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: 7MM3K

Calculation Name: 3GT0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GT0

Chain ID: A

ChEMBL ID:

UniProt ID: Q81C08

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 OptHSide
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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2348808.220527
FMO2-HF: Nuclear repulsion 2263537.421824
FMO2-HF: Total energy -85270.798704
FMO2-MP2: Total energy -85509.519083


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.
-20.147-9.25314.509-8.486-16.918-0.029
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 : 0.010 / q_NPA : 0.012
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].
3A3LYS10.8580.9362.471-9.313-5.9224.990-3.106-5.2760.013
4A4GLN00.0150.0054.569-1.975-1.893-0.001-0.027-0.0540.000
5A5ILE0-0.017-0.0253.0390.1300.7010.080-0.099-0.5510.000
6A6GLY00.0330.0187.051-0.169-0.1690.0000.0000.0000.000
7A7PHE0-0.016-0.0247.8600.0540.0540.0000.0000.0000.000
8A8ILE00.0340.02612.2390.0050.0050.0000.0000.0000.000
9A9GLY0-0.009-0.01015.7570.0290.0290.0000.0000.0000.000
10A10CYS0-0.052-0.04515.167-0.053-0.0530.0000.0000.0000.000
11A11GLY00.0670.04216.605-0.002-0.0020.0000.0000.0000.000
12A12ASN0-0.019-0.02917.397-0.051-0.0510.0000.0000.0000.000
13A13MET00.0320.01614.651-0.049-0.0490.0000.0000.0000.000
14A14GLY00.0660.03712.948-0.051-0.0510.0000.0000.0000.000
15A15MET0-0.0120.00912.446-0.138-0.1380.0000.0000.0000.000
16A16ALA0-0.0340.00114.024-0.071-0.0710.0000.0000.0000.000
17A17MET0-0.0250.0109.157-0.046-0.0460.0000.0000.0000.000
18A18ILE00.0060.0078.943-0.231-0.2310.0000.0000.0000.000
19A19GLY00.0130.0089.938-0.190-0.1900.0000.0000.0000.000
20A20GLY00.0060.00210.356-0.011-0.0110.0000.0000.0000.000
21A21MET00.0240.0124.743-0.391-0.2200.001-0.032-0.1410.000
22A22ILE00.0020.0107.213-0.312-0.3120.0000.0000.0000.000
23A23ASN0-0.052-0.0149.6340.1130.1130.0000.0000.0000.000
24A24LYS10.8300.9058.2700.8710.8710.0000.0000.0000.000
25A25ASN0-0.059-0.0235.4850.4340.4340.0000.0000.0000.000
26A26ILE0-0.0090.0062.570-1.246-0.2971.246-0.434-1.761-0.001
27A27VAL0-0.020-0.0112.067-10.998-9.5014.640-2.722-3.415-0.030
28A28SER00.0100.0154.4771.6461.813-0.001-0.025-0.1410.000
29A29SER00.0420.0037.716-0.012-0.0120.0000.0000.0000.000
30A30ASN0-0.041-0.0279.9400.0060.0060.0000.0000.0000.000
31A31GLN0-0.027-0.0053.863-0.0690.4090.000-0.277-0.2000.001
32A32ILE0-0.024-0.0037.5090.2390.2390.0000.0000.0000.000
33A33ILE0-0.0110.0099.8700.0900.0900.0000.0000.0000.000
34A34CYS0-0.058-0.03412.3500.0200.0200.0000.0000.0000.000
35A35SER00.0750.01814.7370.0150.0150.0000.0000.0000.000
36A36ASP-1-0.799-0.89917.526-0.270-0.2700.0000.0000.0000.000
37A37LEU00.0150.02120.2940.0090.0090.0000.0000.0000.000
38A38ASN0-0.050-0.02923.2350.0020.0020.0000.0000.0000.000
39A39THR00.0780.01623.357-0.021-0.0210.0000.0000.0000.000
40A40ALA0-0.0040.00024.457-0.019-0.0190.0000.0000.0000.000
41A41ASN0-0.051-0.03420.201-0.023-0.0230.0000.0000.0000.000
42A42LEU00.0270.02818.877-0.040-0.0400.0000.0000.0000.000
43A43LYS10.8260.89120.2650.2470.2470.0000.0000.0000.000
44A44ASN00.001-0.00520.929-0.032-0.0320.0000.0000.0000.000
45A45ALA00.0430.01215.996-0.036-0.0360.0000.0000.0000.000
46A46SER0-0.027-0.01117.122-0.058-0.0580.0000.0000.0000.000
47A47GLU-1-0.845-0.90319.146-0.351-0.3510.0000.0000.0000.000
48A48LYS10.8480.94016.7150.5860.5860.0000.0000.0000.000
49A49TYR0-0.021-0.04813.793-0.023-0.0230.0000.0000.0000.000
50A50GLY0-0.0020.01615.297-0.101-0.1010.0000.0000.0000.000
51A51LEU0-0.042-0.01012.149-0.019-0.0190.0000.0000.0000.000
52A52THR00.0200.00514.3770.0840.0840.0000.0000.0000.000
53A53THR0-0.025-0.01615.5450.0040.0040.0000.0000.0000.000
54A54THR0-0.015-0.03917.7970.0290.0290.0000.0000.0000.000
55A55THR0-0.014-0.01820.315-0.004-0.0040.0000.0000.0000.000
56A56ASP-1-0.845-0.91021.710-0.076-0.0760.0000.0000.0000.000
57A57ASN0-0.0050.00118.981-0.047-0.0470.0000.0000.0000.000
58A58ASN00.007-0.01718.3530.0380.0380.0000.0000.0000.000
59A59GLU-1-0.869-0.92018.074-0.234-0.2340.0000.0000.0000.000
60A60VAL0-0.051-0.01813.545-0.012-0.0120.0000.0000.0000.000
61A61ALA0-0.002-0.01013.8580.0210.0210.0000.0000.0000.000
62A62LYS10.8830.96115.1220.1030.1030.0000.0000.0000.000
63A63ASN00.005-0.02112.9740.1050.1050.0000.0000.0000.000
64A64ALA00.0130.02610.2800.0350.0350.0000.0000.0000.000
65A65ASP-1-0.809-0.8986.6221.1501.1500.0000.0000.0000.000
66A66ILE0-0.034-0.0112.932-0.3990.2510.218-0.142-0.7260.000
67A67LEU0-0.0090.0007.207-0.331-0.3310.0000.0000.0000.000
68A68ILE00.006-0.0016.7540.0330.0330.0000.0000.0000.000
69A69LEU00.0070.00710.823-0.034-0.0340.0000.0000.0000.000
70A70SER0-0.030-0.02314.570-0.014-0.0140.0000.0000.0000.000
71A71ILE00.0140.01216.296-0.021-0.0210.0000.0000.0000.000
72A72LYS10.9520.96719.8920.1270.1270.0000.0000.0000.000
73A73PRO00.0890.03922.6370.0100.0100.0000.0000.0000.000
74A74ASP-1-0.924-0.97423.582-0.041-0.0410.0000.0000.0000.000
75A75LEU0-0.033-0.02623.5130.0040.0040.0000.0000.0000.000
76A76TYR0-0.022-0.00917.5090.0120.0120.0000.0000.0000.000
77A77ALA00.0270.01222.3390.0080.0080.0000.0000.0000.000
78A78SER0-0.008-0.00224.9400.0070.0070.0000.0000.0000.000
79A79ILE0-0.014-0.00419.1600.0010.0010.0000.0000.0000.000
80A80ILE0-0.037-0.00119.1310.0070.0070.0000.0000.0000.000
81A81ASN0-0.061-0.04021.2400.0240.0240.0000.0000.0000.000
82A82GLU-1-0.693-0.95719.980-0.065-0.0650.0000.0000.0000.000
83A83ILE0-0.0820.02715.7340.0130.0130.0000.0000.0000.000
84A84LYN0-0.0680.05719.1240.0350.0350.0000.0000.0000.000
85A85GLU-1-0.958-1.02120.6250.1270.1270.0000.0000.0000.000
86A86ILE0-0.110-0.04519.0900.0120.0120.0000.0000.0000.000
87A87ILE0-0.0330.01015.3710.0080.0080.0000.0000.0000.000
88A88LYS10.8710.92610.382-0.817-0.8170.0000.0000.0000.000
89A89ASN0-0.030-0.03915.1790.0140.0140.0000.0000.0000.000
90A90ASP-1-0.887-0.92311.2120.9920.9920.0000.0000.0000.000
91A91ALA00.0240.02210.5800.2410.2410.0000.0000.0000.000
92A92ILE0-0.027-0.0085.971-0.098-0.0980.0000.0000.0000.000
93A93ILE0-0.019-0.0019.446-0.107-0.1070.0000.0000.0000.000
94A94VAL00.0160.0077.5560.0030.0030.0000.0000.0000.000
95A95THR0-0.0020.01310.984-0.063-0.0630.0000.0000.0000.000
96A96ILE00.0220.00812.337-0.010-0.0100.0000.0000.0000.000
97A97ALA0-0.036-0.02915.1820.0130.0130.0000.0000.0000.000
98A98ALA00.0170.01118.0420.0160.0160.0000.0000.0000.000
99A99GLY00.0310.01419.492-0.006-0.0060.0000.0000.0000.000
100A100LYS10.8270.91221.0310.0030.0030.0000.0000.0000.000
101A101SER00.0330.02420.3810.0000.0000.0000.0000.0000.000
102A102ILE00.040-0.00117.277-0.008-0.0080.0000.0000.0000.000
103A103GLU-1-0.903-0.93619.8120.1220.1220.0000.0000.0000.000
104A104SER0-0.075-0.02522.968-0.005-0.0050.0000.0000.0000.000
105A105THR00.004-0.00916.982-0.016-0.0160.0000.0000.0000.000
106A106GLU-1-0.839-0.91719.3530.2520.2520.0000.0000.0000.000
107A107ASN0-0.067-0.05720.9640.0010.0010.0000.0000.0000.000
108A108ALA0-0.059-0.01421.866-0.012-0.0120.0000.0000.0000.000
109A109PHE00.0860.02715.862-0.003-0.0030.0000.0000.0000.000
110A110ASN0-0.072-0.01221.5010.0030.0030.0000.0000.0000.000
111A111LYS10.9030.95418.658-0.270-0.2700.0000.0000.0000.000
112A112LYS10.9610.96320.135-0.343-0.3430.0000.0000.0000.000
113A113VAL00.0030.01615.2200.0350.0350.0000.0000.0000.000
114A114LYS10.8060.90110.425-1.370-1.3700.0000.0000.0000.000
115A115VAL00.015-0.00213.191-0.027-0.0270.0000.0000.0000.000
116A116VAL0-0.003-0.0059.5040.0280.0280.0000.0000.0000.000
117A117ARG10.8820.94212.300-0.132-0.1320.0000.0000.0000.000
118A118VAL00.005-0.01610.4890.0160.0160.0000.0000.0000.000
119A119MET0-0.060-0.02413.970-0.019-0.0190.0000.0000.0000.000
120A120PRO00.0330.02713.8480.0040.0040.0000.0000.0000.000
121A121ASN00.041-0.00415.8600.0010.0010.0000.0000.0000.000
122A122THR00.0520.00818.024-0.032-0.0320.0000.0000.0000.000
123A123PRO00.0170.00919.544-0.031-0.0310.0000.0000.0000.000
124A124ALA00.0780.05114.530-0.017-0.0170.0000.0000.0000.000
125A125LEU0-0.090-0.05615.689-0.057-0.0570.0000.0000.0000.000
126A126VAL0-0.095-0.04617.926-0.018-0.0180.0000.0000.0000.000
127A127GLY0-0.041-0.01015.0440.0060.0060.0000.0000.0000.000
128A128GLU-1-0.901-0.95215.975-0.179-0.1790.0000.0000.0000.000
129A129GLY0-0.033-0.02015.8520.0350.0350.0000.0000.0000.000
130A130MET0-0.051-0.01216.3260.0130.0130.0000.0000.0000.000
131A131SER0-0.041-0.02012.724-0.016-0.0160.0000.0000.0000.000
132A132ALA00.0120.01914.6750.0320.0320.0000.0000.0000.000
133A133LEU0-0.012-0.0199.492-0.025-0.0250.0000.0000.0000.000
134A134CYS0-0.012-0.01213.8110.0280.0280.0000.0000.0000.000
135A135PRO0-0.0020.01012.590-0.017-0.0170.0000.0000.0000.000
136A136ASN00.025-0.01114.3370.0320.0320.0000.0000.0000.000
137A137GLU-1-0.891-0.95815.9040.3940.3940.0000.0000.0000.000
138A138MET0-0.066-0.02416.0090.0180.0180.0000.0000.0000.000
139A139VAL0-0.079-0.01810.4880.1060.1060.0000.0000.0000.000
140A140THR0-0.035-0.04311.4080.0020.0020.0000.0000.0000.000
141A141GLU-1-0.912-0.96911.3830.9320.9320.0000.0000.0000.000
142A142LYS10.8390.9054.628-4.893-4.796-0.001-0.008-0.0870.000
143A143ASP-1-0.767-0.8507.3282.2602.2600.0000.0000.0000.000
144A144LEU00.021-0.0016.559-0.039-0.0390.0000.0000.0000.000
145A145GLU-1-0.821-0.8956.4682.7292.7290.0000.0000.0000.000
146A146ASP-1-0.818-0.9012.6796.9428.1790.883-0.472-1.649-0.002
147A147VAL0-0.014-0.0112.871-4.029-2.9020.375-0.692-0.811-0.009
148A148LEU00.002-0.0055.047-0.414-0.390-0.001-0.002-0.0210.000
149A149ASN0-0.025-0.0133.288-1.027-0.6380.021-0.063-0.3470.000
150A150ILE0-0.0010.0052.409-0.804-0.7792.060-0.380-1.705-0.001
151A151PHE0-0.025-0.0214.9880.1870.226-0.001-0.005-0.0330.000
152A152ASN00.0400.0367.8910.0540.0540.0000.0000.0000.000
153A153SER0-0.077-0.0367.0290.0620.0620.0000.0000.0000.000
154A154PHE0-0.036-0.0228.6160.0400.0400.0000.0000.0000.000
155A155GLY00.0450.02312.2430.0580.0580.0000.0000.0000.000
156A156GLN0-0.0020.01812.8560.0320.0320.0000.0000.0000.000
157A157THR0-0.054-0.06310.240-0.006-0.0060.0000.0000.0000.000
158A158GLU-1-0.869-0.94013.7240.1750.1750.0000.0000.0000.000
159A159ILE0-0.0200.01212.388-0.014-0.0140.0000.0000.0000.000
160A160VAL0-0.011-0.00615.987-0.015-0.0150.0000.0000.0000.000
161A161SER0-0.003-0.00618.6310.0100.0100.0000.0000.0000.000
162A162GLU-1-0.658-0.85519.7840.1030.1030.0000.0000.0000.000
163A163LYS10.9260.96621.660-0.125-0.1250.0000.0000.0000.000
164A164LEU0-0.009-0.00122.830-0.010-0.0100.0000.0000.0000.000
165A165MET0-0.0020.01116.498-0.022-0.0220.0000.0000.0000.000
166A166ASP-1-0.886-0.93322.1970.0130.0130.0000.0000.0000.000
167A167VAL0-0.002-0.01125.461-0.011-0.0110.0000.0000.0000.000
168A168VAL00.0090.00319.370-0.010-0.0100.0000.0000.0000.000
169A169THR0-0.023-0.01822.842-0.021-0.0210.0000.0000.0000.000
170A170SER00.0130.01124.041-0.010-0.0100.0000.0000.0000.000
171A171VAL0-0.0100.00724.399-0.008-0.0080.0000.0000.0000.000
172A172SER00.018-0.00221.688-0.014-0.0140.0000.0000.0000.000
173A173GLY0-0.0200.00024.249-0.013-0.0130.0000.0000.0000.000
174A174SER0-0.041-0.02427.0210.0000.0000.0000.0000.0000.000
175A175SER0-0.028-0.01225.9860.0000.0000.0000.0000.0000.000
176A176PRO00.0220.01526.4000.0000.0000.0000.0000.0000.000
177A177ALA00.0260.01528.9600.0000.0000.0000.0000.0000.000
178A178TYR00.000-0.00431.3990.0040.0040.0000.0000.0000.000
179A179VAL00.0470.01928.1300.0020.0020.0000.0000.0000.000
180A180TYR0-0.022-0.01928.406-0.004-0.0040.0000.0000.0000.000
181A181MET0-0.0140.00333.3540.0020.0020.0000.0000.0000.000
182A182ILE00.0240.00332.2240.0030.0030.0000.0000.0000.000
183A183ILE0-0.026-0.01230.3610.0000.0000.0000.0000.0000.000
184A184GLU-1-0.795-0.87435.015-0.084-0.0840.0000.0000.0000.000
185A185ALA00.0020.01437.9490.0020.0020.0000.0000.0000.000
186A186MET0-0.043-0.02335.1140.0020.0020.0000.0000.0000.000
187A187ALA0-0.016-0.00937.3870.0000.0000.0000.0000.0000.000
188A188ASP-1-0.807-0.89739.385-0.065-0.0650.0000.0000.0000.000
189A189ALA0-0.036-0.01142.6900.0020.0020.0000.0000.0000.000
190A190ALA00.0450.02141.2800.0010.0010.0000.0000.0000.000
191A191VAL0-0.057-0.04142.0240.0000.0000.0000.0000.0000.000
192A192LEU0-0.087-0.03544.5880.0010.0010.0000.0000.0000.000
193A193ASP-1-0.926-0.94146.386-0.043-0.0430.0000.0000.0000.000
194A194GLY0-0.042-0.02047.6040.0000.0000.0000.0000.0000.000
195A195MET0-0.053-0.00540.548-0.005-0.0050.0000.0000.0000.000
196A196PRO00.010-0.00841.701-0.001-0.0010.0000.0000.0000.000
197A197ARG10.8710.91639.5370.0730.0730.0000.0000.0000.000
198A198ASN00.011-0.00236.7060.0010.0010.0000.0000.0000.000
199A199GLN0-0.017-0.01336.089-0.003-0.0030.0000.0000.0000.000
200A200ALA00.0380.01536.873-0.001-0.0010.0000.0000.0000.000
201A201TYR0-0.028-0.04934.179-0.001-0.0010.0000.0000.0000.000
202A202LYS10.9340.98130.6780.1390.1390.0000.0000.0000.000
203A203PHE0-0.027-0.02632.435-0.002-0.0020.0000.0000.0000.000
204A204ALA00.0340.02834.0000.0020.0020.0000.0000.0000.000
205A205ALA00.0350.01129.5670.0030.0030.0000.0000.0000.000
206A206GLN0-0.017-0.00526.609-0.011-0.0110.0000.0000.0000.000
207A207ALA00.0030.00229.8490.0050.0050.0000.0000.0000.000
208A208VAL0-0.004-0.00229.1630.0070.0070.0000.0000.0000.000
209A209LEU0-0.014-0.00423.7150.0060.0060.0000.0000.0000.000
210A210GLY00.0140.00426.4440.0040.0040.0000.0000.0000.000
211A211SER0-0.012-0.02028.3110.0120.0120.0000.0000.0000.000
212A212ALA0-0.0160.00025.9690.0100.0100.0000.0000.0000.000
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