FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: KG9V3

Calculation Name: 2Q4E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Q4E

Chain ID: A

ChEMBL ID:

UniProt ID: Q9SZ83

Base Structure: X-ray

Registration Date: 2023-09-21

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 343
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5261735.881589
FMO2-HF: Nuclear repulsion 5129423.897579
FMO2-HF: Total energy -132311.98401
FMO2-MP2: Total energy -132698.012265


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:6:GLN)


Summations of interaction energy for fragment #1(A:6: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.
-7.63-1.9962.495-3.551-4.575-0.026
Interaction energy analysis for fragmet #1(A:6:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.010
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].
3A8ARG10.8190.8963.8081.5963.389-0.011-0.838-0.9430.003
4A9ILE0-0.014-0.0065.5721.1401.1400.0000.0000.0000.000
5A10GLY00.0340.0197.9530.1290.1290.0000.0000.0000.000
6A11VAL0-0.021-0.01911.4640.1260.1260.0000.0000.0000.000
7A12MET00.0280.02314.1710.0730.0730.0000.0000.0000.000
8A13GLY00.0450.00617.4520.0680.0680.0000.0000.0000.000
9A14CYS0-0.085-0.02119.050-0.033-0.0330.0000.0000.0000.000
10A15ALA00.0330.02420.4530.0440.0440.0000.0000.0000.000
11A16ASP-1-0.756-0.85620.814-0.332-0.3320.0000.0000.0000.000
12A17ILE00.0240.01219.750-0.008-0.0080.0000.0000.0000.000
13A18ALA00.0230.00316.748-0.027-0.0270.0000.0000.0000.000
14A19ARG10.8130.88916.3180.2570.2570.0000.0000.0000.000
15A20LYS10.7820.89417.3720.2840.2840.0000.0000.0000.000
16A21VAL00.0310.00312.959-0.014-0.0140.0000.0000.0000.000
17A22SER00.0290.02012.108-0.134-0.1340.0000.0000.0000.000
18A23ARG10.8300.89811.4370.2260.2260.0000.0000.0000.000
19A24ALA00.0020.00411.7980.0050.0050.0000.0000.0000.000
20A25ILE00.009-0.0196.9280.0160.0160.0000.0000.0000.000
21A26HIS0-0.027-0.0077.329-0.201-0.2010.0000.0000.0000.000
22A27LEU0-0.036-0.0348.1480.0790.0790.0000.0000.0000.000
23A28ALA0-0.0120.0197.0170.2220.2220.0000.0000.0000.000
24A29PRO0-0.0010.0035.637-0.292-0.2920.0000.0000.0000.000
25A30ASN0-0.036-0.0303.3390.0250.8260.027-0.225-0.602-0.001
26A31ALA0-0.034-0.0252.458-7.410-4.9511.864-2.392-1.931-0.028
27A32THR00.0550.0352.2571.1861.7660.616-0.090-1.1060.000
28A33ILE00.0120.0134.411-0.243-0.242-0.001-0.0060.0070.000
29A34SER0-0.003-0.0016.079-0.084-0.0840.0000.0000.0000.000
30A35GLY00.0470.0208.3260.2920.2920.0000.0000.0000.000
31A36VAL0-0.0020.01211.818-0.027-0.0270.0000.0000.0000.000
32A37ALA0-0.0030.01814.8890.0590.0590.0000.0000.0000.000
33A38SER0-0.030-0.04718.5260.0240.0240.0000.0000.0000.000
34A39ARG10.9510.98922.0110.2870.2870.0000.0000.0000.000
35A40SER00.0440.00325.1070.0130.0130.0000.0000.0000.000
36A41LEU00.0460.01522.282-0.013-0.0130.0000.0000.0000.000
37A42GLU-1-0.840-0.90023.196-0.299-0.2990.0000.0000.0000.000
38A43LYS10.9200.94824.2870.2850.2850.0000.0000.0000.000
39A44ALA00.0390.02219.313-0.010-0.0100.0000.0000.0000.000
40A45LYS10.9510.98819.5360.3610.3610.0000.0000.0000.000
41A46ALA00.0030.01321.052-0.010-0.0100.0000.0000.0000.000
42A47PHE0-0.011-0.01516.8650.0170.0170.0000.0000.0000.000
43A48ALA00.0440.01516.672-0.010-0.0100.0000.0000.0000.000
44A49THR0-0.018-0.00817.442-0.006-0.0060.0000.0000.0000.000
45A50ALA00.0030.00019.455-0.005-0.0050.0000.0000.0000.000
46A51ASN0-0.100-0.06016.2560.0150.0150.0000.0000.0000.000
47A52ASN0-0.058-0.02814.6560.0020.0020.0000.0000.0000.000
48A53TYR0-0.046-0.04113.148-0.063-0.0630.0000.0000.0000.000
49A54PRO00.0320.0179.4830.0630.0630.0000.0000.0000.000
50A55GLU-1-0.900-0.95012.681-0.635-0.6350.0000.0000.0000.000
51A56SER0-0.055-0.0299.8430.0210.0210.0000.0000.0000.000
52A57THR0-0.068-0.02410.243-0.015-0.0150.0000.0000.0000.000
53A58LYS10.8050.90012.0131.0581.0580.0000.0000.0000.000
54A59ILE0-0.025-0.02614.607-0.010-0.0100.0000.0000.0000.000
55A60HIS00.0130.02815.5510.1270.1270.0000.0000.0000.000
56A61GLY0-0.052-0.04619.5280.0110.0110.0000.0000.0000.000
57A62SER00.0170.00221.8090.0280.0280.0000.0000.0000.000
58A63TYR00.0150.00520.745-0.048-0.0480.0000.0000.0000.000
59A64GLU-1-0.770-0.89720.551-0.331-0.3310.0000.0000.0000.000
60A65SER0-0.059-0.04620.015-0.002-0.0020.0000.0000.0000.000
61A66LEU0-0.008-0.01113.858-0.026-0.0260.0000.0000.0000.000
62A67LEU0-0.006-0.00516.412-0.081-0.0810.0000.0000.0000.000
63A68GLU-1-0.880-0.92718.324-0.296-0.2960.0000.0000.0000.000
64A69ASP-1-0.796-0.88414.556-0.905-0.9050.0000.0000.0000.000
65A70PRO00.0210.00714.867-0.086-0.0860.0000.0000.0000.000
66A71GLU-1-0.864-0.91410.752-1.063-1.0630.0000.0000.0000.000
67A72ILE0-0.063-0.0349.958-0.442-0.4420.0000.0000.0000.000
68A73ASP-1-0.742-0.8506.135-3.056-3.0560.0000.0000.0000.000
69A74ALA0-0.018-0.0138.9980.3500.3500.0000.0000.0000.000
70A75LEU0-0.008-0.00910.800-0.154-0.1540.0000.0000.0000.000
71A76TYR0-0.042-0.03712.6970.0750.0750.0000.0000.0000.000
72A77VAL00.020-0.00914.2670.0040.0040.0000.0000.0000.000
73A78PRO0-0.031-0.01817.3450.0640.0640.0000.0000.0000.000
74A79LEU0-0.042-0.01020.0430.0330.0330.0000.0000.0000.000
75A80PRO00.0300.01823.1250.0100.0100.0000.0000.0000.000
76A81THR0-0.032-0.05626.199-0.003-0.0030.0000.0000.0000.000
77A82SER0-0.024-0.01527.581-0.004-0.0040.0000.0000.0000.000
78A83LEU0-0.047-0.01025.6950.0030.0030.0000.0000.0000.000
79A84HIS10.8140.88823.4800.2370.2370.0000.0000.0000.000
80A85VAL00.0430.01324.821-0.009-0.0090.0000.0000.0000.000
81A86GLU-1-0.854-0.91227.155-0.216-0.2160.0000.0000.0000.000
82A87TRP0-0.028-0.04922.248-0.020-0.0200.0000.0000.0000.000
83A88ALA00.0000.00820.980-0.040-0.0400.0000.0000.0000.000
84A89ILE00.006-0.00221.451-0.009-0.0090.0000.0000.0000.000
85A90LYS10.8660.93722.9720.2480.2480.0000.0000.0000.000
86A91ALA0-0.025-0.01317.749-0.029-0.0290.0000.0000.0000.000
87A92ALA00.0310.00818.035-0.033-0.0330.0000.0000.0000.000
88A93GLU-1-0.940-0.96018.894-0.152-0.1520.0000.0000.0000.000
89A94LYS10.7810.89218.5950.3130.3130.0000.0000.0000.000
90A95GLY00.0050.00115.938-0.064-0.0640.0000.0000.0000.000
91A96LYS10.7670.89913.4220.6990.6990.0000.0000.0000.000
92A97HIS00.0660.0489.7580.0700.0700.0000.0000.0000.000
93A98ILE00.0040.00413.436-0.177-0.1770.0000.0000.0000.000
94A99LEU0-0.0200.00911.8200.0840.0840.0000.0000.0000.000
95A100LEU0-0.033-0.03014.969-0.037-0.0370.0000.0000.0000.000
96A101GLU-1-0.772-0.87118.687-0.328-0.3280.0000.0000.0000.000
97A102LYS10.8300.93720.5170.2220.2220.0000.0000.0000.000
98A103PRO00.019-0.01023.822-0.007-0.0070.0000.0000.0000.000
99A104VAL0-0.0050.00522.481-0.016-0.0160.0000.0000.0000.000
100A105ALA0-0.0280.01024.900-0.018-0.0180.0000.0000.0000.000
101A106MET00.0060.00627.9790.0040.0040.0000.0000.0000.000
102A107ASN0-0.029-0.02330.9020.0160.0160.0000.0000.0000.000
103A108VAL00.009-0.00530.182-0.008-0.0080.0000.0000.0000.000
104A109THR0-0.0040.00830.4910.0040.0040.0000.0000.0000.000
105A110GLU-1-0.873-0.94429.526-0.124-0.1240.0000.0000.0000.000
106A111PHE0-0.013-0.01822.699-0.009-0.0090.0000.0000.0000.000
107A112ASP-1-0.707-0.82726.218-0.033-0.0330.0000.0000.0000.000
108A113LYS10.9720.99627.1680.0850.0850.0000.0000.0000.000
109A114ILE0-0.031-0.01422.330-0.009-0.0090.0000.0000.0000.000
110A115VAL0-0.043-0.01122.838-0.013-0.0130.0000.0000.0000.000
111A116ASP-1-0.841-0.92223.106-0.008-0.0080.0000.0000.0000.000
112A117ALA0-0.0190.00123.9710.0120.0120.0000.0000.0000.000
113A118CYS0-0.060-0.03819.187-0.031-0.0310.0000.0000.0000.000
114A119GLU-1-0.944-0.96019.4840.0780.0780.0000.0000.0000.000
115A120ALA0-0.068-0.03021.4510.0290.0290.0000.0000.0000.000
116A121ASN0-0.076-0.04718.9130.0170.0170.0000.0000.0000.000
117A122GLY0-0.029-0.00217.6660.0010.0010.0000.0000.0000.000
118A123VAL0-0.051-0.02814.4910.0270.0270.0000.0000.0000.000
119A124GLN0-0.036-0.02512.7940.0200.0200.0000.0000.0000.000
120A125ILE00.009-0.00114.564-0.122-0.1220.0000.0000.0000.000
121A126MET0-0.070-0.03513.2710.1160.1160.0000.0000.0000.000
122A127ASP-1-0.728-0.79917.120-0.200-0.2000.0000.0000.0000.000
123A128GLY00.0790.03417.731-0.020-0.0200.0000.0000.0000.000
124A129THR0-0.093-0.06718.8130.0040.0040.0000.0000.0000.000
125A130MET00.0080.00017.6910.0260.0260.0000.0000.0000.000
126A131TRP00.0650.01619.0850.0180.0180.0000.0000.0000.000
127A132VAL0-0.0120.01319.9140.0200.0200.0000.0000.0000.000
128A133HIS10.8650.92915.9310.1520.1520.0000.0000.0000.000
129A134ASN0-0.024-0.00418.0240.0320.0320.0000.0000.0000.000
130A135PRO00.0990.03418.6570.0160.0160.0000.0000.0000.000
131A136ARG10.8030.86921.1840.0570.0570.0000.0000.0000.000
132A137THR0-0.064-0.03622.7040.0030.0030.0000.0000.0000.000
133A138ALA0-0.020-0.00622.3180.0100.0100.0000.0000.0000.000
134A139LEU00.0280.01824.4050.0060.0060.0000.0000.0000.000
135A140LEU0-0.016-0.02927.512-0.013-0.0130.0000.0000.0000.000
136A141LYS10.8840.93223.992-0.128-0.1280.0000.0000.0000.000
137A142GLU-1-0.787-0.88325.8440.1380.1380.0000.0000.0000.000
138A143PHE0-0.057-0.01129.952-0.001-0.0010.0000.0000.0000.000
139A144LEU0-0.013-0.00531.751-0.005-0.0050.0000.0000.0000.000
140A145SER0-0.033-0.02631.1660.0020.0020.0000.0000.0000.000
141A146ASP-1-0.784-0.87233.6830.0860.0860.0000.0000.0000.000
142A147SER00.0470.01936.432-0.007-0.0070.0000.0000.0000.000
143A148GLU-1-1.007-1.01439.5380.0640.0640.0000.0000.0000.000
144A149ARG10.8910.91835.352-0.079-0.0790.0000.0000.0000.000
145A150PHE00.0410.05337.459-0.007-0.0070.0000.0000.0000.000
146A151GLY0-0.064-0.01639.433-0.006-0.0060.0000.0000.0000.000
147A152GLN0-0.010-0.01739.5800.0070.0070.0000.0000.0000.000
148A153LEU00.0380.01736.182-0.005-0.0050.0000.0000.0000.000
149A154LYS10.8850.94839.951-0.028-0.0280.0000.0000.0000.000
150A155THR00.0290.00241.118-0.003-0.0030.0000.0000.0000.000
151A156VAL00.022-0.00334.9020.0030.0030.0000.0000.0000.000
152A157GLN0-0.038-0.00438.2560.0000.0000.0000.0000.0000.000
153A158SER0-0.0100.00233.275-0.002-0.0020.0000.0000.0000.000
154A159CYS0-0.073-0.01035.169-0.003-0.0030.0000.0000.0000.000
155A160PHE00.0580.00729.097-0.004-0.0040.0000.0000.0000.000
156A161SER0-0.061-0.02534.1080.0020.0020.0000.0000.0000.000
157A162PHE0-0.0220.02530.9230.0010.0010.0000.0000.0000.000
158A163ALA00.012-0.01434.8650.0030.0030.0000.0000.0000.000
159A164GLY0-0.025-0.02636.166-0.005-0.0050.0000.0000.0000.000
160A165ASP-1-0.845-0.92636.415-0.124-0.1240.0000.0000.0000.000
161A166GLU-1-0.838-0.93039.154-0.095-0.0950.0000.0000.0000.000
162A167ASP-1-0.880-0.92835.757-0.150-0.1500.0000.0000.0000.000
163A168PHE0-0.0150.00931.960-0.004-0.0040.0000.0000.0000.000
164A169LEU0-0.027-0.02236.152-0.003-0.0030.0000.0000.0000.000
165A170LYS10.8610.94338.7990.1070.1070.0000.0000.0000.000
166A171ASN0-0.036-0.04935.6510.0010.0010.0000.0000.0000.000
167A172ASP-1-0.791-0.86330.989-0.197-0.1970.0000.0000.0000.000
168A173ILE00.038-0.01127.3320.0090.0090.0000.0000.0000.000
169A174ARG10.7950.88428.1870.1910.1910.0000.0000.0000.000
170A175VAL00.0310.01832.4680.0110.0110.0000.0000.0000.000
171A176LYS10.7630.88934.2790.1520.1520.0000.0000.0000.000
172A177PRO00.0470.02334.895-0.006-0.0060.0000.0000.0000.000
173A178GLY0-0.0020.00035.4690.0010.0010.0000.0000.0000.000
174A179LEU0-0.080-0.03030.609-0.010-0.0100.0000.0000.0000.000
175A180ASP-1-0.745-0.85427.975-0.216-0.2160.0000.0000.0000.000
176A181GLY00.0160.00831.1130.0080.0080.0000.0000.0000.000
177A182LEU0-0.007-0.00430.6550.0090.0090.0000.0000.0000.000
178A183GLY00.0200.01933.8630.0090.0090.0000.0000.0000.000
179A184ALA0-0.006-0.00632.888-0.006-0.0060.0000.0000.0000.000
180A185LEU00.0130.01933.236-0.001-0.0010.0000.0000.0000.000
181A186GLY00.020-0.00930.8250.0010.0010.0000.0000.0000.000
182A187ASP-1-0.866-0.94027.463-0.185-0.1850.0000.0000.0000.000
183A188ALA0-0.018-0.02428.610-0.004-0.0040.0000.0000.0000.000
184A189GLY00.038-0.00931.0070.0070.0070.0000.0000.0000.000
185A190TRP00.0080.01124.1570.0100.0100.0000.0000.0000.000
186A191TYR00.005-0.00223.7680.0020.0020.0000.0000.0000.000
187A192ALA00.0290.02628.4690.0120.0120.0000.0000.0000.000
188A193ILE00.0150.00130.9790.0120.0120.0000.0000.0000.000
189A194ARG10.8470.92322.4340.0840.0840.0000.0000.0000.000
190A195ALA00.0030.00128.6340.0150.0150.0000.0000.0000.000
191A196THR0-0.052-0.02829.9770.0130.0130.0000.0000.0000.000
192A197LEU0-0.007-0.00229.5270.0090.0090.0000.0000.0000.000
193A198LEU0-0.032-0.01125.6150.0120.0120.0000.0000.0000.000
194A199ALA0-0.014-0.01429.1780.0120.0120.0000.0000.0000.000
195A200ASN0-0.023-0.02232.6020.0100.0100.0000.0000.0000.000
196A201ASN0-0.039-0.01729.9140.0120.0120.0000.0000.0000.000
197A202PHE0-0.008-0.00624.9860.0060.0060.0000.0000.0000.000
198A203GLU-1-0.849-0.90629.6890.0670.0670.0000.0000.0000.000
199A204LEU00.005-0.01031.874-0.006-0.0060.0000.0000.0000.000
200A205PRO00.0110.01334.4450.0050.0050.0000.0000.0000.000
201A206LYS10.9150.94637.825-0.025-0.0250.0000.0000.0000.000
202A207THR0-0.054-0.02241.150-0.002-0.0020.0000.0000.0000.000
203A208VAL00.0240.00338.0830.0000.0000.0000.0000.0000.000
204A209THR0-0.0060.01141.350-0.001-0.0010.0000.0000.0000.000
205A210ALA00.0280.03442.0770.0000.0000.0000.0000.0000.000
206A211PHE0-0.039-0.01842.2270.0030.0030.0000.0000.0000.000
207A212PRO00.0360.00245.535-0.003-0.0030.0000.0000.0000.000
208A213GLY0-0.026-0.00547.3740.0000.0000.0000.0000.0000.000
209A214ALA0-0.030-0.00543.157-0.002-0.0020.0000.0000.0000.000
210A215VAL00.0020.00243.1290.0010.0010.0000.0000.0000.000
211A216LEU00.0230.00041.874-0.005-0.0050.0000.0000.0000.000
212A217ASN00.0000.00139.6830.0050.0050.0000.0000.0000.000
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