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: 2JG9R

Calculation Name: 3EOT-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EOT

Chain ID: L

ChEMBL ID:

UniProt ID: P01837

Base Structure: X-ray

Registration Date: 2023-06-26

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 OptHSide
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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2092462.15301
FMO2-HF: Nuclear repulsion 2010179.483494
FMO2-HF: Total energy -82282.669516
FMO2-MP2: Total energy -82523.088473


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(L:1:GLN)


Summations of interaction energy for fragment #1(L:1:GLN)
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.
-10.892-10.5049.637-4.239-5.786-0.031
Interaction energy analysis for fragmet #1(L:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.025
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].
3L3GLN00.0070.0211.894-10.931-11.5967.143-3.012-3.466-0.029
4L4LEU00.010-0.0065.4691.1211.1210.0000.0000.0000.000
5L5THR0-0.007-0.0038.970-0.116-0.1160.0000.0000.0000.000
6L6GLN00.012-0.02211.3850.1450.1450.0000.0000.0000.000
7L7SER0-0.0280.02714.8170.0000.0000.0000.0000.0000.000
8L8PRO00.0790.01618.0700.0350.0350.0000.0000.0000.000
9L9SER00.0500.01117.290-0.044-0.0440.0000.0000.0000.000
10L10SER0-0.007-0.00418.9280.0180.0180.0000.0000.0000.000
11L11LEU0-0.020-0.00122.410-0.009-0.0090.0000.0000.0000.000
12L12SER00.0010.00925.6770.0200.0200.0000.0000.0000.000
13L13ALA00.0160.00029.315-0.007-0.0070.0000.0000.0000.000
14L14SER00.0080.01331.5530.0100.0100.0000.0000.0000.000
15L15VAL00.0240.00134.303-0.005-0.0050.0000.0000.0000.000
16L16GLY0-0.036-0.01235.4790.0040.0040.0000.0000.0000.000
17L17ASP-1-0.849-0.91232.389-0.194-0.1940.0000.0000.0000.000
18L18ARG10.9720.99329.0850.2120.2120.0000.0000.0000.000
19L19VAL0-0.030-0.01925.724-0.016-0.0160.0000.0000.0000.000
20L20THR0-0.028-0.02723.3390.0210.0210.0000.0000.0000.000
21L21ILE0-0.0310.00018.772-0.023-0.0230.0000.0000.0000.000
22L22THR00.0360.01417.2360.0540.0540.0000.0000.0000.000
23L23CYS0-0.065-0.04012.845-0.071-0.0710.0000.0000.0000.000
24L24SER00.0320.01313.5680.0910.0910.0000.0000.0000.000
25L25ALA0-0.010-0.0059.162-0.274-0.2740.0000.0000.0000.000
26L26SER0-0.004-0.0055.3230.3140.3140.0000.0000.0000.000
27L27SER0-0.014-0.0086.5610.2840.2840.0000.0000.0000.000
28L28SER0-0.008-0.0139.0490.0560.0560.0000.0000.0000.000
29L29VAL00.0160.0188.5280.1160.1160.0000.0000.0000.000
30L30ASN00.004-0.00210.806-0.063-0.0630.0000.0000.0000.000
31L31SER00.0890.03313.6940.0280.0280.0000.0000.0000.000
32L32SER0-0.050-0.02616.586-0.021-0.0210.0000.0000.0000.000
33L33ALA0-0.058-0.02411.9450.0530.0530.0000.0000.0000.000
34L34LEU00.0130.01312.1730.0660.0660.0000.0000.0000.000
35L35PHE0-0.042-0.02014.155-0.006-0.0060.0000.0000.0000.000
36L36TRP00.0290.00315.602-0.092-0.0920.0000.0000.0000.000
37L37TYR0-0.040-0.03515.3310.0560.0560.0000.0000.0000.000
38L38GLN00.0100.01119.570-0.041-0.0410.0000.0000.0000.000
39L39GLN0-0.023-0.02119.665-0.001-0.0010.0000.0000.0000.000
40L40LYS10.7880.87822.7210.1050.1050.0000.0000.0000.000
41L41PRO00.0580.02024.8130.0090.0090.0000.0000.0000.000
42L42GLY0-0.0040.00324.6970.0170.0170.0000.0000.0000.000
43L43LYS10.8810.94925.2760.0640.0640.0000.0000.0000.000
44L44ALA00.0460.02722.424-0.017-0.0170.0000.0000.0000.000
45L45PRO00.007-0.01018.481-0.010-0.0100.0000.0000.0000.000
46L46LYS10.9460.98721.5420.0710.0710.0000.0000.0000.000
47L47PRO00.0270.00920.776-0.030-0.0300.0000.0000.0000.000
48L48TRP0-0.020-0.01821.1940.0000.0000.0000.0000.0000.000
49L49ILE00.0070.00421.1670.0020.0020.0000.0000.0000.000
50L50TYR0-0.0040.00519.4800.0020.0020.0000.0000.0000.000
51L51LEU00.0040.01018.730-0.015-0.0150.0000.0000.0000.000
52L52THR00.007-0.01620.3530.0440.0440.0000.0000.0000.000
53L53SER00.0300.04622.531-0.025-0.0250.0000.0000.0000.000
54L54ASN0-0.041-0.03224.2440.0070.0070.0000.0000.0000.000
55L55LEU0-0.032-0.00427.397-0.007-0.0070.0000.0000.0000.000
56L56ALA00.0380.02330.586-0.001-0.0010.0000.0000.0000.000
57L57SER00.036-0.00334.0170.0090.0090.0000.0000.0000.000
58L58GLY00.0170.01037.189-0.002-0.0020.0000.0000.0000.000
59L59VAL0-0.036-0.00531.4090.0030.0030.0000.0000.0000.000
60L60PRO0-0.0130.00032.7800.0060.0060.0000.0000.0000.000
61L61SER00.0670.00628.772-0.004-0.0040.0000.0000.0000.000
62L62ARG10.9430.98127.497-0.048-0.0480.0000.0000.0000.000
63L63PHE0-0.044-0.01926.8470.0010.0010.0000.0000.0000.000
64L64SER00.009-0.00222.7210.0070.0070.0000.0000.0000.000
65L65GLY00.0410.02023.196-0.008-0.0080.0000.0000.0000.000
66L66SER0-0.049-0.02218.2160.0180.0180.0000.0000.0000.000
67L67GLY00.0550.03718.748-0.013-0.0130.0000.0000.0000.000
68L68SER0-0.015-0.02014.0790.0130.0130.0000.0000.0000.000
69L69GLY00.0400.01914.188-0.006-0.0060.0000.0000.0000.000
70L70THR00.0180.00711.7210.0530.0530.0000.0000.0000.000
71L71ASP-1-0.925-0.95513.809-0.719-0.7190.0000.0000.0000.000
72L72TYR00.000-0.01113.7700.1350.1350.0000.0000.0000.000
73L73THR00.015-0.00317.626-0.039-0.0390.0000.0000.0000.000
74L74LEU0-0.0250.02220.4080.0490.0490.0000.0000.0000.000
75L75THR0-0.002-0.02322.247-0.025-0.0250.0000.0000.0000.000
76L76ILE0-0.0060.01425.9240.0210.0210.0000.0000.0000.000
77L77SER0-0.028-0.02628.788-0.008-0.0080.0000.0000.0000.000
78L78SER00.0210.00132.0200.0020.0020.0000.0000.0000.000
79L79LEU0-0.0500.00129.9100.0070.0070.0000.0000.0000.000
80L80GLN00.0440.00832.3670.0160.0160.0000.0000.0000.000
81L81PRO00.0560.01632.530-0.011-0.0110.0000.0000.0000.000
82L82GLU-1-0.959-0.97132.704-0.091-0.0910.0000.0000.0000.000
83L83ASP-1-0.818-0.89528.684-0.147-0.1470.0000.0000.0000.000
84L84PHE0-0.057-0.01127.434-0.023-0.0230.0000.0000.0000.000
85L85ALA0-0.014-0.00524.2390.0220.0220.0000.0000.0000.000
86L86THR0-0.0050.00918.821-0.033-0.0330.0000.0000.0000.000
87L87TYR0-0.006-0.00819.9090.0450.0450.0000.0000.0000.000
88L88TYR0-0.0080.00914.400-0.075-0.0750.0000.0000.0000.000
89L89CYS0-0.0060.04412.4220.0330.0330.0000.0000.0000.000
90L90GLN00.0590.02810.994-0.200-0.2000.0000.0000.0000.000
91L91GLN00.0330.0235.370-0.305-0.261-0.001-0.002-0.0410.000
92L92ILE0-0.022-0.0188.7560.3340.3340.0000.0000.0000.000
93L93SER00.0110.0098.547-0.105-0.1050.0000.0000.0000.000
94L94GLY0-0.015-0.0014.716-0.337-0.309-0.001-0.006-0.0210.000
95L95ASN0-0.061-0.0155.017-0.167-0.1670.0000.0000.0000.000
96L96PRO00.049-0.0031.888-1.468-0.8122.496-1.178-1.975-0.002
97L97TRP00.0090.0054.5271.1471.239-0.001-0.010-0.0810.000
98L98THR0-0.048-0.0253.9040.0380.2710.001-0.031-0.2020.000
99L99PHE00.005-0.0087.0580.1630.1630.0000.0000.0000.000
100L100GLY00.009-0.0018.836-0.492-0.4920.0000.0000.0000.000
101L101GLN0-0.020-0.01111.056-0.007-0.0070.0000.0000.0000.000
102L102GLY0-0.0030.00412.4420.1400.1400.0000.0000.0000.000
103L103THR0-0.041-0.02515.922-0.060-0.0600.0000.0000.0000.000
104L104LYS10.8530.93819.0960.3130.3130.0000.0000.0000.000
105L105VAL00.007-0.00522.306-0.014-0.0140.0000.0000.0000.000
106L106GLU-1-0.801-0.88325.418-0.212-0.2120.0000.0000.0000.000
107L107ILE00.0020.00428.756-0.008-0.0080.0000.0000.0000.000
108L108LYS10.8360.91432.0970.2240.2240.0000.0000.0000.000
109L109ARG10.8480.90234.8690.1170.1170.0000.0000.0000.000
110L110ALA00.0170.01838.247-0.002-0.0020.0000.0000.0000.000
111L111ASP-1-0.789-0.88241.164-0.129-0.1290.0000.0000.0000.000
112L112ALA0-0.027-0.01742.0540.0070.0070.0000.0000.0000.000
113L113ALA00.0490.01742.988-0.004-0.0040.0000.0000.0000.000
114L114PRO0-0.0120.01042.9580.0020.0020.0000.0000.0000.000
115L115THR0-0.002-0.00244.5770.0050.0050.0000.0000.0000.000
116L116VAL00.009-0.00345.6340.0000.0000.0000.0000.0000.000
117L117SER0-0.047-0.01446.8660.0050.0050.0000.0000.0000.000
118L118ILE00.0120.00047.234-0.003-0.0030.0000.0000.0000.000
119L119PHE0-0.018-0.00746.8260.0030.0030.0000.0000.0000.000
120L120PRO00.0160.00549.167-0.002-0.0020.0000.0000.0000.000
121L121PRO00.0020.01149.4290.0010.0010.0000.0000.0000.000
122L122SER0-0.007-0.01449.7430.0010.0010.0000.0000.0000.000
123L123SER0-0.012-0.02551.4970.0010.0010.0000.0000.0000.000
124L124GLU-1-0.774-0.87050.186-0.012-0.0120.0000.0000.0000.000
125L125GLN00.0440.03145.2350.0000.0000.0000.0000.0000.000
126L126LEU00.0340.03149.5300.0010.0010.0000.0000.0000.000
127L127THR0-0.096-0.05052.5270.0020.0020.0000.0000.0000.000
128L128SER0-0.090-0.05448.7630.0020.0020.0000.0000.0000.000
129L129GLY00.0300.01550.1200.0010.0010.0000.0000.0000.000
130L130GLY0-0.048-0.02347.760-0.002-0.0020.0000.0000.0000.000
131L131ALA0-0.003-0.02048.0560.0010.0010.0000.0000.0000.000
132L132SER0-0.025-0.01043.872-0.002-0.0020.0000.0000.0000.000
133L133VAL0-0.022-0.00346.3010.0020.0020.0000.0000.0000.000
134L134VAL00.0020.00842.743-0.005-0.0050.0000.0000.0000.000
135L135CYS0-0.0020.00543.8580.0010.0010.0000.0000.0000.000
136L136PHE0-0.032-0.01241.311-0.005-0.0050.0000.0000.0000.000
137L137LEU00.028-0.00541.2570.0020.0020.0000.0000.0000.000
138L138ASN00.019-0.01140.840-0.009-0.0090.0000.0000.0000.000
139L139ASN0-0.021-0.02440.0960.0040.0040.0000.0000.0000.000
140L140PHE0-0.0120.01137.6680.0020.0020.0000.0000.0000.000
141L141TYR00.0590.02234.244-0.007-0.0070.0000.0000.0000.000
142L142PRO00.021-0.00136.4860.0070.0070.0000.0000.0000.000
143L143LYS10.9060.95128.8390.2170.2170.0000.0000.0000.000
144L144ASP-1-0.927-0.95234.386-0.179-0.1790.0000.0000.0000.000
145L145ILE0-0.038-0.02136.4710.0090.0090.0000.0000.0000.000
146L146ASN0-0.0100.00138.652-0.006-0.0060.0000.0000.0000.000
147L147VAL00.0110.00241.1720.0050.0050.0000.0000.0000.000
148L148LYS10.8360.91842.9160.0790.0790.0000.0000.0000.000
149L149TRP00.0280.00043.3760.0060.0060.0000.0000.0000.000
150L150LYS10.8410.93447.5100.0630.0630.0000.0000.0000.000
151L151ILE00.005-0.01049.6820.0020.0020.0000.0000.0000.000
152L152ASP-1-0.779-0.88053.287-0.038-0.0380.0000.0000.0000.000
153L153GLY00.0110.01655.4300.0000.0000.0000.0000.0000.000
154L154SER0-0.028-0.01753.954-0.003-0.0030.0000.0000.0000.000
155L155GLU-1-0.902-0.93546.514-0.081-0.0810.0000.0000.0000.000
156L156ARG10.8700.93646.9490.0510.0510.0000.0000.0000.000
157L157GLN00.0800.03242.1520.0030.0030.0000.0000.0000.000
158L158ASN0-0.045-0.03342.425-0.003-0.0030.0000.0000.0000.000
159L159GLY00.0630.02741.7820.0040.0040.0000.0000.0000.000
160L160VAL0-0.0240.00240.1430.0030.0030.0000.0000.0000.000
161L161LEU0-0.0100.00335.633-0.006-0.0060.0000.0000.0000.000
162L162ASN00.0270.01935.9590.0110.0110.0000.0000.0000.000
163L163SER0-0.016-0.00333.306-0.010-0.0100.0000.0000.0000.000
164L164TRP00.0340.01332.1570.0060.0060.0000.0000.0000.000
165L165THR0-0.011-0.00431.791-0.001-0.0010.0000.0000.0000.000
166L166ASP-1-0.841-0.94927.039-0.206-0.2060.0000.0000.0000.000
167L167GLN0-0.023-0.00430.2250.0020.0020.0000.0000.0000.000
168L168ASP-1-0.780-0.87131.948-0.084-0.0840.0000.0000.0000.000
169L169SER0-0.046-0.04131.791-0.007-0.0070.0000.0000.0000.000
170L170LYS10.8750.93233.8230.0750.0750.0000.0000.0000.000
171L171ASP-1-0.764-0.85637.512-0.097-0.0970.0000.0000.0000.000
172L172SER0-0.0010.00534.727-0.005-0.0050.0000.0000.0000.000
173L173THR0-0.100-0.06835.974-0.008-0.0080.0000.0000.0000.000
174L174TYR0-0.048-0.06630.805-0.003-0.0030.0000.0000.0000.000
175L175SER00.0440.03836.0350.0090.0090.0000.0000.0000.000
176L176MET0-0.048-0.00536.135-0.008-0.0080.0000.0000.0000.000
177L177SER0-0.0340.00037.3210.0090.0090.0000.0000.0000.000
178L178SER00.017-0.00538.328-0.004-0.0040.0000.0000.0000.000
179L179THR00.013-0.00340.2410.0070.0070.0000.0000.0000.000
180L180LEU00.0100.02141.594-0.003-0.0030.0000.0000.0000.000
181L181THR00.0020.00742.4510.0060.0060.0000.0000.0000.000
182L182LEU0-0.054-0.02144.724-0.002-0.0020.0000.0000.0000.000
183L183THR00.014-0.02347.7100.0010.0010.0000.0000.0000.000
184L184LYS10.9130.93849.6470.0130.0130.0000.0000.0000.000
185L185ASP-1-0.837-0.91652.645-0.019-0.0190.0000.0000.0000.000
186L186GLU-1-0.843-0.89750.488-0.038-0.0380.0000.0000.0000.000
187L187TYR00.0380.01851.727-0.002-0.0020.0000.0000.0000.000
188L188GLU-1-0.859-0.91553.412-0.019-0.0190.0000.0000.0000.000
189L189ARG10.8560.93053.5120.0280.0280.0000.0000.0000.000
190L190HIS10.8240.90353.6090.0370.0370.0000.0000.0000.000
191L191ASN00.001-0.00257.2680.0030.0030.0000.0000.0000.000
192L192SER0-0.0100.01856.9700.0000.0000.0000.0000.0000.000
193L193TYR0-0.037-0.03351.017-0.002-0.0020.0000.0000.0000.000
194L194THR0-0.029-0.02751.5630.0010.0010.0000.0000.0000.000
195L195CYS0-0.0140.01746.511-0.001-0.0010.0000.0000.0000.000
196L196GLU-1-0.859-0.96147.792-0.069-0.0690.0000.0000.0000.000
197L197ALA00.0130.00144.637-0.004-0.0040.0000.0000.0000.000
198L198THR0-0.030-0.02144.4450.0030.0030.0000.0000.0000.000
199L199HIS00.0520.02639.9920.0000.0000.0000.0000.0000.000
200L200LYS10.8490.92040.5330.1380.1380.0000.0000.0000.000
201L201THR0-0.070-0.05243.8680.0030.0030.0000.0000.0000.000
202L202SER00.013-0.01046.3270.0050.0050.0000.0000.0000.000
203L203THR0-0.0090.00747.729-0.003-0.0030.0000.0000.0000.000
204L204SER0-0.037-0.01049.8800.0010.0010.0000.0000.0000.000
205L205PRO00.0050.00548.820-0.001-0.0010.0000.0000.0000.000
206L206ILE00.0130.01147.2470.0040.0040.0000.0000.0000.000
207L207VAL00.0020.00449.319-0.001-0.0010.0000.0000.0000.000
208L208LYS10.8410.92050.3130.0570.0570.0000.0000.0000.000
209L209SER00.0400.00651.684-0.001-0.0010.0000.0000.0000.000
210L210PHE00.0180.02051.4280.0010.0010.0000.0000.0000.000
211L211ASN00.000-0.02756.215-0.003-0.0030.0000.0000.0000.000
212L212ARG10.8520.92356.1780.0290.0290.0000.0000.0000.000
213L213ASN0-0.017-0.00958.2490.0010.0010.0000.0000.0000.000
214L214GLU-1-0.918-0.92561.241-0.030-0.0300.0000.0000.0000.000