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: YZ7K2

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2136367.880332
FMO2-HF: Nuclear repulsion 2054219.137301
FMO2-HF: Total energy -82148.743031
FMO2-MP2: Total energy -82388.202344


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.
-47.537-42.3984.493-4.011-5.617-0.002
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 : -0.932 / q_NPA : -0.966
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].
3L3GLN00.005-0.0043.824-6.565-3.306-0.008-1.484-1.7670.008
4L4MET0-0.033-0.0145.389-5.497-5.507-0.001-0.0020.0130.000
5L5THR0-0.015-0.0098.924-0.660-0.6600.0000.0000.0000.000
6L6GLN00.010-0.03411.926-0.004-0.0040.0000.0000.0000.000
7L7SER0-0.0490.00114.970-0.541-0.5410.0000.0000.0000.000
8L8PRO00.0690.03718.553-0.070-0.0700.0000.0000.0000.000
9L9ALA00.0640.02919.3070.2190.2190.0000.0000.0000.000
10L10SER0-0.018-0.01220.355-0.099-0.0990.0000.0000.0000.000
11L11LEU0-0.031-0.01823.967-0.040-0.0400.0000.0000.0000.000
12L12SER0-0.005-0.01527.0700.0350.0350.0000.0000.0000.000
13L13VAL0-0.058-0.03829.642-0.036-0.0360.0000.0000.0000.000
14L14SER00.0360.00932.335-0.118-0.1180.0000.0000.0000.000
15L15VAL00.009-0.00134.9630.1650.1650.0000.0000.0000.000
16L16GLY0-0.0160.00136.070-0.214-0.2140.0000.0000.0000.000
17L17GLU-1-0.885-0.93933.6519.1529.1520.0000.0000.0000.000
18L18THR0-0.046-0.02730.4820.1140.1140.0000.0000.0000.000
19L19VAL00.0140.01725.8860.0310.0310.0000.0000.0000.000
20L20THR0-0.014-0.01723.4520.0110.0110.0000.0000.0000.000
21L21ILE0-0.0290.00619.2480.0780.0780.0000.0000.0000.000
22L22THR0-0.018-0.01917.4500.0220.0220.0000.0000.0000.000
23L23CYS0-0.061-0.01413.5020.3120.3120.0000.0000.0000.000
24L24ARG10.9030.96013.378-18.881-18.8810.0000.0000.0000.000
25L25ALA00.0440.0258.7791.5441.5440.0000.0000.0000.000
26L26SER00.0380.0185.521-0.949-0.9490.0000.0000.0000.000
27L27GLU-1-0.871-0.9323.98336.27736.393-0.001-0.055-0.0600.000
28L28ASN0-0.034-0.0228.232-0.634-0.6340.0000.0000.0000.000
29L29ILE00.0710.0437.6680.8430.8430.0000.0000.0000.000
30L30TYR0-0.047-0.02310.192-0.959-0.9590.0000.0000.0000.000
31L31ARG10.8930.92913.658-15.072-15.0720.0000.0000.0000.000
32L32ASN0-0.0120.00810.906-1.419-1.4190.0000.0000.0000.000
33L33LEU0-0.007-0.00611.2871.8861.8860.0000.0000.0000.000
34L34ALA0-0.0190.00213.575-1.576-1.5760.0000.0000.0000.000
35L35TRP00.025-0.00315.6201.1471.1470.0000.0000.0000.000
36L36TYR0-0.023-0.02514.955-1.328-1.3280.0000.0000.0000.000
37L37GLN00.0010.00019.7780.0680.0680.0000.0000.0000.000
38L38GLN0-0.016-0.02421.1670.5010.5010.0000.0000.0000.000
39L39LYS10.8880.94923.515-10.553-10.5530.0000.0000.0000.000
40L40GLN00.0680.02326.5350.4330.4330.0000.0000.0000.000
41L41GLY00.004-0.00227.264-0.340-0.3400.0000.0000.0000.000
42L42LYS10.9050.96626.962-10.253-10.2530.0000.0000.0000.000
43L43SER00.0400.01623.1880.2860.2860.0000.0000.0000.000
44L44PRO00.006-0.00118.997-0.426-0.4260.0000.0000.0000.000
45L45GLN0-0.031-0.01421.756-0.557-0.5570.0000.0000.0000.000
46L46LEU00.0010.00718.9900.2340.2340.0000.0000.0000.000
47L47LEU0-0.0060.00421.434-0.599-0.5990.0000.0000.0000.000
48L48VAL0-0.003-0.00519.946-0.491-0.4910.0000.0000.0000.000
49L49TYR00.0340.00618.2620.9560.9560.0000.0000.0000.000
50L50ALA00.0250.01216.815-0.564-0.5640.0000.0000.0000.000
51L51ALA0-0.0150.00316.705-0.524-0.5240.0000.0000.0000.000
52L52THR0-0.092-0.06218.152-0.500-0.5000.0000.0000.0000.000
53L53ASN0-0.0100.01721.538-0.935-0.9350.0000.0000.0000.000
54L54LEU00.0230.01722.9100.4990.4990.0000.0000.0000.000
55L55ALA00.0050.00023.615-0.143-0.1430.0000.0000.0000.000
56L56ALA00.024-0.00725.334-0.386-0.3860.0000.0000.0000.000
57L57GLY0-0.010-0.00528.6770.0970.0970.0000.0000.0000.000
58L58VAL0-0.0370.00625.977-0.140-0.1400.0000.0000.0000.000
59L59PRO00.0190.00529.356-0.184-0.1840.0000.0000.0000.000
60L60SER00.0430.00330.1650.3010.3010.0000.0000.0000.000
61L61ARG10.8170.90331.033-9.525-9.5250.0000.0000.0000.000
62L62PHE0-0.0120.00225.9530.2210.2210.0000.0000.0000.000
63L63SER00.0090.00726.152-0.121-0.1210.0000.0000.0000.000
64L64GLY00.0370.02921.9220.3450.3450.0000.0000.0000.000
65L65SER0-0.040-0.02221.398-0.499-0.4990.0000.0000.0000.000
66L66GLY00.0810.03218.8480.6250.6250.0000.0000.0000.000
67L67SER0-0.043-0.02316.997-0.390-0.3900.0000.0000.0000.000
68L68GLY00.0630.03614.7150.0740.0740.0000.0000.0000.000
69L69THR00.0350.02611.3320.4190.4190.0000.0000.0000.000
70L70GLN00.0170.02413.5601.0381.0380.0000.0000.0000.000
71L71TYR00.006-0.01213.115-1.283-1.2830.0000.0000.0000.000
72L72SER0-0.010-0.01417.4640.1200.1200.0000.0000.0000.000
73L73LEU0-0.0020.01720.575-0.112-0.1120.0000.0000.0000.000
74L74LYS10.9100.95422.412-10.684-10.6840.0000.0000.0000.000
75L75ILE00.0140.01025.935-0.065-0.0650.0000.0000.0000.000
76L76ASN0-0.017-0.04128.7760.1610.1610.0000.0000.0000.000
77L77SER00.0080.01532.269-0.252-0.2520.0000.0000.0000.000
78L78LEU0-0.024-0.00929.776-0.050-0.0500.0000.0000.0000.000
79L79GLN00.020-0.00233.125-0.410-0.4100.0000.0000.0000.000
80L80SER00.0660.01433.5870.2510.2510.0000.0000.0000.000
81L81GLU-1-0.921-0.95832.8809.1019.1010.0000.0000.0000.000
82L82ASP-1-0.722-0.82629.51510.43410.4340.0000.0000.0000.000
83L83PHE0-0.0020.03128.4590.4790.4790.0000.0000.0000.000
84L84GLY0-0.016-0.01626.764-0.115-0.1150.0000.0000.0000.000
85L85SER0-0.022-0.00621.2010.1620.1620.0000.0000.0000.000
86L86TYR0-0.014-0.02320.732-0.182-0.1820.0000.0000.0000.000
87L87TYR00.0120.02915.3390.3980.3980.0000.0000.0000.000
88L89GLN00.0280.00610.635-0.994-0.9940.0000.0000.0000.000
89L90HIS0-0.0140.0234.645-7.350-7.281-0.001-0.005-0.0620.000
90L91PHE0-0.020-0.0329.0120.9350.9350.0000.0000.0000.000
91L92TRP0-0.037-0.0185.162-3.275-3.2750.0000.0000.0000.000
92L93ASN00.0210.0032.6461.1622.8850.895-1.090-1.528-0.011
93L94ILE0-0.0120.0175.1120.1120.276-0.001-0.014-0.1480.000
94L95PRO00.0450.0121.9322.7662.4163.612-1.346-1.9160.001
95L96PHE00.0390.0144.6362.4032.460-0.001-0.007-0.0480.000
96L97THR00.0130.0054.468-5.724-5.613-0.001-0.008-0.1010.000
97L98PHE00.005-0.0037.281-2.369-2.3690.0000.0000.0000.000
98L99GLY0-0.008-0.0129.9322.0922.0920.0000.0000.0000.000
99L100SER00.014-0.00912.022-0.402-0.4020.0000.0000.0000.000
100L101GLY00.0090.01013.881-0.987-0.9870.0000.0000.0000.000
101L102THR0-0.070-0.04417.2100.1190.1190.0000.0000.0000.000
102L103LYS10.9470.97220.511-12.260-12.2600.0000.0000.0000.000
103L104LEU0-0.037-0.02423.729-0.151-0.1510.0000.0000.0000.000
104L105GLU-1-0.768-0.79527.0229.6829.6820.0000.0000.0000.000
105L106ILE00.030-0.00230.111-0.005-0.0050.0000.0000.0000.000
106L107LYS10.9030.96833.177-9.478-9.4780.0000.0000.0000.000
107L108ARG10.8550.91835.691-7.944-7.9440.0000.0000.0000.000
108L109ALA0-0.0080.00238.9460.0790.0790.0000.0000.0000.000
109L110ASP-1-0.797-0.89238.9218.2668.2660.0000.0000.0000.000
110L111ALA0-0.038-0.02240.862-0.219-0.2190.0000.0000.0000.000
111L112ALA00.0390.02141.3950.1990.1990.0000.0000.0000.000
112L113PRO0-0.0210.00841.126-0.046-0.0460.0000.0000.0000.000
113L114THR00.0040.00043.040-0.224-0.2240.0000.0000.0000.000
114L115VAL0-0.012-0.01043.8960.1000.1000.0000.0000.0000.000
115L116SER0-0.040-0.02045.998-0.247-0.2470.0000.0000.0000.000
116L117ILE0-0.019-0.00846.5400.1630.1630.0000.0000.0000.000
117L118PHE0-0.022-0.01547.223-0.161-0.1610.0000.0000.0000.000
118L119PRO00.007-0.00148.9370.1300.1300.0000.0000.0000.000
119L120PRO00.0210.02249.6770.0290.0290.0000.0000.0000.000
120L121SER00.0330.03051.041-0.112-0.1120.0000.0000.0000.000
121L122SER00.032-0.00153.102-0.008-0.0080.0000.0000.0000.000
122L123GLU-1-0.873-0.94953.3845.8845.8840.0000.0000.0000.000
123L124GLN00.0370.01746.335-0.052-0.0520.0000.0000.0000.000
124L125LEU00.0320.03251.6750.0300.0300.0000.0000.0000.000
125L126THR0-0.065-0.02553.919-0.071-0.0710.0000.0000.0000.000
126L127SER0-0.105-0.06151.0660.0110.0110.0000.0000.0000.000
127L128GLY00.0350.02051.9150.0670.0670.0000.0000.0000.000
128L129GLY0-0.036-0.01848.6460.1020.1020.0000.0000.0000.000
129L130ALA00.004-0.01648.036-0.145-0.1450.0000.0000.0000.000
130L131SER0-0.041-0.02244.0720.1060.1060.0000.0000.0000.000
131L132VAL0-0.019-0.00145.638-0.150-0.1500.0000.0000.0000.000
132L133VAL00.0220.01443.0350.2050.2050.0000.0000.0000.000
133L134CYS0-0.060-0.02142.634-0.004-0.0040.0000.0000.0000.000
134L135PHE0-0.0130.00441.8830.2150.2150.0000.0000.0000.000
135L136LEU00.014-0.01139.034-0.173-0.1730.0000.0000.0000.000
136L137ASN00.041-0.00940.2250.4170.4170.0000.0000.0000.000
137L138ASN0-0.004-0.00541.062-0.186-0.1860.0000.0000.0000.000
138L139PHE0-0.0050.00435.313-0.131-0.1310.0000.0000.0000.000
139L140TYR0-0.005-0.02533.8920.1540.1540.0000.0000.0000.000
140L141PRO0-0.0010.00133.702-0.203-0.2030.0000.0000.0000.000
141L142LYS10.9990.98927.302-11.367-11.3670.0000.0000.0000.000
142L143ASP-1-0.937-0.94329.91710.63310.6330.0000.0000.0000.000
143L144ILE0-0.038-0.02432.641-0.344-0.3440.0000.0000.0000.000
144L145ASN0-0.050-0.02132.9610.4140.4140.0000.0000.0000.000
145L146VAL00.0400.02036.043-0.255-0.2550.0000.0000.0000.000
146L147LYS10.9100.97137.952-7.677-7.6770.0000.0000.0000.000
147L148TRP00.024-0.00440.135-0.320-0.3200.0000.0000.0000.000
148L149LYS10.8320.92043.049-6.911-6.9110.0000.0000.0000.000
149L150ILE00.0260.01146.123-0.069-0.0690.0000.0000.0000.000
150L151ASP-1-0.796-0.89248.7906.0276.0270.0000.0000.0000.000
151L152GLY0-0.007-0.00349.902-0.039-0.0390.0000.0000.0000.000
152L153SER0-0.015-0.00947.1250.0830.0830.0000.0000.0000.000
153L154GLU-1-0.949-0.97839.3648.1018.1010.0000.0000.0000.000
154L155ARG10.8490.93142.089-7.353-7.3530.0000.0000.0000.000
155L156GLN00.0420.00935.9000.2820.2820.0000.0000.0000.000
156L157ASN00.005-0.00137.6800.3150.3150.0000.0000.0000.000
157L158GLY00.0440.01638.180-0.221-0.2210.0000.0000.0000.000
158L159VAL00.0030.01736.818-0.168-0.1680.0000.0000.0000.000
159L160LEU0-0.0130.01634.8750.2900.2900.0000.0000.0000.000
160L161ASN00.0320.01433.460-0.489-0.4890.0000.0000.0000.000
161L162SER0-0.021-0.00933.1830.3510.3510.0000.0000.0000.000
162L163TRP00.0470.00430.230-0.156-0.1560.0000.0000.0000.000
163L164THR00.0090.01532.6660.1240.1240.0000.0000.0000.000
164L165ASP-1-0.938-0.96830.11810.70110.7010.0000.0000.0000.000
165L166GLN0-0.069-0.03832.330-0.034-0.0340.0000.0000.0000.000
166L167ASP-1-0.846-0.92434.2857.8727.8720.0000.0000.0000.000
167L168SER0-0.026-0.02737.871-0.045-0.0450.0000.0000.0000.000
168L169LYS10.9130.96438.725-7.106-7.1060.0000.0000.0000.000
169L170ASP-1-0.806-0.88741.1997.5947.5940.0000.0000.0000.000
170L171SER0-0.0080.00137.0900.0400.0400.0000.0000.0000.000
171L172THR0-0.092-0.04937.0950.2020.2020.0000.0000.0000.000
172L173TYR0-0.064-0.08931.6370.3380.3380.0000.0000.0000.000
173L174SER00.0450.03036.484-0.339-0.3390.0000.0000.0000.000
174L175MET0-0.0350.00234.8140.2950.2950.0000.0000.0000.000
175L176SER0-0.022-0.00337.203-0.321-0.3210.0000.0000.0000.000
176L177SER00.0220.00637.4940.2140.2140.0000.0000.0000.000
177L178THR0-0.004-0.01439.157-0.310-0.3100.0000.0000.0000.000
178L179LEU00.0110.02240.1070.1990.1990.0000.0000.0000.000
179L180THR0-0.009-0.00441.809-0.246-0.2460.0000.0000.0000.000
180L181LEU0-0.058-0.02143.3330.1200.1200.0000.0000.0000.000
181L182THR00.0470.01646.199-0.023-0.0230.0000.0000.0000.000
182L183LYS10.9580.97748.772-5.722-5.7220.0000.0000.0000.000
183L184ASP-1-0.871-0.94052.1495.8945.8940.0000.0000.0000.000
184L185GLU-1-0.922-0.98047.8996.5276.5270.0000.0000.0000.000
185L186TYR00.015-0.00250.465-0.036-0.0360.0000.0000.0000.000
186L187GLU-1-0.903-0.97551.7455.6325.6320.0000.0000.0000.000
187L188ARG10.9010.98151.165-6.259-6.2590.0000.0000.0000.000
188L189HIS10.8010.92050.801-6.348-6.3480.0000.0000.0000.000
189L190ASN00.0060.00954.339-0.104-0.1040.0000.0000.0000.000
190L191SER0-0.055-0.01453.216-0.003-0.0030.0000.0000.0000.000
191L192TYR00.0180.00448.2910.1710.1710.0000.0000.0000.000
192L193THR0-0.006-0.03246.915-0.121-0.1210.0000.0000.0000.000
193L195GLU-1-0.857-0.94143.0886.9936.9930.0000.0000.0000.000
194L196ALA00.0320.00840.8090.2230.2230.0000.0000.0000.000
195L197THR0-0.022-0.00438.344-0.186-0.1860.0000.0000.0000.000
196L198HIS00.0660.02337.1450.0680.0680.0000.0000.0000.000
197L199LYS10.8670.93736.946-8.554-8.5540.0000.0000.0000.000
198L200THR0-0.063-0.05738.688-0.170-0.1700.0000.0000.0000.000
199L201SER0-0.042-0.03341.625-0.201-0.2010.0000.0000.0000.000
200L202THR00.0430.03039.4190.0460.0460.0000.0000.0000.000
201L203SER00.0150.01641.7040.0250.0250.0000.0000.0000.000
202L204PRO0-0.016-0.00242.907-0.036-0.0360.0000.0000.0000.000
203L205ILE00.0120.00744.315-0.227-0.2270.0000.0000.0000.000
204L206VAL00.0010.00245.5430.1360.1360.0000.0000.0000.000
205L207LYS10.8900.95747.766-6.519-6.5190.0000.0000.0000.000
206L208SER00.0550.02448.9030.1690.1690.0000.0000.0000.000
207L209PHE0-0.0070.01150.061-0.087-0.0870.0000.0000.0000.000
208L210ASN0-0.013-0.01553.8210.0590.0590.0000.0000.0000.000
209L211ARG10.9050.95954.964-5.760-5.7600.0000.0000.0000.000