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: K3J23

Calculation Name: 3EUH-C-Xray372

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: 2023-06-19

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2408305.869108
FMO2-HF: Nuclear repulsion 2324647.781375
FMO2-HF: Total energy -83658.087733
FMO2-MP2: Total energy -83901.342584


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:19:MET)


Summations of interaction energy for fragment #1(C:19:MET)
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.
-12.145-14.71618.623-6.539-9.5120.017
Interaction energy analysis for fragmet #1(C:19:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.041
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].
3C21VAL00.0420.0113.313-1.8350.1090.040-0.953-1.0320.001
4C22LYS10.8290.9065.7341.2511.2510.0000.0000.0000.000
5C23LEU00.0240.0132.5480.9910.1914.922-0.956-3.166-0.009
6C24ALA0-0.017-0.0123.3340.1380.9890.031-0.247-0.635-0.001
7C25GLN0-0.024-0.0174.2110.8921.0880.001-0.036-0.1610.000
8C26ALA00.0170.0127.2170.3570.3570.0000.0000.0000.000
9C27LEU0-0.024-0.0253.754-0.0620.3100.019-0.061-0.3290.000
10C28ALA0-0.039-0.0087.1440.0760.0760.0000.0000.0000.000
11C29ASN0-0.0030.0128.9010.1490.1490.0000.0000.0000.000
12C30PRO00.011-0.01411.9890.1230.1230.0000.0000.0000.000
13C31LEU00.0200.02114.9760.0650.0650.0000.0000.0000.000
14C32PHE00.0110.0178.7210.0950.0950.0000.0000.0000.000
15C33PRO00.0210.01412.1560.1320.1320.0000.0000.0000.000
16C34ALA00.0100.00913.3480.0740.0740.0000.0000.0000.000
17C35LEU00.0240.02115.3790.0400.0400.0000.0000.0000.000
18C36ASP-1-0.736-0.82211.3541.1251.1250.0000.0000.0000.000
19C37SER0-0.043-0.03614.2500.0530.0530.0000.0000.0000.000
20C38ALA0-0.0130.00016.7330.0000.0000.0000.0000.0000.000
21C39LEU00.0140.02015.235-0.004-0.0040.0000.0000.0000.000
22C40ARG10.7720.85510.321-1.202-1.2020.0000.0000.0000.000
23C41SER0-0.135-0.06717.882-0.028-0.0280.0000.0000.0000.000
24C42GLY00.0090.00220.804-0.036-0.0360.0000.0000.0000.000
25C43ARG10.7120.86021.694-0.193-0.1930.0000.0000.0000.000
26C44HIS0-0.032-0.01521.3620.0330.0330.0000.0000.0000.000
27C45ILE0-0.002-0.00919.461-0.023-0.0230.0000.0000.0000.000
28C46GLY00.0790.02722.702-0.001-0.0010.0000.0000.0000.000
29C47LEU0-0.045-0.04424.924-0.010-0.0100.0000.0000.0000.000
30C48ASP-1-0.836-0.89026.4840.0370.0370.0000.0000.0000.000
31C49GLU-1-0.827-0.89422.7690.1180.1180.0000.0000.0000.000
32C50LEU00.0180.01222.913-0.001-0.0010.0000.0000.0000.000
33C51ASP-1-0.868-0.93420.618-0.125-0.1250.0000.0000.0000.000
34C52ASN0-0.007-0.02818.509-0.037-0.0370.0000.0000.0000.000
35C53HIS0-0.047-0.02718.3110.0000.0000.0000.0000.0000.000
36C54ALA00.0390.01419.308-0.001-0.0010.0000.0000.0000.000
37C55PHE0-0.025-0.00810.987-0.047-0.0470.0000.0000.0000.000
38C56LEU0-0.012-0.02214.545-0.001-0.0010.0000.0000.0000.000
39C57MET0-0.033-0.01715.4440.0360.0360.0000.0000.0000.000
40C58ASP-1-0.875-0.91814.198-0.610-0.6100.0000.0000.0000.000
41C59PHE0-0.023-0.0169.313-0.182-0.1820.0000.0000.0000.000
42C60GLN0-0.043-0.02010.7600.1110.1110.0000.0000.0000.000
43C61GLU-1-0.820-0.8919.800-0.299-0.2990.0000.0000.0000.000
44C62TYR0-0.033-0.0466.2030.0110.0110.0000.0000.0000.000
45C63LEU0-0.021-0.0166.9191.0221.0220.0000.0000.0000.000
46C64GLU-1-0.867-0.9279.5320.7340.7340.0000.0000.0000.000
47C65GLU-1-0.883-0.9495.3990.6010.6010.0000.0000.0000.000
48C66PHE0-0.062-0.0315.2250.8501.017-0.001-0.019-0.1470.000
49C67TYR00.004-0.0527.2110.0310.0310.0000.0000.0000.000
50C68ALA00.0370.02310.045-0.113-0.1130.0000.0000.0000.000
51C69ARG10.8420.9152.260-14.786-20.08713.611-4.267-4.0420.026
52C70TYR0-0.0060.0098.370-0.377-0.3770.0000.0000.0000.000
53C71ASN0-0.048-0.01712.959-0.214-0.2140.0000.0000.0000.000
54C72VAL0-0.022-0.01814.228-0.202-0.2020.0000.0000.0000.000
55C73GLU-1-0.772-0.85514.2560.7000.7000.0000.0000.0000.000
56C74LEU00.0090.00812.709-0.042-0.0420.0000.0000.0000.000
57C75ILE0-0.042-0.01515.707-0.040-0.0400.0000.0000.0000.000
58C76ARG10.9300.97019.060-0.082-0.0820.0000.0000.0000.000
59C77ALA0-0.0150.01120.810-0.003-0.0030.0000.0000.0000.000
60C78PRO0-0.013-0.01024.589-0.019-0.0190.0000.0000.0000.000
61C79GLU-1-0.806-0.88326.6760.1010.1010.0000.0000.0000.000
62C80GLY0-0.002-0.00324.342-0.016-0.0160.0000.0000.0000.000
63C81PHE00.0050.03623.404-0.005-0.0050.0000.0000.0000.000
64C82PHE00.020-0.00617.6610.0240.0240.0000.0000.0000.000
65C83TYR0-0.034-0.05819.946-0.026-0.0260.0000.0000.0000.000
66C84LEU00.0200.02915.0900.0500.0500.0000.0000.0000.000
67C85ARG10.8150.87518.501-0.489-0.4890.0000.0000.0000.000
68C86PRO0-0.019-0.01118.7470.0550.0550.0000.0000.0000.000
69C87ARG10.8760.93317.091-0.787-0.7870.0000.0000.0000.000
70C88SER0-0.012-0.02020.8480.0150.0150.0000.0000.0000.000
71C89THR0-0.005-0.00619.165-0.031-0.0310.0000.0000.0000.000
72C90THR0-0.030-0.01817.7750.1300.1300.0000.0000.0000.000
73C91LEU0-0.0070.00013.819-0.049-0.0490.0000.0000.0000.000
74C92ILE0-0.016-0.00513.642-0.001-0.0010.0000.0000.0000.000
75C93PRO0-0.008-0.00117.939-0.029-0.0290.0000.0000.0000.000
76C94ARG10.8930.94321.812-0.424-0.4240.0000.0000.0000.000
77C95SER0-0.037-0.03023.578-0.033-0.0330.0000.0000.0000.000
78C96VAL0-0.020-0.00926.8790.0090.0090.0000.0000.0000.000
79C97LEU0-0.0070.00929.843-0.009-0.0090.0000.0000.0000.000
80C98SER00.002-0.02332.323-0.005-0.0050.0000.0000.0000.000
81C99GLU-1-0.731-0.88936.0750.1350.1350.0000.0000.0000.000
82C100LEU00.0220.01938.629-0.006-0.0060.0000.0000.0000.000
83C101ASP-1-0.749-0.82134.2840.1680.1680.0000.0000.0000.000
84C102MET00.0030.01033.3770.0000.0000.0000.0000.0000.000
85C103MET0-0.0230.00036.517-0.008-0.0080.0000.0000.0000.000
86C104VAL00.012-0.00337.492-0.006-0.0060.0000.0000.0000.000
87C105GLY00.0490.01335.342-0.007-0.0070.0000.0000.0000.000
88C106LYS10.7950.87036.144-0.142-0.1420.0000.0000.0000.000
89C107ILE00.0100.01338.369-0.006-0.0060.0000.0000.0000.000
90C108LEU0-0.017-0.01534.750-0.007-0.0070.0000.0000.0000.000
91C109CYS0-0.016-0.01935.943-0.005-0.0050.0000.0000.0000.000
92C110TYR0-0.0160.00337.355-0.006-0.0060.0000.0000.0000.000
93C111LEU0-0.009-0.01240.405-0.006-0.0060.0000.0000.0000.000
94C112TYR0-0.062-0.03333.351-0.006-0.0060.0000.0000.0000.000
95C113LEU0-0.025-0.01237.616-0.004-0.0040.0000.0000.0000.000
96C114SER0-0.0100.01740.858-0.005-0.0050.0000.0000.0000.000
97C115PRO00.0380.01444.480-0.003-0.0030.0000.0000.0000.000
98C116GLU-1-0.903-0.96646.2480.0260.0260.0000.0000.0000.000
99C117ARG10.7770.88144.373-0.048-0.0480.0000.0000.0000.000
100C118LEU0-0.0050.00342.631-0.001-0.0010.0000.0000.0000.000
101C119ALA0-0.009-0.00644.478-0.003-0.0030.0000.0000.0000.000
102C120ASN0-0.074-0.04643.495-0.003-0.0030.0000.0000.0000.000
103C121GLU-1-0.903-0.94040.6510.0000.0000.0000.0000.0000.000
104C122GLY00.0410.02039.0160.0010.0010.0000.0000.0000.000
105C123ILE0-0.030-0.01938.9750.0070.0070.0000.0000.0000.000
106C124PHE00.0450.03339.672-0.003-0.0030.0000.0000.0000.000
107C125THR0-0.008-0.02741.9190.0020.0020.0000.0000.0000.000
108C126GLN00.016-0.01740.4720.0060.0060.0000.0000.0000.000
109C127GLN0-0.073-0.02943.8290.0040.0040.0000.0000.0000.000
110C128GLU-1-0.719-0.85945.2310.0440.0440.0000.0000.0000.000
111C129LEU0-0.023-0.00340.0690.0020.0020.0000.0000.0000.000
112C130TYR0-0.035-0.02543.9270.0030.0030.0000.0000.0000.000
113C131ASP-1-0.795-0.89346.2960.0570.0570.0000.0000.0000.000
114C132GLU-1-0.807-0.87744.9990.0560.0560.0000.0000.0000.000
115C133LEU0-0.039-0.03142.7710.0030.0030.0000.0000.0000.000
116C134LEU0-0.044-0.03245.9230.0020.0020.0000.0000.0000.000
117C135THR0-0.051-0.02749.363-0.002-0.0020.0000.0000.0000.000
118C136LEU0-0.035-0.00945.352-0.001-0.0010.0000.0000.0000.000
119C137ALA0-0.029-0.00845.9280.0050.0050.0000.0000.0000.000
120C138ASP-1-0.803-0.91548.0110.0810.0810.0000.0000.0000.000
121C139GLU-1-0.793-0.88449.6530.0730.0730.0000.0000.0000.000
122C140ALA00.0140.01251.1550.0020.0020.0000.0000.0000.000
123C141LYS10.7860.87444.406-0.121-0.1210.0000.0000.0000.000
124C142LEU00.0330.01344.4700.0060.0060.0000.0000.0000.000
125C143LEU00.0220.00747.1920.0030.0030.0000.0000.0000.000
126C144LYS10.8520.93749.067-0.089-0.0890.0000.0000.0000.000
127C145LEU0-0.0460.00342.6350.0050.0050.0000.0000.0000.000
128C146VAL0-0.084-0.02144.9000.0060.0060.0000.0000.0000.000
129C147ASN0-0.004-0.02347.1260.0070.0070.0000.0000.0000.000
130C148ASN00.003-0.00449.6100.0000.0000.0000.0000.0000.000
131C149ARG10.9340.96351.130-0.088-0.0880.0000.0000.0000.000
132C150SER0-0.014-0.01252.694-0.004-0.0040.0000.0000.0000.000
133C151THR0-0.016-0.02054.4400.0010.0010.0000.0000.0000.000
134C152GLY00.0310.02155.593-0.003-0.0030.0000.0000.0000.000
135C153SER0-0.039-0.03255.695-0.004-0.0040.0000.0000.0000.000
136C154ASP-1-0.768-0.89454.9340.0630.0630.0000.0000.0000.000
137C155VAL00.0280.02253.2180.0010.0010.0000.0000.0000.000
138C156ASP-1-0.768-0.85451.2050.0850.0850.0000.0000.0000.000
139C157ARG10.8500.90550.180-0.060-0.0600.0000.0000.0000.000
140C158GLN0-0.010-0.00150.0060.0030.0030.0000.0000.0000.000
141C159LYS10.7870.87147.430-0.080-0.0800.0000.0000.0000.000
142C160LEU00.0120.00545.4260.0060.0060.0000.0000.0000.000
143C161GLN00.0060.01545.0990.0040.0040.0000.0000.0000.000
144C162GLU-1-0.818-0.88643.8930.0880.0880.0000.0000.0000.000
145C163LYS10.8130.91641.503-0.114-0.1140.0000.0000.0000.000
146C164VAL00.0520.02740.3220.0080.0080.0000.0000.0000.000
147C165ARG10.8910.94839.883-0.068-0.0680.0000.0000.0000.000
148C166SER0-0.051-0.03937.7840.0040.0040.0000.0000.0000.000
149C167SER0-0.040-0.04836.0070.0090.0090.0000.0000.0000.000
150C168LEU00.0150.02535.0240.0100.0100.0000.0000.0000.000
151C169ASN0-0.0040.00833.6490.0100.0100.0000.0000.0000.000
152C170ARG10.8400.90931.186-0.175-0.1750.0000.0000.0000.000
153C171LEU00.0490.01230.3520.0140.0140.0000.0000.0000.000
154C172ARG10.8800.95430.294-0.117-0.1170.0000.0000.0000.000
155C173ARG10.8530.92227.373-0.180-0.1800.0000.0000.0000.000
156C174LEU00.0520.01325.9690.0080.0080.0000.0000.0000.000
157C175GLY00.0270.03926.1780.0110.0110.0000.0000.0000.000
158C176MET0-0.042-0.00927.204-0.015-0.0150.0000.0000.0000.000
159C177VAL0-0.016-0.01330.271-0.014-0.0140.0000.0000.0000.000
160C178TRP0-0.023-0.00226.5810.0100.0100.0000.0000.0000.000
161C179PHE00.014-0.02633.0360.0000.0000.0000.0000.0000.000
162C180MET0-0.013-0.00335.173-0.005-0.0050.0000.0000.0000.000
163C181GLY00.0200.01537.729-0.008-0.0080.0000.0000.0000.000
164C182HIS0-0.022-0.01237.6400.0090.0090.0000.0000.0000.000
165C183ASP-1-0.832-0.90839.5560.0590.0590.0000.0000.0000.000
166C184SER0-0.015-0.02338.4620.0000.0000.0000.0000.0000.000
167C185SER0-0.064-0.01039.3800.0030.0030.0000.0000.0000.000
168C186LYS10.8450.91641.599-0.037-0.0370.0000.0000.0000.000
169C187PHE0-0.021-0.02736.9030.0020.0020.0000.0000.0000.000
170C188ARG10.9350.96835.019-0.027-0.0270.0000.0000.0000.000
171C189ILE0-0.037-0.01334.3460.0100.0100.0000.0000.0000.000
172C190THR0-0.014-0.00128.292-0.008-0.0080.0000.0000.0000.000
173C191GLU-1-0.727-0.88527.3570.0970.0970.0000.0000.0000.000
174C192SER00.000-0.02026.9580.0090.0090.0000.0000.0000.000
175C193VAL0-0.012-0.00528.4150.0180.0180.0000.0000.0000.000
176C194PHE00.0320.00330.7460.0030.0030.0000.0000.0000.000
177C195ARG10.7950.89825.823-0.281-0.2810.0000.0000.0000.000
178C196PHE0-0.032-0.00930.4730.0080.0080.0000.0000.0000.000
179C197GLY00.0340.02533.811-0.007-0.0070.0000.0000.0000.000
180C198ALA00.0270.00930.840-0.007-0.0070.0000.0000.0000.000
181C199ASP-1-0.863-0.92332.7610.1450.1450.0000.0000.0000.000
182C200VAL0-0.037-0.02435.636-0.006-0.0060.0000.0000.0000.000
183C201ARG10.7870.89330.712-0.116-0.1160.0000.0000.0000.000
184C202ALA0-0.0140.00433.511-0.007-0.0070.0000.0000.0000.000
185C203GLY00.0200.01935.378-0.001-0.0010.0000.0000.0000.000
186C204ASP-1-0.927-0.97036.5510.1160.1160.0000.0000.0000.000
187C205ASP-1-0.812-0.89839.7820.1070.1070.0000.0000.0000.000
188C206PRO00.0670.02439.2890.0090.0090.0000.0000.0000.000
189C207ARG10.8680.91738.545-0.106-0.1060.0000.0000.0000.000
190C208GLU-1-0.838-0.87437.7350.1620.1620.0000.0000.0000.000
191C209ALA00.0330.01535.1550.0140.0140.0000.0000.0000.000
192C210GLN0-0.030-0.03433.9270.0150.0150.0000.0000.0000.000
193C211ARG10.8130.87933.879-0.147-0.1470.0000.0000.0000.000
194C212ARG10.8570.90827.099-0.210-0.2100.0000.0000.0000.000
195C213LEU0-0.016-0.00529.5020.0200.0200.0000.0000.0000.000
196C214ILE0-0.036-0.01828.9860.0260.0260.0000.0000.0000.000
197C215ARG10.8310.90127.606-0.237-0.2370.0000.0000.0000.000
198C216ASP-1-0.786-0.85725.1610.3130.3130.0000.0000.0000.000
199C217GLY00.0240.01924.4590.0350.0350.0000.0000.0000.000
200C218GLU-1-0.767-0.83024.6540.3250.3250.0000.0000.0000.000
201C219ALA00.0020.00626.786-0.011-0.0110.0000.0000.0000.000
202C220MET00.0060.00029.5030.0350.0350.0000.0000.0000.000
203C221PRO0-0.0010.01931.972-0.012-0.0120.0000.0000.0000.000
204C222ILE0-0.040-0.02735.3950.0090.0090.0000.0000.0000.000
205C223GLU-1-0.880-0.93337.8600.1630.1630.0000.0000.0000.000
206C224ASN0-0.058-0.02640.638-0.003-0.0030.0000.0000.0000.000