FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: QLR1Y

Calculation Name: 4ZCH-A-Xray547

Preferred Name: Tumor necrosis factor ligand superfamily member 13B

Target Type: SINGLE PROTEIN

Ligand Name: tris-hydroxymethyl-methyl-ammonium

Ligand 3-letter code: 144

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4ZCH

Chain ID: A

ChEMBL ID: CHEMBL2364158

UniProt ID: Q9Y275

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 435
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -8348522.413938
FMO2-HF: Nuclear repulsion 8177729.068378
FMO2-HF: Total energy -170793.34556
FMO2-MP2: Total energy -171291.742548


3D Structure Molmil
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:7:HIS)


Summations of interaction energy for fragment #1(A:7:HIS)
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.
-155.225-157.44236.105-12.319-21.568-0.161
Interaction energy analysis for fragmet #1(A:7:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.771 / q_NPA : 0.918
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].
3A9VAL0-0.046-0.0193.801-7.514-6.4900.004-0.465-0.5630.002
30A36ARG10.7850.8933.21863.48364.2250.035-0.250-0.5270.000
31A37GLY00.0390.0343.412-4.146-3.8580.015-0.101-0.2020.000
32A38ARG10.8520.9053.64425.84726.0690.000-0.020-0.2010.000
33A39GLY00.0090.0184.0513.2383.330-0.001-0.015-0.0760.000
45A51ASP0-0.065-0.0814.1692.3942.547-0.001-0.021-0.1310.000
133A140VAL00.020-0.0044.640-3.118-3.091-0.001-0.004-0.0220.000
134A141LYS00.0050.0552.1486.0787.6502.891-1.399-3.064-0.004
135A142LEU0-0.069-0.0282.049-35.839-35.3025.802-3.551-2.788-0.045
136A143GLY00.0910.0612.502-7.961-5.9870.505-1.307-1.172-0.012
137A144GLY0-0.003-0.0572.125-27.226-30.73718.555-7.723-7.320-0.052
138A145GLY0-0.012-0.0122.005-5.277-13.4648.2553.829-3.897-0.041
139A146GLY0-0.028-0.0113.5293.0143.2310.000-0.068-0.1490.000
140A147SER0-0.015-0.0263.120-1.672-0.1500.027-0.714-0.836-0.006
435A444LEU-1-0.829-0.8763.575-75.632-74.5210.019-0.510-0.620-0.003
4A10LEU0-0.026-0.0216.2024.5964.5960.0000.0000.0000.000
5A11HIS00.0850.0739.939-1.129-1.1290.0000.0000.0000.000
6A12LEU0-0.007-0.01112.9090.6220.6220.0000.0000.0000.000
7A13VAL00.0310.02016.3110.2570.2570.0000.0000.0000.000
8A14PRO00.001-0.00219.949-0.100-0.1000.0000.0000.0000.000
9A15ILE0-0.0320.00222.8990.2420.2420.0000.0000.0000.000
10A16ASN0-0.066-0.05624.8910.8540.8540.0000.0000.0000.000
11A17ALA00.0180.01926.467-0.508-0.5080.0000.0000.0000.000
12A18ALA0-0.0060.00928.9820.3370.3370.0000.0000.0000.000
13A19SER00.011-0.01229.5790.3230.3230.0000.0000.0000.000
14A20LYS10.8290.88832.2878.2788.2780.0000.0000.0000.000
15A21ASP-1-0.714-0.84035.228-8.197-8.1970.0000.0000.0000.000
16A22ASP-1-0.897-0.92735.891-8.340-8.3400.0000.0000.0000.000
17A23SER0-0.053-0.03833.655-0.011-0.0110.0000.0000.0000.000
18A24ASP-1-0.895-0.94334.544-8.463-8.4630.0000.0000.0000.000
19A25VAL0-0.053-0.00930.309-0.084-0.0840.0000.0000.0000.000
20A26THR0-0.052-0.04929.2630.2220.2220.0000.0000.0000.000
21A27GLU-1-0.862-0.89025.937-11.747-11.7470.0000.0000.0000.000
22A28VAL0-0.014-0.02123.1320.3450.3450.0000.0000.0000.000
23A29MET0-0.042-0.00523.003-0.452-0.4520.0000.0000.0000.000
24A30TRP00.0290.00218.605-0.089-0.0890.0000.0000.0000.000
25A31GLN00.001-0.00518.5600.5040.5040.0000.0000.0000.000
26A32PRO0-0.034-0.03413.487-0.474-0.4740.0000.0000.0000.000
27A33ALA0-0.0150.00615.6060.8210.8210.0000.0000.0000.000
28A34LEU0-0.019-0.00811.627-0.032-0.0320.0000.0000.0000.000
29A35ARG10.9090.9488.05323.99423.9940.0000.0000.0000.000
34A40LEU0-0.0190.0045.4642.0192.0190.0000.0000.0000.000
35A41GLN0-0.068-0.0418.6250.4170.4170.0000.0000.0000.000
36A42ALA00.0200.01711.7240.4040.4040.0000.0000.0000.000
37A43GLN0-0.027-0.02514.978-0.068-0.0680.0000.0000.0000.000
38A44GLY00.0600.02918.2170.6870.6870.0000.0000.0000.000
39A45TYR00.0490.01720.464-0.447-0.4470.0000.0000.0000.000
40A46GLY00.0410.02518.9880.0800.0800.0000.0000.0000.000
41A47VAL0-0.090-0.04412.506-0.135-0.1350.0000.0000.0000.000
42A48ARG10.9571.00113.67517.52317.5230.0000.0000.0000.000
43A49ILE0-0.003-0.00410.130-1.856-1.8560.0000.0000.0000.000
44A50GLN0-0.017-0.0108.3952.7242.7240.0000.0000.0000.000
46A52ALA00.0170.0138.122-1.469-1.4690.0000.0000.0000.000
47A53GLY00.0460.0208.521-2.294-2.2940.0000.0000.0000.000
48A54VAL0-0.024-0.0098.2422.0212.0210.0000.0000.0000.000
49A55TYR00.000-0.0246.634-8.661-8.6610.0000.0000.0000.000
50A56LEU00.0040.0188.0303.5553.5550.0000.0000.0000.000
51A57LEU0-0.032-0.0119.742-2.077-2.0770.0000.0000.0000.000
52A58TYR00.011-0.01910.8540.8700.8700.0000.0000.0000.000
53A59SER0-0.009-0.00614.9940.0290.0290.0000.0000.0000.000
54A60GLN0-0.030-0.01018.1450.1600.1600.0000.0000.0000.000
55A61VAL00.0190.02021.071-0.119-0.1190.0000.0000.0000.000
56A62LEU0-0.0210.00324.4000.2670.2670.0000.0000.0000.000
57A63PHE00.0050.00127.0690.2160.2160.0000.0000.0000.000
58A64GLN00.0410.01830.649-0.031-0.0310.0000.0000.0000.000
59A65ASP-1-0.839-0.91633.405-9.194-9.1940.0000.0000.0000.000
60A66VAL00.0440.01836.118-0.009-0.0090.0000.0000.0000.000
61A67THR0-0.002-0.00139.5120.0570.0570.0000.0000.0000.000
62A68PHE0-0.019-0.02337.012-0.050-0.0500.0000.0000.0000.000
63A69THR00.0390.00734.970-0.103-0.1030.0000.0000.0000.000
64A70MET0-0.0500.01431.5230.0670.0670.0000.0000.0000.000
65A71GLY00.0600.01228.383-0.011-0.0110.0000.0000.0000.000
66A72GLN0-0.031-0.01921.7940.7940.7940.0000.0000.0000.000
67A73VAL00.003-0.00323.954-0.104-0.1040.0000.0000.0000.000
68A74VAL0-0.0050.01217.254-0.092-0.0920.0000.0000.0000.000
69A75SER00.0070.00420.1460.2880.2880.0000.0000.0000.000
70A76ARG10.7480.85515.82817.11717.1170.0000.0000.0000.000
71A77GLU-1-0.883-0.91919.420-12.233-12.2330.0000.0000.0000.000
72A78GLY00.019-0.00619.785-0.942-0.9420.0000.0000.0000.000
73A79GLN0-0.037-0.02919.4140.2500.2500.0000.0000.0000.000
74A80GLY0-0.0140.00022.2160.3450.3450.0000.0000.0000.000
75A81ARG10.8630.94419.10715.77815.7780.0000.0000.0000.000
76A82GLN00.0590.02523.270-0.587-0.5870.0000.0000.0000.000
77A83GLU-1-0.855-0.92420.482-15.284-15.2840.0000.0000.0000.000
78A84THR0-0.035-0.01321.374-0.629-0.6290.0000.0000.0000.000
79A85LEU0-0.057-0.01715.637-0.294-0.2940.0000.0000.0000.000
80A86PHE00.0270.00216.027-0.202-0.2020.0000.0000.0000.000
81A87ARG10.8120.90121.19111.58411.5840.0000.0000.0000.000
82A88CYS0-0.089-0.02023.4820.1560.1560.0000.0000.0000.000
83A89ILE0-0.028-0.01125.4300.2610.2610.0000.0000.0000.000
84A90ARG10.8700.93326.74411.22911.2290.0000.0000.0000.000
85A91SER00.0190.00331.4570.2910.2910.0000.0000.0000.000
86A92MET0-0.0700.03534.681-0.153-0.1530.0000.0000.0000.000
87A93PRO0-0.024-0.01436.3520.2420.2420.0000.0000.0000.000
88A94SER00.021-0.04739.0250.0860.0860.0000.0000.0000.000
89A95HIS00.010-0.00441.085-0.014-0.0140.0000.0000.0000.000
90A96PRO00.0210.00541.678-0.097-0.0970.0000.0000.0000.000
91A97ASP-1-0.912-0.97541.047-7.870-7.8700.0000.0000.0000.000
92A98ARG0-0.0020.03639.8260.0340.0340.0000.0000.0000.000
93A99ALA0-0.0040.00836.322-0.183-0.1830.0000.0000.0000.000
94A100TYR0-0.046-0.02132.384-0.117-0.1170.0000.0000.0000.000
95A101ASN00.007-0.00430.931-0.058-0.0580.0000.0000.0000.000
96A102SER00.0280.01825.233-0.109-0.1090.0000.0000.0000.000
97A104TYR00.0240.01415.593-0.349-0.3490.0000.0000.0000.000
98A105SER0-0.018-0.04020.0720.2700.2700.0000.0000.0000.000
99A106ALA00.001-0.00815.098-0.843-0.8430.0000.0000.0000.000
100A107GLY00.0480.03015.1151.2191.2190.0000.0000.0000.000
101A108VAL0-0.034-0.02111.075-2.075-2.0750.0000.0000.0000.000
102A109PHE00.0580.02812.0811.5681.5680.0000.0000.0000.000
103A110HIS0-0.026-0.00411.498-3.140-3.1400.0000.0000.0000.000
104A111LEU0-0.015-0.00710.7012.0962.0960.0000.0000.0000.000
105A112HIS00.022-0.00912.185-1.699-1.6990.0000.0000.0000.000
106A113GLN0-0.030-0.02411.5870.5110.5110.0000.0000.0000.000
107A114GLY0-0.042-0.02413.6061.3141.3140.0000.0000.0000.000
108A115ASP-1-0.754-0.86015.027-17.497-17.4970.0000.0000.0000.000
109A116ILE0-0.024-0.01915.325-1.352-1.3520.0000.0000.0000.000
110A117LEU00.0040.00113.5100.4710.4710.0000.0000.0000.000
111A118SER00.0120.00717.2310.1590.1590.0000.0000.0000.000
112A119VAL0-0.006-0.01119.349-0.274-0.2740.0000.0000.0000.000
113A120ILE00.0230.02221.8800.3920.3920.0000.0000.0000.000
114A121ILE00.0300.01225.632-0.129-0.1290.0000.0000.0000.000
115A122PRO0-0.031-0.02328.3270.2910.2910.0000.0000.0000.000
116A123ARG10.8880.94031.0889.2519.2510.0000.0000.0000.000
117A124ALA00.0290.02933.187-0.193-0.1930.0000.0000.0000.000
118A125ARG10.7930.86034.6188.1818.1810.0000.0000.0000.000
119A126ALA00.0100.03331.5550.1520.1520.0000.0000.0000.000
120A127LYS10.9560.96632.9008.0738.0730.0000.0000.0000.000
121A128LEU0-0.003-0.00627.330-0.107-0.1070.0000.0000.0000.000
122A129ASN0-0.044-0.03628.696-0.096-0.0960.0000.0000.0000.000
123A130LEU00.0170.00626.295-0.497-0.4970.0000.0000.0000.000
124A131SER00.0110.01725.623-0.307-0.3070.0000.0000.0000.000
125A132PRO00.0260.00421.496-0.328-0.3280.0000.0000.0000.000
126A133HIS00.0400.02620.791-0.705-0.7050.0000.0000.0000.000
127A134GLY0-0.019-0.01422.5680.0470.0470.0000.0000.0000.000
128A135THR00.005-0.01322.7120.0650.0650.0000.0000.0000.000
129A136PHE0-0.039-0.02417.039-0.245-0.2450.0000.0000.0000.000
130A137LEU00.0080.01315.0170.2660.2660.0000.0000.0000.000
131A138GLY0-0.007-0.01112.430-0.172-0.1720.0000.0000.0000.000
132A139PHE00.0230.0148.2390.7510.7510.0000.0000.0000.000
141A148GLU-1-0.885-0.9434.838-53.633-53.6330.0000.0000.0000.000
142A149THR0-0.022-0.0056.4903.0373.0370.0000.0000.0000.000
143A150VAL00.0010.0267.9053.2443.2440.0000.0000.0000.000
144A151THR0-0.002-0.0139.549-2.383-2.3830.0000.0000.0000.000
145A152GLN0-0.101-0.0657.377-2.650-2.6500.0000.0000.0000.000
146A153ASP-1-0.814-0.89710.410-23.081-23.0810.0000.0000.0000.000
147A154CYS0-0.042-0.02912.414-1.176-1.1760.0000.0000.0000.000
148A155LEU0-0.030-0.00514.4050.5650.5650.0000.0000.0000.000
149A156GLN00.0750.06717.043-0.754-0.7540.0000.0000.0000.000
150A157LEU0-0.0120.00018.9790.3280.3280.0000.0000.0000.000
151A158ILE00.0230.00722.167-0.339-0.3390.0000.0000.0000.000
152A159ALA00.019-0.00224.6390.2590.2590.0000.0000.0000.000
153A160ASP-1-0.848-0.91428.378-9.923-9.9230.0000.0000.0000.000
154A161SER00.004-0.00931.0410.0830.0830.0000.0000.0000.000
155A162GLU-1-0.975-0.97833.389-8.463-8.4630.0000.0000.0000.000
156A163THR0-0.069-0.03434.7120.4190.4190.0000.0000.0000.000
157A164PRO0-0.007-0.00435.902-0.136-0.1360.0000.0000.0000.000
158A165THR00.013-0.00334.853-0.096-0.0960.0000.0000.0000.000
159A166ILE0-0.031-0.01234.4400.2790.2790.0000.0000.0000.000
160A167GLN00.0370.02337.785-0.063-0.0630.0000.0000.0000.000
161A168LYS10.9280.95935.9279.0939.0930.0000.0000.0000.000
162A169GLY00.0240.01240.021-0.131-0.1310.0000.0000.0000.000
163A170SER00.017-0.00142.182-0.029-0.0290.0000.0000.0000.000
164A171TYR0-0.020-0.00635.304-0.168-0.1680.0000.0000.0000.000
165A172THR00.0050.00435.5730.1830.1830.0000.0000.0000.000
166A173PHE0-0.043-0.03032.556-0.279-0.2790.0000.0000.0000.000
167A174VAL00.0320.01329.3920.2910.2910.0000.0000.0000.000
168A175PRO0-0.0050.02431.112-0.191-0.1910.0000.0000.0000.000
169A176TRP0-0.026-0.03126.470-0.339-0.3390.0000.0000.0000.000
170A177LEU00.0520.04026.7920.1970.1970.0000.0000.0000.000
171A178LEU0-0.034-0.02821.021-0.511-0.5110.0000.0000.0000.000
172A179SER0-0.0370.00420.227-0.141-0.1410.0000.0000.0000.000
173A180PHE00.008-0.02612.891-0.702-0.7020.0000.0000.0000.000
174A181LYS10.9650.98517.39415.73415.7340.0000.0000.0000.000
175A182ARG10.9190.9687.80833.20633.2060.0000.0000.0000.000
176A183GLY00.0430.02415.185-0.355-0.3550.0000.0000.0000.000
177A184SER0-0.044-0.04416.0170.8360.8360.0000.0000.0000.000
178A185ALA0-0.008-0.00817.0670.8750.8750.0000.0000.0000.000
179A186LEU0-0.0100.00916.6800.5550.5550.0000.0000.0000.000
180A187GLU-1-0.880-0.94120.158-12.622-12.6220.0000.0000.0000.000
181A188GLU-1-0.859-0.93123.281-11.632-11.6320.0000.0000.0000.000
182A189LYS10.8800.93025.61710.49510.4950.0000.0000.0000.000
183A190GLU-1-0.885-0.95129.126-9.317-9.3170.0000.0000.0000.000
184A191ASN0-0.0040.01229.4300.3160.3160.0000.0000.0000.000
185A192LYS10.7820.89327.90310.57410.5740.0000.0000.0000.000
186A193ILE00.0370.03321.077-0.159-0.1590.0000.0000.0000.000
187A194LEU0-0.043-0.01524.6040.1950.1950.0000.0000.0000.000
188A195VAL0-0.002-0.00221.577-0.675-0.6750.0000.0000.0000.000
189A196LYS10.8220.89422.01113.10513.1050.0000.0000.0000.000
190A197GLU-1-0.790-0.89118.458-17.492-17.4920.0000.0000.0000.000
191A198THR00.0050.00120.976-0.358-0.3580.0000.0000.0000.000
192A199GLY0-0.029-0.02018.711-0.741-0.7410.0000.0000.0000.000
193A200TYR00.0080.01016.4860.7770.7770.0000.0000.0000.000
194A201PHE00.0260.00615.904-1.343-1.3430.0000.0000.0000.000
195A202PHE00.0250.01713.8790.6830.6830.0000.0000.0000.000
196A203ILE0-0.009-0.01315.930-0.267-0.2670.0000.0000.0000.000
197A204TYR0-0.025-0.04315.728-0.111-0.1110.0000.0000.0000.000
198A205GLY00.0210.00419.6040.2030.2030.0000.0000.0000.000
199A206GLN0-0.081-0.01422.547-0.218-0.2180.0000.0000.0000.000
200A207VAL00.0350.02024.5010.1370.1370.0000.0000.0000.000
201A208LEU0-0.0180.00628.211-0.035-0.0350.0000.0000.0000.000
202A209TYR00.024-0.01730.2860.3900.3900.0000.0000.0000.000
203A210THR00.014-0.01933.860-0.042-0.0420.0000.0000.0000.000
204A211ASP-1-0.782-0.86937.155-7.751-7.7510.0000.0000.0000.000
205A212LYS10.9640.97039.5247.0337.0330.0000.0000.0000.000
206A213THR0-0.047-0.02440.0970.2280.2280.0000.0000.0000.000
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