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: 724QK

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2091754.738567
FMO2-HF: Nuclear repulsion 2009473.006397
FMO2-HF: Total energy -82281.73217
FMO2-MP2: Total energy -82522.179648


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.
-8.462-6.6467.139-3.539-5.415-0.019
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 : 0.002 / q_NPA : -0.005
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].
3L3GLN00.0020.0092.181-7.140-5.8603.606-1.977-2.908-0.017
4L4LEU00.009-0.0085.7880.8620.8620.0000.0000.0000.000
5L5THR0-0.006-0.0029.344-0.173-0.1730.0000.0000.0000.000
6L6GLN00.021-0.01811.5740.1940.1940.0000.0000.0000.000
7L7SER0-0.0230.03115.099-0.040-0.0400.0000.0000.0000.000
8L8PRO00.0750.01218.2410.0460.0460.0000.0000.0000.000
9L9SER00.0490.01017.516-0.025-0.0250.0000.0000.0000.000
10L10SER0-0.068-0.02819.1120.0460.0460.0000.0000.0000.000
11L11LEU00.0290.01822.648-0.019-0.0190.0000.0000.0000.000
12L12SER00.0020.00525.9250.0230.0230.0000.0000.0000.000
13L13ALA00.0240.00529.589-0.010-0.0100.0000.0000.0000.000
14L14SER0-0.0040.01531.8650.0100.0100.0000.0000.0000.000
15L15VAL00.0400.00634.690-0.002-0.0020.0000.0000.0000.000
16L16GLY0-0.045-0.01935.8880.0000.0000.0000.0000.0000.000
17L17ASP-1-0.874-0.92932.609-0.151-0.1510.0000.0000.0000.000
18L18ARG10.9570.98629.5200.1340.1340.0000.0000.0000.000
19L19VAL0-0.010-0.01026.088-0.020-0.0200.0000.0000.0000.000
20L20THR0-0.027-0.01523.4490.0300.0300.0000.0000.0000.000
21L21ILE0-0.0320.00119.146-0.032-0.0320.0000.0000.0000.000
22L22THR00.0250.01317.3450.0550.0550.0000.0000.0000.000
23L23CYS0-0.060-0.03113.263-0.117-0.1170.0000.0000.0000.000
24L24SER00.0220.01013.5540.0880.0880.0000.0000.0000.000
25L25ALA0-0.005-0.0029.131-0.247-0.2470.0000.0000.0000.000
26L26SER00.0000.0005.839-0.240-0.2400.0000.0000.0000.000
27L27SER00.002-0.0046.850-0.224-0.2240.0000.0000.0000.000
28L28SER0-0.045-0.0268.8970.1200.1200.0000.0000.0000.000
29L29VAL00.0280.0238.6250.2200.2200.0000.0000.0000.000
30L30ASN0-0.014-0.01010.861-0.140-0.1400.0000.0000.0000.000
31L31SER00.0970.03513.7460.0490.0490.0000.0000.0000.000
32L32SER0-0.039-0.02516.646-0.034-0.0340.0000.0000.0000.000
33L33ALA0-0.058-0.01911.9240.0590.0590.0000.0000.0000.000
34L34LEU00.0210.01912.1560.1610.1610.0000.0000.0000.000
35L35PHE0-0.047-0.02514.155-0.062-0.0620.0000.0000.0000.000
36L36TRP00.0320.00715.644-0.059-0.0590.0000.0000.0000.000
37L37TYR0-0.048-0.04315.3200.0260.0260.0000.0000.0000.000
38L38GLN00.0090.01319.608-0.043-0.0430.0000.0000.0000.000
39L39GLN0-0.029-0.02220.1750.0100.0100.0000.0000.0000.000
40L40LYS10.7770.87223.0570.0070.0070.0000.0000.0000.000
41L41PRO00.0700.03025.0840.0150.0150.0000.0000.0000.000
42L42GLY00.0090.00925.0060.0120.0120.0000.0000.0000.000
43L43LYS10.8740.94625.627-0.022-0.0220.0000.0000.0000.000
44L44ALA00.0400.02022.872-0.009-0.0090.0000.0000.0000.000
45L45PRO00.004-0.01218.958-0.021-0.0210.0000.0000.0000.000
46L46LYS10.9450.98521.768-0.056-0.0560.0000.0000.0000.000
47L47PRO00.0300.01020.811-0.020-0.0200.0000.0000.0000.000
48L48TRP0-0.020-0.01821.235-0.019-0.0190.0000.0000.0000.000
49L49ILE00.0040.00621.211-0.011-0.0110.0000.0000.0000.000
50L50TYR0-0.0010.00319.5550.0310.0310.0000.0000.0000.000
51L51LEU0-0.0030.00518.654-0.040-0.0400.0000.0000.0000.000
52L52THR00.004-0.01220.3530.0650.0650.0000.0000.0000.000
53L53SER00.0130.03422.556-0.038-0.0380.0000.0000.0000.000
54L54ASN0-0.028-0.02524.2930.0130.0130.0000.0000.0000.000
55L55LEU0-0.036-0.00327.841-0.010-0.0100.0000.0000.0000.000
56L56ALA00.0340.01930.633-0.004-0.0040.0000.0000.0000.000
57L57SER00.025-0.00634.0650.0100.0100.0000.0000.0000.000
58L58GLY00.0240.01137.241-0.004-0.0040.0000.0000.0000.000
59L59VAL0-0.033-0.00231.5020.0020.0020.0000.0000.0000.000
60L60PRO0-0.013-0.00332.8310.0100.0100.0000.0000.0000.000
61L61SER00.0590.00128.876-0.002-0.0020.0000.0000.0000.000
62L62ARG10.9570.98927.535-0.129-0.1290.0000.0000.0000.000
63L63PHE0-0.047-0.01826.8830.0030.0030.0000.0000.0000.000
64L64SER00.0080.00022.8080.0150.0150.0000.0000.0000.000
65L65GLY00.0410.01723.243-0.015-0.0150.0000.0000.0000.000
66L66SER0-0.043-0.01818.2990.0370.0370.0000.0000.0000.000
67L67GLY00.0580.03818.792-0.034-0.0340.0000.0000.0000.000
68L68SER0-0.018-0.01714.2800.0500.0500.0000.0000.0000.000
69L69GLY00.0440.01814.246-0.043-0.0430.0000.0000.0000.000
70L70THR0-0.007-0.00411.8280.1230.1230.0000.0000.0000.000
71L71ASP-1-0.902-0.94413.835-0.534-0.5340.0000.0000.0000.000
72L72TYR0-0.004-0.01113.8980.1350.1350.0000.0000.0000.000
73L73THR00.0210.00117.626-0.047-0.0470.0000.0000.0000.000
74L74LEU0-0.0260.02120.4370.0550.0550.0000.0000.0000.000
75L75THR0-0.004-0.03622.279-0.032-0.0320.0000.0000.0000.000
76L76ILE0-0.0090.00525.9540.0250.0250.0000.0000.0000.000
77L77SER0-0.044-0.03628.818-0.013-0.0130.0000.0000.0000.000
78L78SER00.0430.01432.050-0.008-0.0080.0000.0000.0000.000
79L79LEU0-0.041-0.00730.3270.0100.0100.0000.0000.0000.000
80L80GLN00.0440.01932.6830.0070.0070.0000.0000.0000.000
81L81PRO00.0440.00933.004-0.007-0.0070.0000.0000.0000.000
82L82GLU-1-0.964-0.96932.611-0.015-0.0150.0000.0000.0000.000
83L83ASP-1-0.818-0.90429.108-0.051-0.0510.0000.0000.0000.000
84L84PHE0-0.037-0.00527.746-0.015-0.0150.0000.0000.0000.000
85L85ALA0-0.016-0.00724.7800.0270.0270.0000.0000.0000.000
86L86THR0-0.0090.01219.277-0.049-0.0490.0000.0000.0000.000
87L87TYR0-0.009-0.01020.3230.0590.0590.0000.0000.0000.000
88L88TYR0-0.0100.00814.628-0.081-0.0810.0000.0000.0000.000
89L89CYS0-0.0130.02312.3370.0170.0170.0000.0000.0000.000
90L90GLN00.0580.03611.130-0.244-0.2440.0000.0000.0000.000
91L91GLN00.0340.0325.286-0.699-0.659-0.001-0.002-0.0370.000
92L92ILE0-0.027-0.0248.7560.5050.5050.0000.0000.0000.000
93L93SER00.0090.0058.619-0.206-0.2060.0000.0000.0000.000
94L94GLY0-0.0150.0034.757-0.413-0.387-0.001-0.006-0.0180.000
95L95ASN0-0.054-0.0134.994-0.222-0.2220.0000.0000.0000.000
96L96PRO00.041-0.0051.792-1.162-1.0163.536-1.517-2.165-0.002
97L97TRP00.0230.0134.4931.4331.533-0.001-0.011-0.0880.000
98L98THR0-0.058-0.0323.908-0.0710.1530.000-0.026-0.1990.000
99L99PHE00.007-0.0077.098-0.041-0.0410.0000.0000.0000.000
100L100GLY00.0240.0059.439-0.412-0.4120.0000.0000.0000.000
101L101GLN0-0.019-0.01111.6050.0230.0230.0000.0000.0000.000
102L102GLY0-0.0080.00512.8460.1040.1040.0000.0000.0000.000
103L103THR0-0.034-0.02516.393-0.082-0.0820.0000.0000.0000.000
104L104LYS10.9250.97319.4980.2940.2940.0000.0000.0000.000
105L105VAL00.013-0.00522.708-0.023-0.0230.0000.0000.0000.000
106L106GLU-1-0.886-0.94525.836-0.175-0.1750.0000.0000.0000.000
107L107ILE00.0100.00829.146-0.010-0.0100.0000.0000.0000.000
108L108LYS10.8500.92932.6000.1830.1830.0000.0000.0000.000
109L109ARG10.8580.89735.1940.0880.0880.0000.0000.0000.000
110L110ALA00.0050.01638.598-0.005-0.0050.0000.0000.0000.000
111L111ASP-1-0.852-0.93041.244-0.110-0.1100.0000.0000.0000.000
112L112ALA0-0.034-0.01942.3600.0070.0070.0000.0000.0000.000
113L113ALA00.0450.01043.288-0.005-0.0050.0000.0000.0000.000
114L114PRO0-0.0240.00743.1450.0040.0040.0000.0000.0000.000
115L115THR00.0090.00344.7890.0040.0040.0000.0000.0000.000
116L116VAL0-0.002-0.00945.7500.0000.0000.0000.0000.0000.000
117L117SER0-0.064-0.03046.9270.0050.0050.0000.0000.0000.000
118L118ILE00.0220.00047.342-0.003-0.0030.0000.0000.0000.000
119L119PHE0-0.030-0.01247.3520.0040.0040.0000.0000.0000.000
120L120PRO00.0080.00249.282-0.002-0.0020.0000.0000.0000.000
121L121PRO00.0150.01849.5590.0020.0020.0000.0000.0000.000
122L122SER00.0370.02849.8400.0000.0000.0000.0000.0000.000
123L123SER0-0.005-0.00951.6720.0000.0000.0000.0000.0000.000
124L124GLU-1-0.815-0.92250.536-0.002-0.0020.0000.0000.0000.000
125L125GLN00.0460.03445.4730.0000.0000.0000.0000.0000.000
126L126LEU00.0180.03949.697-0.001-0.0010.0000.0000.0000.000
127L127THR0-0.101-0.05852.6670.0000.0000.0000.0000.0000.000
128L128SER0-0.085-0.07049.0140.0010.0010.0000.0000.0000.000
129L129GLY00.0340.01650.2550.0000.0000.0000.0000.0000.000
130L130GLY0-0.043-0.02247.871-0.004-0.0040.0000.0000.0000.000
131L131ALA00.004-0.01848.1490.0020.0020.0000.0000.0000.000
132L132SER0-0.031-0.00244.041-0.003-0.0030.0000.0000.0000.000
133L133VAL0-0.0070.00446.3970.0030.0030.0000.0000.0000.000
134L134VAL00.0020.00543.034-0.005-0.0050.0000.0000.0000.000
135L135CYS0-0.006-0.00343.9450.0010.0010.0000.0000.0000.000
136L136PHE0-0.018-0.00441.079-0.004-0.0040.0000.0000.0000.000
137L137LEU00.015-0.00841.4290.0010.0010.0000.0000.0000.000
138L138ASN00.038-0.00240.940-0.009-0.0090.0000.0000.0000.000
139L139ASN0-0.013-0.01140.3780.0020.0020.0000.0000.0000.000
140L140PHE0-0.0180.01037.8360.0010.0010.0000.0000.0000.000
141L141TYR00.0480.01434.589-0.005-0.0050.0000.0000.0000.000
142L142PRO00.0360.00436.8370.0050.0050.0000.0000.0000.000
143L143LYS10.9891.00229.6680.1780.1780.0000.0000.0000.000
144L144ASP-1-0.948-0.95934.573-0.173-0.1730.0000.0000.0000.000
145L145ILE0-0.014-0.01736.6230.0090.0090.0000.0000.0000.000
146L146ASN0-0.0030.00638.760-0.010-0.0100.0000.0000.0000.000
147L147VAL00.004-0.00441.1480.0070.0070.0000.0000.0000.000
148L148LYS10.8640.94942.8580.0820.0820.0000.0000.0000.000
149L149TRP0-0.029-0.03043.2230.0060.0060.0000.0000.0000.000
150L150LYS10.8570.93847.4760.0680.0680.0000.0000.0000.000
151L151ILE00.011-0.00549.6400.0030.0030.0000.0000.0000.000
152L152ASP-1-0.831-0.91953.253-0.041-0.0410.0000.0000.0000.000
153L153GLY00.0050.01055.3980.0000.0000.0000.0000.0000.000
154L154SER0-0.029-0.01853.860-0.003-0.0030.0000.0000.0000.000
155L155GLU-1-0.914-0.95846.019-0.089-0.0890.0000.0000.0000.000
156L156ARG10.9200.96846.7600.0600.0600.0000.0000.0000.000
157L157GLN00.1280.06142.3830.0030.0030.0000.0000.0000.000
158L158ASN0-0.041-0.03142.348-0.002-0.0020.0000.0000.0000.000
159L159GLY00.0680.02841.7530.0050.0050.0000.0000.0000.000
160L160VAL0-0.0220.00339.9800.0050.0050.0000.0000.0000.000
161L161LEU0-0.0060.00235.465-0.008-0.0080.0000.0000.0000.000
162L162ASN00.0630.03835.9580.0160.0160.0000.0000.0000.000
163L163SER0-0.028-0.01133.290-0.010-0.0100.0000.0000.0000.000
164L164TRP00.0280.00832.1810.0040.0040.0000.0000.0000.000
165L165THR00.0080.00731.906-0.001-0.0010.0000.0000.0000.000
166L166ASP-1-0.943-0.98627.845-0.115-0.1150.0000.0000.0000.000
167L167GLN0-0.016-0.00730.5050.0030.0030.0000.0000.0000.000
168L168ASP-1-0.840-0.91232.246-0.034-0.0340.0000.0000.0000.000
169L169SER0-0.043-0.04232.184-0.002-0.0020.0000.0000.0000.000
170L170LYS10.9350.97934.2380.0220.0220.0000.0000.0000.000
171L171ASP-1-0.765-0.85037.962-0.061-0.0610.0000.0000.0000.000
172L172SER0-0.002-0.00335.430-0.008-0.0080.0000.0000.0000.000
173L173THR0-0.112-0.08336.433-0.010-0.0100.0000.0000.0000.000
174L174TYR0-0.053-0.05630.8860.0000.0000.0000.0000.0000.000
175L175SER00.0540.04436.1710.0060.0060.0000.0000.0000.000
176L176MET0-0.053-0.00936.240-0.008-0.0080.0000.0000.0000.000
177L177SER0-0.054-0.00337.5760.0090.0090.0000.0000.0000.000
178L178SER00.027-0.00838.397-0.006-0.0060.0000.0000.0000.000
179L179THR00.0160.00140.3820.0090.0090.0000.0000.0000.000
180L180LEU0-0.0040.01341.630-0.005-0.0050.0000.0000.0000.000
181L181THR00.0100.00642.4600.0080.0080.0000.0000.0000.000
182L182LEU0-0.060-0.02444.769-0.004-0.0040.0000.0000.0000.000
183L183THR00.0690.02847.7380.0020.0020.0000.0000.0000.000
184L184LYS10.9520.97949.6910.0140.0140.0000.0000.0000.000
185L185ASP-1-0.888-0.95452.714-0.023-0.0230.0000.0000.0000.000
186L186GLU-1-0.878-0.92050.705-0.044-0.0440.0000.0000.0000.000
187L187TYR00.0370.01151.869-0.002-0.0020.0000.0000.0000.000
188L188GLU-1-0.928-0.96753.447-0.020-0.0200.0000.0000.0000.000
189L189ARG10.8410.93053.8520.0350.0350.0000.0000.0000.000
190L190HIS10.8000.88653.7060.0420.0420.0000.0000.0000.000
191L191ASN00.0270.01857.2630.0030.0030.0000.0000.0000.000
192L192SER00.0060.03156.9840.0000.0000.0000.0000.0000.000
193L193TYR0-0.034-0.03950.944-0.004-0.0040.0000.0000.0000.000
194L194THR00.0210.02151.3290.0030.0030.0000.0000.0000.000
195L195CYS0-0.0410.00546.474-0.002-0.0020.0000.0000.0000.000
196L196GLU-1-0.887-0.97147.758-0.067-0.0670.0000.0000.0000.000
197L197ALA00.0160.00344.651-0.005-0.0050.0000.0000.0000.000
198L198THR0-0.029-0.01844.5660.0030.0030.0000.0000.0000.000
199L199HIS00.0420.01440.240-0.002-0.0020.0000.0000.0000.000
200L200LYS10.9420.98140.4000.1280.1280.0000.0000.0000.000
201L201THR0-0.076-0.04144.0110.0020.0020.0000.0000.0000.000
202L202SER00.007-0.01546.5270.0050.0050.0000.0000.0000.000
203L203THR00.0040.01747.853-0.003-0.0030.0000.0000.0000.000
204L204SER0-0.035-0.00649.9700.0000.0000.0000.0000.0000.000
205L205PRO0-0.014-0.01049.0080.0010.0010.0000.0000.0000.000
206L206ILE00.0230.02047.3390.0050.0050.0000.0000.0000.000
207L207VAL00.0120.00949.384-0.002-0.0020.0000.0000.0000.000
208L208LYS10.8760.94550.3460.0460.0460.0000.0000.0000.000
209L209SER00.017-0.02351.721-0.001-0.0010.0000.0000.0000.000
210L210PHE00.0100.01651.4440.0020.0020.0000.0000.0000.000
211L211ASN00.0460.01456.282-0.004-0.0040.0000.0000.0000.000
212L212ARG10.8780.93756.3490.0290.0290.0000.0000.0000.000
213L213ASN0-0.052-0.03258.3200.0020.0020.0000.0000.0000.000
214L214GLU-1-0.941-0.95761.320-0.026-0.0260.0000.0000.0000.000