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: V5Z11

Calculation Name: 4AEH-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AEH

Chain ID: L

ChEMBL ID:

UniProt ID:

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2138778.161782
FMO2-HF: Nuclear repulsion 2056628.510789
FMO2-HF: Total energy -82149.650994
FMO2-MP2: Total energy -82389.082129


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:ASP)


Summations of interaction energy for fragment #1(L:1:ASP)
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.
-49.42-43.6463.72-3.921-5.571-0.001
Interaction energy analysis for fragmet #1(L:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.924 / q_NPA : -0.956
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].
3L3GLN0-0.008-0.0063.688-10.165-6.555-0.006-1.680-1.9240.009
4L4MET0-0.020-0.0075.450-5.300-5.311-0.001-0.0020.0140.000
5L5THR0-0.015-0.0129.026-0.642-0.6420.0000.0000.0000.000
6L6GLN00.001-0.04011.989-0.055-0.0550.0000.0000.0000.000
7L7SER0-0.0530.00115.066-0.539-0.5390.0000.0000.0000.000
8L8PRO00.0710.03618.633-0.071-0.0710.0000.0000.0000.000
9L9ALA00.0600.02719.4270.2210.2210.0000.0000.0000.000
10L10SER0-0.002-0.00320.447-0.060-0.0600.0000.0000.0000.000
11L11LEU0-0.042-0.02324.068-0.041-0.0410.0000.0000.0000.000
12L12SER00.0260.00727.1730.0400.0400.0000.0000.0000.000
13L13VAL0-0.054-0.04029.629-0.059-0.0590.0000.0000.0000.000
14L14SER00.010-0.02232.455-0.163-0.1630.0000.0000.0000.000
15L15VAL0-0.013-0.01035.0980.1600.1600.0000.0000.0000.000
16L16GLY00.0030.01236.217-0.211-0.2110.0000.0000.0000.000
17L17GLU-1-0.775-0.85233.6879.1889.1880.0000.0000.0000.000
18L18THR0-0.032-0.02130.5740.0950.0950.0000.0000.0000.000
19L19VAL00.0030.01426.0510.0170.0170.0000.0000.0000.000
20L20THR0-0.005-0.01723.626-0.055-0.0550.0000.0000.0000.000
21L21ILE0-0.0200.01219.4330.0920.0920.0000.0000.0000.000
22L22THR0-0.008-0.01117.6390.2170.2170.0000.0000.0000.000
23L23CYS0-0.035-0.00413.5670.4160.4160.0000.0000.0000.000
24L24ARG10.8920.94613.430-18.619-18.6190.0000.0000.0000.000
25L25ALA00.0380.0228.8901.5581.5580.0000.0000.0000.000
26L26SER00.0330.0125.680-0.936-0.9360.0000.0000.0000.000
27L27GLU-1-0.836-0.9124.13735.19835.327-0.001-0.033-0.0950.000
28L28ASN0-0.032-0.0238.241-0.681-0.6810.0000.0000.0000.000
29L29ILE00.0740.0437.6360.8030.8030.0000.0000.0000.000
30L30TYR0-0.047-0.02210.203-1.654-1.6540.0000.0000.0000.000
31L31ARG10.8890.92313.667-14.869-14.8690.0000.0000.0000.000
32L32ASN0-0.0110.01010.917-1.546-1.5460.0000.0000.0000.000
33L33LEU0-0.009-0.00911.3021.8501.8500.0000.0000.0000.000
34L34ALA0-0.0200.00013.591-1.549-1.5490.0000.0000.0000.000
35L35TRP00.017-0.00515.6391.1021.1020.0000.0000.0000.000
36L36TYR0-0.026-0.02714.930-1.354-1.3540.0000.0000.0000.000
37L37GLN00.0120.00219.7890.0290.0290.0000.0000.0000.000
38L38GLN0-0.019-0.03121.0780.5710.5710.0000.0000.0000.000
39L39LYS10.8560.92823.507-10.611-10.6110.0000.0000.0000.000
40L40GLN00.0660.02126.5210.5100.5100.0000.0000.0000.000
41L41GLY00.0070.00227.357-0.345-0.3450.0000.0000.0000.000
42L42LYS10.9080.96426.942-10.178-10.1780.0000.0000.0000.000
43L43SER00.0490.02223.2140.4110.4110.0000.0000.0000.000
44L44PRO00.0080.00518.976-0.406-0.4060.0000.0000.0000.000
45L45GLN0-0.044-0.02221.764-0.630-0.6300.0000.0000.0000.000
46L46LEU0-0.0040.00618.9640.2130.2130.0000.0000.0000.000
47L47LEU0-0.0050.00821.461-0.590-0.5900.0000.0000.0000.000
48L48VAL0-0.011-0.01320.092-0.491-0.4910.0000.0000.0000.000
49L49TYR00.0260.00318.2760.9180.9180.0000.0000.0000.000
50L50ALA00.0250.01016.816-0.555-0.5550.0000.0000.0000.000
51L51ALA0-0.0090.00816.624-0.501-0.5010.0000.0000.0000.000
52L52THR0-0.051-0.04718.168-0.212-0.2120.0000.0000.0000.000
53L53ASN0-0.057-0.00721.551-0.821-0.8210.0000.0000.0000.000
54L54LEU00.0210.02222.9240.4920.4920.0000.0000.0000.000
55L55ALA00.0150.00523.531-0.152-0.1520.0000.0000.0000.000
56L56ALA00.026-0.00625.348-0.379-0.3790.0000.0000.0000.000
57L57GLY0-0.007-0.00428.6910.0970.0970.0000.0000.0000.000
58L58VAL0-0.0390.00326.001-0.139-0.1390.0000.0000.0000.000
59L59PRO00.0320.01129.386-0.154-0.1540.0000.0000.0000.000
60L60SER00.0460.00630.1820.3120.3120.0000.0000.0000.000
61L61ARG10.7440.85431.065-9.463-9.4630.0000.0000.0000.000
62L62PHE0-0.0020.00526.2560.2380.2380.0000.0000.0000.000
63L63SER00.0090.00226.181-0.163-0.1630.0000.0000.0000.000
64L64GLY00.0290.02821.9390.3240.3240.0000.0000.0000.000
65L65SER0-0.037-0.02121.416-0.499-0.4990.0000.0000.0000.000
66L66GLY00.0790.03118.8630.6080.6080.0000.0000.0000.000
67L67SER0-0.031-0.01117.001-0.443-0.4430.0000.0000.0000.000
68L68GLY00.0610.03814.6740.0640.0640.0000.0000.0000.000
69L69THR00.0440.03611.2400.4100.4100.0000.0000.0000.000
70L70GLN00.0230.03113.5660.9770.9770.0000.0000.0000.000
71L71TYR00.017-0.01413.043-1.302-1.3020.0000.0000.0000.000
72L72SER0-0.031-0.02417.482-0.033-0.0330.0000.0000.0000.000
73L73LEU00.0040.02220.593-0.111-0.1110.0000.0000.0000.000
74L74LYS10.8780.93022.431-10.668-10.6680.0000.0000.0000.000
75L75ILE00.0110.01226.102-0.067-0.0670.0000.0000.0000.000
76L76ASN0-0.005-0.02528.7950.0440.0440.0000.0000.0000.000
77L77SER00.0030.01132.276-0.267-0.2670.0000.0000.0000.000
78L78LEU0-0.031-0.00929.879-0.058-0.0580.0000.0000.0000.000
79L79GLN00.0590.01933.158-0.372-0.3720.0000.0000.0000.000
80L80SER00.0620.01233.6870.2480.2480.0000.0000.0000.000
81L81GLU-1-0.838-0.91132.6129.1759.1750.0000.0000.0000.000
82L82ASP-1-0.742-0.82329.64610.46310.4630.0000.0000.0000.000
83L83PHE0-0.0090.02728.6020.4480.4480.0000.0000.0000.000
84L84GLY0-0.015-0.01726.932-0.138-0.1380.0000.0000.0000.000
85L85SER0-0.0010.00221.374-0.116-0.1160.0000.0000.0000.000
86L86TYR0-0.008-0.01520.863-0.149-0.1490.0000.0000.0000.000
87L87TYR00.0090.02515.5140.3480.3480.0000.0000.0000.000
88L89GLN00.0200.00210.565-0.997-0.9970.0000.0000.0000.000
89L90HIS0-0.0240.0094.500-6.736-6.662-0.001-0.005-0.0680.000
90L91PHE0-0.018-0.0329.0210.9160.9160.0000.0000.0000.000
91L92TRP0-0.057-0.0265.478-3.106-3.1060.0000.0000.0000.000
92L93ASN00.011-0.0012.6241.7653.3210.943-1.059-1.440-0.011
93L94ILE0-0.0110.0155.1180.0960.252-0.001-0.014-0.1410.000
94L95PRO00.0480.0172.0123.1163.2132.789-1.119-1.7660.001
95L96PHE00.0500.0204.6872.1532.210-0.001-0.006-0.0500.000
96L97THR0-0.0040.0024.497-4.940-4.834-0.001-0.003-0.1010.000
97L98PHE00.010-0.0057.279-2.186-2.1860.0000.0000.0000.000
98L99GLY0-0.006-0.00710.1012.0192.0190.0000.0000.0000.000
99L100SER00.018-0.00512.173-0.359-0.3590.0000.0000.0000.000
100L101GLY00.0050.00314.010-0.967-0.9670.0000.0000.0000.000
101L102THR0-0.074-0.04017.3540.1520.1520.0000.0000.0000.000
102L103LYS10.8890.94520.643-11.904-11.9040.0000.0000.0000.000
103L104LEU0-0.040-0.02023.866-0.170-0.1700.0000.0000.0000.000
104L105GLU-1-0.798-0.83927.1599.9179.9170.0000.0000.0000.000
105L106ILE00.005-0.00930.243-0.016-0.0160.0000.0000.0000.000
106L107LYS10.8170.91033.216-9.378-9.3780.0000.0000.0000.000
107L108ARG10.8370.91535.807-7.958-7.9580.0000.0000.0000.000
108L109ALA00.0060.00739.0480.0820.0820.0000.0000.0000.000
109L110ASP-1-0.807-0.88139.0438.2178.2170.0000.0000.0000.000
110L111ALA0-0.033-0.02140.953-0.218-0.2180.0000.0000.0000.000
111L112ALA00.0440.02341.4830.1950.1950.0000.0000.0000.000
112L113PRO0-0.0160.00841.197-0.040-0.0400.0000.0000.0000.000
113L114THR0-0.0070.00043.127-0.223-0.2230.0000.0000.0000.000
114L115VAL0-0.014-0.01343.9770.0970.0970.0000.0000.0000.000
115L116SER0-0.041-0.02046.087-0.246-0.2460.0000.0000.0000.000
116L117ILE0-0.018-0.00846.6280.1630.1630.0000.0000.0000.000
117L118PHE0-0.012-0.01047.192-0.164-0.1640.0000.0000.0000.000
118L119PRO00.0100.00249.0200.1310.1310.0000.0000.0000.000
119L120PRO00.0120.01549.7110.0280.0280.0000.0000.0000.000
120L121SER0-0.016-0.01151.125-0.094-0.0940.0000.0000.0000.000
121L122SER00.045-0.00553.199-0.003-0.0030.0000.0000.0000.000
122L123GLU-1-0.831-0.89653.3765.9285.9280.0000.0000.0000.000
123L124GLN00.0370.01546.379-0.038-0.0380.0000.0000.0000.000
124L125LEU00.0180.02751.7690.0380.0380.0000.0000.0000.000
125L126THR0-0.057-0.02754.001-0.070-0.0700.0000.0000.0000.000
126L127SER0-0.105-0.05951.1490.0120.0120.0000.0000.0000.000
127L128GLY00.0340.02051.9960.0670.0670.0000.0000.0000.000
128L129GLY0-0.039-0.02048.7230.1020.1020.0000.0000.0000.000
129L130ALA00.001-0.01748.096-0.143-0.1430.0000.0000.0000.000
130L131SER0-0.029-0.01344.1740.1010.1010.0000.0000.0000.000
131L132VAL0-0.0270.00045.720-0.150-0.1500.0000.0000.0000.000
132L133VAL00.0150.01043.0940.2090.2090.0000.0000.0000.000
133L134CYS0-0.049-0.01442.8270.0030.0030.0000.0000.0000.000
134L135PHE0-0.0190.00242.0750.2120.2120.0000.0000.0000.000
135L136LEU00.019-0.00739.103-0.171-0.1710.0000.0000.0000.000
136L137ASN00.023-0.01840.3240.3710.3710.0000.0000.0000.000
137L138ASN0-0.011-0.01641.148-0.173-0.1730.0000.0000.0000.000
138L139PHE00.0010.00935.343-0.137-0.1370.0000.0000.0000.000
139L140TYR00.013-0.02533.6070.1270.1270.0000.0000.0000.000
140L141PRO0-0.002-0.00133.724-0.214-0.2140.0000.0000.0000.000
141L142LYS10.9420.95427.672-11.162-11.1620.0000.0000.0000.000
142L143ASP-1-0.905-0.92730.05310.67210.6720.0000.0000.0000.000
143L144ILE0-0.018-0.01332.711-0.339-0.3390.0000.0000.0000.000
144L145ASN0-0.050-0.02032.7530.3650.3650.0000.0000.0000.000
145L146VAL00.0340.01736.094-0.257-0.2570.0000.0000.0000.000
146L147LYS10.8200.91137.995-7.823-7.8230.0000.0000.0000.000
147L148TRP00.0300.00340.286-0.308-0.3080.0000.0000.0000.000
148L149LYS10.7900.87843.087-6.956-6.9560.0000.0000.0000.000
149L150ILE00.011-0.00146.151-0.067-0.0670.0000.0000.0000.000
150L151ASP-1-0.767-0.87548.8186.0446.0440.0000.0000.0000.000
151L152GLY0-0.007-0.00349.917-0.040-0.0400.0000.0000.0000.000
152L153SER0-0.014-0.00547.2040.0780.0780.0000.0000.0000.000
153L154GLU-1-0.815-0.89139.3948.0978.0970.0000.0000.0000.000
154L155ARG10.8510.92942.307-7.252-7.2520.0000.0000.0000.000
155L156GLN0-0.008-0.02136.3530.2270.2270.0000.0000.0000.000
156L157ASN00.005-0.00137.7900.2800.2800.0000.0000.0000.000
157L158GLY00.0370.01138.219-0.212-0.2120.0000.0000.0000.000
158L159VAL0-0.0030.01137.077-0.171-0.1710.0000.0000.0000.000
159L160LEU0-0.0180.01134.9380.2900.2900.0000.0000.0000.000
160L161ASN00.0300.01433.541-0.492-0.4920.0000.0000.0000.000
161L162SER0-0.015-0.00633.2900.3530.3530.0000.0000.0000.000
162L163TRP00.0580.01130.750-0.181-0.1810.0000.0000.0000.000
163L164THR0-0.0080.00232.7900.1240.1240.0000.0000.0000.000
164L165ASP-1-0.865-0.94429.86410.94110.9410.0000.0000.0000.000
165L166GLN0-0.074-0.03532.458-0.052-0.0520.0000.0000.0000.000
166L167ASP-1-0.835-0.91334.4247.8227.8220.0000.0000.0000.000
167L168SER0-0.029-0.02838.017-0.041-0.0410.0000.0000.0000.000
168L169LYS10.9000.95838.885-7.282-7.2820.0000.0000.0000.000
169L170ASP-1-0.792-0.86841.3277.5697.5690.0000.0000.0000.000
170L171SER00.0030.00637.1980.0500.0500.0000.0000.0000.000
171L172THR0-0.094-0.05937.2200.2040.2040.0000.0000.0000.000
172L173TYR0-0.049-0.05331.2140.2550.2550.0000.0000.0000.000
173L174SER00.0330.02536.619-0.344-0.3440.0000.0000.0000.000
174L175MET0-0.040-0.00334.7940.2810.2810.0000.0000.0000.000
175L176SER0-0.0150.00037.308-0.329-0.3290.0000.0000.0000.000
176L177SER00.0270.00637.5870.2150.2150.0000.0000.0000.000
177L178THR0-0.004-0.01539.236-0.307-0.3070.0000.0000.0000.000
178L179LEU00.0010.01640.1780.1940.1940.0000.0000.0000.000
179L180THR0-0.005-0.00441.854-0.241-0.2410.0000.0000.0000.000
180L181LEU0-0.059-0.01943.3870.1150.1150.0000.0000.0000.000
181L182THR00.0560.01746.252-0.018-0.0180.0000.0000.0000.000
182L183LYS10.8920.92248.826-5.729-5.7290.0000.0000.0000.000
183L184ASP-1-0.883-0.94652.2085.9475.9470.0000.0000.0000.000
184L185GLU-1-0.846-0.91947.9006.5236.5230.0000.0000.0000.000
185L186TYR00.022-0.00250.461-0.036-0.0360.0000.0000.0000.000
186L187GLU-1-0.827-0.91651.7945.6455.6450.0000.0000.0000.000
187L188ARG10.8700.95850.958-6.301-6.3010.0000.0000.0000.000
188L189HIS10.7840.90350.219-6.386-6.3860.0000.0000.0000.000
189L190ASN00.0000.00254.371-0.107-0.1070.0000.0000.0000.000
190L191SER0-0.042-0.01153.563-0.013-0.0130.0000.0000.0000.000
191L192TYR0-0.005-0.00248.3820.1690.1690.0000.0000.0000.000
192L193THR0-0.009-0.02547.109-0.116-0.1160.0000.0000.0000.000
193L195GLU-1-0.818-0.89643.0396.9836.9830.0000.0000.0000.000
194L196ALA00.0300.00840.8640.2240.2240.0000.0000.0000.000
195L197THR0-0.024-0.00738.312-0.184-0.1840.0000.0000.0000.000
196L198HIS00.0570.02637.3730.0670.0670.0000.0000.0000.000
197L199LYS10.8560.91636.847-8.498-8.4980.0000.0000.0000.000
198L200THR0-0.048-0.05338.738-0.168-0.1680.0000.0000.0000.000
199L201SER0-0.033-0.01641.674-0.210-0.2100.0000.0000.0000.000
200L202THR00.0510.02039.4250.0530.0530.0000.0000.0000.000
201L203SER00.0110.01441.7330.0270.0270.0000.0000.0000.000
202L204PRO0-0.015-0.00942.818-0.041-0.0410.0000.0000.0000.000
203L205ILE00.0090.00744.352-0.222-0.2220.0000.0000.0000.000
204L206VAL00.0060.00445.5970.1370.1370.0000.0000.0000.000
205L207LYS10.8800.95547.818-6.531-6.5310.0000.0000.0000.000
206L208SER00.0570.01348.9600.1670.1670.0000.0000.0000.000
207L209PHE00.0010.01250.063-0.089-0.0890.0000.0000.0000.000
208L210ASN00.008-0.00453.8740.0850.0850.0000.0000.0000.000
209L211ARG10.8710.94654.860-5.809-5.8090.0000.0000.0000.000