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: 221GR

Calculation Name: 4XPU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XPU

Chain ID: A

ChEMBL ID:

UniProt ID: P68739

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2428114.408849
FMO2-HF: Nuclear repulsion 2347298.903227
FMO2-HF: Total energy -80815.505622
FMO2-MP2: Total energy -81050.237924


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.
-0.6791.7266.488-3.105-5.788-0.01
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 : 0.039 / q_NPA : 0.025
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].
3A3LEU00.0050.0032.983-3.0720.2410.412-1.429-2.2960.001
4A4ALA00.009-0.0091.7720.529-0.6206.055-1.883-3.023-0.011
5A5SER00.012-0.0023.3411.1141.3550.0210.207-0.4690.000
6A6LEU00.0170.0215.7160.6310.6310.0000.0000.0000.000
7A7ARG10.8610.9286.3920.3290.3290.0000.0000.0000.000
8A8ALA00.0100.0047.4320.1440.1440.0000.0000.0000.000
9A9GLN00.0830.0309.2940.3140.3140.0000.0000.0000.000
10A10GLN00.0100.01610.8720.1640.1640.0000.0000.0000.000
11A11ILE0-0.039-0.03311.7590.0790.0790.0000.0000.0000.000
12A12GLU-1-0.904-0.92613.573-0.522-0.5220.0000.0000.0000.000
13A13LEU00.0310.01515.0450.0510.0510.0000.0000.0000.000
14A14ALA0-0.029-0.02516.4850.0370.0370.0000.0000.0000.000
15A15SER0-0.082-0.05217.5160.0340.0340.0000.0000.0000.000
16A16SER0-0.031-0.01819.3350.0090.0090.0000.0000.0000.000
17A17VAL0-0.055-0.01821.0000.0110.0110.0000.0000.0000.000
18A18ILE0-0.0040.00823.4670.0090.0090.0000.0000.0000.000
19A19ARG10.8070.88023.1390.0870.0870.0000.0000.0000.000
20A20GLU-1-0.808-0.89228.967-0.078-0.0780.0000.0000.0000.000
21A21ASP-1-0.756-0.84332.252-0.057-0.0570.0000.0000.0000.000
22A22ARG10.8430.90530.2210.1010.1010.0000.0000.0000.000
23A23LEU00.0200.01034.133-0.005-0.0050.0000.0000.0000.000
24A24ASP-1-0.875-0.91435.289-0.083-0.0830.0000.0000.0000.000
25A25LYS10.7580.85838.0580.0530.0530.0000.0000.0000.000
26A26ASP-1-0.876-0.92840.174-0.043-0.0430.0000.0000.0000.000
27A27PRO0-0.018-0.01942.1380.0010.0010.0000.0000.0000.000
28A28PRO0-0.030-0.00639.730-0.001-0.0010.0000.0000.0000.000
29A29ASP-1-0.827-0.90741.826-0.039-0.0390.0000.0000.0000.000
30A30LEU0-0.064-0.03639.3790.0030.0030.0000.0000.0000.000
31A31ILE0-0.0070.00037.523-0.003-0.0030.0000.0000.0000.000
32A32ALA00.0480.01233.9660.0020.0020.0000.0000.0000.000
33A33GLY0-0.054-0.02633.6230.0010.0010.0000.0000.0000.000
34A34ALA0-0.011-0.00629.100-0.002-0.0020.0000.0000.0000.000
35A35ASP-1-0.808-0.89829.1550.0020.0020.0000.0000.0000.000
36A36VAL0-0.016-0.00523.997-0.007-0.0070.0000.0000.0000.000
37A37GLY0-0.0090.00825.8880.0080.0080.0000.0000.0000.000
38A38PHE0-0.040-0.02220.2760.0010.0010.0000.0000.0000.000
39A39GLU-1-0.745-0.84725.2300.0170.0170.0000.0000.0000.000
40A40GLN00.025-0.00125.7780.0080.0080.0000.0000.0000.000
41A41GLY00.0120.00825.4640.0070.0070.0000.0000.0000.000
42A42GLY0-0.033-0.01421.8180.0180.0180.0000.0000.0000.000
43A43GLU-1-0.878-0.93020.6000.1130.1130.0000.0000.0000.000
44A44VAL0-0.025-0.00222.488-0.016-0.0160.0000.0000.0000.000
45A45THR0-0.023-0.01821.8660.0110.0110.0000.0000.0000.000
46A46ARG10.8030.88724.271-0.011-0.0110.0000.0000.0000.000
47A47ALA00.006-0.00426.2020.0020.0020.0000.0000.0000.000
48A48ALA0-0.0160.00128.156-0.001-0.0010.0000.0000.0000.000
49A49MET0-0.005-0.00228.521-0.002-0.0020.0000.0000.0000.000
50A50VAL0-0.002-0.00632.9120.0040.0040.0000.0000.0000.000
51A51LEU00.0270.01835.929-0.004-0.0040.0000.0000.0000.000
52A52LEU0-0.016-0.01538.5420.0040.0040.0000.0000.0000.000
53A53LYS10.9120.95341.3670.0220.0220.0000.0000.0000.000
54A54TYR0-0.060-0.00942.4220.0020.0020.0000.0000.0000.000
55A55PRO00.0720.02344.527-0.001-0.0010.0000.0000.0000.000
56A56SER0-0.052-0.05846.6170.0010.0010.0000.0000.0000.000
57A57LEU0-0.025-0.01542.0530.0030.0030.0000.0000.0000.000
58A58GLU-1-0.822-0.86444.584-0.021-0.0210.0000.0000.0000.000
59A59LEU0-0.002-0.00340.820-0.002-0.0020.0000.0000.0000.000
60A60VAL0-0.036-0.02042.1100.0010.0010.0000.0000.0000.000
61A61GLU-1-0.765-0.85138.290-0.043-0.0430.0000.0000.0000.000
62A62TYR00.000-0.00237.4440.0010.0010.0000.0000.0000.000
63A63LYS10.7990.90434.2450.0420.0420.0000.0000.0000.000
64A64VAL00.004-0.00332.2470.0010.0010.0000.0000.0000.000
65A65ALA00.0250.02828.592-0.001-0.0010.0000.0000.0000.000
66A66ARG10.8000.84627.7260.0020.0020.0000.0000.0000.000
67A67ILE00.0030.01421.898-0.005-0.0050.0000.0000.0000.000
68A68ALA00.0370.01922.2010.0110.0110.0000.0000.0000.000
69A69THR0-0.047-0.02618.051-0.028-0.0280.0000.0000.0000.000
70A70THR00.0090.01015.7200.0340.0340.0000.0000.0000.000
71A71MET00.0130.01810.575-0.040-0.0400.0000.0000.0000.000
72A72PRO00.0880.05511.999-0.009-0.0090.0000.0000.0000.000
73A73TYR00.014-0.01014.156-0.031-0.0310.0000.0000.0000.000
74A74ILE00.0580.0288.6880.0910.0910.0000.0000.0000.000
75A75PRO00.015-0.00212.047-0.105-0.1050.0000.0000.0000.000
76A76GLY0-0.018-0.00212.4260.0370.0370.0000.0000.0000.000
77A77PHE00.0440.0098.319-0.035-0.0350.0000.0000.0000.000
78A78LEU0-0.0240.00213.195-0.030-0.0300.0000.0000.0000.000
79A79SER00.0380.01916.257-0.002-0.0020.0000.0000.0000.000
80A80PHE00.003-0.00711.992-0.007-0.0070.0000.0000.0000.000
81A81ARG10.7840.89215.292-0.112-0.1120.0000.0000.0000.000
82A82GLU-1-0.865-0.95317.492-0.008-0.0080.0000.0000.0000.000
83A83TYR00.0350.02118.679-0.006-0.0060.0000.0000.0000.000
84A84PRO00.0230.00718.2560.0020.0020.0000.0000.0000.000
85A85ALA00.0320.02321.2100.0050.0050.0000.0000.0000.000
86A86LEU00.008-0.00323.2050.0040.0040.0000.0000.0000.000
87A87LEU00.0010.01022.4580.0040.0040.0000.0000.0000.000
88A88ALA00.0160.00825.3340.0040.0040.0000.0000.0000.000
89A89ALA0-0.002-0.01727.0360.0050.0050.0000.0000.0000.000
90A90TRP00.0400.00028.2420.0080.0080.0000.0000.0000.000
91A91GLU-1-0.872-0.93927.671-0.100-0.1000.0000.0000.0000.000
92A92MET0-0.074-0.01930.5440.0050.0050.0000.0000.0000.000
93A93LEU0-0.075-0.02132.9160.0070.0070.0000.0000.0000.000
94A94SER0-0.057-0.05735.396-0.005-0.0050.0000.0000.0000.000
95A95GLN0-0.027-0.01238.019-0.001-0.0010.0000.0000.0000.000
96A96LYS10.8380.91632.0140.0800.0800.0000.0000.0000.000
97A97PRO0-0.054-0.01233.9110.0020.0020.0000.0000.0000.000
98A98ASP-1-0.714-0.86035.258-0.058-0.0580.0000.0000.0000.000
99A99LEU0-0.040-0.01933.895-0.003-0.0030.0000.0000.0000.000
100A100VAL00.0080.00529.9940.0040.0040.0000.0000.0000.000
101A101PHE0-0.015-0.01931.9700.0000.0000.0000.0000.0000.000
102A102VAL00.0360.01025.8200.0030.0030.0000.0000.0000.000
103A103ASP-1-0.808-0.91629.2470.0010.0010.0000.0000.0000.000
104A104GLY00.0190.00625.9440.0060.0060.0000.0000.0000.000
105A105HIS10.7740.87923.279-0.010-0.0100.0000.0000.0000.000
106A106GLY00.0820.05923.799-0.006-0.0060.0000.0000.0000.000
107A107ILE00.0650.02822.6090.0070.0070.0000.0000.0000.000
108A108SER0-0.0130.02223.2490.0080.0080.0000.0000.0000.000
109A109HIS00.041-0.00516.4250.0070.0070.0000.0000.0000.000
110A110PRO0-0.018-0.02417.711-0.011-0.0110.0000.0000.0000.000
111A111ARG10.7540.87611.188-0.192-0.1920.0000.0000.0000.000
112A112ARG10.7530.86116.671-0.004-0.0040.0000.0000.0000.000
113A113LEU00.0590.03315.432-0.011-0.0110.0000.0000.0000.000
114A114GLY0-0.041-0.01017.9260.0130.0130.0000.0000.0000.000
115A115VAL00.0320.01020.602-0.021-0.0210.0000.0000.0000.000
116A116ALA0-0.0130.00421.598-0.013-0.0130.0000.0000.0000.000
117A117SER00.001-0.02021.4490.0000.0000.0000.0000.0000.000
118A118HIS0-0.0230.00314.8730.0170.0170.0000.0000.0000.000
119A119PHE00.025-0.00920.142-0.019-0.0190.0000.0000.0000.000
120A120GLY00.0320.00923.123-0.007-0.0070.0000.0000.0000.000
121A121LEU0-0.017-0.00419.831-0.003-0.0030.0000.0000.0000.000
122A122LEU0-0.037-0.02617.847-0.012-0.0120.0000.0000.0000.000
123A123VAL0-0.046-0.01622.236-0.004-0.0040.0000.0000.0000.000
124A124ASP-1-0.831-0.89125.538-0.124-0.1240.0000.0000.0000.000
125A125VAL00.0380.02527.3560.0100.0100.0000.0000.0000.000
126A126PRO0-0.0030.01829.205-0.001-0.0010.0000.0000.0000.000
127A127THR0-0.009-0.01327.1520.0060.0060.0000.0000.0000.000
128A128ILE0-0.036-0.00829.436-0.001-0.0010.0000.0000.0000.000
129A129GLY00.0350.01027.7650.0000.0000.0000.0000.0000.000
130A130VAL0-0.029-0.01928.6290.0040.0040.0000.0000.0000.000
131A131ALA00.0010.01327.7810.0050.0050.0000.0000.0000.000
132A132LYS10.8030.87929.707-0.001-0.0010.0000.0000.0000.000
133A133LYS10.9380.97128.664-0.033-0.0330.0000.0000.0000.000
134A134ARG10.9470.98026.752-0.051-0.0510.0000.0000.0000.000
135A135LEU0-0.038-0.01421.0980.0040.0040.0000.0000.0000.000
136A136CYS0-0.020-0.00422.5950.0100.0100.0000.0000.0000.000
137A137GLY00.0660.03724.738-0.007-0.0070.0000.0000.0000.000
138A138LYS10.9090.94827.456-0.019-0.0190.0000.0000.0000.000
139A139PHE00.0460.02231.135-0.003-0.0030.0000.0000.0000.000
140A140GLU-1-0.881-0.93534.5080.0070.0070.0000.0000.0000.000
141A141PRO0-0.060-0.04238.084-0.001-0.0010.0000.0000.0000.000
142A142LEU0-0.0030.01438.483-0.001-0.0010.0000.0000.0000.000
143A143SER00.016-0.01641.3380.0020.0020.0000.0000.0000.000
144A144SER00.003-0.00344.1910.0000.0000.0000.0000.0000.000
145A145GLU-1-0.816-0.88046.1840.0040.0040.0000.0000.0000.000
146A146PRO0-0.049-0.03345.2360.0000.0000.0000.0000.0000.000
147A147GLY00.0410.00844.336-0.001-0.0010.0000.0000.0000.000
148A148ALA00.0000.01942.863-0.001-0.0010.0000.0000.0000.000
149A149LEU00.012-0.00738.5870.0000.0000.0000.0000.0000.000
150A150ALA00.0210.02337.5850.0010.0010.0000.0000.0000.000
151A151PRO00.0330.03434.577-0.001-0.0010.0000.0000.0000.000
152A152LEU0-0.077-0.03728.0080.0050.0050.0000.0000.0000.000
153A153MET00.0280.02030.315-0.006-0.0060.0000.0000.0000.000
154A154ASP-1-0.792-0.90423.7030.0240.0240.0000.0000.0000.000
155A155LYS10.8120.89121.287-0.028-0.0280.0000.0000.0000.000
156A156GLY00.0570.04427.084-0.003-0.0030.0000.0000.0000.000
157A157GLU-1-0.753-0.82924.595-0.055-0.0550.0000.0000.0000.000
158A158GLN00.022-0.01128.7770.0070.0070.0000.0000.0000.000
159A159LEU0-0.079-0.04324.579-0.004-0.0040.0000.0000.0000.000
160A160ALA0-0.011-0.03228.218-0.003-0.0030.0000.0000.0000.000
161A161TRP00.0020.00030.9200.0050.0050.0000.0000.0000.000
162A162VAL0-0.064-0.02432.9270.0010.0010.0000.0000.0000.000
163A163TRP00.0690.02735.3030.0000.0000.0000.0000.0000.000
164A164ARG10.7770.87538.415-0.008-0.0080.0000.0000.0000.000
165A165SER0-0.004-0.01339.8370.0000.0000.0000.0000.0000.000
166A166LYS10.9080.93841.820-0.002-0.0020.0000.0000.0000.000
167A167ALA00.0690.02844.0700.0020.0020.0000.0000.0000.000
168A168ARG10.9430.96045.393-0.009-0.0090.0000.0000.0000.000
169A169CYS0-0.0310.02040.9170.0020.0020.0000.0000.0000.000
170A170ASN00.0270.00636.8250.0000.0000.0000.0000.0000.000
171A171PRO00.0120.02335.795-0.002-0.0020.0000.0000.0000.000
172A172LEU0-0.0290.01234.3360.0030.0030.0000.0000.0000.000
173A173PHE0-0.021-0.02830.1430.0010.0010.0000.0000.0000.000
174A174ILE00.0230.02430.322-0.001-0.0010.0000.0000.0000.000
175A175ALA00.016-0.00327.6530.0010.0010.0000.0000.0000.000
176A176THR00.0450.03126.7770.0000.0000.0000.0000.0000.000
177A177GLY0-0.012-0.00425.8140.0000.0000.0000.0000.0000.000
178A178HIS00.007-0.01125.182-0.008-0.0080.0000.0000.0000.000
179A179ARG10.7980.88727.1300.1090.1090.0000.0000.0000.000
180A180VAL00.0140.01430.2760.0070.0070.0000.0000.0000.000
181A181SER0-0.001-0.01130.885-0.001-0.0010.0000.0000.0000.000
182A182VAL0-0.013-0.02931.5660.0020.0020.0000.0000.0000.000
183A183ASP-1-0.838-0.91233.103-0.029-0.0290.0000.0000.0000.000
184A184SER00.006-0.02536.2910.0040.0040.0000.0000.0000.000
185A185ALA0-0.0070.00432.8780.0010.0010.0000.0000.0000.000
186A186LEU0-0.048-0.02434.8990.0030.0030.0000.0000.0000.000
187A187ALA00.0340.01637.1820.0020.0020.0000.0000.0000.000
188A188TRP00.0130.00036.6560.0040.0040.0000.0000.0000.000
189A189VAL00.013-0.00435.1270.0020.0020.0000.0000.0000.000
190A190GLN0-0.039-0.02838.2040.0010.0010.0000.0000.0000.000
191A191ARG10.8890.95541.6120.0350.0350.0000.0000.0000.000
192A192CYS0-0.0080.00839.542-0.001-0.0010.0000.0000.0000.000
193A193MET0-0.055-0.00939.5050.0030.0030.0000.0000.0000.000
194A194LYS10.9020.95143.3130.0160.0160.0000.0000.0000.000
195A195GLY00.0530.03145.7590.0010.0010.0000.0000.0000.000
196A196TYR0-0.042-0.01242.5320.0020.0020.0000.0000.0000.000
197A197ARG10.8320.88534.391-0.012-0.0120.0000.0000.0000.000
198A198LEU00.0020.02735.1530.0000.0000.0000.0000.0000.000
199A199PRO00.0410.02436.5490.0010.0010.0000.0000.0000.000
200A200GLU-1-0.768-0.87838.496-0.012-0.0120.0000.0000.0000.000
201A201PRO00.0320.02835.8390.0010.0010.0000.0000.0000.000
202A202THR00.0340.00532.7470.0000.0000.0000.0000.0000.000
203A203ARG10.7720.87735.1930.0120.0120.0000.0000.0000.000
204A204TRP00.031-0.00538.2510.0040.0040.0000.0000.0000.000
205A205ALA00.0150.01633.0990.0010.0010.0000.0000.0000.000
206A206ASP-1-0.829-0.90533.7710.0040.0040.0000.0000.0000.000
207A207ALA0-0.079-0.03135.4250.0030.0030.0000.0000.0000.000
208A208VAL0-0.058-0.01035.1550.0020.0020.0000.0000.0000.000