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: 1JQ2Z

Calculation Name: 3EUH-C-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EUH

Chain ID: C

ChEMBL ID:

UniProt ID: P22524

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 208
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2409270.901429
FMO2-HF: Nuclear repulsion 2325444.39728
FMO2-HF: Total energy -83826.50415
FMO2-MP2: Total energy -84070.467642


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:18:ACE )


Summations of interaction energy for fragment #1(C:18: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.
1.4142.277-0.006-0.403-0.4550
Interaction energy analysis for fragmet #1(C:18:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / 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].
3C20PRO 00.0370.0333.8420.9271.790-0.006-0.403-0.4550.000
4C21VAL 00.0580.0106.9540.0130.0130.0000.0000.0000.000
5C22LYS 11.0111.0079.0130.2620.2620.0000.0000.0000.000
6C23LEU 00.0300.0328.4650.0200.0200.0000.0000.0000.000
7C24ALA 00.0180.0018.0020.0630.0630.0000.0000.0000.000
8C25GLN 0-0.047-0.0159.9980.1120.1120.0000.0000.0000.000
9C26ALA 00.0070.00013.3700.0460.0460.0000.0000.0000.000
10C27LEU 0-0.025-0.03810.6200.0320.0320.0000.0000.0000.000
11C28ALA 0-0.0400.00413.5730.0400.0400.0000.0000.0000.000
12C29ASN 0-0.0020.01615.2440.0610.0610.0000.0000.0000.000
13C30PRO 00.003-0.01818.459-0.005-0.0050.0000.0000.0000.000
14C31LEU 0-0.0080.00021.4300.0080.0080.0000.0000.0000.000
15C32PHE 00.0040.01016.440-0.003-0.0030.0000.0000.0000.000
16C33PRO 00.0430.03118.9520.0040.0040.0000.0000.0000.000
17C34ALA 00.0320.00920.9710.0040.0040.0000.0000.0000.000
18C35LEU 00.0280.02421.8300.0060.0060.0000.0000.0000.000
19C36ASP -1-0.784-0.86119.063-0.271-0.2710.0000.0000.0000.000
20C37SER 0-0.034-0.02921.4110.0110.0110.0000.0000.0000.000
21C38ALA 0-0.0120.00024.2370.0100.0100.0000.0000.0000.000
22C39LEU 00.0280.03021.7400.0090.0090.0000.0000.0000.000
23C40ARG 10.8230.91817.2160.2670.2670.0000.0000.0000.000
24C41SER 0-0.140-0.06724.5500.0130.0130.0000.0000.0000.000
25C42GLY 0-0.008-0.01427.3680.0110.0110.0000.0000.0000.000
26C43ARG 10.7490.87528.6160.1070.1070.0000.0000.0000.000
27C44HIS 0-0.0280.00728.177-0.009-0.0090.0000.0000.0000.000
28C45ILE 0-0.006-0.01126.2250.0050.0050.0000.0000.0000.000
29C46GLY 00.0650.02629.066-0.004-0.0040.0000.0000.0000.000
30C47LEU 0-0.021-0.02531.181-0.003-0.0030.0000.0000.0000.000
31C48ASP -1-0.921-0.95932.717-0.076-0.0760.0000.0000.0000.000
32C49GLU -1-0.870-0.91529.819-0.109-0.1090.0000.0000.0000.000
33C50LEU 00.024-0.00329.578-0.009-0.0090.0000.0000.0000.000
34C51ASP -1-0.857-0.92127.191-0.105-0.1050.0000.0000.0000.000
35C52ASN 0-0.024-0.02025.136-0.019-0.0190.0000.0000.0000.000
36C53HIS 0-0.038-0.03124.754-0.017-0.0170.0000.0000.0000.000
37C54ALA 00.0260.02425.836-0.006-0.0060.0000.0000.0000.000
38C55PHE 0-0.027-0.01817.686-0.014-0.0140.0000.0000.0000.000
39C56LEU 0-0.025-0.02820.976-0.023-0.0230.0000.0000.0000.000
40C57MET 0-0.051-0.02421.196-0.014-0.0140.0000.0000.0000.000
41C58ASP -1-0.977-0.96520.157-0.195-0.1950.0000.0000.0000.000
42C59PHE 0-0.032-0.02915.187-0.027-0.0270.0000.0000.0000.000
43C60GLN 00.0100.01316.837-0.033-0.0330.0000.0000.0000.000
44C61GLU -1-0.884-0.94915.012-0.314-0.3140.0000.0000.0000.000
45C62TYR 00.018-0.00611.048-0.049-0.0490.0000.0000.0000.000
46C63LEU 0-0.002-0.01413.285-0.073-0.0730.0000.0000.0000.000
47C64GLU -1-0.923-0.95915.589-0.250-0.2500.0000.0000.0000.000
48C65GLU -1-0.932-0.96611.023-0.703-0.7030.0000.0000.0000.000
49C66PHE 0-0.077-0.03911.299-0.039-0.0390.0000.0000.0000.000
50C67TYR 0-0.007-0.07312.9760.0210.0210.0000.0000.0000.000
51C68ALA 00.0520.04614.5290.0410.0410.0000.0000.0000.000
52C69ARG 10.8970.9617.3551.2891.2890.0000.0000.0000.000
53C70TYR 0-0.034-0.01214.0290.0580.0580.0000.0000.0000.000
54C71ASN 0-0.058-0.01617.2800.0300.0300.0000.0000.0000.000
55C72VAL 0-0.015-0.02218.8840.0350.0350.0000.0000.0000.000
56C73GLU -1-0.882-0.91919.425-0.186-0.1860.0000.0000.0000.000
57C74LEU 00.0130.01919.0300.0180.0180.0000.0000.0000.000
58C75ILE 0-0.0010.00121.5090.0000.0000.0000.0000.0000.000
59C76ARG 10.9550.98924.7760.1280.1280.0000.0000.0000.000
60C77ALA 0-0.007-0.00226.5120.0050.0050.0000.0000.0000.000
61C78PRO 00.0090.01230.1300.0000.0000.0000.0000.0000.000
62C79GLU -1-0.824-0.90032.432-0.076-0.0760.0000.0000.0000.000
63C80GLY 0-0.053-0.02330.1780.0020.0020.0000.0000.0000.000
64C81PHE 00.0160.04429.445-0.006-0.0060.0000.0000.0000.000
65C82PHE 00.003-0.00923.181-0.005-0.0050.0000.0000.0000.000
66C83TYR 0-0.034-0.08125.8170.0090.0090.0000.0000.0000.000
67C84LEU 0-0.0020.02121.116-0.009-0.0090.0000.0000.0000.000
68C85ARG 10.8300.88424.2140.1470.1470.0000.0000.0000.000
69C86PRO 0-0.046-0.02523.750-0.006-0.0060.0000.0000.0000.000
70C87ARG 10.9940.99920.5150.1900.1900.0000.0000.0000.000
71C88SER 0-0.036-0.03024.9680.0000.0000.0000.0000.0000.000
72C89THR 0-0.022-0.02321.3770.0050.0050.0000.0000.0000.000
73C90THR 0-0.033-0.02321.940-0.019-0.0190.0000.0000.0000.000
74C91LEU 00.0090.00717.5830.0140.0140.0000.0000.0000.000
75C92ILE 0-0.043-0.01319.8090.0030.0030.0000.0000.0000.000
76C93PRO 00.0100.01623.2540.0060.0060.0000.0000.0000.000
77C94ARG 11.0020.99727.0620.0950.0950.0000.0000.0000.000
78C95SER 0-0.059-0.03829.1440.0090.0090.0000.0000.0000.000
79C96VAL 0-0.010-0.00832.743-0.003-0.0030.0000.0000.0000.000
80C97LEU 0-0.037-0.00435.6560.0030.0030.0000.0000.0000.000
81C98SER 0-0.003-0.01938.3070.0030.0030.0000.0000.0000.000
82C99GLU -1-0.809-0.93641.912-0.047-0.0470.0000.0000.0000.000
83C100LEU 0-0.0040.00744.4810.0000.0000.0000.0000.0000.000
84C101ASP -1-0.781-0.86440.652-0.060-0.0600.0000.0000.0000.000
85C102MET 00.0420.03039.271-0.002-0.0020.0000.0000.0000.000
86C103MET 0-0.039-0.00842.5730.0010.0010.0000.0000.0000.000
87C104VAL 00.0340.00943.9030.0010.0010.0000.0000.0000.000
88C105GLY 00.016-0.01541.5110.0000.0000.0000.0000.0000.000
89C106LYS 10.8130.86242.2930.0540.0540.0000.0000.0000.000
90C107ILE 00.0130.04244.2750.0010.0010.0000.0000.0000.000
91C108LEU 0-0.025-0.01041.4450.0010.0010.0000.0000.0000.000
92C109CYS 0-0.016-0.03241.788-0.001-0.0010.0000.0000.0000.000
93C110TYR 0-0.033-0.00143.3360.0010.0010.0000.0000.0000.000
94C111LEU 0-0.017-0.02146.9440.0010.0010.0000.0000.0000.000
95C112TYR 0-0.053-0.02140.0100.0000.0000.0000.0000.0000.000
96C113LEU 0-0.030-0.01043.1540.0000.0000.0000.0000.0000.000
97C114SER 00.0100.01546.7540.0020.0020.0000.0000.0000.000
98C115PRO 00.0250.00850.3360.0000.0000.0000.0000.0000.000
99C116GLU -1-0.953-0.97851.966-0.030-0.0300.0000.0000.0000.000
100C117ARG 10.8680.92550.7290.0370.0370.0000.0000.0000.000
101C118LEU 0-0.0090.01249.124-0.001-0.0010.0000.0000.0000.000
102C119ALA 00.0170.02150.868-0.001-0.0010.0000.0000.0000.000
103C120ASN 0-0.057-0.03650.0940.0010.0010.0000.0000.0000.000
104C121GLU -1-0.952-0.95847.586-0.042-0.0420.0000.0000.0000.000
105C122GLY 0-0.020-0.00945.115-0.002-0.0020.0000.0000.0000.000
106C123ILE 0-0.087-0.05645.312-0.002-0.0020.0000.0000.0000.000
107C124PHE 00.0650.02546.5760.0020.0020.0000.0000.0000.000
108C125THR 00.001-0.01848.623-0.001-0.0010.0000.0000.0000.000
109C126GLN 0-0.029-0.04047.508-0.001-0.0010.0000.0000.0000.000
110C127GLN 0-0.066-0.02350.6040.0000.0000.0000.0000.0000.000
111C128GLU -1-0.815-0.91351.657-0.037-0.0370.0000.0000.0000.000
112C129LEU 0-0.025-0.00746.8680.0000.0000.0000.0000.0000.000
113C130TYR 0-0.012-0.02850.4130.0010.0010.0000.0000.0000.000
114C131ASP -1-0.838-0.92252.644-0.032-0.0320.0000.0000.0000.000
115C132GLU -1-0.866-0.94551.422-0.036-0.0360.0000.0000.0000.000
116C133LEU 0-0.041-0.04349.8070.0000.0000.0000.0000.0000.000
117C134LEU 0-0.050-0.04652.3210.0000.0000.0000.0000.0000.000
118C135THR 0-0.0370.00255.6110.0010.0010.0000.0000.0000.000
119C136LEU 0-0.027-0.00751.1790.0010.0010.0000.0000.0000.000
120C137ALA 0-0.031-0.00152.0730.0000.0000.0000.0000.0000.000
121C138ASP -1-0.823-0.93854.000-0.030-0.0300.0000.0000.0000.000
122C139GLU -1-0.928-0.97056.164-0.029-0.0290.0000.0000.0000.000
123C140ALA 00.0050.00857.2650.0000.0000.0000.0000.0000.000
124C141LYS 10.9240.95452.3020.0350.0350.0000.0000.0000.000
125C142LEU 00.0000.00550.819-0.001-0.0010.0000.0000.0000.000
126C143LEU 00.014-0.00353.305-0.001-0.0010.0000.0000.0000.000
127C144LYS 10.9250.96954.7270.0300.0300.0000.0000.0000.000
128C145LEU 0-0.0310.00848.409-0.001-0.0010.0000.0000.0000.000
129C146VAL 0-0.109-0.04551.182-0.001-0.0010.0000.0000.0000.000
130C147ASN 0-0.023-0.01053.0520.0000.0000.0000.0000.0000.000
131C148ASN 00.0000.00355.2210.0000.0000.0000.0000.0000.000
132C149ARG 10.9140.95156.6990.0250.0250.0000.0000.0000.000
133C150SER 00.0330.01659.1500.0010.0010.0000.0000.0000.000
134C151THR 0-0.012-0.01160.652-0.001-0.0010.0000.0000.0000.000
135C152GLY 00.0440.02562.0040.0010.0010.0000.0000.0000.000
136C153SER 0-0.006-0.00761.9070.0000.0000.0000.0000.0000.000
137C154ASP -1-0.878-0.93061.611-0.027-0.0270.0000.0000.0000.000
138C155VAL 00.0060.00860.139-0.001-0.0010.0000.0000.0000.000
139C156ASP -1-0.837-0.95457.952-0.030-0.0300.0000.0000.0000.000
140C157ARG 10.9941.00456.7290.0270.0270.0000.0000.0000.000
141C158GLN 00.0640.03956.488-0.002-0.0020.0000.0000.0000.000
142C159LYS 10.8360.91353.1650.0330.0330.0000.0000.0000.000
143C160LEU 0-0.019-0.00851.925-0.002-0.0020.0000.0000.0000.000
144C161GLN 0-0.009-0.00451.708-0.001-0.0010.0000.0000.0000.000
145C162GLU -1-0.844-0.90551.045-0.037-0.0370.0000.0000.0000.000
146C163LYS 10.9260.96047.7180.0390.0390.0000.0000.0000.000
147C164VAL 00.0360.01847.085-0.003-0.0030.0000.0000.0000.000
148C165ARG 10.9610.98746.6860.0380.0380.0000.0000.0000.000
149C166SER 0-0.058-0.03944.500-0.003-0.0030.0000.0000.0000.000
150C167SER 0-0.044-0.02742.775-0.002-0.0020.0000.0000.0000.000
151C168LEU 00.0260.04041.771-0.004-0.0040.0000.0000.0000.000
152C169ASN 00.007-0.00141.242-0.006-0.0060.0000.0000.0000.000
153C170ARG 10.8600.91337.5120.0580.0580.0000.0000.0000.000
154C171LEU 00.0370.00937.073-0.006-0.0060.0000.0000.0000.000
155C172ARG 10.9040.97836.9710.0640.0640.0000.0000.0000.000
156C173ARG 10.9020.95834.3870.0690.0690.0000.0000.0000.000
157C174LEU 00.0200.00032.685-0.005-0.0050.0000.0000.0000.000
158C175GLY 00.0050.00532.747-0.006-0.0060.0000.0000.0000.000
159C176MET 0-0.076-0.00633.9760.0020.0020.0000.0000.0000.000
160C177VAL 00.0060.00336.8640.0040.0040.0000.0000.0000.000
161C178TRP 00.0200.01733.899-0.002-0.0020.0000.0000.0000.000
162C179PHE 0-0.012-0.03339.6760.0030.0030.0000.0000.0000.000
163C180MET 0-0.014-0.01542.1720.0000.0000.0000.0000.0000.000
164C181GLY 00.0210.02144.6710.0010.0010.0000.0000.0000.000
165C182HIS 0-0.018-0.01144.978-0.003-0.0030.0000.0000.0000.000
166C183ASP -1-0.836-0.91246.658-0.039-0.0390.0000.0000.0000.000
167C184SER 0-0.032-0.01645.784-0.002-0.0020.0000.0000.0000.000
168C185SER 0-0.086-0.03446.786-0.001-0.0010.0000.0000.0000.000
169C186LYS 10.9830.99148.2330.0380.0380.0000.0000.0000.000
170C187PHE 00.006-0.01543.288-0.002-0.0020.0000.0000.0000.000
171C188ARG 11.0061.01840.5350.0580.0580.0000.0000.0000.000
172C189ILE 0-0.036-0.00541.021-0.003-0.0030.0000.0000.0000.000
173C190THR 00.0470.04034.9650.0020.0020.0000.0000.0000.000
174C191GLU -1-0.726-0.87533.681-0.087-0.0870.0000.0000.0000.000
175C192SER 00.010-0.03032.6820.0010.0010.0000.0000.0000.000
176C193VAL 00.0140.01534.746-0.001-0.0010.0000.0000.0000.000
177C194PHE 00.032-0.00936.4500.0040.0040.0000.0000.0000.000
178C195ARG 10.8440.92131.4770.1040.1040.0000.0000.0000.000
179C196PHE 0-0.0370.00136.1910.0020.0020.0000.0000.0000.000
180C197GLY 00.0180.01839.3840.0040.0040.0000.0000.0000.000
181C198ALA 00.0160.00336.5530.0020.0020.0000.0000.0000.000
182C199ASP -1-0.940-0.96138.438-0.055-0.0550.0000.0000.0000.000
183C200VAL 0-0.012-0.02341.0910.0030.0030.0000.0000.0000.000
184C201ARG 10.7830.89437.1880.0680.0680.0000.0000.0000.000
185C202ALA 0-0.031-0.01438.5600.0010.0010.0000.0000.0000.000
186C203GLY 00.0220.00140.5850.0010.0010.0000.0000.0000.000
187C204ASP -1-0.891-0.94241.555-0.050-0.0500.0000.0000.0000.000
188C205ASP -1-0.878-0.92244.875-0.038-0.0380.0000.0000.0000.000
189C206PRO 00.0850.02244.784-0.002-0.0020.0000.0000.0000.000
190C207ARG 10.9260.95443.8270.0350.0350.0000.0000.0000.000
191C208GLU -1-0.925-0.94242.788-0.043-0.0430.0000.0000.0000.000
192C209ALA 00.0200.00139.989-0.003-0.0030.0000.0000.0000.000
193C210GLN 00.0180.00538.813-0.004-0.0040.0000.0000.0000.000
194C211ARG 10.8930.95338.7040.0440.0440.0000.0000.0000.000
195C212ARG 10.8470.90731.6070.0780.0780.0000.0000.0000.000
196C213LEU 00.001-0.00934.732-0.006-0.0060.0000.0000.0000.000
197C214ILE 0-0.050-0.02133.974-0.005-0.0050.0000.0000.0000.000
198C215ARG 10.8780.94532.1750.0680.0680.0000.0000.0000.000
199C216ASP -1-0.822-0.90330.101-0.094-0.0940.0000.0000.0000.000
200C217GLY 0-0.024-0.00529.240-0.009-0.0090.0000.0000.0000.000
201C218GLU -1-0.817-0.84430.262-0.111-0.1110.0000.0000.0000.000
202C219ALA 0-0.021-0.01632.2520.0020.0020.0000.0000.0000.000
203C220MET 00.0120.00834.742-0.004-0.0040.0000.0000.0000.000
204C221PRO 0-0.0190.00536.8920.0010.0010.0000.0000.0000.000
205C222ILE 0-0.013-0.00540.625-0.001-0.0010.0000.0000.0000.000
206C223GLU -1-0.920-0.95142.968-0.041-0.0410.0000.0000.0000.000
207C224ASN 0-0.044-0.05645.6100.0000.0000.0000.0000.0000.000
208C225NME 0-0.0090.02648.2770.0010.0010.0000.0000.0000.000