FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: ZYQGN

Calculation Name: 4Y66-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y66

Chain ID: C

ChEMBL ID:

UniProt ID: E2RTU1

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 197
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1440763.725499
FMO2-HF: Nuclear repulsion 1361258.05384
FMO2-HF: Total energy -79505.671659
FMO2-MP2: Total energy -79737.219598


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:6:THR)


Summations of interaction energy for fragment #1(C:6: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.
-42.134-37.52820.093-13.195-11.505-0.037
Interaction energy analysis for fragmet #1(C:6:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / 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].
3C8LEU0-0.067-0.0192.275-9.788-3.8222.147-4.016-4.0960.039
4C9ASP-1-0.774-0.8901.761-33.855-36.06617.944-8.937-6.797-0.076
5C10GLU-1-0.835-0.9033.665-0.7870.0640.002-0.242-0.6120.000
6C11LYS10.8490.9155.4980.3350.3350.0000.0000.0000.000
7C12LYS10.7870.8825.3403.2333.2330.0000.0000.0000.000
8C13GLU-1-0.875-0.9347.548-1.236-1.2360.0000.0000.0000.000
9C14ARG10.7930.8869.3070.9240.9240.0000.0000.0000.000
10C15LEU0-0.012-0.02011.3710.1980.1980.0000.0000.0000.000
11C16LEU00.0370.01612.4980.1420.1420.0000.0000.0000.000
12C17GLU-1-0.828-0.90213.445-0.394-0.3940.0000.0000.0000.000
13C18GLU-1-0.817-0.89215.313-0.274-0.2740.0000.0000.0000.000
14C19MET0-0.059-0.02517.1220.0550.0550.0000.0000.0000.000
15C20LEU0-0.032-0.01116.3450.0530.0530.0000.0000.0000.000
16C21LYS10.8160.90119.2540.4160.4160.0000.0000.0000.000
17C22ARG10.8040.89220.2840.3100.3100.0000.0000.0000.000
18C23GLY00.0010.01622.8860.0250.0250.0000.0000.0000.000
19C24GLU-1-0.864-0.90823.883-0.176-0.1760.0000.0000.0000.000
20C25ILE0-0.016-0.01123.938-0.018-0.0180.0000.0000.0000.000
21C26TYR0-0.027-0.05321.5200.0090.0090.0000.0000.0000.000
22C27SER00.0530.03024.0980.0000.0000.0000.0000.0000.000
23C28ASN00.029-0.00922.072-0.006-0.0060.0000.0000.0000.000
24C29LYS10.9650.98222.2500.0440.0440.0000.0000.0000.000
25C30THR00.0120.01023.8200.0000.0000.0000.0000.0000.000
26C31ILE00.0790.04817.9120.0000.0000.0000.0000.0000.000
27C32GLU-1-0.798-0.88519.892-0.053-0.0530.0000.0000.0000.000
28C33THR0-0.038-0.00521.0800.0120.0120.0000.0000.0000.000
29C34LEU00.0200.00318.1020.0020.0020.0000.0000.0000.000
30C35SER0-0.054-0.01617.372-0.031-0.0310.0000.0000.0000.000
31C36LYS10.9250.96317.9690.0740.0740.0000.0000.0000.000
32C37PRO00.0190.01818.540-0.002-0.0020.0000.0000.0000.000
33C38THR0-0.021-0.02913.824-0.024-0.0240.0000.0000.0000.000
34C39GLY00.0190.03013.629-0.067-0.0670.0000.0000.0000.000
35C40ILE0-0.039-0.01311.4640.0590.0590.0000.0000.0000.000
36C41SER00.0320.00614.198-0.011-0.0110.0000.0000.0000.000
37C42SER00.041-0.00515.8830.0040.0040.0000.0000.0000.000
38C43MET0-0.019-0.00817.387-0.007-0.0070.0000.0000.0000.000
39C44VAL0-0.036-0.02411.2930.0260.0260.0000.0000.0000.000
40C45ILE00.0270.01913.478-0.012-0.0120.0000.0000.0000.000
41C46LYS10.8560.92714.800-0.022-0.0220.0000.0000.0000.000
42C47ASN0-0.0040.00512.325-0.031-0.0310.0000.0000.0000.000
43C48VAL0-0.0010.0079.443-0.003-0.0030.0000.0000.0000.000
44C49LEU00.0200.00711.304-0.138-0.1380.0000.0000.0000.000
45C50GLN0-0.054-0.03114.226-0.027-0.0270.0000.0000.0000.000
46C51ALA0-0.001-0.0059.004-0.008-0.0080.0000.0000.0000.000
47C52LEU00.0140.00210.498-0.100-0.1000.0000.0000.0000.000
48C53VAL0-0.038-0.01212.567-0.003-0.0030.0000.0000.0000.000
49C54ASN0-0.0110.00012.7950.0440.0440.0000.0000.0000.000
50C55GLU-1-0.865-0.9188.532-1.563-1.5630.0000.0000.0000.000
51C56ASP-1-0.861-0.92713.164-0.404-0.4040.0000.0000.0000.000
52C57LEU0-0.0030.00710.5620.0200.0200.0000.0000.0000.000
53C58VAL0-0.038-0.02715.2540.0130.0130.0000.0000.0000.000
54C59ASP-1-0.859-0.92017.935-0.265-0.2650.0000.0000.0000.000
55C60THR0-0.066-0.06920.8840.0050.0050.0000.0000.0000.000
56C61ASP-1-0.818-0.89622.860-0.127-0.1270.0000.0000.0000.000
57C62LYS10.7630.85326.3520.0800.0800.0000.0000.0000.000
58C63ILE00.0440.02628.6810.0080.0080.0000.0000.0000.000
59C64GLY00.0400.01930.9830.0070.0070.0000.0000.0000.000
60C65ALA00.0060.00331.2720.0000.0000.0000.0000.0000.000
61C66SER0-0.045-0.01528.0400.0050.0050.0000.0000.0000.000
62C67THR0-0.0330.00423.2920.0080.0080.0000.0000.0000.000
63C68TYR00.005-0.01224.8930.0070.0070.0000.0000.0000.000
64C69TYR00.0510.02419.5760.0080.0080.0000.0000.0000.000
65C70TRP0-0.0020.00721.6640.0150.0150.0000.0000.0000.000
66C71CYS0-0.011-0.00717.581-0.016-0.0160.0000.0000.0000.000
67C72PHE00.0640.04120.8780.0110.0110.0000.0000.0000.000
68C73ALA00.0600.02421.096-0.019-0.0190.0000.0000.0000.000
69C74SER0-0.026-0.01322.152-0.009-0.0090.0000.0000.0000.000
70C75LYS10.8060.92519.0370.3870.3870.0000.0000.0000.000
71C76ARG11.0501.00117.3470.4630.4630.0000.0000.0000.000
72C77SER00.0060.01821.9170.0290.0290.0000.0000.0000.000
73C78GLN00.0650.02625.2770.0220.0220.0000.0000.0000.000
74C79ALA00.0420.04523.5800.0190.0190.0000.0000.0000.000
75C80ALA00.0040.00324.5710.0170.0170.0000.0000.0000.000
76C81ARG10.8610.90926.2940.2070.2070.0000.0000.0000.000
77C82THR0-0.022-0.01629.0260.0170.0170.0000.0000.0000.000
78C83GLU-1-0.812-0.89127.401-0.135-0.1350.0000.0000.0000.000
79C84LEU0-0.026-0.00429.7470.0110.0110.0000.0000.0000.000
80C85ALA00.0140.00231.6570.0110.0110.0000.0000.0000.000
81C86ARG10.8830.92230.2890.1330.1330.0000.0000.0000.000
82C87LEU0-0.016-0.00830.8830.0090.0090.0000.0000.0000.000
83C88GLN0-0.011-0.00734.2620.0050.0050.0000.0000.0000.000
84C89LYS10.8130.91336.8790.0800.0800.0000.0000.0000.000
85C90ALA00.0440.01636.6930.0060.0060.0000.0000.0000.000
86C91LEU0-0.021-0.00437.9120.0060.0060.0000.0000.0000.000
87C92GLU-1-0.843-0.90139.773-0.067-0.0670.0000.0000.0000.000
88C93GLU-1-0.902-0.95741.890-0.068-0.0680.0000.0000.0000.000
89C94GLN00.014-0.00139.8540.0070.0070.0000.0000.0000.000
90C95THR0-0.043-0.02843.1990.0040.0040.0000.0000.0000.000
91C96ASN00.0460.01745.3770.0060.0060.0000.0000.0000.000
92C97PHE0-0.053-0.01645.0660.0040.0040.0000.0000.0000.000
93C98ILE00.0270.00545.4290.0030.0030.0000.0000.0000.000
94C99ASP-1-0.866-0.91948.110-0.046-0.0460.0000.0000.0000.000
95C100LYS10.8530.91850.9090.0480.0480.0000.0000.0000.000
96C101ALA0-0.020-0.00250.2000.0020.0020.0000.0000.0000.000
97C102THR0-0.019-0.03150.8010.0020.0020.0000.0000.0000.000
98C103ALA00.0150.02153.4230.0020.0020.0000.0000.0000.000
99C104ARG10.8140.88655.4720.0310.0310.0000.0000.0000.000
100C105ILE00.008-0.00352.8770.0020.0020.0000.0000.0000.000
101C106GLU-1-0.816-0.90156.923-0.026-0.0260.0000.0000.0000.000
102C107GLU-1-0.835-0.90659.310-0.028-0.0280.0000.0000.0000.000
103C108LEU0-0.068-0.02558.5760.0020.0020.0000.0000.0000.000
104C109LYS10.8610.92358.5110.0270.0270.0000.0000.0000.000
105C110VAL00.0040.01662.6440.0010.0010.0000.0000.0000.000
106C111GLY00.0010.01365.8830.0010.0010.0000.0000.0000.000
107C112ARG10.7630.86062.7710.0200.0200.0000.0000.0000.000
108C113GLU-1-0.843-0.90363.744-0.020-0.0200.0000.0000.0000.000
109C114GLU-1-0.961-0.97760.589-0.016-0.0160.0000.0000.0000.000
110C115THR0-0.017-0.01065.1880.0000.0000.0000.0000.0000.000
111C116GLU-1-0.815-0.92168.431-0.010-0.0100.0000.0000.0000.000
112C117GLU-1-0.808-0.88070.833-0.013-0.0130.0000.0000.0000.000
113C118ARG10.8400.89967.4680.0150.0150.0000.0000.0000.000
114C119SER0-0.032-0.01168.0130.0000.0000.0000.0000.0000.000
115C120SER00.012-0.01369.0430.0000.0000.0000.0000.0000.000
116C121LEU00.0450.01772.7020.0000.0000.0000.0000.0000.000
117C122LEU0-0.055-0.01866.3870.0000.0000.0000.0000.0000.000
118C123LYS10.8470.91767.2530.0100.0100.0000.0000.0000.000
119C124GLU-1-0.925-0.95571.653-0.008-0.0080.0000.0000.0000.000
120C125LYS10.9670.98770.4290.0120.0120.0000.0000.0000.000
121C126LEU0-0.0080.00568.5470.0000.0000.0000.0000.0000.000
122C127ALA00.0280.00972.5920.0000.0000.0000.0000.0000.000
123C128LEU00.0070.00275.4020.0000.0000.0000.0000.0000.000
124C129GLN0-0.014-0.01872.0200.0000.0000.0000.0000.0000.000
125C130VAL00.0330.02073.1290.0000.0000.0000.0000.0000.000
126C131LYS10.9210.95475.9570.0050.0050.0000.0000.0000.000
127C132LEU0-0.024-0.02579.0680.0000.0000.0000.0000.0000.000
128C133GLU-1-0.833-0.87275.030-0.007-0.0070.0000.0000.0000.000
129C134GLU-1-0.896-0.93778.547-0.003-0.0030.0000.0000.0000.000
130C135GLN0-0.0160.01480.7610.0000.0000.0000.0000.0000.000
131C136ARG10.8250.86877.6370.0070.0070.0000.0000.0000.000
132C137GLY00.0070.01181.6910.0000.0000.0000.0000.0000.000
133C138THR0-0.007-0.02082.5180.0000.0000.0000.0000.0000.000
134C139PHE0-0.022-0.02185.9590.0000.0000.0000.0000.0000.000
135C140ARG10.9190.96381.5830.0040.0040.0000.0000.0000.000
136C141ASP-1-0.771-0.87684.763-0.002-0.0020.0000.0000.0000.000
137C142LEU0-0.046-0.01187.4790.0000.0000.0000.0000.0000.000
138C143LEU0-0.028-0.01188.9700.0000.0000.0000.0000.0000.000
139C144LYS10.7910.89584.8680.0020.0020.0000.0000.0000.000
140C145ASN0-0.088-0.06488.2650.0010.0010.0000.0000.0000.000
141C146ASP-1-0.818-0.89692.128-0.002-0.0020.0000.0000.0000.000
142C147PRO00.0330.00695.9010.0000.0000.0000.0000.0000.000
143C148ASP-1-0.916-0.95297.612-0.001-0.0010.0000.0000.0000.000
144C149VAL0-0.013-0.01097.4050.0000.0000.0000.0000.0000.000
145C150ALA00.0120.00495.6770.0000.0000.0000.0000.0000.000
146C151GLN0-0.018-0.01097.5470.0000.0000.0000.0000.0000.000
147C152LYS10.9770.986100.8420.0000.0000.0000.0000.0000.000
148C153LEU0-0.0030.00695.5440.0000.0000.0000.0000.0000.000
149C154ARG10.8990.96197.1540.0010.0010.0000.0000.0000.000
150C155ASN00.0480.029100.3450.0000.0000.0000.0000.0000.000
151C156TYR00.014-0.008102.6610.0000.0000.0000.0000.0000.000
152C157THR0-0.011-0.01198.2570.0000.0000.0000.0000.0000.000
153C158ASP-1-0.883-0.948101.5180.0010.0010.0000.0000.0000.000
154C159ILE0-0.0050.000103.7130.0000.0000.0000.0000.0000.000
155C160ALA0-0.009-0.005102.8120.0000.0000.0000.0000.0000.000
156C161LYS10.8560.92399.393-0.001-0.0010.0000.0000.0000.000
157C162GLN0-0.055-0.021103.6790.0000.0000.0000.0000.0000.000
158C163GLU-1-0.850-0.926107.3200.0020.0020.0000.0000.0000.000
159C164ALA0-0.013-0.006103.6740.0000.0000.0000.0000.0000.000
160C165ASN00.0150.019103.6300.0000.0000.0000.0000.0000.000
161C166LEU00.0440.032106.7040.0000.0000.0000.0000.0000.000
162C167TRP0-0.014-0.024108.5080.0000.0000.0000.0000.0000.000
163C168THR0-0.0030.006104.9060.0000.0000.0000.0000.0000.000
164C169ASP-1-0.824-0.890107.6570.0030.0030.0000.0000.0000.000
165C170ASN0-0.033-0.020110.7120.0000.0000.0000.0000.0000.000
166C171ILE00.0120.014106.8650.0000.0000.0000.0000.0000.000
167C172PHE00.0350.013104.6480.0000.0000.0000.0000.0000.000
168C173CYS0-0.094-0.052110.6490.0000.0000.0000.0000.0000.000
169C174LEU00.0090.005112.8140.0000.0000.0000.0000.0000.000
170C175GLN00.0660.034108.7750.0000.0000.0000.0000.0000.000
171C176LYS10.9460.970112.464-0.003-0.0030.0000.0000.0000.000
172C177TYR00.0070.012114.8490.0000.0000.0000.0000.0000.000
173C178MET00.009-0.009112.9020.0000.0000.0000.0000.0000.000
174C179LEU0-0.0140.004111.0320.0000.0000.0000.0000.0000.000
175C180THR0-0.082-0.049115.2930.0000.0000.0000.0000.0000.000
176C181LYS10.9130.943118.794-0.003-0.0030.0000.0000.0000.000
177C182LEU0-0.013-0.003117.9470.0000.0000.0000.0000.0000.000
178C183GLN0-0.052-0.004118.1870.0000.0000.0000.0000.0000.000
179C184MET00.0220.028113.2510.0000.0000.0000.0000.0000.000
180C185ASP-1-0.783-0.878109.3590.0050.0050.0000.0000.0000.000
181C186LYS10.9680.978106.446-0.005-0.0050.0000.0000.0000.000
182C187LYS10.9730.994103.653-0.006-0.0060.0000.0000.0000.000
183C188THR0-0.023-0.022106.4770.0000.0000.0000.0000.0000.000
184C189VAL0-0.026-0.015108.8940.0000.0000.0000.0000.0000.000
185C190SER0-0.019-0.012104.5150.0000.0000.0000.0000.0000.000
186C191THR0-0.059-0.055102.7410.0000.0000.0000.0000.0000.000
187C192ALA0-0.029-0.006105.1030.0000.0000.0000.0000.0000.000
188C193LEU0-0.045-0.032107.7910.0000.0000.0000.0000.0000.000
189C194GLY00.0070.019103.3770.0000.0000.0000.0000.0000.000
190C195ILE0-0.055-0.013102.3080.0000.0000.0000.0000.0000.000
191C196THR0-0.028-0.03298.2310.0000.0000.0000.0000.0000.000
192C197GLY0-0.021-0.02498.9770.0000.0000.0000.0000.0000.000
193C198GLU-1-0.909-0.94593.2170.0050.0050.0000.0000.0000.000
194C199PHE0-0.099-0.04297.5230.0000.0000.0000.0000.0000.000
195C200ASP-1-0.838-0.92099.6930.0030.0030.0000.0000.0000.000
196C201TYR0-0.143-0.098101.3580.0000.0000.0000.0000.0000.000
197C202LEU0-0.048-0.02298.5730.0000.0000.0000.0000.0000.000