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: M37ZZ

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2427743.267827
FMO2-HF: Nuclear repulsion 2346929.098378
FMO2-HF: Total energy -80814.16945
FMO2-MP2: Total energy -81048.803941


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.
0.6750.53911.562-3.418-8.008-0.016
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 : -0.016 / q_NPA : -0.020
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].
3A3LEU00.0310.0052.111-4.076-1.1662.140-1.755-3.295-0.011
4A4ALA0-0.033-0.0291.9662.133-1.1349.396-2.034-4.095-0.005
5A5SER0-0.002-0.0053.3911.2261.3070.0270.378-0.4860.000
6A6LEU00.0560.0325.3090.4510.591-0.001-0.007-0.1320.000
7A7ARG10.8920.9486.5120.7010.7010.0000.0000.0000.000
8A8ALA0-0.0020.0037.2750.1650.1650.0000.0000.0000.000
9A9GLN00.0940.0358.9590.2160.2160.0000.0000.0000.000
10A10GLN0-0.0230.00910.9250.0690.0690.0000.0000.0000.000
11A11ILE0-0.070-0.04612.0590.0750.0750.0000.0000.0000.000
12A12GLU-1-0.886-0.92913.405-0.459-0.4590.0000.0000.0000.000
13A13LEU00.0230.00114.9310.0500.0500.0000.0000.0000.000
14A14ALA0-0.033-0.03116.6980.0340.0340.0000.0000.0000.000
15A15SER0-0.044-0.03017.9200.0300.0300.0000.0000.0000.000
16A16SER0-0.035-0.00319.1350.0140.0140.0000.0000.0000.000
17A17VAL0-0.052-0.00621.3020.0210.0210.0000.0000.0000.000
18A18ILE0-0.0190.01423.539-0.003-0.0030.0000.0000.0000.000
19A19ARG10.8700.91323.0900.1340.1340.0000.0000.0000.000
20A20GLU-1-0.793-0.87129.199-0.076-0.0760.0000.0000.0000.000
21A21ASP-1-0.728-0.80832.298-0.047-0.0470.0000.0000.0000.000
22A22ARG10.8280.89029.5960.0850.0850.0000.0000.0000.000
23A23LEU00.0130.01034.1090.0000.0000.0000.0000.0000.000
24A24ASP-1-0.843-0.91935.229-0.046-0.0460.0000.0000.0000.000
25A25LYS10.8060.88937.8860.0150.0150.0000.0000.0000.000
26A26ASP-1-0.912-0.92440.430-0.026-0.0260.0000.0000.0000.000
27A27PRO0-0.030-0.03742.2110.0000.0000.0000.0000.0000.000
28A28PRO0-0.008-0.00839.5700.0010.0010.0000.0000.0000.000
29A29ASP-1-0.832-0.90241.633-0.008-0.0080.0000.0000.0000.000
30A30LEU0-0.073-0.04339.6760.0040.0040.0000.0000.0000.000
31A31ILE0-0.0240.00237.539-0.003-0.0030.0000.0000.0000.000
32A32ALA00.0480.00433.9600.0040.0040.0000.0000.0000.000
33A33GLY0-0.051-0.01433.807-0.004-0.0040.0000.0000.0000.000
34A34ALA0-0.018-0.01829.0000.0030.0030.0000.0000.0000.000
35A35ASP-1-0.846-0.92629.1420.0530.0530.0000.0000.0000.000
36A36VAL0-0.010-0.01223.5830.0040.0040.0000.0000.0000.000
37A37GLY0-0.0130.00125.045-0.003-0.0030.0000.0000.0000.000
38A38PHE0-0.067-0.03419.8430.0080.0080.0000.0000.0000.000
39A39GLU-1-0.769-0.87924.9710.1060.1060.0000.0000.0000.000
40A40GLN00.008-0.01125.6000.0150.0150.0000.0000.0000.000
41A41GLY00.0110.00925.0650.0150.0150.0000.0000.0000.000
42A42GLY0-0.028-0.01121.3860.0200.0200.0000.0000.0000.000
43A43GLU-1-0.892-0.93120.8570.3390.3390.0000.0000.0000.000
44A44VAL0-0.0150.00222.586-0.001-0.0010.0000.0000.0000.000
45A45THR0-0.044-0.01321.533-0.004-0.0040.0000.0000.0000.000
46A46ARG10.9040.93823.922-0.083-0.0830.0000.0000.0000.000
47A47ALA00.0190.00426.218-0.003-0.0030.0000.0000.0000.000
48A48ALA0-0.037-0.00528.1610.0010.0010.0000.0000.0000.000
49A49MET0-0.019-0.00728.570-0.007-0.0070.0000.0000.0000.000
50A50VAL0-0.017-0.01433.0160.0020.0020.0000.0000.0000.000
51A51LEU00.0400.02436.145-0.004-0.0040.0000.0000.0000.000
52A52LEU0-0.037-0.02138.6360.0020.0020.0000.0000.0000.000
53A53LYS10.9480.99541.382-0.011-0.0110.0000.0000.0000.000
54A54TYR0-0.0320.02142.3200.0010.0010.0000.0000.0000.000
55A55PRO00.045-0.00244.3810.0000.0000.0000.0000.0000.000
56A56SER0-0.063-0.03546.5510.0000.0000.0000.0000.0000.000
57A57LEU0-0.024-0.02742.4560.0010.0010.0000.0000.0000.000
58A58GLU-1-0.899-0.94644.3920.0110.0110.0000.0000.0000.000
59A59LEU0-0.017-0.00740.817-0.001-0.0010.0000.0000.0000.000
60A60VAL0-0.013-0.00942.1350.0000.0000.0000.0000.0000.000
61A61GLU-1-0.794-0.86638.5280.0280.0280.0000.0000.0000.000
62A62TYR0-0.008-0.00237.3740.0000.0000.0000.0000.0000.000
63A63LYS10.8770.95234.323-0.036-0.0360.0000.0000.0000.000
64A64VAL00.001-0.00231.8800.0000.0000.0000.0000.0000.000
65A65ALA00.0410.03328.4280.0020.0020.0000.0000.0000.000
66A66ARG10.8200.88327.754-0.100-0.1000.0000.0000.0000.000
67A67ILE00.0120.01321.845-0.001-0.0010.0000.0000.0000.000
68A68ALA00.0200.01521.9920.0010.0010.0000.0000.0000.000
69A69THR0-0.058-0.04717.661-0.013-0.0130.0000.0000.0000.000
70A70THR00.0180.01215.6840.0190.0190.0000.0000.0000.000
71A71MET00.0110.02110.2870.0460.0460.0000.0000.0000.000
72A72PRO00.0700.04111.610-0.077-0.0770.0000.0000.0000.000
73A73TYR0-0.005-0.02613.049-0.038-0.0380.0000.0000.0000.000
74A74ILE00.0520.0357.9720.0610.0610.0000.0000.0000.000
75A75PRO00.0240.00311.518-0.099-0.0990.0000.0000.0000.000
76A76GLY0-0.042-0.02311.759-0.005-0.0050.0000.0000.0000.000
77A77PHE00.024-0.0048.454-0.096-0.0960.0000.0000.0000.000
78A78LEU0-0.0090.01212.9530.0170.0170.0000.0000.0000.000
79A79SER00.017-0.03516.3140.0120.0120.0000.0000.0000.000
80A80PHE00.015-0.00412.531-0.006-0.0060.0000.0000.0000.000
81A81ARG10.8470.93414.719-0.251-0.2510.0000.0000.0000.000
82A82GLU-1-0.877-0.95317.0160.0680.0680.0000.0000.0000.000
83A83TYR00.0400.01018.411-0.003-0.0030.0000.0000.0000.000
84A84PRO00.013-0.00218.193-0.006-0.0060.0000.0000.0000.000
85A85ALA00.0350.03021.0910.0000.0000.0000.0000.0000.000
86A86LEU0-0.010-0.01123.114-0.006-0.0060.0000.0000.0000.000
87A87LEU00.0010.01022.456-0.006-0.0060.0000.0000.0000.000
88A88ALA00.0370.01525.267-0.002-0.0020.0000.0000.0000.000
89A89ALA0-0.007-0.01627.075-0.003-0.0030.0000.0000.0000.000
90A90TRP00.0290.00328.383-0.003-0.0030.0000.0000.0000.000
91A91GLU-1-0.959-0.98827.3470.0280.0280.0000.0000.0000.000
92A92MET0-0.072-0.01330.8860.0020.0020.0000.0000.0000.000
93A93LEU0-0.102-0.04033.324-0.001-0.0010.0000.0000.0000.000
94A94SER0-0.087-0.08635.582-0.003-0.0030.0000.0000.0000.000
95A95GLN00.009-0.01038.209-0.005-0.0050.0000.0000.0000.000
96A96LYS10.8940.96332.033-0.012-0.0120.0000.0000.0000.000
97A97PRO0-0.037-0.00133.869-0.001-0.0010.0000.0000.0000.000
98A98ASP-1-0.760-0.89735.290-0.016-0.0160.0000.0000.0000.000
99A99LEU0-0.047-0.02633.720-0.005-0.0050.0000.0000.0000.000
100A100VAL00.0010.00330.0150.0070.0070.0000.0000.0000.000
101A101PHE0-0.031-0.02031.955-0.006-0.0060.0000.0000.0000.000
102A102VAL00.033-0.00525.9620.0050.0050.0000.0000.0000.000
103A103ASP-1-0.854-0.92529.4360.0280.0280.0000.0000.0000.000
104A104GLY00.0180.00625.9170.0090.0090.0000.0000.0000.000
105A105HIS10.7430.84823.513-0.003-0.0030.0000.0000.0000.000
106A106GLY00.0860.06124.0800.0010.0010.0000.0000.0000.000
107A107ILE00.0720.03122.968-0.001-0.0010.0000.0000.0000.000
108A108SER0-0.0030.04123.446-0.004-0.0040.0000.0000.0000.000
109A109HIS00.057-0.00516.4900.0000.0000.0000.0000.0000.000
110A110PRO0-0.050-0.03017.675-0.020-0.0200.0000.0000.0000.000
111A111ARG10.8140.89510.8860.0760.0760.0000.0000.0000.000
112A112ARG10.8180.91217.1350.0830.0830.0000.0000.0000.000
113A113LEU00.0630.03016.063-0.007-0.0070.0000.0000.0000.000
114A114GLY0-0.056-0.01418.3680.0140.0140.0000.0000.0000.000
115A115VAL00.0690.02120.727-0.015-0.0150.0000.0000.0000.000
116A116ALA00.0040.00921.634-0.003-0.0030.0000.0000.0000.000
117A117SER00.009-0.00721.7870.0010.0010.0000.0000.0000.000
118A118HIS0-0.0100.05015.318-0.004-0.0040.0000.0000.0000.000
119A119PHE00.020-0.00520.531-0.006-0.0060.0000.0000.0000.000
120A120GLY00.0310.01423.304-0.002-0.0020.0000.0000.0000.000
121A121LEU0-0.029-0.01119.937-0.002-0.0020.0000.0000.0000.000
122A122LEU0-0.043-0.02918.156-0.007-0.0070.0000.0000.0000.000
123A123VAL0-0.024-0.00522.3640.0040.0040.0000.0000.0000.000
124A124ASP-1-0.876-0.92725.823-0.069-0.0690.0000.0000.0000.000
125A125VAL00.0100.00527.4110.0060.0060.0000.0000.0000.000
126A126PRO00.0060.04029.471-0.003-0.0030.0000.0000.0000.000
127A127THR0-0.017-0.03827.5060.0100.0100.0000.0000.0000.000
128A128ILE0-0.037-0.00929.787-0.008-0.0080.0000.0000.0000.000
129A129GLY00.0170.00928.0320.0060.0060.0000.0000.0000.000
130A130VAL0-0.020-0.01128.857-0.003-0.0030.0000.0000.0000.000
131A131ALA00.0240.01927.8980.0070.0070.0000.0000.0000.000
132A132LYS10.8840.93029.860-0.044-0.0440.0000.0000.0000.000
133A133LYS10.9460.96328.555-0.042-0.0420.0000.0000.0000.000
134A134ARG10.9530.98927.019-0.002-0.0020.0000.0000.0000.000
135A135LEU0-0.035-0.00621.2050.0070.0070.0000.0000.0000.000
136A136CYS0-0.044-0.01622.4420.0040.0040.0000.0000.0000.000
137A137GLY00.1010.05724.8930.0000.0000.0000.0000.0000.000
138A138LYS10.8910.92627.4810.0480.0480.0000.0000.0000.000
139A139PHE00.0350.01431.119-0.003-0.0030.0000.0000.0000.000
140A140GLU-1-0.881-0.93234.558-0.023-0.0230.0000.0000.0000.000
141A141PRO0-0.068-0.03837.7220.0010.0010.0000.0000.0000.000
142A142LEU00.0030.01438.2720.0000.0000.0000.0000.0000.000
143A143SER00.0620.03841.3400.0020.0020.0000.0000.0000.000
144A144SER0-0.044-0.03844.0850.0000.0000.0000.0000.0000.000
145A145GLU-1-0.817-0.91045.914-0.004-0.0040.0000.0000.0000.000
146A146PRO0-0.062-0.04845.1580.0000.0000.0000.0000.0000.000
147A147GLY00.004-0.00244.168-0.001-0.0010.0000.0000.0000.000
148A148ALA00.0150.03342.884-0.002-0.0020.0000.0000.0000.000
149A149LEU0-0.011-0.02438.7780.0020.0020.0000.0000.0000.000
150A150ALA00.0300.02737.659-0.001-0.0010.0000.0000.0000.000
151A151PRO00.0270.02134.9070.0010.0010.0000.0000.0000.000
152A152LEU0-0.089-0.04328.0900.0030.0030.0000.0000.0000.000
153A153MET00.0160.00930.812-0.008-0.0080.0000.0000.0000.000
154A154ASP-1-0.831-0.94124.146-0.073-0.0730.0000.0000.0000.000
155A155LYS10.8630.94021.4380.1030.1030.0000.0000.0000.000
156A156GLY00.0280.02227.007-0.007-0.0070.0000.0000.0000.000
157A157GLU-1-0.859-0.92125.616-0.118-0.1180.0000.0000.0000.000
158A158GLN00.007-0.00929.4590.0040.0040.0000.0000.0000.000
159A159LEU0-0.050-0.02525.055-0.002-0.0020.0000.0000.0000.000
160A160ALA0-0.022-0.03128.5110.0020.0020.0000.0000.0000.000
161A161TRP0-0.0010.00231.0380.0000.0000.0000.0000.0000.000
162A162VAL0-0.055-0.01533.1650.0040.0040.0000.0000.0000.000
163A163TRP00.0990.04035.4620.0000.0000.0000.0000.0000.000
164A164ARG10.8070.90338.4930.0000.0000.0000.0000.0000.000
165A165SER0-0.022-0.01740.1310.0000.0000.0000.0000.0000.000
166A166LYS10.9170.94641.869-0.012-0.0120.0000.0000.0000.000
167A167ALA00.0470.02043.7610.0000.0000.0000.0000.0000.000
168A168ARG10.9500.96144.989-0.011-0.0110.0000.0000.0000.000
169A169CYS0-0.0200.02340.6010.0040.0040.0000.0000.0000.000
170A170ASN00.012-0.00136.503-0.005-0.0050.0000.0000.0000.000
171A171PRO00.0240.02435.8740.0010.0010.0000.0000.0000.000
172A172LEU0-0.035-0.00534.3230.0040.0040.0000.0000.0000.000
173A173PHE0-0.021-0.02530.219-0.003-0.0030.0000.0000.0000.000
174A174ILE00.0230.02330.7600.0020.0020.0000.0000.0000.000
175A175ALA0-0.009-0.01128.067-0.004-0.0040.0000.0000.0000.000
176A176THR00.0120.03628.1860.0030.0030.0000.0000.0000.000
177A177GLY00.017-0.00726.195-0.001-0.0010.0000.0000.0000.000
178A178HIS00.0450.00225.517-0.016-0.0160.0000.0000.0000.000
179A179ARG10.8240.92627.4360.0660.0660.0000.0000.0000.000
180A180VAL00.0220.02030.4720.0070.0070.0000.0000.0000.000
181A181SER0-0.008-0.02431.355-0.003-0.0030.0000.0000.0000.000
182A182VAL00.006-0.01831.7700.0050.0050.0000.0000.0000.000
183A183ASP-1-0.825-0.90933.292-0.039-0.0390.0000.0000.0000.000
184A184SER0-0.028-0.07036.3280.0050.0050.0000.0000.0000.000
185A185ALA0-0.036-0.01033.0000.0050.0050.0000.0000.0000.000
186A186LEU0-0.031-0.01935.0290.0050.0050.0000.0000.0000.000
187A187ALA00.0190.01837.4510.0040.0040.0000.0000.0000.000
188A188TRP00.0490.01337.1730.0060.0060.0000.0000.0000.000
189A189VAL00.002-0.01335.4000.0040.0040.0000.0000.0000.000
190A190GLN0-0.034-0.03038.4540.0030.0030.0000.0000.0000.000
191A191ARG10.9130.97641.8760.0220.0220.0000.0000.0000.000
192A192CYS0-0.0140.00739.8230.0020.0020.0000.0000.0000.000
193A193MET0-0.0510.00639.0720.0040.0040.0000.0000.0000.000
194A194LYS11.0561.02843.425-0.010-0.0100.0000.0000.0000.000
195A195GLY0-0.0030.00146.071-0.001-0.0010.0000.0000.0000.000
196A196TYR0-0.063-0.03142.4700.0020.0020.0000.0000.0000.000
197A197ARG10.8520.91534.622-0.022-0.0220.0000.0000.0000.000
198A198LEU00.0090.02735.140-0.003-0.0030.0000.0000.0000.000
199A199PRO00.0420.02336.5620.0000.0000.0000.0000.0000.000
200A200GLU-1-0.765-0.88538.3910.0180.0180.0000.0000.0000.000
201A201PRO00.0560.03535.9600.0040.0040.0000.0000.0000.000
202A202THR00.037-0.00232.4630.0020.0020.0000.0000.0000.000
203A203ARG10.7960.90035.087-0.018-0.0180.0000.0000.0000.000
204A204TRP00.008-0.00937.9380.0050.0050.0000.0000.0000.000
205A205ALA0-0.020-0.00733.0510.0040.0040.0000.0000.0000.000
206A206ASP-1-0.822-0.91932.9730.0450.0450.0000.0000.0000.000
207A207ALA0-0.117-0.04334.8530.0040.0040.0000.0000.0000.000
208A208VAL0-0.066-0.00335.1870.0080.0080.0000.0000.0000.000