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: VQ8R1

Calculation Name: 1YJE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YJE

Chain ID: A

ChEMBL ID:

UniProt ID: P22829

Base Structure: X-ray

Registration Date: 2023-09-20

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2790954.521393
FMO2-HF: Nuclear repulsion 2702238.715269
FMO2-HF: Total energy -88715.806124
FMO2-MP2: Total energy -88974.174815


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(A:362:ASN)


Summations of interaction energy for fragment #1(A:362:ASN)
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.
-30.474-34.98523.688-9.944-9.2320.061
Interaction energy analysis for fragmet #1(A:362:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.080 / q_NPA : 0.060
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].
3A364LEU00.0890.0392.684-2.1140.9041.007-1.697-2.3280.011
4A365THR0-0.017-0.0331.779-21.662-29.86722.641-8.000-6.4350.047
5A366SER00.004-0.0053.706-4.408-3.7610.041-0.244-0.4440.003
6A367LEU00.0250.0285.810-0.926-0.9260.0000.0000.0000.000
7A368ILE0-0.017-0.0035.901-0.913-0.9130.0000.0000.0000.000
8A369ARG10.8360.8997.403-0.976-0.9760.0000.0000.0000.000
9A370ALA00.0240.0169.698-0.252-0.2520.0000.0000.0000.000
10A371HIS00.0150.00911.290-0.176-0.1760.0000.0000.0000.000
11A372LEU00.0120.00811.842-0.183-0.1830.0000.0000.0000.000
12A373ASP-1-0.831-0.89812.6770.2930.2930.0000.0000.0000.000
13A374SER0-0.077-0.03215.389-0.068-0.0680.0000.0000.0000.000
14A375GLY0-0.0040.00417.757-0.006-0.0060.0000.0000.0000.000
15A376PRO0-0.0280.00019.186-0.035-0.0350.0000.0000.0000.000
16A377ASN00.0530.01121.8090.0220.0220.0000.0000.0000.000
17A378THR00.0250.00222.198-0.024-0.0240.0000.0000.0000.000
18A379ALA00.0110.01124.512-0.015-0.0150.0000.0000.0000.000
19A380LYS10.7670.87226.463-0.154-0.1540.0000.0000.0000.000
20A381LEU00.0440.03425.6940.0060.0060.0000.0000.0000.000
21A382ASP-1-0.850-0.91428.7010.1110.1110.0000.0000.0000.000
22A383TYR00.0630.01730.9990.0050.0050.0000.0000.0000.000
23A384SER0-0.051-0.03134.699-0.007-0.0070.0000.0000.0000.000
24A385LYS10.9450.97534.550-0.130-0.1300.0000.0000.0000.000
25A386PHE0-0.0140.01035.7140.0020.0020.0000.0000.0000.000
26A387GLN0-0.012-0.01537.685-0.007-0.0070.0000.0000.0000.000
27A388GLU-1-0.807-0.91138.6520.1260.1260.0000.0000.0000.000
28A389LEU0-0.039-0.01041.054-0.006-0.0060.0000.0000.0000.000
29A390VAL00.0230.00642.6890.0040.0040.0000.0000.0000.000
30A391LEU0-0.009-0.00745.435-0.001-0.0010.0000.0000.0000.000
31A392PRO00.010-0.00644.6720.0020.0020.0000.0000.0000.000
32A393ARG10.8960.95942.826-0.107-0.1070.0000.0000.0000.000
33A394PHE00.0230.02446.2200.0020.0020.0000.0000.0000.000
34A395GLY00.004-0.00449.254-0.001-0.0010.0000.0000.0000.000
35A396LYS10.7830.88346.330-0.090-0.0900.0000.0000.0000.000
36A397GLU-1-0.830-0.90643.3750.0980.0980.0000.0000.0000.000
37A398ASP-1-0.817-0.89446.3650.0840.0840.0000.0000.0000.000
38A399ALA00.0700.01445.1620.0050.0050.0000.0000.0000.000
39A400GLY0-0.0090.00943.6180.0040.0040.0000.0000.0000.000
40A401ASP-1-0.848-0.93141.2390.1090.1090.0000.0000.0000.000
41A402VAL00.0200.01639.7930.0090.0090.0000.0000.0000.000
42A403GLN0-0.005-0.00238.4620.0030.0030.0000.0000.0000.000
43A404GLN0-0.009-0.00336.7520.0060.0060.0000.0000.0000.000
44A405PHE0-0.005-0.01333.8880.0120.0120.0000.0000.0000.000
45A406TYR00.0640.01634.2300.0160.0160.0000.0000.0000.000
46A407ASP-1-0.838-0.90633.9290.1310.1310.0000.0000.0000.000
47A408LEU0-0.092-0.04631.3520.0110.0110.0000.0000.0000.000
48A409LEU0-0.0080.01629.6660.0220.0220.0000.0000.0000.000
49A410SER00.0320.00329.0790.0120.0120.0000.0000.0000.000
50A411GLY0-0.010-0.00329.1420.0020.0020.0000.0000.0000.000
51A412SER0-0.038-0.07325.5720.0200.0200.0000.0000.0000.000
52A413LEU00.0230.03524.3820.0320.0320.0000.0000.0000.000
53A414ASP-1-0.770-0.87524.0890.2000.2000.0000.0000.0000.000
54A415VAL0-0.126-0.06220.8670.0080.0080.0000.0000.0000.000
55A416ILE0-0.022-0.01420.0260.0440.0440.0000.0000.0000.000
56A417ARG10.8910.94519.514-0.155-0.1550.0000.0000.0000.000
57A418LYS10.9290.95518.672-0.198-0.1980.0000.0000.0000.000
58A419TRP0-0.063-0.03213.572-0.045-0.0450.0000.0000.0000.000
59A420ALA00.0480.02514.7170.0730.0730.0000.0000.0000.000
60A421GLU-1-0.867-0.94714.7100.2510.2510.0000.0000.0000.000
61A422LYS10.7270.87311.900-0.345-0.3450.0000.0000.0000.000
62A423ILE00.0110.01810.2090.1160.1160.0000.0000.0000.000
63A424PRO0-0.036-0.0316.138-0.131-0.1310.0000.0000.0000.000
64A425GLY00.0260.0169.0000.1730.1730.0000.0000.0000.000
65A426PHE0-0.007-0.00811.6400.0050.0050.0000.0000.0000.000
66A427ILE00.0250.00113.141-0.032-0.0320.0000.0000.0000.000
67A428GLU-1-0.929-0.96511.629-0.049-0.0490.0000.0000.0000.000
68A429LEU0-0.069-0.01615.834-0.008-0.0080.0000.0000.0000.000
69A430SER0-0.005-0.01118.298-0.020-0.0200.0000.0000.0000.000
70A431PRO00.032-0.01222.0560.0180.0180.0000.0000.0000.000
71A432GLY0-0.0230.00323.9930.0050.0050.0000.0000.0000.000
72A433ASP-1-0.736-0.85621.2170.1670.1670.0000.0000.0000.000
73A434GLN0-0.046-0.01418.2590.0150.0150.0000.0000.0000.000
74A435ASP-1-0.800-0.92921.5240.2140.2140.0000.0000.0000.000
75A436LEU0-0.0030.02424.6140.0100.0100.0000.0000.0000.000
76A437LEU0-0.023-0.01318.7570.0120.0120.0000.0000.0000.000
77A438LEU0-0.035-0.01421.0560.0290.0290.0000.0000.0000.000
78A439GLU-1-0.825-0.91422.9030.1880.1880.0000.0000.0000.000
79A440SER00.0250.00624.974-0.003-0.0030.0000.0000.0000.000
80A441ALA0-0.042-0.00921.6780.0080.0080.0000.0000.0000.000
81A442PHE0-0.0010.01723.7340.0220.0220.0000.0000.0000.000
82A443LEU00.0200.00825.1590.0150.0150.0000.0000.0000.000
83A444GLU-1-0.761-0.86123.1380.3710.3710.0000.0000.0000.000
84A445LEU0-0.006-0.01518.7790.0310.0310.0000.0000.0000.000
85A446PHE0-0.014-0.00822.1660.0200.0200.0000.0000.0000.000
86A447ILE0-0.005-0.00124.9570.0030.0030.0000.0000.0000.000
87A448LEU0-0.0050.00318.7330.0000.0000.0000.0000.0000.000
88A449ARG10.8760.92316.631-0.556-0.5560.0000.0000.0000.000
89A450LEU0-0.047-0.00521.490-0.006-0.0060.0000.0000.0000.000
90A451ALA00.0130.01424.625-0.014-0.0140.0000.0000.0000.000
91A452TYR0-0.059-0.02616.7850.0020.0020.0000.0000.0000.000
92A453ARG10.8790.94321.391-0.366-0.3660.0000.0000.0000.000
93A454SER0-0.021-0.01423.275-0.038-0.0380.0000.0000.0000.000
94A455LYS10.8710.91826.827-0.173-0.1730.0000.0000.0000.000
95A456PRO00.0230.01228.672-0.021-0.0210.0000.0000.0000.000
96A457GLY0-0.036-0.01731.671-0.013-0.0130.0000.0000.0000.000
97A458GLU-1-0.787-0.88632.2900.1470.1470.0000.0000.0000.000
98A459GLY00.0070.00534.152-0.008-0.0080.0000.0000.0000.000
99A460LYS10.7360.87632.261-0.140-0.1400.0000.0000.0000.000
100A461LEU00.0430.02330.0540.0170.0170.0000.0000.0000.000
101A462ILE0-0.018-0.00426.180-0.014-0.0140.0000.0000.0000.000
102A463PHE00.0690.02826.3330.0310.0310.0000.0000.0000.000
103A464CYS0-0.041-0.00523.7310.0030.0030.0000.0000.0000.000
104A465SER00.0410.01723.9030.0130.0130.0000.0000.0000.000
105A466GLY00.024-0.00526.132-0.015-0.0150.0000.0000.0000.000
106A467LEU0-0.042-0.00326.975-0.012-0.0120.0000.0000.0000.000
107A468VAL0-0.0190.00629.9200.0140.0140.0000.0000.0000.000
108A469LEU00.004-0.01131.857-0.013-0.0130.0000.0000.0000.000
109A470HIS00.0530.03134.0540.0130.0130.0000.0000.0000.000
110A471ARG10.9260.96236.103-0.149-0.1490.0000.0000.0000.000
111A472LEU0-0.023-0.01837.031-0.001-0.0010.0000.0000.0000.000
112A473GLN0-0.029-0.02438.333-0.001-0.0010.0000.0000.0000.000
113A474CYS0-0.042-0.00935.4800.0010.0010.0000.0000.0000.000
114A475ALA0-0.006-0.00837.8420.0000.0000.0000.0000.0000.000
115A476ARG10.8250.92040.010-0.091-0.0910.0000.0000.0000.000
116A477GLY00.0530.02739.2150.0000.0000.0000.0000.0000.000
117A478PHE0-0.011-0.01132.0420.0040.0040.0000.0000.0000.000
118A479GLY00.0700.03737.4190.0020.0020.0000.0000.0000.000
119A480ASP-1-0.879-0.94738.4380.1450.1450.0000.0000.0000.000
120A481TRP0-0.0010.02131.1770.0050.0050.0000.0000.0000.000
121A482ILE00.0080.00432.5440.0150.0150.0000.0000.0000.000
122A483ASP-1-0.777-0.90833.6840.1630.1630.0000.0000.0000.000
123A484ASN0-0.045-0.01834.1200.0070.0070.0000.0000.0000.000
124A485ILE00.0330.02028.7360.0160.0160.0000.0000.0000.000
125A486LEU0-0.006-0.00629.4510.0190.0190.0000.0000.0000.000
126A487ALA0-0.060-0.01231.1500.0020.0020.0000.0000.0000.000
127A488PHE00.0610.01923.6280.0100.0100.0000.0000.0000.000
128A489SER0-0.042-0.03426.1620.0130.0130.0000.0000.0000.000
129A490ARG10.9140.93426.402-0.172-0.1720.0000.0000.0000.000
130A491SER0-0.066-0.03727.5180.0010.0010.0000.0000.0000.000
131A492LEU0-0.023-0.01721.4280.0150.0150.0000.0000.0000.000
132A493HIS0-0.042-0.03123.1750.0260.0260.0000.0000.0000.000
133A494SER0-0.072-0.04124.877-0.015-0.0150.0000.0000.0000.000
134A495LEU0-0.093-0.02721.434-0.015-0.0150.0000.0000.0000.000
135A496GLY00.0220.02821.442-0.002-0.0020.0000.0000.0000.000
136A497VAL0-0.014-0.02416.0770.0300.0300.0000.0000.0000.000
137A498ASP-1-0.786-0.86312.4151.1281.1280.0000.0000.0000.000
138A499VAL00.0510.01311.5280.0700.0700.0000.0000.0000.000
139A500PRO00.025-0.0048.1430.1330.1330.0000.0000.0000.000
140A501ALA00.0430.0249.8230.1860.1860.0000.0000.0000.000
141A502PHE00.0320.00512.431-0.058-0.0580.0000.0000.0000.000
142A503ALA0-0.0160.0089.972-0.102-0.1020.0000.0000.0000.000
143A504CYS0-0.039-0.0208.7010.2020.2020.0000.0000.0000.000
144A505LEU0-0.012-0.00211.130-0.210-0.2100.0000.0000.0000.000
145A506SER0-0.009-0.03114.675-0.112-0.1120.0000.0000.0000.000
146A507ALA00.0250.00712.020-0.111-0.1110.0000.0000.0000.000
147A508LEU0-0.035-0.01613.714-0.109-0.1090.0000.0000.0000.000
148A509VAL0-0.0260.00015.843-0.090-0.0900.0000.0000.0000.000
149A510LEU0-0.039-0.01216.062-0.063-0.0630.0000.0000.0000.000
150A511ILE0-0.046-0.02013.656-0.065-0.0650.0000.0000.0000.000
151A512THR0-0.022-0.03116.9550.0350.0350.0000.0000.0000.000
152A513ASP-1-0.871-0.94319.7390.2360.2360.0000.0000.0000.000
153A514ARG10.8530.92822.116-0.328-0.3280.0000.0000.0000.000
154A515HIS0-0.003-0.02025.797-0.011-0.0110.0000.0000.0000.000
155A516GLY00.0250.01328.144-0.006-0.0060.0000.0000.0000.000
156A517LEU0-0.0330.00222.078-0.004-0.0040.0000.0000.0000.000
157A518GLN00.0100.01924.397-0.006-0.0060.0000.0000.0000.000
158A519ASP-1-0.856-0.93121.7860.0840.0840.0000.0000.0000.000
159A520PRO00.0250.01421.2210.0150.0150.0000.0000.0000.000
160A521ARG10.8850.93517.117-0.097-0.0970.0000.0000.0000.000
161A522ARG10.7870.86616.981-0.115-0.1150.0000.0000.0000.000
162A523VAL0-0.0010.01315.8560.0380.0380.0000.0000.0000.000
163A524GLU-1-0.848-0.92616.6120.2640.2640.0000.0000.0000.000
164A525GLU-1-0.809-0.86513.3920.1780.1780.0000.0000.0000.000
165A526LEU0-0.015-0.00410.2690.0640.0640.0000.0000.0000.000
166A527GLN00.0820.04711.8810.1490.1490.0000.0000.0000.000
167A528ASN0-0.039-0.04013.2010.1390.1390.0000.0000.0000.000
168A529ARG10.8640.9358.149-0.184-0.1840.0000.0000.0000.000
169A530ILE00.0190.0148.3690.4350.4350.0000.0000.0000.000
170A531ALA0-0.0070.00010.0560.2300.2300.0000.0000.0000.000
171A532SER0-0.035-0.0189.6180.0350.0350.0000.0000.0000.000
172A533CYS0-0.016-0.0055.7670.4040.433-0.001-0.003-0.0250.000
173A534LEU0-0.0030.0067.9130.0690.0690.0000.0000.0000.000
174A535LYS10.9390.96110.693-0.606-0.6060.0000.0000.0000.000
175A536GLU-1-0.947-0.9838.2550.4810.4810.0000.0000.0000.000
176A537HIS0-0.020-0.0158.291-0.047-0.0470.0000.0000.0000.000
177A538MET0-0.054-0.03110.007-0.279-0.2790.0000.0000.0000.000
178A539ALA0-0.069-0.02813.077-0.136-0.1360.0000.0000.0000.000
179A540ALA0-0.026-0.00210.768-0.125-0.1250.0000.0000.0000.000
180A541VAL0-0.072-0.02412.113-0.124-0.1240.0000.0000.0000.000
181A549SER00.0360.00820.6750.0090.0090.0000.0000.0000.000
182A550CYS00.0250.00918.250-0.023-0.0230.0000.0000.0000.000
183A551LEU00.1030.06415.2730.0120.0120.0000.0000.0000.000
184A552SER00.017-0.00618.3110.0040.0040.0000.0000.0000.000
185A553ARG10.9050.94221.889-0.307-0.3070.0000.0000.0000.000
186A554LEU00.0420.02816.009-0.018-0.0180.0000.0000.0000.000
187A555LEU00.0220.00117.921-0.013-0.0130.0000.0000.0000.000
188A556GLY0-0.006-0.00321.103-0.028-0.0280.0000.0000.0000.000
189A557LYS10.8010.89622.339-0.341-0.3410.0000.0000.0000.000
190A558LEU00.0270.00720.296-0.016-0.0160.0000.0000.0000.000
191A559PRO00.0060.00124.354-0.018-0.0180.0000.0000.0000.000
192A560GLU-1-0.728-0.81127.4860.2660.2660.0000.0000.0000.000
193A561LEU00.0110.01722.684-0.014-0.0140.0000.0000.0000.000
194A562ARG10.8630.89924.396-0.326-0.3260.0000.0000.0000.000
195A563THR0-0.011-0.00928.693-0.022-0.0220.0000.0000.0000.000
196A564LEU00.000-0.00628.909-0.011-0.0110.0000.0000.0000.000
197A565CYS0-0.054-0.01927.653-0.001-0.0010.0000.0000.0000.000
198A566THR0-0.0060.00330.333-0.013-0.0130.0000.0000.0000.000
199A567GLN0-0.010-0.02333.7940.0000.0000.0000.0000.0000.000
200A568GLY00.0250.00232.783-0.009-0.0090.0000.0000.0000.000
201A569LEU00.0170.00532.393-0.009-0.0090.0000.0000.0000.000
202A570GLN0-0.021-0.00935.218-0.006-0.0060.0000.0000.0000.000
203A571ARG10.7880.88137.364-0.131-0.1310.0000.0000.0000.000
204A572ILE00.0190.00133.056-0.006-0.0060.0000.0000.0000.000
205A573PHE00.0000.00437.598-0.007-0.0070.0000.0000.0000.000
206A574CYS0-0.069-0.04540.289-0.008-0.0080.0000.0000.0000.000
207A575LEU0-0.013-0.00538.387-0.005-0.0050.0000.0000.0000.000
208A576LYS10.8480.92139.877-0.114-0.1140.0000.0000.0000.000
209A577LEU0-0.061-0.02642.550-0.005-0.0050.0000.0000.0000.000
210A578GLU-1-0.826-0.89244.3780.0990.0990.0000.0000.0000.000
211A579ASP-1-0.930-0.96644.7610.0850.0850.0000.0000.0000.000
212A580LEU0-0.060-0.02545.548-0.004-0.0040.0000.0000.0000.000
213A581VAL0-0.039-0.02442.010-0.003-0.0030.0000.0000.0000.000
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