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: ZVLKN

Calculation Name: 1QIL-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1QIL

Chain ID: C

ChEMBL ID:

UniProt ID: P06886

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2191032.545194
FMO2-HF: Nuclear repulsion 2114831.40122
FMO2-HF: Total energy -76201.143974
FMO2-MP2: Total energy -76427.651751


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(C:1:SER)


Summations of interaction energy for fragment #1(C:1:SER)
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.
-0.0872.6050.434-1.369-1.756-0.003
Interaction energy analysis for fragmet #1(C:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.001
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].
3C3ASN00.0430.0063.869-0.3391.012-0.016-0.649-0.6860.002
4C4ASP-1-0.829-0.8996.3350.0720.0720.0000.0000.0000.000
5C5ASN00.0250.0159.0770.1920.1920.0000.0000.0000.000
6C6ILE0-0.041-0.0177.6800.0700.0700.0000.0000.0000.000
7C7LYS10.8390.9075.3180.1080.1080.0000.0000.0000.000
8C8ASP-1-0.851-0.9249.4150.0900.0900.0000.0000.0000.000
9C9LEU0-0.079-0.03712.5900.0290.0290.0000.0000.0000.000
10C10LEU0-0.013-0.0078.7340.0480.0480.0000.0000.0000.000
11C11ASP-1-0.848-0.89812.4610.6070.6070.0000.0000.0000.000
12C12TRP0-0.023-0.00314.674-0.037-0.0370.0000.0000.0000.000
13C13TYR0-0.064-0.06216.332-0.029-0.0290.0000.0000.0000.000
14C14SER0-0.023-0.01715.1710.0290.0290.0000.0000.0000.000
15C15SER0-0.062-0.03717.715-0.019-0.0190.0000.0000.0000.000
16C16GLY0-0.036-0.02319.895-0.032-0.0320.0000.0000.0000.000
17C17SER00.0000.00323.057-0.008-0.0080.0000.0000.0000.000
18C18ASP-1-0.794-0.86626.0140.1430.1430.0000.0000.0000.000
19C19THR0-0.022-0.03129.528-0.009-0.0090.0000.0000.0000.000
20C20PHE0-0.0250.00632.8350.0040.0040.0000.0000.0000.000
21C21THR00.0240.01436.535-0.002-0.0020.0000.0000.0000.000
22C22ASN0-0.027-0.02039.643-0.002-0.0020.0000.0000.0000.000
23C23SER0-0.011-0.00338.9980.0000.0000.0000.0000.0000.000
24C24GLU-1-0.870-0.91741.9390.0360.0360.0000.0000.0000.000
25C25VAL00.0000.01142.4160.0020.0020.0000.0000.0000.000
26C26LEU0-0.034-0.03743.529-0.002-0.0020.0000.0000.0000.000
27C27ASP-1-0.886-0.95543.3710.0180.0180.0000.0000.0000.000
28C28ASN0-0.083-0.05441.7060.0030.0030.0000.0000.0000.000
29C29SER00.0280.01541.579-0.004-0.0040.0000.0000.0000.000
30C30LEU00.007-0.00139.9180.0000.0000.0000.0000.0000.000
31C31GLY00.0370.02336.8920.0000.0000.0000.0000.0000.000
32C32SER0-0.084-0.04635.7950.0040.0040.0000.0000.0000.000
33C33MET00.0210.03637.3630.0000.0000.0000.0000.0000.000
34C34ARG10.9310.97338.034-0.039-0.0390.0000.0000.0000.000
35C35ILE00.0430.02037.952-0.003-0.0030.0000.0000.0000.000
36C36LYS10.8680.93640.277-0.055-0.0550.0000.0000.0000.000
37C37ASN00.0090.01136.738-0.005-0.0050.0000.0000.0000.000
38C38THR00.0330.00340.6300.0000.0000.0000.0000.0000.000
39C39ASP-1-0.801-0.86137.8630.0890.0890.0000.0000.0000.000
40C40GLY0-0.0080.00241.3940.0000.0000.0000.0000.0000.000
41C41SER0-0.082-0.05737.628-0.004-0.0040.0000.0000.0000.000
42C42ILE0-0.022-0.01838.786-0.005-0.0050.0000.0000.0000.000
43C43SER00.0190.00034.6710.0080.0080.0000.0000.0000.000
44C44LEU0-0.033-0.00434.610-0.006-0.0060.0000.0000.0000.000
45C45ILE0-0.019-0.00432.5330.0050.0050.0000.0000.0000.000
46C46ILE00.0120.00529.335-0.006-0.0060.0000.0000.0000.000
47C47PHE00.040-0.00532.1360.0050.0050.0000.0000.0000.000
48C48PRO0-0.016-0.01129.304-0.004-0.0040.0000.0000.0000.000
49C49SER0-0.010-0.00832.092-0.011-0.0110.0000.0000.0000.000
50C50PRO0-0.001-0.00633.5850.0050.0050.0000.0000.0000.000
51C51TYR0-0.048-0.03134.0150.0000.0000.0000.0000.0000.000
52C52TYR0-0.034-0.04032.8800.0050.0050.0000.0000.0000.000
53C53SER00.0610.03736.3060.0030.0030.0000.0000.0000.000
54C54PRO0-0.046-0.01537.347-0.001-0.0010.0000.0000.0000.000
55C55ALA00.0390.01640.147-0.001-0.0010.0000.0000.0000.000
56C56PHE0-0.042-0.00839.4340.0000.0000.0000.0000.0000.000
57C57THR0-0.009-0.03044.6520.0000.0000.0000.0000.0000.000
58C58LYS10.9360.95947.075-0.025-0.0250.0000.0000.0000.000
59C59GLY00.0120.01347.584-0.001-0.0010.0000.0000.0000.000
60C60GLU-1-0.826-0.87746.2250.0250.0250.0000.0000.0000.000
61C61LYS10.7850.86044.741-0.038-0.0380.0000.0000.0000.000
62C62VAL00.0070.00739.876-0.002-0.0020.0000.0000.0000.000
63C63ASP-1-0.806-0.89937.4720.0670.0670.0000.0000.0000.000
64C64LEU0-0.054-0.02134.131-0.005-0.0050.0000.0000.0000.000
65C65ASN0-0.004-0.02331.3290.0010.0010.0000.0000.0000.000
66C66THR00.010-0.00629.201-0.003-0.0030.0000.0000.0000.000
67C67LYS10.8620.93520.719-0.187-0.1870.0000.0000.0000.000
68C68ARG10.8880.93125.340-0.192-0.1920.0000.0000.0000.000
69C69THR0-0.024-0.02024.7690.0120.0120.0000.0000.0000.000
70C70LYS10.8610.94724.495-0.071-0.0710.0000.0000.0000.000
71C71LYS10.9390.96725.958-0.171-0.1710.0000.0000.0000.000
72C72SER0-0.0010.00127.583-0.009-0.0090.0000.0000.0000.000
73C73GLN0-0.036-0.01531.2320.0030.0030.0000.0000.0000.000
74C74HIS00.0620.02934.103-0.005-0.0050.0000.0000.0000.000
75C75THR0-0.056-0.04037.7020.0010.0010.0000.0000.0000.000
76C76SER00.012-0.01440.4040.0020.0020.0000.0000.0000.000
77C77GLU-1-0.852-0.88643.4480.0500.0500.0000.0000.0000.000
78C78GLY00.0070.01142.8390.0000.0000.0000.0000.0000.000
79C79THR0-0.089-0.04841.8860.0020.0020.0000.0000.0000.000
80C80TYR00.0260.01132.4700.0030.0030.0000.0000.0000.000
81C81ILE0-0.018-0.01335.300-0.004-0.0040.0000.0000.0000.000
82C82HIS00.0580.02232.0800.0130.0130.0000.0000.0000.000
83C83PHE00.022-0.01330.250-0.010-0.0100.0000.0000.0000.000
84C84GLN0-0.0050.00029.1340.0010.0010.0000.0000.0000.000
85C85ILE0-0.032-0.00726.068-0.011-0.0110.0000.0000.0000.000
86C86SER00.013-0.02229.0430.0060.0060.0000.0000.0000.000
87C87GLY00.0170.03431.2230.0080.0080.0000.0000.0000.000
88C88VAL0-0.016-0.00931.9950.0070.0070.0000.0000.0000.000
89C89THR0-0.0140.00835.729-0.005-0.0050.0000.0000.0000.000
90C90ASN00.0440.00038.3950.0050.0050.0000.0000.0000.000
91C91THR0-0.004-0.01840.6580.0020.0020.0000.0000.0000.000
92C92GLU-1-0.895-0.91942.7450.0320.0320.0000.0000.0000.000
93C93LYS10.7790.89539.683-0.063-0.0630.0000.0000.0000.000
94C94LEU00.0120.00840.271-0.004-0.0040.0000.0000.0000.000
95C95PRO0-0.025-0.02643.5330.0030.0030.0000.0000.0000.000
96C96THR00.0050.00642.5840.0020.0020.0000.0000.0000.000
97C97PRO0-0.0100.00438.431-0.002-0.0020.0000.0000.0000.000
98C98ILE00.0000.00236.9900.0000.0000.0000.0000.0000.000
99C99GLU-1-0.839-0.91032.6440.1070.1070.0000.0000.0000.000
100C100LEU00.0400.03030.772-0.008-0.0080.0000.0000.0000.000
101C101PRO00.0390.03631.2680.0090.0090.0000.0000.0000.000
102C102LEU0-0.040-0.02624.304-0.010-0.0100.0000.0000.0000.000
103C103LYS10.8180.90226.689-0.026-0.0260.0000.0000.0000.000
104C104VAL00.0410.01620.311-0.010-0.0100.0000.0000.0000.000
105C105LYS10.8310.91121.2030.0040.0040.0000.0000.0000.000
106C106VAL0-0.002-0.01215.0440.0030.0030.0000.0000.0000.000
107C107HIS0-0.044-0.02912.0620.0260.0260.0000.0000.0000.000
108C108GLY00.0570.04317.282-0.013-0.0130.0000.0000.0000.000
109C109LYS10.8590.92619.425-0.124-0.1240.0000.0000.0000.000
110C110ASP-1-0.818-0.89021.0360.0550.0550.0000.0000.0000.000
111C111SER0-0.045-0.03719.8550.0180.0180.0000.0000.0000.000
112C112PRO0-0.002-0.01222.092-0.005-0.0050.0000.0000.0000.000
113C113LEU00.0150.02423.3980.0260.0260.0000.0000.0000.000
114C114LYS10.9030.94522.115-0.315-0.3150.0000.0000.0000.000
115C115TYR00.010-0.00323.7320.0200.0200.0000.0000.0000.000
116C116TRP00.0030.01025.6530.0100.0100.0000.0000.0000.000
117C117PRO00.0310.02628.159-0.006-0.0060.0000.0000.0000.000
118C118LYS10.8180.89531.150-0.104-0.1040.0000.0000.0000.000
119C119PHE00.003-0.00629.4250.0040.0040.0000.0000.0000.000
120C120ASP-1-0.771-0.90135.6110.0710.0710.0000.0000.0000.000
121C121LYS10.7970.91336.005-0.063-0.0630.0000.0000.0000.000
122C122LYS10.7880.89038.805-0.027-0.0270.0000.0000.0000.000
123C123GLN00.0430.01538.120-0.002-0.0020.0000.0000.0000.000
124C124LEU00.010-0.00132.0940.0070.0070.0000.0000.0000.000
125C125ALA00.0260.02331.760-0.008-0.0080.0000.0000.0000.000
126C126ILE00.0170.00828.6300.0060.0060.0000.0000.0000.000
127C127SER0-0.051-0.05326.7570.0070.0070.0000.0000.0000.000
128C128THR00.006-0.00726.2570.0080.0080.0000.0000.0000.000
129C129LEU00.0070.00827.1720.0130.0130.0000.0000.0000.000
130C130ASP-1-0.713-0.81922.2940.0390.0390.0000.0000.0000.000
131C131PHE0-0.015-0.01822.1900.0130.0130.0000.0000.0000.000
132C132GLU-1-0.868-0.93422.6010.1830.1830.0000.0000.0000.000
133C133ILE0-0.022-0.00822.2690.0210.0210.0000.0000.0000.000
134C134ARG10.7770.86817.1560.0100.0100.0000.0000.0000.000
135C135ALA00.0480.03918.6720.0450.0450.0000.0000.0000.000
136C136GLN00.024-0.00119.9540.0490.0490.0000.0000.0000.000
137C137LEU0-0.010-0.01117.3570.0350.0350.0000.0000.0000.000
138C138THR0-0.003-0.01114.5020.0530.0530.0000.0000.0000.000
139C139GLN0-0.048-0.01415.4720.1680.1680.0000.0000.0000.000
140C140ILE0-0.077-0.02718.1360.0310.0310.0000.0000.0000.000
141C141HIS0-0.0120.00716.8290.0070.0070.0000.0000.0000.000
142C142GLY0-0.0010.00912.9170.0050.0050.0000.0000.0000.000
143C143LEU0-0.013-0.02011.3830.1310.1310.0000.0000.0000.000
144C144TYR0-0.056-0.0589.6640.1030.1030.0000.0000.0000.000
145C145ARG10.8520.9177.955-0.723-0.7230.0000.0000.0000.000
146C146SER0-0.016-0.0305.1581.0941.0940.0000.0000.0000.000
147C147SER00.015-0.0242.442-1.0300.2090.451-0.713-0.977-0.005
148C148ASP-1-0.768-0.8314.9370.1640.266-0.001-0.007-0.0930.000
149C149LYS10.8130.9148.208-0.682-0.6820.0000.0000.0000.000
150C150THR00.013-0.0027.3140.1650.1650.0000.0000.0000.000
151C151GLY00.0460.02010.474-0.053-0.0530.0000.0000.0000.000
152C152GLY00.0040.01314.0150.0650.0650.0000.0000.0000.000
153C153TYR0-0.112-0.07817.451-0.012-0.0120.0000.0000.0000.000
154C154TRP00.001-0.00420.7360.0230.0230.0000.0000.0000.000
155C155LYS10.8840.92023.4060.0100.0100.0000.0000.0000.000
156C156ILE00.0070.02527.1190.0070.0070.0000.0000.0000.000
157C157THR0-0.003-0.01130.280-0.014-0.0140.0000.0000.0000.000
158C158MET00.0270.03633.4520.0090.0090.0000.0000.0000.000
159C159ASN00.044-0.00336.861-0.005-0.0050.0000.0000.0000.000
160C160ASP-1-0.828-0.88139.903-0.014-0.0140.0000.0000.0000.000
161C161GLY0-0.023-0.01538.392-0.002-0.0020.0000.0000.0000.000
162C162SER0-0.024-0.02336.906-0.007-0.0070.0000.0000.0000.000
163C163THR0-0.060-0.03431.4980.0020.0020.0000.0000.0000.000
164C164TYR00.0220.01430.194-0.004-0.0040.0000.0000.0000.000
165C165GLN0-0.008-0.01224.7110.0120.0120.0000.0000.0000.000
166C166SER0-0.028-0.01422.725-0.012-0.0120.0000.0000.0000.000
167C167ASP-1-0.747-0.83118.032-0.251-0.2510.0000.0000.0000.000
168C168LEU00.0180.01216.1430.0190.0190.0000.0000.0000.000
169C169SER0-0.015-0.02113.9200.0130.0130.0000.0000.0000.000
170C170LYS10.8540.91214.5690.2690.2690.0000.0000.0000.000
171C171LYS10.9410.99017.194-0.015-0.0150.0000.0000.0000.000
172C172PHE0-0.0010.00719.171-0.020-0.0200.0000.0000.0000.000
173C173GLU-1-0.793-0.85822.686-0.082-0.0820.0000.0000.0000.000
174C174TYR00.055-0.00223.4160.0080.0080.0000.0000.0000.000
175C175ASN0-0.050-0.03526.8730.0060.0060.0000.0000.0000.000
176C176THR0-0.076-0.05929.2730.0000.0000.0000.0000.0000.000
177C177GLU-1-0.724-0.79529.6070.0220.0220.0000.0000.0000.000
178C178LYS10.8900.94931.0210.0460.0460.0000.0000.0000.000
179C179PRO00.0410.01033.8800.0050.0050.0000.0000.0000.000
180C180PRO0-0.030-0.01135.0740.0000.0000.0000.0000.0000.000
181C181ILE0-0.0070.01132.851-0.004-0.0040.0000.0000.0000.000
182C182ASN0-0.028-0.03436.8740.0090.0090.0000.0000.0000.000
183C183ILE00.007-0.01034.778-0.003-0.0030.0000.0000.0000.000
184C184ASP-1-0.801-0.89436.9830.0310.0310.0000.0000.0000.000
185C185GLU-1-0.857-0.91439.3020.0130.0130.0000.0000.0000.000
186C186ILE0-0.036-0.01832.836-0.006-0.0060.0000.0000.0000.000
187C187LYS10.8200.91936.2560.0090.0090.0000.0000.0000.000
188C188THR0-0.095-0.07831.4840.0020.0020.0000.0000.0000.000
189C189ILE00.0290.01427.033-0.004-0.0040.0000.0000.0000.000
190C190GLU-1-0.783-0.85725.9410.0110.0110.0000.0000.0000.000
191C191ALA00.0320.00521.298-0.006-0.0060.0000.0000.0000.000
192C192GLU-1-0.875-0.90720.117-0.039-0.0390.0000.0000.0000.000
193C193ILE00.0120.00813.749-0.036-0.0360.0000.0000.0000.000
194C194ASN0-0.036-0.04311.577-0.032-0.0320.0000.0000.0000.000