FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 39ZGL

Calculation Name: 2V3C-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2V3C

Chain ID: C

ChEMBL ID:

UniProt ID: Q58440

Base Structure: X-ray

Registration Date: 2023-06-22

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 403
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6262676.677419
FMO2-HF: Nuclear repulsion 6106605.832085
FMO2-HF: Total energy -156070.845335
FMO2-MP2: Total energy -156529.834644


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:2:MET)


Summations of interaction energy for fragment #1(C:2: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.
-41.856-38.40531.021-11.68-22.786-0.071
Interaction energy analysis for fragmet #1(C:2:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.027
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].
3C4LYS10.9410.9653.465-2.730-0.6790.050-0.947-1.1530.005
4C5LEU0-0.036-0.0082.065-3.683-2.7773.197-1.531-2.5720.003
5C6GLY00.0950.0423.376-0.2920.0170.026-0.008-0.326-0.001
6C7GLU-1-0.859-0.9166.2400.8430.8430.0000.0000.0000.000
7C8ASN0-0.038-0.0196.806-0.164-0.1640.0000.0000.0000.000
8C9LEU0-0.020-0.0047.419-0.125-0.1250.0000.0000.0000.000
9C10ASN00.0720.0239.091-0.022-0.0220.0000.0000.0000.000
10C11LYS10.7800.87110.954-0.532-0.5320.0000.0000.0000.000
11C12ALA0-0.038-0.01612.587-0.039-0.0390.0000.0000.0000.000
12C13LEU00.0300.01213.290-0.027-0.0270.0000.0000.0000.000
13C14ASN0-0.023-0.00915.555-0.015-0.0150.0000.0000.0000.000
14C15LYS10.8250.90217.182-0.312-0.3120.0000.0000.0000.000
15C16LEU0-0.046-0.00618.551-0.019-0.0190.0000.0000.0000.000
16C17LYS10.9640.97021.457-0.123-0.1230.0000.0000.0000.000
17C18ALA00.0140.00223.451-0.014-0.0140.0000.0000.0000.000
18C19ALA0-0.052-0.02826.7830.0010.0010.0000.0000.0000.000
19C20ALA00.0300.02628.026-0.005-0.0050.0000.0000.0000.000
20C21PHE00.007-0.00128.0030.0110.0110.0000.0000.0000.000
21C22VAL00.0000.00224.3680.0010.0010.0000.0000.0000.000
22C23ASP-1-0.671-0.84527.8150.1510.1510.0000.0000.0000.000
23C24LYS10.8750.92528.138-0.175-0.1750.0000.0000.0000.000
24C25LYS10.9190.97326.315-0.175-0.1750.0000.0000.0000.000
25C26LEU00.0130.00622.1540.0190.0190.0000.0000.0000.000
26C27ILE00.0610.03521.6170.0190.0190.0000.0000.0000.000
27C28LYS10.8800.92220.276-0.260-0.2600.0000.0000.0000.000
28C29GLU-1-0.906-0.93419.7770.3170.3170.0000.0000.0000.000
29C30VAL00.0820.04716.2590.0310.0310.0000.0000.0000.000
30C31ILE00.0100.00215.7540.0540.0540.0000.0000.0000.000
31C32LYS10.8240.90315.363-0.308-0.3080.0000.0000.0000.000
32C33ASP-1-0.820-0.90213.1340.5680.5680.0000.0000.0000.000
33C34ILE00.0450.03411.2430.0960.0960.0000.0000.0000.000
34C35GLN00.0420.02810.4260.1160.1160.0000.0000.0000.000
35C36ARG10.8350.89711.036-0.588-0.5880.0000.0000.0000.000
36C37ALA0-0.0020.0117.1550.0840.0840.0000.0000.0000.000
37C38LEU00.0470.0126.4960.2590.2590.0000.0000.0000.000
38C39ILE0-0.014-0.0107.6130.1400.1400.0000.0000.0000.000
39C40GLN0-0.042-0.0247.491-0.076-0.0760.0000.0000.0000.000
40C41ALA0-0.0020.0203.501-0.1920.0770.009-0.082-0.1970.000
41C42ASP-1-0.809-0.9034.8361.2091.343-0.001-0.004-0.1280.000
42C43VAL00.0110.0137.3880.0890.0890.0000.0000.0000.000
43C44ASN00.0080.0109.693-0.265-0.2650.0000.0000.0000.000
44C45VAL00.0570.01913.428-0.018-0.0180.0000.0000.0000.000
45C46LYS10.9430.97214.774-0.441-0.4410.0000.0000.0000.000
46C47LEU0-0.008-0.00213.249-0.071-0.0710.0000.0000.0000.000
47C48VAL00.0140.02011.680-0.048-0.0480.0000.0000.0000.000
48C49LEU00.007-0.00114.406-0.059-0.0590.0000.0000.0000.000
49C50LYS10.9010.95517.876-0.459-0.4590.0000.0000.0000.000
50C51MET00.0430.04113.518-0.004-0.0040.0000.0000.0000.000
51C52SER0-0.014-0.03816.765-0.030-0.0300.0000.0000.0000.000
52C53LYS10.9490.97518.233-0.303-0.3030.0000.0000.0000.000
53C54GLU-1-0.833-0.89220.6330.2330.2330.0000.0000.0000.000
54C55ILE00.0220.01816.276-0.024-0.0240.0000.0000.0000.000
55C56GLU-1-0.865-0.92720.8890.2510.2510.0000.0000.0000.000
56C57ARG10.7760.87923.638-0.240-0.2400.0000.0000.0000.000
57C58ARG10.9550.93321.633-0.240-0.2400.0000.0000.0000.000
58C59ALA00.0610.03422.751-0.018-0.0180.0000.0000.0000.000
59C60LEU0-0.166-0.08524.647-0.011-0.0110.0000.0000.0000.000
60C61GLU-1-0.970-0.99727.1920.1640.1640.0000.0000.0000.000
61C62GLU-1-0.868-0.92228.4570.1380.1380.0000.0000.0000.000
62C63LYS10.8170.92827.618-0.141-0.1410.0000.0000.0000.000
63C64THR00.021-0.00629.356-0.010-0.0100.0000.0000.0000.000
64C65PRO0-0.065-0.05229.9470.0050.0050.0000.0000.0000.000
65C66LYS10.8810.92830.274-0.071-0.0710.0000.0000.0000.000
66C67GLY00.0720.05329.1260.0100.0100.0000.0000.0000.000
67C68LEU00.0550.02424.772-0.002-0.0020.0000.0000.0000.000
68C69SER0-0.0270.00428.267-0.009-0.0090.0000.0000.0000.000
69C70LYN0-0.043-0.01427.2490.0110.0110.0000.0000.0000.000
70C71LYS10.8420.90123.503-0.039-0.0390.0000.0000.0000.000
71C72GLU-1-0.734-0.86122.7270.0690.0690.0000.0000.0000.000
72C73HIS00.0140.01622.7080.0210.0210.0000.0000.0000.000
73C74ILE0-0.002-0.00119.9550.0160.0160.0000.0000.0000.000
74C75ILE0-0.011-0.00517.7330.0350.0350.0000.0000.0000.000
75C76LYS10.9730.99418.069-0.114-0.1140.0000.0000.0000.000
76C77ILE0-0.055-0.02319.5690.0210.0210.0000.0000.0000.000
77C78VAL0-0.023-0.02214.5150.0400.0400.0000.0000.0000.000
78C79TYR00.0080.00713.7170.0930.0930.0000.0000.0000.000
79C80GLU-1-0.876-0.94615.1610.2350.2350.0000.0000.0000.000
80C81GLU-1-0.818-0.89317.1020.3800.3800.0000.0000.0000.000
81C82LEU0-0.031-0.0279.4050.0910.0910.0000.0000.0000.000
82C83VAL00.005-0.00312.2950.1470.1470.0000.0000.0000.000
83C84LYS10.8700.94013.183-0.277-0.2770.0000.0000.0000.000
84C85LEU0-0.095-0.03710.7850.0360.0360.0000.0000.0000.000
85C86LEU0-0.029-0.0347.0820.2360.2360.0000.0000.0000.000
86C87GLY00.003-0.00810.6550.0250.0250.0000.0000.0000.000
87C88GLU-1-0.918-0.94813.3340.2510.2510.0000.0000.0000.000
88C89GLU-1-0.843-0.94816.4630.0660.0660.0000.0000.0000.000
89C90ALA0-0.0200.00316.7710.0140.0140.0000.0000.0000.000
90C91LYN0-0.048-0.01314.162-0.001-0.0010.0000.0000.0000.000
91C92LYS10.8580.93116.335-0.079-0.0790.0000.0000.0000.000
92C93LEU0-0.069-0.03117.743-0.002-0.0020.0000.0000.0000.000
93C94GLU-1-0.803-0.88419.7800.0100.0100.0000.0000.0000.000
94C95LEU0-0.014-0.02022.112-0.017-0.0170.0000.0000.0000.000
95C96ASN00.002-0.02225.2280.0000.0000.0000.0000.0000.000
96C97PRO0-0.0020.02928.831-0.002-0.0020.0000.0000.0000.000
97C98LYS10.8510.90831.8370.0320.0320.0000.0000.0000.000
98C99LYS10.8060.89932.9660.0740.0740.0000.0000.0000.000
99C100GLN00.0510.01332.111-0.001-0.0010.0000.0000.0000.000
100C101ASN0-0.018-0.00827.4210.0060.0060.0000.0000.0000.000
101C102VAL0-0.020-0.02228.263-0.011-0.0110.0000.0000.0000.000
102C103ILE00.0380.02721.4470.0090.0090.0000.0000.0000.000
103C104LEU00.0190.00624.413-0.014-0.0140.0000.0000.0000.000
104C105LEU0-0.035-0.00718.2800.0080.0080.0000.0000.0000.000
105C106VAL00.0510.00820.1050.0000.0000.0000.0000.0000.000
106C107GLY00.0590.01317.9120.0120.0120.0000.0000.0000.000
107C108ILE0-0.0070.01717.051-0.028-0.0280.0000.0000.0000.000
108C109GLN00.0920.05517.314-0.035-0.0350.0000.0000.0000.000
109C110GLY0-0.036-0.03016.2280.0300.0300.0000.0000.0000.000
110C111SER00.0250.01013.247-0.091-0.0910.0000.0000.0000.000
111C112GLY0-0.025-0.01313.157-0.077-0.0770.0000.0000.0000.000
112C113LYN0-0.024-0.00114.089-0.022-0.0220.0000.0000.0000.000
113C114THR00.0740.03617.225-0.014-0.0140.0000.0000.0000.000
114C115THR00.0080.00216.058-0.005-0.0050.0000.0000.0000.000
115C116THR0-0.044-0.04413.815-0.083-0.0830.0000.0000.0000.000
116C117ALA00.0860.06916.3610.0080.0080.0000.0000.0000.000
117C118ALA0-0.007-0.00519.9870.0040.0040.0000.0000.0000.000
118C119LYS10.8590.92212.4790.6080.6080.0000.0000.0000.000
119C120LEU00.0420.02817.031-0.012-0.0120.0000.0000.0000.000
120C121ALA00.0250.01818.1770.0160.0160.0000.0000.0000.000
121C122ARG10.8000.87318.0960.4560.4560.0000.0000.0000.000
122C123TYR00.0030.00116.517-0.010-0.0100.0000.0000.0000.000
123C124ILE00.032-0.00518.8960.0160.0160.0000.0000.0000.000
124C125GLN00.002-0.00121.957-0.001-0.0010.0000.0000.0000.000
125C126LYS10.8830.94817.1550.4630.4630.0000.0000.0000.000
126C127ARG10.9140.97518.9470.1710.1710.0000.0000.0000.000
127C128GLY00.0450.03423.0540.0190.0190.0000.0000.0000.000
128C129LEU0-0.051-0.01625.7700.0130.0130.0000.0000.0000.000
129C130LYS10.8700.92627.3970.1080.1080.0000.0000.0000.000
130C131PRO00.0010.00924.2340.0120.0120.0000.0000.0000.000
131C132ALA0-0.021-0.01026.925-0.007-0.0070.0000.0000.0000.000
132C133LEU0-0.011-0.01023.1970.0020.0020.0000.0000.0000.000
133C134ILE0-0.001-0.01127.2810.0040.0040.0000.0000.0000.000
134C135ALA0-0.013-0.00427.459-0.001-0.0010.0000.0000.0000.000
135C136ALA00.0360.01828.1650.0040.0040.0000.0000.0000.000
136C137ASP-1-0.786-0.89725.951-0.071-0.0710.0000.0000.0000.000
137C138THR0-0.042-0.00528.790-0.004-0.0040.0000.0000.0000.000
138C139TYR0-0.072-0.04623.834-0.016-0.0160.0000.0000.0000.000
139C140ARG10.8700.93020.8910.2370.2370.0000.0000.0000.000
140C141PRO00.1160.04027.756-0.013-0.0130.0000.0000.0000.000
141C142ALA00.0390.02325.939-0.006-0.0060.0000.0000.0000.000
142C143ALA0-0.092-0.05224.157-0.025-0.0250.0000.0000.0000.000
143C144TYR00.0640.02525.105-0.021-0.0210.0000.0000.0000.000
144C145GLU-1-0.888-0.94526.858-0.195-0.1950.0000.0000.0000.000
145C146GLN00.0000.02020.958-0.023-0.0230.0000.0000.0000.000
146C147LEU00.0030.01321.890-0.027-0.0270.0000.0000.0000.000
147C148LYS10.8180.89024.0920.1630.1630.0000.0000.0000.000
148C149GLN00.016-0.01625.3280.0030.0030.0000.0000.0000.000
149C150LEU0-0.064-0.02219.562-0.016-0.0160.0000.0000.0000.000
150C151ALA00.009-0.00723.468-0.006-0.0060.0000.0000.0000.000
151C152GLU-1-0.758-0.85426.026-0.170-0.1700.0000.0000.0000.000
152C153LYS10.8430.94122.3230.3480.3480.0000.0000.0000.000
153C154ILE0-0.053-0.02422.863-0.011-0.0110.0000.0000.0000.000
154C155HIS00.0480.02926.3330.0230.0230.0000.0000.0000.000
155C156VAL00.0060.01424.6780.0130.0130.0000.0000.0000.000
156C157PRO00.0070.00628.028-0.002-0.0020.0000.0000.0000.000
157C158ILE00.005-0.00327.214-0.001-0.0010.0000.0000.0000.000
158C159TYR0-0.025-0.01830.2660.0040.0040.0000.0000.0000.000
159C160GLY00.0270.00330.904-0.005-0.0050.0000.0000.0000.000
160C161ASP-1-0.845-0.89332.273-0.083-0.0830.0000.0000.0000.000
161C162GLU-1-0.904-0.95033.258-0.097-0.0970.0000.0000.0000.000
162C163THR0-0.009-0.02335.2070.0030.0030.0000.0000.0000.000
163C164ARG10.8180.91837.7950.0720.0720.0000.0000.0000.000
164C165THR00.007-0.00433.728-0.002-0.0020.0000.0000.0000.000
165C166LYS10.8800.93735.7230.0390.0390.0000.0000.0000.000
166C167SER00.0580.03131.790-0.003-0.0030.0000.0000.0000.000
167C168PRO0-0.004-0.00433.826-0.001-0.0010.0000.0000.0000.000
168C169VAL0-0.041-0.03736.0130.0030.0030.0000.0000.0000.000
169C170ASP-1-0.878-0.92734.963-0.052-0.0520.0000.0000.0000.000
170C171ILE00.0400.00231.060-0.005-0.0050.0000.0000.0000.000
171C172VAL00.0210.02333.904-0.001-0.0010.0000.0000.0000.000
172C173LYS10.8360.92736.9980.0490.0490.0000.0000.0000.000
173C174GLU-1-0.792-0.90333.286-0.064-0.0640.0000.0000.0000.000
174C175GLY00.0380.02234.206-0.004-0.0040.0000.0000.0000.000
175C176MET0-0.082-0.04235.075-0.001-0.0010.0000.0000.0000.000
176C177GLU-1-0.844-0.91136.114-0.083-0.0830.0000.0000.0000.000
177C178LYS10.8170.90131.4490.0950.0950.0000.0000.0000.000
178C179PHE00.0570.01834.690-0.004-0.0040.0000.0000.0000.000
179C180LYS10.9070.94736.1160.0620.0620.0000.0000.0000.000
180C181LYS10.8330.90933.2940.1130.1130.0000.0000.0000.000
181C182ALA0-0.0010.01431.101-0.005-0.0050.0000.0000.0000.000
182C183ASP-1-0.781-0.87529.764-0.082-0.0820.0000.0000.0000.000
183C184VAL0-0.031-0.00625.3970.0080.0080.0000.0000.0000.000
184C185LEU0-0.0140.00428.203-0.012-0.0120.0000.0000.0000.000
185C186ILE0-0.014-0.00821.8180.0060.0060.0000.0000.0000.000
186C187ILE00.013-0.00524.839-0.008-0.0080.0000.0000.0000.000
187C188ASP-1-0.792-0.90122.507-0.152-0.1520.0000.0000.0000.000
188C189THR00.016-0.01424.1500.0050.0050.0000.0000.0000.000
189C190ALA0-0.053-0.02121.7750.0180.0180.0000.0000.0000.000
190C191GLY00.0640.05323.760-0.017-0.0170.0000.0000.0000.000
191C192ARG10.8610.93723.8320.0760.0760.0000.0000.0000.000
192C193HIS0-0.044-0.02223.8020.0080.0080.0000.0000.0000.000
193C194LYS10.8740.92616.6090.0150.0150.0000.0000.0000.000
194C195GLU-1-0.933-0.96820.6370.1060.1060.0000.0000.0000.000
195C196GLH0-0.020-0.03919.339-0.006-0.0060.0000.0000.0000.000
196C197LYS10.9810.98422.813-0.121-0.1210.0000.0000.0000.000
197C198GLY00.0400.02726.548-0.005-0.0050.0000.0000.0000.000
198C199LEU00.0050.01521.004-0.004-0.0040.0000.0000.0000.000
199C200LEU0-0.020-0.02622.903-0.006-0.0060.0000.0000.0000.000
200C201GLU-1-0.901-0.94426.5780.0510.0510.0000.0000.0000.000
201C202GLU-1-0.840-0.92127.658-0.019-0.0190.0000.0000.0000.000
202C203MET0-0.0030.00325.012-0.003-0.0030.0000.0000.0000.000
203C204LYS10.8240.90328.058-0.039-0.0390.0000.0000.0000.000
204C205GLN00.001-0.00531.063-0.005-0.0050.0000.0000.0000.000
205C206ILE00.006-0.00128.788-0.003-0.0030.0000.0000.0000.000
206C207LYS10.8930.95527.915-0.072-0.0720.0000.0000.0000.000
207C208GLU-1-0.855-0.89931.1580.0310.0310.0000.0000.0000.000
208C209ILE0-0.061-0.02033.775-0.002-0.0020.0000.0000.0000.000
209C210THR0-0.011-0.01731.459-0.010-0.0100.0000.0000.0000.000
210C211ASN0-0.045-0.02032.5670.0030.0030.0000.0000.0000.000
211C212PRO0-0.011-0.00327.014-0.003-0.0030.0000.0000.0000.000
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