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: LN999

Calculation Name: 3L9D-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3L9D

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8DU97

Base Structure: X-ray

Registration Date: 2023-09-23

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2416031.436526
FMO2-HF: Nuclear repulsion 2332586.701756
FMO2-HF: Total energy -83444.734771
FMO2-MP2: Total energy -83688.051432


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-13.726-4.07510.207-4.201-15.658-0.028
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.003
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].
3A3TRP00.041-0.0192.616-4.4531.7605.045-2.676-8.582-0.015
4A4GLU-1-0.942-0.9614.210-1.047-1.2250.0300.387-0.2380.000
5A5GLU-1-0.866-0.9196.5870.2140.2140.0000.0000.0000.000
6A6PHE0-0.009-0.0082.565-3.625-2.4722.995-0.896-3.253-0.011
7A7LEU0-0.010-0.0324.529-0.323-0.196-0.001-0.014-0.1130.000
8A8ASP-1-0.883-0.9186.799-0.208-0.2080.0000.0000.0000.000
9A9PRO00.0600.0258.0700.0290.0290.0000.0000.0000.000
10A10TYR00.009-0.0075.9710.2180.2180.0000.0000.0000.000
11A11ILE0-0.032-0.02510.6010.0580.0580.0000.0000.0000.000
12A12GLN0-0.018-0.01712.7680.0380.0380.0000.0000.0000.000
13A13ALA00.0290.02813.7230.0280.0280.0000.0000.0000.000
14A14VAL0-0.016-0.01614.0030.0350.0350.0000.0000.0000.000
15A15GLY0-0.038-0.01316.3110.0260.0260.0000.0000.0000.000
16A16GLU-1-0.805-0.89518.041-0.167-0.1670.0000.0000.0000.000
17A17LEU00.008-0.00717.1010.0210.0210.0000.0000.0000.000
18A18LYS10.8520.94118.8690.2420.2420.0000.0000.0000.000
19A19ILE0-0.026-0.01022.7000.0150.0150.0000.0000.0000.000
20A20LYS10.8590.93220.9450.1570.1570.0000.0000.0000.000
21A21PHE00.0470.02621.5360.0100.0100.0000.0000.0000.000
22A22ARG10.8770.92125.2910.1490.1490.0000.0000.0000.000
23A23GLY00.0150.00228.4780.0080.0080.0000.0000.0000.000
24A24ILE00.0150.02828.5470.0070.0070.0000.0000.0000.000
25A25ARG10.8410.91731.6990.0900.0900.0000.0000.0000.000
26A26LYS10.9220.95331.8820.0920.0920.0000.0000.0000.000
27A27GLN0-0.045-0.02632.3600.0080.0080.0000.0000.0000.000
28A28PHE00.0350.01234.6130.0040.0040.0000.0000.0000.000
29A29ARG10.8930.96137.2460.0690.0690.0000.0000.0000.000
30A30LYS10.9170.96638.4740.0620.0620.0000.0000.0000.000
31A31GLN0-0.0100.00439.8810.0020.0020.0000.0000.0000.000
32A32LYS10.8510.92142.5800.0480.0480.0000.0000.0000.000
33A33ARG10.9350.97938.9770.0580.0580.0000.0000.0000.000
34A34HIS00.0480.00937.6990.0000.0000.0000.0000.0000.000
35A35SER0-0.066-0.05234.441-0.001-0.0010.0000.0000.0000.000
36A36PRO0-0.0060.01233.601-0.002-0.0020.0000.0000.0000.000
37A37ILE0-0.0150.00828.352-0.004-0.0040.0000.0000.0000.000
38A38GLU-1-0.751-0.85132.040-0.075-0.0750.0000.0000.0000.000
39A39PHE0-0.053-0.04327.9880.0000.0000.0000.0000.0000.000
40A40VAL00.0320.02623.560-0.003-0.0030.0000.0000.0000.000
41A41THR0-0.045-0.01523.029-0.001-0.0010.0000.0000.0000.000
42A42GLY00.0900.03119.163-0.001-0.0010.0000.0000.0000.000
43A43ARG10.8810.93715.4890.3230.3230.0000.0000.0000.000
44A44VAL00.0900.0629.4060.0010.0010.0000.0000.0000.000
45A45LYS10.7960.9119.8250.5780.5780.0000.0000.0000.000
46A46PRO0-0.005-0.0139.811-0.059-0.0590.0000.0000.0000.000
47A47ILE00.1010.0505.976-0.053-0.0530.0000.0000.0000.000
48A48GLU-1-0.795-0.8957.556-0.663-0.6630.0000.0000.0000.000
49A49SER0-0.032-0.02110.2570.0580.0580.0000.0000.0000.000
50A50ILE00.0020.0004.666-0.0340.043-0.001-0.002-0.0740.000
51A51LYS10.8830.9255.3500.8000.8000.0000.0000.0000.000
52A52GLU-1-0.770-0.8667.706-0.094-0.0940.0000.0000.0000.000
53A53LYS10.7960.87510.4230.3100.3100.0000.0000.0000.000
54A54MET0-0.0230.0064.564-0.470-0.305-0.001-0.023-0.1400.000
55A55VAL00.0040.0039.1340.1160.1160.0000.0000.0000.000
56A56LEU0-0.013-0.01911.9050.0360.0360.0000.0000.0000.000
57A57ARG10.7840.87612.0240.3590.3590.0000.0000.0000.000
58A58GLY00.0330.03512.8960.0180.0180.0000.0000.0000.000
59A59ILE0-0.0120.0097.6550.0810.0810.0000.0000.0000.000
60A60LYS10.9130.9457.943-0.237-0.2370.0000.0000.0000.000
61A61LYS10.8980.9192.429-5.730-4.4691.078-0.463-1.8760.001
62A62GLU-1-0.799-0.9003.459-0.0010.6660.026-0.322-0.372-0.002
63A63ASN0-0.040-0.0295.888-0.015-0.0150.0000.0000.0000.000
64A64LEU0-0.032-0.0162.557-0.435-0.2691.036-0.192-1.010-0.001
65A65THR0-0.004-0.0096.4200.0260.0260.0000.0000.0000.000
66A66GLN0-0.064-0.0318.2330.1430.1430.0000.0000.0000.000
67A67ASP-1-0.773-0.86010.090-0.106-0.1060.0000.0000.0000.000
68A68MET0-0.130-0.0618.0910.0030.0030.0000.0000.0000.000
69A69GLN00.038-0.00210.440-0.048-0.0480.0000.0000.0000.000
70A70ASP-1-0.734-0.83112.145-0.424-0.4240.0000.0000.0000.000
71A71ILE00.0020.0126.2680.0120.0120.0000.0000.0000.000
72A72ALA00.0280.01910.0070.0400.0400.0000.0000.0000.000
73A73GLY00.0230.01612.6580.0240.0240.0000.0000.0000.000
74A74LEU0-0.037-0.04115.9660.0130.0130.0000.0000.0000.000
75A75ARG10.8770.93819.5430.1850.1850.0000.0000.0000.000
76A76ILE00.0030.00623.0590.0040.0040.0000.0000.0000.000
77A77MET0-0.031-0.00125.5660.0000.0000.0000.0000.0000.000
78A78VAL00.010-0.00429.2780.0020.0020.0000.0000.0000.000
79A79GLN0-0.021-0.02432.6090.0020.0020.0000.0000.0000.000
80A80PHE00.0340.01936.1730.0020.0020.0000.0000.0000.000
81A81VAL00.016-0.00435.179-0.004-0.0040.0000.0000.0000.000
82A82ASP-1-0.764-0.83435.351-0.060-0.0600.0000.0000.0000.000
83A83ASP-1-0.704-0.83934.976-0.071-0.0710.0000.0000.0000.000
84A84VAL0-0.007-0.01230.060-0.004-0.0040.0000.0000.0000.000
85A85ASN0-0.003-0.00931.478-0.005-0.0050.0000.0000.0000.000
86A86ASP-1-0.859-0.92133.447-0.067-0.0670.0000.0000.0000.000
87A87VAL0-0.072-0.04928.288-0.002-0.0020.0000.0000.0000.000
88A88LEU0-0.0050.00627.732-0.006-0.0060.0000.0000.0000.000
89A89GLU-1-0.837-0.90829.465-0.072-0.0720.0000.0000.0000.000
90A90LEU0-0.072-0.04330.8990.0000.0000.0000.0000.0000.000
91A91LEU0-0.052-0.03524.605-0.004-0.0040.0000.0000.0000.000
92A92ARG10.8080.86926.8150.0780.0780.0000.0000.0000.000
93A93GLN0-0.050-0.01228.6110.0040.0040.0000.0000.0000.000
94A94ARG10.7620.85725.4920.1210.1210.0000.0000.0000.000
95A95LYS10.9670.96226.5360.0720.0720.0000.0000.0000.000
96A96ASP-1-0.789-0.84923.811-0.122-0.1220.0000.0000.0000.000
97A97MET0-0.0190.00120.924-0.017-0.0170.0000.0000.0000.000
98A98LYS10.8520.94221.1740.1270.1270.0000.0000.0000.000
99A99VAL00.0250.01921.212-0.017-0.0170.0000.0000.0000.000
100A100ILE0-0.029-0.01717.0930.0120.0120.0000.0000.0000.000
101A101GLN0-0.0060.00619.0010.0230.0230.0000.0000.0000.000
102A102GLU-1-0.762-0.82822.704-0.106-0.1060.0000.0000.0000.000
103A103ARG10.8550.91419.4160.1570.1570.0000.0000.0000.000
104A104ASP-1-0.746-0.84425.777-0.086-0.0860.0000.0000.0000.000
105A105TYR0-0.018-0.01623.770-0.002-0.0020.0000.0000.0000.000
106A106ILE0-0.020-0.01929.2410.0010.0010.0000.0000.0000.000
107A107ASN0-0.013-0.03332.2390.0070.0070.0000.0000.0000.000
108A108ASN0-0.060-0.00530.8610.0090.0090.0000.0000.0000.000
109A109LEU00.053-0.01733.641-0.003-0.0030.0000.0000.0000.000
110A110LYS10.7960.91833.8200.0660.0660.0000.0000.0000.000
111A111PRO00.0360.03336.895-0.004-0.0040.0000.0000.0000.000
112A112SER0-0.033-0.01536.2450.0020.0020.0000.0000.0000.000
113A113GLY00.0260.00632.3440.0000.0000.0000.0000.0000.000
114A114TYR0-0.022-0.04423.459-0.002-0.0020.0000.0000.0000.000
115A115ARG10.8060.90329.3530.0750.0750.0000.0000.0000.000
116A116SER0-0.020-0.02624.575-0.004-0.0040.0000.0000.0000.000
117A117TYR00.016-0.01626.8310.0050.0050.0000.0000.0000.000
118A118HIS0-0.045-0.02620.4540.0060.0060.0000.0000.0000.000
119A119VAL00.0370.01222.4150.0120.0120.0000.0000.0000.000
120A120ILE0-0.0150.00016.683-0.016-0.0160.0000.0000.0000.000
121A121VAL0-0.005-0.01518.1570.0260.0260.0000.0000.0000.000
122A122GLU-1-0.807-0.90816.631-0.180-0.1800.0000.0000.0000.000
123A123TYR0-0.048-0.08015.9150.0340.0340.0000.0000.0000.000
124A124PRO00.0140.01115.648-0.030-0.0300.0000.0000.0000.000
125A125VAL0-0.027-0.00913.1090.0040.0040.0000.0000.0000.000
126A126ASP-1-0.829-0.91415.327-0.104-0.1040.0000.0000.0000.000
127A127THR00.0330.03512.4270.0010.0010.0000.0000.0000.000
128A128ILE00.007-0.01415.6640.0210.0210.0000.0000.0000.000
129A129SER0-0.039-0.01213.4010.0260.0260.0000.0000.0000.000
130A130GLY00.0540.03015.5320.0220.0220.0000.0000.0000.000
131A131GLN0-0.041-0.02915.395-0.023-0.0230.0000.0000.0000.000
132A132ARG10.8160.91210.6770.1060.1060.0000.0000.0000.000
133A133ILE00.0340.02613.448-0.002-0.0020.0000.0000.0000.000
134A134ILE0-0.0190.00110.110-0.059-0.0590.0000.0000.0000.000
135A135MET0-0.0050.01411.6820.0960.0960.0000.0000.0000.000
136A136ALA0-0.018-0.01412.488-0.071-0.0710.0000.0000.0000.000
137A137GLU-1-0.809-0.87715.052-0.195-0.1950.0000.0000.0000.000
138A138ILE0-0.040-0.02317.493-0.006-0.0060.0000.0000.0000.000
139A139GLN0-0.0090.00120.0450.0310.0310.0000.0000.0000.000
140A140ILE0-0.0030.00223.1760.0000.0000.0000.0000.0000.000
141A141ARG10.8050.88723.5950.1530.1530.0000.0000.0000.000
142A142THR00.040-0.02329.029-0.002-0.0020.0000.0000.0000.000
143A143LEU00.015-0.01331.020-0.007-0.0070.0000.0000.0000.000
144A144ALA00.0240.02532.110-0.004-0.0040.0000.0000.0000.000
145A145MET00.0170.03529.768-0.005-0.0050.0000.0000.0000.000
146A146ASN00.0110.00626.020-0.015-0.0150.0000.0000.0000.000
147A147PHE00.0030.02227.795-0.008-0.0080.0000.0000.0000.000
148A148TRP00.0550.02128.382-0.006-0.0060.0000.0000.0000.000
149A149ALA00.0150.01925.813-0.002-0.0020.0000.0000.0000.000
150A150THR0-0.060-0.04924.197-0.021-0.0210.0000.0000.0000.000
151A151ILE00.0140.02225.459-0.005-0.0050.0000.0000.0000.000
152A152GLU-1-0.841-0.91925.657-0.123-0.1230.0000.0000.0000.000
153A153HIS00.0270.01918.3490.0050.0050.0000.0000.0000.000
154A154SER0-0.043-0.03722.714-0.010-0.0100.0000.0000.0000.000
155A155LEU0-0.036-0.01924.1320.0020.0020.0000.0000.0000.000
156A156ASN0-0.066-0.04123.0760.0030.0030.0000.0000.0000.000
157A157TYR00.0170.00317.1980.0020.0020.0000.0000.0000.000
158A158LYS10.8860.95121.7410.0910.0910.0000.0000.0000.000
159A159TYR0-0.017-0.02424.6330.0070.0070.0000.0000.0000.000
160A160HIS00.0400.03120.3790.0030.0030.0000.0000.0000.000
161A161GLY00.0150.01823.2980.0050.0050.0000.0000.0000.000
162A162GLU-1-0.961-0.96425.444-0.045-0.0450.0000.0000.0000.000
163A163PHE0-0.075-0.05426.9780.0020.0020.0000.0000.0000.000
164A164PRO00.0200.01030.6250.0050.0050.0000.0000.0000.000
165A165GLU-1-0.746-0.85434.064-0.047-0.0470.0000.0000.0000.000
166A166ASP-1-0.800-0.87737.072-0.052-0.0520.0000.0000.0000.000
167A167ILE00.0360.01431.245-0.001-0.0010.0000.0000.0000.000
168A168LYS10.9010.94933.2500.0460.0460.0000.0000.0000.000
169A169ARG10.8520.90634.2280.0420.0420.0000.0000.0000.000
170A170ARG10.8660.92435.6110.0550.0550.0000.0000.0000.000
171A171LEU00.0270.03329.953-0.002-0.0020.0000.0000.0000.000
172A172GLU-1-0.822-0.90733.891-0.053-0.0530.0000.0000.0000.000
173A173LEU0-0.0090.01035.7480.0010.0010.0000.0000.0000.000
174A174THR0-0.012-0.03234.9950.0000.0000.0000.0000.0000.000
175A175SER0-0.054-0.01433.698-0.001-0.0010.0000.0000.0000.000
176A176LYS10.8680.92035.2250.0540.0540.0000.0000.0000.000
177A177ILE0-0.0080.00238.8080.0010.0010.0000.0000.0000.000
178A178ALA0-0.004-0.00734.8780.0000.0000.0000.0000.0000.000
179A179PHE00.0280.01436.2140.0000.0000.0000.0000.0000.000
180A180GLN00.011-0.01037.8320.0030.0030.0000.0000.0000.000
181A181LEU0-0.0140.01038.0550.0010.0010.0000.0000.0000.000
182A182ASP-1-0.760-0.85535.369-0.079-0.0790.0000.0000.0000.000
183A183GLU-1-0.820-0.91338.824-0.061-0.0610.0000.0000.0000.000
184A184GLU-1-0.845-0.90441.460-0.042-0.0420.0000.0000.0000.000
185A185MET0-0.030-0.00941.0870.0010.0010.0000.0000.0000.000
186A186ARG10.7520.82839.3990.0580.0580.0000.0000.0000.000
187A187GLN0-0.071-0.03942.5270.0020.0020.0000.0000.0000.000
188A188ILE00.0200.01645.8300.0020.0020.0000.0000.0000.000
189A189ARG10.8140.87941.4300.0520.0520.0000.0000.0000.000
190A190ASP-1-0.896-0.94044.253-0.050-0.0500.0000.0000.0000.000
191A191ASP-1-0.877-0.92446.411-0.042-0.0420.0000.0000.0000.000
192A192ILE00.0350.01643.424-0.001-0.0010.0000.0000.0000.000
193A193LYS10.7670.88039.5510.0600.0600.0000.0000.0000.000
194A194GLU-1-0.930-0.96644.648-0.040-0.0400.0000.0000.0000.000
195A195ALA00.0250.00548.0790.0000.0000.0000.0000.0000.000
196A196GLN0-0.081-0.04941.491-0.003-0.0030.0000.0000.0000.000
197A197LEU0-0.046-0.02742.897-0.001-0.0010.0000.0000.0000.000
198A198LEU00.0390.03346.2760.0010.0010.0000.0000.0000.000
199A199PHE00.0110.01542.1900.0000.0000.0000.0000.0000.000