FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: Q136Y

Calculation Name: 5D0Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D0Q

Chain ID: A

ChEMBL ID:

UniProt ID: P0A940

Base Structure: X-ray

Registration Date: 2023-06-20

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 766
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -16359513.604481
FMO2-HF: Nuclear repulsion 16060244.1339
FMO2-HF: Total energy -299269.470581
FMO2-MP2: Total energy -300148.716457


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:24:PHE)


Summations of interaction energy for fragment #1(A:24:PHE)
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.
-24.612-20.17730.892-11.037-24.29-0.04
Interaction energy analysis for fragmet #1(A:24:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.022
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].
3A26VAL00.0330.0292.497-1.9281.3810.765-1.278-2.7960.008
4A27LYS10.8880.9384.611-0.951-0.5940.002-0.049-0.3100.000
5A28ASP-1-0.868-0.9325.981-0.356-0.3560.0000.0000.0000.000
6A29ILE0-0.080-0.0426.323-0.297-0.2970.0000.0000.0000.000
7A30HIS00.0320.0188.6120.1500.1500.0000.0000.0000.000
8A31PHE0-0.018-0.01710.520-0.073-0.0730.0000.0000.0000.000
9A32GLU-1-0.909-0.96013.277-0.196-0.1960.0000.0000.0000.000
10A33GLY0-0.044-0.02615.880-0.010-0.0100.0000.0000.0000.000
11A34LEU00.0300.01116.332-0.005-0.0050.0000.0000.0000.000
12A35GLN0-0.039-0.02819.826-0.002-0.0020.0000.0000.0000.000
13A36ARG10.8830.96223.6600.1890.1890.0000.0000.0000.000
14A37VAL0-0.0040.00119.8440.0080.0080.0000.0000.0000.000
15A38ALA00.0150.01321.221-0.003-0.0030.0000.0000.0000.000
16A39VAL00.0670.01116.003-0.017-0.0170.0000.0000.0000.000
17A40GLY00.0130.00816.731-0.037-0.0370.0000.0000.0000.000
18A41ALA00.009-0.00618.146-0.017-0.0170.0000.0000.0000.000
19A42ALA00.0480.03315.677-0.006-0.0060.0000.0000.0000.000
20A43LEU00.019-0.00211.776-0.042-0.0420.0000.0000.0000.000
21A44LEU0-0.081-0.04414.504-0.040-0.0400.0000.0000.0000.000
22A45SER0-0.0300.00316.525-0.001-0.0010.0000.0000.0000.000
23A46MET0-0.043-0.0069.2200.0210.0210.0000.0000.0000.000
24A47PRO0-0.0280.00011.7780.0250.0250.0000.0000.0000.000
25A48VAL00.0290.0167.5970.0170.0170.0000.0000.0000.000
26A49ARG10.8720.9209.1380.5880.5880.0000.0000.0000.000
27A50THR00.0210.0017.889-0.202-0.2020.0000.0000.0000.000
28A51GLY0-0.0280.0067.9010.0610.0610.0000.0000.0000.000
29A52ASP-1-0.871-0.9337.552-0.606-0.6060.0000.0000.0000.000
30A53THR0-0.079-0.0522.951-0.770-0.0790.148-0.305-0.5330.001
31A54VAL0-0.0040.0112.013-1.743-0.1202.261-1.332-2.5520.000
32A55ASN0-0.044-0.0322.127-8.754-7.5975.678-3.357-3.478-0.043
33A56ASP-1-0.857-0.9644.440-0.796-0.647-0.001-0.012-0.1360.000
34A57GLU-1-0.948-0.9697.182-0.484-0.4840.0000.0000.0000.000
35A58ASP-1-0.862-0.9346.260-2.320-2.3200.0000.0000.0000.000
36A59ILE00.0100.0104.8450.2690.2690.0000.0000.0000.000
37A60SER00.0260.0108.0120.2820.2820.0000.0000.0000.000
38A61ASN0-0.029-0.01511.0700.2880.2880.0000.0000.0000.000
39A62THR00.0560.0158.2720.1580.1580.0000.0000.0000.000
40A63ILE0-0.0090.00510.5820.1070.1070.0000.0000.0000.000
41A64ARG10.9220.95212.7910.6130.6130.0000.0000.0000.000
42A65ALA0-0.0050.00714.3310.0600.0600.0000.0000.0000.000
43A66LEU00.0100.00111.9260.0550.0550.0000.0000.0000.000
44A67PHE00.0040.00816.1030.0510.0510.0000.0000.0000.000
45A68ALA0-0.029-0.00218.6780.0370.0370.0000.0000.0000.000
46A69THR0-0.100-0.06018.6450.0370.0370.0000.0000.0000.000
47A70GLY00.0260.02221.3450.0220.0220.0000.0000.0000.000
48A71ASN0-0.027-0.01821.5240.0430.0430.0000.0000.0000.000
49A72PHE0-0.021-0.03017.7660.0100.0100.0000.0000.0000.000
50A73GLU-1-0.969-0.98421.267-0.162-0.1620.0000.0000.0000.000
51A74ASP-1-0.962-0.99117.642-0.266-0.2660.0000.0000.0000.000
52A75VAL00.0140.01412.905-0.013-0.0130.0000.0000.0000.000
53A76ARG10.9370.98312.5700.2220.2220.0000.0000.0000.000
54A77VAL00.0250.0026.709-0.024-0.0240.0000.0000.0000.000
55A78LEU0-0.031-0.0166.9840.0490.0490.0000.0000.0000.000
56A79ARG10.8790.9482.428-7.680-5.5767.837-2.511-7.4300.022
57A80ASP-1-0.896-0.9424.6330.0180.076-0.001-0.011-0.0460.000
58A81GLY00.0180.0184.591-0.292-0.081-0.001-0.094-0.1160.000
59A82ASP-1-0.942-1.0111.783-3.172-4.87012.705-6.294-4.713-0.011
60A83THR0-0.030-0.0022.5593.993-0.3991.4354.381-1.424-0.017
61A84LEU0-0.0030.0072.979-0.6460.1780.065-0.165-0.7240.000
62A85LEU00.0310.0154.6840.1640.206-0.001-0.010-0.0320.000
63A86VAL0-0.014-0.0138.226-0.017-0.0170.0000.0000.0000.000
64A87GLN0-0.016-0.00810.7480.0750.0750.0000.0000.0000.000
65A88VAL0-0.0100.00013.907-0.025-0.0250.0000.0000.0000.000
66A89LYS10.9500.97516.5440.2200.2200.0000.0000.0000.000
67A90GLU-1-0.811-0.92020.139-0.206-0.2060.0000.0000.0000.000
68A91ARG10.8940.95422.6650.2050.2050.0000.0000.0000.000
69A92PRO0-0.085-0.00225.1910.0120.0120.0000.0000.0000.000
70A93THR00.006-0.00228.5480.0000.0000.0000.0000.0000.000
71A94ILE00.0290.03731.1110.0080.0080.0000.0000.0000.000
72A95ALA0-0.051-0.02534.577-0.001-0.0010.0000.0000.0000.000
73A96SER00.004-0.01237.1110.0020.0020.0000.0000.0000.000
74A97ILE00.0540.03738.692-0.002-0.0020.0000.0000.0000.000
75A98THR0-0.077-0.03941.8500.0040.0040.0000.0000.0000.000
76A99PHE00.0610.02544.837-0.002-0.0020.0000.0000.0000.000
77A100SER0-0.016-0.01647.7490.0030.0030.0000.0000.0000.000
78A101GLY0-0.0110.00150.3970.0000.0000.0000.0000.0000.000
79A102ASN0-0.037-0.00751.1820.0010.0010.0000.0000.0000.000
80A103LYS10.9050.94253.2550.0460.0460.0000.0000.0000.000
81A104SER0-0.024-0.00556.1800.0010.0010.0000.0000.0000.000
82A105VAL00.0250.03051.0690.0000.0000.0000.0000.0000.000
83A106LYS10.9570.96652.9410.0520.0520.0000.0000.0000.000
84A107ASP-1-0.771-0.89749.093-0.059-0.0590.0000.0000.0000.000
85A108ASP-1-0.996-1.01548.407-0.061-0.0610.0000.0000.0000.000
86A109MET00.0180.01048.578-0.001-0.0010.0000.0000.0000.000
87A110LEU00.0360.03646.649-0.002-0.0020.0000.0000.0000.000
88A111LYS10.8700.94843.7630.0660.0660.0000.0000.0000.000
89A112GLN00.015-0.01043.517-0.003-0.0030.0000.0000.0000.000
90A113ASN00.0120.02044.412-0.002-0.0020.0000.0000.0000.000
91A114LEU0-0.042-0.01839.999-0.003-0.0030.0000.0000.0000.000
92A115GLU-1-0.934-0.98539.455-0.089-0.0890.0000.0000.0000.000
93A116ALA0-0.046-0.00539.172-0.005-0.0050.0000.0000.0000.000
94A117SER0-0.027-0.02038.9020.0000.0000.0000.0000.0000.000
95A118GLY0-0.0340.00235.010-0.005-0.0050.0000.0000.0000.000
96A119VAL0-0.0080.00735.100-0.003-0.0030.0000.0000.0000.000
97A120ARG11.0070.99835.8830.1110.1110.0000.0000.0000.000
98A121VAL0-0.029-0.03336.262-0.004-0.0040.0000.0000.0000.000
99A122GLY0-0.032-0.01134.7050.0010.0010.0000.0000.0000.000
100A123GLU-1-0.885-0.95231.230-0.148-0.1480.0000.0000.0000.000
101A124SER0-0.060-0.02927.3460.0050.0050.0000.0000.0000.000
102A125LEU00.0190.00429.3440.0030.0030.0000.0000.0000.000
103A126ASP-1-0.805-0.91727.529-0.190-0.1900.0000.0000.0000.000
104A127ARG10.9460.97228.5050.1360.1360.0000.0000.0000.000
105A128THR0-0.026-0.02227.3550.0080.0080.0000.0000.0000.000
106A129THR00.0460.04030.1900.0020.0020.0000.0000.0000.000
107A130ILE0-0.034-0.01232.9340.0060.0060.0000.0000.0000.000
108A131ALA00.0430.01535.2230.0050.0050.0000.0000.0000.000
109A132ASP-1-0.912-0.95435.218-0.110-0.1100.0000.0000.0000.000
110A133ILE0-0.010-0.00435.1870.0040.0040.0000.0000.0000.000
111A134GLU-1-0.929-0.97638.816-0.077-0.0770.0000.0000.0000.000
112A135LYS10.9560.97540.9550.0770.0770.0000.0000.0000.000
113A136GLY00.0370.02041.3260.0030.0030.0000.0000.0000.000
114A137LEU0-0.063-0.04242.4870.0040.0040.0000.0000.0000.000
115A138GLU-1-0.921-0.97544.931-0.063-0.0630.0000.0000.0000.000
116A139ASP-1-0.889-0.94445.767-0.068-0.0680.0000.0000.0000.000
117A140PHE0-0.058-0.02046.8130.0020.0020.0000.0000.0000.000
118A141TYR0-0.095-0.13348.6590.0030.0030.0000.0000.0000.000
119A142TYR00.0100.01349.2130.0040.0040.0000.0000.0000.000
120A143SER0-0.074-0.03152.6690.0030.0030.0000.0000.0000.000
121A144VAL00.0140.00254.9480.0020.0020.0000.0000.0000.000
122A145GLY00.0550.03256.6190.0020.0020.0000.0000.0000.000
123A146LYS10.8450.93254.8080.0460.0460.0000.0000.0000.000
124A147TYR00.0920.03554.525-0.002-0.0020.0000.0000.0000.000
125A148SER0-0.071-0.04454.5910.0000.0000.0000.0000.0000.000
126A149ALA0-0.035-0.00952.1920.0010.0010.0000.0000.0000.000
127A150SER0-0.0270.01248.469-0.001-0.0010.0000.0000.0000.000
128A151VAL0-0.010-0.00144.5160.0020.0020.0000.0000.0000.000
129A152LYS10.9740.98742.2960.0680.0680.0000.0000.0000.000
130A153ALA00.0110.00839.4080.0010.0010.0000.0000.0000.000
131A154VAL0-0.057-0.02440.3580.0000.0000.0000.0000.0000.000
132A155VAL00.0040.00333.592-0.002-0.0020.0000.0000.0000.000
133A156THR0-0.013-0.00936.7770.0010.0010.0000.0000.0000.000
134A157PRO00.0130.02233.034-0.002-0.0020.0000.0000.0000.000
135A158LEU0-0.002-0.01233.8540.0060.0060.0000.0000.0000.000
136A159PRO0-0.034-0.02533.512-0.003-0.0030.0000.0000.0000.000
137A160ARG10.9420.97229.7830.1000.1000.0000.0000.0000.000
138A161ASN00.0580.02126.3080.0000.0000.0000.0000.0000.000
139A162ARG10.8800.95229.1790.0980.0980.0000.0000.0000.000
140A163VAL00.0310.00632.0990.0020.0020.0000.0000.0000.000
141A164ASP-1-0.945-0.96434.605-0.081-0.0810.0000.0000.0000.000
142A165LEU00.0500.00837.443-0.002-0.0020.0000.0000.0000.000
143A166LYS10.9430.99139.7120.0670.0670.0000.0000.0000.000
144A167LEU00.000-0.01141.324-0.001-0.0010.0000.0000.0000.000
145A168VAL0-0.027-0.01644.6500.0030.0030.0000.0000.0000.000
146A169PHE00.0580.03346.995-0.001-0.0010.0000.0000.0000.000
147A170GLN0-0.039-0.02650.0640.0000.0000.0000.0000.0000.000
148A171GLU-1-0.713-0.81752.915-0.050-0.0500.0000.0000.0000.000
149A172GLY00.0060.00855.0420.0010.0010.0000.0000.0000.000
150A173VAL0-0.015-0.01957.5230.0000.0000.0000.0000.0000.000
151A174SER0-0.043-0.03260.984-0.001-0.0010.0000.0000.0000.000
152A175ALA00.0070.00562.1420.0020.0020.0000.0000.0000.000
153A176GLU-1-0.843-0.88762.235-0.037-0.0370.0000.0000.0000.000
154A177ILE0-0.128-0.06062.966-0.001-0.0010.0000.0000.0000.000
155A178GLN00.0940.01566.2270.0010.0010.0000.0000.0000.000
156A179GLN0-0.041-0.01668.4360.0000.0000.0000.0000.0000.000
157A180ILE00.0350.01767.235-0.001-0.0010.0000.0000.0000.000
158A181ASN0-0.080-0.03468.9080.0010.0010.0000.0000.0000.000
159A182ILE00.0400.01669.385-0.001-0.0010.0000.0000.0000.000
160A183VAL00.0030.01170.8720.0010.0010.0000.0000.0000.000
161A184GLY00.023-0.00671.792-0.001-0.0010.0000.0000.0000.000
162A185ASN0-0.051-0.00874.2580.0000.0000.0000.0000.0000.000
163A186HIS0-0.094-0.04475.9650.0010.0010.0000.0000.0000.000
164A187ALA0-0.037-0.01278.1290.0010.0010.0000.0000.0000.000
165A188PHE00.0210.01576.5080.0000.0000.0000.0000.0000.000
166A189THR00.0320.00478.1630.0000.0000.0000.0000.0000.000
167A190THR00.027-0.00575.242-0.001-0.0010.0000.0000.0000.000
168A191ASP-1-0.935-0.96775.328-0.027-0.0270.0000.0000.0000.000
169A192GLU-1-0.846-0.93876.349-0.028-0.0280.0000.0000.0000.000
170A193LEU0-0.0350.01172.900-0.001-0.0010.0000.0000.0000.000
171A194ILE0-0.016-0.02071.000-0.001-0.0010.0000.0000.0000.000
172A195SER0-0.087-0.05871.783-0.001-0.0010.0000.0000.0000.000
173A196HIS00.0080.00471.0580.0000.0000.0000.0000.0000.000
174A197PHE0-0.080-0.02166.975-0.001-0.0010.0000.0000.0000.000
175A198GLN0-0.065-0.02667.7160.0000.0000.0000.0000.0000.000
176A199LEU00.0060.01769.9900.0010.0010.0000.0000.0000.000
177A217GLN00.0760.04561.0190.0010.0010.0000.0000.0000.000
178A218LYS10.8290.90656.1310.0480.0480.0000.0000.0000.000
179A219LEU00.0420.00957.4790.0000.0000.0000.0000.0000.000
180A220ALA00.0340.01756.1760.0010.0010.0000.0000.0000.000
181A221GLY00.0630.04058.2750.0010.0010.0000.0000.0000.000
182A222ASP-1-0.822-0.92960.285-0.039-0.0390.0000.0000.0000.000
183A223LEU0-0.052-0.01559.8260.0010.0010.0000.0000.0000.000
184A224GLU-1-0.946-0.98658.446-0.046-0.0460.0000.0000.0000.000
185A225THR00.0370.04862.5580.0010.0010.0000.0000.0000.000
186A226LEU00.0230.02965.7420.0010.0010.0000.0000.0000.000
187A227ARG10.9280.95461.0170.0430.0430.0000.0000.0000.000
188A228SER0-0.032-0.04464.7070.0010.0010.0000.0000.0000.000
189A229TYR0-0.0110.01967.1520.0010.0010.0000.0000.0000.000
190A230TYR0-0.007-0.02769.7390.0010.0010.0000.0000.0000.000
191A231LEU0-0.045-0.03065.6500.0010.0010.0000.0000.0000.000
192A232ASP-1-0.938-0.95569.508-0.033-0.0330.0000.0000.0000.000
193A233ARG10.8340.92271.9790.0310.0310.0000.0000.0000.000
194A234GLY0-0.0070.00673.6040.0010.0010.0000.0000.0000.000
195A235TYR0-0.039-0.02372.3250.0010.0010.0000.0000.0000.000
196A236ALA00.0150.00469.673-0.001-0.0010.0000.0000.0000.000
197A237ARG10.9000.96168.3770.0280.0280.0000.0000.0000.000
198A238PHE00.0190.01266.8510.0000.0000.0000.0000.0000.000
199A239ASN0-0.044-0.03462.558-0.001-0.0010.0000.0000.0000.000
200A240ILE00.006-0.01462.5220.0010.0010.0000.0000.0000.000
201A241ASP-1-0.841-0.88562.774-0.036-0.0360.0000.0000.0000.000
202A242SER0-0.057-0.04062.286-0.001-0.0010.0000.0000.0000.000
203A243THR00.0310.00359.7440.0010.0010.0000.0000.0000.000
204A244GLN0-0.0270.00060.891-0.001-0.0010.0000.0000.0000.000
205A245VAL00.0310.01659.6310.0010.0010.0000.0000.0000.000
206A246SER0-0.0160.00160.798-0.001-0.0010.0000.0000.0000.000
207A247LEU00.008-0.01057.7830.0000.0000.0000.0000.0000.000
208A248THR00.0180.02962.2820.0020.0020.0000.0000.0000.000
209A249PRO00.0250.00463.783-0.001-0.0010.0000.0000.0000.000
210A250ASP-1-0.931-0.96663.721-0.038-0.0380.0000.0000.0000.000
211A251LYS10.8540.91358.8200.0400.0400.0000.0000.0000.000
212A252LYS10.9320.96658.4380.0400.0400.0000.0000.0000.000
213A253GLY00.0630.05060.4810.0000.0000.0000.0000.0000.000
214A254ILE0-0.059-0.04059.6060.0000.0000.0000.0000.0000.000
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