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: 98VR2

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2009532.840769
FMO2-HF: Nuclear repulsion 1935632.888036
FMO2-HF: Total energy -73899.952734
FMO2-MP2: Total energy -74112.789201


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.
-13.554-9.64613.663-4.364-13.204-0.001
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 : -0.039 / q_NPA : -0.033
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].
3A3ALA00.0480.0342.969-1.903-0.1750.034-0.605-1.1560.001
4A4ASP-1-0.798-0.9054.9281.0911.250-0.001-0.007-0.1500.000
5A5ARG10.9470.9595.2860.3100.3100.0000.0000.0000.000
6A6LEU0-0.089-0.0203.0100.821-0.5214.227-0.424-2.4610.001
7A7PHE0-0.021-0.0226.9090.1990.1990.0000.0000.0000.000
8A8ASN0-0.0240.00010.312-0.217-0.2170.0000.0000.0000.000
9A9ALA0-0.032-0.01411.847-0.100-0.1000.0000.0000.0000.000
10A10MET0-0.047-0.0077.396-0.091-0.0910.0000.0000.0000.000
11A11GLU-1-0.888-0.94811.8440.4310.4310.0000.0000.0000.000
12A12ARG10.8920.9489.8610.1770.1770.0000.0000.0000.000
13A13ASN0-0.049-0.02812.748-0.134-0.1340.0000.0000.0000.000
14A14GLU-1-0.893-0.95814.3390.0630.0630.0000.0000.0000.000
15A15PRO0-0.030-0.01315.0580.0350.0350.0000.0000.0000.000
16A16ALA00.0140.00417.357-0.018-0.0180.0000.0000.0000.000
17A17PRO00.0360.01119.7970.0190.0190.0000.0000.0000.000
18A18GLY0-0.041-0.01821.0960.0200.0200.0000.0000.0000.000
19A19MET0-0.040-0.00415.5280.0620.0620.0000.0000.0000.000
20A20VAL0-0.035-0.02913.236-0.067-0.0670.0000.0000.0000.000
21A21LEU00.0270.02411.5810.1050.1050.0000.0000.0000.000
22A22VAL0-0.034-0.0257.756-0.041-0.0410.0000.0000.0000.000
23A23ALA00.0590.0357.476-0.097-0.0970.0000.0000.0000.000
24A24ALA00.0380.0142.3070.3570.8020.532-0.364-0.613-0.001
25A25PRO0-0.050-0.0382.401-1.850-1.5302.929-1.304-1.9450.009
26A26SER0-0.027-0.0213.697-0.731-0.5320.001-0.045-0.1540.000
27A27MET0-0.0080.0275.3860.2740.288-0.001-0.001-0.0110.000
28A28GLU-1-0.917-0.9737.702-0.605-0.6050.0000.0000.0000.000
29A29SER0-0.064-0.01611.1680.1180.1180.0000.0000.0000.000
30A30GLU-1-0.896-0.96713.724-0.240-0.2400.0000.0000.0000.000
31A31ASP-1-0.910-0.94916.357-0.221-0.2210.0000.0000.0000.000
32A32PHE0-0.055-0.03311.9990.0520.0520.0000.0000.0000.000
33A33ALA00.0290.04210.384-0.001-0.0010.0000.0000.0000.000
34A34ARG10.8190.9087.7210.1410.1410.0000.0000.0000.000
35A35SER00.0090.00110.6990.1180.1180.0000.0000.0000.000
36A36VAL0-0.007-0.01411.1170.0830.0830.0000.0000.0000.000
37A37ILE00.0040.00613.418-0.002-0.0020.0000.0000.0000.000
38A38LEU0-0.0050.00915.4650.0330.0330.0000.0000.0000.000
39A39ILE00.0150.01716.126-0.043-0.0430.0000.0000.0000.000
40A40ILE0-0.053-0.05719.5070.0350.0350.0000.0000.0000.000
41A41GLU-1-0.899-0.95322.6610.0140.0140.0000.0000.0000.000
42A42HIS00.0040.01720.038-0.025-0.0250.0000.0000.0000.000
43A43SER0-0.0080.00123.3060.0130.0130.0000.0000.0000.000
44A44GLU-1-0.974-0.99224.842-0.084-0.0840.0000.0000.0000.000
45A45TYR0-0.0200.00326.808-0.013-0.0130.0000.0000.0000.000
46A46ALA00.0250.00523.290-0.018-0.0180.0000.0000.0000.000
47A47THR0-0.032-0.02018.5110.0160.0160.0000.0000.0000.000
48A48PHE00.0280.01220.862-0.029-0.0290.0000.0000.0000.000
49A49GLY00.015-0.01218.8170.0320.0320.0000.0000.0000.000
50A50VAL0-0.034-0.00319.842-0.025-0.0250.0000.0000.0000.000
51A51ASN00.0390.00315.9110.0870.0870.0000.0000.0000.000
52A52LEU0-0.032-0.02517.1410.0040.0040.0000.0000.0000.000
53A53ALA0-0.031-0.02015.4590.0180.0180.0000.0000.0000.000
54A54SER00.0030.01317.4780.0020.0020.0000.0000.0000.000
55A55ARG10.9140.96619.756-0.062-0.0620.0000.0000.0000.000
56A56SER00.0270.00223.452-0.017-0.0170.0000.0000.0000.000
57A57ASP-1-0.939-0.98026.0460.0120.0120.0000.0000.0000.000
58A58VAL0-0.0160.00129.3610.0000.0000.0000.0000.0000.000
59A59ALA0-0.023-0.01130.9750.0080.0080.0000.0000.0000.000
60A60VAL00.0690.01631.671-0.006-0.0060.0000.0000.0000.000
61A61PHE0-0.030-0.02233.920-0.003-0.0030.0000.0000.0000.000
62A62ASN0-0.027-0.02636.142-0.002-0.0020.0000.0000.0000.000
63A63VAL0-0.0410.00133.309-0.005-0.0050.0000.0000.0000.000
64A64ILE00.0200.01233.320-0.002-0.0020.0000.0000.0000.000
65A65PRO0-0.0010.00237.3770.0070.0070.0000.0000.0000.000
66A66GLU-1-0.872-0.93739.3700.0250.0250.0000.0000.0000.000
67A67TRP00.0700.01835.3660.0100.0100.0000.0000.0000.000
68A68VAL0-0.054-0.01736.0190.0080.0080.0000.0000.0000.000
69A69PRO0-0.020-0.02336.4630.0080.0080.0000.0000.0000.000
70A70CYS0-0.030-0.00535.0240.0070.0070.0000.0000.0000.000
71A71VAL0-0.071-0.00230.7330.0090.0090.0000.0000.0000.000
72A72THR00.0110.00628.435-0.001-0.0010.0000.0000.0000.000
73A73LYS10.9300.97630.170-0.105-0.1050.0000.0000.0000.000
74A74PRO0-0.013-0.01926.9640.0130.0130.0000.0000.0000.000
75A75GLN0-0.009-0.01329.265-0.004-0.0040.0000.0000.0000.000
76A76ALA0-0.025-0.01128.405-0.009-0.0090.0000.0000.0000.000
77A77LEU00.0220.01628.0790.0100.0100.0000.0000.0000.000
78A78TYR00.0070.01021.740-0.001-0.0010.0000.0000.0000.000
79A79ILE00.0080.00421.270-0.005-0.0050.0000.0000.0000.000
80A80GLY00.0010.00020.6650.0050.0050.0000.0000.0000.000
81A81GLY00.0320.01519.475-0.006-0.0060.0000.0000.0000.000
82A82PRO00.0290.02518.8750.0230.0230.0000.0000.0000.000
83A83LEU00.0110.02721.8000.0040.0040.0000.0000.0000.000
84A84ASN0-0.005-0.02524.3980.0100.0100.0000.0000.0000.000
85A85GLN00.0560.01123.1820.0170.0170.0000.0000.0000.000
86A86GLN0-0.047-0.01427.5370.0040.0040.0000.0000.0000.000
87A87SER0-0.054-0.01829.3680.0050.0050.0000.0000.0000.000
88A88VAL00.011-0.00228.686-0.002-0.0020.0000.0000.0000.000
89A89VAL00.0360.03525.8670.0020.0020.0000.0000.0000.000
90A90GLY00.0420.01028.1300.0040.0040.0000.0000.0000.000
91A91VAL00.0030.01424.0820.0010.0010.0000.0000.0000.000
92A92GLY00.001-0.00727.3090.0030.0030.0000.0000.0000.000
93A93VAL0-0.029-0.00726.0770.0150.0150.0000.0000.0000.000
94A94THR00.0400.01128.722-0.004-0.0040.0000.0000.0000.000
95A95ALA00.0020.00531.6130.0140.0140.0000.0000.0000.000
96A96GLN0-0.035-0.04732.7950.0010.0010.0000.0000.0000.000
97A97GLY0-0.008-0.00735.861-0.007-0.0070.0000.0000.0000.000
98A98VAL0-0.0290.00934.980-0.005-0.0050.0000.0000.0000.000
99A99ASP-1-0.897-0.94934.7840.1170.1170.0000.0000.0000.000
100A100ALA00.018-0.01032.513-0.007-0.0070.0000.0000.0000.000
101A101ALA0-0.0090.00834.530-0.007-0.0070.0000.0000.0000.000
102A102ARG10.8750.93436.107-0.083-0.0830.0000.0000.0000.000
103A103VAL0-0.015-0.00536.975-0.002-0.0020.0000.0000.0000.000
104A104ASP-1-0.858-0.91737.2320.0470.0470.0000.0000.0000.000
105A105ASN0-0.066-0.03637.273-0.006-0.0060.0000.0000.0000.000
106A106LEU0-0.055-0.02733.1420.0040.0040.0000.0000.0000.000
107A107THR00.0380.03329.678-0.004-0.0040.0000.0000.0000.000
108A108ARG10.9430.96426.986-0.140-0.1400.0000.0000.0000.000
109A109LEU0-0.0080.02423.724-0.006-0.0060.0000.0000.0000.000
110A110ALA00.024-0.00222.7360.0030.0030.0000.0000.0000.000
111A111ASN0-0.042-0.02522.529-0.007-0.0070.0000.0000.0000.000
112A112ARG10.9100.95326.121-0.191-0.1910.0000.0000.0000.000
113A113LEU0-0.0030.02621.621-0.013-0.0130.0000.0000.0000.000
114A114VAL00.0090.00326.121-0.006-0.0060.0000.0000.0000.000
115A115MET00.0410.02926.9430.0000.0000.0000.0000.0000.000
116A116VAL0-0.026-0.02229.2390.0020.0020.0000.0000.0000.000
117A117ASN00.0280.01732.465-0.010-0.0100.0000.0000.0000.000
118A118LEU0-0.001-0.01831.7440.0020.0020.0000.0000.0000.000
119A119GLY0-0.0010.00735.747-0.003-0.0030.0000.0000.0000.000
120A120ALA0-0.050-0.01538.305-0.001-0.0010.0000.0000.0000.000
121A121ASP-1-0.827-0.91340.0600.0380.0380.0000.0000.0000.000
122A122PRO00.009-0.00839.3870.0060.0060.0000.0000.0000.000
123A123GLU-1-0.971-0.99840.2870.0500.0500.0000.0000.0000.000
124A124GLU-1-0.926-0.95641.2050.0570.0570.0000.0000.0000.000
125A125ILE00.019-0.00335.6280.0060.0060.0000.0000.0000.000
126A126LYS10.9550.98137.473-0.076-0.0760.0000.0000.0000.000
127A127PRO0-0.077-0.03737.6850.0080.0080.0000.0000.0000.000
128A128LEU0-0.021-0.00536.9680.0080.0080.0000.0000.0000.000
129A129VAL00.0200.01132.3990.0090.0090.0000.0000.0000.000
130A130SER0-0.091-0.04730.8840.0010.0010.0000.0000.0000.000
131A131GLY0-0.031-0.02229.6260.0040.0040.0000.0000.0000.000
132A132MET00.0270.00729.190-0.001-0.0010.0000.0000.0000.000
133A133ARG10.8580.95623.306-0.150-0.1500.0000.0000.0000.000
134A134LEU00.0320.01327.754-0.003-0.0030.0000.0000.0000.000
135A135PHE0-0.002-0.01321.9010.0070.0070.0000.0000.0000.000
136A136ALA00.0240.02125.757-0.003-0.0030.0000.0000.0000.000
137A137GLY00.0410.02024.631-0.008-0.0080.0000.0000.0000.000
138A138HIS0-0.069-0.03621.9070.0190.0190.0000.0000.0000.000
139A139ALA00.0050.00517.541-0.024-0.0240.0000.0000.0000.000
140A140GLU-1-0.900-0.95919.634-0.111-0.1110.0000.0000.0000.000
141A141TRP0-0.088-0.04313.7270.0300.0300.0000.0000.0000.000
142A142ALA00.0530.01519.2030.0360.0360.0000.0000.0000.000
143A143PRO00.0690.02220.428-0.020-0.0200.0000.0000.0000.000
144A144GLY0-0.029-0.00920.025-0.016-0.0160.0000.0000.0000.000
145A145GLN0-0.059-0.02815.3210.0100.0100.0000.0000.0000.000
146A146LEU00.0350.01413.170-0.071-0.0710.0000.0000.0000.000
147A147ALA0-0.001-0.00613.544-0.064-0.0640.0000.0000.0000.000
148A148GLN00.0260.01913.778-0.116-0.1160.0000.0000.0000.000
149A149GLU-1-0.760-0.87410.807-0.784-0.7840.0000.0000.0000.000
150A150ILE0-0.050-0.0319.304-0.314-0.3140.0000.0000.0000.000
151A151GLU-1-0.997-0.9929.099-0.621-0.6210.0000.0000.0000.000
152A152ASN0-0.122-0.0578.8150.0490.0490.0000.0000.0000.000
153A153GLY0-0.017-0.0025.464-0.531-0.5310.0000.0000.0000.000
154A154ASP-1-0.865-0.9274.199-4.114-4.065-0.001-0.037-0.0120.000
155A155TRP0-0.045-0.0566.3240.2770.2770.0000.0000.0000.000
156A156PHE0-0.042-0.0125.8830.1760.1760.0000.0000.0000.000
157A157VAL00.0440.0277.9170.0020.0020.0000.0000.0000.000
158A158ALA0-0.004-0.00111.1440.2070.2070.0000.0000.0000.000
159A159PRO00.0160.00812.963-0.125-0.1250.0000.0000.0000.000
160A160ALA00.0200.02816.0260.0670.0670.0000.0000.0000.000
161A161LEU0-0.046-0.03917.925-0.016-0.0160.0000.0000.0000.000
162A162PRO00.0410.00320.343-0.019-0.0190.0000.0000.0000.000
163A163SER0-0.005-0.00720.202-0.019-0.0190.0000.0000.0000.000
164A164ASP-1-0.750-0.85117.3970.4960.4960.0000.0000.0000.000
165A165VAL0-0.0030.00619.737-0.027-0.0270.0000.0000.0000.000
166A166THR0-0.075-0.04622.801-0.022-0.0220.0000.0000.0000.000
167A167ALA00.0330.03221.201-0.011-0.0110.0000.0000.0000.000
168A168PRO00.0190.00123.281-0.027-0.0270.0000.0000.0000.000
169A169GLY00.0240.00223.4830.0110.0110.0000.0000.0000.000
170A170SER0-0.060-0.01923.784-0.008-0.0080.0000.0000.0000.000
171A171VAL0-0.0080.00118.7480.0050.0050.0000.0000.0000.000
172A172ASP-1-0.786-0.85814.6430.3950.3950.0000.0000.0000.000
173A173VAL00.0360.00415.5730.0790.0790.0000.0000.0000.000
174A174TRP00.012-0.0096.5290.1500.1500.0000.0000.0000.000
175A175GLY0-0.016-0.01011.2160.2260.2260.0000.0000.0000.000
176A176ASP-1-0.879-0.95112.3230.6680.6680.0000.0000.0000.000
177A177VAL0-0.027-0.01211.1000.0850.0850.0000.0000.0000.000
178A178MET0-0.0050.0014.3990.0700.182-0.001-0.006-0.1050.000
179A179ARG10.8040.8799.465-0.457-0.4570.0000.0000.0000.000
180A180ARG10.7370.87012.082-0.740-0.7400.0000.0000.0000.000
181A181GLN0-0.047-0.0078.448-0.097-0.0970.0000.0000.0000.000
182A182PRO00.0400.0178.599-0.033-0.0330.0000.0000.0000.000
183A183MET0-0.0150.0127.3630.8180.8180.0000.0000.0000.000
184A184PRO0-0.005-0.0152.451-1.103-0.6341.282-0.331-1.4200.000
185A185LEU00.0610.0153.173-0.0050.4421.119-0.227-1.3390.000
186A186PRO00.0570.0235.402-0.841-0.789-0.001-0.005-0.0450.000
187A187LEU0-0.082-0.0305.891-0.516-0.5160.0000.0000.0000.000
188A188TYR0-0.021-0.0132.609-3.941-2.6853.544-1.008-3.793-0.011
189A189SER0-0.080-0.0226.309-0.293-0.2930.0000.0000.0000.000
190A190THR0-0.003-0.0299.323-0.134-0.1340.0000.0000.0000.000
191A191PHE0-0.011-0.01412.3470.0460.0460.0000.0000.0000.000
192A192PRO00.0400.02016.100-0.038-0.0380.0000.0000.0000.000
193A193VAL0-0.036-0.00217.947-0.014-0.0140.0000.0000.0000.000