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: 3M85L

Calculation Name: 3OQH-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3OQH

Chain ID: A

ChEMBL ID:

UniProt ID: Q65EX3

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 -2876343.845151
FMO2-HF: Nuclear repulsion 2786799.714764
FMO2-HF: Total energy -89544.130387
FMO2-MP2: Total energy -89805.680512


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:12:LEU)


Summations of interaction energy for fragment #1(A:12:LEU)
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.
-114.903-106.15115.757-11.862-12.643-0.093
Interaction energy analysis for fragmet #1(A:12:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.810 / q_NPA : 0.901
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].
3A14LYS10.8720.9673.85425.66927.803-0.022-1.120-0.992-0.002
39A50ARG10.8300.8993.73634.15034.6110.005-0.067-0.3980.000
40A51LEU00.0020.0003.996-3.419-3.1650.004-0.076-0.1810.000
42A53ALA00.0170.0194.5420.0720.157-0.001-0.007-0.0760.000
43A54TRP0-0.083-0.0552.335-2.042-1.0341.618-0.687-1.938-0.008
44A55ALA00.0330.0103.8161.0821.2560.011-0.052-0.1320.000
46A57ARG10.8840.9641.81142.84642.6413.674-1.149-2.3210.007
223A234GLU-1-0.755-0.8434.661-40.839-40.700-0.001-0.028-0.1100.000
224A235ALA-1-0.876-0.9222.080-104.737-100.03510.469-8.676-6.495-0.090
4A15THR0-0.001-0.0166.2902.8922.8920.0000.0000.0000.000
5A16GLU-1-0.872-0.9359.503-21.362-21.3620.0000.0000.0000.000
6A17THR0-0.0120.00513.008-0.093-0.0930.0000.0000.0000.000
7A18LEU0-0.025-0.00616.0020.4600.4600.0000.0000.0000.000
8A19THR00.002-0.10219.2410.8800.8800.0000.0000.0000.000
9A20GLN00.054-0.00219.786-1.286-1.2860.0000.0000.0000.000
10A21ASN0-0.031-0.01321.1100.0100.0100.0000.0000.0000.000
11A22CYS-1-0.814-0.75317.564-15.742-15.7420.0000.0000.0000.000
12A23ASN00.0070.00115.811-1.846-1.8460.0000.0000.0000.000
13A24GLU-1-0.852-0.90817.403-15.263-15.2630.0000.0000.0000.000
14A25ILE0-0.027-0.00217.034-0.178-0.1780.0000.0000.0000.000
15A26LEU0-0.037-0.01410.757-0.568-0.5680.0000.0000.0000.000
16A27LYS10.7710.86313.89414.85314.8530.0000.0000.0000.000
17A28ARG10.8500.90816.19014.13514.1350.0000.0000.0000.000
18A29ARG10.7960.9018.93327.18627.1860.0000.0000.0000.000
19A30ARG10.8470.91614.60912.94412.9440.0000.0000.0000.000
20A31HIS00.0240.01515.585-0.065-0.0650.0000.0000.0000.000
21A32VAL0-0.0280.00210.640-0.493-0.4930.0000.0000.0000.000
22A33LEU00.0210.01614.0110.3470.3470.0000.0000.0000.000
23A34VAL00.0330.00210.574-0.574-0.5740.0000.0000.0000.000
24A35GLY00.0250.02013.4031.1371.1370.0000.0000.0000.000
25A36ILE0-0.029-0.02512.751-1.064-1.0640.0000.0000.0000.000
26A37SER0-0.0200.00815.5900.7920.7920.0000.0000.0000.000
27A38PRO00.0240.00818.179-0.355-0.3550.0000.0000.0000.000
28A39PHE0-0.050-0.04320.7520.1890.1890.0000.0000.0000.000
29A40ASN00.015-0.00316.606-0.627-0.6270.0000.0000.0000.000
30A41SER00.0250.00316.837-0.682-0.6820.0000.0000.0000.000
31A42ARG10.8250.9199.11827.46927.4690.0000.0000.0000.000
32A43PHE00.0070.00212.015-1.707-1.7070.0000.0000.0000.000
33A44SER00.0090.00712.1950.8600.8600.0000.0000.0000.000
34A45GLU-1-0.782-0.88912.155-17.091-17.0910.0000.0000.0000.000
35A46ASP-1-0.867-0.9349.172-22.021-22.0210.0000.0000.0000.000
36A47TYR0-0.071-0.0237.348-3.225-3.2250.0000.0000.0000.000
37A48ILE00.0140.0037.583-1.757-1.7570.0000.0000.0000.000
38A49HIS00.008-0.0168.6730.1100.1100.0000.0000.0000.000
41A52ILE00.0200.0095.943-0.077-0.0770.0000.0000.0000.000
45A56VAL00.010-0.0097.5811.0981.0980.0000.0000.0000.000
47A58GLU-1-0.929-0.9485.779-37.961-37.9610.0000.0000.0000.000
48A59PHE0-0.029-0.0238.6591.0391.0390.0000.0000.0000.000
49A60GLN0-0.0140.01211.8160.0610.0610.0000.0000.0000.000
50A61SER0-0.029-0.02514.6101.1941.1940.0000.0000.0000.000
51A62VAL0-0.013-0.00310.597-0.841-0.8410.0000.0000.0000.000
52A63SER00.0550.04313.8810.8630.8630.0000.0000.0000.000
53A64VAL0-0.043-0.01913.909-0.902-0.9020.0000.0000.0000.000
54A65LEU0-0.0130.00716.3750.9310.9310.0000.0000.0000.000
55A66LEU0-0.012-0.00917.865-0.526-0.5260.0000.0000.0000.000
56A67ALA0-0.018-0.02820.3280.3550.3550.0000.0000.0000.000
57A68GLY00.0290.02123.2510.1130.1130.0000.0000.0000.000
58A69LYS10.9010.93126.8109.4059.4050.0000.0000.0000.000
59A70GLU-1-0.729-0.86329.570-9.647-9.6470.0000.0000.0000.000
60A71ALA0-0.038-0.02226.087-0.110-0.1100.0000.0000.0000.000
61A72ALA0-0.074-0.04827.961-0.048-0.0480.0000.0000.0000.000
62A73ASN00.1060.05631.275-0.014-0.0140.0000.0000.0000.000
63A74LEU0-0.0040.01325.9660.0500.0500.0000.0000.0000.000
64A75LEU0-0.107-0.06127.4080.1420.1420.0000.0000.0000.000
65A76GLU-1-0.832-0.92831.201-8.411-8.4110.0000.0000.0000.000
66A77ALA00.0260.04832.2910.2240.2240.0000.0000.0000.000
67A78LEU0-0.031-0.01929.3310.0290.0290.0000.0000.0000.000
68A79GLY00.0420.02033.6650.0880.0880.0000.0000.0000.000
69A80THR0-0.124-0.06633.2480.1420.1420.0000.0000.0000.000
70A81PRO00.0480.01635.535-0.028-0.0280.0000.0000.0000.000
71A82HIS00.1480.08236.280-0.036-0.0360.0000.0000.0000.000
72A83GLY00.0240.02235.758-0.197-0.1970.0000.0000.0000.000
73A84LYS10.8480.91034.5868.2338.2330.0000.0000.0000.000
74A85ALA00.0310.02132.194-0.267-0.2670.0000.0000.0000.000
75A86GLU-1-0.831-0.91131.094-8.954-8.9540.0000.0000.0000.000
76A87ARG10.9060.94231.1357.9447.9440.0000.0000.0000.000
77A88LYS10.9010.96528.8779.3599.3590.0000.0000.0000.000
78A89VAL00.0660.03426.532-0.394-0.3940.0000.0000.0000.000
79A90ARG10.9130.96226.2288.5308.5300.0000.0000.0000.000
80A91LYS10.9480.97425.26710.99810.9980.0000.0000.0000.000
81A92GLU-1-0.874-0.91820.781-13.580-13.5800.0000.0000.0000.000
82A93VAL00.0640.03321.986-0.525-0.5250.0000.0000.0000.000
83A94SER0-0.036-0.01921.947-0.270-0.2700.0000.0000.0000.000
84A95ARG10.8980.95219.28913.84613.8460.0000.0000.0000.000
85A96ASN0-0.016-0.03217.607-0.083-0.0830.0000.0000.0000.000
86A97ARG10.9040.97517.19711.56011.5600.0000.0000.0000.000
87A98ARG10.9540.97418.43111.59211.5920.0000.0000.0000.000
88A99PHE0-0.067-0.03914.657-0.119-0.1190.0000.0000.0000.000
89A100ALA00.0320.01213.921-0.881-0.8810.0000.0000.0000.000
90A101GLU-1-0.851-0.94014.651-13.109-13.1090.0000.0000.0000.000
91A102LYS10.8860.94414.72115.73615.7360.0000.0000.0000.000
92A103ALA0-0.018-0.00410.716-0.446-0.4460.0000.0000.0000.000
93A104LEU0-0.006-0.00111.462-1.279-1.2790.0000.0000.0000.000
94A105GLU-1-0.915-0.95913.484-13.748-13.7480.0000.0000.0000.000
95A106ALA0-0.075-0.03611.9920.0310.0310.0000.0000.0000.000
96A107HIS0-0.101-0.0688.135-1.990-1.9900.0000.0000.0000.000
97A108GLY00.0140.02011.437-0.304-0.3040.0000.0000.0000.000
98A109GLY0-0.0140.00213.6940.2640.2640.0000.0000.0000.000
99A110ASN00.005-0.01014.5900.5540.5540.0000.0000.0000.000
100A111PRO0-0.004-0.01717.548-0.342-0.3420.0000.0000.0000.000
101A112GLU-1-0.932-0.96418.699-11.068-11.0680.0000.0000.0000.000
102A113ASP-1-0.903-0.91317.852-13.340-13.3400.0000.0000.0000.000
103A114ILE0-0.047-0.03617.180-0.835-0.8350.0000.0000.0000.000
104A115HIS00.0510.02319.7130.3850.3850.0000.0000.0000.000
105A116THR0-0.095-0.08821.607-0.395-0.3950.0000.0000.0000.000
106A117PHE00.0650.03023.6140.1720.1720.0000.0000.0000.000
107A118SER00.001-0.00225.6000.2440.2440.0000.0000.0000.000
108A119ASP-1-0.862-0.88225.645-10.675-10.6750.0000.0000.0000.000
109A120PHE00.0560.02324.9670.2990.2990.0000.0000.0000.000
110A121ALA00.0210.01730.2610.2120.2120.0000.0000.0000.000
111A122ASN0-0.030-0.03133.3000.2970.2970.0000.0000.0000.000
112A123GLN00.006-0.00628.9320.2050.2050.0000.0000.0000.000
113A124THR00.007-0.01533.937-0.082-0.0820.0000.0000.0000.000
114A125ALA00.0390.03930.7330.0720.0720.0000.0000.0000.000
115A126TYR00.0520.01428.0140.1580.1580.0000.0000.0000.000
116A127ARG10.9120.96231.0868.0578.0570.0000.0000.0000.000
117A128ASN0-0.004-0.00934.4570.2350.2350.0000.0000.0000.000
118A129LEU0-0.0070.00728.2710.0500.0500.0000.0000.0000.000
119A130ARG10.8000.89031.1579.1919.1910.0000.0000.0000.000
120A131MET0-0.017-0.00233.4720.1690.1690.0000.0000.0000.000
121A132GLU-1-0.803-0.86932.317-9.445-9.4450.0000.0000.0000.000
122A133VAL0-0.003-0.01230.1310.0210.0210.0000.0000.0000.000
123A134GLU-1-0.841-0.92333.441-8.472-8.4720.0000.0000.0000.000
124A135ALA00.0020.00836.5240.1540.1540.0000.0000.0000.000
125A136ALA00.0250.01635.1100.1190.1190.0000.0000.0000.000
126A137PHE00.0000.00334.656-0.019-0.0190.0000.0000.0000.000
127A138PHE00.0010.00236.9050.0960.0960.0000.0000.0000.000
128A139ASP-1-0.897-0.94040.605-7.355-7.3550.0000.0000.0000.000
129A140GLN0-0.021-0.01036.770-0.147-0.1470.0000.0000.0000.000
130A141THR00.016-0.00537.891-0.202-0.2020.0000.0000.0000.000
131A142HIS0-0.042-0.01833.8480.0240.0240.0000.0000.0000.000
132A143PHE00.0570.02130.414-0.272-0.2720.0000.0000.0000.000
133A144ARG10.8840.94633.3857.6127.6120.0000.0000.0000.000
134A145ASN00.010-0.00434.584-0.100-0.1000.0000.0000.0000.000
135A146ALA00.0360.02630.267-0.199-0.1990.0000.0000.0000.000
136A147CYS0-0.006-0.00429.896-0.469-0.4690.0000.0000.0000.000
137A148LEU00.0130.01330.393-0.237-0.2370.0000.0000.0000.000
138A149GLU-1-0.832-0.88728.874-10.976-10.9760.0000.0000.0000.000
139A150MET0-0.0210.00223.336-0.274-0.2740.0000.0000.0000.000
140A151SER0-0.016-0.02026.469-0.254-0.2540.0000.0000.0000.000
141A152HIS10.9500.96428.52510.17410.1740.0000.0000.0000.000
142A153ALA00.0070.00323.870-0.127-0.1270.0000.0000.0000.000
143A154ALA0-0.0030.00823.994-0.567-0.5670.0000.0000.0000.000
144A155ILE0-0.010-0.00825.1830.0180.0180.0000.0000.0000.000
145A156LEU00.0070.01725.530-0.122-0.1220.0000.0000.0000.000
146A157GLY00.0360.00921.705-0.710-0.7100.0000.0000.0000.000
147A158ARG10.8370.94519.91913.28113.2810.0000.0000.0000.000
148A159ALA00.0240.01823.3310.4090.4090.0000.0000.0000.000
149A160ARG10.8360.91325.38710.90910.9090.0000.0000.0000.000
150A161GLY0-0.030-0.02029.037-0.048-0.0480.0000.0000.0000.000
151A162THR0-0.055-0.03432.3370.0590.0590.0000.0000.0000.000
152A163ARG10.9280.97532.9188.6288.6280.0000.0000.0000.000
153A164MET0-0.016-0.00333.939-0.035-0.0350.0000.0000.0000.000
154A165ASP-1-0.911-0.96229.558-10.457-10.4570.0000.0000.0000.000
155A166VAL00.0290.01931.938-0.108-0.1080.0000.0000.0000.000
156A167VAL0-0.053-0.02932.1830.3230.3230.0000.0000.0000.000
157A168GLU-1-0.922-0.95234.192-8.216-8.2160.0000.0000.0000.000
158A169VAL0-0.064-0.05731.7480.0160.0160.0000.0000.0000.000
159A170SER00.0550.00635.2240.0310.0310.0000.0000.0000.000
160A171ALA00.0450.01037.008-0.205-0.2050.0000.0000.0000.000
161A172ASP-1-0.817-0.90237.934-7.652-7.6520.0000.0000.0000.000
162A173MET0-0.106-0.01534.287-0.073-0.0730.0000.0000.0000.000
163A174LEU0-0.037-0.02232.157-0.326-0.3260.0000.0000.0000.000
164A175GLU-1-0.933-0.97534.277-7.903-7.9030.0000.0000.0000.000
165A176LEU0-0.0050.01734.954-0.035-0.0350.0000.0000.0000.000
166A177ALA0-0.019-0.02630.428-0.190-0.1900.0000.0000.0000.000
167A178VAL0-0.034-0.02930.460-0.408-0.4080.0000.0000.0000.000
168A179GLU-1-0.824-0.91831.512-8.694-8.6940.0000.0000.0000.000
169A180TYR0-0.042-0.01722.759-0.427-0.4270.0000.0000.0000.000
170A181VAL0-0.014-0.00926.901-0.256-0.2560.0000.0000.0000.000
171A182ILE00.0160.00128.000-0.230-0.2300.0000.0000.0000.000
172A183ALA0-0.0160.00428.7860.0140.0140.0000.0000.0000.000
173A184GLU-1-0.867-0.94822.694-13.023-13.0230.0000.0000.0000.000
174A185LEU00.013-0.00424.764-0.362-0.3620.0000.0000.0000.000
175A186PRO00.0070.00825.839-0.255-0.2550.0000.0000.0000.000
176A187PHE00.0310.00821.798-0.069-0.0690.0000.0000.0000.000
177A188PHE0-0.023-0.01720.373-0.747-0.7470.0000.0000.0000.000
178A189ILE0-0.044-0.01922.582-0.298-0.2980.0000.0000.0000.000
179A190ALA00.009-0.00425.1140.0480.0480.0000.0000.0000.000
180A191ALA00.0570.02921.2720.2940.2940.0000.0000.0000.000
181A192PRO0-0.031-0.01122.3550.1820.1820.0000.0000.0000.000
182A193ASP-1-0.873-0.93824.411-10.183-10.1830.0000.0000.0000.000
183A194ILE0-0.093-0.03825.5090.3600.3600.0000.0000.0000.000
184A195LEU0-0.011-0.01220.8890.1960.1960.0000.0000.0000.000
185A196GLY00.0050.02024.707-0.029-0.0290.0000.0000.0000.000
186A197VAL0-0.0170.00520.3970.0850.0850.0000.0000.0000.000
187A198GLU-1-0.864-0.93122.945-12.083-12.0830.0000.0000.0000.000
188A199GLU-1-0.761-0.86419.547-13.924-13.9240.0000.0000.0000.000
189A200THR0-0.067-0.05217.484-0.554-0.5540.0000.0000.0000.000
190A201LEU0-0.0130.01113.5740.1090.1090.0000.0000.0000.000
191A202LEU0-0.0070.01515.265-0.464-0.4640.0000.0000.0000.000
192A203ALA00.0030.00610.840-0.521-0.5210.0000.0000.0000.000
193A204TYR0-0.018-0.03412.9840.6510.6510.0000.0000.0000.000
194A205HIS0-0.019-0.00511.490-1.376-1.3760.0000.0000.0000.000
195A206ARG10.8190.91112.86615.21815.2180.0000.0000.0000.000
196A207PRO00.0910.04416.503-0.227-0.2270.0000.0000.0000.000
197A208TRP00.0100.00718.7420.3770.3770.0000.0000.0000.000
198A209LYS10.9010.94421.26611.27411.2740.0000.0000.0000.000
199A210LEU00.0040.00224.7250.2560.2560.0000.0000.0000.000
200A211GLY00.0930.02423.2640.3880.3880.0000.0000.0000.000
201A212GLU-1-0.913-0.96622.641-13.564-13.5640.0000.0000.0000.000
202A213GLN0-0.074-0.02425.0830.1140.1140.0000.0000.0000.000
203A214ILE0-0.018-0.00326.4110.3510.3510.0000.0000.0000.000
204A215SER0-0.093-0.04625.0500.1920.1920.0000.0000.0000.000
205A216ARG10.8090.88926.60711.64011.6400.0000.0000.0000.000
206A217ASN0-0.015-0.00430.1430.5620.5620.0000.0000.0000.000
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