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: GYNV1

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1761617.392868
FMO2-HF: Nuclear repulsion 1691864.82747
FMO2-HF: Total energy -69752.565398
FMO2-MP2: Total energy -69955.852662


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.
-41.11-37.77213.26-7.745-8.852-0.011
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 : -0.058 / q_NPA : -0.050
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].
3A15LYS10.9240.9762.141-8.862-5.9663.710-3.064-3.542-0.034
4A16VAL00.0210.0004.5691.4681.590-0.001-0.006-0.1150.000
5A17PHE00.020-0.0037.068-0.185-0.1850.0000.0000.0000.000
6A18ARG10.7700.84710.7661.5251.5250.0000.0000.0000.000
7A19ALA00.0240.02714.279-0.019-0.0190.0000.0000.0000.000
8A20LEU0-0.036-0.00917.3970.0740.0740.0000.0000.0000.000
9A21TYR00.0140.00520.0020.1090.1090.0000.0000.0000.000
10A22THR00.0070.00721.333-0.070-0.0700.0000.0000.0000.000
11A23PHE0-0.049-0.01121.1380.0000.0000.0000.0000.0000.000
12A24GLU-1-0.855-0.91023.239-0.337-0.3370.0000.0000.0000.000
13A25PRO0-0.066-0.00624.031-0.005-0.0050.0000.0000.0000.000
14A26ARG10.8120.85823.7720.4370.4370.0000.0000.0000.000
15A27THR00.001-0.00825.2840.0240.0240.0000.0000.0000.000
16A28PRO0-0.030-0.01625.552-0.024-0.0240.0000.0000.0000.000
17A29ASP-1-0.884-0.93722.034-0.117-0.1170.0000.0000.0000.000
18A30GLU-1-0.788-0.86220.765-0.461-0.4610.0000.0000.0000.000
19A31LEU0-0.041-0.02016.2170.0390.0390.0000.0000.0000.000
20A32TYR0-0.062-0.06420.268-0.027-0.0270.0000.0000.0000.000
21A33ILE0-0.067-0.02316.805-0.019-0.0190.0000.0000.0000.000
22A34GLU-1-0.839-0.91220.353-0.372-0.3720.0000.0000.0000.000
23A35GLU-1-0.967-0.99420.132-0.740-0.7400.0000.0000.0000.000
24A36GLY00.0490.03219.0870.0500.0500.0000.0000.0000.000
25A37ASP-1-0.825-0.88816.880-0.710-0.7100.0000.0000.0000.000
26A38ILE0-0.049-0.02110.846-0.174-0.1740.0000.0000.0000.000
27A39ILE00.0000.01611.7900.2230.2230.0000.0000.0000.000
28A40TYR0-0.058-0.0736.982-0.812-0.8120.0000.0000.0000.000
29A41ILE00.0270.0117.4430.7760.7760.0000.0000.0000.000
30A42THR0-0.029-0.0275.170-1.511-1.5110.0000.0000.0000.000
31A43ASP-1-0.888-0.9284.824-0.618-0.540-0.001-0.007-0.0700.000
32A44MET0-0.035-0.0197.484-0.535-0.5350.0000.0000.0000.000
33A45SER0-0.056-0.0379.9100.0730.0730.0000.0000.0000.000
34A46ASP-1-0.771-0.86911.369-0.397-0.3970.0000.0000.0000.000
35A47THR0-0.059-0.02714.763-0.128-0.1280.0000.0000.0000.000
36A48ASN0-0.050-0.02817.624-0.071-0.0710.0000.0000.0000.000
37A49TRP0-0.028-0.00517.041-0.035-0.0350.0000.0000.0000.000
38A50TRP00.012-0.00611.943-0.124-0.1240.0000.0000.0000.000
39A51LYS10.9730.98711.321-0.352-0.3520.0000.0000.0000.000
40A52GLY00.0120.00711.071-0.153-0.1530.0000.0000.0000.000
41A53THR0-0.021-0.01911.2420.3250.3250.0000.0000.0000.000
42A54SER00.030-0.00312.445-0.287-0.2870.0000.0000.0000.000
43A55LYS10.8050.88514.7760.6730.6730.0000.0000.0000.000
44A56GLY0-0.0090.00415.6540.0890.0890.0000.0000.0000.000
45A57ARG10.9000.95716.6370.2680.2680.0000.0000.0000.000
46A58THR0-0.015-0.03414.183-0.024-0.0240.0000.0000.0000.000
47A59GLY00.0140.01516.2330.0820.0820.0000.0000.0000.000
48A60LEU0-0.032-0.01315.935-0.071-0.0710.0000.0000.0000.000
49A61ILE00.0260.00914.304-0.007-0.0070.0000.0000.0000.000
50A62PRO00.0160.01016.773-0.054-0.0540.0000.0000.0000.000
51A63SER0-0.009-0.01216.105-0.057-0.0570.0000.0000.0000.000
52A64ASN0-0.027-0.02617.039-0.092-0.0920.0000.0000.0000.000
53A65TYR0-0.022-0.01617.193-0.070-0.0700.0000.0000.0000.000
54A66VAL0-0.013-0.01412.700-0.059-0.0590.0000.0000.0000.000
55A67ALA0-0.046-0.01515.534-0.145-0.1450.0000.0000.0000.000
56A68GLU-1-0.888-0.93417.378-0.669-0.6690.0000.0000.0000.000
57A69GLN0-0.082-0.05419.2010.0600.0600.0000.0000.0000.000
58A70ALA00.0060.00814.7240.0210.0210.0000.0000.0000.000
59A71GLU-1-0.809-0.87214.276-1.396-1.3960.0000.0000.0000.000
60A72SER00.007-0.0079.793-0.096-0.0960.0000.0000.0000.000
61A73ILE0-0.037-0.0239.1130.3130.3130.0000.0000.0000.000
62A74ASP-1-0.852-0.9087.397-3.725-3.7250.0000.0000.0000.000
63A75ASN0-0.065-0.0456.504-0.719-0.7190.0000.0000.0000.000
64A76PRO00.0590.0376.3680.8180.8180.0000.0000.0000.000
65A77LEU00.0580.0347.6680.4990.4990.0000.0000.0000.000
66A78HIS0-0.045-0.0329.0610.0860.0860.0000.0000.0000.000
67A79GLU-1-0.798-0.86011.886-1.141-1.1410.0000.0000.0000.000
68A80ALA00.0230.00412.3930.1960.1960.0000.0000.0000.000
69A81ALA00.002-0.00313.5430.1510.1510.0000.0000.0000.000
70A82LYS10.9140.96115.3870.6260.6260.0000.0000.0000.000
71A83ARG10.8340.91616.4270.8860.8860.0000.0000.0000.000
72A84GLY00.0520.04018.6720.0250.0250.0000.0000.0000.000
73A85ASN00.0060.00216.2620.1060.1060.0000.0000.0000.000
74A86LEU00.0360.00415.905-0.049-0.0490.0000.0000.0000.000
75A87SER00.0070.00116.2000.0720.0720.0000.0000.0000.000
76A88TRP0-0.0010.00610.5760.1550.1550.0000.0000.0000.000
77A89LEU0-0.002-0.00411.733-0.139-0.1390.0000.0000.0000.000
78A90ARG10.8950.91511.156-0.031-0.0310.0000.0000.0000.000
79A91GLU-1-0.752-0.84311.441-0.665-0.6650.0000.0000.0000.000
80A92CYS0-0.051-0.0187.448-0.283-0.2830.0000.0000.0000.000
81A93LEU0-0.054-0.0266.7920.0090.0090.0000.0000.0000.000
82A94ASP-1-0.890-0.9428.6480.9800.9800.0000.0000.0000.000
83A95ASN0-0.101-0.0566.9640.4310.4310.0000.0000.0000.000
84A96ARG10.8970.9471.948-30.545-31.5609.457-4.324-4.1180.024
85A97VAL0-0.018-0.0082.6862.4993.4180.094-0.282-0.731-0.001
86A98GLY0-0.008-0.0063.4851.1341.4720.001-0.062-0.2760.000
87A99VAL00.0410.0095.608-1.282-1.2820.0000.0000.0000.000
88A100ASN0-0.023-0.0159.050-0.583-0.5830.0000.0000.0000.000
89A101GLY00.0070.0127.4580.0150.0150.0000.0000.0000.000
90A102LEU0-0.031-0.0278.332-0.198-0.1980.0000.0000.0000.000
91A103ASP-1-0.709-0.8289.895-1.007-1.0070.0000.0000.0000.000
92A104LYS10.9010.92111.0812.2412.2410.0000.0000.0000.000
93A105ALA0-0.066-0.03714.0530.1030.1030.0000.0000.0000.000
94A106GLY00.0470.03614.6710.1010.1010.0000.0000.0000.000
95A107SER00.012-0.01015.3460.1750.1750.0000.0000.0000.000
96A108THR00.0640.03012.469-0.154-0.1540.0000.0000.0000.000
97A109ALA00.0270.00911.068-0.082-0.0820.0000.0000.0000.000
98A110LEU00.0360.01613.068-0.029-0.0290.0000.0000.0000.000
99A111TYR00.0130.00816.150-0.022-0.0220.0000.0000.0000.000
100A112TRP0-0.005-0.03214.8430.0230.0230.0000.0000.0000.000
101A113ALA00.0170.02417.011-0.013-0.0130.0000.0000.0000.000
102A114CYS0-0.051-0.01618.7360.0230.0230.0000.0000.0000.000
103A115HIS0-0.0050.00121.179-0.026-0.0260.0000.0000.0000.000
104A116GLY00.018-0.00421.431-0.004-0.0040.0000.0000.0000.000
105A117GLY0-0.042-0.01522.8060.0070.0070.0000.0000.0000.000
106A118HIS0-0.010-0.00219.9080.0530.0530.0000.0000.0000.000
107A119LYS10.8920.92721.014-0.037-0.0370.0000.0000.0000.000
108A120ASP-1-0.809-0.90520.868-0.085-0.0850.0000.0000.0000.000
109A121ILE0-0.0160.00115.7930.0390.0390.0000.0000.0000.000
110A122VAL0-0.034-0.01517.4020.0610.0610.0000.0000.0000.000
111A123GLU-1-0.861-0.94519.1500.1770.1770.0000.0000.0000.000
112A124MET00.0280.05614.7370.0470.0470.0000.0000.0000.000
113A125LEU00.0050.00612.6230.1180.1180.0000.0000.0000.000
114A126PHE0-0.002-0.01815.6420.1400.1400.0000.0000.0000.000
115A127THR0-0.047-0.02616.5940.0820.0820.0000.0000.0000.000
116A128GLN0-0.025-0.00811.9380.2890.2890.0000.0000.0000.000
117A129PRO00.006-0.00112.285-0.105-0.1050.0000.0000.0000.000
118A130ASN0-0.036-0.03413.4780.1340.1340.0000.0000.0000.000
119A131ILE0-0.0010.03014.0070.0380.0380.0000.0000.0000.000
120A132GLU-1-0.817-0.89614.7300.4800.4800.0000.0000.0000.000
121A133LEU0-0.048-0.03516.590-0.099-0.0990.0000.0000.0000.000
122A134ASN0-0.066-0.06019.546-0.128-0.1280.0000.0000.0000.000
123A135GLN0-0.030-0.01415.7160.0620.0620.0000.0000.0000.000
124A136GLN0-0.046-0.03018.797-0.036-0.0360.0000.0000.0000.000
125A137ASN00.0000.01218.5090.0230.0230.0000.0000.0000.000
126A138LYS10.8970.92818.0310.5360.5360.0000.0000.0000.000
127A139LEU0-0.0070.00720.9120.0040.0040.0000.0000.0000.000
128A140GLY00.0320.01623.0310.0220.0220.0000.0000.0000.000
129A141ASP-1-0.839-0.90023.545-0.071-0.0710.0000.0000.0000.000
130A142THR00.026-0.00521.443-0.001-0.0010.0000.0000.0000.000
131A143ALA00.018-0.01119.394-0.041-0.0410.0000.0000.0000.000
132A144LEU00.0360.02421.398-0.024-0.0240.0000.0000.0000.000
133A145HIS00.0060.02425.055-0.006-0.0060.0000.0000.0000.000
134A146ALA0-0.0050.00522.662-0.018-0.0180.0000.0000.0000.000
135A147ALA00.011-0.00124.643-0.017-0.0170.0000.0000.0000.000
136A148ALA0-0.015-0.01326.046-0.005-0.0050.0000.0000.0000.000
137A149TRP00.0030.00726.148-0.011-0.0110.0000.0000.0000.000
138A150LYS10.8490.95126.1290.1760.1760.0000.0000.0000.000
139A151GLY00.0400.02128.562-0.004-0.0040.0000.0000.0000.000
140A152TYR00.012-0.00527.3720.0030.0030.0000.0000.0000.000
141A153ALA00.0470.00529.1450.0140.0140.0000.0000.0000.000
142A154ASP-1-0.781-0.89429.5120.0330.0330.0000.0000.0000.000
143A155ILE00.0080.01023.8520.0220.0220.0000.0000.0000.000
144A156VAL0-0.025-0.01025.9870.0250.0250.0000.0000.0000.000
145A157GLN00.000-0.00128.1520.0180.0180.0000.0000.0000.000
146A158LEU0-0.031-0.00924.2220.0240.0240.0000.0000.0000.000
147A159LEU00.001-0.01221.4070.0400.0400.0000.0000.0000.000
148A160LEU0-0.028-0.00524.8020.0330.0330.0000.0000.0000.000
149A161ALA0-0.029-0.01527.7220.0200.0200.0000.0000.0000.000
150A162LYS10.8290.93420.035-0.490-0.4900.0000.0000.0000.000
151A163GLY00.0290.01523.8530.0510.0510.0000.0000.0000.000
152A164ALA0-0.068-0.03623.6170.0100.0100.0000.0000.0000.000
153A165ARG10.8360.88024.785-0.259-0.2590.0000.0000.0000.000
154A166THR00.0280.00427.113-0.018-0.0180.0000.0000.0000.000
155A167ASP-1-0.851-0.88829.3900.1580.1580.0000.0000.0000.000
156A168LEU0-0.0050.00824.323-0.010-0.0100.0000.0000.0000.000
157A169ARG10.8130.88128.516-0.045-0.0450.0000.0000.0000.000
158A170ASN0-0.011-0.00727.1550.0130.0130.0000.0000.0000.000
159A171ILE00.0340.00625.2790.0090.0090.0000.0000.0000.000
160A172GLU-1-0.881-0.92229.098-0.106-0.1060.0000.0000.0000.000
161A173LYS10.9050.95131.3750.0370.0370.0000.0000.0000.000
162A174LYS10.8360.92731.4520.1030.1030.0000.0000.0000.000
163A175LEU0-0.015-0.01530.5950.0030.0030.0000.0000.0000.000
164A176ALA00.0440.02128.133-0.015-0.0150.0000.0000.0000.000
165A177PHE00.006-0.00629.964-0.012-0.0120.0000.0000.0000.000
166A178ASP-1-0.813-0.90133.6750.0020.0020.0000.0000.0000.000
167A179MET0-0.054-0.02328.257-0.016-0.0160.0000.0000.0000.000
168A180ALA0-0.034-0.01031.987-0.011-0.0110.0000.0000.0000.000
169A181THR0-0.034-0.01932.1530.0050.0050.0000.0000.0000.000
170A182ASN0-0.034-0.01933.9580.0090.0090.0000.0000.0000.000
171A183ALA00.0520.01336.5700.0080.0080.0000.0000.0000.000
172A184ALA00.0110.02036.1320.0090.0090.0000.0000.0000.000
173A185CYS0-0.0240.01232.3860.0110.0110.0000.0000.0000.000
174A186ALA00.0370.00834.0100.0120.0120.0000.0000.0000.000
175A187SER0-0.044-0.04036.4780.0080.0080.0000.0000.0000.000
176A188LEU0-0.049-0.00932.2040.0090.0090.0000.0000.0000.000
177A189LEU0-0.020-0.00330.0590.0140.0140.0000.0000.0000.000
178A190LYS10.9020.97834.140-0.032-0.0320.0000.0000.0000.000