.0000.0000.000
8A8ASN0-0.056-0.02810.406-0.169-0.1690.0000.0000.0000.000
9A9ALA0-0.034-0.01412.155-0.140-0.1400.0000.0000.0000.000
10A10MET0-0.052-0.0217.903-0.050-0.0500.0000.0000.0000.000
11A11GLU-1-0.913-0.95311.7970.5910.5910.0000.0000.0000.000
12A12ARG10.8130.89810.2920.0290.0290.0000.0000.0000.000
13A13ASN0-0.070-0.03612.313-0.134-0.1340.0000.0000.0000.000
14A14GLU-1-0.859-0.94114.4610.1680.1680.0000.0000.0000.000
15A15PRO0-0.039-0.01915.7920.0320.0320.0000.0000.0000.000
16A16ALA00.0170.00817.881-0.021-0.0210.0000.0000.0000.000
17A17PRO00.0410.01120.3020.0180.0180.0000.0000.0000.000
18A18GLY0-0.042-0.02321.7160.0170.0170.0000.0000.0000.000
19A19MET0-0.041-0.00315.7540.0500.0500.0000.0000.0000.000
20A20VAL0-0.046-0.02914.120-0.068-0.0680.0000.0000.0000.000
21A21LEU00.0300.02612.2420.1290.1290.0000.0000.0000.000
22A22VAL0-0.027-0.0207.964-0.084-0.0840.0000.0000.0000.000
23A23ALA00.0610.0388.1310.0030.0030.0000.0000.0000.000
24A24ALA00.0400.0163.3860.3510.5500.004-0.053-0.1500.000
25A25PRO0-0.051-0.0361.978-1.201-1.2823.704-1.478-2.1450.004
26A26SER0-0.028-0.0123.891-0.370-0.223-0.001-0.025-0.1220.000
27A27MET0-0.0090.0215.7460.2420.2420.0000.0000.0000.000
28A28GLU-1-0.927-0.9748.116-0.778-0.7780.0000.0000.0000.000
29A29SER0-0.028-0.00911.4840.0930.0930.0000.0000.0000.000
30A30GLU-1-0.905-0.96514.013-0.281-0.2810.0000.0000.0000.000
31A31ASP-1-0.932-0.95616.412-0.219-0.2190.0000.0000.0000.000
32A32PHE0-0.033-0.03212.6210.0610.0610.0000.0000.0000.000
33A33ALA00.0260.04110.7420.0020.0020.0000.0000.0000.000
34A34ARG10.8040.9067.4860.5940.5940.0000.0000.0000.000
35A35SER0-0.003-0.00610.4520.1550.1550.0000.0000.0000.000
36A36VAL0-0.012-0.02411.3850.0760.0760.0000.0000.0000.000
37A37ILE00.0110.01713.7700.0020.0020.0000.0000.0000.000
38A38LEU0-0.0160.00715.9020.0380.0380.0000.0000.0000.000
39A39ILE00.0130.01816.776-0.043-0.0430.0000.0000.0000.000
40A40ILE0-0.068-0.06120.0230.0280.0280.0000.0000.0000.000
41A41GLU-1-0.810-0.88723.3440.0500.0500.0000.0000.0000.000
42A42HIS0-0.032-0.00920.451-0.023-0.0230.0000.0000.0000.000
43A43SER0-0.049-0.03623.9000.0110.0110.0000.0000.0000.000
44A44GLU-1-0.987-1.00025.788-0.026-0.0260.0000.0000.0000.000
45A45TYR0-0.0090.01127.632-0.012-0.0120.0000.0000.0000.000
46A46ALA00.001-0.00524.035-0.018-0.0180.0000.0000.0000.000
47A47THR0-0.023-0.01319.1870.0160.0160.0000.0000.0000.000
48A48PHE00.0080.00421.619-0.027-0.0270.0000.0000.0000.000
49A49GLY00.023-0.00819.5470.0350.0350.0000.0000.0000.000
50A50VAL0-0.040-0.01120.253-0.030-0.0300.0000.0000.0000.000
51A51ASN00.0220.00216.1390.0810.0810.0000.0000.0000.000
52A52LEU0-0.024-0.02417.536-0.003-0.0030.0000.0000.0000.000
53A53ALA0-0.036-0.01815.4460.0090.0090.0000.0000.0000.000
54A54SER00.0170.01717.370-0.016-0.0160.0000.0000.0000.000
55A55ARG10.8300.90519.713-0.016-0.0160.0000.0000.0000.000
56A56SER00.0260.00323.426-0.020-0.0200.0000.0000.0000.000
57A57ASP-1-0.852-0.92226.143-0.013-0.0130.0000.0000.0000.000
58A58VAL0-0.011-0.00229.4860.0020.0020.0000.0000.0000.000
59A59ALA0-0.002-0.00231.2000.0080.0080.0000.0000.0000.000
60A60VAL00.0260.00431.703-0.004-0.0040.0000.0000.0000.000
61A61PHE0-0.017-0.01734.021-0.002-0.0020.0000.0000.0000.000
62A62ASN0-0.034-0.01836.0770.0010.0010.0000.0000.0000.000
63A63VAL0-0.041-0.01533.674-0.006-0.0060.0000.0000.0000.000
64A64ILE00.0190.01933.291-0.001-0.0010.0000.0000.0000.000
65A65PRO0-0.0060.00337.3250.0060.0060.0000.0000.0000.000
66A66GLU-1-0.847-0.93439.3500.0280.0280.0000.0000.0000.000
67A67TRP00.0700.02035.3580.0110.0110.0000.0000.0000.000
68A68VAL0-0.052-0.01935.6960.0080.0080.0000.0000.0000.000
69A69PRO0-0.017-0.02036.0580.0070.0070.0000.0000.0000.000
70A70CYS0-0.041-0.02034.9660.0070.0070.0000.0000.0000.000
71A71VAL0-0.0620.00130.3480.0090.0090.0000.0000.0000.000
72A72THR00.001-0.00528.935-0.003-0.0030.0000.0000.0000.000
73A73LYS10.9260.97329.387-0.083-0.0830.0000.0000.0000.000
74A74PRO0-0.002-0.00126.7430.0120.0120.0000.0000.0000.000
75A75GLN00.015-0.00229.129-0.002-0.0020.0000.0000.0000.000
76A76ALA0-0.021-0.01628.767-0.008-0.0080.0000.0000.0000.000
77A77LEU00.0160.02028.2120.0110.0110.0000.0000.0000.000
78A78TYR00.0120.01121.629-0.007-0.0070.0000.0000.0000.000
79A79ILE0-0.001-0.00121.150-0.001-0.0010.0000.0000.0000.000
80A80GLY00.0120.01020.5560.0010.0010.0000.0000.0000.000
81A81GLY00.0480.02119.7960.0000.0000.0000.0000.0000.000
82A82PRO00.0330.03019.3090.0160.0160.0000.0000.0000.000
83A83LEU0-0.0270.00722.2940.0040.0040.0000.0000.0000.000
84A84ASN00.013-0.01024.7500.0100.0100.0000.0000.0000.000
85A85GLN00.0420.01123.3380.0140.0140.0000.0000.0000.000
86A86GLN0-0.059-0.02227.7440.0030.0030.0000.0000.0000.000
87A87SER0-0.044-0.01429.8450.0050.0050.0000.0000.0000.000
88A88VAL00.001-0.00629.030-0.003-0.0030.0000.0000.0000.000
89A89VAL00.0490.03526.0350.0050.0050.0000.0000.0000.000
90A90GLY00.0380.01528.1500.0020.0020.0000.0000.0000.000
91A91VAL0-0.005-0.00124.6190.0040.0040.0000.0000.0000.000
92A92GLY00.0170.00227.682-0.003-0.0030.0000.0000.0000.000
93A93VAL0-0.048-0.00826.6680.0150.0150.0000.0000.0000.000
94A94THR00.0570.02629.324-0.005-0.0050.0000.0000.0000.000
95A95ALA00.0110.01032.2420.0120.0120.0000.0000.0000.000
96A96GLN00.011-0.02233.5410.0050.0050.0000.0000.0000.000
97A97GLY0-0.023-0.01136.352-0.008-0.0080.0000.0000.0000.000
98A98VAL0-0.034-0.00135.584-0.004-0.0040.0000.0000.0000.000
99A99ASP-1-0.845-0.91435.0420.1300.1300.0000.0000.0000.000
100A100ALA00.035-0.00132.960-0.007-0.0070.0000.0000.0000.000
101A101ALA0-0.041-0.00934.974-0.007-0.0070.0000.0000.0000.000
102A102ARG10.8140.90136.653-0.104-0.1040.0000.0000.0000.000
103A103VAL00.0160.00737.507-0.003-0.0030.0000.0000.0000.000
104A104ASP-1-0.884-0.92737.5320.0630.0630.0000.0000.0000.000
105A105ASN0-0.045-0.03437.332-0.005-0.0050.0000.0000.0000.000
106A106LEU0-0.034-0.01933.4920.0020.0020.0000.0000.0000.000
107A107THR00.0540.03129.8340.0030.0030.0000.0000.0000.000
108A108ARG10.8990.93326.631-0.169-0.1690.0000.0000.0000.000
109A109LEU0-0.0090.01824.1780.0000.0000.0000.0000.0000.000
110A110ALA00.0370.01223.0490.0060.0060.0000.0000.0000.000
111A111ASN0-0.031-0.02022.695-0.011-0.0110.0000.0000.0000.000
112A112ARG10.8740.93526.466-0.192-0.1920.0000.0000.0000.000
113A113LEU0-0.0120.01822.067-0.016-0.0160.0000.0000.0000.000
114A114VAL0-0.005-0.00126.573-0.004-0.0040.0000.0000.0000.000
115A115MET00.0390.02527.041-0.004-0.0040.0000.0000.0000.000
116A116VAL0-0.046-0.02929.3520.0020.0020.0000.0000.0000.000
117A117ASN00.0200.00132.599-0.011-0.0110.0000.0000.0000.000
118A118LEU0-0.012-0.01631.8460.0010.0010.0000.0000.0000.000
119A119GLY0-0.0080.00535.969-0.004-0.0040.0000.0000.0000.000
120A120ALA0-0.043-0.01038.650-0.001-0.0010.0000.0000.0000.000
121A121ASP-1-0.839-0.91840.4060.0410.0410.0000.0000.0000.000
122A122PRO00.013-0.00839.4960.0060.0060.0000.0000.0000.000
123A123GLU-1-0.955-0.99140.3600.0540.0540.0000.0000.0000.000
124A124GLU-1-0.903-0.92640.8990.0640.0640.0000.0000.0000.000
125A125ILE00.011-0.00835.6990.0070.0070.0000.0000.0000.000
126A126LYS10.9040.95136.396-0.084-0.0840.0000.0000.0000.000
127A127PRO0-0.068-0.02238.3870.0080.0080.0000.0000.0000.000
128A128LEU00.0050.00637.4540.0080.0080.0000.0000.0000.000
129A129VAL00.0140.00932.7820.0100.0100.0000.0000.0000.000
130A130SER0-0.049-0.02930.926-0.005-0.0050.0000.0000.0000.000
131A131GLY0-0.050-0.02530.3760.0020.0020.0000.0000.0000.000
132A132MET00.0190.00929.5120.0040.0040.0000.0000.0000.000
133A133ARG10.8140.91523.661-0.133-0.1330.0000.0000.0000.000
134A134LEU00.0370.01627.703-0.001-0.0010.0000.0000.0000.000
135A135PHE00.008-0.00722.1410.0030.0030.0000.0000.0000.000
136A136ALA00.0180.02025.823-0.002-0.0020.0000.0000.0000.000
137A137GLY00.0340.01424.823-0.010-0.0100.0000.0000.0000.000
138A138HIS0-0.065-0.04522.2830.0220.0220.0000.0000.0000.000
139A139ALA0-0.0070.00418.181-0.028-0.0280.0000.0000.0000.000
140A140GLU-1-0.828-0.93820.240-0.047-0.0470.0000.0000.0000.000
141A141TRP0-0.092-0.05014.4320.0190.0190.0000.0000.0000.000
142A142ALA00.0440.01320.2560.0280.0280.0000.0000.0000.000
143A143PRO00.0600.01921.368-0.011-0.0110.0000.0000.0000.000
144A144GLY0-0.018-0.00120.659-0.016-0.0160.0000.0000.0000.000
145A145GLN0-0.084-0.04816.0590.0100.0100.0000.0000.0000.000
146A146LEU00.0410.01414.048-0.047-0.0470.0000.0000.0000.000
147A147ALA00.0050.00114.381-0.017-0.0170.0000.0000.0000.000
148A148GLN0-0.011-0.00814.432-0.037-0.0370.0000.0000.0000.000
149A149GLU-1-0.747-0.84911.557-0.525-0.5250.0000.0000.0000.000
150A150ILE0-0.031-0.0099.989-0.214-0.2140.0000.0000.0000.000
151A151GLU-1-0.943-0.96810.411-0.155-0.1550.0000.0000.0000.000
152A152ASN0-0.134-0.0769.744-0.046-0.0460.0000.0000.0000.000
153A153GLY0-0.012-0.0036.220-0.429-0.4290.0000.0000.0000.000
154A154ASP-1-0.852-0.9255.239-2.309-2.3090.0000.0000.0000.000
155A155TRP0-0.025-0.0457.2710.1570.1570.0000.0000.0000.000
156A156PHE0-0.043-0.0126.2900.1970.1970.0000.0000.0000.000
157A157VAL00.0420.0268.444-0.024-0.0240.0000.0000.0000.000
158A158ALA00.0030.00911.3670.1940.1940.0000.0000.0000.000
159A159PRO00.0140.00813.251-0.130-0.1300.0000.0000.0000.000
160A160ALA00.0310.03116.5070.0570.0570.0000.0000.0000.000
161A161LEU0-0.033-0.03218.344-0.015-0.0150.0000.0000.0000.000
162A162PRO00.014-0.01120.866-0.020-0.0200.0000.0000.0000.000
163A163SER00.0000.01119.968-0.022-0.0220.0000.0000.0000.000
164A164ASP-1-0.744-0.83217.9230.4540.4540.0000.0000.0000.000
165A165VAL00.0140.01420.342-0.029-0.0290.0000.0000.0000.000
166A166THR0-0.073-0.06223.381-0.026-0.0260.0000.0000.0000.000
167A167ALA00.0250.02821.841-0.015-0.0150.0000.0000.0000.000
168A168PRO00.0250.00423.946-0.024-0.0240.0000.0000.0000.000
169A169GLY00.020-0.00123.8320.0090.0090.0000.0000.0000.000
170A170SER0-0.037-0.00323.642-0.017-0.0170.0000.0000.0000.000
171A171VAL0-0.022-0.01019.2410.0040.0040.0000.0000.0000.000
172A172ASP-1-0.764-0.84914.3150.2880.2880.0000.0000.0000.000
173A173VAL00.0290.00115.9570.0830.0830.0000.0000.0000.000
174A174TRP00.0310.0116.0220.1430.1430.0000.0000.0000.000
175A175GLY0-0.022-0.01111.4570.2230.2230.0000.0000.0000.000
176A176ASP-1-0.839-0.92612.3210.6510.6510.0000.0000.0000.000
177A177VAL0-0.022-0.01111.7180.0830.0830.0000.0000.0000.000
178A178MET0-0.0070.0064.6910.1570.238-0.001-0.002-0.0780.000
179A179ARG10.7540.8429.598-0.340-0.3400.0000.0000.0000.000
180A180ARG10.7220.84112.135-0.704-0.7040.0000.0000.0000.000
181A181GLN0-0.047-0.0158.332-0.083-0.0830.0000.0000.0000.000
182A182PRO00.0300.0058.5690.0010.0010.0000.0000.0000.000
183A183MET0-0.0200.0067.3050.8530.8530.0000.0000.0000.000
184A184PRO0-0.007-0.0162.575-1.055-1.0442.374-0.546-1.8380.004
185A185LEU00.0450.0182.928-0.767-0.6632.365-0.457-2.013-0.001
186A186PRO00.0510.0225.417-0.912-0.860-0.001-0.008-0.0430.000
187A187LEU0-0.073-0.0246.110-0.576-0.5760.0000.0000.0000.000
188A188TYR0-0.020-0.0142.598-4.943-3.7404.477-1.271-4.409-0.013
189A189SER0-0.060-0.0156.170-0.310-0.3100.0000.0000.0000.000
190A190THR0-0.025-0.0419.298-0.191-0.1910.0000.0000.0000.000
191A191PHE00.0290.00212.4130.0960.0960.0000.0000.0000.000
192A192PRO00.0130.00816.195-0.052-0.0520.0000.0000.0000.000
193A193VAL0-0.0280.00617.695-0.007-0.0070.0000.0000.0000.000