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: GR7Q1

Calculation Name: 4L5H-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4L5H

Chain ID: A

ChEMBL ID:

UniProt ID: O04708

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 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2121898.075958
FMO2-HF: Nuclear repulsion 2043450.598481
FMO2-HF: Total energy -78447.477477
FMO2-MP2: Total energy -78663.949729


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:25:ALA)


Summations of interaction energy for fragment #1(A:25: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.
-164.028-158.21316.103-9.651-12.27-0.097
Interaction energy analysis for fragmet #1(A:25:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.798 / q_NPA : 0.914
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].
3A27PHE00.027-0.0022.406-3.028-0.4750.956-1.396-2.113-0.008
34A58THR0-0.015-0.0163.367-6.179-5.9170.004-0.089-0.1780.000
35A59VAL00.0120.0183.1229.16110.0330.005-0.338-0.539-0.001
36A60ASN00.019-0.0011.888-42.405-43.8978.293-4.077-2.725-0.052
37A61PRO00.0260.0103.5040.9191.2160.004-0.036-0.2660.000
38A62GLY00.0130.0155.1554.8204.814-0.001-0.0010.0080.000
84A110LEU0-0.011-0.0032.366-3.655-3.4321.894-0.572-1.546-0.006
85A111ASN0-0.050-0.0324.084-6.071-5.908-0.001-0.036-0.1250.000
91A117ASP-1-0.740-0.8313.727-57.036-56.5770.004-0.164-0.299-0.001
182A213GLY0-0.023-0.0134.1463.7543.798-0.001-0.014-0.0290.000
184A215ASN0-0.045-0.0232.368-27.313-24.9912.678-2.207-2.793-0.022
185A216TYR00.006-0.0382.2789.1859.3342.269-0.720-1.698-0.007
186A217LYS10.8900.9535.26421.18221.151-0.001-0.0010.0330.000
4A28ASP-1-0.898-0.9495.872-21.622-21.6220.0000.0000.0000.000
5A29ILE00.0040.0089.3620.1550.1550.0000.0000.0000.000
6A30LEU00.0250.01512.0671.2831.2830.0000.0000.0000.000
7A31ASN0-0.013-0.02615.2430.1770.1770.0000.0000.0000.000
8A32LYS10.8560.92118.39215.12015.1200.0000.0000.0000.000
9A33CYS0-0.069-0.01718.2061.0641.0640.0000.0000.0000.000
10A34THR00.0100.01123.598-0.105-0.1050.0000.0000.0000.000
11A35TYR00.0060.00324.1300.2690.2690.0000.0000.0000.000
12A36THR0-0.042-0.04024.064-0.293-0.2930.0000.0000.0000.000
13A37VAL0-0.0160.00819.1070.2690.2690.0000.0000.0000.000
14A38TRP00.014-0.01620.448-0.307-0.3070.0000.0000.0000.000
15A39ALA00.0190.03114.859-0.111-0.1110.0000.0000.0000.000
16A40ALA00.0220.00615.2220.5620.5620.0000.0000.0000.000
17A41ALA00.0110.01210.206-0.924-0.9240.0000.0000.0000.000
18A42SER0-0.0330.01711.5881.6731.6730.0000.0000.0000.000
19A43PRO00.037-0.0057.933-0.506-0.5060.0000.0000.0000.000
20A44GLY00.039-0.0049.497-2.476-2.4760.0000.0000.0000.000
21A45GLY00.0370.04211.0740.8820.8820.0000.0000.0000.000
22A46GLY0-0.002-0.02814.877-0.055-0.0550.0000.0000.0000.000
23A47ARG10.9240.98116.71817.15017.1500.0000.0000.0000.000
24A48ARG10.8320.88718.40812.08012.0800.0000.0000.0000.000
25A49LEU0-0.0160.00015.887-0.313-0.3130.0000.0000.0000.000
26A50ASP-1-0.763-0.84020.563-11.790-11.7900.0000.0000.0000.000
27A51SER0-0.035-0.03922.224-0.490-0.4900.0000.0000.0000.000
28A52GLY00.0240.01221.4520.3320.3320.0000.0000.0000.000
29A53GLN0-0.035-0.00319.999-0.702-0.7020.0000.0000.0000.000
30A54SER00.0250.00214.573-0.266-0.2660.0000.0000.0000.000
31A55TRP0-0.061-0.03313.5090.7470.7470.0000.0000.0000.000
32A56THR00.0120.0148.898-0.556-0.5560.0000.0000.0000.000
33A57ILE0-0.0030.0126.4231.1661.1660.0000.0000.0000.000
39A63THR0-0.066-0.0385.9455.2425.2420.0000.0000.0000.000
40A64THR00.0150.0037.999-2.157-2.1570.0000.0000.0000.000
41A65ASN00.000-0.00810.775-0.603-0.6030.0000.0000.0000.000
42A66ALA00.0470.0578.0561.1421.1420.0000.0000.0000.000
43A67ARG10.8160.90410.07419.13319.1330.0000.0000.0000.000
44A68ILE0-0.027-0.0097.449-0.366-0.3660.0000.0000.0000.000
45A69TRP0-0.037-0.02511.4980.7220.7220.0000.0000.0000.000
46A70GLY00.0550.02215.158-0.402-0.4020.0000.0000.0000.000
47A71ARG10.7550.86618.09916.16516.1650.0000.0000.0000.000
48A72THR00.0630.03621.505-0.106-0.1060.0000.0000.0000.000
49A73SER0-0.031-0.04725.0040.0080.0080.0000.0000.0000.000
50A74CYS0-0.0730.01224.0110.0060.0060.0000.0000.0000.000
51A75THR0-0.014-0.00827.1470.3010.3010.0000.0000.0000.000
52A76PHE0-0.017-0.02423.801-0.207-0.2070.0000.0000.0000.000
53A77ASP-1-0.799-0.89928.684-10.451-10.4510.0000.0000.0000.000
54A78ALA0-0.025-0.02628.688-0.385-0.3850.0000.0000.0000.000
55A79ASN0-0.074-0.02727.936-0.215-0.2150.0000.0000.0000.000
56A80GLY00.0180.01924.766-0.393-0.3930.0000.0000.0000.000
57A81ARG10.9250.96325.13511.32711.3270.0000.0000.0000.000
58A82GLY00.000-0.00927.8670.3460.3460.0000.0000.0000.000
59A83LYS10.9120.96227.61910.16610.1660.0000.0000.0000.000
60A85GLU-1-0.894-0.93626.521-9.939-9.9390.0000.0000.0000.000
61A86THR0-0.004-0.00524.258-0.136-0.1360.0000.0000.0000.000
62A87GLY00.0660.03321.160-0.334-0.3340.0000.0000.0000.000
63A88ASP-1-0.828-0.90421.072-12.998-12.9980.0000.0000.0000.000
64A89CYS0-0.0290.00716.6010.5800.5800.0000.0000.0000.000
65A90ASN0-0.019-0.02122.064-0.510-0.5100.0000.0000.0000.000
66A91GLY00.0450.02625.0990.2760.2760.0000.0000.0000.000
67A92LEU0-0.059-0.02321.6490.3730.3730.0000.0000.0000.000
68A93LEU0-0.0050.00521.300-0.336-0.3360.0000.0000.0000.000
69A94GLU-1-0.945-0.97418.258-17.260-17.2600.0000.0000.0000.000
70A96GLN00.015-0.00716.507-0.688-0.6880.0000.0000.0000.000
71A97GLY00.0060.00417.302-0.131-0.1310.0000.0000.0000.000
72A98TYR0-0.054-0.05214.4070.2980.2980.0000.0000.0000.000
73A99GLY00.0120.02018.2340.6740.6740.0000.0000.0000.000
74A100SER0-0.065-0.04320.2860.2410.2410.0000.0000.0000.000
75A101PRO0-0.0250.00823.2130.0040.0040.0000.0000.0000.000
76A102PRO0-0.030-0.00624.2700.4560.4560.0000.0000.0000.000
77A103ASN0-0.040-0.06819.106-0.161-0.1610.0000.0000.0000.000
78A104THR00.0380.01717.6100.0860.0860.0000.0000.0000.000
79A105LEU0-0.058-0.01514.748-0.740-0.7400.0000.0000.0000.000
80A106ALA00.0430.01910.3370.4950.4950.0000.0000.0000.000
81A107GLU-1-0.831-0.91411.029-20.106-20.1060.0000.0000.0000.000
82A108PHE00.026-0.0205.462-2.383-2.3830.0000.0000.0000.000
83A109ALA0-0.0240.0008.2380.7970.7970.0000.0000.0000.000
86A112GLN0-0.0110.0047.0705.6065.6060.0000.0000.0000.000
87A113PRO00.015-0.01610.610-0.006-0.0060.0000.0000.0000.000
88A114ASN0-0.018-0.01613.4120.0210.0210.0000.0000.0000.000
89A115ASN0-0.0160.00510.210-0.927-0.9270.0000.0000.0000.000
90A116LEU00.0080.0169.500-0.907-0.9070.0000.0000.0000.000
92A118TYR0-0.010-0.0187.1033.7223.7220.0000.0000.0000.000
93A119ILE0-0.008-0.0147.118-2.506-2.5060.0000.0000.0000.000
94A120ASP-1-0.807-0.9139.951-18.603-18.6030.0000.0000.0000.000
95A121ILE0-0.008-0.00612.339-1.051-1.0510.0000.0000.0000.000
96A122SER00.0040.01315.0411.4531.4530.0000.0000.0000.000
97A123LEU00.029-0.00417.4370.0560.0560.0000.0000.0000.000
98A124VAL00.0100.01220.3140.8400.8400.0000.0000.0000.000
99A125ASP-1-0.824-0.90619.667-14.346-14.3460.0000.0000.0000.000
100A126GLY0-0.008-0.02022.0070.1900.1900.0000.0000.0000.000
101A127PHE0-0.004-0.01021.701-0.595-0.5950.0000.0000.0000.000
102A128ASN0-0.017-0.02421.1200.1470.1470.0000.0000.0000.000
103A129ILE0-0.0050.01520.2530.4500.4500.0000.0000.0000.000
104A130PRO0-0.0080.01720.443-0.513-0.5130.0000.0000.0000.000
105A131MET00.011-0.00114.693-0.527-0.5270.0000.0000.0000.000
106A132ASP-1-0.850-0.91213.532-19.026-19.0260.0000.0000.0000.000
107A133PHE0-0.024-0.0106.937-1.160-1.1600.0000.0000.0000.000
108A134SER0-0.040-0.0319.8901.5531.5530.0000.0000.0000.000
109A135GLY00.0300.0087.067-3.204-3.2040.0000.0000.0000.000
110A136CYS0-0.109-0.0307.2863.5403.5400.0000.0000.0000.000
111A137ARG10.8050.88810.19718.49018.4900.0000.0000.0000.000
112A138GLY00.0240.01711.366-1.690-1.6900.0000.0000.0000.000
113A139ILE0-0.005-0.00712.5571.1381.1380.0000.0000.0000.000
114A140GLN00.0330.00714.956-0.259-0.2590.0000.0000.0000.000
115A141CYS0-0.081-0.02717.6790.5800.5800.0000.0000.0000.000
116A142SER00.039-0.00820.342-0.003-0.0030.0000.0000.0000.000
117A143VAL00.0080.01522.3410.4140.4140.0000.0000.0000.000
118A144ASP-1-0.833-0.91325.667-10.318-10.3180.0000.0000.0000.000
119A145ILE0-0.030-0.02424.7970.4270.4270.0000.0000.0000.000
120A146ASN00.012-0.00526.2090.2420.2420.0000.0000.0000.000
121A147GLY0-0.041-0.03629.5830.3080.3080.0000.0000.0000.000
122A148GLN0-0.007-0.00231.4870.3190.3190.0000.0000.0000.000
123A149CYS0-0.128-0.00926.7380.6410.6410.0000.0000.0000.000
124A150PRO00.0320.02132.1340.2470.2470.0000.0000.0000.000
125A151SER00.008-0.00434.473-0.200-0.2000.0000.0000.0000.000
126A152GLU-1-0.844-0.91535.817-8.284-8.2840.0000.0000.0000.000
127A153LEU0-0.016-0.01430.026-0.137-0.1370.0000.0000.0000.000
128A154LYS10.8800.95130.9998.9828.9820.0000.0000.0000.000
129A155ALA00.0120.00829.4080.1740.1740.0000.0000.0000.000
130A156PRO0-0.007-0.01631.1470.0380.0380.0000.0000.0000.000
131A157GLY00.0220.01428.415-0.294-0.2940.0000.0000.0000.000
132A158GLY0-0.005-0.00726.928-0.465-0.4650.0000.0000.0000.000
133A160ASN00.0620.02126.323-0.867-0.8670.0000.0000.0000.000
134A161ASN00.0010.00224.5210.5720.5720.0000.0000.0000.000
135A162PRO00.0470.01826.9420.1710.1710.0000.0000.0000.000
136A163CYS0-0.019-0.00926.757-0.216-0.2160.0000.0000.0000.000
137A164THR0-0.023-0.01125.852-0.087-0.0870.0000.0000.0000.000
138A165VAL0-0.036-0.01528.0980.1050.1050.0000.0000.0000.000
139A166PHE0-0.016-0.01131.8400.3000.3000.0000.0000.0000.000
140A167LYS10.8570.92228.43210.53110.5310.0000.0000.0000.000
141A168THR00.0360.01033.1880.1580.1580.0000.0000.0000.000
142A169ASN00.0740.03331.805-0.562-0.5620.0000.0000.0000.000
143A170GLU-1-0.971-0.97831.526-8.876-8.8760.0000.0000.0000.000
144A171TYR00.000-0.00929.878-0.230-0.2300.0000.0000.0000.000
145A173CYS0-0.078-0.01226.594-0.266-0.2660.0000.0000.0000.000
146A174THR00.007-0.01128.300-0.231-0.2310.0000.0000.0000.000
147A175ASP-1-0.906-0.93930.021-9.201-9.2010.0000.0000.0000.000
148A176GLY00.0070.01229.6400.2160.2160.0000.0000.0000.000
149A177PRO00.006-0.00627.344-0.004-0.0040.0000.0000.0000.000
150A178GLY0-0.020-0.00728.5330.3100.3100.0000.0000.0000.000
151A179SER0-0.068-0.02430.4520.3360.3360.0000.0000.0000.000
152A181GLY00.0370.00029.618-0.077-0.0770.0000.0000.0000.000
153A182PRO0-0.050-0.02128.770-0.004-0.0040.0000.0000.0000.000
154A183THR00.0810.06230.4680.3340.3340.0000.0000.0000.000
155A184THR00.009-0.00231.888-0.285-0.2850.0000.0000.0000.000
156A185TYR0-0.020-0.02731.752-0.178-0.1780.0000.0000.0000.000
157A186SER0-0.008-0.00327.442-0.309-0.3090.0000.0000.0000.000
158A187LYS10.9700.97627.9589.3649.3640.0000.0000.0000.000
159A188PHE0-0.0110.01628.883-0.089-0.0890.0000.0000.0000.000
160A189PHE00.0500.01924.864-0.068-0.0680.0000.0000.0000.000
161A190LYS10.8120.91122.20513.07013.0700.0000.0000.0000.000
162A191ASP-1-0.949-0.98326.308-9.920-9.9200.0000.0000.0000.000
163A192ARG10.7540.87226.9599.9949.9940.0000.0000.0000.000
164A194PRO00.0660.03922.593-0.355-0.3550.0000.0000.0000.000
165A195ASP-1-0.806-0.88318.257-14.787-14.7870.0000.0000.0000.000
166A196ALA00.0160.00718.321-0.845-0.8450.0000.0000.0000.000
167A197TYR0-0.044-0.04116.0200.6050.6050.0000.0000.0000.000
168A198SER0-0.059-0.05420.2680.2530.2530.0000.0000.0000.000
169A199TYR0-0.005-0.02023.8200.4840.4840.0000.0000.0000.000
170A200PRO00.024-0.00322.374-0.446-0.4460.0000.0000.0000.000
171A201GLN0-0.024-0.01122.179-0.004-0.0040.0000.0000.0000.000
172A202ASP-1-0.775-0.86221.957-12.318-12.3180.0000.0000.0000.000
173A203ASP-1-0.784-0.85419.697-14.857-14.8570.0000.0000.0000.000
174A204LYS10.9050.93919.75311.21211.2120.0000.0000.0000.000
175A205THR0-0.050-0.01521.6100.0480.0480.0000.0000.0000.000
176A206SER0-0.013-0.01218.6180.2060.2060.0000.0000.0000.000
177A207LEU0-0.0260.00313.490-1.000-1.0000.0000.0000.0000.000
178A208PHE0-0.022-0.00813.0870.8140.8140.0000.0000.0000.000
179A209THR0-0.007-0.01110.636-1.011-1.0110.0000.0000.0000.000
180A211PRO00.0270.0158.478-1.214-1.2140.0000.0000.0000.000
181A212SER0-0.039-0.0235.251-3.329-3.3290.0000.0000.0000.000
183A214THR0-0.057-0.0284.8182.7552.7550.0000.0000.0000.000
187A218VAL00.0410.0158.7780.3260.3260.0000.0000.0000.000
188A219THR0-0.041-0.02711.3010.5690.5690.0000.0000.0000.000
189A220PHE00.0090.01014.9830.3900.3900.0000.0000.0000.000
190A222PRO-1-0.848-0.89617.616-13.650-13.6500.0000.0000.0000.000