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: QVY6Y

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 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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2810301.269688
FMO2-HF: Nuclear repulsion 2719236.780262
FMO2-HF: Total energy -91064.489426
FMO2-MP2: Total energy -91330.022662


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.
31.31535.9896.632-4.559-6.7470.009
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 : -0.894 / q_NPA : -0.957
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].
3A255TYR00.0820.0243.808-12.564-10.140-0.014-1.021-1.3900.003
4A256PHE00.0150.0231.807-11.227-10.8235.486-2.623-3.2680.001
5A257LEU0-0.004-0.0122.542-8.056-6.7421.151-0.813-1.6510.005
6A258PHE0-0.048-0.0104.912-4.375-4.248-0.001-0.008-0.1170.000
7A259GLU-1-0.868-0.9478.03222.94722.9470.0000.0000.0000.000
8A260GLU-1-0.889-0.9677.13320.17720.1770.0000.0000.0000.000
9A261LYS10.8880.9769.251-22.058-22.0580.0000.0000.0000.000
10A262PHE0-0.040-0.04111.129-1.998-1.9980.0000.0000.0000.000
11A263ARG10.9100.98212.540-19.485-19.4850.0000.0000.0000.000
12A264GLY00.010-0.00312.661-1.692-1.6920.0000.0000.0000.000
13A265SER00.0770.04912.1041.1511.1510.0000.0000.0000.000
14A266ARG10.8220.91210.669-21.028-21.0280.0000.0000.0000.000
15A267GLU-1-0.897-0.95214.02316.98816.9880.0000.0000.0000.000
16A268LEU0-0.0120.01416.311-0.869-0.8690.0000.0000.0000.000
17A269VAL00.013-0.00514.549-0.936-0.9360.0000.0000.0000.000
18A270LYS10.8630.91417.566-15.210-15.2100.0000.0000.0000.000
19A271ALA0-0.077-0.04019.347-0.791-0.7910.0000.0000.0000.000
20A272ARG10.9220.96118.052-15.323-15.3230.0000.0000.0000.000
21A273LEU00.0330.01418.844-0.541-0.5410.0000.0000.0000.000
22A274ARG10.9410.98822.735-12.498-12.4980.0000.0000.0000.000
23A275ARG10.8610.93224.117-12.350-12.3500.0000.0000.0000.000
24A276TYR00.034-0.00923.870-0.364-0.3640.0000.0000.0000.000
25A277ILE00.0570.04124.754-0.127-0.1270.0000.0000.0000.000
26A278PRO0-0.049-0.02428.287-0.257-0.2570.0000.0000.0000.000
27A279TYR0-0.032-0.02129.923-0.421-0.4210.0000.0000.0000.000
28A280PHE0-0.004-0.02226.7570.0060.0060.0000.0000.0000.000
29A281LYS10.9340.97230.206-8.672-8.6720.0000.0000.0000.000
30A282GLY00.0240.01331.640-0.237-0.2370.0000.0000.0000.000
31A283CYS0-0.0610.01029.769-0.202-0.2020.0000.0000.0000.000
32A284ARG10.9230.95330.275-9.926-9.9260.0000.0000.0000.000
33A285ARG10.9270.95228.117-9.853-9.8530.0000.0000.0000.000
34A286VAL00.0400.03824.780-0.151-0.1510.0000.0000.0000.000
35A287LEU0-0.014-0.00621.5610.3290.3290.0000.0000.0000.000
36A288ASP-1-0.827-0.93518.61715.92715.9270.0000.0000.0000.000
37A289ILE0-0.019-0.03918.7280.7010.7010.0000.0000.0000.000
38A290GLY0-0.045-0.01414.965-0.037-0.0370.0000.0000.0000.000
39A291CYS0-0.0010.01513.6580.1730.1730.0000.0000.0000.000
40A292GLY00.0780.03910.7960.1360.1360.0000.0000.0000.000
41A293ARG10.7960.8948.692-24.361-24.3610.0000.0000.0000.000
42A294GLY00.0360.00410.885-0.789-0.7890.0000.0000.0000.000
43A295GLU-1-0.852-0.95312.95820.38920.3890.0000.0000.0000.000
44A296PHE00.0280.00516.260-1.075-1.0750.0000.0000.0000.000
45A297LEU00.0090.01116.168-0.683-0.6830.0000.0000.0000.000
46A298GLU-1-0.837-0.90616.67316.03216.0320.0000.0000.0000.000
47A299LEU00.0110.00319.385-0.690-0.6900.0000.0000.0000.000
48A300CYS0-0.057-0.01322.157-0.692-0.6920.0000.0000.0000.000
49A301LYS10.9060.95220.850-14.530-14.5300.0000.0000.0000.000
50A302GLU-1-0.951-0.97522.23512.59812.5980.0000.0000.0000.000
51A303GLU-1-0.964-0.98825.32210.15210.1520.0000.0000.0000.000
52A304GLY0-0.053-0.01227.435-0.427-0.4270.0000.0000.0000.000
53A305ILE0-0.118-0.06026.619-0.378-0.3780.0000.0000.0000.000
54A306GLU-1-0.960-0.97426.13611.74311.7430.0000.0000.0000.000
55A307SER0-0.049-0.05022.655-0.025-0.0250.0000.0000.0000.000
56A308ILE0-0.0110.00520.5510.2170.2170.0000.0000.0000.000
57A309GLY00.0380.01217.653-0.225-0.2250.0000.0000.0000.000
58A310VAL0-0.048-0.00616.8760.2700.2700.0000.0000.0000.000
59A311ASP-1-0.759-0.91311.40525.76025.7600.0000.0000.0000.000
60A312ILE00.0080.01411.8390.1220.1220.0000.0000.0000.000
61A313ASN0-0.0060.0075.2510.5830.5830.0000.0000.0000.000
62A314GLU-1-0.771-0.8948.26625.86525.8650.0000.0000.0000.000
63A315ASP-1-0.868-0.9473.93759.77660.1810.010-0.094-0.3210.000
64A316MET0-0.050-0.0086.126-1.103-1.1030.0000.0000.0000.000
65A317ILE00.0190.0088.315-2.700-2.7000.0000.0000.0000.000
66A318LYS10.9230.9727.819-35.108-35.1080.0000.0000.0000.000
67A319PHE0-0.075-0.0256.928-2.111-2.1110.0000.0000.0000.000
68A320CYS0-0.071-0.0279.522-2.515-2.5150.0000.0000.0000.000
69A321GLU-1-0.956-0.97912.82720.19320.1930.0000.0000.0000.000
70A322GLY00.0060.02114.419-1.155-1.1550.0000.0000.0000.000
71A323LYS10.8730.94313.854-20.489-20.4890.0000.0000.0000.000
72A324PHE00.005-0.01114.877-1.171-1.1710.0000.0000.0000.000
73A325ASN00.0460.04418.2380.6310.6310.0000.0000.0000.000
74A326VAL00.0120.00514.382-0.156-0.1560.0000.0000.0000.000
75A327VAL0-0.026-0.00717.439-0.115-0.1150.0000.0000.0000.000
76A328LYS10.8790.92811.795-24.827-24.8270.0000.0000.0000.000
77A329SER0-0.022-0.03415.096-1.178-1.1780.0000.0000.0000.000
78A330ASP-1-0.780-0.87216.56716.10116.1010.0000.0000.0000.000
79A331ALA00.0340.01618.547-0.641-0.6410.0000.0000.0000.000
80A332ILE00.0260.02120.464-0.519-0.5190.0000.0000.0000.000
81A333GLU-1-0.868-0.95121.89211.92811.9280.0000.0000.0000.000
82A334TYR00.0210.00621.046-0.584-0.5840.0000.0000.0000.000
83A335LEU00.0000.00423.087-0.520-0.5200.0000.0000.0000.000
84A336LYS10.8750.94625.846-12.142-12.1420.0000.0000.0000.000
85A337SER0-0.142-0.05925.452-0.385-0.3850.0000.0000.0000.000
86A338LEU0-0.0090.00425.654-0.146-0.1460.0000.0000.0000.000
87A339PRO00.0080.00629.211-0.277-0.2770.0000.0000.0000.000
88A340ASP-1-0.808-0.92732.2959.2429.2420.0000.0000.0000.000
89A341LYS10.8260.90034.576-8.252-8.2520.0000.0000.0000.000
90A342TYR0-0.0110.00828.055-0.252-0.2520.0000.0000.0000.000
91A343LEU0-0.021-0.01626.376-0.099-0.0990.0000.0000.0000.000
92A344ASP-1-0.921-0.96229.6279.3559.3550.0000.0000.0000.000
93A345GLY00.0740.02428.892-0.269-0.2690.0000.0000.0000.000
94A346VAL0-0.026-0.00624.6010.2800.2800.0000.0000.0000.000
95A347MET0-0.0210.01221.491-0.507-0.5070.0000.0000.0000.000
96A348ILE0-0.025-0.01720.8820.4910.4910.0000.0000.0000.000
97A349SER00.029-0.00518.837-0.298-0.2980.0000.0000.0000.000
98A350HIS00.031-0.00816.8180.9870.9870.0000.0000.0000.000
99A351PHE00.0400.02216.3191.0071.0070.0000.0000.0000.000
100A352VAL00.0340.00017.9870.2310.2310.0000.0000.0000.000
101A353GLU-1-0.796-0.88517.98215.85515.8550.0000.0000.0000.000
102A354HIS10.8450.92213.716-20.927-20.9270.0000.0000.0000.000
103A355LEU0-0.053-0.02517.2030.6290.6290.0000.0000.0000.000
104A356ASP-1-0.912-0.93919.78112.97512.9750.0000.0000.0000.000
105A357PRO0-0.001-0.01022.188-0.265-0.2650.0000.0000.0000.000
106A358GLU-1-0.897-0.95825.26311.72811.7280.0000.0000.0000.000
107A359ARG10.8240.90720.577-14.437-14.4370.0000.0000.0000.000
108A360LEU00.0190.01024.7560.0930.0930.0000.0000.0000.000
109A361PHE00.007-0.01026.596-0.117-0.1170.0000.0000.0000.000
110A362GLU-1-0.851-0.94927.52611.23511.2350.0000.0000.0000.000
111A363LEU00.0290.02422.572-0.076-0.0760.0000.0000.0000.000
112A364LEU00.0520.01226.402-0.081-0.0810.0000.0000.0000.000
113A365SER0-0.0080.00828.834-0.392-0.3920.0000.0000.0000.000
114A366LEU0-0.026-0.01426.810-0.278-0.2780.0000.0000.0000.000
115A367CYS0-0.021-0.01126.690-0.022-0.0220.0000.0000.0000.000
116A368TYR0-0.019-0.01229.188-0.301-0.3010.0000.0000.0000.000
117A369SER0-0.043-0.01332.792-0.313-0.3130.0000.0000.0000.000
118A370LYS10.7950.90129.047-10.275-10.2750.0000.0000.0000.000
119A371MET0-0.0230.02630.2250.1680.1680.0000.0000.0000.000
120A372LYS10.9561.00732.536-8.788-8.7880.0000.0000.0000.000
121A373TYR0-0.003-0.01435.5440.0510.0510.0000.0000.0000.000
122A374SER0-0.131-0.09737.579-0.043-0.0430.0000.0000.0000.000
123A375SER00.0770.04632.416-0.008-0.0080.0000.0000.0000.000
124A376TYR00.0260.00231.559-0.293-0.2930.0000.0000.0000.000
125A377ILE0-0.0160.00427.0520.2590.2590.0000.0000.0000.000
126A378VAL0-0.009-0.01425.980-0.327-0.3270.0000.0000.0000.000
127A379ILE00.016-0.00523.9650.4900.4900.0000.0000.0000.000
128A380GLU-1-0.934-0.95221.16813.35813.3580.0000.0000.0000.000
129A381SER00.0000.00421.6570.6160.6160.0000.0000.0000.000
130A382PRO00.0550.03920.047-0.605-0.6050.0000.0000.0000.000
131A383ASN0-0.0060.00823.043-0.472-0.4720.0000.0000.0000.000
132A384PRO0-0.040-0.02326.303-0.032-0.0320.0000.0000.0000.000
133A385THR0-0.111-0.09427.826-0.362-0.3620.0000.0000.0000.000
134A386SER00.0320.03229.263-0.490-0.4900.0000.0000.0000.000
135A387LEU0-0.005-0.00828.8400.3960.3960.0000.0000.0000.000
136A388TYR00.0460.01623.9180.5120.5120.0000.0000.0000.000
137A389SER00.0470.01824.2030.4290.4290.0000.0000.0000.000
138A390LEU0-0.030-0.00623.9380.5630.5630.0000.0000.0000.000
139A391ILE0-0.043-0.02124.0280.3880.3880.0000.0000.0000.000
140A392ASN0-0.001-0.01420.4800.7520.7520.0000.0000.0000.000
141A393PHE0-0.0120.01419.8180.8760.8760.0000.0000.0000.000
142A394TYR0-0.026-0.02819.5670.5600.5600.0000.0000.0000.000
143A395ILE0-0.0190.01615.2030.3690.3690.0000.0000.0000.000
144A396ASP-1-0.805-0.87113.33625.09925.0990.0000.0000.0000.000
145A397PRO00.009-0.01413.058-0.866-0.8660.0000.0000.0000.000
146A398THR0-0.112-0.07310.959-0.327-0.3270.0000.0000.0000.000
147A399HIS0-0.060-0.03214.310-0.018-0.0180.0000.0000.0000.000
148A400LYS10.8920.95517.268-17.203-17.2030.0000.0000.0000.000
149A401LYS10.9180.95820.453-12.141-12.1410.0000.0000.0000.000
150A402PRO00.0200.01123.3280.1740.1740.0000.0000.0000.000
151A403VAL00.0360.02523.274-0.426-0.4260.0000.0000.0000.000
152A404HIS00.0190.02225.9320.0830.0830.0000.0000.0000.000
153A405PRO00.0660.02129.328-0.035-0.0350.0000.0000.0000.000
154A406GLU-1-0.898-0.96630.6648.5278.5270.0000.0000.0000.000
155A407THR0-0.061-0.02129.414-0.271-0.2710.0000.0000.0000.000
156A408LEU00.0240.01426.357-0.101-0.1010.0000.0000.0000.000
157A409LYS10.9620.96930.715-8.384-8.3840.0000.0000.0000.000
158A410PHE0-0.0060.00433.987-0.213-0.2130.0000.0000.0000.000
159A411ILE00.0280.01430.426-0.196-0.1960.0000.0000.0000.000
160A412LEU00.007-0.00530.435-0.193-0.1930.0000.0000.0000.000
161A413GLU-1-0.932-0.96533.8587.9997.9990.0000.0000.0000.000
162A414TYR0-0.073-0.03236.801-0.293-0.2930.0000.0000.0000.000
163A415LEU0-0.064-0.02532.237-0.139-0.1390.0000.0000.0000.000
164A416GLY00.0040.01536.726-0.081-0.0810.0000.0000.0000.000
165A417PHE0-0.082-0.02931.740-0.150-0.1500.0000.0000.0000.000
166A418ARG10.9290.96036.920-7.883-7.8830.0000.0000.0000.000
167A419ASP-1-0.923-0.98637.3168.1388.1380.0000.0000.0000.000
168A420VAL0-0.017-0.00534.1310.1220.1220.0000.0000.0000.000
169A421LYS10.8780.96234.766-8.964-8.9640.0000.0000.0000.000
170A422ILE00.004-0.01231.6280.2920.2920.0000.0000.0000.000
171A423GLU-1-0.935-0.97030.7789.2059.2050.0000.0000.0000.000
172A424PHE00.0080.00329.5920.2960.2960.0000.0000.0000.000
173A425PHE0-0.029-0.02826.395-0.294-0.2940.0000.0000.0000.000
174A426GLU-1-0.797-0.90022.52512.57412.5740.0000.0000.0000.000
175A427GLU-1-0.793-0.83525.9459.3829.3820.0000.0000.0000.000
176A428CYS00.0020.01927.1070.2660.2660.0000.0000.0000.000
177A429GLU-1-0.917-0.96325.56610.87310.8730.0000.0000.0000.000
178A430GLU-1-0.933-0.99328.9078.6928.6920.0000.0000.0000.000
179A431LEU00.000-0.00229.706-0.136-0.1360.0000.0000.0000.000
180A432THR0-0.077-0.01828.2670.0840.0840.0000.0000.0000.000
181A433LYS10.7680.88530.656-9.359-9.3590.0000.0000.0000.000
182A434LEU00.006-0.00133.565-0.141-0.1410.0000.0000.0000.000
183A435ALA00.0450.01737.0070.0100.0100.0000.0000.0000.000
184A436LYS10.8740.93339.409-7.480-7.4800.0000.0000.0000.000
185A437ILE0-0.014-0.01042.715-0.008-0.0080.0000.0000.0000.000
186A438ASP-1-0.867-0.91746.0296.5926.5920.0000.0000.0000.000
187A439SER0-0.009-0.04248.888-0.054-0.0540.0000.0000.0000.000
188A440ASN00.0060.01152.316-0.036-0.0360.0000.0000.0000.000
189A441THR0-0.032-0.01355.556-0.082-0.0820.0000.0000.0000.000
190A442VAL0-0.022-0.00453.225-0.079-0.0790.0000.0000.0000.000
191A443SER0-0.005-0.00155.6870.0360.0360.0000.0000.0000.000
192A444GLU-1-0.830-0.91854.6395.6435.6430.0000.0000.0000.000
193A445GLU-1-0.883-0.94753.7185.6175.6170.0000.0000.0000.000
194A446VAL0-0.048-0.02052.6380.0940.0940.0000.0000.0000.000
195A447ILE0-0.001-0.00949.5170.1470.1470.0000.0000.0000.000
196A448ARG10.9110.95449.327-5.890-5.8900.0000.0000.0000.000
197A449VAL0-0.007-0.00648.9890.1330.1330.0000.0000.0000.000
198A450ILE00.0120.01246.2830.1520.1520.0000.0000.0000.000
199A451ASN00.0470.01044.8230.3320.3320.0000.0000.0000.000
200A452GLU-1-0.910-0.95544.0376.6176.6170.0000.0000.0000.000
201A453ASN0-0.041-0.02744.0080.1560.1560.0000.0000.0000.000
202A454ILE00.0180.01739.9460.1890.1890.0000.0000.0000.000
203A455GLU-1-0.937-0.96039.3428.1798.1790.0000.0000.0000.000
204A456LYS10.9310.95639.193-6.788-6.7880.0000.0000.0000.000
205A457LEU00.0020.00238.3120.1950.1950.0000.0000.0000.000
206A458ASN00.0330.00935.4380.4290.4290.0000.0000.0000.000
207A459ARG10.7820.89534.356-8.528-8.5280.0000.0000.0000.000
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