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

tag_button

FMODB ID: VKQ71

Calculation Name: 3CDL-A-Xray372

Preferred Name:
Warning: Undefined array key "pref_name" in /home/FMODBwui_src/fmodbwui/detail.php on line 446

Target Type:
Warning: Undefined array key "target_type" in /home/FMODBwui_src/fmodbwui/detail.php on line 447

Ligand Name:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

ligand 3-letter code:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

PDB ID: 3CDL

Chain ID: A

ChEMBL ID:
Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

UniProt ID: Q87Z81

Base Structure: X-ray

Registration Date: 2023-09-27

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2168206.801643
FMO2-HF: Nuclear repulsion 2089636.603419
FMO2-HF: Total energy -78570.198224
FMO2-MP2: Total energy -78801.032005


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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-0.4513.459-0.036-1.676-2.199-0.002
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.009
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].
3A5ASP-1-0.907-0.9163.8310.1973.564-0.035-1.610-1.722-0.002
4A6GLN00.005-0.0094.541-0.936-0.710-0.001-0.010-0.2150.000
5A7LYS10.9240.9634.0170.4840.8010.000-0.056-0.2620.000
6A8ARG11.0361.0377.485-0.577-0.5770.0000.0000.0000.000
7A9GLU-1-0.747-0.8579.9020.2690.2690.0000.0000.0000.000
8A10SER0-0.005-0.00110.182-0.093-0.0930.0000.0000.0000.000
9A11ILE0-0.053-0.03210.764-0.060-0.0600.0000.0000.0000.000
10A12VAL00.0010.00513.465-0.025-0.0250.0000.0000.0000.000
11A13GLN00.018-0.00315.149-0.003-0.0030.0000.0000.0000.000
12A14ALA0-0.0220.00515.869-0.022-0.0220.0000.0000.0000.000
13A15ALA0-0.007-0.01017.531-0.012-0.0120.0000.0000.0000.000
14A16ILE0-0.0040.00019.373-0.010-0.0100.0000.0000.0000.000
15A17ALA0-0.0060.00320.656-0.009-0.0090.0000.0000.0000.000
16A18GLU-1-0.834-0.91320.9450.0060.0060.0000.0000.0000.000
17A19PHE0-0.058-0.04221.680-0.006-0.0060.0000.0000.0000.000
18A20GLY0-0.0010.00524.952-0.004-0.0040.0000.0000.0000.000
19A21ASP-1-0.914-0.93726.0300.0340.0340.0000.0000.0000.000
20A22ARG10.8660.92426.208-0.017-0.0170.0000.0000.0000.000
21A23GLY00.0710.03828.610-0.003-0.0030.0000.0000.0000.000
22A24PHE00.005-0.00123.943-0.004-0.0040.0000.0000.0000.000
23A25GLU-1-0.864-0.94326.3220.0360.0360.0000.0000.0000.000
24A26ILE0-0.0070.01228.058-0.004-0.0040.0000.0000.0000.000
25A27THR0-0.041-0.01822.615-0.009-0.0090.0000.0000.0000.000
26A28SER00.008-0.00223.2970.0050.0050.0000.0000.0000.000
27A29MET00.0670.01517.028-0.003-0.0030.0000.0000.0000.000
28A30ASP-1-0.926-0.99217.860-0.048-0.0480.0000.0000.0000.000
29A31ARG10.8870.96718.919-0.009-0.0090.0000.0000.0000.000
30A32ILE00.0210.00516.168-0.003-0.0030.0000.0000.0000.000
31A33ALA0-0.032-0.02314.6010.0010.0010.0000.0000.0000.000
32A34ALA0-0.0150.00314.611-0.022-0.0220.0000.0000.0000.000
33A35ARG10.8780.93916.584-0.032-0.0320.0000.0000.0000.000
34A36ALA0-0.005-0.00612.7340.0090.0090.0000.0000.0000.000
35A37GLU-1-0.967-0.96011.999-0.133-0.1330.0000.0000.0000.000
36A38VAL0-0.071-0.0368.484-0.091-0.0910.0000.0000.0000.000
37A39SER00.0420.00710.5640.0560.0560.0000.0000.0000.000
38A40LYS10.9990.99312.3100.0580.0580.0000.0000.0000.000
39A41ARG10.9450.96312.4070.1440.1440.0000.0000.0000.000
40A42THR0-0.013-0.0077.2440.0060.0060.0000.0000.0000.000
41A43VAL00.0650.0479.9070.0450.0450.0000.0000.0000.000
42A44TYR0-0.051-0.03812.5840.0350.0350.0000.0000.0000.000
43A45ASN0-0.043-0.0178.5590.0680.0680.0000.0000.0000.000
44A46HIS00.0050.0197.0000.0190.0190.0000.0000.0000.000
45A47PHE00.0310.01412.0470.0390.0390.0000.0000.0000.000
46A48PRO0-0.015-0.00215.466-0.041-0.0410.0000.0000.0000.000
47A49SER0-0.027-0.01817.359-0.023-0.0230.0000.0000.0000.000
48A50LYS10.8940.92119.855-0.028-0.0280.0000.0000.0000.000
49A51GLU-1-0.774-0.87821.8880.0760.0760.0000.0000.0000.000
50A52GLU-1-0.940-0.97317.1300.2270.2270.0000.0000.0000.000
51A53LEU0-0.029-0.01517.4880.0160.0160.0000.0000.0000.000
52A54PHE00.0130.00420.5070.0090.0090.0000.0000.0000.000
53A55ALA00.0160.01122.1620.0020.0020.0000.0000.0000.000
54A56GLU-1-0.870-0.94417.3280.2860.2860.0000.0000.0000.000
55A57MET0-0.021-0.01419.2890.0030.0030.0000.0000.0000.000
56A58LEU0-0.018-0.00123.093-0.007-0.0070.0000.0000.0000.000
57A59GLN0-0.0010.01620.516-0.025-0.0250.0000.0000.0000.000
58A60ARG10.8140.89615.972-0.288-0.2880.0000.0000.0000.000
59A61LEU0-0.014-0.00223.096-0.007-0.0070.0000.0000.0000.000
60A62TRP0-0.038-0.03826.283-0.009-0.0090.0000.0000.0000.000
61A63ASN0-0.030-0.01622.1550.0110.0110.0000.0000.0000.000
62A64CYS0-0.0010.02125.6690.0000.0000.0000.0000.0000.000
63A65ALA0-0.061-0.02028.087-0.011-0.0110.0000.0000.0000.000
64A66PRO0-0.042-0.01728.2230.0000.0000.0000.0000.0000.000
65A67PRO0-0.0080.00425.6880.0060.0060.0000.0000.0000.000
66A68GLN00.001-0.02927.900-0.005-0.0050.0000.0000.0000.000
67A69SER0-0.025-0.01631.0690.0020.0020.0000.0000.0000.000
68A70GLU-1-0.856-0.91233.9150.0740.0740.0000.0000.0000.000
69A71VAL0-0.061-0.04535.9320.0030.0030.0000.0000.0000.000
70A72VAL0-0.0100.01038.740-0.003-0.0030.0000.0000.0000.000
71A73TYR0-0.092-0.09940.791-0.002-0.0020.0000.0000.0000.000
72A74ARG10.9680.97843.659-0.062-0.0620.0000.0000.0000.000
73A75PRO00.0430.02346.844-0.002-0.0020.0000.0000.0000.000
74A76LEU0-0.021-0.01650.009-0.002-0.0020.0000.0000.0000.000
75A77VAL0-0.0010.02948.104-0.001-0.0010.0000.0000.0000.000
76A78SER0-0.043-0.06251.3440.0000.0000.0000.0000.0000.000
77A79LEU00.0450.01550.1810.0030.0030.0000.0000.0000.000
78A80ARG10.9570.95749.106-0.036-0.0360.0000.0000.0000.000
79A81GLU-1-0.756-0.82848.0820.0480.0480.0000.0000.0000.000
80A82GLN0-0.011-0.00145.0570.0050.0050.0000.0000.0000.000
81A83LEU00.0070.00744.1350.0030.0030.0000.0000.0000.000
82A84LEU00.0230.00145.1120.0010.0010.0000.0000.0000.000
83A85GLU-1-0.945-0.96840.4780.0720.0720.0000.0000.0000.000
84A86LEU0-0.014-0.00640.2170.0040.0040.0000.0000.0000.000
85A87LEU0-0.031-0.01540.0240.0030.0030.0000.0000.0000.000
86A88TRP00.0360.01640.4780.0020.0020.0000.0000.0000.000
87A89GLY0-0.025-0.00936.9660.0020.0020.0000.0000.0000.000
88A90LYS10.8930.94734.224-0.078-0.0780.0000.0000.0000.000
89A91MET0-0.001-0.00436.9430.0010.0010.0000.0000.0000.000
90A92ARG10.9360.96635.024-0.074-0.0740.0000.0000.0000.000
91A93ASN0-0.0010.00931.6010.0030.0030.0000.0000.0000.000
92A94LEU0-0.041-0.02033.3150.0000.0000.0000.0000.0000.000
93A95THR0-0.039-0.01236.022-0.004-0.0040.0000.0000.0000.000
94A96ASP-1-0.877-0.93229.5330.0920.0920.0000.0000.0000.000
95A97SER00.015-0.00830.4890.0040.0040.0000.0000.0000.000
96A98SER00.0670.04626.0270.0000.0000.0000.0000.0000.000
97A99PHE00.0010.00527.6560.0020.0020.0000.0000.0000.000
98A100LEU0-0.023-0.02729.445-0.001-0.0010.0000.0000.0000.000
99A101ASP-1-0.872-0.92427.8470.0600.0600.0000.0000.0000.000
100A102LEU0-0.030-0.01723.606-0.002-0.0020.0000.0000.0000.000
101A103ALA0-0.017-0.03027.502-0.001-0.0010.0000.0000.0000.000
102A104ARG10.8750.95330.880-0.055-0.0550.0000.0000.0000.000
103A105VAL0-0.0210.00425.679-0.004-0.0040.0000.0000.0000.000
104A106VAL00.004-0.00427.596-0.004-0.0040.0000.0000.0000.000
105A107VAL0-0.024-0.01429.870-0.003-0.0030.0000.0000.0000.000
106A108GLY00.0200.00532.569-0.004-0.0040.0000.0000.0000.000
107A109ALA00.000-0.01129.151-0.005-0.0050.0000.0000.0000.000
108A110THR0-0.0090.00431.1770.0000.0000.0000.0000.0000.000
109A111ILE0-0.048-0.01333.864-0.003-0.0030.0000.0000.0000.000
110A112HIS0-0.077-0.03932.565-0.003-0.0030.0000.0000.0000.000
111A113SER00.0240.02731.941-0.003-0.0030.0000.0000.0000.000
112A114PRO00.0370.00434.2620.0040.0040.0000.0000.0000.000
113A115GLU-1-0.934-0.96830.9370.0450.0450.0000.0000.0000.000
114A116ARG10.8240.89328.177-0.054-0.0540.0000.0000.0000.000
115A117ALA0-0.003-0.01332.3090.0060.0060.0000.0000.0000.000
116A118GLN0-0.075-0.03135.0050.0030.0030.0000.0000.0000.000
117A119VAL0-0.0080.01830.3010.0000.0000.0000.0000.0000.000
118A120TRP0-0.042-0.01026.2760.0080.0080.0000.0000.0000.000
119A121LEU00.007-0.01632.7160.0010.0010.0000.0000.0000.000
120A122ALA00.0510.03634.9250.0040.0040.0000.0000.0000.000
121A123ARG10.8090.92331.111-0.089-0.0890.0000.0000.0000.000
122A124ILE00.011-0.00736.740-0.001-0.0010.0000.0000.0000.000
123A125ASN0-0.013-0.04536.2840.0010.0010.0000.0000.0000.000
124A126GLU-1-0.663-0.81531.3300.0870.0870.0000.0000.0000.000
125A127ARG10.7390.86032.289-0.066-0.0660.0000.0000.0000.000
126A128GLU-1-0.905-0.95234.3600.0580.0580.0000.0000.0000.000
127A129GLU-1-0.861-0.93836.6260.0730.0730.0000.0000.0000.000
128A130THR00.0250.02636.090-0.001-0.0010.0000.0000.0000.000
129A131PHE00.007-0.01238.307-0.002-0.0020.0000.0000.0000.000
130A132SER0-0.0130.00941.380-0.004-0.0040.0000.0000.0000.000
131A133ALA00.019-0.00740.767-0.003-0.0030.0000.0000.0000.000
132A134TRP00.0230.01442.446-0.003-0.0030.0000.0000.0000.000
133A135ILE00.0030.01044.042-0.003-0.0030.0000.0000.0000.000
134A136ARG10.9490.97043.013-0.062-0.0620.0000.0000.0000.000
135A137ALA0-0.0040.00045.510-0.002-0.0020.0000.0000.0000.000
136A138ALA00.0640.03247.539-0.002-0.0020.0000.0000.0000.000
137A139GLN0-0.105-0.05150.025-0.001-0.0010.0000.0000.0000.000
138A140LYS10.8560.93249.411-0.049-0.0490.0000.0000.0000.000
139A141ASP-1-0.805-0.86751.2270.0440.0440.0000.0000.0000.000
140A142GLY00.0120.02353.144-0.001-0.0010.0000.0000.0000.000
141A143ARG10.8500.91951.817-0.045-0.0450.0000.0000.0000.000
142A144LEU0-0.0230.00050.1270.0000.0000.0000.0000.0000.000
143A145LYS10.8990.94554.365-0.032-0.0320.0000.0000.0000.000
144A146PRO0-0.024-0.00554.4830.0020.0020.0000.0000.0000.000
145A147VAL00.0110.00351.103-0.001-0.0010.0000.0000.0000.000
146A148ASP-1-0.833-0.92247.7120.0490.0490.0000.0000.0000.000
147A149PRO00.011-0.00545.7040.0000.0000.0000.0000.0000.000
148A150GLY00.0330.01644.2450.0010.0010.0000.0000.0000.000
149A151PHE0-0.024-0.00345.2290.0010.0010.0000.0000.0000.000
150A152ALA00.0300.01248.001-0.001-0.0010.0000.0000.0000.000
151A153ALA00.0160.00142.9630.0000.0000.0000.0000.0000.000
152A154THR0-0.0040.00743.8070.0010.0010.0000.0000.0000.000
153A155GLN00.0270.01944.8410.0010.0010.0000.0000.0000.000
154A156MET00.0090.02444.993-0.001-0.0010.0000.0000.0000.000
155A157HIS10.8640.92538.881-0.063-0.0630.0000.0000.0000.000
156A158ALA0-0.0080.01843.2590.0000.0000.0000.0000.0000.000
157A159LEU00.0280.02945.334-0.001-0.0010.0000.0000.0000.000
158A160LEU00.0260.02341.7150.0000.0000.0000.0000.0000.000
159A161LYS10.9230.93938.455-0.060-0.0600.0000.0000.0000.000
160A162SER0-0.071-0.04642.017-0.001-0.0010.0000.0000.0000.000
161A163PHE0-0.0050.00644.429-0.002-0.0020.0000.0000.0000.000
162A164ALA00.0220.00040.499-0.001-0.0010.0000.0000.0000.000
163A165PHE0-0.0140.00434.5100.0040.0040.0000.0000.0000.000
164A166TRP00.0510.00338.5490.0010.0010.0000.0000.0000.000
165A167PRO00.0440.03740.550-0.001-0.0010.0000.0000.0000.000
166A168GLN0-0.039-0.02437.2400.0000.0000.0000.0000.0000.000
167A169VAL00.000-0.00334.666-0.001-0.0010.0000.0000.0000.000
168A170THR0-0.086-0.06536.620-0.002-0.0020.0000.0000.0000.000
169A171PHE00.0030.00439.269-0.002-0.0020.0000.0000.0000.000
170A172ASN0-0.016-0.00135.2330.0000.0000.0000.0000.0000.000
171A173ALA0-0.0110.01238.575-0.002-0.0020.0000.0000.0000.000
172A174ALA00.0300.00939.8420.0020.0020.0000.0000.0000.000
173A175LEU00.0090.01235.7260.0000.0000.0000.0000.0000.000
174A176LEU0-0.0200.01139.917-0.002-0.0020.0000.0000.0000.000
175A177THR00.0300.00341.8760.0020.0020.0000.0000.0000.000
176A178PRO00.0560.00542.6160.0010.0010.0000.0000.0000.000
177A179GLN00.0480.01744.4010.0020.0020.0000.0000.0000.000
178A180GLU-1-0.843-0.91146.1270.0340.0340.0000.0000.0000.000
179A181GLN0-0.069-0.03740.3350.0020.0020.0000.0000.0000.000
180A182SER00.023-0.01044.6980.0010.0010.0000.0000.0000.000
181A183ASN00.0180.02346.9680.0000.0000.0000.0000.0000.000
182A184VAL0-0.036-0.00945.2060.0000.0000.0000.0000.0000.000
183A185VAL0-0.008-0.00943.6980.0010.0010.0000.0000.0000.000
184A186GLU-1-0.890-0.94646.8900.0410.0410.0000.0000.0000.000
185A187SER0-0.033-0.01550.503-0.001-0.0010.0000.0000.0000.000
186A188ALA00.0300.01047.821-0.001-0.0010.0000.0000.0000.000
187A189LEU00.0140.00048.4020.0000.0000.0000.0000.0000.000
188A190ASN0-0.020-0.00150.6220.0000.0000.0000.0000.0000.000
189A191MET0-0.032-0.00552.777-0.001-0.0010.0000.0000.0000.000
190A192PHE00.006-0.00849.5590.0000.0000.0000.0000.0000.000
191A193LEU0-0.038-0.01851.1450.0000.0000.0000.0000.0000.000
192A194GLY00.0180.01854.281-0.001-0.0010.0000.0000.0000.000
193A195TRP0-0.048-0.01155.412-0.002-0.0020.0000.0000.0000.000
194A196TYR0-0.004-0.04152.180-0.001-0.0010.0000.0000.0000.000
195A197GLU-1-0.949-0.96855.2250.0380.0380.0000.0000.0000.000
196A198ILE0-0.087-0.05056.206-0.002-0.0020.0000.0000.0000.000
197A199PRO0-0.0090.00458.2680.0010.0010.0000.0000.0000.000