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: KG953

Calculation Name: 3DLI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DLI

Chain ID: A

ChEMBL ID:

UniProt ID: O30190

Base Structure: X-ray

Registration Date: 2023-09-21

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2811994.145096
FMO2-HF: Nuclear repulsion 2720927.699528
FMO2-HF: Total energy -91066.445568
FMO2-MP2: Total energy -91331.897277


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:253:ASP)


Summations of interaction energy for fragment #1(A:253: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.
-2.36100000000017.0564.092-5.6-7.9090.039
Interaction energy analysis for fragmet #1(A:253:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.861 / q_NPA : -0.953
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].
3A255TYR00.0740.0212.945-18.735-14.7140.158-1.939-2.2400.014
4A256PHE0-0.0070.0142.228-19.307-15.4642.293-2.594-3.5420.022
5A257LEU00.001-0.0122.118-9.939-8.7441.644-1.052-1.7870.003
6A258PHE0-0.026-0.0015.008-5.539-5.399-0.001-0.008-0.1310.000
7A259GLU-1-0.849-0.9427.92924.27224.2720.0000.0000.0000.000
8A260GLU-1-0.858-0.9397.10321.85121.8510.0000.0000.0000.000
9A261LYS10.8490.9559.311-23.449-23.4490.0000.0000.0000.000
10A262PHE0-0.032-0.03911.219-2.291-2.2910.0000.0000.0000.000
11A263ARG10.8550.94512.601-21.241-21.2410.0000.0000.0000.000
12A264GLY00.0060.00612.711-1.918-1.9180.0000.0000.0000.000
13A265SER00.035-0.00212.1061.2041.2040.0000.0000.0000.000
14A266ARG10.8200.89210.779-21.623-21.6230.0000.0000.0000.000
15A267GLU-1-0.871-0.91314.00617.42317.4230.0000.0000.0000.000
16A268LEU0-0.0090.00916.419-0.861-0.8610.0000.0000.0000.000
17A269VAL00.012-0.00514.613-0.996-0.9960.0000.0000.0000.000
18A270LYS10.8090.86617.567-15.856-15.8560.0000.0000.0000.000
19A271ALA0-0.055-0.02719.402-0.813-0.8130.0000.0000.0000.000
20A272ARG10.8790.94617.579-16.344-16.3440.0000.0000.0000.000
21A273LEU00.0080.00218.862-0.578-0.5780.0000.0000.0000.000
22A274ARG10.8890.95022.826-12.875-12.8750.0000.0000.0000.000
23A275ARG10.8110.90124.000-12.875-12.8750.0000.0000.0000.000
24A276TYR0-0.025-0.04423.234-0.757-0.7570.0000.0000.0000.000
25A277ILE00.0380.03024.758-0.150-0.1500.0000.0000.0000.000
26A278PRO0-0.029-0.01928.340-0.285-0.2850.0000.0000.0000.000
27A279TYR0-0.074-0.03829.315-0.466-0.4660.0000.0000.0000.000
28A280PHE0-0.007-0.01826.028-0.005-0.0050.0000.0000.0000.000
29A281LYS10.9500.98630.009-8.827-8.8270.0000.0000.0000.000
30A282GLY00.0320.01731.683-0.241-0.2410.0000.0000.0000.000
31A283CYS0-0.0400.01529.682-0.212-0.2120.0000.0000.0000.000
32A284ARG10.8120.87029.256-10.229-10.2290.0000.0000.0000.000
33A285ARG10.9040.95527.946-9.829-9.8290.0000.0000.0000.000
34A286VAL00.0290.03024.423-0.149-0.1490.0000.0000.0000.000
35A287LEU0-0.016-0.00721.3980.3250.3250.0000.0000.0000.000
36A288ASP-1-0.833-0.93917.88816.51716.5170.0000.0000.0000.000
37A289ILE0-0.011-0.03118.4300.7020.7020.0000.0000.0000.000
38A290GLY0-0.036-0.00814.6160.0110.0110.0000.0000.0000.000
39A291CYS0-0.0050.01013.3230.3500.3500.0000.0000.0000.000
40A292GLY00.0700.04010.3570.1970.1970.0000.0000.0000.000
41A293ARG10.7750.8808.845-26.300-26.3000.0000.0000.0000.000
42A294GLY00.0520.01510.949-1.042-1.0420.0000.0000.0000.000
43A295GLU-1-0.824-0.93913.55721.04521.0450.0000.0000.0000.000
44A296PHE00.0420.00716.310-1.146-1.1460.0000.0000.0000.000
45A297LEU00.0240.01916.157-0.784-0.7840.0000.0000.0000.000
46A298GLU-1-0.789-0.85816.28117.07717.0770.0000.0000.0000.000
47A299LEU00.0020.00919.385-0.741-0.7410.0000.0000.0000.000
48A300CYS0-0.043-0.00822.178-0.719-0.7190.0000.0000.0000.000
49A301LYS10.9130.95321.106-14.480-14.4800.0000.0000.0000.000
50A302GLU-1-0.860-0.91121.85413.04013.0400.0000.0000.0000.000
51A303GLU-1-0.946-0.98425.30510.42010.4200.0000.0000.0000.000
52A304GLY0-0.045-0.00627.429-0.432-0.4320.0000.0000.0000.000
53A305ILE0-0.108-0.05326.656-0.370-0.3700.0000.0000.0000.000
54A306GLU-1-0.877-0.93126.15311.36411.3640.0000.0000.0000.000
55A307SER0-0.032-0.03522.671-0.069-0.0690.0000.0000.0000.000
56A308ILE0-0.0070.00220.6830.2230.2230.0000.0000.0000.000
57A309GLY00.0390.02317.448-0.208-0.2080.0000.0000.0000.000
58A310VAL0-0.047-0.01416.7920.1960.1960.0000.0000.0000.000
59A311ASP-1-0.766-0.91111.27126.88826.8880.0000.0000.0000.000
60A312ILE00.0000.00911.9870.0290.0290.0000.0000.0000.000
61A313ASN0-0.023-0.0155.1940.3760.406-0.0010.001-0.0300.000
62A314GLU-1-0.787-0.8968.68625.13625.1360.0000.0000.0000.000
63A315ASP-1-0.802-0.9054.64946.97747.165-0.001-0.008-0.1790.000
64A316MET0-0.0300.0175.986-0.700-0.7000.0000.0000.0000.000
65A317ILE00.001-0.0038.235-2.663-2.6630.0000.0000.0000.000
66A318LYS10.8550.9337.698-37.671-37.6710.0000.0000.0000.000
67A319PHE0-0.073-0.0326.886-1.969-1.9690.0000.0000.0000.000
68A320CYS0-0.056-0.0099.475-2.473-2.4730.0000.0000.0000.000
69A321GLU-1-0.949-0.98013.05120.04920.0490.0000.0000.0000.000
70A322GLY00.0020.01914.341-1.160-1.1600.0000.0000.0000.000
71A323LYS10.8340.92514.003-20.348-20.3480.0000.0000.0000.000
72A324PHE0-0.021-0.03114.944-1.261-1.2610.0000.0000.0000.000
73A325ASN00.0190.03018.2270.3790.3790.0000.0000.0000.000
74A326VAL00.0310.00614.312-0.121-0.1210.0000.0000.0000.000
75A327VAL0-0.018-0.00517.537-0.218-0.2180.0000.0000.0000.000
76A328LYS10.8840.93412.061-24.164-24.1640.0000.0000.0000.000
77A329SER0-0.017-0.02215.348-1.174-1.1740.0000.0000.0000.000
78A330ASP-1-0.759-0.84816.59616.32116.3210.0000.0000.0000.000
79A331ALA00.0240.00818.571-0.675-0.6750.0000.0000.0000.000
80A332ILE00.0030.00920.338-0.573-0.5730.0000.0000.0000.000
81A333GLU-1-0.801-0.90822.13112.00712.0070.0000.0000.0000.000
82A334TYR00.0100.00521.078-0.557-0.5570.0000.0000.0000.000
83A335LEU0-0.017-0.00623.139-0.519-0.5190.0000.0000.0000.000
84A336LYS10.7820.88225.783-12.422-12.4220.0000.0000.0000.000
85A337SER0-0.140-0.05825.484-0.325-0.3250.0000.0000.0000.000
86A338LEU0-0.0050.00225.697-0.129-0.1290.0000.0000.0000.000
87A339PRO00.0110.00029.249-0.263-0.2630.0000.0000.0000.000
88A340ASP-1-0.812-0.92032.2389.4839.4830.0000.0000.0000.000
89A341LYS10.8290.90334.488-8.365-8.3650.0000.0000.0000.000
90A342TYR00.0140.02027.837-0.246-0.2460.0000.0000.0000.000
91A343LEU0-0.008-0.00726.348-0.102-0.1020.0000.0000.0000.000
92A344ASP-1-0.817-0.91829.3949.2959.2950.0000.0000.0000.000
93A345GLY00.0310.01128.488-0.276-0.2760.0000.0000.0000.000
94A346VAL0-0.025-0.01024.3120.2670.2670.0000.0000.0000.000
95A347MET00.0120.02821.236-0.632-0.6320.0000.0000.0000.000
96A348ILE0-0.002-0.01320.3320.5200.5200.0000.0000.0000.000
97A349SER0-0.009-0.01518.356-0.213-0.2130.0000.0000.0000.000
98A350HIS0-0.026-0.02016.1411.3321.3320.0000.0000.0000.000
99A351PHE00.0750.03615.5950.9600.9600.0000.0000.0000.000
100A352VAL00.0310.00317.3670.1840.1840.0000.0000.0000.000
101A353GLU-1-0.766-0.84617.31516.92916.9290.0000.0000.0000.000
102A354HIS10.8300.88412.879-21.801-21.8010.0000.0000.0000.000
103A355LEU0-0.062-0.01416.6200.6590.6590.0000.0000.0000.000
104A356ASP-1-0.881-0.93919.33013.17813.1780.0000.0000.0000.000
105A357PRO00.012-0.01021.812-0.277-0.2770.0000.0000.0000.000
106A358GLU-1-0.909-0.95124.79411.71611.7160.0000.0000.0000.000
107A359ARG10.7870.88020.700-14.606-14.6060.0000.0000.0000.000
108A360LEU00.0120.00424.2060.0820.0820.0000.0000.0000.000
109A361PHE00.016-0.00726.171-0.113-0.1130.0000.0000.0000.000
110A362GLU-1-0.777-0.91227.34511.45811.4580.0000.0000.0000.000
111A363LEU00.0400.02822.398-0.084-0.0840.0000.0000.0000.000
112A364LEU00.0490.01725.963-0.096-0.0960.0000.0000.0000.000
113A365SER00.0190.01528.436-0.426-0.4260.0000.0000.0000.000
114A366LEU0-0.059-0.02426.973-0.325-0.3250.0000.0000.0000.000
115A367CYS0-0.023-0.01226.346-0.015-0.0150.0000.0000.0000.000
116A368TYR0-0.024-0.01228.882-0.278-0.2780.0000.0000.0000.000
117A369SER0-0.058-0.02432.559-0.326-0.3260.0000.0000.0000.000
118A370LYS10.7910.89729.000-10.210-10.2100.0000.0000.0000.000
119A371MET0-0.0240.02529.9070.1910.1910.0000.0000.0000.000
120A372LYS10.8400.93832.267-9.511-9.5110.0000.0000.0000.000
121A373TYR00.0030.00335.2120.0570.0570.0000.0000.0000.000
122A374SER0-0.091-0.06537.225-0.024-0.0240.0000.0000.0000.000
123A375SER00.0410.02132.0630.0040.0040.0000.0000.0000.000
124A376TYR00.0310.00231.005-0.318-0.3180.0000.0000.0000.000
125A377ILE0-0.0140.00026.6660.2710.2710.0000.0000.0000.000
126A378VAL0-0.018-0.01825.150-0.334-0.3340.0000.0000.0000.000
127A379ILE0-0.001-0.00223.2350.5190.5190.0000.0000.0000.000
128A380GLU-1-0.797-0.85520.76913.96313.9630.0000.0000.0000.000
129A381SER0-0.030-0.02720.7550.6660.6660.0000.0000.0000.000
130A382PRO00.0540.03219.274-0.573-0.5730.0000.0000.0000.000
131A383ASN00.0090.01622.181-0.490-0.4900.0000.0000.0000.000
132A384PRO0-0.0330.00025.6550.0030.0030.0000.0000.0000.000
133A385THR0-0.104-0.08426.930-0.387-0.3870.0000.0000.0000.000
134A386SER00.0240.02828.794-0.491-0.4910.0000.0000.0000.000
135A387LEU00.010-0.00828.2020.4200.4200.0000.0000.0000.000
136A388TYR00.0370.01924.1200.5610.5610.0000.0000.0000.000
137A389SER00.015-0.01223.9200.3760.3760.0000.0000.0000.000
138A390LEU0-0.037-0.01423.2520.6170.6170.0000.0000.0000.000
139A391ILE0-0.032-0.01723.8980.4170.4170.0000.0000.0000.000
140A392ASN00.015-0.00720.4200.6330.6330.0000.0000.0000.000
141A393PHE0-0.0130.01619.1950.9890.9890.0000.0000.0000.000
142A394TYR0-0.030-0.02518.6960.6500.6500.0000.0000.0000.000
143A395ILE0-0.0220.01715.0650.3730.3730.0000.0000.0000.000
144A396ASP-1-0.763-0.84012.48126.91526.9150.0000.0000.0000.000
145A397PRO00.001-0.01312.313-0.986-0.9860.0000.0000.0000.000
146A398THR0-0.123-0.07710.387-0.455-0.4550.0000.0000.0000.000
147A399HIS0-0.069-0.04513.702-0.097-0.0970.0000.0000.0000.000
148A400LYS10.8680.93016.377-18.397-18.3970.0000.0000.0000.000
149A401LYS10.9210.96319.850-12.368-12.3680.0000.0000.0000.000
150A402PRO00.0290.00922.6340.1980.1980.0000.0000.0000.000
151A403VAL00.0340.02422.694-0.485-0.4850.0000.0000.0000.000
152A404HIS00.0240.01625.1950.0700.0700.0000.0000.0000.000
153A405PRO00.0640.02528.447-0.044-0.0440.0000.0000.0000.000
154A406GLU-1-0.797-0.90729.8818.6958.6950.0000.0000.0000.000
155A407THR0-0.027-0.01028.987-0.251-0.2510.0000.0000.0000.000
156A408LEU0-0.0070.00225.608-0.118-0.1180.0000.0000.0000.000
157A409LYS10.8700.91130.064-8.712-8.7120.0000.0000.0000.000
158A410PHE0-0.013-0.00233.315-0.221-0.2210.0000.0000.0000.000
159A411ILE00.0200.00830.031-0.202-0.2020.0000.0000.0000.000
160A412LEU00.005-0.00130.117-0.210-0.2100.0000.0000.0000.000
161A413GLU-1-0.865-0.90433.3287.9907.9900.0000.0000.0000.000
162A414TYR0-0.044-0.02436.472-0.293-0.2930.0000.0000.0000.000
163A415LEU0-0.063-0.02031.992-0.146-0.1460.0000.0000.0000.000
164A416GLY0-0.0160.00336.295-0.088-0.0880.0000.0000.0000.000
165A417PHE0-0.063-0.02231.134-0.152-0.1520.0000.0000.0000.000
166A418ARG10.8080.88536.408-8.174-8.1740.0000.0000.0000.000
167A419ASP-1-0.929-0.98936.7188.2678.2670.0000.0000.0000.000
168A420VAL0-0.007-0.00133.4740.1410.1410.0000.0000.0000.000
169A421LYS10.8480.92134.046-9.208-9.2080.0000.0000.0000.000
170A422ILE00.003-0.01430.7260.3210.3210.0000.0000.0000.000
171A423GLU-1-0.884-0.91830.3479.3609.3600.0000.0000.0000.000
172A424PHE00.003-0.00329.0800.3330.3330.0000.0000.0000.000
173A425PHE0-0.015-0.01926.155-0.274-0.2740.0000.0000.0000.000
174A426GLU-1-0.752-0.87822.61613.06913.0690.0000.0000.0000.000
175A427GLU-1-0.796-0.85125.9909.6709.6700.0000.0000.0000.000
176A428CYS00.0020.02627.1820.3010.3010.0000.0000.0000.000
177A429GLU-1-0.895-0.95725.94611.00711.0070.0000.0000.0000.000
178A430GLU-1-0.952-0.99828.9828.8598.8590.0000.0000.0000.000
179A431LEU0-0.001-0.00129.981-0.158-0.1580.0000.0000.0000.000
180A432THR0-0.071-0.01728.3260.0880.0880.0000.0000.0000.000
181A433LYS10.7580.88930.749-9.881-9.8810.0000.0000.0000.000
182A434LEU00.007-0.00133.652-0.153-0.1530.0000.0000.0000.000
183A435ALA00.0440.01737.0980.0100.0100.0000.0000.0000.000
184A436LYS10.8350.89739.497-7.738-7.7380.0000.0000.0000.000
185A437ILE0-0.047-0.02942.799-0.013-0.0130.0000.0000.0000.000
186A438ASP-1-0.848-0.90746.1166.6856.6850.0000.0000.0000.000
187A439SER00.003-0.02948.971-0.056-0.0560.0000.0000.0000.000
188A440ASN0-0.0040.00452.403-0.018-0.0180.0000.0000.0000.000
189A441THR0-0.034-0.01655.642-0.086-0.0860.0000.0000.0000.000
190A442VAL0-0.028-0.00953.351-0.079-0.0790.0000.0000.0000.000
191A443SER0-0.001-0.00855.7740.0480.0480.0000.0000.0000.000
192A444GLU-1-0.829-0.91554.7115.7495.7490.0000.0000.0000.000
193A445GLU-1-0.883-0.93853.7975.6645.6640.0000.0000.0000.000
194A446VAL0-0.043-0.01952.8560.1070.1070.0000.0000.0000.000
195A447ILE00.002-0.00749.6130.1560.1560.0000.0000.0000.000
196A448ARG10.8450.88749.409-6.026-6.0260.0000.0000.0000.000
197A449VAL0-0.010-0.00749.0660.1490.1490.0000.0000.0000.000
198A450ILE00.0050.00346.4550.1650.1650.0000.0000.0000.000
199A451ASN00.0450.01444.9070.3480.3480.0000.0000.0000.000
200A452GLU-1-0.848-0.88744.1146.6956.6950.0000.0000.0000.000
201A453ASN0-0.024-0.02144.0840.1840.1840.0000.0000.0000.000
202A454ILE00.0520.03740.0070.1850.1850.0000.0000.0000.000
203A455GLU-1-0.809-0.87138.8378.4338.4330.0000.0000.0000.000
204A456LYS10.8670.92839.265-6.854-6.8540.0000.0000.0000.000
205A457LEU00.0050.00138.4020.2000.2000.0000.0000.0000.000
206A458ASN00.0370.01035.5170.4020.4020.0000.0000.0000.000
207A459ARG10.7310.86233.986-8.709-8.7090.0000.0000.0000.000
208A460ILE0-0.0030.00233.8950.2450.2450.0000.0000.0000.000
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210A462PHE00.006-0.01230.0090.3870.3870.0000.0000.0000.000
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