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: 64V6Z

Calculation Name: 3WYH-A-Xray547

Preferred Name:

Target Type:

Ligand Name: hexaethylene glycol | tris(hydroxyethyl)aminomethane

Ligand 3-letter code: P6G | TAM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3WYH

Chain ID: A

ChEMBL ID:

UniProt ID: P00719

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 185
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2053245.13319
FMO2-HF: Nuclear repulsion 1981360.293793
FMO2-HF: Total energy -71884.839397
FMO2-MP2: Total energy -72095.448738


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:1:ARG)


Summations of interaction energy for fragment #1(A:1:ARG)
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.
223.333238.389.782-8.395-16.435-0.072
Interaction energy analysis for fragmet #1(A:1:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.814 / q_NPA : 1.911
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].
3A3GLY00.0460.0213.0410.8613.1060.298-0.987-1.555-0.006
4A4SER00.000-0.0083.7647.5097.6050.009-0.018-0.0870.000
53A53LYS10.8200.8994.19085.77286.045-0.001-0.012-0.2600.000
54A54LYS10.8500.9203.63431.79032.3900.002-0.286-0.316-0.002
56A56GLY00.0300.0183.1330.8871.2160.044-0.080-0.294-0.001
57A57GLN0-0.080-0.0522.374-22.012-18.4525.480-2.968-6.072-0.020
58A58LYS10.9380.9733.52053.55752.9590.1391.031-0.5720.000
60A60SER0-0.033-0.0092.9500.6451.0610.058-0.118-0.356-0.001
61A61VAL0-0.015-0.0063.7127.1017.4430.003-0.063-0.2820.000
62A62ASP-1-0.749-0.8632.641-127.189-124.1140.579-1.601-2.053-0.017
63A63PRO0-0.012-0.0102.2089.26010.1313.069-1.246-2.694-0.009
64A64ALA00.0260.0144.53311.33911.460-0.001-0.016-0.1040.000
181A181LYS10.7930.8753.117102.812103.3490.015-0.221-0.3310.000
185A185TYR-1-0.915-0.9833.256-137.078-133.8980.088-1.810-1.459-0.016
5A5TYR0-0.035-0.0337.0638.5448.5440.0000.0000.0000.000
6A6GLY00.0880.0598.1673.5713.5710.0000.0000.0000.000
7A7ASP-1-0.853-0.9347.732-66.623-66.6230.0000.0000.0000.000
8A8VAL00.0410.0197.1715.2825.2820.0000.0000.0000.000
9A9ASN0-0.045-0.0326.7915.9345.9340.0000.0000.0000.000
10A10ARG10.8660.93310.52046.58746.5870.0000.0000.0000.000
11A11VAL0-0.0310.00812.6612.4192.4190.0000.0000.0000.000
12A12ASP-1-0.770-0.84614.780-30.522-30.5220.0000.0000.0000.000
13A13THR0-0.019-0.04116.0620.1720.1720.0000.0000.0000.000
14A14THR00.0120.01018.6760.7420.7420.0000.0000.0000.000
15A15GLY0-0.025-0.01719.3830.7240.7240.0000.0000.0000.000
16A16ALA0-0.0160.00120.3850.6270.6270.0000.0000.0000.000
17A17SER00.028-0.00322.6691.0791.0790.0000.0000.0000.000
18A18SER00.036-0.01926.389-0.412-0.4120.0000.0000.0000.000
19A19LYS10.8280.91928.53019.81819.8180.0000.0000.0000.000
20A20SER0-0.004-0.03223.7090.0290.0290.0000.0000.0000.000
21A21ALA00.0020.00525.565-0.317-0.3170.0000.0000.0000.000
22A22LYS10.9750.99126.69917.68617.6860.0000.0000.0000.000
23A23PRO0-0.029-0.01427.7680.4620.4620.0000.0000.0000.000
24A24GLU-1-0.833-0.89023.893-24.383-24.3830.0000.0000.0000.000
25A25LYS10.9380.96427.03318.18018.1800.0000.0000.0000.000
26A26LEU0-0.0170.01423.9410.1050.1050.0000.0000.0000.000
27A27ASN0-0.009-0.01128.622-0.280-0.2800.0000.0000.0000.000
28A28TYR00.0100.00623.5810.5080.5080.0000.0000.0000.000
29A29SER0-0.012-0.01625.851-0.496-0.4960.0000.0000.0000.000
30A30GLY00.0700.04023.4040.0020.0020.0000.0000.0000.000
31A31VAL00.020-0.00818.534-0.565-0.5650.0000.0000.0000.000
32A32ALA00.0220.01019.156-1.250-1.2500.0000.0000.0000.000
33A33ALA0-0.0030.01821.445-0.047-0.0470.0000.0000.0000.000
34A34SER00.015-0.03717.587-0.024-0.0240.0000.0000.0000.000
35A35ARG10.8680.93113.29935.40335.4030.0000.0000.0000.000
36A36LYS10.8630.93017.39625.24025.2400.0000.0000.0000.000
37A37ILE0-0.036-0.02919.8070.3460.3460.0000.0000.0000.000
38A38ALA00.0150.01214.363-0.183-0.1830.0000.0000.0000.000
39A39GLU-1-0.852-0.90516.246-28.505-28.5050.0000.0000.0000.000
40A40ARG10.8640.92717.67423.93023.9300.0000.0000.0000.000
41A41ASP-1-0.757-0.83017.086-29.270-29.2700.0000.0000.0000.000
42A42LEU0-0.0100.02312.495-1.534-1.5340.0000.0000.0000.000
43A43GLN00.0540.02015.411-2.674-2.6740.0000.0000.0000.000
44A44SER0-0.051-0.02418.0470.6950.6950.0000.0000.0000.000
45A45MET0-0.023-0.00311.936-0.431-0.4310.0000.0000.0000.000
46A46ASP-1-0.776-0.87412.664-47.081-47.0810.0000.0000.0000.000
47A47ARG10.9320.98714.29728.56428.5640.0000.0000.0000.000
48A48TYR00.029-0.00113.3780.8900.8900.0000.0000.0000.000
49A49LYS10.8370.9439.04246.62646.6260.0000.0000.0000.000
50A50ALA00.0340.0138.402-6.878-6.8780.0000.0000.0000.000
51A51LEU00.0190.0058.031-4.839-4.8390.0000.0000.0000.000
52A52ILE00.0320.0147.215-3.806-3.8060.0000.0000.0000.000
55A55VAL00.0270.0126.025-3.070-3.0700.0000.0000.0000.000
59A59LEU00.007-0.0036.1115.0815.0810.0000.0000.0000.000
65A65VAL00.0090.0006.3278.4638.4630.0000.0000.0000.000
66A66ILE0-0.019-0.0016.0245.0165.0160.0000.0000.0000.000
67A67ALA00.0290.0068.9985.0715.0710.0000.0000.0000.000
68A68GLY00.017-0.00110.3804.1654.1650.0000.0000.0000.000
69A69ILE00.0080.00312.2353.2933.2930.0000.0000.0000.000
70A70ILE00.0060.00812.1012.7862.7860.0000.0000.0000.000
71A71SER0-0.056-0.03614.8512.6562.6560.0000.0000.0000.000
72A72ARG10.7620.85416.63029.57429.5740.0000.0000.0000.000
73A73GLU-1-0.819-0.88817.740-28.299-28.2990.0000.0000.0000.000
74A74SER0-0.025-0.02318.2401.4531.4530.0000.0000.0000.000
75A75HIS10.7510.85719.47028.16728.1670.0000.0000.0000.000
76A76ALA00.010-0.01216.5230.4810.4810.0000.0000.0000.000
77A77GLY00.016-0.01218.2670.3680.3680.0000.0000.0000.000
78A78LYS10.8100.90620.68929.26929.2690.0000.0000.0000.000
79A79ALA0-0.0140.00123.5341.0151.0150.0000.0000.0000.000
80A80LEU0-0.083-0.02421.2290.5850.5850.0000.0000.0000.000
81A81ARG10.9630.97725.75320.67320.6730.0000.0000.0000.000
82A82ASN00.002-0.00527.985-0.134-0.1340.0000.0000.0000.000
83A83GLY00.0380.02223.878-0.057-0.0570.0000.0000.0000.000
84A84TRP0-0.004-0.00623.874-1.066-1.0660.0000.0000.0000.000
85A85GLY00.0620.01625.6010.2250.2250.0000.0000.0000.000
86A86ASP-1-0.839-0.92025.485-21.495-21.4950.0000.0000.0000.000
87A87ASN0-0.056-0.03327.2630.7320.7320.0000.0000.0000.000
88A88GLY00.0410.03929.6150.5850.5850.0000.0000.0000.000
89A89ASN0-0.065-0.03327.7150.6210.6210.0000.0000.0000.000
90A90GLY00.0570.04423.802-0.491-0.4910.0000.0000.0000.000
91A91PHE00.001-0.01020.8320.2960.2960.0000.0000.0000.000
92A92GLY00.0390.01019.694-1.241-1.2410.0000.0000.0000.000
93A93LEU0-0.0100.00115.4350.2590.2590.0000.0000.0000.000
94A94MET0-0.049-0.00911.490-1.135-1.1350.0000.0000.0000.000
95A95GLN0-0.0180.00316.6061.1921.1920.0000.0000.0000.000
96A96VAL0-0.0020.00817.7250.4700.4700.0000.0000.0000.000
97A97ASP-1-0.781-0.86420.248-21.648-21.6480.0000.0000.0000.000
98A98ARG10.9130.93823.79219.83919.8390.0000.0000.0000.000
99A99ARG10.8190.89826.10121.63121.6310.0000.0000.0000.000
100A100SER00.0030.00724.8280.0700.0700.0000.0000.0000.000
101A101HIS10.8610.92121.10425.94025.9400.0000.0000.0000.000
102A102LYS11.0241.02923.86922.76022.7600.0000.0000.0000.000
103A103PRO00.0370.02621.804-1.064-1.0640.0000.0000.0000.000
104A104VAL0-0.059-0.03018.6390.9480.9480.0000.0000.0000.000
105A105GLY0-0.030-0.01719.614-1.375-1.3750.0000.0000.0000.000
106A106GLU-1-0.875-0.93420.054-26.263-26.2630.0000.0000.0000.000
107A107TRP00.0190.00819.413-1.975-1.9750.0000.0000.0000.000
108A108ASN00.013-0.00117.604-0.954-0.9540.0000.0000.0000.000
109A109GLY00.0500.03216.361-1.500-1.5000.0000.0000.0000.000
110A110GLU-1-0.824-0.90910.872-46.871-46.8710.0000.0000.0000.000
111A111ARG10.9690.97013.29627.48427.4840.0000.0000.0000.000
112A112HIS00.0540.06215.869-0.603-0.6030.0000.0000.0000.000
113A113LEU00.0420.01410.994-0.772-0.7720.0000.0000.0000.000
114A114MET0-0.044-0.01110.762-4.465-4.4650.0000.0000.0000.000
115A115GLN00.0520.01912.133-0.377-0.3770.0000.0000.0000.000
116A116GLY00.0500.01314.2760.8430.8430.0000.0000.0000.000
117A117THR0-0.002-0.0247.580-1.718-1.7180.0000.0000.0000.000
118A118GLU-1-0.906-0.96810.975-39.231-39.2310.0000.0000.0000.000
119A119ILE0-0.0310.00213.1351.3871.3870.0000.0000.0000.000
120A120LEU00.0380.0379.9830.8260.8260.0000.0000.0000.000
121A121ILE0-0.009-0.0098.7020.7440.7440.0000.0000.0000.000
122A122SER0-0.089-0.05512.7521.9581.9580.0000.0000.0000.000
123A123MET00.0130.01016.1982.1102.1100.0000.0000.0000.000
124A124ILE00.0500.01410.9401.0041.0040.0000.0000.0000.000
125A125LYS10.8890.95412.73140.82340.8230.0000.0000.0000.000
126A126ALA0-0.0110.00316.7721.4391.4390.0000.0000.0000.000
127A127ILE0-0.0080.00517.9051.4701.4700.0000.0000.0000.000
128A128GLN0-0.049-0.02913.891-1.059-1.0590.0000.0000.0000.000
129A129LYS10.9470.97818.51524.63824.6380.0000.0000.0000.000
130A130LYS10.8030.90721.76724.26624.2660.0000.0000.0000.000
131A131PHE00.001-0.00321.7621.2941.2940.0000.0000.0000.000
132A132PRO00.0430.02221.284-1.017-1.0170.0000.0000.0000.000
133A133ARG10.9450.96822.36420.98120.9810.0000.0000.0000.000
134A134TRP0-0.022-0.00119.495-0.076-0.0760.0000.0000.0000.000
135A135THR00.0420.00617.085-0.978-0.9780.0000.0000.0000.000
136A136LYS10.9500.97210.90344.30544.3050.0000.0000.0000.000
137A137GLU-1-0.826-0.92511.909-44.921-44.9210.0000.0000.0000.000
138A138GLN00.0540.04714.046-0.300-0.3000.0000.0000.0000.000
139A139GLN00.000-0.02815.608-0.930-0.9300.0000.0000.0000.000
140A140LEU0-0.038-0.0029.6240.2270.2270.0000.0000.0000.000
141A141LYS10.8050.89313.44330.49830.4980.0000.0000.0000.000
142A142GLY00.0670.01316.0530.9440.9440.0000.0000.0000.000
143A143GLY0-0.012-0.02015.4491.0831.0830.0000.0000.0000.000
144A144ILE0-0.015-0.01112.0340.1570.1570.0000.0000.0000.000
145A145SER0-0.034-0.03015.9011.3961.3960.0000.0000.0000.000
146A146ALA0-0.016-0.01918.9821.1731.1730.0000.0000.0000.000
147A147TYR0-0.093-0.05815.4500.0440.0440.0000.0000.0000.000
148A148ASN0-0.0100.00918.5351.4491.4490.0000.0000.0000.000
149A149ALA00.0570.02321.6511.0181.0180.0000.0000.0000.000
150A150GLY00.0430.03422.6181.0001.0000.0000.0000.0000.000
151A151PRO00.003-0.02321.6000.2270.2270.0000.0000.0000.000
152A152GLY0-0.0150.00023.2230.5560.5560.0000.0000.0000.000
153A153ASN0-0.008-0.00325.6551.5381.5380.0000.0000.0000.000
154A154VAL00.0280.02321.3110.4150.4150.0000.0000.0000.000
155A155ARG10.8810.92524.66219.97719.9770.0000.0000.0000.000
156A156SER00.0080.01526.0510.5810.5810.0000.0000.0000.000
157A157TYR0-0.030-0.04418.840-1.217-1.2170.0000.0000.0000.000
158A158GLU-1-0.838-0.93523.496-23.256-23.2560.0000.0000.0000.000
159A159ARG10.9080.94625.61220.94420.9440.0000.0000.0000.000
160A160MET0-0.0660.00219.700-0.136-0.1360.0000.0000.0000.000
161A161ASP-1-0.712-0.82121.563-28.409-28.4090.0000.0000.0000.000
162A162ILE0-0.0410.01124.5510.4150.4150.0000.0000.0000.000
163A163GLY00.0360.03028.3960.0380.0380.0000.0000.0000.000
164A164THR0-0.086-0.05423.185-0.401-0.4010.0000.0000.0000.000
165A165THR00.020-0.00624.6440.4970.4970.0000.0000.0000.000
166A166HIS0-0.030-0.03325.154-0.384-0.3840.0000.0000.0000.000
167A167ASP-1-0.817-0.89027.119-20.161-20.1610.0000.0000.0000.000
168A168ASP-1-0.703-0.79623.269-25.075-25.0750.0000.0000.0000.000
169A169TYR0-0.049-0.04517.530-1.728-1.7280.0000.0000.0000.000
170A170ALA00.0370.00217.495-1.601-1.6010.0000.0000.0000.000
171A171ASN00.011-0.00216.812-2.110-2.1100.0000.0000.0000.000
172A172ASP-1-0.730-0.79217.393-31.346-31.3460.0000.0000.0000.000
173A173VAL00.0190.01113.566-1.582-1.5820.0000.0000.0000.000
174A174VAL0-0.0010.00512.686-3.396-3.3960.0000.0000.0000.000
175A175ALA0-0.0150.00012.606-2.236-2.2360.0000.0000.0000.000
176A176ARG10.7870.86713.82030.38930.3890.0000.0000.0000.000
177A177ALA00.0010.0048.974-1.849-1.8490.0000.0000.0000.000
178A178GLN0-0.032-0.0398.821-2.942-2.9420.0000.0000.0000.000
179A179TYR00.0160.01810.522-0.619-0.6190.0000.0000.0000.000
180A180TYR00.0290.0038.672-0.917-0.9170.0000.0000.0000.000
182A182GLN0-0.0010.0156.568-1.444-1.4440.0000.0000.0000.000
183A183HIS0-0.014-0.0039.1864.5664.5660.0000.0000.0000.000
184A184GLY00.0320.0157.2491.5401.5400.0000.0000.0000.000