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: 4J9ZN

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 OptAll
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 -2816372.810008
FMO2-HF: Nuclear repulsion 2725305.57307
FMO2-HF: Total energy -91067.236937
FMO2-MP2: Total energy -91332.582522


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.
-24.075-15.00810.148-8.305-10.9090.088
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 : -0.809 / q_NPA : -0.929
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].
3A255TYR00.0360.0041.986-29.764-26.7876.961-4.690-5.2480.055
4A256PHE0-0.0060.0042.187-25.967-21.2202.857-3.092-4.5120.032
5A257LEU0-0.001-0.0092.519-10.818-9.6130.332-0.520-1.0160.001
6A258PHE0-0.032-0.0025.478-5.866-5.8660.0000.0000.0000.000
7A259GLU-1-0.810-0.9107.22725.74325.7430.0000.0000.0000.000
8A260GLU-1-0.874-0.9377.32722.46722.4670.0000.0000.0000.000
9A261LYS10.8500.9489.599-24.364-24.3640.0000.0000.0000.000
10A262PHE0-0.021-0.02611.435-2.417-2.4170.0000.0000.0000.000
11A263ARG10.8130.91612.299-22.604-22.6040.0000.0000.0000.000
12A264GLY00.005-0.00212.786-1.790-1.7900.0000.0000.0000.000
13A265SER00.031-0.00411.9371.1871.1870.0000.0000.0000.000
14A266ARG10.7780.85710.505-22.230-22.2300.0000.0000.0000.000
15A267GLU-1-0.867-0.91513.81217.67817.6780.0000.0000.0000.000
16A268LEU00.0030.01516.515-0.901-0.9010.0000.0000.0000.000
17A269VAL00.0060.00314.082-0.946-0.9460.0000.0000.0000.000
18A270LYS10.8150.86817.238-16.142-16.1420.0000.0000.0000.000
19A271ALA0-0.043-0.02319.147-0.796-0.7960.0000.0000.0000.000
20A272ARG10.8070.90117.833-16.836-16.8360.0000.0000.0000.000
21A273LEU00.010-0.00418.139-0.730-0.7300.0000.0000.0000.000
22A274ARG10.8390.92322.113-12.912-12.9120.0000.0000.0000.000
23A275ARG10.7940.89923.116-13.410-13.4100.0000.0000.0000.000
24A276TYR0-0.023-0.05022.435-0.780-0.7800.0000.0000.0000.000
25A277ILE00.0430.03424.387-0.269-0.2690.0000.0000.0000.000
26A278PRO0-0.015-0.01728.065-0.319-0.3190.0000.0000.0000.000
27A279TYR0-0.045-0.01428.732-0.534-0.5340.0000.0000.0000.000
28A280PHE0-0.005-0.01225.574-0.051-0.0510.0000.0000.0000.000
29A281LYS10.8990.94829.647-9.021-9.0210.0000.0000.0000.000
30A282GLY00.0350.02230.924-0.284-0.2840.0000.0000.0000.000
31A283CYS0-0.063-0.00529.415-0.187-0.1870.0000.0000.0000.000
32A284ARG10.7890.86129.436-10.209-10.2090.0000.0000.0000.000
33A285ARG10.9310.96827.803-9.953-9.9530.0000.0000.0000.000
34A286VAL00.0310.02724.121-0.092-0.0920.0000.0000.0000.000
35A287LEU0-0.010-0.00521.0850.2390.2390.0000.0000.0000.000
36A288ASP-1-0.847-0.94617.38917.02317.0230.0000.0000.0000.000
37A289ILE0-0.026-0.03418.1650.6920.6920.0000.0000.0000.000
38A290GLY0-0.004-0.00614.203-0.106-0.1060.0000.0000.0000.000
39A291CYS0-0.0260.00313.1050.6520.6520.0000.0000.0000.000
40A292GLY00.0870.0549.896-0.052-0.0520.0000.0000.0000.000
41A293ARG10.7550.8438.325-28.064-28.0640.0000.0000.0000.000
42A294GLY00.0700.03210.488-1.419-1.4190.0000.0000.0000.000
43A295GLU-1-0.817-0.91513.01521.72921.7290.0000.0000.0000.000
44A296PHE00.0530.01716.017-1.240-1.2400.0000.0000.0000.000
45A297LEU00.0260.01715.848-0.844-0.8440.0000.0000.0000.000
46A298GLU-1-0.785-0.85716.04617.27317.2730.0000.0000.0000.000
47A299LEU00.0040.00118.993-0.739-0.7390.0000.0000.0000.000
48A300CYS0-0.084-0.01821.767-0.760-0.7600.0000.0000.0000.000
49A301LYS10.8920.94120.958-14.442-14.4420.0000.0000.0000.000
50A302GLU-1-0.861-0.91021.56413.33513.3350.0000.0000.0000.000
51A303GLU-1-0.870-0.94524.94510.79910.7990.0000.0000.0000.000
52A304GLY0-0.050-0.01127.304-0.399-0.3990.0000.0000.0000.000
53A305ILE0-0.078-0.03826.149-0.360-0.3600.0000.0000.0000.000
54A306GLU-1-0.874-0.91825.75911.35211.3520.0000.0000.0000.000
55A307SER0-0.037-0.04322.466-0.094-0.0940.0000.0000.0000.000
56A308ILE00.000-0.00420.7150.0910.0910.0000.0000.0000.000
57A309GLY00.0280.02217.277-0.178-0.1780.0000.0000.0000.000
58A310VAL0-0.033-0.01416.676-0.041-0.0410.0000.0000.0000.000
59A311ASP-1-0.761-0.90210.93428.25628.2560.0000.0000.0000.000
60A312ILE00.0080.00611.479-0.823-0.8230.0000.0000.0000.000
61A313ASN0-0.014-0.0194.807-0.281-0.232-0.001-0.001-0.0470.000
62A314GLU-1-0.787-0.8978.58725.58225.5820.0000.0000.0000.000
63A315ASP-1-0.801-0.8985.09140.95441.043-0.001-0.002-0.0860.000
64A316MET0-0.0270.0135.614-0.769-0.7690.0000.0000.0000.000
65A317ILE0-0.0110.0018.229-2.989-2.9890.0000.0000.0000.000
66A318LYS10.8260.9157.953-34.003-34.0030.0000.0000.0000.000
67A319PHE0-0.062-0.0276.729-1.899-1.8990.0000.0000.0000.000
68A320CYS0-0.054-0.0109.389-2.312-2.3120.0000.0000.0000.000
69A321GLU-1-0.876-0.94812.97019.80519.8050.0000.0000.0000.000
70A322GLY0-0.028-0.00214.155-1.167-1.1670.0000.0000.0000.000
71A323LYS10.8150.90513.693-20.274-20.2740.0000.0000.0000.000
72A324PHE0-0.016-0.01514.805-1.227-1.2270.0000.0000.0000.000
73A325ASN0-0.0020.01018.0850.3800.3800.0000.0000.0000.000
74A326VAL00.0020.00814.5210.0590.0590.0000.0000.0000.000
75A327VAL0-0.001-0.00317.321-0.433-0.4330.0000.0000.0000.000
76A328LYS10.8730.92812.068-24.337-24.3370.0000.0000.0000.000
77A329SER0-0.037-0.04015.550-1.284-1.2840.0000.0000.0000.000
78A330ASP-1-0.765-0.85216.52016.49316.4930.0000.0000.0000.000
79A331ALA00.0470.02318.325-0.729-0.7290.0000.0000.0000.000
80A332ILE0-0.0330.00419.961-0.690-0.6900.0000.0000.0000.000
81A333GLU-1-0.784-0.90022.02212.15812.1580.0000.0000.0000.000
82A334TYR00.0210.01821.057-0.533-0.5330.0000.0000.0000.000
83A335LEU0-0.0020.00023.096-0.618-0.6180.0000.0000.0000.000
84A336LYS10.7500.84825.661-12.587-12.5870.0000.0000.0000.000
85A337SER0-0.092-0.04325.461-0.342-0.3420.0000.0000.0000.000
86A338LEU0-0.0170.01125.596-0.264-0.2640.0000.0000.0000.000
87A339PRO00.008-0.00328.998-0.270-0.2700.0000.0000.0000.000
88A340ASP-1-0.835-0.92131.8519.7399.7390.0000.0000.0000.000
89A341LYS10.8140.89834.140-8.614-8.6140.0000.0000.0000.000
90A342TYR00.0260.03127.754-0.274-0.2740.0000.0000.0000.000
91A343LEU0-0.006-0.01426.291-0.015-0.0150.0000.0000.0000.000
92A344ASP-1-0.814-0.91929.3879.3959.3950.0000.0000.0000.000
93A345GLY00.0070.00728.430-0.262-0.2620.0000.0000.0000.000
94A346VAL0-0.022-0.00923.7250.2450.2450.0000.0000.0000.000
95A347MET00.0120.02320.635-0.672-0.6720.0000.0000.0000.000
96A348ILE00.005-0.00219.6370.4560.4560.0000.0000.0000.000
97A349SER00.003-0.01217.160-0.071-0.0710.0000.0000.0000.000
98A350HIS0-0.017-0.01415.3121.4401.4400.0000.0000.0000.000
99A351PHE00.0780.04414.7171.1201.1200.0000.0000.0000.000
100A352VAL00.008-0.01516.624-0.043-0.0430.0000.0000.0000.000
101A353GLU-1-0.769-0.86016.86417.36717.3670.0000.0000.0000.000
102A354HIS10.8450.90411.904-23.189-23.1890.0000.0000.0000.000
103A355LEU0-0.0330.02015.8220.5900.5900.0000.0000.0000.000
104A356ASP-1-0.882-0.94918.44114.04214.0420.0000.0000.0000.000
105A357PRO0-0.011-0.01520.989-0.348-0.3480.0000.0000.0000.000
106A358GLU-1-0.890-0.94723.92011.83811.8380.0000.0000.0000.000
107A359ARG10.7930.88520.595-14.701-14.7010.0000.0000.0000.000
108A360LEU0-0.011-0.00423.265-0.019-0.0190.0000.0000.0000.000
109A361PHE00.027-0.00625.307-0.150-0.1500.0000.0000.0000.000
110A362GLU-1-0.791-0.89526.49011.72511.7250.0000.0000.0000.000
111A363LEU00.0380.01621.965-0.137-0.1370.0000.0000.0000.000
112A364LEU00.0330.01925.544-0.167-0.1670.0000.0000.0000.000
113A365SER00.0320.00828.168-0.413-0.4130.0000.0000.0000.000
114A366LEU0-0.049-0.00726.627-0.340-0.3400.0000.0000.0000.000
115A367CYS0-0.029-0.01726.059-0.050-0.0500.0000.0000.0000.000
116A368TYR0-0.023-0.01528.591-0.280-0.2800.0000.0000.0000.000
117A369SER0-0.062-0.02132.241-0.372-0.3720.0000.0000.0000.000
118A370LYS10.8470.89928.665-10.417-10.4170.0000.0000.0000.000
119A371MET0-0.0420.02029.6810.1230.1230.0000.0000.0000.000
120A372LYS10.8410.92232.051-9.599-9.5990.0000.0000.0000.000
121A373TYR00.0330.01534.9320.0850.0850.0000.0000.0000.000
122A374SER0-0.103-0.06337.0770.0180.0180.0000.0000.0000.000
123A375SER00.0360.01731.877-0.019-0.0190.0000.0000.0000.000
124A376TYR00.0330.01530.515-0.346-0.3460.0000.0000.0000.000
125A377ILE0-0.003-0.00526.3230.2450.2450.0000.0000.0000.000
126A378VAL0-0.022-0.00824.438-0.364-0.3640.0000.0000.0000.000
127A379ILE00.0150.00422.6080.5160.5160.0000.0000.0000.000
128A380GLU-1-0.775-0.84919.91114.55414.5540.0000.0000.0000.000
129A381SER0-0.038-0.03519.8360.6160.6160.0000.0000.0000.000
130A382PRO00.0400.02418.326-0.628-0.6280.0000.0000.0000.000
131A383ASN00.0000.01021.210-0.458-0.4580.0000.0000.0000.000
132A384PRO0-0.0260.00124.947-0.015-0.0150.0000.0000.0000.000
133A385THR0-0.085-0.07526.286-0.395-0.3950.0000.0000.0000.000
134A386SER00.0240.02327.886-0.534-0.5340.0000.0000.0000.000
135A387LEU00.017-0.00127.3330.4590.4590.0000.0000.0000.000
136A388TYR00.0300.01623.8250.6080.6080.0000.0000.0000.000
137A389SER00.008-0.01223.0230.4240.4240.0000.0000.0000.000
138A390LEU0-0.055-0.02122.5270.6510.6510.0000.0000.0000.000
139A391ILE0-0.033-0.02123.2980.3370.3370.0000.0000.0000.000
140A392ASN00.017-0.00619.8160.7450.7450.0000.0000.0000.000
141A393PHE00.0170.02118.5171.0761.0760.0000.0000.0000.000
142A394TYR0-0.041-0.02617.8060.8150.8150.0000.0000.0000.000
143A395ILE0-0.0120.01114.1290.3950.3950.0000.0000.0000.000
144A396ASP-1-0.755-0.83211.53229.38329.3830.0000.0000.0000.000
145A397PRO0-0.042-0.03111.734-1.073-1.0730.0000.0000.0000.000
146A398THR0-0.085-0.0659.837-0.220-0.2200.0000.0000.0000.000
147A399HIS0-0.067-0.03913.062-0.062-0.0620.0000.0000.0000.000
148A400LYS10.8320.91215.835-18.906-18.9060.0000.0000.0000.000
149A401LYS10.9350.95219.293-12.977-12.9770.0000.0000.0000.000
150A402PRO00.0190.02121.9010.2250.2250.0000.0000.0000.000
151A403VAL00.0290.02422.072-0.572-0.5720.0000.0000.0000.000
152A404HIS00.0360.02524.5970.0960.0960.0000.0000.0000.000
153A405PRO00.0600.02427.562-0.095-0.0950.0000.0000.0000.000
154A406GLU-1-0.784-0.89629.2228.8718.8710.0000.0000.0000.000
155A407THR0-0.027-0.01528.404-0.284-0.2840.0000.0000.0000.000
156A408LEU00.0010.01124.825-0.053-0.0530.0000.0000.0000.000
157A409LYS10.8560.91129.130-8.916-8.9160.0000.0000.0000.000
158A410PHE0-0.0060.00032.490-0.186-0.1860.0000.0000.0000.000
159A411ILE00.0120.01129.236-0.217-0.2170.0000.0000.0000.000
160A412LEU0-0.002-0.00429.570-0.200-0.2000.0000.0000.0000.000
161A413GLU-1-0.876-0.92532.6298.1388.1380.0000.0000.0000.000
162A414TYR0-0.037-0.01635.916-0.309-0.3090.0000.0000.0000.000
163A415LEU0-0.045-0.01231.795-0.163-0.1630.0000.0000.0000.000
164A416GLY0-0.0200.00835.941-0.085-0.0850.0000.0000.0000.000
165A417PHE0-0.043-0.01530.573-0.118-0.1180.0000.0000.0000.000
166A418ARG10.7460.84035.915-8.404-8.4040.0000.0000.0000.000
167A419ASP-1-0.852-0.94735.9728.3708.3700.0000.0000.0000.000
168A420VAL0-0.0130.01033.2230.1690.1690.0000.0000.0000.000
169A421LYS10.8620.91733.452-9.458-9.4580.0000.0000.0000.000
170A422ILE00.0030.00429.9050.3240.3240.0000.0000.0000.000
171A423GLU-1-0.874-0.92129.3719.6089.6080.0000.0000.0000.000
172A424PHE00.015-0.00428.1170.3300.3300.0000.0000.0000.000
173A425PHE0-0.008-0.01525.166-0.316-0.3160.0000.0000.0000.000
174A426GLU-1-0.730-0.85722.25013.45313.4530.0000.0000.0000.000
175A427GLU-1-0.807-0.86925.4719.8929.8920.0000.0000.0000.000
176A428CYS0-0.0070.02527.0320.2260.2260.0000.0000.0000.000
177A429GLU-1-0.891-0.95526.28811.09711.0970.0000.0000.0000.000
178A430GLU-1-0.956-0.98728.9438.9108.9100.0000.0000.0000.000
179A431LEU00.000-0.00330.360-0.211-0.2110.0000.0000.0000.000
180A432THR0-0.054-0.01627.9710.1520.1520.0000.0000.0000.000
181A433LYS10.7710.89130.729-10.050-10.0500.0000.0000.0000.000
182A434LEU0-0.018-0.00633.717-0.169-0.1690.0000.0000.0000.000
183A435ALA00.0420.02137.225-0.054-0.0540.0000.0000.0000.000
184A436LYS10.8060.88139.313-7.907-7.9070.0000.0000.0000.000
185A437ILE0-0.021-0.01242.8030.0020.0020.0000.0000.0000.000
186A438ASP-1-0.861-0.91046.1756.7576.7570.0000.0000.0000.000
187A439SER0-0.026-0.03749.058-0.072-0.0720.0000.0000.0000.000
188A440ASN00.0060.00352.6440.0070.0070.0000.0000.0000.000
189A441THR0-0.037-0.01455.997-0.088-0.0880.0000.0000.0000.000
190A442VAL0-0.023-0.00453.583-0.076-0.0760.0000.0000.0000.000
191A443SER0-0.018-0.03256.2960.0350.0350.0000.0000.0000.000
192A444GLU-1-0.827-0.92254.5615.8385.8380.0000.0000.0000.000
193A445GLU-1-0.890-0.91953.5405.7355.7350.0000.0000.0000.000
194A446VAL0-0.023-0.01552.6700.1290.1290.0000.0000.0000.000
195A447ILE00.0260.01149.7300.1550.1550.0000.0000.0000.000
196A448ARG10.8580.92049.037-6.098-6.0980.0000.0000.0000.000
197A449VAL0-0.008-0.01048.3800.1610.1610.0000.0000.0000.000
198A450ILE00.0070.00546.2030.1690.1690.0000.0000.0000.000
199A451ASN00.0550.00844.6050.3530.3530.0000.0000.0000.000
200A452GLU-1-0.800-0.87343.6446.8666.8660.0000.0000.0000.000
201A453ASN0-0.024-0.01543.1530.2080.2080.0000.0000.0000.000
202A454ILE00.0320.02340.0580.1890.1890.0000.0000.0000.000
203A455GLU-1-0.775-0.86037.9538.6868.6860.0000.0000.0000.000
204A456LYS10.7890.87838.449-6.879-6.8790.0000.0000.0000.000
205A457LEU00.0040.00937.5490.1810.1810.0000.0000.0000.000
206A458ASN00.0310.00534.9320.4560.4560.0000.0000.0000.000
207A459ARG10.7250.83833.542-8.828-8.8280.0000.0000.0000.000
208A460ILE00.0100.01633.1270.2260.2260.0000.0000.0000.000
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