Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: YNV72

Calculation Name: 2GAU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GAU

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MAW7

Base Structure: X-ray

Registration Date: 2023-09-27

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2676185.620546
FMO2-HF: Nuclear repulsion 2587940.909312
FMO2-HF: Total energy -88244.711234
FMO2-MP2: Total energy -88503.275542


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:10:LEU)


Summations of interaction energy for fragment #1(A:10:LEU)
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.
-17.358-9.1227.313-4.97-10.578-0.017
Interaction energy analysis for fragmet #1(A:10:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.011
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].
3A12HIS00.0260.0013.237-1.6821.0020.105-1.196-1.593-0.001
4A13LEU0-0.071-0.0322.5210.1971.3231.350-0.528-1.9480.000
5A14LEU0-0.029-0.0025.0680.8240.8240.0000.0000.0000.000
6A15ARG10.8740.9127.7870.3870.3870.0000.0000.0000.000
7A16ASP-1-0.874-0.92110.133-0.425-0.4250.0000.0000.0000.000
8A17VAL00.0540.01710.4980.0470.0470.0000.0000.0000.000
9A18TRP00.0530.0465.391-0.007-0.0070.0000.0000.0000.000
10A19SER0-0.093-0.0569.8850.1090.1090.0000.0000.0000.000
11A20LEU0-0.061-0.02913.0610.1130.1130.0000.0000.0000.000
12A21LEU0-0.0510.0039.5080.0500.0500.0000.0000.0000.000
13A22ASN00.0220.01312.986-0.044-0.0440.0000.0000.0000.000
14A23GLU-1-0.894-0.97510.950-0.989-0.9890.0000.0000.0000.000
15A24GLU-1-0.890-0.93711.456-0.658-0.6580.0000.0000.0000.000
16A25GLU-1-0.840-0.93012.133-0.834-0.8340.0000.0000.0000.000
17A26ARG10.8690.9307.8920.8910.8910.0000.0000.0000.000
18A27GLU-1-0.902-0.9387.077-1.399-1.3990.0000.0000.0000.000
19A28LEU0-0.0240.0007.991-0.150-0.1500.0000.0000.0000.000
20A29LEU0-0.042-0.0295.934-0.076-0.0760.0000.0000.0000.000
21A30ASP-1-0.868-0.9622.937-11.082-8.5300.393-1.682-1.263-0.015
22A31LYS10.8690.9524.2800.5860.745-0.001-0.023-0.1340.000
23A32GLU-1-0.921-0.9707.081-0.506-0.5060.0000.0000.0000.000
24A33ILE0-0.106-0.0342.326-0.7650.1511.366-0.550-1.732-0.006
25A34GLN00.0330.0124.003-0.1720.1920.002-0.092-0.2740.000
26A35PRO0-0.031-0.0152.169-0.258-0.4672.620-0.511-1.9000.005
27A36PHE00.0220.0124.263-0.455-0.3630.002-0.023-0.0710.000
28A37PRO0-0.0060.0047.8670.0280.0280.0000.0000.0000.000
29A38CYS0-0.0040.00510.163-0.130-0.1300.0000.0000.0000.000
30A39LYS10.9991.01112.450-0.257-0.2570.0000.0000.0000.000
31A40LYS10.9450.97115.577-0.186-0.1860.0000.0000.0000.000
32A41ALA0-0.065-0.04218.4350.0020.0020.0000.0000.0000.000
33A42SER0-0.033-0.00515.975-0.014-0.0140.0000.0000.0000.000
34A43THR0-0.027-0.03318.097-0.008-0.0080.0000.0000.0000.000
35A44VAL00.0020.00012.9860.0130.0130.0000.0000.0000.000
36A45PHE00.0020.00315.540-0.023-0.0230.0000.0000.0000.000
37A46SER0-0.039-0.02718.3180.0180.0180.0000.0000.0000.000
38A47GLU-1-0.909-0.97322.099-0.048-0.0480.0000.0000.0000.000
39A48GLY00.002-0.00924.9770.0080.0080.0000.0000.0000.000
40A49ASP-1-0.829-0.91220.619-0.046-0.0460.0000.0000.0000.000
41A50ILE00.0270.00421.749-0.010-0.0100.0000.0000.0000.000
42A51PRO0-0.044-0.02618.7060.0020.0020.0000.0000.0000.000
43A52ASN00.0690.04315.680-0.022-0.0220.0000.0000.0000.000
44A53ASN0-0.036-0.02011.559-0.102-0.1020.0000.0000.0000.000
45A54LEU00.0000.01212.6070.0660.0660.0000.0000.0000.000
46A55PHE00.0100.00010.482-0.057-0.0570.0000.0000.0000.000
47A56TYR00.0290.0227.156-0.032-0.0320.0000.0000.0000.000
48A57LEU0-0.042-0.0218.8200.1270.1270.0000.0000.0000.000
49A58TYR00.0310.0206.653-0.020-0.0200.0000.0000.0000.000
50A59GLU-1-0.834-0.9198.8570.6520.6520.0000.0000.0000.000
51A60GLY00.0300.01911.0550.0220.0220.0000.0000.0000.000
52A61LYS10.8650.93314.324-0.191-0.1910.0000.0000.0000.000
53A62ILE00.0310.03713.6550.0230.0230.0000.0000.0000.000
54A63LYS10.8570.93217.509-0.079-0.0790.0000.0000.0000.000
55A64ILE0-0.0050.00118.4290.0000.0000.0000.0000.0000.000
56A65LEU0-0.049-0.03922.1360.0000.0000.0000.0000.0000.000
57A66ARG11.0451.02325.2530.0580.0580.0000.0000.0000.000
58A67GLU-1-0.844-0.88527.978-0.014-0.0140.0000.0000.0000.000
59A68GLY0-0.015-0.01230.7820.0040.0040.0000.0000.0000.000
60A69VAL00.0140.00833.1560.0000.0000.0000.0000.0000.000
61A70TYR0-0.039-0.02435.7440.0010.0010.0000.0000.0000.000
62A71GLY00.0120.00936.8710.0020.0020.0000.0000.0000.000
63A72ARG10.8280.91635.3180.0110.0110.0000.0000.0000.000
64A73PHE00.0810.04828.747-0.001-0.0010.0000.0000.0000.000
65A74HIS0-0.042-0.03129.367-0.005-0.0050.0000.0000.0000.000
66A75ILE00.0060.00325.055-0.001-0.0010.0000.0000.0000.000
67A76SER0-0.048-0.03024.958-0.006-0.0060.0000.0000.0000.000
68A77ARG10.9330.96718.1460.1400.1400.0000.0000.0000.000
69A78ILE0-0.018-0.01220.3650.0110.0110.0000.0000.0000.000
70A79VAL0-0.034-0.00715.507-0.009-0.0090.0000.0000.0000.000
71A80LYS10.9610.98417.2280.1200.1200.0000.0000.0000.000
72A81PRO00.001-0.01612.714-0.042-0.0420.0000.0000.0000.000
73A82GLY00.0290.01411.758-0.010-0.0100.0000.0000.0000.000
74A83GLN0-0.034-0.00812.730-0.038-0.0380.0000.0000.0000.000
75A84PHE00.0910.03910.4080.0370.0370.0000.0000.0000.000
76A85PHE0-0.068-0.06412.3230.0570.0570.0000.0000.0000.000
77A86GLY00.0540.01514.862-0.023-0.0230.0000.0000.0000.000
78A87MET0-0.0210.01516.080-0.015-0.0150.0000.0000.0000.000
79A88ARG10.8610.92617.7130.1130.1130.0000.0000.0000.000
80A89PRO0-0.0010.01320.0570.0020.0020.0000.0000.0000.000
81A90TYR00.0770.04118.555-0.008-0.0080.0000.0000.0000.000
82A91PHE0-0.012-0.02617.897-0.003-0.0030.0000.0000.0000.000
83A92ALA0-0.053-0.02022.4490.0060.0060.0000.0000.0000.000
84A93GLU-1-0.934-0.94424.274-0.182-0.1820.0000.0000.0000.000
85A94GLU-1-0.974-0.98124.864-0.107-0.1070.0000.0000.0000.000
86A95THR0-0.003-0.00924.333-0.013-0.0130.0000.0000.0000.000
87A96CYS0-0.049-0.02220.411-0.010-0.0100.0000.0000.0000.000
88A97SER00.0490.01723.4420.0090.0090.0000.0000.0000.000
89A98SER0-0.084-0.05523.1300.0040.0040.0000.0000.0000.000
90A99THR00.0970.04521.638-0.008-0.0080.0000.0000.0000.000
91A100ALA0-0.049-0.00717.347-0.001-0.0010.0000.0000.0000.000
92A101ILE00.0230.00818.4340.0140.0140.0000.0000.0000.000
93A102ALA00.0350.03215.650-0.013-0.0130.0000.0000.0000.000
94A103VAL0-0.041-0.02517.4730.0000.0000.0000.0000.0000.000
95A104GLU-1-0.895-0.96916.3810.2040.2040.0000.0000.0000.000
96A105ASN0-0.011-0.00814.299-0.037-0.0370.0000.0000.0000.000
97A106SER00.004-0.00512.201-0.023-0.0230.0000.0000.0000.000
98A107LYS10.8420.9276.677-0.872-0.8720.0000.0000.0000.000
99A108VAL00.004-0.0047.898-0.123-0.1230.0000.0000.0000.000
100A109LEU00.0200.0132.386-0.5180.0341.476-0.365-1.6630.000
101A110ALA00.002-0.0055.911-0.136-0.1360.0000.0000.0000.000
102A111ILE00.007-0.0057.156-0.247-0.2470.0000.0000.0000.000
103A112PRO00.1040.0688.9870.1450.1450.0000.0000.0000.000
104A113VAL00.011-0.00712.227-0.083-0.0830.0000.0000.0000.000
105A114GLU-1-0.865-0.92815.337-0.398-0.3980.0000.0000.0000.000
106A115ALA00.0190.01311.150-0.010-0.0100.0000.0000.0000.000
107A116ILE0-0.051-0.02911.586-0.045-0.0450.0000.0000.0000.000
108A117GLU-1-0.892-0.96214.075-0.325-0.3250.0000.0000.0000.000
109A118ALA0-0.015-0.00815.2860.0340.0340.0000.0000.0000.000
110A119LEU00.0020.00310.7960.0240.0240.0000.0000.0000.000
111A120LEU0-0.072-0.04415.4590.0470.0470.0000.0000.0000.000
112A121LYS10.8700.93918.4670.3810.3810.0000.0000.0000.000
113A122GLY00.0240.03719.0270.0420.0420.0000.0000.0000.000
114A123ASN00.0110.01016.2220.0740.0740.0000.0000.0000.000
115A124THR00.0450.00119.455-0.009-0.0090.0000.0000.0000.000
116A125SER0-0.008-0.00918.7990.0410.0410.0000.0000.0000.000
117A126PHE00.0350.02812.4630.0030.0030.0000.0000.0000.000
118A127CYS0-0.0020.00317.4880.0240.0240.0000.0000.0000.000
119A128ARG10.9190.94020.3900.3120.3120.0000.0000.0000.000
120A129TYR0-0.0110.01314.3130.0290.0290.0000.0000.0000.000
121A130PHE00.0520.00413.4050.0550.0550.0000.0000.0000.000
122A131LEU00.0230.02519.1290.0410.0410.0000.0000.0000.000
123A132LYS10.9480.98021.4670.2530.2530.0000.0000.0000.000
124A133ALA0-0.029-0.01318.4980.0310.0310.0000.0000.0000.000
125A134LEU00.0420.00520.5540.0310.0310.0000.0000.0000.000
126A135ALA00.0310.03022.8390.0240.0240.0000.0000.0000.000
127A136LYS10.8730.93022.9110.1670.1670.0000.0000.0000.000
128A137GLU-1-0.923-0.96421.336-0.117-0.1170.0000.0000.0000.000
129A138LEU00.0240.02724.4100.0160.0160.0000.0000.0000.000
130A139GLY00.0410.02127.7270.0130.0130.0000.0000.0000.000
131A140TYR0-0.107-0.06723.0170.0170.0170.0000.0000.0000.000
132A141ALA00.0220.01127.7360.0130.0130.0000.0000.0000.000
133A142GLU-1-0.887-0.94729.359-0.085-0.0850.0000.0000.0000.000
134A143ARG10.9390.96929.2740.0860.0860.0000.0000.0000.000
135A144ARG10.8230.90229.1760.0420.0420.0000.0000.0000.000
136A145THR00.0300.01632.6640.0080.0080.0000.0000.0000.000
137A146VAL00.0250.03935.1770.0050.0050.0000.0000.0000.000
138A147THR0-0.015-0.01834.9100.0040.0040.0000.0000.0000.000
139A148LEU0-0.071-0.04632.6970.0060.0060.0000.0000.0000.000
140A149THR0-0.021-0.03237.0360.0040.0040.0000.0000.0000.000
141A150GLN00.0070.01840.1850.0020.0020.0000.0000.0000.000
142A151LYS10.8040.90837.1950.0290.0290.0000.0000.0000.000
143A152HIS00.0730.03241.6600.0020.0020.0000.0000.0000.000
144A153VAL00.001-0.01841.0200.0000.0000.0000.0000.0000.000
145A154ARG10.8430.90040.286-0.002-0.0020.0000.0000.0000.000
146A155GLY00.0650.03940.0240.0010.0010.0000.0000.0000.000
147A156ARG10.8930.95937.0680.0100.0100.0000.0000.0000.000
148A157LEU0-0.0040.00234.6890.0000.0000.0000.0000.0000.000
149A158ALA00.0320.01334.9960.0020.0020.0000.0000.0000.000
150A159GLU-1-0.852-0.91733.072-0.033-0.0330.0000.0000.0000.000
151A160THR0-0.019-0.01430.285-0.002-0.0020.0000.0000.0000.000
152A161LEU0-0.008-0.01330.1950.0020.0020.0000.0000.0000.000
153A162LEU0-0.0090.00030.3350.0030.0030.0000.0000.0000.000
154A163ILE0-0.0070.00626.689-0.002-0.0020.0000.0000.0000.000
155A164LEU0-0.037-0.01125.538-0.002-0.0020.0000.0000.0000.000
156A165LYS10.9730.98525.4560.0060.0060.0000.0000.0000.000
157A166GLU-1-0.998-0.98825.442-0.040-0.0400.0000.0000.0000.000
158A167ASN0-0.072-0.03921.952-0.013-0.0130.0000.0000.0000.000
159A168PHE0-0.024-0.04319.0440.0020.0020.0000.0000.0000.000
160A169GLY00.0320.04622.2860.0150.0150.0000.0000.0000.000
161A170PHE0-0.060-0.03924.671-0.001-0.0010.0000.0000.0000.000
162A171GLU-1-0.747-0.79924.1720.1360.1360.0000.0000.0000.000
163A172ASN00.026-0.00525.044-0.011-0.0110.0000.0000.0000.000
164A173ASP-1-0.798-0.85727.4780.0630.0630.0000.0000.0000.000
165A174GLY00.0010.00729.216-0.007-0.0070.0000.0000.0000.000
166A175ALA0-0.021-0.01630.349-0.008-0.0080.0000.0000.0000.000
167A176THR0-0.123-0.10228.559-0.007-0.0070.0000.0000.0000.000
168A177LEU0-0.042-0.01227.3730.0030.0030.0000.0000.0000.000
169A178SER00.0370.03722.2290.0020.0020.0000.0000.0000.000
170A179ILE0-0.060-0.03722.4140.0130.0130.0000.0000.0000.000
171A180TYR0-0.114-0.13823.657-0.012-0.0120.0000.0000.0000.000
172A181LEU0-0.0110.00124.2810.0050.0050.0000.0000.0000.000
173A182SER0-0.037-0.02327.290-0.002-0.0020.0000.0000.0000.000
174A183ARG10.9950.98429.970-0.052-0.0520.0000.0000.0000.000
175A184GLU-1-0.836-0.92631.5620.0380.0380.0000.0000.0000.000
176A185GLU-1-0.829-0.89425.3750.0590.0590.0000.0000.0000.000
177A186LEU00.0220.00829.497-0.008-0.0080.0000.0000.0000.000
178A187ALA0-0.024-0.01131.412-0.006-0.0060.0000.0000.0000.000
179A188THR0-0.014-0.00330.531-0.006-0.0060.0000.0000.0000.000
180A189LEU0-0.033-0.01527.048-0.007-0.0070.0000.0000.0000.000
181A190SER00.0030.01630.682-0.008-0.0080.0000.0000.0000.000
182A191ASN0-0.043-0.01734.1120.0010.0010.0000.0000.0000.000
183A192MET0-0.058-0.01836.1790.0000.0000.0000.0000.0000.000
184A193THR00.0760.04037.1830.0020.0020.0000.0000.0000.000
185A194VAL00.1170.04135.6060.0000.0000.0000.0000.0000.000
186A195SER0-0.0120.00238.1930.0010.0010.0000.0000.0000.000
187A196ASN00.036-0.00241.3870.0010.0010.0000.0000.0000.000
188A197ALA00.0540.04836.646-0.001-0.0010.0000.0000.0000.000
189A198ILE0-0.031-0.02337.9760.0010.0010.0000.0000.0000.000
190A199ARG10.9650.99540.034-0.013-0.0130.0000.0000.0000.000
191A200THR0-0.009-0.03340.265-0.001-0.0010.0000.0000.0000.000
192A201LEU0-0.013-0.00735.6230.0000.0000.0000.0000.0000.000
193A202SER0-0.0010.01239.7920.0010.0010.0000.0000.0000.000
194A203THR00.0120.00742.9370.0000.0000.0000.0000.0000.000
195A204PHE00.013-0.00738.385-0.001-0.0010.0000.0000.0000.000
196A205VAL0-0.0080.00639.9810.0000.0000.0000.0000.0000.000
197A206SER0-0.023-0.00542.3440.0000.0000.0000.0000.0000.000
198A207GLU-1-0.842-0.90644.6020.0070.0070.0000.0000.0000.000
199A208ARG10.9370.97643.099-0.023-0.0230.0000.0000.0000.000
200A209MET0-0.0250.00640.054-0.001-0.0010.0000.0000.0000.000
201A210LEU0-0.035-0.02435.4130.0010.0010.0000.0000.0000.000
202A211ALA00.0360.02036.990-0.001-0.0010.0000.0000.0000.000
203A212LEU0-0.043-0.03135.5540.0020.0020.0000.0000.0000.000
204A213ASP-1-0.826-0.90234.2460.0740.0740.0000.0000.0000.000
205A214GLY00.0600.03333.3040.0060.0060.0000.0000.0000.000
206A215LYS10.8720.91427.115-0.100-0.1000.0000.0000.0000.000
207A216ARG10.9010.96929.271-0.096-0.0960.0000.0000.0000.000
208A217ILE0-0.006-0.00430.617-0.005-0.0050.0000.0000.0000.000
209A218LYS10.9630.99731.407-0.055-0.0550.0000.0000.0000.000
210A219ILE0-0.014-0.02631.694-0.005-0.0050.0000.0000.0000.000
211A220ILE0-0.033-0.01534.8980.0020.0020.0000.0000.0000.000
212A221ASP-1-0.795-0.87437.9880.0070.0070.0000.0000.0000.000
213A222CYS0-0.030-0.02934.695-0.002-0.0020.0000.0000.0000.000
214A223ASP-1-0.824-0.89937.018-0.007-0.0070.0000.0000.0000.000
215A224ARG10.8050.86639.724-0.013-0.0130.0000.0000.0000.000
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