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: VQ961

Calculation Name: 1ES9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ES9

Chain ID: A

ChEMBL ID:

UniProt ID: Q29460

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2594782.860166
FMO2-HF: Nuclear repulsion 2511769.894968
FMO2-HF: Total energy -83012.965198
FMO2-MP2: Total energy -83258.560574


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:5:GLU)


Summations of interaction energy for fragment #1(A:5:GLU)
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.
-165.374-168.26228.463-13.903-11.6720.159
Interaction energy analysis for fragmet #1(A:5:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.793 / q_NPA : -0.896
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].
3A7PRO0-0.0080.0003.6263.4015.3210.018-0.785-1.1540.002
4A8ALA0-0.036-0.0105.115-1.586-1.459-0.001-0.004-0.1210.000
5A9SER00.006-0.0105.531-4.141-4.1410.0000.0000.0000.000
6A10LYS10.8480.9411.772-142.555-147.49428.447-13.093-10.4150.157
7A11PRO0-0.0110.0124.637-3.870-3.866-0.001-0.0210.0180.000
8A12THR0-0.036-0.0357.4793.0183.0180.0000.0000.0000.000
9A13PRO00.0220.0179.693-1.907-1.9070.0000.0000.0000.000
10A14VAL0-0.017-0.00912.8811.5381.5380.0000.0000.0000.000
11A15GLN0-0.025-0.00814.8820.2940.2940.0000.0000.0000.000
12A16ASP-1-0.766-0.88416.45813.47813.4780.0000.0000.0000.000
13A17VAL0-0.030-0.02118.7980.2110.2110.0000.0000.0000.000
14A18GLN0-0.056-0.02821.578-0.464-0.4640.0000.0000.0000.000
15A19GLY00.0190.01724.650-0.486-0.4860.0000.0000.0000.000
16A20ASP-1-0.801-0.88525.58212.03512.0350.0000.0000.0000.000
17A21GLY00.0160.01023.128-0.162-0.1620.0000.0000.0000.000
18A22LYS10.7880.87223.828-12.532-12.5320.0000.0000.0000.000
19A23TRP0-0.020-0.02115.5720.1140.1140.0000.0000.0000.000
20A24MET00.0220.01316.8480.2140.2140.0000.0000.0000.000
21A25SER0-0.016-0.00921.166-0.309-0.3090.0000.0000.0000.000
22A26LEU0-0.046-0.01423.207-0.395-0.3950.0000.0000.0000.000
23A27HIS10.8030.90118.844-16.700-16.7000.0000.0000.0000.000
24A28HIS00.0470.00120.464-0.059-0.0590.0000.0000.0000.000
25A29ARG10.8570.92623.842-11.506-11.5060.0000.0000.0000.000
26A30PHE0-0.0070.00422.175-0.486-0.4860.0000.0000.0000.000
27A31VAL00.0160.01621.463-0.146-0.1460.0000.0000.0000.000
28A32ALA0-0.0080.00024.336-0.307-0.3070.0000.0000.0000.000
29A33ASP-1-0.859-0.94027.68610.39310.3930.0000.0000.0000.000
30A34SER0-0.044-0.05224.299-0.366-0.3660.0000.0000.0000.000
31A35LYS10.8020.88427.226-10.458-10.4580.0000.0000.0000.000
32A36ASP-1-0.852-0.89628.8599.6959.6950.0000.0000.0000.000
33A37LYS10.8120.90831.370-10.135-10.1350.0000.0000.0000.000
34A38GLU-1-0.784-0.89831.17710.46510.4650.0000.0000.0000.000
35A39PRO0-0.0540.00428.657-0.271-0.2710.0000.0000.0000.000
36A40GLU-1-0.756-0.85630.9659.2149.2140.0000.0000.0000.000
37A41VAL0-0.042-0.02928.6860.2420.2420.0000.0000.0000.000
38A42VAL00.0130.01324.162-0.109-0.1090.0000.0000.0000.000
39A43PHE00.0140.00525.0850.3380.3380.0000.0000.0000.000
40A44ILE00.0110.00118.950-0.004-0.0040.0000.0000.0000.000
41A45GLY00.052-0.00519.5290.1090.1090.0000.0000.0000.000
42A46ASP-1-0.812-0.91019.33214.60314.6030.0000.0000.0000.000
43A47SER00.017-0.00221.079-0.664-0.6640.0000.0000.0000.000
44A48LEU0-0.024-0.00423.921-0.589-0.5890.0000.0000.0000.000
45A49VAL00.0240.03623.202-0.514-0.5140.0000.0000.0000.000
46A50GLN00.0360.02825.182-0.262-0.2620.0000.0000.0000.000
47A51LEU0-0.011-0.00926.886-0.413-0.4130.0000.0000.0000.000
48A52MET0-0.0090.02028.281-0.465-0.4650.0000.0000.0000.000
49A53HIS00.0120.00230.533-0.271-0.2710.0000.0000.0000.000
50A54GLN0-0.083-0.04032.286-0.408-0.4080.0000.0000.0000.000
51A55CYS0-0.046-0.01533.291-0.389-0.3890.0000.0000.0000.000
52A56GLU-1-0.723-0.83533.8238.3758.3750.0000.0000.0000.000
53A57ILE0-0.049-0.01935.5910.0210.0210.0000.0000.0000.000
54A58TRP00.0570.00729.630-0.048-0.0480.0000.0000.0000.000
55A59ARG10.7950.86835.818-7.490-7.4900.0000.0000.0000.000
56A60GLU-1-0.737-0.84739.0827.4127.4120.0000.0000.0000.000
57A61LEU0-0.066-0.01235.810-0.099-0.0990.0000.0000.0000.000
58A62PHE00.035-0.01832.8060.0190.0190.0000.0000.0000.000
59A63SER0-0.017-0.00734.9250.1360.1360.0000.0000.0000.000
60A64PRO0-0.019-0.01036.845-0.008-0.0080.0000.0000.0000.000
61A65LEU0-0.057-0.01634.536-0.070-0.0700.0000.0000.0000.000
62A66HIS00.0140.00634.3380.3420.3420.0000.0000.0000.000
63A67ALA00.0110.01530.8080.2700.2700.0000.0000.0000.000
64A68LEU00.0120.01428.171-0.161-0.1610.0000.0000.0000.000
65A69ASN0-0.069-0.05527.1150.5640.5640.0000.0000.0000.000
66A70PHE00.0230.01422.604-0.154-0.1540.0000.0000.0000.000
67A71GLY00.0310.01122.3050.8250.8250.0000.0000.0000.000
68A72ILE0-0.027-0.01919.910-0.501-0.5010.0000.0000.0000.000
69A73GLY0-0.015-0.02221.2670.5040.5040.0000.0000.0000.000
70A74GLY0-0.0030.00020.0580.0060.0060.0000.0000.0000.000
71A75ASP-1-0.769-0.85916.75818.80918.8090.0000.0000.0000.000
72A76SER0-0.019-0.01312.641-0.726-0.7260.0000.0000.0000.000
73A77THR0-0.033-0.04010.253-0.249-0.2490.0000.0000.0000.000
74A78GLN00.0750.0328.326-1.436-1.4360.0000.0000.0000.000
75A79HIS00.0310.02410.194-0.073-0.0730.0000.0000.0000.000
76A80VAL00.0500.01813.319-0.553-0.5530.0000.0000.0000.000
77A81LEU0-0.036-0.0098.787-0.730-0.7300.0000.0000.0000.000
78A82TRP00.0690.03210.423-1.843-1.8430.0000.0000.0000.000
79A83ARG10.7160.84112.382-17.596-17.5960.0000.0000.0000.000
80A84LEU0-0.021-0.01215.659-1.183-1.1830.0000.0000.0000.000
81A85GLU-1-0.852-0.93610.49128.36628.3660.0000.0000.0000.000
82A86ASN0-0.105-0.04912.706-1.232-1.2320.0000.0000.0000.000
83A87GLY00.0480.00316.599-0.793-0.7930.0000.0000.0000.000
84A88GLU-1-0.750-0.86019.40415.12215.1220.0000.0000.0000.000
85A89LEU00.0020.01018.440-0.700-0.7000.0000.0000.0000.000
86A90GLU-1-0.798-0.86620.99914.07914.0790.0000.0000.0000.000
87A91HIS0-0.037-0.01723.617-0.503-0.5030.0000.0000.0000.000
88A92ILE0-0.0110.02424.528-0.370-0.3700.0000.0000.0000.000
89A93ARG10.8930.95527.114-10.121-10.1210.0000.0000.0000.000
90A94PRO00.0120.03726.246-0.315-0.3150.0000.0000.0000.000
91A95LYS10.8150.86928.414-8.923-8.9230.0000.0000.0000.000
92A96ILE0-0.060-0.02427.2640.0820.0820.0000.0000.0000.000
93A97VAL00.0380.02821.378-0.023-0.0230.0000.0000.0000.000
94A98VAL0-0.034-0.01824.378-0.093-0.0930.0000.0000.0000.000
95A99VAL00.0220.01217.8160.2680.2680.0000.0000.0000.000
96A100TRP0-0.049-0.04020.703-0.464-0.4640.0000.0000.0000.000
97A101VAL00.0530.02415.905-0.047-0.0470.0000.0000.0000.000
98A102GLY00.0400.00615.2280.1940.1940.0000.0000.0000.000
99A103THR00.0080.01616.3000.2410.2410.0000.0000.0000.000
100A104ASN0-0.028-0.02717.203-0.763-0.7630.0000.0000.0000.000
101A105ASN00.0260.02911.119-0.897-0.8970.0000.0000.0000.000
102A106HIS0-0.013-0.02414.315-0.305-0.3050.0000.0000.0000.000
103A107GLY00.0450.02412.8930.6550.6550.0000.0000.0000.000
104A108HIS00.0070.0238.9900.0840.0840.0000.0000.0000.000
105A109THR00.0540.02311.134-1.364-1.3640.0000.0000.0000.000
106A110ALA00.0630.02112.7880.6700.6700.0000.0000.0000.000
107A111GLU-1-0.777-0.88311.92817.49617.4960.0000.0000.0000.000
108A112GLN00.0130.0176.660-0.693-0.6930.0000.0000.0000.000
109A113VAL00.0240.0179.7181.2071.2070.0000.0000.0000.000
110A114THR00.023-0.00112.139-0.404-0.4040.0000.0000.0000.000
111A115GLY0-0.026-0.0109.269-0.460-0.4600.0000.0000.0000.000
112A116GLY0-0.004-0.0029.5380.9430.9430.0000.0000.0000.000
113A117ILE00.010-0.00810.314-0.405-0.4050.0000.0000.0000.000
114A118LYS10.9330.95912.458-19.644-19.6440.0000.0000.0000.000
115A119ALA00.0030.0149.555-0.589-0.5890.0000.0000.0000.000
116A120ILE00.0050.00711.657-0.653-0.6530.0000.0000.0000.000
117A121VAL0-0.021-0.01514.429-0.928-0.9280.0000.0000.0000.000
118A122GLN0-0.035-0.02313.950-1.502-1.5020.0000.0000.0000.000
119A123LEU00.0410.02113.485-0.701-0.7010.0000.0000.0000.000
120A124VAL0-0.020-0.01415.735-0.933-0.9330.0000.0000.0000.000
121A125ASN0-0.063-0.04318.676-1.304-1.3040.0000.0000.0000.000
122A126GLU-1-0.885-0.92215.44519.22319.2230.0000.0000.0000.000
123A127ARG10.7970.86318.643-14.593-14.5930.0000.0000.0000.000
124A128GLN0-0.052-0.03220.442-1.102-1.1020.0000.0000.0000.000
125A129PRO00.0740.05323.188-0.342-0.3420.0000.0000.0000.000
126A130GLN0-0.094-0.06724.564-0.297-0.2970.0000.0000.0000.000
127A131ALA0-0.0040.01324.683-0.371-0.3710.0000.0000.0000.000
128A132ARG10.8560.92725.490-9.790-9.7900.0000.0000.0000.000
129A133VAL00.0220.00920.0860.1450.1450.0000.0000.0000.000
130A134VAL0-0.0020.00523.526-0.049-0.0490.0000.0000.0000.000
131A135VAL0-0.012-0.00819.3730.4990.4990.0000.0000.0000.000
132A136LEU00.0010.00322.414-0.407-0.4070.0000.0000.0000.000
133A137GLY00.003-0.00721.9920.6530.6530.0000.0000.0000.000
134A138LEU0-0.078-0.03317.772-0.175-0.1750.0000.0000.0000.000
135A139LEU00.0320.02622.397-0.300-0.3000.0000.0000.0000.000
136A140PRO0-0.0040.01524.6630.5590.5590.0000.0000.0000.000
137A141ARG10.9280.94820.520-13.817-13.8170.0000.0000.0000.000
138A142GLY00.0030.00527.2630.0120.0120.0000.0000.0000.000
139A143GLN00.0280.01729.341-0.123-0.1230.0000.0000.0000.000
140A144HIS00.0450.02432.186-0.175-0.1750.0000.0000.0000.000
141A145PRO00.0320.00630.3950.4080.4080.0000.0000.0000.000
142A146ASN0-0.040-0.03626.0000.4340.4340.0000.0000.0000.000
143A147PRO00.0570.00922.3480.1270.1270.0000.0000.0000.000
144A148LEU0-0.0080.00420.5680.5940.5940.0000.0000.0000.000
145A149ARG10.7760.90722.525-9.667-9.6670.0000.0000.0000.000
146A150GLU-1-0.843-0.91323.51911.35011.3500.0000.0000.0000.000
147A151LYS10.8350.92314.293-18.498-18.4980.0000.0000.0000.000
148A152ASN0-0.030-0.03619.5591.0561.0560.0000.0000.0000.000
149A153ARG10.8410.90021.235-11.803-11.8030.0000.0000.0000.000
150A154ARG10.8230.90717.543-14.490-14.4900.0000.0000.0000.000
151A155VAL0-0.013-0.01916.1450.4160.4160.0000.0000.0000.000
152A156ASN00.0170.00918.4530.6480.6480.0000.0000.0000.000
153A157GLU-1-0.855-0.91020.95412.42212.4220.0000.0000.0000.000
154A158LEU0-0.019-0.00215.453-0.137-0.1370.0000.0000.0000.000
155A159VAL0-0.002-0.00116.7860.3250.3250.0000.0000.0000.000
156A160ARG10.8540.92518.729-11.813-11.8130.0000.0000.0000.000
157A161ALA0-0.017-0.01120.165-0.301-0.3010.0000.0000.0000.000
158A162ALA0-0.044-0.02217.134-0.066-0.0660.0000.0000.0000.000
159A163LEU00.003-0.01318.8620.0160.0160.0000.0000.0000.000
160A164ALA0-0.0030.01321.566-0.406-0.4060.0000.0000.0000.000
161A165GLY0-0.0180.00422.655-0.459-0.4590.0000.0000.0000.000
162A166HIS0-0.042-0.03018.3170.6640.6640.0000.0000.0000.000
163A167PRO00.0210.00723.629-0.123-0.1230.0000.0000.0000.000
164A168ARG10.7960.89225.147-12.324-12.3240.0000.0000.0000.000
165A169ALA00.0370.03022.0080.1830.1830.0000.0000.0000.000
166A170HIS0-0.036-0.02524.062-0.533-0.5330.0000.0000.0000.000
167A171PHE00.0490.03021.1820.0940.0940.0000.0000.0000.000
168A172LEU00.0000.00324.784-0.530-0.5300.0000.0000.0000.000
169A173ASP-1-0.775-0.87726.36811.75411.7540.0000.0000.0000.000
170A174ALA0-0.020-0.00927.786-0.363-0.3630.0000.0000.0000.000
171A175ASP-1-0.797-0.90329.2589.7369.7360.0000.0000.0000.000
172A176PRO0-0.034-0.01131.076-0.137-0.1370.0000.0000.0000.000
173A177GLY0-0.004-0.00333.744-0.265-0.2650.0000.0000.0000.000
174A178PHE0-0.047-0.04830.684-0.147-0.1470.0000.0000.0000.000
175A179VAL0-0.053-0.02130.654-0.024-0.0240.0000.0000.0000.000
176A180HIS00.0280.01433.743-0.178-0.1780.0000.0000.0000.000
177A181SER00.0290.00236.9620.1000.1000.0000.0000.0000.000
178A182ASP-1-0.849-0.89239.1797.8507.8500.0000.0000.0000.000
179A183GLY0-0.0110.00235.0920.0800.0800.0000.0000.0000.000
180A184THR0-0.030-0.04334.3460.3620.3620.0000.0000.0000.000
181A185ILE0-0.022-0.01030.4200.1360.1360.0000.0000.0000.000
182A186SER0-0.008-0.01634.874-0.087-0.0870.0000.0000.0000.000
183A187HIS00.0290.00335.9560.2890.2890.0000.0000.0000.000
184A188HIS00.0040.00837.0890.1070.1070.0000.0000.0000.000
185A189ASP-1-0.859-0.87535.0368.3628.3620.0000.0000.0000.000
186A190MET0-0.022-0.01929.1850.3080.3080.0000.0000.0000.000
187A191TYR00.0290.02631.008-0.011-0.0110.0000.0000.0000.000
188A192ASP-1-0.788-0.86729.72710.59110.5910.0000.0000.0000.000
189A193TYR0-0.031-0.01830.2450.2500.2500.0000.0000.0000.000
190A194LEU0-0.0030.00023.6040.3960.3960.0000.0000.0000.000
191A195HIS10.8210.87825.830-11.293-11.2930.0000.0000.0000.000
192A196LEU00.0020.01929.167-0.296-0.2960.0000.0000.0000.000
193A197SER0-0.011-0.03531.6830.0300.0300.0000.0000.0000.000
194A198ARG10.8710.88835.039-8.124-8.1240.0000.0000.0000.000
195A199LEU0-0.0300.00737.377-0.049-0.0490.0000.0000.0000.000
196A200GLY00.0930.03334.408-0.014-0.0140.0000.0000.0000.000
197A201TYR0-0.017-0.05628.5150.1350.1350.0000.0000.0000.000
198A202THR0-0.021-0.00334.003-0.052-0.0520.0000.0000.0000.000
199A203PRO0-0.036-0.01535.144-0.067-0.0670.0000.0000.0000.000
200A204VAL00.0280.02329.7820.0540.0540.0000.0000.0000.000
201A205CYS0-0.026-0.00732.1930.2850.2850.0000.0000.0000.000
202A206ARG10.9880.99333.468-7.855-7.8550.0000.0000.0000.000
203A207ALA00.0010.01132.919-0.089-0.0890.0000.0000.0000.000
204A208LEU00.0140.00328.3720.0400.0400.0000.0000.0000.000
205A209HIS0-0.027-0.00731.7550.0120.0120.0000.0000.0000.000
206A210SER00.0090.00934.719-0.076-0.0760.0000.0000.0000.000
207A211LEU0-0.035-0.01428.764-0.069-0.0690.0000.0000.0000.000
208A212LEU00.015-0.01329.3410.0550.0550.0000.0000.0000.000
209A213LEU00.0300.01433.005-0.064-0.0640.0000.0000.0000.000
210A214ARG10.8800.96732.052-9.406-9.4060.0000.0000.0000.000
211A215LEU0-0.085-0.04729.8800.1310.1310.0000.0000.0000.000
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