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: 3J88L

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2410519.197316
FMO2-HF: Nuclear repulsion 2327075.079704
FMO2-HF: Total energy -83444.117613
FMO2-MP2: Total energy -83687.4159


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.
-12.907-2.9847.509-3.921-13.511-0.025
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 : -0.021 / q_NPA : -0.013
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].
3A3TRP00.036-0.0182.762-4.3292.2672.802-2.431-6.968-0.015
4A4GLU-1-0.935-0.9634.605-0.950-0.8930.0080.082-0.1470.000
5A5GLU-1-0.866-0.9136.3890.3680.3680.0000.0000.0000.000
6A6PHE0-0.005-0.0072.676-3.132-1.6631.839-0.718-2.591-0.009
7A7LEU0-0.007-0.0404.522-0.284-0.170-0.001-0.015-0.0970.000
8A8ASP-1-0.905-0.9306.941-0.158-0.1580.0000.0000.0000.000
9A9PRO00.0680.0258.2380.0160.0160.0000.0000.0000.000
10A10TYR0-0.018-0.0216.2930.1370.1370.0000.0000.0000.000
11A11ILE0-0.022-0.02311.0790.0370.0370.0000.0000.0000.000
12A12GLN0-0.0180.00013.1780.0230.0230.0000.0000.0000.000
13A13ALA00.0440.03114.0390.0200.0200.0000.0000.0000.000
14A14VAL0-0.018-0.01614.6730.0240.0240.0000.0000.0000.000
15A15GLY0-0.0180.00017.0240.0180.0180.0000.0000.0000.000
16A16GLU-1-0.808-0.89818.333-0.114-0.1140.0000.0000.0000.000
17A17LEU00.0020.00217.5100.0140.0140.0000.0000.0000.000
18A18LYS10.8590.94819.8190.1770.1770.0000.0000.0000.000
19A19ILE0-0.027-0.01722.9310.0100.0100.0000.0000.0000.000
20A20LYS10.8460.92921.5490.1040.1040.0000.0000.0000.000
21A21PHE00.037-0.00321.6590.0090.0090.0000.0000.0000.000
22A22ARG10.8590.92325.5670.1140.1140.0000.0000.0000.000
23A23GLY00.009-0.00328.8810.0050.0050.0000.0000.0000.000
24A24ILE00.0300.03328.5850.0050.0050.0000.0000.0000.000
25A25ARG10.8370.92231.9400.0680.0680.0000.0000.0000.000
26A26LYS10.9160.95032.1450.0700.0700.0000.0000.0000.000
27A27GLN0-0.043-0.02332.6420.0060.0060.0000.0000.0000.000
28A28PHE00.0280.02034.8340.0030.0030.0000.0000.0000.000
29A29ARG10.9120.96237.6480.0520.0520.0000.0000.0000.000
30A30LYS10.9400.97738.7600.0450.0450.0000.0000.0000.000
31A31GLN0-0.033-0.00239.8500.0020.0020.0000.0000.0000.000
32A32LYS10.9140.96142.8800.0360.0360.0000.0000.0000.000
33A33ARG10.9400.97539.6960.0400.0400.0000.0000.0000.000
34A34HIS00.0730.03238.3020.0000.0000.0000.0000.0000.000
35A35SER0-0.061-0.04434.9370.0000.0000.0000.0000.0000.000
36A36PRO00.0180.02133.842-0.001-0.0010.0000.0000.0000.000
37A37ILE00.0010.01128.876-0.003-0.0030.0000.0000.0000.000
38A38GLU-1-0.805-0.89732.274-0.057-0.0570.0000.0000.0000.000
39A39PHE0-0.055-0.04428.365-0.001-0.0010.0000.0000.0000.000
40A40VAL00.0320.02724.106-0.002-0.0020.0000.0000.0000.000
41A41THR0-0.027-0.00423.416-0.004-0.0040.0000.0000.0000.000
42A42GLY00.0660.01519.8420.0010.0010.0000.0000.0000.000
43A43ARG10.8900.94616.1440.2510.2510.0000.0000.0000.000
44A44VAL00.0830.05810.1090.0020.0020.0000.0000.0000.000
45A45LYS10.7770.90210.3620.3780.3780.0000.0000.0000.000
46A46PRO00.010-0.01210.128-0.042-0.0420.0000.0000.0000.000
47A47ILE00.0920.0356.149-0.024-0.0240.0000.0000.0000.000
48A48GLU-1-0.790-0.8957.949-0.625-0.6250.0000.0000.0000.000
49A49SER0-0.045-0.02110.4460.0540.0540.0000.0000.0000.000
50A50ILE00.000-0.0065.0960.0500.0500.0000.0000.0000.000
51A51LYS10.9060.9485.5970.8120.8120.0000.0000.0000.000
52A52GLU-1-0.872-0.9237.893-0.034-0.0340.0000.0000.0000.000
53A53LYS10.9080.94510.5970.2440.2440.0000.0000.0000.000
54A54MET0-0.0390.0074.432-0.367-0.218-0.001-0.015-0.1330.000
55A55VAL00.0100.0039.4540.1100.1100.0000.0000.0000.000
56A56LEU0-0.027-0.02011.8400.0300.0300.0000.0000.0000.000
57A57ARG10.7860.87111.6310.2530.2530.0000.0000.0000.000
58A58GLY00.0410.03812.7960.0200.0200.0000.0000.0000.000
59A59ILE0-0.0200.0047.6940.0480.0480.0000.0000.0000.000
60A60LYS10.9170.9437.882-0.363-0.3630.0000.0000.0000.000
61A61LYS10.9230.9322.345-6.475-5.2731.570-0.513-2.2590.001
62A62GLU-1-0.825-0.9133.8411.0791.4070.004-0.099-0.232-0.001
63A63ASN0-0.051-0.0295.980-0.056-0.0560.0000.0000.0000.000
64A64LEU0-0.010-0.0082.459-0.436-0.4281.288-0.212-1.084-0.001
65A65THR0-0.010-0.0066.388-0.030-0.0300.0000.0000.0000.000
66A66GLN0-0.065-0.0377.9630.1050.1050.0000.0000.0000.000
67A67ASP-1-0.761-0.8559.8970.0220.0220.0000.0000.0000.000
68A68MET0-0.133-0.0608.0980.0100.0100.0000.0000.0000.000
69A69GLN00.0500.01210.503-0.012-0.0120.0000.0000.0000.000
70A70ASP-1-0.722-0.83912.504-0.298-0.2980.0000.0000.0000.000
71A71ILE00.0090.0196.7050.0120.0120.0000.0000.0000.000
72A72ALA00.0350.02310.6120.0340.0340.0000.0000.0000.000
73A73GLY00.0340.02913.3210.0170.0170.0000.0000.0000.000
74A74LEU0-0.061-0.06116.4400.0090.0090.0000.0000.0000.000
75A75ARG10.9090.96520.0510.1460.1460.0000.0000.0000.000
76A76ILE00.0010.00123.3890.0020.0020.0000.0000.0000.000
77A77MET0-0.029-0.00625.8100.0010.0010.0000.0000.0000.000
78A78VAL00.0270.00629.5940.0020.0020.0000.0000.0000.000
79A79GLN00.014-0.00432.7980.0000.0000.0000.0000.0000.000
80A80PHE00.0150.00636.2990.0010.0010.0000.0000.0000.000
81A81VAL00.0350.01235.252-0.002-0.0020.0000.0000.0000.000
82A82ASP-1-0.760-0.85135.498-0.041-0.0410.0000.0000.0000.000
83A83ASP-1-0.782-0.88535.205-0.050-0.0500.0000.0000.0000.000
84A84VAL0-0.005-0.01130.334-0.003-0.0030.0000.0000.0000.000
85A85ASN00.0370.00831.947-0.004-0.0040.0000.0000.0000.000
86A86ASP-1-0.883-0.92333.879-0.044-0.0440.0000.0000.0000.000
87A87VAL0-0.079-0.05628.727-0.002-0.0020.0000.0000.0000.000
88A88LEU0-0.028-0.00828.001-0.004-0.0040.0000.0000.0000.000
89A89GLU-1-0.848-0.92430.172-0.042-0.0420.0000.0000.0000.000
90A90LEU0-0.071-0.03731.0980.0000.0000.0000.0000.0000.000
91A91LEU0-0.031-0.03125.149-0.002-0.0020.0000.0000.0000.000
92A92ARG10.8150.88327.0360.0470.0470.0000.0000.0000.000
93A93GLN0-0.045-0.00428.8100.0040.0040.0000.0000.0000.000
94A94ARG10.7800.86925.7310.0790.0790.0000.0000.0000.000
95A95LYS10.9790.96927.0490.0370.0370.0000.0000.0000.000
96A96ASP-1-0.796-0.84923.775-0.080-0.0800.0000.0000.0000.000
97A97MET0-0.0130.00221.006-0.013-0.0130.0000.0000.0000.000
98A98LYS10.9170.97221.1300.0650.0650.0000.0000.0000.000
99A99VAL00.0380.01721.331-0.013-0.0130.0000.0000.0000.000
100A100ILE0-0.032-0.00817.4440.0130.0130.0000.0000.0000.000
101A101GLN0-0.0100.00119.0960.0170.0170.0000.0000.0000.000
102A102GLU-1-0.762-0.83622.783-0.067-0.0670.0000.0000.0000.000
103A103ARG10.8810.93319.7490.0920.0920.0000.0000.0000.000
104A104ASP-1-0.761-0.85825.882-0.056-0.0560.0000.0000.0000.000
105A105TYR0-0.050-0.04323.9530.0010.0010.0000.0000.0000.000
106A106ILE00.000-0.01429.281-0.001-0.0010.0000.0000.0000.000
107A107ASN0-0.022-0.02732.3360.0030.0030.0000.0000.0000.000
108A108ASN0-0.0130.02530.6420.0070.0070.0000.0000.0000.000
109A109LEU0-0.013-0.04633.402-0.002-0.0020.0000.0000.0000.000
110A110LYS10.8200.93633.7650.0420.0420.0000.0000.0000.000
111A111PRO00.0490.03137.007-0.003-0.0030.0000.0000.0000.000
112A112SER0-0.004-0.00736.4860.0010.0010.0000.0000.0000.000
113A113GLY00.0130.01032.6680.0000.0000.0000.0000.0000.000
114A114TYR0-0.029-0.04523.638-0.002-0.0020.0000.0000.0000.000
115A115ARG10.8870.95329.3920.0550.0550.0000.0000.0000.000
116A116SER0-0.047-0.02124.793-0.004-0.0040.0000.0000.0000.000
117A117TYR00.031-0.00426.6360.0050.0050.0000.0000.0000.000
118A118HIS0-0.060-0.03120.4630.0020.0020.0000.0000.0000.000
119A119VAL00.0400.01622.4850.0090.0090.0000.0000.0000.000
120A120ILE0-0.0190.00516.840-0.014-0.0140.0000.0000.0000.000
121A121VAL0-0.013-0.01418.3560.0190.0190.0000.0000.0000.000
122A122GLU-1-0.877-0.93716.474-0.113-0.1130.0000.0000.0000.000
123A123TYR0-0.044-0.08616.0450.0270.0270.0000.0000.0000.000
124A124PRO00.0080.00815.622-0.023-0.0230.0000.0000.0000.000
125A125VAL0-0.026-0.00913.2350.0040.0040.0000.0000.0000.000
126A126ASP-1-0.851-0.92015.337-0.057-0.0570.0000.0000.0000.000
127A127THR00.0100.00012.260-0.003-0.0030.0000.0000.0000.000
128A128ILE00.034-0.00315.6380.0150.0150.0000.0000.0000.000
129A129SER0-0.0240.00313.2970.0210.0210.0000.0000.0000.000
130A130GLY00.0320.02015.6640.0240.0240.0000.0000.0000.000
131A131GLN0-0.039-0.01615.238-0.017-0.0170.0000.0000.0000.000
132A132ARG10.8430.92310.1460.0470.0470.0000.0000.0000.000
133A133ILE00.0390.02613.115-0.009-0.0090.0000.0000.0000.000
134A134ILE0-0.0200.00210.063-0.042-0.0420.0000.0000.0000.000
135A135MET00.0070.01611.7790.0700.0700.0000.0000.0000.000
136A136ALA0-0.045-0.02112.941-0.048-0.0480.0000.0000.0000.000
137A137GLU-1-0.806-0.88715.542-0.139-0.1390.0000.0000.0000.000
138A138ILE0-0.044-0.01717.666-0.004-0.0040.0000.0000.0000.000
139A139GLN0-0.026-0.02319.9640.0210.0210.0000.0000.0000.000
140A140ILE0-0.0050.00323.305-0.001-0.0010.0000.0000.0000.000
141A141ARG10.8560.91123.5470.1140.1140.0000.0000.0000.000
142A142THR00.0610.00529.181-0.002-0.0020.0000.0000.0000.000
143A143LEU00.015-0.00731.236-0.005-0.0050.0000.0000.0000.000
144A144ALA00.0360.02632.180-0.004-0.0040.0000.0000.0000.000
145A145MET00.0140.03929.951-0.004-0.0040.0000.0000.0000.000
146A146ASN00.0160.00826.244-0.011-0.0110.0000.0000.0000.000
147A147PHE0-0.0100.00728.248-0.006-0.0060.0000.0000.0000.000
148A148TRP00.0430.01628.545-0.004-0.0040.0000.0000.0000.000
149A149ALA00.0030.00425.712-0.003-0.0030.0000.0000.0000.000
150A150THR0-0.077-0.05324.986-0.011-0.0110.0000.0000.0000.000
151A151ILE0-0.005-0.00125.780-0.006-0.0060.0000.0000.0000.000
152A152GLU-1-0.873-0.94025.784-0.090-0.0900.0000.0000.0000.000
153A153HIS00.0310.02318.5630.0040.0040.0000.0000.0000.000
154A154SER0-0.046-0.02522.996-0.010-0.0100.0000.0000.0000.000
155A155LEU0-0.050-0.02424.4630.0000.0000.0000.0000.0000.000
156A156ASN0-0.046-0.03823.3220.0000.0000.0000.0000.0000.000
157A157TYR00.0190.00917.2210.0010.0010.0000.0000.0000.000
158A158LYS10.9160.96822.0460.0820.0820.0000.0000.0000.000
159A159TYR0-0.037-0.03824.4400.0030.0030.0000.0000.0000.000
160A160HIS00.0290.02619.9860.0060.0060.0000.0000.0000.000
161A161GLY0-0.0160.00423.4010.0070.0070.0000.0000.0000.000
162A162GLU-1-0.972-0.96825.566-0.031-0.0310.0000.0000.0000.000
163A163PHE0-0.075-0.04427.3970.0000.0000.0000.0000.0000.000
164A164PRO00.0190.00031.1000.0040.0040.0000.0000.0000.000
165A165GLU-1-0.727-0.84434.382-0.034-0.0340.0000.0000.0000.000
166A166ASP-1-0.813-0.89137.476-0.042-0.0420.0000.0000.0000.000
167A167ILE00.0450.01431.688-0.001-0.0010.0000.0000.0000.000
168A168LYS10.9370.97533.7280.0350.0350.0000.0000.0000.000
169A169ARG10.8560.90934.7130.0330.0330.0000.0000.0000.000
170A170ARG10.8760.93536.1420.0460.0460.0000.0000.0000.000
171A171LEU00.0170.01930.373-0.001-0.0010.0000.0000.0000.000
172A172GLU-1-0.839-0.91634.281-0.038-0.0380.0000.0000.0000.000
173A173LEU0-0.0240.01536.1770.0000.0000.0000.0000.0000.000
174A174THR0-0.008-0.03635.2950.0000.0000.0000.0000.0000.000
175A175SER0-0.049-0.02834.0050.0000.0000.0000.0000.0000.000
176A176LYS10.8740.91935.5060.0380.0380.0000.0000.0000.000
177A177ILE0-0.014-0.00338.8960.0010.0010.0000.0000.0000.000
178A178ALA0-0.020-0.01135.0150.0000.0000.0000.0000.0000.000
179A179PHE00.0310.01036.6240.0000.0000.0000.0000.0000.000
180A180GLN00.0150.00438.0940.0020.0020.0000.0000.0000.000
181A181LEU00.0090.02638.5010.0010.0010.0000.0000.0000.000
182A182ASP-1-0.785-0.88235.768-0.056-0.0560.0000.0000.0000.000
183A183GLU-1-0.860-0.93839.390-0.039-0.0390.0000.0000.0000.000
184A184GLU-1-0.906-0.96041.845-0.031-0.0310.0000.0000.0000.000
185A185MET0-0.018-0.00941.6730.0010.0010.0000.0000.0000.000
186A186ARG10.7130.80939.7930.0400.0400.0000.0000.0000.000
187A187GLN0-0.020-0.00342.7460.0020.0020.0000.0000.0000.000
188A188ILE00.0250.02646.3430.0010.0010.0000.0000.0000.000
189A189ARG10.8200.88941.7850.0350.0350.0000.0000.0000.000
190A190ASP-1-0.910-0.96144.912-0.034-0.0340.0000.0000.0000.000
191A191ASP-1-0.885-0.92547.162-0.030-0.0300.0000.0000.0000.000
192A192ILE00.0080.00043.834-0.001-0.0010.0000.0000.0000.000
193A193LYS10.7800.88739.8870.0420.0420.0000.0000.0000.000
194A194GLU-1-0.915-0.95345.228-0.029-0.0290.0000.0000.0000.000
195A195ALA00.0210.01248.4440.0000.0000.0000.0000.0000.000
196A196GLN0-0.024-0.01441.687-0.002-0.0020.0000.0000.0000.000
197A197LEU0-0.090-0.03743.744-0.001-0.0010.0000.0000.0000.000
198A198LEU0-0.0130.00246.8910.0010.0010.0000.0000.0000.000
199A199PHE00.0050.00042.679-0.001-0.0010.0000.0000.0000.000