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: 2LL7R

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2354563.747557
FMO2-HF: Nuclear repulsion 2269291.887372
FMO2-HF: Total energy -85271.860185
FMO2-MP2: Total energy -85510.471728


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.
-20.132-12.32822.374-10.657-19.523-0.045
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 : -0.002 / q_NPA : 0.007
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].
3A3LYS10.8520.9332.557-8.174-6.3147.364-3.465-5.7590.015
4A4GLN00.0210.0054.482-2.195-2.0770.000-0.046-0.0730.000
5A5ILE0-0.026-0.0203.1640.1640.5970.032-0.074-0.3910.000
6A6GLY00.0330.0137.202-0.085-0.0850.0000.0000.0000.000
7A7PHE0-0.008-0.0247.9980.0270.0270.0000.0000.0000.000
8A8ILE00.0280.02312.4670.0160.0160.0000.0000.0000.000
9A9GLY00.0080.01016.0970.0350.0350.0000.0000.0000.000
10A10CYS0-0.035-0.02415.375-0.050-0.0500.0000.0000.0000.000
11A11GLY00.0730.03816.631-0.015-0.0150.0000.0000.0000.000
12A12ASN0-0.044-0.03217.466-0.052-0.0520.0000.0000.0000.000
13A13MET00.0490.02814.908-0.049-0.0490.0000.0000.0000.000
14A14GLY00.0610.03713.298-0.057-0.0570.0000.0000.0000.000
15A15MET0-0.042-0.00712.852-0.134-0.1340.0000.0000.0000.000
16A16ALA0-0.0320.00714.198-0.075-0.0750.0000.0000.0000.000
17A17MET0-0.0270.0039.585-0.064-0.0640.0000.0000.0000.000
18A18ILE00.0170.0119.099-0.242-0.2420.0000.0000.0000.000
19A19GLY00.0080.0069.918-0.207-0.2070.0000.0000.0000.000
20A20GLY0-0.003-0.00410.471-0.011-0.0110.0000.0000.0000.000
21A21MET00.0170.0084.918-0.376-0.2280.000-0.023-0.1240.000
22A22ILE00.0110.0157.205-0.321-0.3210.0000.0000.0000.000
23A23ASN0-0.055-0.0189.5430.1400.1400.0000.0000.0000.000
24A24LYS10.8410.9097.9550.9900.9900.0000.0000.0000.000
25A25ASN0-0.057-0.0295.2020.5760.5760.0000.0000.0000.000
26A26ILE0-0.0050.0112.418-1.251-0.7092.301-0.642-2.201-0.001
27A27VAL0-0.006-0.0041.934-12.296-12.3708.529-4.007-4.447-0.043
28A28SER00.0090.0074.3261.8042.015-0.001-0.038-0.1720.000
29A29SER00.015-0.0017.4940.0270.0270.0000.0000.0000.000
30A30ASN0-0.013-0.0179.7410.0560.0560.0000.0000.0000.000
31A31GLN0-0.032-0.0033.9160.0160.471-0.001-0.270-0.1850.001
32A32ILE0-0.025-0.0057.5740.1910.1910.0000.0000.0000.000
33A33ILE0-0.0030.0059.9080.1360.1360.0000.0000.0000.000
34A34CYS0-0.050-0.02612.3810.0060.0060.0000.0000.0000.000
35A35SER00.0810.00914.7720.0190.0190.0000.0000.0000.000
36A36ASP-1-0.804-0.90817.831-0.336-0.3360.0000.0000.0000.000
37A37LEU00.0140.02320.6180.0150.0150.0000.0000.0000.000
38A38ASN0-0.035-0.01923.5650.0120.0120.0000.0000.0000.000
39A39THR00.0720.01323.584-0.024-0.0240.0000.0000.0000.000
40A40ALA0-0.0030.00624.303-0.022-0.0220.0000.0000.0000.000
41A41ASN0-0.051-0.03720.126-0.023-0.0230.0000.0000.0000.000
42A42LEU00.0320.03218.664-0.042-0.0420.0000.0000.0000.000
43A43LYS10.8260.89520.2620.2830.2830.0000.0000.0000.000
44A44ASN00.006-0.00320.939-0.042-0.0420.0000.0000.0000.000
45A45ALA00.0420.00916.003-0.039-0.0390.0000.0000.0000.000
46A46SER0-0.019-0.00516.790-0.064-0.0640.0000.0000.0000.000
47A47GLU-1-0.846-0.90818.870-0.393-0.3930.0000.0000.0000.000
48A48LYS10.8450.93316.8390.6340.6340.0000.0000.0000.000
49A49TYR0-0.015-0.04213.741-0.017-0.0170.0000.0000.0000.000
50A50GLY0-0.0030.00514.930-0.121-0.1210.0000.0000.0000.000
51A51LEU0-0.0350.00212.123-0.018-0.0180.0000.0000.0000.000
52A52THR00.0160.00714.2050.1430.1430.0000.0000.0000.000
53A53THR0-0.044-0.03115.5070.0020.0020.0000.0000.0000.000
54A54THR0-0.006-0.02417.9230.0390.0390.0000.0000.0000.000
55A55THR0-0.016-0.02220.441-0.006-0.0060.0000.0000.0000.000
56A56ASP-1-0.846-0.90921.779-0.138-0.1380.0000.0000.0000.000
57A57ASN00.0110.00018.873-0.055-0.0550.0000.0000.0000.000
58A58ASN0-0.009-0.01318.3140.0270.0270.0000.0000.0000.000
59A59GLU-1-0.873-0.91518.039-0.321-0.3210.0000.0000.0000.000
60A60VAL0-0.056-0.01913.617-0.015-0.0150.0000.0000.0000.000
61A61ALA00.004-0.00413.9950.0110.0110.0000.0000.0000.000
62A62LYS10.8720.93915.2560.1450.1450.0000.0000.0000.000
63A63ASN0-0.013-0.01713.1150.0910.0910.0000.0000.0000.000
64A64ALA00.0060.02610.0620.0260.0260.0000.0000.0000.000
65A65ASP-1-0.790-0.8996.7620.9910.9910.0000.0000.0000.000
66A66ILE0-0.045-0.0142.857-0.3100.3270.238-0.148-0.7270.000
67A67LEU0-0.0030.0067.131-0.333-0.3330.0000.0000.0000.000
68A68ILE00.0040.0037.0490.0660.0660.0000.0000.0000.000
69A69LEU0-0.0010.00411.041-0.020-0.0200.0000.0000.0000.000
70A70SER0-0.002-0.04014.7370.0010.0010.0000.0000.0000.000
71A71ILE0-0.044-0.00616.428-0.007-0.0070.0000.0000.0000.000
72A72LYS10.9330.95920.0240.1530.1530.0000.0000.0000.000
73A73PRO00.0670.02622.1680.0080.0080.0000.0000.0000.000
74A74ASP-1-0.911-0.96623.372-0.080-0.0800.0000.0000.0000.000
75A75LEU0-0.001-0.00923.8030.0080.0080.0000.0000.0000.000
76A76TYR0-0.011-0.00517.6810.0120.0120.0000.0000.0000.000
77A77ALA00.0380.01722.4240.0080.0080.0000.0000.0000.000
78A78SER0-0.0150.00225.1610.0090.0090.0000.0000.0000.000
79A79ILE00.001-0.00219.1200.0010.0010.0000.0000.0000.000
80A80ILE0-0.042-0.04519.5550.0030.0030.0000.0000.0000.000
81A81ASN0-0.061-0.04321.6820.0290.0290.0000.0000.0000.000
82A82GLU-1-0.807-0.90820.698-0.121-0.1210.0000.0000.0000.000
83A83ILE0-0.059-0.01015.9940.0190.0190.0000.0000.0000.000
84A84LYN0-0.0310.00318.8950.0240.0240.0000.0000.0000.000
85A85GLU-1-0.954-0.98120.5950.0820.0820.0000.0000.0000.000
86A86ILE0-0.049-0.02719.0850.0230.0230.0000.0000.0000.000
87A87ILE0-0.0160.02315.1050.0000.0000.0000.0000.0000.000
88A88LYS10.8580.91110.437-0.675-0.6750.0000.0000.0000.000
89A89ASN0-0.006-0.01314.8490.0170.0170.0000.0000.0000.000
90A90ASP-1-0.859-0.91011.3000.8450.8450.0000.0000.0000.000
91A91ALA00.0190.02010.3680.2360.2360.0000.0000.0000.000
92A92ILE0-0.056-0.0235.630-0.050-0.0500.0000.0000.0000.000
93A93ILE0-0.0100.0069.097-0.160-0.1600.0000.0000.0000.000
94A94VAL0-0.005-0.0057.7650.0230.0230.0000.0000.0000.000
95A95THR00.0150.01411.136-0.057-0.0570.0000.0000.0000.000
96A96ILE00.0240.01712.7110.0060.0060.0000.0000.0000.000
97A97ALA0-0.015-0.01515.5110.0170.0170.0000.0000.0000.000
98A98ALA00.0730.04917.9260.0170.0170.0000.0000.0000.000
99A99GLY0-0.024-0.01919.5560.0210.0210.0000.0000.0000.000
100A100LYS10.8580.92121.2140.0440.0440.0000.0000.0000.000
101A101SER00.0500.03620.714-0.005-0.0050.0000.0000.0000.000
102A102ILE00.0150.00017.313-0.012-0.0120.0000.0000.0000.000
103A103GLU-1-0.892-0.93019.7170.0840.0840.0000.0000.0000.000
104A104SER0-0.073-0.04023.108-0.007-0.0070.0000.0000.0000.000
105A105THR0-0.035-0.01217.165-0.022-0.0220.0000.0000.0000.000
106A106GLU-1-0.836-0.92719.5130.1990.1990.0000.0000.0000.000
107A107ASN0-0.072-0.05621.2170.0010.0010.0000.0000.0000.000
108A108ALA0-0.0350.00322.692-0.009-0.0090.0000.0000.0000.000
109A109PHE00.0630.00915.835-0.004-0.0040.0000.0000.0000.000
110A110ASN0-0.071-0.00721.4790.0050.0050.0000.0000.0000.000
111A111LYS10.8250.91718.559-0.184-0.1840.0000.0000.0000.000
112A112LYS10.8590.90620.312-0.313-0.3130.0000.0000.0000.000
113A113VAL00.0170.01115.0910.0210.0210.0000.0000.0000.000
114A114LYS10.8040.90010.459-1.262-1.2620.0000.0000.0000.000
115A115VAL00.013-0.00213.124-0.040-0.0400.0000.0000.0000.000
116A116VAL00.001-0.0089.6840.0390.0390.0000.0000.0000.000
117A117ARG10.8300.93112.747-0.091-0.0910.0000.0000.0000.000
118A118VAL00.003-0.01810.8020.0240.0240.0000.0000.0000.000
119A119MET0-0.042-0.01914.261-0.031-0.0310.0000.0000.0000.000
120A120PRO00.0500.03913.8890.0090.0090.0000.0000.0000.000
121A121ASN00.025-0.01215.8740.0020.0020.0000.0000.0000.000
122A122THR00.0430.00318.288-0.034-0.0340.0000.0000.0000.000
123A123PRO00.0170.00519.751-0.030-0.0300.0000.0000.0000.000
124A124ALA00.0710.04614.791-0.014-0.0140.0000.0000.0000.000
125A125LEU0-0.081-0.05515.883-0.060-0.0600.0000.0000.0000.000
126A126VAL0-0.095-0.04518.157-0.009-0.0090.0000.0000.0000.000
127A127GLY0-0.025-0.00115.1970.0120.0120.0000.0000.0000.000
128A128GLU-1-0.812-0.88915.725-0.175-0.1750.0000.0000.0000.000
129A129GLY0-0.030-0.01316.0210.0330.0330.0000.0000.0000.000
130A130MET0-0.055-0.01416.4400.0160.0160.0000.0000.0000.000
131A131SER0-0.013-0.00412.990-0.009-0.0090.0000.0000.0000.000
132A132ALA00.0010.00914.9240.0390.0390.0000.0000.0000.000
133A133LEU0-0.005-0.0119.722-0.035-0.0350.0000.0000.0000.000
134A134CYS0-0.020-0.00414.1570.0350.0350.0000.0000.0000.000
135A135PRO00.0190.01412.676-0.025-0.0250.0000.0000.0000.000
136A136ASN00.032-0.00714.4190.0250.0250.0000.0000.0000.000
137A137GLU-1-0.836-0.92815.8930.3720.3720.0000.0000.0000.000
138A138MET0-0.055-0.00915.7180.0230.0230.0000.0000.0000.000
139A139VAL0-0.071-0.01810.3600.1010.1010.0000.0000.0000.000
140A140THR0-0.026-0.03911.2810.0200.0200.0000.0000.0000.000
141A141GLU-1-0.920-0.97111.2190.9690.9690.0000.0000.0000.000
142A142LYS10.8270.8944.465-5.638-5.481-0.001-0.033-0.1220.000
143A143ASP-1-0.767-0.8497.0932.2222.2220.0000.0000.0000.000
144A144LEU00.0400.0076.706-0.189-0.1890.0000.0000.0000.000
145A145GLU-1-0.819-0.8796.3363.1203.1200.0000.0000.0000.000
146A146ASP-1-0.792-0.8922.6567.9539.2171.662-0.730-2.197-0.006
147A147VAL0-0.009-0.0092.756-4.394-3.2770.590-0.730-0.977-0.011
148A148LEU00.0130.0005.041-0.402-0.380-0.001-0.003-0.0190.000
149A149ASN0-0.052-0.0272.999-1.421-0.8410.072-0.118-0.5340.000
150A150ILE0-0.001-0.0022.494-0.872-0.5761.591-0.326-1.5620.000
151A151PHE0-0.020-0.0174.9930.2020.240-0.001-0.004-0.0330.000
152A152ASN00.0250.0337.9230.1060.1060.0000.0000.0000.000
153A153SER0-0.076-0.0376.7970.0530.0530.0000.0000.0000.000
154A154PHE0-0.036-0.0218.8570.0470.0470.0000.0000.0000.000
155A155GLY00.0090.00412.2660.0640.0640.0000.0000.0000.000
156A156GLN00.0080.00112.7580.0320.0320.0000.0000.0000.000
157A157THR0-0.070-0.06310.141-0.015-0.0150.0000.0000.0000.000
158A158GLU-1-0.835-0.91713.6000.1830.1830.0000.0000.0000.000
159A159ILE0-0.043-0.01212.657-0.016-0.0160.0000.0000.0000.000
160A160VAL0-0.009-0.01016.378-0.008-0.0080.0000.0000.0000.000
161A161SER0-0.001-0.00418.8570.0060.0060.0000.0000.0000.000
162A162GLU-1-0.671-0.86420.1840.0600.0600.0000.0000.0000.000
163A163LYS10.9340.97021.859-0.111-0.1110.0000.0000.0000.000
164A164LEU0-0.009-0.00422.712-0.006-0.0060.0000.0000.0000.000
165A165MET00.0000.01716.454-0.021-0.0210.0000.0000.0000.000
166A166ASP-1-0.871-0.92021.967-0.015-0.0150.0000.0000.0000.000
167A167VAL00.006-0.00125.407-0.011-0.0110.0000.0000.0000.000
168A168VAL00.0410.01919.390-0.009-0.0090.0000.0000.0000.000
169A169THR0-0.023-0.01922.882-0.024-0.0240.0000.0000.0000.000
170A170SER00.0150.00424.048-0.009-0.0090.0000.0000.0000.000
171A171VAL0-0.028-0.00324.770-0.005-0.0050.0000.0000.0000.000
172A172SER0-0.020-0.01822.045-0.014-0.0140.0000.0000.0000.000
173A173GLY0-0.023-0.00224.340-0.014-0.0140.0000.0000.0000.000
174A174SER0-0.033-0.02727.3730.0000.0000.0000.0000.0000.000
175A175SER0-0.020-0.00525.9280.0000.0000.0000.0000.0000.000
176A176PRO00.0160.00326.3350.0010.0010.0000.0000.0000.000
177A177ALA00.0150.01828.9170.0010.0010.0000.0000.0000.000
178A178TYR0-0.001-0.00731.5490.0040.0040.0000.0000.0000.000
179A179VAL00.0450.01827.8470.0020.0020.0000.0000.0000.000
180A180TYR0-0.013-0.01928.259-0.005-0.0050.0000.0000.0000.000
181A181MET0-0.0120.00832.9990.0030.0030.0000.0000.0000.000
182A182ILE00.0310.00932.1450.0040.0040.0000.0000.0000.000
183A183ILE0-0.027-0.00730.1420.0010.0010.0000.0000.0000.000
184A184GLU-1-0.806-0.89034.778-0.092-0.0920.0000.0000.0000.000
185A185ALA00.0100.01537.7070.0030.0030.0000.0000.0000.000
186A186MET0-0.049-0.02735.3610.0030.0030.0000.0000.0000.000
187A187ALA0-0.019-0.00737.4100.0010.0010.0000.0000.0000.000
188A188ASP-1-0.808-0.90039.364-0.068-0.0680.0000.0000.0000.000
189A189ALA0-0.034-0.00542.6140.0020.0020.0000.0000.0000.000
190A190ALA00.0580.02341.0890.0010.0010.0000.0000.0000.000
191A191VAL0-0.061-0.03142.024-0.001-0.0010.0000.0000.0000.000
192A192LEU0-0.073-0.03244.5550.0010.0010.0000.0000.0000.000
193A193ASP-1-0.935-0.95346.099-0.046-0.0460.0000.0000.0000.000
194A194GLY0-0.036-0.01447.2330.0010.0010.0000.0000.0000.000
195A195MET0-0.066-0.01540.504-0.005-0.0050.0000.0000.0000.000
196A196PRO00.012-0.01041.498-0.002-0.0020.0000.0000.0000.000
197A197ARG10.8870.92639.2590.0780.0780.0000.0000.0000.000
198A198ASN00.003-0.00136.5950.0020.0020.0000.0000.0000.000
199A199GLN0-0.024-0.01235.824-0.005-0.0050.0000.0000.0000.000
200A200ALA00.0430.02236.745-0.001-0.0010.0000.0000.0000.000
201A201TYR0-0.031-0.05234.039-0.001-0.0010.0000.0000.0000.000
202A202LYS10.9290.97730.6930.1410.1410.0000.0000.0000.000
203A203PHE0-0.016-0.02132.271-0.003-0.0030.0000.0000.0000.000
204A204ALA00.0250.02533.7760.0030.0030.0000.0000.0000.000
205A205ALA00.0310.00429.4560.0030.0030.0000.0000.0000.000
206A206GLN0-0.037-0.01526.645-0.011-0.0110.0000.0000.0000.000
207A207ALA00.0190.01329.6630.0050.0050.0000.0000.0000.000
208A208VAL00.0090.01529.3210.0080.0080.0000.0000.0000.000
209A209LEU0-0.0150.00023.6800.0060.0060.0000.0000.0000.000
210A210GLY00.0230.00426.4090.0040.0040.0000.0000.0000.000
211A211SER0-0.033-0.03028.1680.0130.0130.0000.0000.0000.000
212A212ALA0-0.017-0.01225.9150.0100.0100.0000.0000.0000.000
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