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: 89Y2Y

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1838510.737467
FMO2-HF: Nuclear repulsion 1769182.752529
FMO2-HF: Total energy -69327.984938
FMO2-MP2: Total energy -69529.837178


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.
-13.882-6.6891.842-3.602-5.432-0.017
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 : 0.015 / q_NPA : 0.002
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].
3A3GLY0-0.001-0.0123.703-1.8240.354-0.006-1.043-1.1290.004
4A4VAL00.003-0.0084.8370.1340.213-0.001-0.012-0.0660.000
5A5ASP-1-0.820-0.8482.249-3.222-2.6430.959-0.497-1.041-0.002
6A6LEU0-0.043-0.0332.807-8.144-5.4600.373-1.594-1.463-0.016
7A7SER0-0.019-0.0452.872-0.3790.9720.490-0.599-1.241-0.003
8A8THR00.0540.0123.441-0.005-0.1440.0300.180-0.0710.000
9A9ASP-1-0.808-0.8506.6340.1090.1090.0000.0000.0000.000
10A10LEU00.0110.0166.443-0.080-0.0800.0000.0000.0000.000
11A11GLN0-0.006-0.0286.2790.1110.1110.0000.0000.0000.000
12A12ASP-1-0.861-0.9168.9400.1340.1340.0000.0000.0000.000
13A13TRP0-0.067-0.01911.3320.0380.0380.0000.0000.0000.000
14A14ILE00.0440.0139.7580.0040.0040.0000.0000.0000.000
15A15ARG10.8590.93411.4860.1950.1950.0000.0000.0000.000
16A16LEU0-0.065-0.03414.9920.0300.0300.0000.0000.0000.000
17A17SER0-0.072-0.04016.0700.0030.0030.0000.0000.0000.000
18A18GLY00.0380.02618.0850.0020.0020.0000.0000.0000.000
19A19MET0-0.115-0.03115.0670.0040.0040.0000.0000.0000.000
20A20ASN0-0.068-0.03815.5010.0550.0550.0000.0000.0000.000
21A21MET00.000-0.0127.6090.0160.0160.0000.0000.0000.000
22A22ILE0-0.0160.00111.8060.1150.1150.0000.0000.0000.000
23A23GLN00.0320.0184.685-0.607-0.528-0.001-0.004-0.0740.000
24A24GLY00.0950.0427.5170.2500.2500.0000.0000.0000.000
25A25SER0-0.129-0.0886.1480.5110.5110.0000.0000.0000.000
26A26GLU-1-0.957-0.9718.446-0.349-0.3490.0000.0000.0000.000
27A27THR0-0.093-0.05011.4370.1660.1660.0000.0000.0000.000
28A28ASN0-0.033-0.03513.393-0.030-0.0300.0000.0000.0000.000
29A29ASP-1-0.911-0.96715.047-0.691-0.6910.0000.0000.0000.000
30A30GLY0-0.0190.01511.031-0.022-0.0220.0000.0000.0000.000
31A31ARG10.8310.89810.6320.4680.4680.0000.0000.0000.000
32A32THR00.002-0.0186.9750.1450.1450.0000.0000.0000.000
33A33ILE0-0.026-0.00110.0150.1480.1480.0000.0000.0000.000
34A34LEU00.0160.00210.338-0.014-0.0140.0000.0000.0000.000
35A35TRP0-0.031-0.02214.3400.0500.0500.0000.0000.0000.000
36A36ASN00.1250.06517.932-0.001-0.0010.0000.0000.0000.000
37A37LYS10.9930.98220.3750.1400.1400.0000.0000.0000.000
38A38GLY0-0.015-0.01523.3930.0050.0050.0000.0000.0000.000
39A39GLY0-0.022-0.00821.8040.0000.0000.0000.0000.0000.000
40A40GLU-1-0.937-0.95022.862-0.209-0.2090.0000.0000.0000.000
41A41VAL00.0280.01820.4620.0020.0020.0000.0000.0000.000
42A42ARG10.8720.93018.6320.3590.3590.0000.0000.0000.000
43A43TYR00.0490.01814.7900.0320.0320.0000.0000.0000.000
44A44PHE00.0020.00013.902-0.025-0.0250.0000.0000.0000.000
45A45ILE0-0.013-0.0038.2310.0520.0520.0000.0000.0000.000
46A46ASP-1-0.787-0.90010.976-0.953-0.9530.0000.0000.0000.000
47A47ARG10.8520.9288.4861.3241.3240.0000.0000.0000.000
48A48LEU00.0230.01912.2510.0820.0820.0000.0000.0000.000
49A49ALA0-0.032-0.03315.9560.0210.0210.0000.0000.0000.000
50A50GLY0-0.0070.00215.5080.0390.0390.0000.0000.0000.000
51A51TRP0-0.0140.00313.8580.0350.0350.0000.0000.0000.000
52A52TYR0-0.008-0.0037.222-0.097-0.0970.0000.0000.0000.000
53A53VAL0-0.028-0.02711.2240.1060.1060.0000.0000.0000.000
54A54ILE00.0260.01411.469-0.105-0.1050.0000.0000.0000.000
55A55THR0-0.052-0.04414.2410.0860.0860.0000.0000.0000.000
56A56SER00.009-0.03016.862-0.051-0.0510.0000.0000.0000.000
57A57SER0-0.048-0.03019.5200.0330.0330.0000.0000.0000.000
58A58ASP-1-0.726-0.81122.526-0.228-0.2280.0000.0000.0000.000
59A59ARG10.8460.86525.3710.2070.2070.0000.0000.0000.000
60A60MET0-0.066-0.02223.7040.0030.0030.0000.0000.0000.000
61A61SER0-0.060-0.01726.0390.0010.0010.0000.0000.0000.000
62A62ARG10.9550.97125.2090.2260.2260.0000.0000.0000.000
63A63GLU-1-0.790-0.85019.135-0.510-0.5100.0000.0000.0000.000
64A64GLY0-0.061-0.02422.1390.0310.0310.0000.0000.0000.000
65A65TYR0-0.069-0.06618.710-0.036-0.0360.0000.0000.0000.000
66A66GLU-1-0.816-0.88116.995-0.361-0.3610.0000.0000.0000.000
67A67PHE0-0.013-0.02612.5000.0550.0550.0000.0000.0000.000
68A68ALA00.0080.01914.162-0.067-0.0670.0000.0000.0000.000
69A69ALA00.0200.00511.5200.0770.0770.0000.0000.0000.000
70A70ALA00.0420.02512.426-0.076-0.0760.0000.0000.0000.000
71A71SER0-0.010-0.0168.6770.0750.0750.0000.0000.0000.000
72A72MET00.0790.0473.9760.4430.642-0.001-0.021-0.1780.000
73A73SER0-0.0110.0096.091-0.162-0.1620.0000.0000.0000.000
74A74VAL00.0150.0087.653-0.022-0.0220.0000.0000.0000.000
75A75ILE0-0.010-0.0027.4740.0360.0360.0000.0000.0000.000
76A76GLU-1-0.755-0.8584.545-2.289-2.106-0.001-0.012-0.1690.000
77A77LYS10.8180.9268.5530.0410.0410.0000.0000.0000.000
78A78TYR00.0320.01311.9570.0650.0650.0000.0000.0000.000
79A79LEU00.003-0.0029.1050.0490.0490.0000.0000.0000.000
80A80TYR0-0.045-0.0688.9110.0250.0250.0000.0000.0000.000
81A81GLY00.0180.00113.1750.0520.0520.0000.0000.0000.000
82A82TYR0-0.079-0.03915.3980.0350.0350.0000.0000.0000.000
83A83PHE00.0530.00413.3780.0050.0050.0000.0000.0000.000
84A84GLY00.0240.02016.7140.0350.0350.0000.0000.0000.000
85A85GLY00.020-0.00318.0460.0320.0320.0000.0000.0000.000
86A86SER00.0140.00919.6460.0100.0100.0000.0000.0000.000
87A87VAL0-0.012-0.00216.7690.0170.0170.0000.0000.0000.000
88A88ARG10.7190.83920.0390.0490.0490.0000.0000.0000.000
89A89SER00.011-0.00923.1090.0080.0080.0000.0000.0000.000
90A90GLU-1-0.935-0.95422.039-0.104-0.1040.0000.0000.0000.000
91A91ARG10.8370.92820.0790.0090.0090.0000.0000.0000.000
92A92GLU-1-0.964-0.97226.120-0.041-0.0410.0000.0000.0000.000
93A93LEU0-0.044-0.00725.3120.0090.0090.0000.0000.0000.000
94A94PRO0-0.013-0.00428.913-0.010-0.0100.0000.0000.0000.000
95A95ALA00.0320.00828.557-0.001-0.0010.0000.0000.0000.000
96A96ILE00.0240.01223.4690.0100.0100.0000.0000.0000.000
97A97ARG10.7160.83727.7700.0400.0400.0000.0000.0000.000
98A98ALA00.0330.01223.7150.0130.0130.0000.0000.0000.000
99A99PRO0-0.045-0.02724.463-0.004-0.0040.0000.0000.0000.000
100A100PHE00.001-0.02625.107-0.011-0.0110.0000.0000.0000.000
101A101GLN0-0.040-0.02226.948-0.009-0.0090.0000.0000.0000.000
102A102PRO00.0390.01129.3270.0030.0030.0000.0000.0000.000
103A103GLU-1-0.852-0.92530.112-0.045-0.0450.0000.0000.0000.000
104A104GLU-1-0.755-0.83128.247-0.043-0.0430.0000.0000.0000.000
105A105LEU0-0.0190.01424.283-0.001-0.0010.0000.0000.0000.000
106A106MET0-0.033-0.00322.9530.0060.0060.0000.0000.0000.000
107A107PRO00.012-0.00525.587-0.007-0.0070.0000.0000.0000.000
108A108GLU-1-0.888-0.94522.6500.0330.0330.0000.0000.0000.000
109A109TYR0-0.017-0.02019.067-0.010-0.0100.0000.0000.0000.000
110A110SER0-0.013-0.00724.5360.0000.0000.0000.0000.0000.000
111A111ILE0-0.003-0.00924.123-0.012-0.0120.0000.0000.0000.000
112A112GLY00.0180.01425.3380.0110.0110.0000.0000.0000.000
113A113THR0-0.025-0.01926.400-0.010-0.0100.0000.0000.0000.000
114A114MET0-0.0020.00721.3690.0040.0040.0000.0000.0000.000
115A115THR0-0.017-0.01926.093-0.004-0.0040.0000.0000.0000.000
116A116PHE00.0430.02117.684-0.004-0.0040.0000.0000.0000.000
117A117ALA00.0150.01520.8310.0050.0050.0000.0000.0000.000
118A118GLY00.0190.01222.9670.0030.0030.0000.0000.0000.000
119A119ARG10.9220.97026.1880.2050.2050.0000.0000.0000.000
120A120GLN00.0280.02726.510-0.015-0.0150.0000.0000.0000.000
121A121ARG10.8240.90322.2610.2720.2720.0000.0000.0000.000
122A122ASP-1-0.793-0.89624.653-0.145-0.1450.0000.0000.0000.000
123A123THR0-0.019-0.02521.666-0.021-0.0210.0000.0000.0000.000
124A124LEU00.0350.02918.3900.0170.0170.0000.0000.0000.000
125A125ILE0-0.033-0.00820.212-0.014-0.0140.0000.0000.0000.000
126A126ASP-1-0.752-0.85619.053-0.004-0.0040.0000.0000.0000.000
127A127SER00.0460.01021.667-0.001-0.0010.0000.0000.0000.000
128A128SER0-0.133-0.08421.615-0.001-0.0010.0000.0000.0000.000
129A129GLY0-0.004-0.00824.049-0.003-0.0030.0000.0000.0000.000
130A130THR0-0.045-0.01619.346-0.018-0.0180.0000.0000.0000.000
131A131VAL0-0.051-0.02318.6560.0030.0030.0000.0000.0000.000
132A132VAL00.0290.01015.498-0.015-0.0150.0000.0000.0000.000
133A133ALA0-0.020-0.01914.941-0.064-0.0640.0000.0000.0000.000
134A134ILE00.0020.00816.8660.0460.0460.0000.0000.0000.000
135A135THR0-0.049-0.02418.611-0.040-0.0400.0000.0000.0000.000
136A136ALA00.0150.02720.9730.0190.0190.0000.0000.0000.000
137A137ALA00.0690.01023.371-0.005-0.0050.0000.0000.0000.000
138A138ASP-1-0.880-0.93624.802-0.157-0.1570.0000.0000.0000.000
139A139ARG10.9310.95819.0540.3110.3110.0000.0000.0000.000
140A140LEU0-0.070-0.02119.349-0.008-0.0080.0000.0000.0000.000
141A141VAL0-0.0010.01821.3640.0150.0150.0000.0000.0000.000
142A142GLU-1-0.856-0.87221.121-0.149-0.1490.0000.0000.0000.000
143A143LEU0-0.026-0.01914.7450.0090.0090.0000.0000.0000.000
144A144SER0-0.042-0.04218.2200.0280.0280.0000.0000.0000.000
145A145HIS10.8780.92220.4080.0500.0500.0000.0000.0000.000
146A146TYR0-0.044-0.04816.1070.0380.0380.0000.0000.0000.000
147A147LEU0-0.050-0.03014.2710.0320.0320.0000.0000.0000.000
148A148ASP-1-0.911-0.95016.5810.1290.1290.0000.0000.0000.000
149A149VAL0-0.0070.03018.1850.0330.0330.0000.0000.0000.000
150A150SER0-0.038-0.03915.6040.0040.0040.0000.0000.0000.000
151A151VAL00.0830.02410.457-0.047-0.0470.0000.0000.0000.000
152A152ASN0-0.020-0.01813.845-0.037-0.0370.0000.0000.0000.000
153A153VAL00.0640.04816.466-0.029-0.0290.0000.0000.0000.000
154A154ILE0-0.0040.01614.528-0.031-0.0310.0000.0000.0000.000
155A155LYS10.8170.89512.270-0.284-0.2840.0000.0000.0000.000
156A156ASP-1-0.880-0.95517.3430.1500.1500.0000.0000.0000.000
157A157SER0-0.026-0.02120.652-0.012-0.0120.0000.0000.0000.000
158A158PHE0-0.025-0.01217.957-0.011-0.0110.0000.0000.0000.000
159A159LEU0-0.043-0.01419.111-0.011-0.0110.0000.0000.0000.000
160A160ASP-1-0.804-0.87422.8110.0440.0440.0000.0000.0000.000
161A161SER0-0.041-0.03725.842-0.012-0.0120.0000.0000.0000.000
162A162GLU-1-0.886-0.93329.1570.0000.0000.0000.0000.0000.000
163A163GLY0-0.029-0.00925.886-0.007-0.0070.0000.0000.0000.000
164A164LYS10.8050.92325.840-0.016-0.0160.0000.0000.0000.000
165A165PRO00.023-0.01923.5950.0060.0060.0000.0000.0000.000
166A166LEU0-0.011-0.01420.082-0.006-0.0060.0000.0000.0000.000
167A167PHE00.0040.01520.729-0.010-0.0100.0000.0000.0000.000
168A168THR0-0.037-0.01026.7690.0110.0110.0000.0000.0000.000
169A169LEU00.0500.03129.546-0.010-0.0100.0000.0000.0000.000
170A170TRP00.0410.00229.4520.0070.0070.0000.0000.0000.000
171A171LYS10.8210.91733.3700.0090.0090.0000.0000.0000.000
172A172ASP-1-0.851-0.91235.244-0.004-0.0040.0000.0000.0000.000
173A173TYR00.0220.01134.6180.0040.0040.0000.0000.0000.000
174A174LYS10.8740.91836.9030.0110.0110.0000.0000.0000.000
175A175GLY0-0.0070.02038.8480.0000.0000.0000.0000.0000.000