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: YVLR2

Calculation Name: 4CTI-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4CTI

Chain ID: C

ChEMBL ID:

UniProt ID: P0AEJ4

Base Structure: X-ray

Registration Date: 2023-09-24

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 OptH
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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2175863.950625
FMO2-HF: Nuclear repulsion 2091156.035804
FMO2-HF: Total energy -84707.914821
FMO2-MP2: Total energy -84954.441982


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:280:ILE)


Summations of interaction energy for fragment #1(C:280:ILE)
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.
-7.173-4.8526.302-1.975-6.647-0.001
Interaction energy analysis for fragmet #1(C:280:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.002
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].
3C282ARG10.9880.9903.809-3.769-2.135-0.010-0.658-0.9660.003
4C283PRO00.0360.0152.299-0.292-0.7351.9340.169-1.661-0.001
5C284ILE00.0470.0373.048-0.8410.0290.087-0.176-0.781-0.001
6C285ILE0-0.029-0.0085.8550.3180.3180.0000.0000.0000.000
7C286GLU-1-0.905-0.9517.9760.7420.7420.0000.0000.0000.000
8C287LEU0-0.015-0.0156.927-0.030-0.0300.0000.0000.0000.000
9C288SER0-0.029-0.0239.859-0.009-0.0090.0000.0000.0000.000
10C289ASN00.0190.00511.9780.1170.1170.0000.0000.0000.000
11C290THR0-0.021-0.00812.7100.0230.0230.0000.0000.0000.000
12C291PHE0-0.030-0.03111.8960.0000.0000.0000.0000.0000.000
13C292ASP-1-0.885-0.93215.844-0.075-0.0750.0000.0000.0000.000
14C293LYS10.9220.95717.193-0.075-0.0750.0000.0000.0000.000
15C294ILE0-0.035-0.02317.3360.0030.0030.0000.0000.0000.000
16C295ALA0-0.041-0.01819.9110.0020.0020.0000.0000.0000.000
17C296GLU-1-0.949-0.96221.7380.0000.0000.0000.0000.0000.000
18C297GLY0-0.0070.00423.7710.0110.0110.0000.0000.0000.000
19C298ASN0-0.003-0.00722.0020.0030.0030.0000.0000.0000.000
20C299LEU0-0.025-0.01021.905-0.008-0.0080.0000.0000.0000.000
21C300GLU-1-0.868-0.91823.447-0.010-0.0100.0000.0000.0000.000
22C301ALA0-0.073-0.02618.8740.0150.0150.0000.0000.0000.000
23C302GLU-1-0.933-0.96615.9390.1320.1320.0000.0000.0000.000
24C303VAL0-0.014-0.00413.3430.0010.0010.0000.0000.0000.000
25C304PRO00.0570.04010.7360.0000.0000.0000.0000.0000.000
26C305HIS0-0.011-0.0276.944-0.104-0.1040.0000.0000.0000.000
27C306GLN00.0650.0289.607-0.138-0.1380.0000.0000.0000.000
28C307ASN0-0.067-0.03711.910-0.089-0.0890.0000.0000.0000.000
29C308ARG10.8360.8802.287-1.288-0.6800.586-0.285-0.9080.003
30C309ALA0-0.021-0.0169.343-0.068-0.0680.0000.0000.0000.000
31C310ASP-1-0.722-0.8103.903-1.590-1.3020.001-0.067-0.2220.000
32C311GLU-1-0.877-0.9585.206-1.806-1.8060.0000.0000.0000.000
33C312ILE00.000-0.0042.030-0.058-0.6943.704-0.958-2.109-0.005
34C313GLY00.0440.0376.1620.3130.3130.0000.0000.0000.000
35C314ILE0-0.053-0.0279.1940.1530.1530.0000.0000.0000.000
36C315LEU00.0170.0148.1480.1240.1240.0000.0000.0000.000
37C316ALA00.0690.0369.7630.1080.1080.0000.0000.0000.000
38C317LYS10.8860.94311.4820.4030.4030.0000.0000.0000.000
39C318SER0-0.086-0.05113.7470.0630.0630.0000.0000.0000.000
40C319ILE00.0170.02011.7640.0380.0380.0000.0000.0000.000
41C320GLU-1-0.795-0.87015.645-0.043-0.0430.0000.0000.0000.000
42C321ARG10.8910.93817.2460.3010.3010.0000.0000.0000.000
43C322LEU00.0080.00718.9010.0200.0200.0000.0000.0000.000
44C323ARG10.8620.90319.1800.0750.0750.0000.0000.0000.000
45C324ARG10.9320.96220.5620.1030.1030.0000.0000.0000.000
46C325SER0-0.030-0.01223.5580.0110.0110.0000.0000.0000.000
47C326LEU0-0.012-0.01122.2070.0090.0090.0000.0000.0000.000
48C327LYS10.8880.92825.3060.0360.0360.0000.0000.0000.000
49C328GLN0-0.018-0.00427.0310.0080.0080.0000.0000.0000.000
50C329LEU0-0.022-0.02227.7140.0030.0030.0000.0000.0000.000
51C330ALA0-0.090-0.04629.0040.0030.0030.0000.0000.0000.000
52C331ASP-1-0.902-0.94130.895-0.031-0.0310.0000.0000.0000.000
53C332ASP-1-0.902-0.94133.273-0.048-0.0480.0000.0000.0000.000
54C333ARG10.9350.96628.8310.0660.0660.0000.0000.0000.000
55C334THR0-0.009-0.00935.6160.0010.0010.0000.0000.0000.000
56C335LEU0-0.001-0.00837.7350.0010.0010.0000.0000.0000.000
57C336LEU00.0340.02638.2120.0010.0010.0000.0000.0000.000
58C337MET00.0310.01941.0570.0020.0020.0000.0000.0000.000
59C338ALA0-0.0020.00242.9180.0020.0020.0000.0000.0000.000
60C339GLY00.0100.00843.8380.0020.0020.0000.0000.0000.000
61C340VAL00.0150.00744.9230.0010.0010.0000.0000.0000.000
62C341SER00.000-0.00347.3160.0020.0020.0000.0000.0000.000
63C342HIS0-0.054-0.03448.4070.0030.0030.0000.0000.0000.000
64C343ASP-1-0.890-0.95348.873-0.036-0.0360.0000.0000.0000.000
65C344LEU0-0.059-0.03151.1170.0010.0010.0000.0000.0000.000
66C345ARG10.9901.00849.7720.0260.0260.0000.0000.0000.000
67C346THR00.0230.04254.9240.0020.0020.0000.0000.0000.000
68C347PRO0-0.084-0.04655.8600.0010.0010.0000.0000.0000.000
69C348LEU00.0930.04455.5120.0010.0010.0000.0000.0000.000
70C349THR0-0.012-0.02858.4340.0010.0010.0000.0000.0000.000
71C350ARG10.9120.94159.1850.0260.0260.0000.0000.0000.000
72C351ILE00.0050.01460.8060.0010.0010.0000.0000.0000.000
73C352ARG10.9250.96560.3600.0170.0170.0000.0000.0000.000
74C353LEU0-0.040-0.01664.6640.0010.0010.0000.0000.0000.000
75C354ALA0-0.010-0.00766.9430.0010.0010.0000.0000.0000.000
76C355THR0-0.043-0.04766.9820.0000.0000.0000.0000.0000.000
77C356GLU-1-0.918-0.95269.468-0.012-0.0120.0000.0000.0000.000
78C357MET0-0.110-0.03371.6800.0000.0000.0000.0000.0000.000
79C358MET0-0.059-0.00771.3000.0000.0000.0000.0000.0000.000
80C359SER0-0.003-0.00374.7550.0010.0010.0000.0000.0000.000
81C360GLU-1-0.888-0.95276.843-0.011-0.0110.0000.0000.0000.000
82C361GLN0-0.090-0.04878.5220.0000.0000.0000.0000.0000.000
83C362ASP-1-0.915-0.95474.296-0.016-0.0160.0000.0000.0000.000
84C363GLY00.0760.03373.7680.0000.0000.0000.0000.0000.000
85C364TYR00.013-0.00572.4760.0000.0000.0000.0000.0000.000
86C365LEU0-0.0060.00470.391-0.001-0.0010.0000.0000.0000.000
87C366ALA00.0410.02468.860-0.001-0.0010.0000.0000.0000.000
88C367GLU-1-0.961-0.97767.815-0.013-0.0130.0000.0000.0000.000
89C368SER0-0.025-0.02866.2570.0000.0000.0000.0000.0000.000
90C369ILE00.0300.01963.969-0.001-0.0010.0000.0000.0000.000
91C370ASN0-0.001-0.01263.012-0.001-0.0010.0000.0000.0000.000
92C371LYS10.9320.96462.1940.0150.0150.0000.0000.0000.000
93C372ASP-1-0.846-0.91260.310-0.022-0.0220.0000.0000.0000.000
94C373ILE0-0.083-0.04358.513-0.001-0.0010.0000.0000.0000.000
95C374GLU-1-0.884-0.94557.361-0.017-0.0170.0000.0000.0000.000
96C375GLU-1-0.937-0.95955.619-0.024-0.0240.0000.0000.0000.000
97C376CYS0-0.076-0.04554.052-0.002-0.0020.0000.0000.0000.000
98C377ASN0-0.033-0.02052.589-0.002-0.0020.0000.0000.0000.000
99C378ALA00.0440.02951.9450.0000.0000.0000.0000.0000.000
100C379ILE0-0.021-0.00749.154-0.001-0.0010.0000.0000.0000.000
101C380ILE0-0.040-0.03147.740-0.002-0.0020.0000.0000.0000.000
102C381GLU-1-0.935-0.97246.957-0.019-0.0190.0000.0000.0000.000
103C382GLN00.0020.00646.707-0.001-0.0010.0000.0000.0000.000
104C383PHE00.002-0.01440.619-0.001-0.0010.0000.0000.0000.000
105C384ILE0-0.015-0.01242.499-0.002-0.0020.0000.0000.0000.000
106C385ASP-1-0.876-0.94141.918-0.018-0.0180.0000.0000.0000.000
107C386TYR00.004-0.00837.0460.0020.0020.0000.0000.0000.000
108C387LEU0-0.0480.00637.432-0.001-0.0010.0000.0000.0000.000
109C388ARG10.9020.96737.1740.0190.0190.0000.0000.0000.000
110C389THR0-0.121-0.08134.4860.0020.0020.0000.0000.0000.000
111C399ASP-1-0.806-0.93142.5730.0280.0280.0000.0000.0000.000
112C400LEU0-0.025-0.02243.712-0.002-0.0020.0000.0000.0000.000
113C401ASN00.023-0.02045.802-0.004-0.0040.0000.0000.0000.000
114C402ALA00.0340.04447.351-0.002-0.0020.0000.0000.0000.000
115C403VAL00.013-0.00245.047-0.002-0.0020.0000.0000.0000.000
116C404LEU0-0.034-0.01547.900-0.002-0.0020.0000.0000.0000.000
117C405GLY00.0140.00550.129-0.001-0.0010.0000.0000.0000.000
118C406GLU-1-0.985-0.99949.2650.0100.0100.0000.0000.0000.000
119C407VAL0-0.077-0.04749.260-0.001-0.0010.0000.0000.0000.000
120C408ILE0-0.0350.01352.282-0.001-0.0010.0000.0000.0000.000
121C409ALA0-0.0120.00755.763-0.001-0.0010.0000.0000.0000.000
122C417GLU-1-0.921-0.96662.9000.0010.0010.0000.0000.0000.000
123C418ILE0-0.007-0.00457.3280.0000.0000.0000.0000.0000.000
124C419GLU-1-0.807-0.89659.9800.0060.0060.0000.0000.0000.000
125C420THR0-0.023-0.01856.8270.0000.0000.0000.0000.0000.000
126C421ALA0-0.035-0.02056.2460.0010.0010.0000.0000.0000.000
127C422LEU00.0180.00852.0590.0010.0010.0000.0000.0000.000
128C423TYR00.0330.02149.9300.0010.0010.0000.0000.0000.000
129C424PRO0-0.0060.00052.2900.0000.0000.0000.0000.0000.000
130C425GLY00.0410.01749.6700.0020.0020.0000.0000.0000.000
131C426SER0-0.043-0.00346.3900.0020.0020.0000.0000.0000.000
132C427ILE0-0.011-0.00843.040-0.001-0.0010.0000.0000.0000.000
133C428GLU-1-0.797-0.90238.2590.0370.0370.0000.0000.0000.000
134C429VAL0-0.049-0.02036.3530.0010.0010.0000.0000.0000.000
135C430LYS10.8940.95632.236-0.035-0.0350.0000.0000.0000.000
136C431MET00.0100.00035.408-0.002-0.0020.0000.0000.0000.000
137C432HIS00.0670.03235.2330.0020.0020.0000.0000.0000.000
138C433PRO00.0360.00838.438-0.003-0.0030.0000.0000.0000.000
139C434LEU00.0180.00640.934-0.001-0.0010.0000.0000.0000.000
140C435SER0-0.0150.00238.502-0.004-0.0040.0000.0000.0000.000
141C436ILE00.0540.02739.960-0.002-0.0020.0000.0000.0000.000
142C437LYS10.9290.96843.072-0.007-0.0070.0000.0000.0000.000
143C438ARG10.8760.94840.0750.0150.0150.0000.0000.0000.000
144C439ALA00.0250.01343.069-0.001-0.0010.0000.0000.0000.000
145C440VAL00.0430.01345.105-0.001-0.0010.0000.0000.0000.000
146C441ALA00.0120.01448.3360.0000.0000.0000.0000.0000.000
147C442ASN0-0.030-0.03146.203-0.003-0.0030.0000.0000.0000.000
148C443MET0-0.026-0.00947.427-0.001-0.0010.0000.0000.0000.000
149C444VAL00.0560.03250.1150.0000.0000.0000.0000.0000.000
150C445VAL0-0.020-0.00152.001-0.001-0.0010.0000.0000.0000.000
151C446ASN0-0.065-0.05051.481-0.002-0.0020.0000.0000.0000.000
152C447ALA0-0.010-0.01553.524-0.001-0.0010.0000.0000.0000.000
153C448ALA00.0610.05355.7090.0000.0000.0000.0000.0000.000
154C449ARG10.8660.94752.2910.0140.0140.0000.0000.0000.000
155C450TYR0-0.066-0.05654.734-0.002-0.0020.0000.0000.0000.000
156C451GLY00.0150.01758.7280.0000.0000.0000.0000.0000.000
157C452ASN0-0.090-0.04260.189-0.001-0.0010.0000.0000.0000.000
158C453GLY00.0500.01262.9910.0000.0000.0000.0000.0000.000
159C454TRP0-0.123-0.05262.3310.0010.0010.0000.0000.0000.000
160C455ILE00.0420.03156.381-0.001-0.0010.0000.0000.0000.000
161C456LYS10.7970.89457.260-0.005-0.0050.0000.0000.0000.000
162C457VAL00.0080.00452.1060.0000.0000.0000.0000.0000.000
163C458SER0-0.053-0.02552.7820.0010.0010.0000.0000.0000.000
164C459SER0-0.018-0.02349.268-0.001-0.0010.0000.0000.0000.000
165C460GLY00.001-0.01148.9050.0000.0000.0000.0000.0000.000
166C461THR0-0.032-0.03245.4560.0010.0010.0000.0000.0000.000
167C462GLU-1-0.915-0.95644.8340.0290.0290.0000.0000.0000.000
168C463PRO0-0.0760.04339.9450.0030.0030.0000.0000.0000.000
169C464ASN00.060-0.01538.1200.0020.0020.0000.0000.0000.000
170C465ARG10.7910.88439.201-0.042-0.0420.0000.0000.0000.000
171C466ALA00.046-0.01841.052-0.001-0.0010.0000.0000.0000.000
172C467TRP0-0.0600.00043.0950.0000.0000.0000.0000.0000.000
173C468PHE00.0080.00543.4880.0010.0010.0000.0000.0000.000
174C469GLN00.0630.03347.356-0.001-0.0010.0000.0000.0000.000
175C470VAL0-0.0100.00450.0570.0010.0010.0000.0000.0000.000
176C471GLU-1-0.895-0.93552.5500.0050.0050.0000.0000.0000.000
177C472ASP-1-0.743-0.88355.365-0.001-0.0010.0000.0000.0000.000
178C473ASP-1-0.894-0.93958.094-0.001-0.0010.0000.0000.0000.000
179C474GLY00.0040.01859.663-0.001-0.0010.0000.0000.0000.000
180C475PRO0-0.096-0.04158.5030.0010.0010.0000.0000.0000.000
181C499SER0-0.010-0.02047.7160.0010.0010.0000.0000.0000.000
182C500GLY00.1040.04749.2660.0000.0000.0000.0000.0000.000
183C501THR00.0150.01349.2440.0000.0000.0000.0000.0000.000
184C502GLY00.0540.02747.5850.0010.0010.0000.0000.0000.000
185C503LEU00.0010.00643.359-0.001-0.0010.0000.0000.0000.000
186C504GLY00.0530.02744.4610.0000.0000.0000.0000.0000.000
187C505LEU00.007-0.00245.2460.0010.0010.0000.0000.0000.000
188C506ALA00.0050.01441.1750.0010.0010.0000.0000.0000.000
189C507ILE0-0.024-0.00240.518-0.001-0.0010.0000.0000.0000.000
190C508VAL00.002-0.00340.8750.0020.0020.0000.0000.0000.000
191C509GLN0-0.029-0.01538.0360.0020.0020.0000.0000.0000.000
192C510ARG10.9020.94433.2400.0300.0300.0000.0000.0000.000
193C511ILE0-0.047-0.01936.2870.0020.0020.0000.0000.0000.000
194C512VAL0-0.021-0.01137.4800.0040.0040.0000.0000.0000.000
195C513ASP-1-0.839-0.91534.037-0.010-0.0100.0000.0000.0000.000
196C514ASN0-0.055-0.00932.744-0.003-0.0030.0000.0000.0000.000
197C515HIS0-0.106-0.06332.6320.0050.0050.0000.0000.0000.000
198C516ASN0-0.048-0.02029.9290.0010.0010.0000.0000.0000.000
199C517GLY00.0310.02833.4700.0050.0050.0000.0000.0000.000
200C518MET0-0.025-0.01236.757-0.002-0.0020.0000.0000.0000.000
201C519LEU00.009-0.00139.4160.0020.0020.0000.0000.0000.000
202C520GLU-1-0.838-0.89342.4790.0100.0100.0000.0000.0000.000
203C521LEU00.006-0.00345.5950.0000.0000.0000.0000.0000.000
204C522GLY00.009-0.00648.6740.0010.0010.0000.0000.0000.000
205C523THR00.0090.01451.9900.0010.0010.0000.0000.0000.000
206C524SER0-0.010-0.02351.1440.0010.0010.0000.0000.0000.000
207C525GLH0-0.083-0.06849.5650.0020.0020.0000.0000.0000.000
208C526ARG10.8290.91054.657-0.007-0.0070.0000.0000.0000.000
209C527GLY0-0.0020.02457.8480.0000.0000.0000.0000.0000.000
210C528GLY00.0780.04558.281-0.001-0.0010.0000.0000.0000.000
211C529LEU0-0.013-0.01852.3040.0010.0010.0000.0000.0000.000
212C530SER00.0060.00951.4990.0010.0010.0000.0000.0000.000
213C531ILE0-0.009-0.01347.252-0.001-0.0010.0000.0000.0000.000
214C532ARG10.8500.92246.346-0.010-0.0100.0000.0000.0000.000
215C533ALA00.0030.00242.876-0.001-0.0010.0000.0000.0000.000
216C534TRP0-0.040-0.02040.6200.0040.0040.0000.0000.0000.000
217C535LEU00.005-0.00737.031-0.001-0.0010.0000.0000.0000.000