Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: ZY2GN

Calculation Name: 4Y66-C-Xray323

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 199
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1445259.963455
FMO2-HF: Nuclear repulsion 1365586.24902
FMO2-HF: Total energy -79673.714435
FMO2-MP2: Total energy -79906.229463


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:5:ACE )


Summations of interaction energy for fragment #1(C:5:ACE )
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.
0.5472.5070.071-1.096-0.935-0.004
Interaction energy analysis for fragmet #1(C:5:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.016
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].
3C7SER 00.0930.0343.8350.9411.729-0.006-0.372-0.4100.001
4C8LEU 0-0.057-0.0216.7490.3530.3530.0000.0000.0000.000
5C9ASP -1-0.830-0.9343.277-1.350-0.1780.077-0.724-0.525-0.005
6C10GLU -1-0.909-0.9424.884-0.496-0.4960.0000.0000.0000.000
7C11LYS 10.8890.9406.9120.4750.4750.0000.0000.0000.000
8C12LYS 10.8390.8928.2480.0180.0180.0000.0000.0000.000
9C13GLU -1-0.886-0.9248.0100.5710.5710.0000.0000.0000.000
10C14ARG 10.8160.91410.115-0.057-0.0570.0000.0000.0000.000
11C15LEU 0-0.025-0.03412.465-0.002-0.0020.0000.0000.0000.000
12C16LEU 00.0710.02313.129-0.012-0.0120.0000.0000.0000.000
13C17GLU -1-0.920-0.94714.1030.1470.1470.0000.0000.0000.000
14C18GLU -1-0.906-0.97215.7660.0230.0230.0000.0000.0000.000
15C19MET 0-0.085-0.04518.042-0.008-0.0080.0000.0000.0000.000
16C20LEU 0-0.025-0.00116.534-0.006-0.0060.0000.0000.0000.000
17C21LYS 10.9410.98319.930-0.072-0.0720.0000.0000.0000.000
18C22ARG 10.8740.92621.864-0.034-0.0340.0000.0000.0000.000
19C23GLY 00.0250.03923.394-0.004-0.0040.0000.0000.0000.000
20C24GLU -1-0.923-0.93624.8950.0150.0150.0000.0000.0000.000
21C25ILE 0-0.019-0.02125.3380.0020.0020.0000.0000.0000.000
22C26TYR 0-0.016-0.02623.378-0.006-0.0060.0000.0000.0000.000
23C27SER 00.0440.00526.261-0.001-0.0010.0000.0000.0000.000
24C28ASN 00.0440.00525.3480.0000.0000.0000.0000.0000.000
25C29LYS 10.9660.96025.1570.0210.0210.0000.0000.0000.000
26C30THR 00.0700.05326.895-0.003-0.0030.0000.0000.0000.000
27C31ILE 00.0870.10620.517-0.001-0.0010.0000.0000.0000.000
28C32GLU -1-0.887-0.94222.192-0.055-0.0550.0000.0000.0000.000
29C33THR 0-0.052-0.08023.802-0.005-0.0050.0000.0000.0000.000
30C34LEU 0-0.014-0.02119.641-0.003-0.0030.0000.0000.0000.000
31C35SER 0-0.029-0.00719.437-0.003-0.0030.0000.0000.0000.000
32C36LYS 10.9280.96819.7550.0280.0280.0000.0000.0000.000
33C37PRO 0-0.0170.00619.826-0.006-0.0060.0000.0000.0000.000
34C38THR 0-0.012-0.01115.248-0.003-0.0030.0000.0000.0000.000
35C39GLY 00.0370.03315.048-0.016-0.0160.0000.0000.0000.000
36C40ILE 0-0.032-0.00513.354-0.041-0.0410.0000.0000.0000.000
37C41SER 00.0360.00816.6250.0250.0250.0000.0000.0000.000
38C42SER 00.0440.01219.423-0.003-0.0030.0000.0000.0000.000
39C43MET 0-0.0120.00121.7140.0020.0020.0000.0000.0000.000
40C44VAL 0-0.027-0.03115.357-0.004-0.0040.0000.0000.0000.000
41C45ILE 00.0170.02917.341-0.001-0.0010.0000.0000.0000.000
42C46LYS 10.9300.95717.6600.0540.0540.0000.0000.0000.000
43C47ASN 0-0.018-0.00716.5630.0200.0200.0000.0000.0000.000
44C48VAL 0-0.0100.00312.373-0.007-0.0070.0000.0000.0000.000
45C49LEU 0-0.0060.00214.4530.0270.0270.0000.0000.0000.000
46C50GLN 0-0.024-0.00616.8590.0170.0170.0000.0000.0000.000
47C51ALA 0-0.017-0.02712.1110.0100.0100.0000.0000.0000.000
48C52LEU 00.0470.01912.2790.0260.0260.0000.0000.0000.000
49C53VAL 0-0.053-0.00914.5140.0220.0220.0000.0000.0000.000
50C54ASN 0-0.018-0.01415.2600.0130.0130.0000.0000.0000.000
51C55GLU -1-0.878-0.91510.4180.1260.1260.0000.0000.0000.000
52C56ASP -1-0.848-0.91314.7940.1230.1230.0000.0000.0000.000
53C57LEU 0-0.021-0.00112.1350.0190.0190.0000.0000.0000.000
54C58VAL 0-0.083-0.05416.305-0.001-0.0010.0000.0000.0000.000
55C59ASP -1-0.866-0.92319.1450.0680.0680.0000.0000.0000.000
56C60THR 0-0.072-0.04022.565-0.010-0.0100.0000.0000.0000.000
57C61ASP -1-0.815-0.90724.3220.0270.0270.0000.0000.0000.000
58C62LYS 10.8090.90327.9420.0000.0000.0000.0000.0000.000
59C63ILE 00.0380.03330.7830.0010.0010.0000.0000.0000.000
60C64GLY 0-0.013-0.00433.918-0.001-0.0010.0000.0000.0000.000
61C65ALA 00.0450.00434.7670.0000.0000.0000.0000.0000.000
62C66SER 0-0.072-0.03330.988-0.002-0.0020.0000.0000.0000.000
63C67THR 00.0000.00025.9740.0020.0020.0000.0000.0000.000
64C68TYR 0-0.026-0.02627.171-0.004-0.0040.0000.0000.0000.000
65C69TYR 00.0140.00021.5610.0000.0000.0000.0000.0000.000
66C70TRP 0-0.002-0.00123.470-0.004-0.0040.0000.0000.0000.000
67C71CYS 00.0440.02719.5210.0100.0100.0000.0000.0000.000
68C72PHE 00.0430.03021.938-0.002-0.0020.0000.0000.0000.000
69C73ALA 00.0450.01721.3660.0120.0120.0000.0000.0000.000
70C74SER 0-0.050-0.03322.3900.0110.0110.0000.0000.0000.000
71C75LYS 10.8770.95219.063-0.110-0.1100.0000.0000.0000.000
72C76ARG 11.0521.00417.377-0.216-0.2160.0000.0000.0000.000
73C77SER 0-0.0060.00821.797-0.010-0.0100.0000.0000.0000.000
74C78GLN 00.0140.01824.905-0.006-0.0060.0000.0000.0000.000
75C79ALA 00.0620.02923.605-0.005-0.0050.0000.0000.0000.000
76C80ALA 0-0.0070.00324.360-0.005-0.0050.0000.0000.0000.000
77C81ARG 10.9110.93326.036-0.090-0.0900.0000.0000.0000.000
78C82THR 0-0.011-0.00228.841-0.007-0.0070.0000.0000.0000.000
79C83GLU -1-0.812-0.89726.9300.0610.0610.0000.0000.0000.000
80C84LEU 0-0.037-0.00629.509-0.003-0.0030.0000.0000.0000.000
81C85ALA 00.017-0.00931.381-0.004-0.0040.0000.0000.0000.000
82C86ARG 10.8960.93829.383-0.059-0.0590.0000.0000.0000.000
83C87LEU 0-0.047-0.01730.294-0.005-0.0050.0000.0000.0000.000
84C88GLN 00.0160.00633.9610.0000.0000.0000.0000.0000.000
85C89LYS 10.8820.95436.503-0.038-0.0380.0000.0000.0000.000
86C90ALA 00.0190.00936.337-0.003-0.0030.0000.0000.0000.000
87C91LEU 0-0.019-0.00737.480-0.002-0.0020.0000.0000.0000.000
88C92GLU -1-0.891-0.95139.2340.0350.0350.0000.0000.0000.000
89C93GLU -1-0.967-0.98141.7780.0290.0290.0000.0000.0000.000
90C94GLN 00.000-0.01240.069-0.004-0.0040.0000.0000.0000.000
91C95THR 0-0.031-0.02342.604-0.002-0.0020.0000.0000.0000.000
92C96ASN 00.0430.03644.883-0.002-0.0020.0000.0000.0000.000
93C97PHE 0-0.036-0.02045.399-0.002-0.0020.0000.0000.0000.000
94C98ILE 00.0290.00444.399-0.001-0.0010.0000.0000.0000.000
95C99ASP -1-0.894-0.93547.7260.0260.0260.0000.0000.0000.000
96C100LYS 10.9100.94550.369-0.022-0.0220.0000.0000.0000.000
97C101ALA 0-0.0210.00350.142-0.001-0.0010.0000.0000.0000.000
98C102THR 00.003-0.01250.714-0.001-0.0010.0000.0000.0000.000
99C103ALA 00.0290.03553.228-0.001-0.0010.0000.0000.0000.000
100C104ARG 10.8220.89255.553-0.016-0.0160.0000.0000.0000.000
101C105ILE 0-0.011-0.02852.743-0.001-0.0010.0000.0000.0000.000
102C106GLU -1-0.882-0.94656.3130.0180.0180.0000.0000.0000.000
103C107GLU -1-0.844-0.90358.8170.0150.0150.0000.0000.0000.000
104C108LEU 0-0.091-0.05059.425-0.001-0.0010.0000.0000.0000.000
105C109LYS 10.8840.93557.221-0.018-0.0180.0000.0000.0000.000
106C110VAL 00.0240.03462.0080.0000.0000.0000.0000.0000.000
107C111GLY 0-0.046-0.01365.1690.0000.0000.0000.0000.0000.000
108C112ARG 10.8010.89563.003-0.012-0.0120.0000.0000.0000.000
109C113GLU -1-0.839-0.91663.7130.0140.0140.0000.0000.0000.000
110C114GLU -1-0.992-0.99460.4080.0130.0130.0000.0000.0000.000
111C115THR 00.0340.01565.0570.0000.0000.0000.0000.0000.000
112C116GLU -1-0.869-0.92568.1030.0080.0080.0000.0000.0000.000
113C117GLU -1-0.823-0.91470.8720.0090.0090.0000.0000.0000.000
114C118ARG 10.9660.99765.773-0.011-0.0110.0000.0000.0000.000
115C119SER 0-0.068-0.03867.1240.0000.0000.0000.0000.0000.000
116C120SER 0-0.008-0.02668.8690.0000.0000.0000.0000.0000.000
117C121LEU 00.0510.01672.5920.0000.0000.0000.0000.0000.000
118C122LEU 0-0.115-0.04866.3510.0000.0000.0000.0000.0000.000
119C123LYS 10.9110.94966.434-0.008-0.0080.0000.0000.0000.000
120C124GLU -1-0.894-0.94271.6920.0060.0060.0000.0000.0000.000
121C125LYS 11.0021.00070.793-0.008-0.0080.0000.0000.0000.000
122C126LEU 0-0.024-0.00669.0620.0000.0000.0000.0000.0000.000
123C127ALA 00.0250.01272.8950.0000.0000.0000.0000.0000.000
124C128LEU 00.000-0.00175.7260.0000.0000.0000.0000.0000.000
125C129GLN 0-0.073-0.04172.6500.0000.0000.0000.0000.0000.000
126C130VAL 00.0520.03274.2190.0000.0000.0000.0000.0000.000
127C131LYS 10.9590.99476.746-0.004-0.0040.0000.0000.0000.000
128C132LEU 0-0.003-0.02680.0520.0000.0000.0000.0000.0000.000
129C133GLU -1-0.876-0.92375.8510.0040.0040.0000.0000.0000.000
130C134GLU -1-0.905-0.94279.4180.0030.0030.0000.0000.0000.000
131C135GLN 0-0.066-0.04081.4920.0000.0000.0000.0000.0000.000
132C136ARG 10.8430.91078.403-0.004-0.0040.0000.0000.0000.000
133C137GLY 00.0240.01482.6540.0000.0000.0000.0000.0000.000
134C138THR 00.0230.01483.6230.0000.0000.0000.0000.0000.000
135C139PHE 0-0.012-0.01486.9940.0000.0000.0000.0000.0000.000
136C140ARG 10.9100.94783.514-0.002-0.0020.0000.0000.0000.000
137C141ASP -1-0.919-0.95286.2100.0020.0020.0000.0000.0000.000
138C142LEU 0-0.071-0.03588.7510.0000.0000.0000.0000.0000.000
139C143LEU 0-0.050-0.02190.4820.0000.0000.0000.0000.0000.000
140C144LYS 10.9000.95885.393-0.001-0.0010.0000.0000.0000.000
141C145ASN 0-0.033-0.01689.5390.0000.0000.0000.0000.0000.000
142C146ASP -1-0.828-0.92193.4980.0010.0010.0000.0000.0000.000
143C147PRO 00.0360.00996.7910.0000.0000.0000.0000.0000.000
144C148ASP -1-0.910-0.95298.8170.0010.0010.0000.0000.0000.000
145C149VAL 00.0120.01498.5100.0000.0000.0000.0000.0000.000
146C150ALA 00.001-0.00197.0560.0000.0000.0000.0000.0000.000
147C151GLN 0-0.055-0.04298.9490.0000.0000.0000.0000.0000.000
148C152LYS 10.9630.986102.3070.0000.0000.0000.0000.0000.000
149C153LEU 00.009-0.00597.3330.0000.0000.0000.0000.0000.000
150C154ARG 10.9290.97098.638-0.001-0.0010.0000.0000.0000.000
151C155ASN 00.0620.055102.1030.0000.0000.0000.0000.0000.000
152C156TYR 00.014-0.012104.4710.0000.0000.0000.0000.0000.000
153C157THR 0-0.0330.000100.5170.0000.0000.0000.0000.0000.000
154C158ASP -1-0.933-0.976103.5880.0010.0010.0000.0000.0000.000
155C159ILE 0-0.025-0.011105.5930.0000.0000.0000.0000.0000.000
156C160ALA 0-0.0020.000105.0810.0000.0000.0000.0000.0000.000
157C161LYS 10.9580.971100.6550.0000.0000.0000.0000.0000.000
158C162GLN 0-0.0120.001105.5900.0000.0000.0000.0000.0000.000
159C163GLU -1-0.886-0.951108.8650.0000.0000.0000.0000.0000.000
160C164ALA 0-0.012-0.006106.0750.0000.0000.0000.0000.0000.000
161C165ASN 00.0280.018105.6360.0000.0000.0000.0000.0000.000
162C166LEU 00.0500.039108.5120.0000.0000.0000.0000.0000.000
163C167TRP 0-0.010-0.017110.5080.0000.0000.0000.0000.0000.000
164C168THR 0-0.0090.004107.1970.0000.0000.0000.0000.0000.000
165C169ASP -1-0.850-0.898109.8330.0000.0000.0000.0000.0000.000
166C170ASN 0-0.048-0.032112.7790.0000.0000.0000.0000.0000.000
167C171ILE 0-0.0080.012109.2500.0000.0000.0000.0000.0000.000
168C172PHE 00.0720.024107.3050.0000.0000.0000.0000.0000.000
169C173CYS 0-0.082-0.046113.1490.0000.0000.0000.0000.0000.000
170C174LEU 00.0150.018115.3620.0000.0000.0000.0000.0000.000
171C175GLN 00.0570.029111.1160.0000.0000.0000.0000.0000.000
172C176LYS 10.9530.971115.1300.0000.0000.0000.0000.0000.000
173C177TYR 0-0.004-0.007117.4920.0000.0000.0000.0000.0000.000
174C178MET 0-0.004-0.012115.7160.0000.0000.0000.0000.0000.000
175C179LEU 0-0.0280.001113.6600.0000.0000.0000.0000.0000.000
176C180THR 0-0.045-0.028118.0450.0000.0000.0000.0000.0000.000
177C181LYS 10.9210.949121.2740.0010.0010.0000.0000.0000.000
178C182LEU 00.0090.005121.1790.0000.0000.0000.0000.0000.000
179C183GLN 0-0.064-0.007120.9110.0000.0000.0000.0000.0000.000
180C184MET 00.0120.023116.9440.0000.0000.0000.0000.0000.000
181C185ASP -1-0.803-0.921112.180-0.002-0.0020.0000.0000.0000.000
182C186LYS 10.9630.997109.0250.0010.0010.0000.0000.0000.000
183C187LYS 10.9820.988106.0990.0020.0020.0000.0000.0000.000
184C188THR 0-0.006-0.009109.2560.0000.0000.0000.0000.0000.000
185C189VAL 00.000-0.012111.7870.0000.0000.0000.0000.0000.000
186C190SER 0-0.079-0.023107.6740.0000.0000.0000.0000.0000.000
187C191THR 0-0.033-0.019105.5120.0000.0000.0000.0000.0000.000
188C192ALA 0-0.0150.005107.6250.0000.0000.0000.0000.0000.000
189C193LEU 0-0.064-0.045110.2880.0000.0000.0000.0000.0000.000
190C194GLY 00.0140.029106.2810.0000.0000.0000.0000.0000.000
191C195ILE 0-0.053-0.025105.6890.0000.0000.0000.0000.0000.000
192C196THR 0-0.015-0.012100.4340.0000.0000.0000.0000.0000.000
193C197GLY 0-0.019-0.029101.8780.0000.0000.0000.0000.0000.000
194C198GLU -1-0.936-0.97495.405-0.001-0.0010.0000.0000.0000.000
195C199PHE 0-0.088-0.036100.0740.0000.0000.0000.0000.0000.000
196C200ASP -1-0.840-0.902102.0770.0000.0000.0000.0000.0000.000
197C201TYR 0-0.130-0.105103.8090.0000.0000.0000.0000.0000.000
198C202LEU 0-0.060-0.038100.9200.0000.0000.0000.0000.0000.000
199C203NME 0-0.037-0.01699.4070.0000.0000.0000.0000.0000.000