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: RMK78

Calculation Name: 4XKA-A-Xray547

Preferred Name:

Target Type:

Ligand Name: tris(hydroxyethyl)aminomethane

Ligand 3-letter code: TAM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4XKA

Chain ID: A

ChEMBL ID:

UniProt ID: P54651

Base Structure: X-ray

Registration Date: 2025-10-04

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 215
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2560979.209897
FMO2-HF: Nuclear repulsion 2476289.63534
FMO2-HF: Total energy -84689.574557
FMO2-MP2: Total energy -84937.268166


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:5:GLN)


Summations of interaction energy for fragment #1(A:5:GLN)
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.
-166.339-165.64211.952-6.302-6.346-0.066
Interaction energy analysis for fragmet #1(A:5:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.783 / q_NPA : 0.874
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].
3A7GLU-1-0.835-0.8771.810-78.195-78.18611.956-6.130-5.835-0.066
4A8ARG10.8970.9214.80228.94229.012-0.001-0.007-0.0620.000
85A89LYS10.8900.9193.48049.12249.370-0.001-0.111-0.1360.000
159A163ALA0-0.0090.0034.366-8.827-8.787-0.001-0.027-0.0110.000
160A164LEU00.0130.0094.0945.6575.987-0.001-0.027-0.3020.000
5A9PHE0-0.0080.0016.6590.6830.6830.0000.0000.0000.000
6A10THR00.0280.02411.5770.5990.5990.0000.0000.0000.000
7A11PHE0-0.023-0.01315.363-0.259-0.2590.0000.0000.0000.000
8A12GLN0-0.006-0.00417.6930.0800.0800.0000.0000.0000.000
9A13ALA00.006-0.00120.0900.1330.1330.0000.0000.0000.000
10A14GLU-1-0.805-0.91423.475-12.066-12.0660.0000.0000.0000.000
11A15ILE00.0050.01420.0670.3660.3660.0000.0000.0000.000
12A16ASN00.0380.01319.873-0.113-0.1130.0000.0000.0000.000
13A17GLN0-0.0070.02623.1340.3660.3660.0000.0000.0000.000
14A18LEU00.002-0.00325.1000.2910.2910.0000.0000.0000.000
15A19MET0-0.019-0.01219.4650.1560.1560.0000.0000.0000.000
16A20SER0-0.018-0.02224.8740.1620.1620.0000.0000.0000.000
17A21LEU0-0.021-0.00727.0980.3140.3140.0000.0000.0000.000
18A22ILE0-0.047-0.01726.6260.3440.3440.0000.0000.0000.000
19A23ILE0-0.0220.00123.8590.1130.1130.0000.0000.0000.000
20A24ASN0-0.043-0.01727.7850.1990.1990.0000.0000.0000.000
21A25THR0-0.065-0.03731.1910.4780.4780.0000.0000.0000.000
22A26PHE0-0.004-0.00533.909-0.108-0.1080.0000.0000.0000.000
23A27TYR0-0.004-0.02734.4520.0920.0920.0000.0000.0000.000
24A28SER00.0090.00836.377-0.181-0.1810.0000.0000.0000.000
25A29ASN0-0.0070.00637.8220.0830.0830.0000.0000.0000.000
26A30LYS10.9640.96432.8039.4759.4750.0000.0000.0000.000
27A31GLU-1-0.802-0.87832.906-8.835-8.8350.0000.0000.0000.000
28A32VAL00.0010.00432.252-0.125-0.1250.0000.0000.0000.000
29A33PHE00.0450.02127.793-0.117-0.1170.0000.0000.0000.000
30A34LEU0-0.0300.00029.109-0.319-0.3190.0000.0000.0000.000
31A35ARG10.8390.90030.9209.3009.3000.0000.0000.0000.000
32A36GLU-1-0.816-0.90128.523-10.375-10.3750.0000.0000.0000.000
33A37LEU0-0.032-0.01224.099-0.332-0.3320.0000.0000.0000.000
34A38ILE00.0060.00427.183-0.262-0.2620.0000.0000.0000.000
35A39SER0-0.0030.00229.9000.1740.1740.0000.0000.0000.000
36A40ASN0-0.035-0.02723.9120.3250.3250.0000.0000.0000.000
37A41ALA00.0220.02325.786-0.318-0.3180.0000.0000.0000.000
38A42SER00.0200.00726.7870.0890.0890.0000.0000.0000.000
39A43ASP-1-0.922-0.95627.151-11.121-11.1210.0000.0000.0000.000
40A44ALA0-0.055-0.02723.885-0.114-0.1140.0000.0000.0000.000
41A45LEU0-0.0070.00925.565-0.146-0.1460.0000.0000.0000.000
42A46ASP-1-0.832-0.88628.294-9.921-9.9210.0000.0000.0000.000
43A47LYS10.8850.94724.04012.93112.9310.0000.0000.0000.000
44A48ILE00.0290.02324.5500.0960.0960.0000.0000.0000.000
45A49ARG10.8960.94527.2679.5959.5950.0000.0000.0000.000
46A50TYR0-0.025-0.00529.9990.2760.2760.0000.0000.0000.000
47A51GLN00.0100.00024.2150.0630.0630.0000.0000.0000.000
48A52SER0-0.032-0.02929.7000.2590.2590.0000.0000.0000.000
49A53LEU0-0.064-0.02931.6940.3110.3110.0000.0000.0000.000
50A54THR0-0.087-0.03331.9130.3310.3310.0000.0000.0000.000
51A55ASP-1-0.817-0.89729.351-10.555-10.5550.0000.0000.0000.000
52A56ALA00.0160.00830.694-0.306-0.3060.0000.0000.0000.000
53A57SER0-0.055-0.04529.051-0.325-0.3250.0000.0000.0000.000
54A58VAL0-0.0020.00126.074-0.475-0.4750.0000.0000.0000.000
55A59LEU00.025-0.00625.723-0.522-0.5220.0000.0000.0000.000
56A60GLU-1-0.947-0.96726.518-10.970-10.9700.0000.0000.0000.000
57A61SER0-0.081-0.04521.5700.0340.0340.0000.0000.0000.000
58A62LYS10.8870.94122.85513.10713.1070.0000.0000.0000.000
59A63THR00.0500.04025.2890.0750.0750.0000.0000.0000.000
60A64GLU-1-0.879-0.93227.723-11.310-11.3100.0000.0000.0000.000
61A65LEU0-0.0200.01228.096-0.432-0.4320.0000.0000.0000.000
62A66GLU-1-0.872-0.94728.359-10.591-10.5910.0000.0000.0000.000
63A67ILE00.0340.01127.520-0.513-0.5130.0000.0000.0000.000
64A68LYS10.8250.91726.30311.61811.6180.0000.0000.0000.000
65A69ILE00.0150.00526.429-0.457-0.4570.0000.0000.0000.000
66A70ILE00.006-0.01324.1420.4330.4330.0000.0000.0000.000
67A71PRO0-0.0200.01026.183-0.440-0.4400.0000.0000.0000.000
68A72ASP-1-0.848-0.92725.098-12.103-12.1030.0000.0000.0000.000
69A73LYS10.8750.90826.9429.1629.1620.0000.0000.0000.000
70A74THR0-0.0200.00326.9860.1420.1420.0000.0000.0000.000
71A75ALA0-0.026-0.01822.388-0.200-0.2000.0000.0000.0000.000
72A76LYS10.8270.90523.49610.76510.7650.0000.0000.0000.000
73A77THR0-0.0040.00020.891-0.340-0.3400.0000.0000.0000.000
74A78LEU00.000-0.00224.2000.6500.6500.0000.0000.0000.000
75A79THR0-0.018-0.00221.210-0.840-0.8400.0000.0000.0000.000
76A80LEU0-0.023-0.01722.8880.8090.8090.0000.0000.0000.000
77A81ILE0-0.011-0.01121.553-0.860-0.8600.0000.0000.0000.000
78A82ASP-1-0.790-0.89922.793-13.714-13.7140.0000.0000.0000.000
79A83SER0-0.020-0.03622.715-0.598-0.5980.0000.0000.0000.000
80A84GLY00.0350.00523.9560.3920.3920.0000.0000.0000.000
81A85ILE0-0.064-0.04121.778-0.342-0.3420.0000.0000.0000.000
82A86GLY00.0710.04219.163-0.436-0.4360.0000.0000.0000.000
83A87MET0-0.083-0.03815.5650.7410.7410.0000.0000.0000.000
84A88THR00.031-0.00213.359-1.199-1.1990.0000.0000.0000.000
86A90THR0-0.008-0.01610.462-0.446-0.4460.0000.0000.0000.000
87A91ASP-1-0.828-0.89312.434-16.296-16.2960.0000.0000.0000.000
88A92MET0-0.0200.01311.8350.1120.1120.0000.0000.0000.000
89A93VAL00.0090.0009.8160.5300.5300.0000.0000.0000.000
90A94LYS10.8360.92812.78117.35317.3530.0000.0000.0000.000
91A95ASN0-0.024-0.03416.2971.1631.1630.0000.0000.0000.000
92A96LEU00.0280.03214.9030.8500.8500.0000.0000.0000.000
93A97GLY00.0520.04515.6660.0550.0550.0000.0000.0000.000
94A98THR0-0.094-0.06116.4640.6710.6710.0000.0000.0000.000
95A99ILE0-0.012-0.00319.1760.4170.4170.0000.0000.0000.000
96A100ALA00.0370.02022.3250.2730.2730.0000.0000.0000.000
97A101ARG10.9490.96723.67611.44311.4430.0000.0000.0000.000
98A102SER00.0380.01327.489-0.175-0.1750.0000.0000.0000.000
99A103GLY00.0360.01829.9500.0400.0400.0000.0000.0000.000
100A104THR00.020-0.01126.8150.2550.2550.0000.0000.0000.000
101A105LYS10.8550.94425.09111.47711.4770.0000.0000.0000.000
102A106ASN00.0530.02029.550-0.125-0.1250.0000.0000.0000.000
103A107PHE00.0150.01430.7160.1640.1640.0000.0000.0000.000
104A108MET00.0120.02527.7710.0540.0540.0000.0000.0000.000
105A109GLU-1-0.934-0.95031.245-8.909-8.9090.0000.0000.0000.000
106A110GLN0-0.020-0.01434.2220.0790.0790.0000.0000.0000.000
107A111LEU0-0.042-0.01231.0790.1630.1630.0000.0000.0000.000
108A112GLN0-0.034-0.04630.396-0.038-0.0380.0000.0000.0000.000
109A113SER0-0.099-0.05134.6490.2260.2260.0000.0000.0000.000
110A114GLY00.0050.00837.5240.2320.2320.0000.0000.0000.000
111A115ALA0-0.044-0.01739.2040.1510.1510.0000.0000.0000.000
112A116ALA0-0.031-0.01236.7320.0990.0990.0000.0000.0000.000
113A117ASP-1-0.731-0.83836.923-8.713-8.7130.0000.0000.0000.000
114A118ILE00.0410.00431.315-0.144-0.1440.0000.0000.0000.000
115A119SER0-0.077-0.05933.128-0.248-0.2480.0000.0000.0000.000
116A120MET0-0.0070.02035.1200.0500.0500.0000.0000.0000.000
117A121ILE0-0.020-0.00527.524-0.077-0.0770.0000.0000.0000.000
118A122GLY00.0580.02629.449-0.262-0.2620.0000.0000.0000.000
119A123GLN0-0.033-0.01030.216-0.105-0.1050.0000.0000.0000.000
120A124PHE0-0.035-0.01929.7580.0420.0420.0000.0000.0000.000
121A125GLY0-0.038-0.02526.673-0.280-0.2800.0000.0000.0000.000
122A126VAL00.0000.00924.217-0.512-0.5120.0000.0000.0000.000
123A127GLY00.0830.03325.851-0.124-0.1240.0000.0000.0000.000
124A128PHE0-0.0020.01618.6420.2690.2690.0000.0000.0000.000
125A129TYR00.011-0.02519.3040.2730.2730.0000.0000.0000.000
126A130SER00.009-0.01024.1950.1320.1320.0000.0000.0000.000
127A131ALA00.0250.01123.5850.3310.3310.0000.0000.0000.000
128A132TYR0-0.012-0.03318.6490.1540.1540.0000.0000.0000.000
129A133LEU0-0.044-0.01425.4940.3430.3430.0000.0000.0000.000
130A134VAL0-0.042-0.03027.4190.3650.3650.0000.0000.0000.000
131A135ALA00.0210.02423.2170.0110.0110.0000.0000.0000.000
132A136ASP-1-0.850-0.92223.423-12.423-12.4230.0000.0000.0000.000
133A137THR0-0.061-0.02617.019-0.693-0.6930.0000.0000.0000.000
134A138VAL0-0.029-0.00218.5770.6280.6280.0000.0000.0000.000
135A139ILE00.0290.02213.353-1.054-1.0540.0000.0000.0000.000
136A140VAL0-0.025-0.02314.7741.5911.5910.0000.0000.0000.000
137A141HIS00.001-0.01812.754-0.830-0.8300.0000.0000.0000.000
138A142SER0-0.022-0.02513.6702.0382.0380.0000.0000.0000.000
139A143LYS10.8900.94713.82817.87317.8730.0000.0000.0000.000
140A144ASN0-0.0100.01415.9541.4341.4340.0000.0000.0000.000
141A145ASN00.0450.01717.554-0.860-0.8600.0000.0000.0000.000
142A146ASP-1-0.936-0.96217.730-15.578-15.5780.0000.0000.0000.000
143A147ASP-1-0.834-0.91811.249-27.412-27.4120.0000.0000.0000.000
144A148GLU-1-0.924-0.95810.105-24.208-24.2080.0000.0000.0000.000
145A149GLN0-0.031-0.01911.5002.2572.2570.0000.0000.0000.000
146A150TYR0-0.024-0.0166.320-6.515-6.5150.0000.0000.0000.000
147A151VAL0-0.009-0.0048.2433.4253.4250.0000.0000.0000.000
148A152TRP00.027-0.0069.432-3.631-3.6310.0000.0000.0000.000
149A153GLU-1-0.896-0.95211.646-23.305-23.3050.0000.0000.0000.000
150A154SER0-0.015-0.03312.998-0.282-0.2820.0000.0000.0000.000
151A155SER00.0390.02015.7660.4440.4440.0000.0000.0000.000
152A156ALA00.0180.00418.6580.9510.9510.0000.0000.0000.000
153A157GLY0-0.0010.00218.327-0.756-0.7560.0000.0000.0000.000
154A158GLY0-0.0020.00619.254-0.021-0.0210.0000.0000.0000.000
155A159GLU-1-0.872-0.93413.511-21.888-21.8880.0000.0000.0000.000
156A160PHE00.0080.03111.5120.6070.6070.0000.0000.0000.000
157A161THR0-0.064-0.0278.283-1.776-1.7760.0000.0000.0000.000
158A162ILE00.0230.0027.0932.5392.5390.0000.0000.0000.000
161A165ASP-1-0.777-0.8555.850-30.561-30.5610.0000.0000.0000.000
162A166HIS0-0.026-0.0105.5103.8693.8690.0000.0000.0000.000
163A167THR0-0.099-0.0679.4942.9082.9080.0000.0000.0000.000
164A168GLU-1-0.914-0.97012.668-17.156-17.1560.0000.0000.0000.000
165A169PRO0-0.020-0.00915.086-0.202-0.2020.0000.0000.0000.000
166A170LEU0-0.025-0.01316.5381.1171.1170.0000.0000.0000.000
167A171GLY0-0.039-0.00418.2721.0711.0710.0000.0000.0000.000
168A172ARG10.7670.85319.34712.97812.9780.0000.0000.0000.000
169A173GLY0-0.0080.02719.6770.7320.7320.0000.0000.0000.000
170A174THR0-0.033-0.03418.166-1.688-1.6880.0000.0000.0000.000
171A175LYS10.9140.97615.77020.19020.1900.0000.0000.0000.000
172A176ILE00.0020.00417.732-1.204-1.2040.0000.0000.0000.000
173A177VAL00.003-0.00317.9070.8010.8010.0000.0000.0000.000
174A178LEU0-0.017-0.00519.463-0.594-0.5940.0000.0000.0000.000
175A179HIS00.0510.02117.1161.0611.0610.0000.0000.0000.000
176A180MET0-0.031-0.01922.2060.0050.0050.0000.0000.0000.000
177A181LYS10.8900.95225.97512.13512.1350.0000.0000.0000.000
178A182GLU-1-0.812-0.89228.164-10.582-10.5820.0000.0000.0000.000
179A183ASP-1-0.904-0.94630.596-9.903-9.9030.0000.0000.0000.000
180A184GLN0-0.079-0.06130.2380.3390.3390.0000.0000.0000.000
181A185LEU00.0450.01928.567-0.147-0.1470.0000.0000.0000.000
182A186ASP-1-0.762-0.85931.756-9.033-9.0330.0000.0000.0000.000
183A187TYR0-0.057-0.03831.4270.2280.2280.0000.0000.0000.000
184A188LEU0-0.0070.00327.957-0.158-0.1580.0000.0000.0000.000
185A189ASP-1-0.853-0.91131.876-8.972-8.9720.0000.0000.0000.000
186A190GLU-1-0.839-0.92535.575-8.369-8.3690.0000.0000.0000.000
187A191THR0-0.035-0.03736.816-0.015-0.0150.0000.0000.0000.000
188A192LYS10.8180.91036.2679.0739.0730.0000.0000.0000.000
189A193ILE00.0500.02631.2770.0480.0480.0000.0000.0000.000
190A194LYS10.9820.98835.0537.9767.9760.0000.0000.0000.000
191A195ASN0-0.056-0.03237.3230.0720.0720.0000.0000.0000.000
192A196LEU0-0.013-0.00435.7410.0920.0920.0000.0000.0000.000
193A197VAL00.0690.02932.592-0.065-0.0650.0000.0000.0000.000
194A198LYS10.9441.00135.3047.6007.6000.0000.0000.0000.000
195A199LYS10.8040.88338.7718.2668.2660.0000.0000.0000.000
196A200HIS0-0.052-0.03634.9500.0900.0900.0000.0000.0000.000
197A201SER0-0.007-0.04135.058-0.218-0.2180.0000.0000.0000.000
198A202GLU-1-0.973-0.97036.710-7.514-7.5140.0000.0000.0000.000
199A203PHE0-0.032-0.01939.2430.1200.1200.0000.0000.0000.000
200A204ILE0-0.0030.01133.160-0.075-0.0750.0000.0000.0000.000
201A205GLN0-0.0020.01236.3170.0590.0590.0000.0000.0000.000
202A206TYR0-0.007-0.04032.178-0.024-0.0240.0000.0000.0000.000
203A207PRO0-0.010-0.00333.1410.1080.1080.0000.0000.0000.000
204A208ILE00.0510.02931.471-0.397-0.3970.0000.0000.0000.000
205A209SER0-0.062-0.02630.7140.3660.3660.0000.0000.0000.000
206A210LEU0-0.0110.00430.693-0.363-0.3630.0000.0000.0000.000
207A211LEU00.0120.00727.7850.2800.2800.0000.0000.0000.000
208A212THR0-0.065-0.05931.5010.2050.2050.0000.0000.0000.000
209A213ILE00.0350.03628.3950.2130.2130.0000.0000.0000.000
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