Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: G6QL1

Calculation Name: 5H4U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H4U

Chain ID: A

ChEMBL ID:

UniProt ID: D3GDK4

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2313156.571359
FMO2-HF: Nuclear repulsion 2231575.076224
FMO2-HF: Total energy -81581.495135
FMO2-MP2: Total energy -81806.355159


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:LEU)


Summations of interaction energy for fragment #1(A:1: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.
-7.741-0.73.425-4.088-6.375-0.018
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / 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].
3A3SER0-0.018-0.0203.625-1.6351.323-0.010-1.471-1.4780.007
4A4GLY00.0320.0275.359-0.0130.015-0.001-0.002-0.0240.000
5A5SER00.0130.0069.0570.0910.0910.0000.0000.0000.000
6A6GLY00.0350.00312.509-0.038-0.0380.0000.0000.0000.000
7A7VAL0-0.0050.01214.4230.0300.0300.0000.0000.0000.000
8A8THR0-0.055-0.05616.3120.0020.0020.0000.0000.0000.000
9A9THR00.005-0.01718.7600.0180.0180.0000.0000.0000.000
10A10ARG10.7420.86221.3430.1110.1110.0000.0000.0000.000
11A11TYR0-0.0090.00320.6060.0030.0030.0000.0000.0000.000
12A12TRP00.011-0.03023.6910.0070.0070.0000.0000.0000.000
13A13ASP-1-0.764-0.89026.046-0.009-0.0090.0000.0000.0000.000
14A14CYS0-0.099-0.04027.3150.0070.0070.0000.0000.0000.000
15A15CYS0-0.075-0.01526.0470.0030.0030.0000.0000.0000.000
16A16LYS10.8400.92324.737-0.107-0.1070.0000.0000.0000.000
17A17PRO0-0.022-0.00320.202-0.003-0.0030.0000.0000.0000.000
18A18SER00.022-0.01318.1000.0180.0180.0000.0000.0000.000
19A19CYS0-0.019-0.0179.6490.0070.0070.0000.0000.0000.000
20A20SER0-0.045-0.02818.0780.0270.0270.0000.0000.0000.000
21A21TRP0-0.022-0.00720.973-0.003-0.0030.0000.0000.0000.000
22A22GLY00.0250.00620.3700.0250.0250.0000.0000.0000.000
23A23GLY00.010-0.00219.908-0.016-0.0160.0000.0000.0000.000
24A24LYS10.8310.92516.650-0.116-0.1160.0000.0000.0000.000
25A25ALA00.008-0.01312.5950.0220.0220.0000.0000.0000.000
26A26SER0-0.0070.01013.160-0.049-0.0490.0000.0000.0000.000
27A27VAL0-0.007-0.02213.4250.1140.1140.0000.0000.0000.000
28A28THR00.0100.01215.767-0.031-0.0310.0000.0000.0000.000
29A29LYS10.8970.94218.435-0.256-0.2560.0000.0000.0000.000
30A30PRO00.0500.02618.5550.0290.0290.0000.0000.0000.000
31A31VAL0-0.023-0.00917.285-0.003-0.0030.0000.0000.0000.000
32A32ARG10.8300.92519.817-0.127-0.1270.0000.0000.0000.000
33A33THR00.0570.01423.208-0.012-0.0120.0000.0000.0000.000
34A34CYS0-0.132-0.05324.8720.0040.0040.0000.0000.0000.000
35A35LYS11.0021.00529.238-0.062-0.0620.0000.0000.0000.000
36A36ALA00.0820.03732.198-0.001-0.0010.0000.0000.0000.000
37A37ASN00.0140.01433.8610.0000.0000.0000.0000.0000.000
38A38GLY00.0710.04130.392-0.003-0.0030.0000.0000.0000.000
39A39ASN00.0220.01529.7090.0040.0040.0000.0000.0000.000
40A40THR0-0.0020.00030.5520.0060.0060.0000.0000.0000.000
41A41THR00.0440.00627.593-0.004-0.0040.0000.0000.0000.000
42A42ILE0-0.053-0.00129.087-0.005-0.0050.0000.0000.0000.000
43A43ASP-1-0.765-0.88128.8720.1360.1360.0000.0000.0000.000
44A44SER0-0.058-0.01224.600-0.003-0.0030.0000.0000.0000.000
45A45ASN0-0.007-0.02026.2890.0040.0040.0000.0000.0000.000
46A46THR0-0.049-0.02428.589-0.010-0.0100.0000.0000.0000.000
47A47GLN00.0910.06129.3530.0020.0020.0000.0000.0000.000
48A48SER00.044-0.00128.125-0.001-0.0010.0000.0000.0000.000
49A49GLY00.0380.03130.076-0.004-0.0040.0000.0000.0000.000
50A51ASN0-0.057-0.03428.225-0.010-0.0100.0000.0000.0000.000
51A52GLY00.0250.01832.5340.0020.0020.0000.0000.0000.000
52A53GLY0-0.048-0.01933.6610.0020.0020.0000.0000.0000.000
53A54SER00.012-0.00433.613-0.004-0.0040.0000.0000.0000.000
54A55SER0-0.072-0.02528.6810.0020.0020.0000.0000.0000.000
55A56TYR00.028-0.00728.903-0.003-0.0030.0000.0000.0000.000
56A57VAL00.0360.03423.4390.0140.0140.0000.0000.0000.000
57A59ASN00.032-0.01625.689-0.009-0.0090.0000.0000.0000.000
58A60ASP-1-0.893-0.95524.4000.0900.0900.0000.0000.0000.000
59A61GLN0-0.089-0.05220.696-0.002-0.0020.0000.0000.0000.000
60A62GLN0-0.003-0.00722.174-0.021-0.0210.0000.0000.0000.000
61A63PRO0-0.034-0.00220.7040.0100.0100.0000.0000.0000.000
62A64PHE0-0.027-0.02818.5270.0050.0050.0000.0000.0000.000
63A65THR00.0220.00720.413-0.015-0.0150.0000.0000.0000.000
64A66GLN0-0.009-0.00517.7630.0220.0220.0000.0000.0000.000
65A67GLY00.0280.02419.697-0.010-0.0100.0000.0000.0000.000
66A68ASN00.004-0.00820.7850.0040.0040.0000.0000.0000.000
67A69VAL0-0.0200.00414.748-0.022-0.0220.0000.0000.0000.000
68A70GLY00.0560.02817.4390.0240.0240.0000.0000.0000.000
69A71TYR0-0.012-0.01913.965-0.006-0.0060.0000.0000.0000.000
70A72GLY00.0570.01415.949-0.006-0.0060.0000.0000.0000.000
71A73PHE0-0.0300.00115.8690.0220.0220.0000.0000.0000.000
72A74ALA00.0090.00414.809-0.028-0.0280.0000.0000.0000.000
73A75ALA00.0110.01416.0410.0430.0430.0000.0000.0000.000
74A76ALA0-0.005-0.00812.533-0.038-0.0380.0000.0000.0000.000
75A77SER00.0280.00514.3810.0520.0520.0000.0000.0000.000
76A78ILE0-0.045-0.0208.191-0.055-0.0550.0000.0000.0000.000
77A79SER0-0.001-0.02310.553-0.086-0.0860.0000.0000.0000.000
78A80GLY00.0250.03211.698-0.062-0.0620.0000.0000.0000.000
79A81GLN00.006-0.0065.7790.3050.3050.0000.0000.0000.000
80A82PRO00.0310.02410.3830.0330.0330.0000.0000.0000.000
81A83GLU-1-0.644-0.80711.3000.1530.1530.0000.0000.0000.000
82A84SER00.0040.00612.2500.0590.0590.0000.0000.0000.000
83A85GLN0-0.043-0.0255.8480.3500.3500.0000.0000.0000.000
84A86THR00.0310.0287.3600.1580.1580.0000.0000.0000.000
85A88CYS0-0.0560.00711.6980.1390.1390.0000.0000.0000.000
86A89ALA00.0160.0186.9570.1410.1410.0000.0000.0000.000
87A90CYS0-0.076-0.0226.886-0.358-0.3580.0000.0000.0000.000
88A91TYR00.0760.0265.8140.1590.1590.0000.0000.0000.000
89A92GLU-1-0.870-0.8977.337-0.242-0.2420.0000.0000.0000.000
90A93MET00.0310.0108.905-0.197-0.1970.0000.0000.0000.000
91A94THR0-0.041-0.01811.6740.0580.0580.0000.0000.0000.000
92A95PHE00.0410.00514.106-0.045-0.0450.0000.0000.0000.000
93A96THR0-0.044-0.04516.186-0.017-0.0170.0000.0000.0000.000
94A97ASN00.0630.03918.5100.0050.0050.0000.0000.0000.000
95A98THR00.0620.05522.0710.0150.0150.0000.0000.0000.000
96A99ALA00.0580.02424.379-0.003-0.0030.0000.0000.0000.000
97A100ILE0-0.051-0.01120.8160.0070.0070.0000.0000.0000.000
98A101SER0-0.038-0.01520.518-0.027-0.0270.0000.0000.0000.000
99A102GLY00.0210.00918.3750.0180.0180.0000.0000.0000.000
100A103GLN0-0.031-0.00917.9240.0040.0040.0000.0000.0000.000
101A104LYS10.8790.91210.9540.2810.2810.0000.0000.0000.000
102A105MET0-0.033-0.00214.2780.0430.0430.0000.0000.0000.000
103A106ILE0-0.015-0.00810.057-0.052-0.0520.0000.0000.0000.000
104A107VAL00.0200.00911.6740.0390.0390.0000.0000.0000.000
105A108GLN0-0.015-0.01311.309-0.029-0.0290.0000.0000.0000.000
106A109VAL00.0080.01311.284-0.036-0.0360.0000.0000.0000.000
107A110THR0-0.013-0.02213.3560.0690.0690.0000.0000.0000.000
108A111ASN00.0540.01816.2810.0280.0280.0000.0000.0000.000
109A112THR00.0190.01616.065-0.018-0.0180.0000.0000.0000.000
110A113GLY00.0040.01617.3490.0110.0110.0000.0000.0000.000
111A114SER00.001-0.00719.4660.0160.0160.0000.0000.0000.000
112A115ASP-1-0.937-0.95618.233-0.214-0.2140.0000.0000.0000.000
113A116LEU0-0.0150.00019.4060.0050.0050.0000.0000.0000.000
114A117ASN00.0230.00818.169-0.055-0.0550.0000.0000.0000.000
115A118GLY00.0350.03515.6500.0010.0010.0000.0000.0000.000
116A119ASN0-0.040-0.02711.271-0.029-0.0290.0000.0000.0000.000
117A120HIS00.010-0.00514.0820.0260.0260.0000.0000.0000.000
118A121PHE0-0.022-0.0249.8330.0260.0260.0000.0000.0000.000
119A122ASP-1-0.826-0.87416.083-0.156-0.1560.0000.0000.0000.000
120A123LEU00.007-0.01817.1820.0260.0260.0000.0000.0000.000
121A124MET0-0.018-0.00119.5490.0120.0120.0000.0000.0000.000
122A125ILE0-0.014-0.01521.7210.0070.0070.0000.0000.0000.000
123A126PRO0-0.041-0.00624.672-0.003-0.0030.0000.0000.0000.000
124A127GLY00.0660.02328.169-0.003-0.0030.0000.0000.0000.000
125A128GLY0-0.031-0.01427.296-0.004-0.0040.0000.0000.0000.000
126A129GLY00.0520.03728.251-0.009-0.0090.0000.0000.0000.000
127A130VAL0-0.071-0.01828.0430.0000.0000.0000.0000.0000.000
128A131GLY00.0580.03227.7070.0000.0000.0000.0000.0000.000
129A132ILE00.0440.02425.7530.0070.0070.0000.0000.0000.000
130A133PHE00.0040.01024.9890.0070.0070.0000.0000.0000.000
131A134ASN00.019-0.02229.651-0.001-0.0010.0000.0000.0000.000
132A135GLY00.0420.01630.7010.0030.0030.0000.0000.0000.000
133A137GLN0-0.046-0.00933.3910.0030.0030.0000.0000.0000.000
134A138SER00.0390.01935.3360.0020.0020.0000.0000.0000.000
135A139GLN0-0.047-0.01230.5990.0000.0000.0000.0000.0000.000
136A140TRP0-0.051-0.05831.4140.0010.0010.0000.0000.0000.000
137A141GLY00.0180.02536.769-0.001-0.0010.0000.0000.0000.000
138A142ALA0-0.054-0.01135.916-0.003-0.0030.0000.0000.0000.000
139A143PRO00.0730.02037.6400.0020.0020.0000.0000.0000.000
140A144SER00.0670.03137.6970.0000.0000.0000.0000.0000.000
141A145ASN0-0.069-0.03436.4990.0030.0030.0000.0000.0000.000
142A146GLY00.0300.00834.016-0.005-0.0050.0000.0000.0000.000
143A147TRP0-0.009-0.02231.0450.0000.0000.0000.0000.0000.000
144A148GLY00.0230.01634.181-0.004-0.0040.0000.0000.0000.000
145A149GLN00.0160.01033.8020.0050.0050.0000.0000.0000.000
146A150ARG10.8810.93532.1260.0360.0360.0000.0000.0000.000
147A151TYR00.026-0.00527.9260.0000.0000.0000.0000.0000.000
148A152GLY00.0400.02929.029-0.003-0.0030.0000.0000.0000.000
149A153GLY00.0180.00730.0610.0000.0000.0000.0000.0000.000
150A154ILE0-0.050-0.02132.143-0.001-0.0010.0000.0000.0000.000
151A155SER00.0120.00532.996-0.009-0.0090.0000.0000.0000.000
152A156SER0-0.041-0.02834.949-0.005-0.0050.0000.0000.0000.000
153A157GLN00.001-0.00433.8030.0020.0020.0000.0000.0000.000
154A158SER00.0490.02235.0580.0040.0040.0000.0000.0000.000
155A159GLU-1-0.755-0.88336.673-0.043-0.0430.0000.0000.0000.000
156A160CYS0-0.067-0.02626.986-0.010-0.0100.0000.0000.0000.000
157A161ASN0-0.074-0.04535.4300.0070.0070.0000.0000.0000.000
158A162GLN0-0.010-0.00738.0470.0030.0030.0000.0000.0000.000
159A163LEU0-0.0120.01431.9320.0020.0020.0000.0000.0000.000
160A164PRO00.0530.03333.9300.0010.0010.0000.0000.0000.000
161A165THR00.0560.01234.585-0.002-0.0020.0000.0000.0000.000
162A166SER0-0.025-0.00832.314-0.002-0.0020.0000.0000.0000.000
163A167LEU00.0090.00928.7480.0030.0030.0000.0000.0000.000
164A168ARG10.8990.95330.0930.0020.0020.0000.0000.0000.000
165A169ALA00.0180.02828.395-0.006-0.0060.0000.0000.0000.000
166A170GLY00.0590.02426.135-0.007-0.0070.0000.0000.0000.000
167A172ASN00.021-0.01229.214-0.011-0.0110.0000.0000.0000.000
168A173TRP0-0.0010.00120.047-0.010-0.0100.0000.0000.0000.000
169A174ARG10.8180.89625.6630.0640.0640.0000.0000.0000.000
170A175PHE00.021-0.01026.698-0.011-0.0110.0000.0000.0000.000
171A176GLY00.0040.02428.301-0.001-0.0010.0000.0000.0000.000
172A177TRP0-0.040-0.02718.241-0.009-0.0090.0000.0000.0000.000
173A178PHE0-0.010-0.01120.577-0.013-0.0130.0000.0000.0000.000
174A179LYS10.8810.93924.2350.1190.1190.0000.0000.0000.000
175A180ASN00.0070.00727.419-0.002-0.0020.0000.0000.0000.000
176A181ALA0-0.0240.01124.005-0.004-0.0040.0000.0000.0000.000
177A182ASP-1-0.811-0.90325.657-0.129-0.1290.0000.0000.0000.000
178A183ASN0-0.030-0.01122.534-0.009-0.0090.0000.0000.0000.000
179A184PRO0-0.0250.00619.930-0.014-0.0140.0000.0000.0000.000
180A185SER00.0440.02118.141-0.015-0.0150.0000.0000.0000.000
181A186MET0-0.063-0.01312.400-0.010-0.0100.0000.0000.0000.000
182A187LYS10.9530.99011.1140.5810.5810.0000.0000.0000.000
183A188PHE00.012-0.0177.2720.0880.0880.0000.0000.0000.000
184A189THR0-0.008-0.0163.365-0.856-0.4440.036-0.081-0.3660.000
185A190GLN00.0230.0312.228-2.2110.1672.105-1.556-2.926-0.011
186A191VAL00.0050.0012.539-1.851-0.6561.296-0.974-1.516-0.014
187A192ARG10.9530.9674.521-0.994-0.924-0.001-0.004-0.0650.000
188A194PRO00.0520.03010.0110.0190.0190.0000.0000.0000.000
189A195THR00.0790.02012.590-0.010-0.0100.0000.0000.0000.000
190A196ILE0-0.0200.00915.785-0.012-0.0120.0000.0000.0000.000
191A197LEU00.0140.01712.795-0.021-0.0210.0000.0000.0000.000
192A198THR00.0350.00813.654-0.022-0.0220.0000.0000.0000.000
193A199GLN0-0.0120.00716.484-0.007-0.0070.0000.0000.0000.000
194A200LYS10.8690.94519.328-0.109-0.1090.0000.0000.0000.000
195A201SER0-0.024-0.03716.2600.0010.0010.0000.0000.0000.000
196A202GLN0-0.023-0.01319.1520.0010.0010.0000.0000.0000.000
197A204VAL00.014-0.00613.2830.0180.0180.0000.0000.0000.000
198A205ARG10.8560.9067.924-1.086-1.0860.0000.0000.0000.000
199A206THR00.0250.00311.9370.0650.0650.0000.0000.0000.000
200A207PRO0-0.054-0.00611.028-0.029-0.0290.0000.0000.0000.000
201A208GLY0-0.0070.0127.290-0.013-0.0130.0000.0000.0000.000