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

tag_button

FMODB ID: RM838

Calculation Name: 3LD9-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol

Ligand 3-letter code: EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3LD9

Chain ID: A

ChEMBL ID:

UniProt ID: Q2GHN3

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 187
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2123189.063875
FMO2-HF: Nuclear repulsion 2047933.130297
FMO2-HF: Total energy -75255.933578
FMO2-MP2: Total energy -75475.099899


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:-2:PRO)


Summations of interaction energy for fragment #1(A:-2:PRO)
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.
-209.501-201.72813.979-10.363-11.39-0.117
Interaction energy analysis for fragmet #1(A:-2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.762 / q_NPA : 0.871
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].
3A0SER0-0.074-0.0153.770-2.396-0.771-0.020-0.766-0.838-0.001
31A28TYR0-0.025-0.0222.555-8.339-6.8170.859-0.746-1.636-0.007
32A29GLY00.0200.0203.586-7.806-7.0520.008-0.382-0.381-0.003
35A32ASN0-0.103-0.0802.399-12.287-10.3513.612-2.073-3.475-0.025
36A33VAL00.0260.0314.127-4.602-4.4260.000-0.062-0.1130.000
89A86LYS10.8270.9203.11228.99530.1400.049-0.489-0.705-0.002
90A87LYS10.8840.9601.807-0.865-0.6439.470-5.791-3.902-0.079
91A88ILE00.0700.0383.8304.1984.5910.001-0.054-0.3400.000
4A1MET00.0220.0226.0343.0033.0030.0000.0000.0000.000
5A2PHE0-0.035-0.0238.053-0.457-0.4570.0000.0000.0000.000
6A3ILE00.0580.0289.8941.4391.4390.0000.0000.0000.000
7A4THR0-0.031-0.00912.9110.0930.0930.0000.0000.0000.000
8A5PHE00.0530.02814.6000.1360.1360.0000.0000.0000.000
9A6GLU-1-0.733-0.85818.806-12.967-12.9670.0000.0000.0000.000
10A7GLY00.0630.03822.3150.0750.0750.0000.0000.0000.000
11A8ILE00.0190.00926.014-0.090-0.0900.0000.0000.0000.000
12A9ASP-1-0.880-0.93527.791-11.178-11.1780.0000.0000.0000.000
13A10GLY0-0.028-0.01829.2230.2530.2530.0000.0000.0000.000
14A11SER0-0.028-0.01726.5020.0240.0240.0000.0000.0000.000
15A12GLY00.0660.03625.274-0.307-0.3070.0000.0000.0000.000
16A13LYS10.8490.93021.60812.38012.3800.0000.0000.0000.000
17A14THR0-0.024-0.03520.183-0.473-0.4730.0000.0000.0000.000
18A15THR00.0090.01919.789-0.695-0.6950.0000.0000.0000.000
19A16GLN00.0540.02419.239-1.104-1.1040.0000.0000.0000.000
20A17SER0-0.064-0.03615.891-1.013-1.0130.0000.0000.0000.000
21A18HIS0-0.067-0.04414.844-1.266-1.2660.0000.0000.0000.000
22A19LEU00.0680.04115.367-0.970-0.9700.0000.0000.0000.000
23A20LEU00.0110.00511.905-0.811-0.8110.0000.0000.0000.000
24A21ALA00.007-0.00610.950-2.020-2.0200.0000.0000.0000.000
25A22GLU-1-0.931-0.95610.754-18.439-18.4390.0000.0000.0000.000
26A23TYR00.0180.00511.582-1.532-1.5320.0000.0000.0000.000
27A24LEU00.005-0.0077.530-1.616-1.6160.0000.0000.0000.000
28A25SER0-0.059-0.0526.929-4.625-4.6250.0000.0000.0000.000
29A26GLU-1-0.962-0.9798.200-22.226-22.2260.0000.0000.0000.000
30A27ILE0-0.060-0.0036.488-0.104-0.1040.0000.0000.0000.000
33A30VAL00.0790.0205.568-3.720-3.7200.0000.0000.0000.000
34A31ASN0-0.051-0.0276.5471.0911.0910.0000.0000.0000.000
37A34VAL0-0.035-0.0156.8393.1293.1290.0000.0000.0000.000
38A35LEU00.0210.0249.6160.3290.3290.0000.0000.0000.000
39A36THR0-0.068-0.06012.7071.1381.1380.0000.0000.0000.000
40A37ARG10.8620.89715.69413.41913.4190.0000.0000.0000.000
41A38GLU-1-0.771-0.85419.076-14.639-14.6390.0000.0000.0000.000
42A39PRO00.0090.00521.9570.2060.2060.0000.0000.0000.000
43A40GLY00.028-0.01022.4980.4090.4090.0000.0000.0000.000
44A41GLY00.0740.05118.968-0.166-0.1660.0000.0000.0000.000
45A42THR00.0150.00318.862-0.355-0.3550.0000.0000.0000.000
46A43LEU00.0480.01621.5510.4770.4770.0000.0000.0000.000
47A44LEU00.0050.02524.5580.5310.5310.0000.0000.0000.000
48A45ASN0-0.018-0.02622.2950.8720.8720.0000.0000.0000.000
49A46GLU-1-0.746-0.85822.590-12.728-12.7280.0000.0000.0000.000
50A47SER0-0.049-0.02926.0860.5010.5010.0000.0000.0000.000
51A48VAL00.005-0.00828.8690.3950.3950.0000.0000.0000.000
52A49ARG10.9130.96524.58912.22912.2290.0000.0000.0000.000
53A50ASN0-0.030-0.02329.1300.2680.2680.0000.0000.0000.000
54A51LEU0-0.044-0.01531.7430.3330.3330.0000.0000.0000.000
55A52LEU00.0280.01030.4270.2650.2650.0000.0000.0000.000
56A53PHE0-0.026-0.00732.0910.2200.2200.0000.0000.0000.000
57A54LYS10.8840.93434.1328.7518.7510.0000.0000.0000.000
58A55ALA0-0.0140.00636.9020.2670.2670.0000.0000.0000.000
59A56GLN0-0.013-0.00938.6620.0130.0130.0000.0000.0000.000
60A57GLY0-0.010-0.00341.7530.0790.0790.0000.0000.0000.000
61A58LEU0-0.037-0.01035.3630.0960.0960.0000.0000.0000.000
62A59ASP-1-0.818-0.90539.681-7.949-7.9490.0000.0000.0000.000
63A60SER00.0660.03036.823-0.214-0.2140.0000.0000.0000.000
64A61LEU00.0310.01635.573-0.311-0.3110.0000.0000.0000.000
65A62SER0-0.020-0.02435.391-0.336-0.3360.0000.0000.0000.000
66A63GLU-1-0.869-0.92832.477-9.506-9.5060.0000.0000.0000.000
67A64LEU00.0150.01430.203-0.382-0.3820.0000.0000.0000.000
68A65LEU0-0.005-0.00630.454-0.409-0.4090.0000.0000.0000.000
69A66PHE0-0.021-0.00930.673-0.296-0.2960.0000.0000.0000.000
70A67PHE0-0.010-0.01827.224-0.459-0.4590.0000.0000.0000.000
71A68ILE00.0130.01725.989-0.575-0.5750.0000.0000.0000.000
72A69ALA00.0110.00726.005-0.447-0.4470.0000.0000.0000.000
73A70MET0-0.079-0.03025.007-0.326-0.3260.0000.0000.0000.000
74A71ARG10.8540.91921.15112.62912.6290.0000.0000.0000.000
75A72ARG10.8930.95521.21413.10913.1090.0000.0000.0000.000
76A73GLU-1-0.843-0.90921.439-13.830-13.8300.0000.0000.0000.000
77A74HIS0-0.026-0.02316.867-1.424-1.4240.0000.0000.0000.000
78A75PHE00.0410.01815.736-1.114-1.1140.0000.0000.0000.000
79A76VAL0-0.027-0.01716.345-1.175-1.1750.0000.0000.0000.000
80A77LYS10.7930.87017.09713.27413.2740.0000.0000.0000.000
81A78ILE0-0.0070.01313.406-0.755-0.7550.0000.0000.0000.000
82A79ILE00.0160.03312.543-2.167-2.1670.0000.0000.0000.000
83A80LYS10.8730.92411.52816.87816.8780.0000.0000.0000.000
84A81PRO00.003-0.01211.384-2.215-2.2150.0000.0000.0000.000
85A82SER0-0.005-0.0078.306-2.633-2.6330.0000.0000.0000.000
86A83LEU00.0580.0426.757-6.259-6.2590.0000.0000.0000.000
87A84MET0-0.060-0.0387.416-2.282-2.2820.0000.0000.0000.000
88A85GLN0-0.024-0.0115.994-2.317-2.3170.0000.0000.0000.000
92A89VAL0-0.061-0.0275.6231.8101.8100.0000.0000.0000.000
93A90ILE00.0410.0319.2730.7850.7850.0000.0000.0000.000
94A91CYS0-0.057-0.02912.1140.7780.7780.0000.0000.0000.000
95A92ASP-1-0.799-0.87315.623-13.581-13.5810.0000.0000.0000.000
96A93ARG10.7940.87518.90312.20812.2080.0000.0000.0000.000
97A94PHE00.0420.00718.283-0.772-0.7720.0000.0000.0000.000
98A95ILE00.009-0.00120.8110.6770.6770.0000.0000.0000.000
99A96ASP-1-0.778-0.85421.762-13.345-13.3450.0000.0000.0000.000
100A97SER0-0.010-0.05624.1270.6920.6920.0000.0000.0000.000
101A98THR0-0.072-0.00925.6490.4170.4170.0000.0000.0000.000
102A99ILE00.0240.01027.5730.4420.4420.0000.0000.0000.000
103A100ALA00.0250.02428.6990.4220.4220.0000.0000.0000.000
104A101TYR00.0320.00828.8780.3240.3240.0000.0000.0000.000
105A102GLN0-0.027-0.03730.5400.0480.0480.0000.0000.0000.000
106A103GLY00.0350.01332.2090.2550.2550.0000.0000.0000.000
107A104TYR0-0.068-0.05233.0840.2110.2110.0000.0000.0000.000
108A105GLY00.0040.01134.4230.2810.2810.0000.0000.0000.000
109A106GLN0-0.093-0.06035.3770.4860.4860.0000.0000.0000.000
110A107GLY0-0.0100.01737.2680.2270.2270.0000.0000.0000.000
111A108ILE0-0.054-0.02235.1450.1490.1490.0000.0000.0000.000
112A109ASP-1-0.809-0.88536.141-8.788-8.7880.0000.0000.0000.000
113A110CYS00.0410.00332.593-0.233-0.2330.0000.0000.0000.000
114A111SER0-0.057-0.03331.918-0.334-0.3340.0000.0000.0000.000
115A112LEU00.0070.00232.559-0.230-0.2300.0000.0000.0000.000
116A113ILE0-0.002-0.00128.766-0.286-0.2860.0000.0000.0000.000
117A114ASP-1-0.861-0.92728.002-11.369-11.3690.0000.0000.0000.000
118A115GLN0-0.034-0.02127.645-0.345-0.3450.0000.0000.0000.000
119A116LEU0-0.026-0.01428.654-0.232-0.2320.0000.0000.0000.000
120A117ASN00.0390.00924.267-0.467-0.4670.0000.0000.0000.000
121A118ASP-1-0.841-0.89023.947-13.370-13.3700.0000.0000.0000.000
122A119LEU0-0.058-0.00824.479-0.188-0.1880.0000.0000.0000.000
123A120VAL0-0.086-0.04623.243-0.145-0.1450.0000.0000.0000.000
124A121ILE0-0.036-0.01518.889-0.656-0.6560.0000.0000.0000.000
125A122ASP-1-0.796-0.87817.209-17.356-17.3560.0000.0000.0000.000
126A123VAL0-0.069-0.03712.705-0.655-0.6550.0000.0000.0000.000
127A124TYR0-0.024-0.04616.1520.0650.0650.0000.0000.0000.000
128A125PRO0-0.033-0.02014.600-1.078-1.0780.0000.0000.0000.000
129A126ASP-1-0.846-0.91411.355-25.208-25.2080.0000.0000.0000.000
130A127ILE0-0.031-0.01512.0631.1031.1030.0000.0000.0000.000
131A128THR0-0.026-0.01915.182-0.387-0.3870.0000.0000.0000.000
132A129PHE00.0420.01614.1070.5960.5960.0000.0000.0000.000
133A130ILE0-0.037-0.01719.3710.1290.1290.0000.0000.0000.000
134A131ILE00.0200.00920.725-0.008-0.0080.0000.0000.0000.000
135A132ASP-1-0.869-0.92624.544-9.896-9.8960.0000.0000.0000.000
136A133VAL0-0.038-0.01928.195-0.084-0.0840.0000.0000.0000.000
137A134ASP-2-1.793-1.88031.173-17.282-17.2820.0000.0000.0000.000
138A151ASP-1-0.845-0.94840.728-7.329-7.3290.0000.0000.0000.000
139A152MET0-0.0110.00039.593-0.220-0.2200.0000.0000.0000.000
140A153GLU-1-0.845-0.90640.347-7.679-7.6790.0000.0000.0000.000
141A154PHE0-0.051-0.03634.870-0.195-0.1950.0000.0000.0000.000
142A155TYR00.0010.00034.090-0.230-0.2300.0000.0000.0000.000
143A156TYR0-0.001-0.00535.684-0.181-0.1810.0000.0000.0000.000
144A157ARG10.8550.91736.3377.7047.7040.0000.0000.0000.000
145A158VAL0-0.022-0.00731.284-0.242-0.2420.0000.0000.0000.000
146A159ARG10.9040.94831.7918.5338.5330.0000.0000.0000.000
147A160ASP-1-0.859-0.92032.075-8.746-8.7460.0000.0000.0000.000
148A161GLY00.014-0.00332.135-0.150-0.1500.0000.0000.0000.000
149A162PHE0-0.029-0.01825.461-0.356-0.3560.0000.0000.0000.000
150A163TYR0-0.032-0.02428.070-0.218-0.2180.0000.0000.0000.000
151A164ASP-1-0.828-0.88630.040-9.315-9.3150.0000.0000.0000.000
152A165ILE0-0.053-0.02125.219-0.172-0.1720.0000.0000.0000.000
153A166ALA00.0460.01825.445-0.358-0.3580.0000.0000.0000.000
154A167LYS10.8460.91826.4939.0819.0810.0000.0000.0000.000
155A168LYS10.8270.91627.96110.98710.9870.0000.0000.0000.000
156A169ASN0-0.088-0.05722.963-0.534-0.5340.0000.0000.0000.000
157A170PRO00.0530.03322.919-0.561-0.5610.0000.0000.0000.000
158A171HIS0-0.0080.01019.8230.0610.0610.0000.0000.0000.000
159A172ARG10.8260.87617.79614.29814.2980.0000.0000.0000.000
160A173CYS0-0.070-0.02318.555-0.581-0.5810.0000.0000.0000.000
161A174HIS10.8820.93718.11915.74515.7450.0000.0000.0000.000
162A175VAL00.0160.00521.297-0.273-0.2730.0000.0000.0000.000
163A176ILE0-0.040-0.00719.726-0.041-0.0410.0000.0000.0000.000
164A177THR00.0010.00424.3340.1030.1030.0000.0000.0000.000
165A178ASP-1-0.874-0.97526.853-11.207-11.2070.0000.0000.0000.000
166A179LYS10.8110.91028.0708.6188.6180.0000.0000.0000.000
167A180SER0-0.032-0.03229.230-0.181-0.1810.0000.0000.0000.000
168A181GLU-1-0.842-0.91430.424-8.517-8.5170.0000.0000.0000.000
169A182THR0-0.104-0.06730.8860.2240.2240.0000.0000.0000.000
170A183TYR0-0.076-0.02928.6000.0880.0880.0000.0000.0000.000
171A184ASP-1-0.903-0.92632.159-8.852-8.8520.0000.0000.0000.000
172A185ILE0-0.042-0.03226.687-0.165-0.1650.0000.0000.0000.000
173A186ASP-1-0.817-0.90727.653-10.862-10.8620.0000.0000.0000.000
174A187ASP-1-0.796-0.89327.656-10.241-10.2410.0000.0000.0000.000
175A188ILE0-0.043-0.01823.932-0.559-0.5590.0000.0000.0000.000
176A189ASN0-0.049-0.04423.394-1.072-1.0720.0000.0000.0000.000
177A190PHE0-0.030-0.00523.082-0.537-0.5370.0000.0000.0000.000
178A191VAL00.0220.02021.502-0.498-0.4980.0000.0000.0000.000
179A192HIS00.0100.00715.775-0.644-0.6440.0000.0000.0000.000
180A193LEU0-0.025-0.01218.444-0.838-0.8380.0000.0000.0000.000
181A194GLU-1-0.810-0.89819.459-13.138-13.1380.0000.0000.0000.000
182A195VAL0-0.036-0.02515.492-0.582-0.5820.0000.0000.0000.000
183A196ILE0-0.029-0.01614.375-1.007-1.0070.0000.0000.0000.000
184A197LYS10.8040.90214.99711.96911.9690.0000.0000.0000.000
185A198VAL0-0.052-0.02616.0020.1100.1100.0000.0000.0000.000
186A199LEU0-0.107-0.05210.691-0.692-0.6920.0000.0000.0000.000
187A200GLN-1-1.011-0.98211.958-20.186-20.1860.0000.0000.0000.000