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: G53N1

Calculation Name: 4QLP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4QLP

Chain ID: A

ChEMBL ID:

UniProt ID: O05442

Base Structure: X-ray

Registration Date: 2023-09-23

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1837783.314305
FMO2-HF: Nuclear repulsion 1768455.734943
FMO2-HF: Total energy -69327.579362
FMO2-MP2: Total energy -69529.403669


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:THR)


Summations of interaction energy for fragment #1(A:1:THR)
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.
-7.683-1.6891.214-2.785-4.42-0.011
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.004
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].
3A3GLY0-0.017-0.0233.735-1.3230.518-0.007-0.845-0.9890.003
4A4VAL00.003-0.0104.170-1.118-1.002-0.001-0.039-0.0760.000
5A5ASP-1-0.821-0.8552.361-2.814-2.1540.646-0.375-0.931-0.001
6A6LEU0-0.055-0.0403.002-2.704-0.8960.260-1.083-0.984-0.010
7A7SER0-0.014-0.0382.987-1.284-0.0460.295-0.488-1.045-0.003
8A8THR00.0410.0013.551-0.167-0.2260.0230.094-0.0570.000
9A9ASP-1-0.793-0.8436.6950.4650.4650.0000.0000.0000.000
10A10LEU00.0110.0126.549-0.190-0.1900.0000.0000.0000.000
11A11GLN0-0.019-0.0346.038-0.224-0.2240.0000.0000.0000.000
12A12ASP-1-0.946-0.9679.1090.3630.3630.0000.0000.0000.000
13A13TRP0-0.067-0.02711.453-0.020-0.0200.0000.0000.0000.000
14A14ILE00.0470.0139.878-0.038-0.0380.0000.0000.0000.000
15A15ARG10.9610.99411.8360.0260.0260.0000.0000.0000.000
16A16LEU0-0.064-0.03615.163-0.004-0.0040.0000.0000.0000.000
17A17SER0-0.072-0.03216.285-0.015-0.0150.0000.0000.0000.000
18A18GLY00.0350.02618.253-0.013-0.0130.0000.0000.0000.000
19A19MET0-0.112-0.03015.195-0.021-0.0210.0000.0000.0000.000
20A20ASN0-0.094-0.05815.6840.0620.0620.0000.0000.0000.000
21A21MET00.001-0.0087.7270.0430.0430.0000.0000.0000.000
22A22ILE0-0.021-0.00611.9060.1040.1040.0000.0000.0000.000
23A23GLN00.0360.0294.887-0.561-0.5610.0000.0000.0000.000
24A24GLY00.0930.0407.5940.1980.1980.0000.0000.0000.000
25A25SER0-0.136-0.0936.3370.5490.5490.0000.0000.0000.000
26A26GLU-1-0.949-0.9698.541-0.377-0.3770.0000.0000.0000.000
27A27THR0-0.094-0.03711.5530.2160.2160.0000.0000.0000.000
28A28ASN0-0.036-0.03913.472-0.078-0.0780.0000.0000.0000.000
29A29ASP-1-0.946-0.97815.150-0.830-0.8300.0000.0000.0000.000
30A30GLY0-0.0300.00811.077-0.064-0.0640.0000.0000.0000.000
31A31ARG10.8200.88310.6460.4950.4950.0000.0000.0000.000
32A32THR00.009-0.0126.9740.0850.0850.0000.0000.0000.000
33A33ILE0-0.038-0.00410.0510.1660.1660.0000.0000.0000.000
34A34LEU00.011-0.00110.5450.0230.0230.0000.0000.0000.000
35A35TRP0-0.017-0.01314.5020.0180.0180.0000.0000.0000.000
36A36ASN00.1380.08018.1010.0080.0080.0000.0000.0000.000
37A37LYS10.9880.97920.5440.0690.0690.0000.0000.0000.000
38A38GLY0-0.018-0.01723.5750.0010.0010.0000.0000.0000.000
39A39GLY0-0.024-0.00621.942-0.008-0.0080.0000.0000.0000.000
40A40GLU-1-0.957-0.96822.980-0.157-0.1570.0000.0000.0000.000
41A41VAL00.0390.02820.445-0.005-0.0050.0000.0000.0000.000
42A42ARG10.8730.93518.5560.3570.3570.0000.0000.0000.000
43A43TYR00.019-0.01715.0100.0200.0200.0000.0000.0000.000
44A44PHE0-0.004-0.00513.931-0.019-0.0190.0000.0000.0000.000
45A45ILE0-0.015-0.0068.7300.0710.0710.0000.0000.0000.000
46A46ASP-1-0.780-0.89311.007-1.294-1.2940.0000.0000.0000.000
47A47ARG10.8870.9417.7092.3822.3820.0000.0000.0000.000
48A48LEU00.0320.02111.8310.1020.1020.0000.0000.0000.000
49A49ALA0-0.039-0.03315.5720.0340.0340.0000.0000.0000.000
50A50GLY0-0.0050.00314.8200.0580.0580.0000.0000.0000.000
51A51TRP0-0.0030.00813.5500.0310.0310.0000.0000.0000.000
52A52TYR0-0.015-0.0106.923-0.316-0.3160.0000.0000.0000.000
53A53VAL0-0.025-0.02511.1780.1980.1980.0000.0000.0000.000
54A54ILE00.0310.01512.273-0.107-0.1070.0000.0000.0000.000
55A55THR0-0.056-0.03314.7760.0700.0700.0000.0000.0000.000
56A56SER00.013-0.02617.320-0.036-0.0360.0000.0000.0000.000
57A57SER0-0.030-0.01919.9290.0160.0160.0000.0000.0000.000
58A58ASP-1-0.725-0.82922.706-0.183-0.1830.0000.0000.0000.000
59A59ARG10.8470.87625.5810.1640.1640.0000.0000.0000.000
60A60MET0-0.069-0.02623.752-0.003-0.0030.0000.0000.0000.000
61A61SER0-0.069-0.01926.067-0.007-0.0070.0000.0000.0000.000
62A62ARG10.9460.96525.2450.2340.2340.0000.0000.0000.000
63A63GLU-1-0.780-0.84919.451-0.533-0.5330.0000.0000.0000.000
64A64GLY0-0.033-0.01122.5980.0220.0220.0000.0000.0000.000
65A65TYR0-0.081-0.06818.962-0.041-0.0410.0000.0000.0000.000
66A66GLU-1-0.828-0.88817.692-0.265-0.2650.0000.0000.0000.000
67A67PHE0-0.031-0.03113.2400.0560.0560.0000.0000.0000.000
68A68ALA00.0180.02414.498-0.085-0.0850.0000.0000.0000.000
69A69ALA00.0150.00511.8450.1040.1040.0000.0000.0000.000
70A70ALA00.0450.02312.415-0.139-0.1390.0000.0000.0000.000
71A71SER0-0.013-0.0148.5190.0040.0040.0000.0000.0000.000
72A72MET00.0860.0453.9540.2610.433-0.001-0.015-0.1560.000
73A73SER0-0.0080.0146.4320.3360.3360.0000.0000.0000.000
74A74VAL00.0140.0048.103-0.004-0.0040.0000.0000.0000.000
75A75ILE0-0.009-0.0018.2030.0250.0250.0000.0000.0000.000
76A76GLU-1-0.755-0.8634.2230.0920.310-0.001-0.034-0.1820.000
77A77LYS10.8440.9448.692-0.352-0.3520.0000.0000.0000.000
78A78TYR00.0430.03312.0370.0000.0000.0000.0000.0000.000
79A79LEU00.000-0.0049.286-0.006-0.0060.0000.0000.0000.000
80A80TYR0-0.050-0.0688.8390.0230.0230.0000.0000.0000.000
81A81GLY00.0190.00413.1890.0040.0040.0000.0000.0000.000
82A82TYR0-0.047-0.00215.424-0.007-0.0070.0000.0000.0000.000
83A83PHE00.0490.00313.301-0.015-0.0150.0000.0000.0000.000
84A84GLY00.0250.02216.7870.0180.0180.0000.0000.0000.000
85A85GLY00.024-0.00218.0990.0140.0140.0000.0000.0000.000
86A86SER00.0160.00519.8000.0050.0050.0000.0000.0000.000
87A87VAL0-0.0080.00616.8810.0070.0070.0000.0000.0000.000
88A88ARG10.7230.84120.138-0.057-0.0570.0000.0000.0000.000
89A89SER00.005-0.01323.1860.0020.0020.0000.0000.0000.000
90A90GLU-1-0.924-0.94722.136-0.009-0.0090.0000.0000.0000.000
91A91ARG10.8410.93420.636-0.121-0.1210.0000.0000.0000.000
92A92GLU-1-0.970-0.98026.2260.0200.0200.0000.0000.0000.000
93A93LEU0-0.043-0.00625.4170.0030.0030.0000.0000.0000.000
94A94PRO0-0.017-0.00628.986-0.011-0.0110.0000.0000.0000.000
95A95ALA00.0320.01028.6100.0050.0050.0000.0000.0000.000
96A96ILE00.0200.01223.6700.0040.0040.0000.0000.0000.000
97A97ARG10.7690.88627.790-0.014-0.0140.0000.0000.0000.000
98A98ALA00.0410.01823.7430.0150.0150.0000.0000.0000.000
99A99PRO0-0.054-0.03024.457-0.010-0.0100.0000.0000.0000.000
100A100PHE00.011-0.01625.303-0.005-0.0050.0000.0000.0000.000
101A101GLN0-0.064-0.03127.299-0.014-0.0140.0000.0000.0000.000
102A102PRO00.0410.00729.8640.0050.0050.0000.0000.0000.000
103A103GLU-1-0.874-0.93930.813-0.013-0.0130.0000.0000.0000.000
104A104GLU-1-0.775-0.86828.5210.0130.0130.0000.0000.0000.000
105A105LEU0-0.0300.01024.8070.0060.0060.0000.0000.0000.000
106A106MET0-0.048-0.00823.2550.0020.0020.0000.0000.0000.000
107A107PRO00.025-0.00626.121-0.011-0.0110.0000.0000.0000.000
108A108GLU-1-0.911-0.94722.8070.0790.0790.0000.0000.0000.000
109A109TYR0-0.017-0.01918.699-0.004-0.0040.0000.0000.0000.000
110A110SER0-0.006-0.00624.947-0.002-0.0020.0000.0000.0000.000
111A111ILE00.000-0.00524.854-0.010-0.0100.0000.0000.0000.000
112A112GLY00.0140.00625.6410.0080.0080.0000.0000.0000.000
113A113THR0-0.026-0.01626.655-0.007-0.0070.0000.0000.0000.000
114A114MET0-0.0040.00221.164-0.001-0.0010.0000.0000.0000.000
115A115THR0-0.048-0.06926.1600.0040.0040.0000.0000.0000.000
116A116PHE00.0350.01517.532-0.011-0.0110.0000.0000.0000.000
117A117ALA00.0130.01520.9620.0160.0160.0000.0000.0000.000
118A118GLY00.0170.00523.0110.0130.0130.0000.0000.0000.000
119A119ARG10.9180.96726.2970.2240.2240.0000.0000.0000.000
120A120GLN00.0630.08326.636-0.025-0.0250.0000.0000.0000.000
121A121ARG10.8360.91222.5350.2900.2900.0000.0000.0000.000
122A122ASP-1-0.789-0.89025.115-0.137-0.1370.0000.0000.0000.000
123A123THR0-0.017-0.02321.971-0.020-0.0200.0000.0000.0000.000
124A124LEU00.0350.02818.9420.0210.0210.0000.0000.0000.000
125A125ILE0-0.043-0.01120.456-0.025-0.0250.0000.0000.0000.000
126A126ASP-1-0.756-0.86419.150-0.029-0.0290.0000.0000.0000.000
127A127SER00.0350.00621.855-0.012-0.0120.0000.0000.0000.000
128A128SER0-0.124-0.07621.561-0.007-0.0070.0000.0000.0000.000
129A129GLY0-0.002-0.00724.027-0.007-0.0070.0000.0000.0000.000
130A130THR0-0.041-0.01318.971-0.027-0.0270.0000.0000.0000.000
131A131VAL0-0.047-0.02018.7070.0140.0140.0000.0000.0000.000
132A132VAL00.0270.01115.686-0.034-0.0340.0000.0000.0000.000
133A133ALA0-0.022-0.02115.173-0.054-0.0540.0000.0000.0000.000
134A134ILE0-0.0020.00817.2120.0370.0370.0000.0000.0000.000
135A135THR0-0.032-0.01519.067-0.030-0.0300.0000.0000.0000.000
136A136ALA00.0230.02521.5320.0130.0130.0000.0000.0000.000
137A137ALA00.0630.01024.0890.0040.0040.0000.0000.0000.000
138A138ASP-1-0.886-0.93925.550-0.096-0.0960.0000.0000.0000.000
139A139ARG10.9100.93519.2930.2150.2150.0000.0000.0000.000
140A140LEU0-0.074-0.02420.0710.0070.0070.0000.0000.0000.000
141A141VAL00.0010.02022.1020.0200.0200.0000.0000.0000.000
142A142GLU-1-0.840-0.87420.944-0.012-0.0120.0000.0000.0000.000
143A143LEU0-0.033-0.02315.3770.0210.0210.0000.0000.0000.000
144A144SER0-0.037-0.03618.6550.0380.0380.0000.0000.0000.000
145A145HIS10.8790.92120.812-0.025-0.0250.0000.0000.0000.000
146A146TYR0-0.051-0.05216.0630.0430.0430.0000.0000.0000.000
147A147LEU0-0.066-0.04714.8260.0570.0570.0000.0000.0000.000
148A148ASP-1-0.890-0.93616.9500.2040.2040.0000.0000.0000.000
149A149VAL00.0010.03518.0200.0280.0280.0000.0000.0000.000
150A150SER0-0.040-0.03915.5500.0320.0320.0000.0000.0000.000
151A151VAL00.0860.02110.375-0.055-0.0550.0000.0000.0000.000
152A152ASN0-0.018-0.01413.778-0.036-0.0360.0000.0000.0000.000
153A153VAL00.0530.04016.421-0.038-0.0380.0000.0000.0000.000
154A154ILE00.0010.00714.536-0.038-0.0380.0000.0000.0000.000
155A155LYS10.8380.90912.504-0.539-0.5390.0000.0000.0000.000
156A156ASP-1-0.879-0.94817.3500.2700.2700.0000.0000.0000.000
157A157SER0-0.026-0.01120.650-0.028-0.0280.0000.0000.0000.000
158A158PHE0-0.025-0.01618.229-0.020-0.0200.0000.0000.0000.000
159A159LEU0-0.043-0.01619.229-0.019-0.0190.0000.0000.0000.000
160A160ASP-1-0.821-0.88622.8530.1180.1180.0000.0000.0000.000
161A161SER0-0.032-0.02325.863-0.011-0.0110.0000.0000.0000.000
162A162GLU-1-0.894-0.95029.1910.0590.0590.0000.0000.0000.000
163A163GLY0-0.036-0.01325.895-0.009-0.0090.0000.0000.0000.000
164A164LYS10.8520.96425.824-0.079-0.0790.0000.0000.0000.000
165A165PRO00.020-0.01923.6070.0090.0090.0000.0000.0000.000
166A166LEU0-0.021-0.02120.055-0.013-0.0130.0000.0000.0000.000
167A167PHE0-0.0050.01520.861-0.016-0.0160.0000.0000.0000.000
168A168THR0-0.058-0.03026.7440.0040.0040.0000.0000.0000.000
169A169LEU00.0600.03629.546-0.007-0.0070.0000.0000.0000.000
170A170TRP00.0450.00529.6520.0000.0000.0000.0000.0000.000
171A171LYS10.8420.92133.387-0.041-0.0410.0000.0000.0000.000
172A172ASP-1-0.866-0.92335.1850.0410.0410.0000.0000.0000.000
173A173TYR0-0.008-0.01434.8340.0010.0010.0000.0000.0000.000
174A174LYS10.8970.94736.895-0.029-0.0290.0000.0000.0000.000
175A175GLY0-0.0060.01938.848-0.002-0.0020.0000.0000.0000.000