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: RL4M8

Calculation Name: 2XWC-A-Xray547

Preferred Name:

Target Type:

Ligand Name: tris(hydroxyethyl)aminomethane | glycerol | zinc ion

Ligand 3-letter code: TAM | GOL | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2XWC

Chain ID: A

ChEMBL ID:

UniProt ID: O15350

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 206
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2358074.082123
FMO2-HF: Nuclear repulsion 2275441.791613
FMO2-HF: Total energy -82632.29051
FMO2-MP2: Total energy -82868.717934


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:112:ALA)


Summations of interaction energy for fragment #1(A:112:ALA)
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.
-16.241-10.841.718-3.497-3.62-0.034
Interaction energy analysis for fragmet #1(A:112:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.867 / q_NPA : 0.934
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].
3A114VAL00.0530.0303.8066.4867.885-0.009-0.603-0.786-0.001
118A230VAL0-0.022-0.0023.750-3.238-2.9900.001-0.083-0.1650.000
119A231THR0-0.095-0.0872.407-23.659-19.9601.726-2.792-2.633-0.033
120A232GLY00.0030.0163.765-0.388-0.3330.000-0.019-0.0360.000
4A115ILE00.0230.0165.9432.9202.9200.0000.0000.0000.000
5A116PRO00.0020.0009.6660.8150.8150.0000.0000.0000.000
6A117SER0-0.018-0.00911.6361.6861.6860.0000.0000.0000.000
7A118ASN00.025-0.00514.5571.5061.5060.0000.0000.0000.000
8A119THR00.0160.01517.6390.5310.5310.0000.0000.0000.000
9A120ASP-1-0.820-0.89620.537-12.782-12.7820.0000.0000.0000.000
10A121TYR0-0.033-0.00722.6820.2910.2910.0000.0000.0000.000
11A122PRO00.0320.01524.588-0.051-0.0510.0000.0000.0000.000
12A123GLY00.0610.04926.9420.0880.0880.0000.0000.0000.000
13A124PRO0-0.020-0.00627.3590.3990.3990.0000.0000.0000.000
14A125HIS0-0.021-0.02228.4160.1190.1190.0000.0000.0000.000
15A126HIS10.8670.92730.7259.7999.7990.0000.0000.0000.000
16A127PHE00.0500.03924.0780.2180.2180.0000.0000.0000.000
17A128GLU-1-0.925-0.96628.772-9.615-9.6150.0000.0000.0000.000
18A129VAL00.006-0.00125.646-0.093-0.0930.0000.0000.0000.000
19A130THR0-0.022-0.01729.0700.0400.0400.0000.0000.0000.000
20A131PHE0-0.006-0.00727.932-0.190-0.1900.0000.0000.0000.000
21A132GLN00.0380.03233.2950.0730.0730.0000.0000.0000.000
22A133GLN00.0350.01536.662-0.227-0.2270.0000.0000.0000.000
23A134SER00.0060.01236.399-0.050-0.0500.0000.0000.0000.000
24A135SER00.0280.01038.4010.2570.2570.0000.0000.0000.000
25A136THR00.0430.02339.153-0.184-0.1840.0000.0000.0000.000
26A137ALA00.0290.02241.5650.0580.0580.0000.0000.0000.000
27A138LYS10.9860.96940.2997.0767.0760.0000.0000.0000.000
28A139SER0-0.027-0.01839.923-0.073-0.0730.0000.0000.0000.000
29A140ALA0-0.0270.00837.7230.0200.0200.0000.0000.0000.000
30A141THR00.0330.01235.072-0.127-0.1270.0000.0000.0000.000
31A142TRP00.0410.00632.207-0.392-0.3920.0000.0000.0000.000
32A143THR0-0.053-0.03133.2370.3250.3250.0000.0000.0000.000
33A144TYR00.0760.02930.285-0.393-0.3930.0000.0000.0000.000
34A145SER0-0.047-0.04032.9010.3090.3090.0000.0000.0000.000
35A146PRO0-0.012-0.02933.214-0.294-0.2940.0000.0000.0000.000
36A147LEU0-0.0100.00834.647-0.136-0.1360.0000.0000.0000.000
37A148LEU00.0310.01231.763-0.126-0.1260.0000.0000.0000.000
38A149LYS10.9170.96829.57510.26410.2640.0000.0000.0000.000
39A150LYS10.8340.92527.00810.96410.9640.0000.0000.0000.000
40A151LEU0-0.0080.00427.2870.4760.4760.0000.0000.0000.000
41A152TYR0-0.035-0.04727.990-0.369-0.3690.0000.0000.0000.000
42A153CYS0-0.083-0.05927.7370.5400.5400.0000.0000.0000.000
43A154GLN00.0350.02229.3070.0320.0320.0000.0000.0000.000
44A155ILE0-0.0280.00326.048-0.142-0.1420.0000.0000.0000.000
45A156ALA0-0.024-0.02027.1840.3820.3820.0000.0000.0000.000
46A157LYS10.8650.94028.6489.3019.3010.0000.0000.0000.000
47A158THR0-0.005-0.01129.599-0.274-0.2740.0000.0000.0000.000
48A160PRO00.0040.01228.689-0.361-0.3610.0000.0000.0000.000
49A161ILE0-0.013-0.01525.528-0.082-0.0820.0000.0000.0000.000
50A162GLN0-0.0140.01029.8160.0900.0900.0000.0000.0000.000
51A163ILE00.0060.00026.369-0.323-0.3230.0000.0000.0000.000
52A164LYS10.8860.93830.2189.0549.0540.0000.0000.0000.000
53A165VAL00.0060.00330.078-0.409-0.4090.0000.0000.0000.000
54A166SER00.0000.00432.6960.2170.2170.0000.0000.0000.000
55A167THR00.007-0.00534.2120.2330.2330.0000.0000.0000.000
56A168PRO00.0300.01833.210-0.296-0.2960.0000.0000.0000.000
57A169PRO0-0.0030.02128.3760.0470.0470.0000.0000.0000.000
58A170PRO00.0160.00328.1460.2780.2780.0000.0000.0000.000
59A171PRO00.0260.01129.145-0.274-0.2740.0000.0000.0000.000
60A172GLY0-0.018-0.00627.183-0.233-0.2330.0000.0000.0000.000
61A173THR0-0.024-0.02224.861-0.633-0.6330.0000.0000.0000.000
62A174ALA0-0.012-0.00221.7130.3650.3650.0000.0000.0000.000
63A175ILE0-0.006-0.00822.6910.0310.0310.0000.0000.0000.000
64A176ARG10.8260.88714.20919.43619.4360.0000.0000.0000.000
65A177ALA00.0130.01319.2370.3270.3270.0000.0000.0000.000
66A178MET00.009-0.00811.367-0.980-0.9800.0000.0000.0000.000
67A179PRO0-0.0220.00814.4660.5820.5820.0000.0000.0000.000
68A180VAL00.010-0.01212.674-1.803-1.8030.0000.0000.0000.000
69A181TYR00.0270.01513.1671.6811.6810.0000.0000.0000.000
70A182LYS10.8720.91915.80713.29113.2910.0000.0000.0000.000
71A183LYS10.8820.96018.19213.99213.9920.0000.0000.0000.000
72A184ALA00.0500.01616.308-0.986-0.9860.0000.0000.0000.000
73A185GLU-1-0.853-0.94014.832-17.690-17.6900.0000.0000.0000.000
74A186HIS00.0340.01913.7130.2120.2120.0000.0000.0000.000
75A187VAL0-0.0040.02212.216-1.317-1.3170.0000.0000.0000.000
76A188THR0-0.008-0.0147.633-0.851-0.8510.0000.0000.0000.000
77A189ASP-1-0.911-0.9397.543-30.327-30.3270.0000.0000.0000.000
78A190VAL0-0.066-0.0376.7930.9220.9220.0000.0000.0000.000
79A191VAL0-0.039-0.0119.5591.4771.4770.0000.0000.0000.000
80A192LYS10.8850.9499.74124.13124.1310.0000.0000.0000.000
81A193ARG10.8240.87614.60713.78513.7850.0000.0000.0000.000
82A194CYS0-0.073-0.06216.875-0.471-0.4710.0000.0000.0000.000
83A195PRO00.1090.02717.2790.4610.4610.0000.0000.0000.000
84A196ASN0-0.033-0.02319.6570.0410.0410.0000.0000.0000.000
85A197HIS0-0.048-0.10022.3250.9010.9010.0000.0000.0000.000
86A198GLU-1-0.968-0.97616.672-16.670-16.6700.0000.0000.0000.000
87A199LEU0-0.017-0.01820.0360.2070.2070.0000.0000.0000.000
88A200GLY00.0130.02523.1110.5150.5150.0000.0000.0000.000
89A201ARG10.8660.91926.2039.1519.1510.0000.0000.0000.000
90A202ASP-1-0.865-0.93828.234-9.897-9.8970.0000.0000.0000.000
91A203PHE0-0.022-0.02426.875-0.415-0.4150.0000.0000.0000.000
92A204ASN00.0050.01623.807-0.618-0.6180.0000.0000.0000.000
93A205GLU-1-0.819-0.89426.553-9.267-9.2670.0000.0000.0000.000
94A206GLY0-0.027-0.02029.8380.0760.0760.0000.0000.0000.000
95A207GLN0-0.027-0.01626.536-0.236-0.2360.0000.0000.0000.000
96A208SER00.0100.00625.894-0.085-0.0850.0000.0000.0000.000
97A209ALA0-0.0030.01422.369-0.439-0.4390.0000.0000.0000.000
98A210PRO00.0020.00017.9670.2150.2150.0000.0000.0000.000
99A211ALA00.0280.01720.030-0.064-0.0640.0000.0000.0000.000
100A212SER00.0450.02515.1320.1830.1830.0000.0000.0000.000
101A213HIS0-0.030-0.01314.560-0.203-0.2030.0000.0000.0000.000
102A214LEU0-0.0110.00216.8490.8250.8250.0000.0000.0000.000
103A215ILE0-0.028-0.01718.2750.8790.8790.0000.0000.0000.000
104A216ARG10.9030.93720.14912.26812.2680.0000.0000.0000.000
105A217VAL0-0.0030.00422.9610.1120.1120.0000.0000.0000.000
106A218GLU-1-0.813-0.88525.581-9.607-9.6070.0000.0000.0000.000
107A219GLY00.001-0.01429.2470.0350.0350.0000.0000.0000.000
108A220ASN00.0150.01827.4450.0110.0110.0000.0000.0000.000
109A221ASN00.0180.00427.969-0.495-0.4950.0000.0000.0000.000
110A222LEU0-0.018-0.00326.961-0.056-0.0560.0000.0000.0000.000
111A223SER0-0.026-0.02823.474-0.476-0.4760.0000.0000.0000.000
112A224GLN0-0.050-0.01619.487-0.540-0.5400.0000.0000.0000.000
113A225TYR00.0430.00618.024-0.368-0.3680.0000.0000.0000.000
114A226VAL0-0.014-0.00612.536-0.093-0.0930.0000.0000.0000.000
115A227ASP-1-0.777-0.87210.723-22.717-22.7170.0000.0000.0000.000
116A228ASP-1-0.805-0.8996.709-37.144-37.1440.0000.0000.0000.000
117A229PRO0-0.008-0.0057.397-3.355-3.3550.0000.0000.0000.000
121A233ARG10.7830.8715.88737.99237.9920.0000.0000.0000.000
122A234GLN0-0.007-0.0128.5231.2191.2190.0000.0000.0000.000
123A235SER0-0.046-0.02412.0660.3040.3040.0000.0000.0000.000
124A236VAL00.0380.02415.1210.1120.1120.0000.0000.0000.000
125A237VAL0-0.003-0.00817.414-0.046-0.0460.0000.0000.0000.000
126A238VAL00.0240.01920.1780.3420.3420.0000.0000.0000.000
127A239PRO00.017-0.00123.929-0.275-0.2750.0000.0000.0000.000
128A240TYR0-0.013-0.01126.1690.1520.1520.0000.0000.0000.000
129A241GLU-1-0.907-0.94127.979-9.775-9.7750.0000.0000.0000.000
130A242PRO0-0.012-0.01131.532-0.064-0.0640.0000.0000.0000.000
131A243PRO00.0110.02234.2280.0440.0440.0000.0000.0000.000
132A244GLN00.0200.03036.5940.1320.1320.0000.0000.0000.000
133A245VAL00.0320.00239.976-0.014-0.0140.0000.0000.0000.000
134A246GLY0-0.0070.00042.4950.1460.1460.0000.0000.0000.000
135A247THR0-0.099-0.05839.9060.0160.0160.0000.0000.0000.000
136A248GLU-1-0.837-0.91637.495-8.306-8.3060.0000.0000.0000.000
137A249PHE0-0.025-0.02434.072-0.232-0.2320.0000.0000.0000.000
138A250THR0-0.007-0.00330.4520.2490.2490.0000.0000.0000.000
139A251THR0-0.039-0.02831.798-0.176-0.1760.0000.0000.0000.000
140A252ILE00.0180.00926.034-0.031-0.0310.0000.0000.0000.000
141A253LEU00.0090.01429.4470.0300.0300.0000.0000.0000.000
142A254TYR00.0250.01222.602-0.449-0.4490.0000.0000.0000.000
143A255ASN0-0.062-0.04325.4630.4310.4310.0000.0000.0000.000
144A256PHE00.021-0.00221.283-0.575-0.5750.0000.0000.0000.000
145A257MET00.0240.00821.8630.6780.6780.0000.0000.0000.000
146A258CYS-1-0.767-0.72920.984-13.668-13.6680.0000.0000.0000.000
147A259ASN00.0210.01023.1000.2260.2260.0000.0000.0000.000
148A260SER00.025-0.00422.708-0.264-0.2640.0000.0000.0000.000
149A261SER0-0.016-0.02723.433-0.304-0.3040.0000.0000.0000.000
150A262CYS0-0.021-0.00522.4120.2270.2270.0000.0000.0000.000
151A263VAL00.0440.03216.720-0.174-0.1740.0000.0000.0000.000
152A264GLY00.0240.00519.626-0.581-0.5810.0000.0000.0000.000
153A265GLY0-0.005-0.00222.4030.6210.6210.0000.0000.0000.000
154A266MET00.0130.00724.446-0.584-0.5840.0000.0000.0000.000
155A267ASN0-0.028-0.00226.007-0.285-0.2850.0000.0000.0000.000
156A268ARG10.9070.95923.70611.43911.4390.0000.0000.0000.000
157A269ARG10.8610.92317.17516.44616.4460.0000.0000.0000.000
158A270PRO00.0480.03920.820-0.188-0.1880.0000.0000.0000.000
159A271ILE00.010-0.00617.451-0.828-0.8280.0000.0000.0000.000
160A272LEU0-0.035-0.02018.2870.9640.9640.0000.0000.0000.000
161A273ILE00.002-0.00118.162-1.013-1.0130.0000.0000.0000.000
162A274ILE0-0.010-0.01515.1720.7650.7650.0000.0000.0000.000
163A275ILE0-0.0020.00418.873-0.239-0.2390.0000.0000.0000.000
164A276THR0-0.025-0.04817.5500.2080.2080.0000.0000.0000.000
165A277LEU00.0080.02320.4840.2350.2350.0000.0000.0000.000
166A278GLU-1-0.790-0.85617.324-18.385-18.3850.0000.0000.0000.000
167A279MET00.0590.02621.2660.7740.7740.0000.0000.0000.000
168A280ARG10.9450.97821.15912.88912.8890.0000.0000.0000.000
169A281ASP-1-0.852-0.93620.125-14.964-14.9640.0000.0000.0000.000
170A282GLY00.0070.01116.921-1.002-1.0020.0000.0000.0000.000
171A283GLN0-0.079-0.03117.370-0.395-0.3950.0000.0000.0000.000
172A284VAL0-0.034-0.02117.4720.6600.6600.0000.0000.0000.000
173A285LEU00.0140.00620.2650.3580.3580.0000.0000.0000.000
174A286GLY00.001-0.01222.9630.6040.6040.0000.0000.0000.000
175A287ARG10.8300.90817.22516.43816.4380.0000.0000.0000.000
176A288ARG10.8260.90822.37412.04612.0460.0000.0000.0000.000
177A289SER00.0060.00320.708-0.740-0.7400.0000.0000.0000.000
178A290PHE00.0370.02322.6760.6210.6210.0000.0000.0000.000
179A291GLU-1-0.810-0.88622.856-13.324-13.3240.0000.0000.0000.000
180A292GLY00.0280.02323.0970.5850.5850.0000.0000.0000.000
181A293ARG10.6820.80923.94010.34210.3420.0000.0000.0000.000
182A294ILE00.0220.01723.9700.3270.3270.0000.0000.0000.000
183A295CYS-1-0.732-0.82126.791-10.085-10.0850.0000.0000.0000.000
184A296ALA00.0330.00129.6660.0970.0970.0000.0000.0000.000
185A297CYS0-0.145-0.11532.9270.3970.3970.0000.0000.0000.000
186A298PRO00.1140.06331.7940.1510.1510.0000.0000.0000.000
187A299GLY00.004-0.00433.5970.0280.0280.0000.0000.0000.000
188A300ARG10.8540.91336.6018.2378.2370.0000.0000.0000.000
189A301ASP-1-0.794-0.88431.314-9.718-9.7180.0000.0000.0000.000
190A302ARG10.8540.92134.2338.5758.5750.0000.0000.0000.000
191A303LYS10.8480.92335.0437.8047.8040.0000.0000.0000.000
192A304ALA00.0350.02035.8550.1000.1000.0000.0000.0000.000
193A305ASP-1-0.762-0.83531.427-10.085-10.0850.0000.0000.0000.000
194A306GLU-1-0.788-0.85434.924-8.427-8.4270.0000.0000.0000.000
195A307ASP-1-0.887-0.92937.508-7.516-7.5160.0000.0000.0000.000
196A308HIS10.8110.87736.3608.3818.3810.0000.0000.0000.000
197A309TYR0-0.059-0.02734.322-0.130-0.1300.0000.0000.0000.000
198A310ARG10.8630.90237.5697.9057.9050.0000.0000.0000.000
199A311GLU-1-0.879-0.91140.355-7.780-7.7800.0000.0000.0000.000
200A312ALA00.0060.00738.3930.1220.1220.0000.0000.0000.000
201A313GLU-1-0.823-0.89638.525-8.438-8.4380.0000.0000.0000.000
202A314ASN0-0.100-0.06441.3050.2400.2400.0000.0000.0000.000
203A315LEU0-0.036-0.01041.8440.1710.1710.0000.0000.0000.000
204A316TYR0-0.098-0.04838.470-0.013-0.0130.0000.0000.0000.000
205A317PHE0-0.048-0.02744.6580.1480.1480.0000.0000.0000.000
206A318GLN-1-0.935-0.95346.929-6.568-6.5680.0000.0000.0000.000