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: VKRY1

Calculation Name: 3EHR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EHR

Chain ID: A

ChEMBL ID:

UniProt ID: Q92882

Base Structure: X-ray

Registration Date: 2023-09-26

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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1756324.071045
FMO2-HF: Nuclear repulsion 1686572.319313
FMO2-HF: Total energy -69751.751732
FMO2-MP2: Total energy -69955.011314


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:13:GLN)


Summations of interaction energy for fragment #1(A:13:GLN)
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.
-42.101-38.35311.038-7.04-7.744-0.005
Interaction energy analysis for fragmet #1(A:13:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.047
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].
3A15LYS10.9390.9692.109-8.056-5.6043.838-2.854-3.436-0.031
4A16VAL00.0140.0074.7931.8261.946-0.001-0.009-0.1090.000
5A17PHE00.0320.0117.277-0.109-0.1090.0000.0000.0000.000
6A18ARG10.8930.97310.9161.4871.4870.0000.0000.0000.000
7A19ALA00.0240.02314.307-0.029-0.0290.0000.0000.0000.000
8A20LEU0-0.033-0.01617.3610.0810.0810.0000.0000.0000.000
9A21TYR00.003-0.00320.0660.1140.1140.0000.0000.0000.000
10A22THR00.0330.01121.481-0.076-0.0760.0000.0000.0000.000
11A23PHE0-0.112-0.03721.1540.0060.0060.0000.0000.0000.000
12A24GLU-1-0.852-0.92423.090-0.359-0.3590.0000.0000.0000.000
13A25PRO0-0.0490.00723.763-0.006-0.0060.0000.0000.0000.000
14A26ARG10.8010.86122.9930.5250.5250.0000.0000.0000.000
15A27THR0-0.014-0.00524.2850.0440.0440.0000.0000.0000.000
16A28PRO00.005-0.01324.900-0.025-0.0250.0000.0000.0000.000
17A29ASP-1-0.918-0.95621.280-0.177-0.1770.0000.0000.0000.000
18A30GLU-1-0.798-0.87820.129-0.537-0.5370.0000.0000.0000.000
19A31LEU0-0.041-0.01616.1960.0450.0450.0000.0000.0000.000
20A32TYR0-0.072-0.06320.373-0.013-0.0130.0000.0000.0000.000
21A33ILE0-0.039-0.01217.1080.0030.0030.0000.0000.0000.000
22A34GLU-1-0.876-0.93320.329-0.418-0.4180.0000.0000.0000.000
23A35GLU-1-0.974-0.99520.181-0.754-0.7540.0000.0000.0000.000
24A36GLY00.0330.02118.9320.0430.0430.0000.0000.0000.000
25A37ASP-1-0.945-0.96717.364-0.731-0.7310.0000.0000.0000.000
26A38ILE0-0.078-0.04411.179-0.180-0.1800.0000.0000.0000.000
27A39ILE0-0.016-0.00711.6350.1960.1960.0000.0000.0000.000
28A40TYR0-0.066-0.0607.330-0.765-0.7650.0000.0000.0000.000
29A41ILE00.0330.0127.7520.7600.7600.0000.0000.0000.000
30A42THR0-0.025-0.0274.173-1.600-1.476-0.001-0.032-0.0920.000
31A43ASP-1-0.906-0.9414.130-2.486-2.322-0.001-0.054-0.1090.000
32A44MET0-0.042-0.0216.863-0.418-0.4180.0000.0000.0000.000
33A45SER0-0.061-0.0289.1890.1500.1500.0000.0000.0000.000
34A46ASP-1-0.887-0.92811.025-0.434-0.4340.0000.0000.0000.000
35A47THR0-0.034-0.02414.069-0.139-0.1390.0000.0000.0000.000
36A48ASN00.001-0.00216.960-0.097-0.0970.0000.0000.0000.000
37A49TRP0-0.0020.01116.523-0.015-0.0150.0000.0000.0000.000
38A50TRP00.0340.00411.247-0.215-0.2150.0000.0000.0000.000
39A51LYS10.9740.99210.809-0.075-0.0750.0000.0000.0000.000
40A52GLY00.0230.00510.298-0.292-0.2920.0000.0000.0000.000
41A53THR0-0.021-0.01811.7800.3210.3210.0000.0000.0000.000
42A54SER00.0370.01312.773-0.244-0.2440.0000.0000.0000.000
43A55LYS11.0161.00915.3840.6360.6360.0000.0000.0000.000
44A56GLY0-0.017-0.00316.2920.0840.0840.0000.0000.0000.000
45A57ARG10.9280.97017.5490.3010.3010.0000.0000.0000.000
46A58THR0-0.013-0.02413.292-0.034-0.0340.0000.0000.0000.000
47A59GLY00.0280.01315.3240.0950.0950.0000.0000.0000.000
48A60LEU0-0.023-0.00515.118-0.122-0.1220.0000.0000.0000.000
49A61ILE00.0270.00813.8850.0220.0220.0000.0000.0000.000
50A62PRO0-0.0080.00416.171-0.062-0.0620.0000.0000.0000.000
51A63SER00.008-0.00815.466-0.042-0.0420.0000.0000.0000.000
52A64ASN0-0.022-0.02816.426-0.108-0.1080.0000.0000.0000.000
53A65TYR0-0.020-0.00417.200-0.049-0.0490.0000.0000.0000.000
54A66VAL0-0.016-0.00412.618-0.038-0.0380.0000.0000.0000.000
55A67ALA0-0.049-0.02215.617-0.112-0.1120.0000.0000.0000.000
56A68GLU-1-0.915-0.95316.879-0.738-0.7380.0000.0000.0000.000
57A69GLN0-0.032-0.02418.9830.0850.0850.0000.0000.0000.000
58A70ALA00.0110.01814.6580.0230.0230.0000.0000.0000.000
59A71GLU-1-0.877-0.92214.322-1.357-1.3570.0000.0000.0000.000
60A72SER0-0.008-0.0179.405-0.086-0.0860.0000.0000.0000.000
61A73ILE0-0.050-0.0259.0950.3600.3600.0000.0000.0000.000
62A74ASP-1-0.868-0.9367.367-3.949-3.9490.0000.0000.0000.000
63A75ASN0-0.062-0.0446.754-0.643-0.6430.0000.0000.0000.000
64A76PRO00.0670.0366.5310.7080.7080.0000.0000.0000.000
65A77LEU00.0570.0278.0840.4420.4420.0000.0000.0000.000
66A78HIS0-0.048-0.0368.8250.0570.0570.0000.0000.0000.000
67A79GLU-1-0.882-0.94811.935-1.333-1.3330.0000.0000.0000.000
68A80ALA0-0.0070.00312.8530.1760.1760.0000.0000.0000.000
69A81ALA00.011-0.00413.9180.1350.1350.0000.0000.0000.000
70A82LYS10.9160.96715.7860.6240.6240.0000.0000.0000.000
71A83ARG10.8890.94117.3600.8380.8380.0000.0000.0000.000
72A84GLY00.0420.04018.8010.0290.0290.0000.0000.0000.000
73A85ASN0-0.028-0.01316.8980.0860.0860.0000.0000.0000.000
74A86LEU00.0670.01316.591-0.044-0.0440.0000.0000.0000.000
75A87SER0-0.039-0.01916.8210.0230.0230.0000.0000.0000.000
76A88TRP00.0320.01111.2920.1700.1700.0000.0000.0000.000
77A89LEU00.0210.00412.495-0.101-0.1010.0000.0000.0000.000
78A90ARG10.8900.91111.982-0.019-0.0190.0000.0000.0000.000
79A91GLU-1-0.781-0.85612.174-0.732-0.7320.0000.0000.0000.000
80A92CYS0-0.036-0.0128.208-0.173-0.1730.0000.0000.0000.000
81A93LEU0-0.053-0.0307.8630.1140.1140.0000.0000.0000.000
82A94ASP-1-0.907-0.9459.4590.9050.9050.0000.0000.0000.000
83A95ASN0-0.122-0.0617.8150.3870.3870.0000.0000.0000.000
84A96ARG10.9120.9632.139-29.412-29.0497.202-4.015-3.5490.026
85A97VAL0-0.0090.0053.4611.5191.8850.002-0.068-0.3000.000
86A98GLY0-0.010-0.0063.9701.1251.284-0.001-0.008-0.1490.000
87A99VAL00.0320.0036.015-0.956-0.9560.0000.0000.0000.000
88A100ASN0-0.017-0.0129.226-0.546-0.5460.0000.0000.0000.000
89A101GLY0-0.0080.0127.2350.0800.0800.0000.0000.0000.000
90A102LEU0-0.034-0.0268.078-0.277-0.2770.0000.0000.0000.000
91A103ASP-1-0.772-0.8819.873-0.881-0.8810.0000.0000.0000.000
92A104LYS10.9140.93311.1362.0302.0300.0000.0000.0000.000
93A105ALA0-0.076-0.03214.1840.1060.1060.0000.0000.0000.000
94A106GLY00.0550.02914.8670.0910.0910.0000.0000.0000.000
95A107SER00.0140.01415.0370.1660.1660.0000.0000.0000.000
96A108THR00.0870.04512.429-0.131-0.1310.0000.0000.0000.000
97A109ALA00.0680.01711.361-0.099-0.0990.0000.0000.0000.000
98A110LEU00.0370.01613.261-0.032-0.0320.0000.0000.0000.000
99A111TYR00.002-0.00316.314-0.010-0.0100.0000.0000.0000.000
100A112TRP00.003-0.01014.8330.0060.0060.0000.0000.0000.000
101A113ALA00.0140.02217.334-0.014-0.0140.0000.0000.0000.000
102A114CYS0-0.055-0.01618.9510.0190.0190.0000.0000.0000.000
103A115HIS0-0.020-0.01121.114-0.018-0.0180.0000.0000.0000.000
104A116GLY00.011-0.00121.738-0.006-0.0060.0000.0000.0000.000
105A117GLY0-0.068-0.02923.2660.0020.0020.0000.0000.0000.000
106A118HIS00.0220.01820.4500.0380.0380.0000.0000.0000.000
107A119LYS10.8950.93421.627-0.044-0.0440.0000.0000.0000.000
108A120ASP-1-0.817-0.90322.140-0.086-0.0860.0000.0000.0000.000
109A121ILE0-0.034-0.01516.3300.0390.0390.0000.0000.0000.000
110A122VAL0-0.026-0.01318.0710.0600.0600.0000.0000.0000.000
111A123GLU-1-0.886-0.94919.5590.1860.1860.0000.0000.0000.000
112A124MET00.0370.05315.7970.0410.0410.0000.0000.0000.000
113A125LEU00.0070.01213.1670.1020.1020.0000.0000.0000.000
114A126PHE00.002-0.01616.1170.1340.1340.0000.0000.0000.000
115A127THR0-0.069-0.04617.3270.0610.0610.0000.0000.0000.000
116A128GLN0-0.037-0.01812.4800.2570.2570.0000.0000.0000.000
117A129PRO0-0.002-0.00813.064-0.075-0.0750.0000.0000.0000.000
118A130ASN0-0.034-0.02314.088-0.008-0.0080.0000.0000.0000.000
119A131ILE00.0050.02614.1520.0720.0720.0000.0000.0000.000
120A132GLU-1-0.872-0.94314.7800.6100.6100.0000.0000.0000.000
121A133LEU0-0.066-0.03516.539-0.099-0.0990.0000.0000.0000.000
122A134ASN0-0.038-0.02319.479-0.123-0.1230.0000.0000.0000.000
123A135GLN00.0080.00215.5770.0800.0800.0000.0000.0000.000
124A136GLN0-0.069-0.03618.497-0.036-0.0360.0000.0000.0000.000
125A137ASN0-0.0060.00718.5120.0350.0350.0000.0000.0000.000
126A138LYS10.9450.96319.0230.3780.3780.0000.0000.0000.000
127A139LEU0-0.016-0.00621.2130.0080.0080.0000.0000.0000.000
128A140GLY00.0350.02022.9000.0140.0140.0000.0000.0000.000
129A141ASP-1-0.858-0.90822.958-0.033-0.0330.0000.0000.0000.000
130A142THR00.047-0.00521.2150.0080.0080.0000.0000.0000.000
131A143ALA00.017-0.02119.464-0.043-0.0430.0000.0000.0000.000
132A144LEU00.0360.01821.390-0.029-0.0290.0000.0000.0000.000
133A145HIS0-0.0070.01824.905-0.008-0.0080.0000.0000.0000.000
134A146ALA00.0150.01522.856-0.019-0.0190.0000.0000.0000.000
135A147ALA00.0130.00524.745-0.017-0.0170.0000.0000.0000.000
136A148ALA0-0.013-0.01126.171-0.007-0.0070.0000.0000.0000.000
137A149TRP0-0.0010.00626.282-0.011-0.0110.0000.0000.0000.000
138A150LYS10.8850.96526.4180.1360.1360.0000.0000.0000.000
139A151GLY00.0210.01228.721-0.006-0.0060.0000.0000.0000.000
140A152TYR0-0.023-0.00827.554-0.001-0.0010.0000.0000.0000.000
141A153ALA00.0580.00629.5320.0120.0120.0000.0000.0000.000
142A154ASP-1-0.788-0.90430.0610.0420.0420.0000.0000.0000.000
143A155ILE00.0170.00924.2700.0210.0210.0000.0000.0000.000
144A156VAL0-0.0110.00026.2360.0250.0250.0000.0000.0000.000
145A157GLN00.002-0.00228.1860.0170.0170.0000.0000.0000.000
146A158LEU0-0.030-0.01024.6550.0240.0240.0000.0000.0000.000
147A159LEU00.012-0.00521.3800.0400.0400.0000.0000.0000.000
148A160LEU0-0.018-0.00624.8950.0340.0340.0000.0000.0000.000
149A161ALA0-0.025-0.00727.9220.0210.0210.0000.0000.0000.000
150A162LYS10.8600.95620.508-0.498-0.4980.0000.0000.0000.000
151A163GLY00.0330.01224.0250.0520.0520.0000.0000.0000.000
152A164ALA0-0.071-0.03024.0330.0110.0110.0000.0000.0000.000
153A165ARG10.8310.88824.979-0.307-0.3070.0000.0000.0000.000
154A166THR00.016-0.00427.050-0.016-0.0160.0000.0000.0000.000
155A167ASP-1-0.841-0.89229.1190.2000.2000.0000.0000.0000.000
156A168LEU0-0.0090.00524.254-0.001-0.0010.0000.0000.0000.000
157A169ARG10.8820.91728.304-0.084-0.0840.0000.0000.0000.000
158A170ASN00.0070.01126.9310.0170.0170.0000.0000.0000.000
159A171ILE00.028-0.00325.9700.0050.0050.0000.0000.0000.000
160A172GLU-1-0.964-0.97829.168-0.080-0.0800.0000.0000.0000.000
161A173LYS10.8760.93331.4560.0000.0000.0000.0000.0000.000
162A174LYS10.9370.99431.4290.0590.0590.0000.0000.0000.000
163A175LEU0-0.015-0.00330.3520.0070.0070.0000.0000.0000.000
164A176ALA00.0510.01828.075-0.015-0.0150.0000.0000.0000.000
165A177PHE00.001-0.01429.811-0.015-0.0150.0000.0000.0000.000
166A178ASP-1-0.837-0.92133.3940.0240.0240.0000.0000.0000.000
167A179MET0-0.067-0.02328.403-0.014-0.0140.0000.0000.0000.000
168A180ALA0-0.034-0.00632.013-0.011-0.0110.0000.0000.0000.000
169A181THR0-0.0070.00132.5280.0020.0020.0000.0000.0000.000
170A182ASN0-0.039-0.03034.1690.0070.0070.0000.0000.0000.000
171A183ALA00.0540.00536.7290.0080.0080.0000.0000.0000.000
172A184ALA0-0.0030.01536.1720.0090.0090.0000.0000.0000.000
173A185CYS0-0.0080.00732.4230.0120.0120.0000.0000.0000.000
174A186ALA00.0270.01134.1830.0120.0120.0000.0000.0000.000
175A187SER0-0.059-0.03636.5530.0120.0120.0000.0000.0000.000
176A188LEU0-0.026-0.00732.4490.0080.0080.0000.0000.0000.000
177A189LEU0-0.0160.00130.1390.0140.0140.0000.0000.0000.000
178A190LYS10.8870.97534.250-0.040-0.0400.0000.0000.0000.000