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: VN141

Calculation Name: 1AD2-A-Xray547

Preferred Name:

Target Type:

Ligand Name: (4r)-2-methylpentane-2,4-diol | mercury (ii) ion

Ligand 3-letter code: MRD | HG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1AD2

Chain ID: A

ChEMBL ID:

UniProt ID: P27150

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 224
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2472138.700429
FMO2-HF: Nuclear repulsion 2388064.65186
FMO2-HF: Total energy -84074.048569
FMO2-MP2: Total energy -84322.83576


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:LYS)


Summations of interaction energy for fragment #1(A:5:LYS)
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.
59.67162.4721.514-9.82-14.494-0.02
Interaction energy analysis for fragmet #1(A:5:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.873 / q_NPA : 0.930
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].
3A7TYR00.1450.0572.227-15.570-13.46015.859-7.638-10.331-0.025
4A8ARG10.8970.9632.15526.22726.5005.631-2.113-3.7920.006
5A9ALA00.0510.0223.2711.9282.3440.024-0.069-0.371-0.001
6A10LEU0-0.047-0.0155.2061.6501.6500.0000.0000.0000.000
7A11LEU00.007-0.0146.5721.3961.3960.0000.0000.0000.000
8A12GLU-1-0.859-0.9267.469-23.828-23.8280.0000.0000.0000.000
9A13LYS10.8650.9389.71620.02120.0210.0000.0000.0000.000
10A14VAL0-0.038-0.01611.8701.0551.0550.0000.0000.0000.000
11A15ASP-1-0.786-0.88813.957-14.669-14.6690.0000.0000.0000.000
12A16PRO0-0.055-0.03814.8390.4410.4410.0000.0000.0000.000
13A17ASN0-0.064-0.03817.4070.6540.6540.0000.0000.0000.000
14A18LYS10.8340.93420.15512.60512.6050.0000.0000.0000.000
15A19ILE0-0.060-0.02821.621-0.270-0.2700.0000.0000.0000.000
16A20TYR00.0180.00217.1590.2050.2050.0000.0000.0000.000
17A21THR00.017-0.01923.3840.2650.2650.0000.0000.0000.000
18A22ILE0-0.019-0.00724.486-0.503-0.5030.0000.0000.0000.000
19A23ASP-1-0.783-0.88424.927-10.285-10.2850.0000.0000.0000.000
20A24GLU-1-0.813-0.85622.033-11.769-11.7690.0000.0000.0000.000
21A25ALA00.0100.00120.196-0.501-0.5010.0000.0000.0000.000
22A26ALA0-0.0140.00120.118-0.606-0.6060.0000.0000.0000.000
23A27HIS10.8390.90021.19211.14511.1450.0000.0000.0000.000
24A28LEU00.0450.02814.679-0.331-0.3310.0000.0000.0000.000
25A29VAL0-0.010-0.01215.778-0.931-0.9310.0000.0000.0000.000
26A30LYS10.8590.92615.79612.18112.1810.0000.0000.0000.000
27A31GLU-1-0.877-0.92413.107-16.397-16.3970.0000.0000.0000.000
28A32LEU0-0.058-0.02611.105-1.543-1.5430.0000.0000.0000.000
29A33ALA00.0230.02611.286-1.593-1.5930.0000.0000.0000.000
30A34THR0-0.0030.0179.7320.8620.8620.0000.0000.0000.000
31A35ALA0-0.052-0.03810.197-2.947-2.9470.0000.0000.0000.000
32A36LYS10.9300.95912.37520.59920.5990.0000.0000.0000.000
33A37PHE0-0.001-0.00615.2330.0730.0730.0000.0000.0000.000
34A38ASP-1-0.761-0.87117.903-14.148-14.1480.0000.0000.0000.000
35A39GLU-1-0.805-0.89314.149-20.754-20.7540.0000.0000.0000.000
36A40THR0-0.001-0.01018.3260.8900.8900.0000.0000.0000.000
37A41VAL00.0270.02419.075-0.784-0.7840.0000.0000.0000.000
38A42GLU-1-0.823-0.88920.512-13.488-13.4880.0000.0000.0000.000
39A43VAL00.0080.01021.853-0.318-0.3180.0000.0000.0000.000
40A44HIS0-0.038-0.04420.2820.4270.4270.0000.0000.0000.000
41A45ALA00.002-0.00323.6920.0700.0700.0000.0000.0000.000
42A46LYS10.9130.96322.64612.74512.7450.0000.0000.0000.000
43A47LEU00.0310.01127.2380.1730.1730.0000.0000.0000.000
44A48GLY0-0.061-0.03031.013-0.085-0.0850.0000.0000.0000.000
45A49ILE0-0.048-0.02232.8600.2430.2430.0000.0000.0000.000
46A50ASP-1-0.812-0.90434.082-8.688-8.6880.0000.0000.0000.000
47A51PRO0-0.023-0.01731.4510.1360.1360.0000.0000.0000.000
48A52ARG10.9160.95532.9889.0409.0400.0000.0000.0000.000
49A53ARG10.8210.89536.8737.5467.5460.0000.0000.0000.000
50A54SER00.0150.00339.099-0.093-0.0930.0000.0000.0000.000
51A55ASP-1-0.766-0.84140.977-7.263-7.2630.0000.0000.0000.000
52A56GLN0-0.006-0.01638.298-0.151-0.1510.0000.0000.0000.000
53A57ASN0-0.062-0.03635.244-0.452-0.4520.0000.0000.0000.000
54A58VAL0-0.0010.00433.9280.1630.1630.0000.0000.0000.000
55A59ARG10.8520.90434.8398.2298.2290.0000.0000.0000.000
56A60GLY00.0350.02536.2390.2470.2470.0000.0000.0000.000
57A61THR00.0160.01735.692-0.230-0.2300.0000.0000.0000.000
58A62VAL0-0.022-0.01032.3400.1250.1250.0000.0000.0000.000
59A63SER00.0180.00935.562-0.012-0.0120.0000.0000.0000.000
60A64LEU0-0.049-0.01730.0300.0300.0300.0000.0000.0000.000
61A65PRO0-0.0020.00933.2380.0970.0970.0000.0000.0000.000
62A66HIS0-0.059-0.05130.7940.0980.0980.0000.0000.0000.000
63A67GLY00.0080.00530.974-0.297-0.2970.0000.0000.0000.000
64A68LEU00.0190.01831.584-0.041-0.0410.0000.0000.0000.000
65A69GLY00.0680.03034.4470.1800.1800.0000.0000.0000.000
66A70LYS10.9050.93837.7897.2927.2920.0000.0000.0000.000
67A71GLN0-0.027-0.01634.671-0.029-0.0290.0000.0000.0000.000
68A72VAL0-0.0120.01632.644-0.176-0.1760.0000.0000.0000.000
69A73ARG10.8510.90631.4679.8689.8680.0000.0000.0000.000
70A74VAL0-0.016-0.02233.607-0.357-0.3570.0000.0000.0000.000
71A75LEU0-0.0040.00831.5350.2260.2260.0000.0000.0000.000
72A76ALA0-0.003-0.00934.132-0.211-0.2110.0000.0000.0000.000
73A77ILE0-0.038-0.02131.9060.0880.0880.0000.0000.0000.000
74A78ALA00.0160.00036.094-0.065-0.0650.0000.0000.0000.000
75A79LYS10.8640.91338.6138.1758.1750.0000.0000.0000.000
76A80GLY00.0230.01241.8580.0660.0660.0000.0000.0000.000
77A81GLU-1-0.865-0.94045.676-6.841-6.8410.0000.0000.0000.000
78A82LYS10.8620.92342.2287.0827.0820.0000.0000.0000.000
79A83ILE0-0.0170.00241.878-0.130-0.1300.0000.0000.0000.000
80A84LYS10.8490.90543.7296.5956.5950.0000.0000.0000.000
81A85GLU-1-0.811-0.89443.755-7.179-7.1790.0000.0000.0000.000
82A86ALA0-0.005-0.02140.813-0.045-0.0450.0000.0000.0000.000
83A87GLU-1-0.828-0.91142.708-6.864-6.8640.0000.0000.0000.000
84A88GLU-1-0.923-0.95445.097-6.347-6.3470.0000.0000.0000.000
85A89ALA0-0.099-0.04243.0020.0480.0480.0000.0000.0000.000
86A90GLY0-0.0200.00343.607-0.074-0.0740.0000.0000.0000.000
87A91ALA0-0.046-0.03238.776-0.156-0.1560.0000.0000.0000.000
88A92ASP-1-0.822-0.88037.771-8.159-8.1590.0000.0000.0000.000
89A93TYR0-0.048-0.03934.8730.1250.1250.0000.0000.0000.000
90A94VAL00.0320.02038.123-0.150-0.1500.0000.0000.0000.000
91A95GLY0-0.016-0.00638.6790.0800.0800.0000.0000.0000.000
92A96GLY00.0800.05538.589-0.056-0.0560.0000.0000.0000.000
93A97GLU-1-0.879-0.96635.497-8.838-8.8380.0000.0000.0000.000
94A98GLU-1-0.876-0.94635.204-8.166-8.1660.0000.0000.0000.000
95A99ILE0-0.038-0.01634.275-0.146-0.1460.0000.0000.0000.000
96A100ILE0-0.012-0.01529.937-0.275-0.2750.0000.0000.0000.000
97A101GLN00.0210.01031.029-0.485-0.4850.0000.0000.0000.000
98A102LYS11.0261.01832.1188.5028.5020.0000.0000.0000.000
99A103ILE0-0.0230.00827.372-0.157-0.1570.0000.0000.0000.000
100A104LEU0-0.094-0.04727.008-0.448-0.4480.0000.0000.0000.000
101A105ASP-1-0.945-0.96128.235-9.925-9.9250.0000.0000.0000.000
102A106GLY0-0.021-0.00927.8130.0750.0750.0000.0000.0000.000
103A107TRP0-0.081-0.04428.861-0.065-0.0650.0000.0000.0000.000
104A108MET00.004-0.02924.380-0.312-0.3120.0000.0000.0000.000
105A109ASP-1-0.896-0.92329.480-9.788-9.7880.0000.0000.0000.000
106A110PHE0-0.013-0.02228.0520.2910.2910.0000.0000.0000.000
107A111ASP-1-0.816-0.86129.488-10.341-10.3410.0000.0000.0000.000
108A112ALA0-0.034-0.02129.172-0.324-0.3240.0000.0000.0000.000
109A113VAL0-0.0050.00828.7830.2240.2240.0000.0000.0000.000
110A114VAL0-0.033-0.01830.833-0.181-0.1810.0000.0000.0000.000
111A115ALA00.0170.00332.7320.0820.0820.0000.0000.0000.000
112A116THR00.0420.00334.598-0.004-0.0040.0000.0000.0000.000
113A117PRO0-0.028-0.02834.697-0.223-0.2230.0000.0000.0000.000
114A118ASP-1-0.840-0.89635.076-8.208-8.2080.0000.0000.0000.000
115A119VAL00.0590.04333.9850.0320.0320.0000.0000.0000.000
116A120MET0-0.039-0.01228.420-0.260-0.2600.0000.0000.0000.000
117A121GLY0-0.0100.01129.989-0.393-0.3930.0000.0000.0000.000
118A122ALA00.0330.01729.852-0.366-0.3660.0000.0000.0000.000
119A123VAL00.0310.00728.355-0.361-0.3610.0000.0000.0000.000
120A124GLY0-0.007-0.00826.047-0.443-0.4430.0000.0000.0000.000
121A125SER0-0.056-0.02524.862-0.715-0.7150.0000.0000.0000.000
122A126LYS10.9160.95625.1829.6309.6300.0000.0000.0000.000
123A127LEU00.0550.03025.089-0.257-0.2570.0000.0000.0000.000
124A128GLY00.0210.02322.720-0.432-0.4320.0000.0000.0000.000
125A129ARG10.9250.95315.95916.84716.8470.0000.0000.0000.000
126A130ILE00.0040.00418.868-0.914-0.9140.0000.0000.0000.000
127A131LEU00.0410.00821.086-0.383-0.3830.0000.0000.0000.000
128A132GLY00.0230.01820.151-0.020-0.0200.0000.0000.0000.000
129A133PRO0-0.048-0.02115.656-0.174-0.1740.0000.0000.0000.000
130A134ARG10.9110.95817.45114.46614.4660.0000.0000.0000.000
131A135GLY0-0.034-0.01020.2030.3760.3760.0000.0000.0000.000
132A136LEU00.000-0.00222.0390.4630.4630.0000.0000.0000.000
133A137LEU0-0.011-0.00422.3830.3110.3110.0000.0000.0000.000
134A138PRO00.0020.01425.435-0.045-0.0450.0000.0000.0000.000
135A139ASN00.000-0.01625.0740.0360.0360.0000.0000.0000.000
136A140PRO00.0540.02828.3210.1660.1660.0000.0000.0000.000
137A141LYS10.8640.92225.48912.02712.0270.0000.0000.0000.000
138A142ALA0-0.0010.00427.295-0.105-0.1050.0000.0000.0000.000
139A143GLY00.0080.01529.3050.1590.1590.0000.0000.0000.000
140A144THR00.0500.02729.3240.2200.2200.0000.0000.0000.000
141A145VAL0-0.021-0.01730.886-0.005-0.0050.0000.0000.0000.000
142A146GLY00.0160.00433.6640.0200.0200.0000.0000.0000.000
143A147PHE00.030-0.00537.358-0.016-0.0160.0000.0000.0000.000
144A148ASN0-0.023-0.00240.1790.0290.0290.0000.0000.0000.000
145A149ILE00.0490.02337.126-0.088-0.0880.0000.0000.0000.000
146A150GLY00.0350.00439.998-0.107-0.1070.0000.0000.0000.000
147A151GLU-1-0.920-0.95641.774-7.223-7.2230.0000.0000.0000.000
148A152ILE0-0.029-0.00735.347-0.080-0.0800.0000.0000.0000.000
149A153ILE0-0.0010.00337.771-0.179-0.1790.0000.0000.0000.000
150A154ARG10.9380.97739.0966.9066.9060.0000.0000.0000.000
151A155GLU-1-0.792-0.86237.826-7.866-7.8660.0000.0000.0000.000
152A156ILE00.0130.00433.755-0.081-0.0810.0000.0000.0000.000
153A157LYS10.8110.88636.9708.2038.2030.0000.0000.0000.000
154A158ALA0-0.091-0.04239.8690.1710.1710.0000.0000.0000.000
155A159GLY0-0.011-0.00637.3150.0730.0730.0000.0000.0000.000
156A160ARG10.7530.85036.4827.5927.5920.0000.0000.0000.000
157A161ILE00.0200.01329.819-0.137-0.1370.0000.0000.0000.000
158A162GLU-1-0.809-0.91633.595-8.572-8.5720.0000.0000.0000.000
159A163PHE0-0.057-0.02231.085-0.426-0.4260.0000.0000.0000.000
160A164ARG10.9700.96930.89310.01110.0110.0000.0000.0000.000
161A165ASN0-0.0230.00029.771-0.178-0.1780.0000.0000.0000.000
162A166ASP-1-0.882-0.92525.729-11.712-11.7120.0000.0000.0000.000
163A167LYS10.9930.97627.10311.35011.3500.0000.0000.0000.000
164A168THR0-0.066-0.05124.4680.0780.0780.0000.0000.0000.000
165A169GLY00.0320.02927.7680.0290.0290.0000.0000.0000.000
166A170ALA0-0.036-0.01024.7820.0480.0480.0000.0000.0000.000
167A171ILE00.005-0.00626.7360.2460.2460.0000.0000.0000.000
168A172HIS10.8220.89422.55612.93312.9330.0000.0000.0000.000
169A173ALA00.0340.03125.6040.2820.2820.0000.0000.0000.000
170A174PRO00.0120.01524.385-0.365-0.3650.0000.0000.0000.000
171A175VAL00.007-0.00724.5470.4830.4830.0000.0000.0000.000
172A176GLY00.0280.00924.9310.4450.4450.0000.0000.0000.000
173A177LYS10.8480.94121.88613.50213.5020.0000.0000.0000.000
174A178ALA00.0590.02817.8640.3380.3380.0000.0000.0000.000
175A179CYS0-0.015-0.02519.8850.1870.1870.0000.0000.0000.000
176A180PHE0-0.040-0.01322.0450.4740.4740.0000.0000.0000.000
177A181PRO00.0330.01323.739-0.339-0.3390.0000.0000.0000.000
178A182PRO00.0100.01122.986-0.016-0.0160.0000.0000.0000.000
179A183GLU-1-0.799-0.91624.846-10.307-10.3070.0000.0000.0000.000
180A184LYS10.9610.98428.1699.5939.5930.0000.0000.0000.000
181A185LEU0-0.0250.00122.0980.0370.0370.0000.0000.0000.000
182A186ALA00.0160.00426.278-0.001-0.0010.0000.0000.0000.000
183A187ASP-1-0.840-0.90027.852-8.916-8.9160.0000.0000.0000.000
184A188ASN0-0.031-0.04528.3790.4850.4850.0000.0000.0000.000
185A189ILE0-0.018-0.01023.9360.0010.0010.0000.0000.0000.000
186A190ARG10.7920.84428.3329.6199.6190.0000.0000.0000.000
187A191ALA00.0040.00831.6850.2300.2300.0000.0000.0000.000
188A192PHE00.0140.00028.1020.1590.1590.0000.0000.0000.000
189A193ILE0-0.010-0.00528.1300.1490.1490.0000.0000.0000.000
190A194ARG10.9540.97132.3188.1988.1980.0000.0000.0000.000
191A195ALA00.0320.02434.8970.2520.2520.0000.0000.0000.000
192A196LEU0-0.0070.01130.5660.1660.1660.0000.0000.0000.000
193A197GLU-1-0.906-0.96934.616-8.540-8.5400.0000.0000.0000.000
194A198ALA0-0.041-0.01036.8580.1910.1910.0000.0000.0000.000
195A199HIS10.8480.91337.0418.2488.2480.0000.0000.0000.000
196A200LYS10.9100.97538.0737.6727.6720.0000.0000.0000.000
197A201PRO0-0.0010.01938.1330.1520.1520.0000.0000.0000.000
198A202GLU-1-0.858-0.94041.156-7.088-7.0880.0000.0000.0000.000
199A203GLY00.0000.00443.7250.0670.0670.0000.0000.0000.000
200A204ALA0-0.049-0.01838.567-0.079-0.0790.0000.0000.0000.000
201A205LYS10.9700.97640.4787.0277.0270.0000.0000.0000.000
202A206GLY00.0100.00738.721-0.164-0.1640.0000.0000.0000.000
203A207THR0-0.035-0.03433.4930.1320.1320.0000.0000.0000.000
204A208PHE00.0550.03234.561-0.196-0.1960.0000.0000.0000.000
205A209LEU00.0550.02730.835-0.280-0.2800.0000.0000.0000.000
206A210ARG10.9330.97529.2009.7919.7910.0000.0000.0000.000
207A211SER0-0.047-0.02624.838-0.264-0.2640.0000.0000.0000.000
208A212VAL00.0370.01925.628-0.028-0.0280.0000.0000.0000.000
209A213TYR0-0.013-0.02120.037-0.174-0.1740.0000.0000.0000.000
210A214VAL00.0320.02420.2870.3630.3630.0000.0000.0000.000
211A215THR00.0030.00215.971-0.796-0.7960.0000.0000.0000.000
212A216THR00.003-0.01214.1820.7690.7690.0000.0000.0000.000
213A217THR00.008-0.01014.5800.0480.0480.0000.0000.0000.000
214A218MET0-0.077-0.0406.984-0.939-0.9390.0000.0000.0000.000
215A219GLY00.0410.04210.023-2.593-2.5930.0000.0000.0000.000
216A220PRO0-0.043-0.0289.9290.3460.3460.0000.0000.0000.000
217A221SER0-0.022-0.00612.4900.9290.9290.0000.0000.0000.000
218A222VAL00.0310.02216.236-0.002-0.0020.0000.0000.0000.000
219A223ARG10.9410.97218.28512.25612.2560.0000.0000.0000.000
220A224ILE00.0180.00521.6420.1120.1120.0000.0000.0000.000
221A225ASN00.0360.02224.5820.2470.2470.0000.0000.0000.000
222A226PRO0-0.033-0.01128.2290.0470.0470.0000.0000.0000.000
223A227HIS10.8020.88730.3379.1159.1150.0000.0000.0000.000
224A228SER-1-0.714-0.82128.941-9.531-9.5310.0000.0000.0000.000