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: VNJM1

Calculation Name: 5F1A-A-Xray547

Preferred Name: Cyclooxygenase-2

Target Type: SINGLE PROTEIN

Ligand Name: protoporphyrin ix containing co | octyl beta-d-glucopyranoside | 2-acetamido-2-deoxy-beta-d-glucopyranose | alpha-d-mannopyranose | 2-hydroxybenzoic acid | acrylic acid | 1,2-ethanediol

Ligand 3-letter code: COH | BOG | NAG | MAN | SAL | AKR | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5F1A

Chain ID: A

ChEMBL ID: CHEMBL230

UniProt ID: P35354

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 548
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -12580806.895866
FMO2-HF: Nuclear repulsion 12356371.683384
FMO2-HF: Total energy -224435.212482
FMO2-MP2: Total energy -225085.339656


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:33:LYS)


Summations of interaction energy for fragment #1(A:33: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.
-209.349-199.60722.616-17.579-14.779-0.216
Interaction energy analysis for fragmet #1(A:33:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.685 / q_NPA : 1.828
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].
3A35PRO00.1020.0603.8332.9314.217-0.006-0.507-0.7740.000
5A37CYS0-0.075-0.0171.825-44.432-44.98510.179-5.839-3.786-0.076
19A52PHE0-0.042-0.0552.569-18.211-14.9601.908-2.462-2.697-0.041
20A53ASP-1-0.940-0.9514.659-68.127-67.995-0.001-0.010-0.1200.000
124A158ASP-1-0.840-0.9241.962-176.495-171.25710.532-8.704-7.067-0.099
125A160PRO0-0.012-0.0043.3153.8154.1750.005-0.055-0.3100.000
126A161THR00.0210.0045.1034.3164.344-0.001-0.002-0.0250.000
4A36CYS00.023-0.0116.5397.4487.4480.0000.0000.0000.000
6A38SER0-0.001-0.0057.5342.2792.2790.0000.0000.0000.000
7A39HIS0-0.035-0.01210.3973.0163.0160.0000.0000.0000.000
8A40PRO00.0240.02211.8623.0803.0800.0000.0000.0000.000
9A41CYS0-0.0830.00014.6600.2080.2080.0000.0000.0000.000
10A42GLN00.0250.00417.4151.5371.5370.0000.0000.0000.000
11A43ASN0-0.047-0.03920.4010.5280.5280.0000.0000.0000.000
12A44ARG10.8400.89221.25224.05024.0500.0000.0000.0000.000
13A45GLY00.0330.02720.5430.2590.2590.0000.0000.0000.000
14A46VAL0-0.075-0.04016.659-0.996-0.9960.0000.0000.0000.000
15A48MET0-0.021-0.00712.3230.3950.3950.0000.0000.0000.000
16A49SER00.0300.0147.609-0.280-0.2800.0000.0000.0000.000
17A50VAL0-0.042-0.0299.5582.9642.9640.0000.0000.0000.000
18A51GLY00.0410.0257.6620.9280.9280.0000.0000.0000.000
21A54GLN00.0730.0427.2681.1081.1080.0000.0000.0000.000
22A55TYR0-0.037-0.0429.495-4.379-4.3790.0000.0000.0000.000
23A56LYS10.9610.97411.31334.16334.1630.0000.0000.0000.000
24A58ASP-1-0.886-0.91917.165-26.223-26.2230.0000.0000.0000.000
25A59CYS0-0.0100.01719.105-0.436-0.4360.0000.0000.0000.000
26A60THR0-0.018-0.02923.0471.7581.7580.0000.0000.0000.000
27A61ARG10.9010.93925.69321.93421.9340.0000.0000.0000.000
28A62THR00.005-0.00123.5270.5020.5020.0000.0000.0000.000
29A63GLY00.0010.02926.9460.3660.3660.0000.0000.0000.000
30A64PHE00.005-0.01625.5220.6730.6730.0000.0000.0000.000
31A65TYR00.0360.01225.088-0.368-0.3680.0000.0000.0000.000
32A66GLY00.0290.00923.651-0.055-0.0550.0000.0000.0000.000
33A67GLU-1-0.938-0.97517.659-33.035-33.0350.0000.0000.0000.000
34A68ASN00.1020.05116.668-3.058-3.0580.0000.0000.0000.000
35A70SER00.0520.02821.9290.6760.6760.0000.0000.0000.000
36A71THR0-0.0120.00223.7521.0321.0320.0000.0000.0000.000
37A72PRO0-0.0150.00727.0980.0340.0340.0000.0000.0000.000
38A73GLU-1-0.887-0.95229.960-19.433-19.4330.0000.0000.0000.000
39A74PHE00.022-0.00532.4110.1530.1530.0000.0000.0000.000
40A75LEU00.0540.01936.0630.2270.2270.0000.0000.0000.000
41A76THR0-0.013-0.01830.4420.4780.4780.0000.0000.0000.000
42A77ARG10.9100.96331.44619.12019.1200.0000.0000.0000.000
43A78ILE00.0010.01135.2760.2080.2080.0000.0000.0000.000
44A79LYS10.9410.96633.52517.98617.9860.0000.0000.0000.000
45A80LEU0-0.033-0.02630.6750.0920.0920.0000.0000.0000.000
46A81PHE0-0.0080.00134.9120.1090.1090.0000.0000.0000.000
47A82LEU00.0100.01337.9210.3610.3610.0000.0000.0000.000
48A83LYS10.8910.96534.60017.30917.3090.0000.0000.0000.000
49A84PRO00.0050.01537.314-0.164-0.1640.0000.0000.0000.000
50A85THR00.0520.02135.107-0.194-0.1940.0000.0000.0000.000
51A86PRO00.0610.02432.6600.5360.5360.0000.0000.0000.000
52A87ASN00.0660.03034.5000.4390.4390.0000.0000.0000.000
53A88THR0-0.0110.00237.9260.5150.5150.0000.0000.0000.000
54A89VAL0-0.014-0.01339.0300.4190.4190.0000.0000.0000.000
55A90HIS0-0.0030.00439.0510.2330.2330.0000.0000.0000.000
56A91TYR00.0420.01941.0560.3440.3440.0000.0000.0000.000
57A92ILE00.009-0.01543.7440.3610.3610.0000.0000.0000.000
58A93LEU0-0.015-0.00441.9800.3240.3240.0000.0000.0000.000
59A94THR00.0170.01444.3670.2520.2520.0000.0000.0000.000
60A95HIS0-0.0260.00946.4090.4170.4170.0000.0000.0000.000
61A96PHE00.004-0.01748.2430.0700.0700.0000.0000.0000.000
62A97LYS10.9881.00752.36711.50211.5020.0000.0000.0000.000
63A98GLY00.0160.00553.5880.0590.0590.0000.0000.0000.000
64A99PHE00.0210.01250.4260.1370.1370.0000.0000.0000.000
65A100TRP00.0260.00047.3240.0550.0550.0000.0000.0000.000
66A101ASN0-0.035-0.02152.996-0.077-0.0770.0000.0000.0000.000
67A102VAL00.0260.02956.2100.1760.1760.0000.0000.0000.000
68A103VAL00.0000.00050.9440.0330.0330.0000.0000.0000.000
69A104ASN0-0.050-0.04351.778-0.198-0.1980.0000.0000.0000.000
70A105ASN0-0.045-0.03154.2350.0570.0570.0000.0000.0000.000
71A105ILE00.0150.02456.0080.1930.1930.0000.0000.0000.000
72A106PRO00.031-0.00254.871-0.223-0.2230.0000.0000.0000.000
73A107PHE00.0130.02353.211-0.236-0.2360.0000.0000.0000.000
74A108LEU00.0450.01651.776-0.265-0.2650.0000.0000.0000.000
75A109ARG10.8480.91050.14811.85111.8510.0000.0000.0000.000
76A110ASN00.0580.02549.018-0.314-0.3140.0000.0000.0000.000
77A111ALA00.0200.01047.793-0.334-0.3340.0000.0000.0000.000
78A112ILE0-0.003-0.00345.458-0.380-0.3800.0000.0000.0000.000
79A113MET00.0130.04242.845-0.368-0.3680.0000.0000.0000.000
80A114SER00.006-0.00343.237-0.476-0.4760.0000.0000.0000.000
81A115TYR0-0.0090.00439.020-0.587-0.5870.0000.0000.0000.000
82A116VAL0-0.0060.01639.720-0.531-0.5310.0000.0000.0000.000
83A117LEU00.0430.02038.488-0.521-0.5210.0000.0000.0000.000
84A118THR0-0.027-0.01837.662-0.476-0.4760.0000.0000.0000.000
85A119SER0-0.099-0.06735.937-0.597-0.5970.0000.0000.0000.000
86A120ARG10.8550.91733.47216.83716.8370.0000.0000.0000.000
87A121SER00.009-0.01932.663-0.633-0.6330.0000.0000.0000.000
88A122HIS00.0100.01530.964-0.361-0.3610.0000.0000.0000.000
89A123LEU0-0.0030.00828.380-0.723-0.7230.0000.0000.0000.000
90A124ILE0-0.0050.00527.203-1.027-1.0270.0000.0000.0000.000
91A125ASP-1-0.849-0.89623.565-24.748-24.7480.0000.0000.0000.000
92A126SER00.021-0.00326.8470.3100.3100.0000.0000.0000.000
93A127PRO0-0.009-0.01428.6230.5670.5670.0000.0000.0000.000
94A128PRO0-0.0130.01825.743-0.464-0.4640.0000.0000.0000.000
95A129THR0-0.019-0.01821.425-0.360-0.3600.0000.0000.0000.000
96A130TYR00.0430.02817.339-0.729-0.7290.0000.0000.0000.000
97A131ASN00.0600.03118.5950.2470.2470.0000.0000.0000.000
98A132ALA0-0.005-0.02017.082-1.249-1.2490.0000.0000.0000.000
99A133ASP-1-0.787-0.85115.281-34.743-34.7430.0000.0000.0000.000
100A134TYR0-0.039-0.01214.728-2.029-2.0290.0000.0000.0000.000
101A135GLY00.021-0.00512.7181.5651.5650.0000.0000.0000.000
102A136TYR0-0.006-0.01012.9500.2750.2750.0000.0000.0000.000
103A137LYS10.9230.96015.81331.07531.0750.0000.0000.0000.000
104A138SER00.0350.01418.676-0.095-0.0950.0000.0000.0000.000
105A139TRP00.0810.02820.6720.6990.6990.0000.0000.0000.000
106A140GLU-1-0.839-0.88421.247-24.669-24.6690.0000.0000.0000.000
107A141ALA0-0.011-0.00820.2920.8060.8060.0000.0000.0000.000
108A142PHE0-0.0230.00522.4351.0121.0120.0000.0000.0000.000
109A143SER0-0.050-0.03725.6201.0531.0530.0000.0000.0000.000
110A144ASN00.006-0.00425.2391.7871.7870.0000.0000.0000.000
111A145LEU00.027-0.00226.676-0.528-0.5280.0000.0000.0000.000
112A146SER0-0.0040.01526.9330.5580.5580.0000.0000.0000.000
113A147TYR0-0.095-0.06520.1680.3750.3750.0000.0000.0000.000
114A148TYR0-0.054-0.03323.8491.1681.1680.0000.0000.0000.000
115A149THR0-0.023-0.03022.887-0.977-0.9770.0000.0000.0000.000
116A150ARG10.7660.87615.52533.00433.0040.0000.0000.0000.000
117A151ALA0-0.003-0.00420.931-0.203-0.2030.0000.0000.0000.000
118A152LEU0-0.039-0.01916.7860.1530.1530.0000.0000.0000.000
119A153PRO0-0.0010.01313.9220.3710.3710.0000.0000.0000.000
120A154PRO00.0030.01212.310-0.298-0.2980.0000.0000.0000.000
121A155VAL0-0.0070.0008.232-2.450-2.4500.0000.0000.0000.000
122A156PRO0-0.001-0.0175.596-0.937-0.9370.0000.0000.0000.000
123A157ASP-1-0.899-0.9426.599-60.619-60.6190.0000.0000.0000.000
127A162PRO00.010-0.0048.066-3.315-3.3150.0000.0000.0000.000
128A163LEU00.0110.01910.3620.8110.8110.0000.0000.0000.000
129A164GLY00.0310.0188.1961.7661.7660.0000.0000.0000.000
130A165VAL0-0.010-0.0117.222-6.277-6.2770.0000.0000.0000.000
131A166LYS10.8210.9049.22235.14235.1420.0000.0000.0000.000
132A167GLY00.0500.02812.478-1.026-1.0260.0000.0000.0000.000
133A168LYS10.8550.92913.12525.59425.5940.0000.0000.0000.000
134A169LYS10.8800.9146.96560.13160.1310.0000.0000.0000.000
135A170GLN0-0.0120.00111.277-2.696-2.6960.0000.0000.0000.000
136A171LEU0-0.007-0.00214.0250.9360.9360.0000.0000.0000.000
137A172PRO00.0440.03116.5260.3700.3700.0000.0000.0000.000
138A173ASP-1-0.747-0.89020.294-23.950-23.9500.0000.0000.0000.000
139A174SER0-0.027-0.02422.4670.7360.7360.0000.0000.0000.000
140A175ASN0-0.039-0.03823.9280.9510.9510.0000.0000.0000.000
141A176GLU-1-0.907-0.95025.590-21.625-21.6250.0000.0000.0000.000
142A177ILE0-0.014-0.00321.7900.6640.6640.0000.0000.0000.000
143A178VAL0-0.032-0.01926.4550.7610.7610.0000.0000.0000.000
144A179GLU-1-0.848-0.91829.322-17.765-17.7650.0000.0000.0000.000
145A180LYS10.8220.91228.36320.51820.5180.0000.0000.0000.000
146A181LEU0-0.0080.00026.7190.5250.5250.0000.0000.0000.000
147A182LEU0-0.0110.00327.7550.3580.3580.0000.0000.0000.000
148A183LEU0-0.035-0.01132.0290.5140.5140.0000.0000.0000.000
149A184ARG10.7320.86834.99115.01115.0110.0000.0000.0000.000
150A185ARG10.8220.90434.46216.81416.8140.0000.0000.0000.000
151A186LYS10.9590.96440.86613.18513.1850.0000.0000.0000.000
152A187PHE00.0130.01142.222-0.297-0.2970.0000.0000.0000.000
153A188ILE0-0.0110.00739.2620.3470.3470.0000.0000.0000.000
154A189PRO00.0350.01742.421-0.260-0.2600.0000.0000.0000.000
155A190ASP-1-0.725-0.86942.528-14.449-14.4490.0000.0000.0000.000
156A191PRO0-0.054-0.02442.8430.2880.2880.0000.0000.0000.000
157A192GLN0-0.029-0.00341.883-0.016-0.0160.0000.0000.0000.000
158A193GLY00.0520.02645.3730.1470.1470.0000.0000.0000.000
159A194SER0-0.032-0.02943.4300.1710.1710.0000.0000.0000.000
160A195ASN00.0050.00745.534-0.249-0.2490.0000.0000.0000.000
161A196MET0-0.039-0.01343.649-0.397-0.3970.0000.0000.0000.000
162A197MET00.0030.02946.134-0.211-0.2110.0000.0000.0000.000
163A198PHE00.0360.02440.093-0.220-0.2200.0000.0000.0000.000
164A199ALA0-0.007-0.00641.521-0.350-0.3500.0000.0000.0000.000
165A200PHE00.006-0.00741.356-0.364-0.3640.0000.0000.0000.000
166A201PHE0-0.0010.01742.843-0.161-0.1610.0000.0000.0000.000
167A202ALA00.0140.00038.536-0.260-0.2600.0000.0000.0000.000
168A203GLN0-0.0400.00637.769-0.146-0.1460.0000.0000.0000.000
169A204HIS00.009-0.00738.794-0.402-0.4020.0000.0000.0000.000
170A205PHE00.0270.00737.930-0.180-0.1800.0000.0000.0000.000
171A206THR00.0440.01034.824-0.279-0.2790.0000.0000.0000.000
172A207HIS0-0.037-0.00935.287-0.535-0.5350.0000.0000.0000.000
173A208GLN00.0240.01436.8190.2150.2150.0000.0000.0000.000
174A209PHE0-0.008-0.00132.915-0.168-0.1680.0000.0000.0000.000
175A210PHE0-0.033-0.01230.009-0.777-0.7770.0000.0000.0000.000
176A211LYS10.8070.89631.52217.32117.3210.0000.0000.0000.000
177A212THR00.0050.02726.624-0.092-0.0920.0000.0000.0000.000
178A213ASP-1-0.746-0.85828.206-19.945-19.9450.0000.0000.0000.000
179A214HIS0-0.028-0.03226.821-0.346-0.3460.0000.0000.0000.000
180A215LYS10.8100.90428.31719.79719.7970.0000.0000.0000.000
181A216ARG10.9430.99026.03322.00722.0070.0000.0000.0000.000
182A217GLY00.0320.01622.997-1.127-1.1270.0000.0000.0000.000
183A218PRO0-0.032-0.02521.1140.5670.5670.0000.0000.0000.000
184A219ALA00.0450.01720.1560.2900.2900.0000.0000.0000.000
185A220PHE0-0.008-0.00321.9880.3190.3190.0000.0000.0000.000
186A221THR00.0040.00525.6130.6780.6780.0000.0000.0000.000
187A222ASN0-0.048-0.04229.210-0.002-0.0020.0000.0000.0000.000
188A223GLY00.007-0.01032.2350.6810.6810.0000.0000.0000.000
189A224LEU0-0.041-0.02231.657-0.392-0.3920.0000.0000.0000.000
190A225GLY00.0360.02133.694-0.131-0.1310.0000.0000.0000.000
191A226HIS0-0.048-0.03128.2420.1310.1310.0000.0000.0000.000
192A227GLY00.0320.00233.334-0.266-0.2660.0000.0000.0000.000
193A228VAL0-0.037-0.00636.0480.0830.0830.0000.0000.0000.000
194A229ASP-1-0.766-0.87038.580-15.639-15.6390.0000.0000.0000.000
195A230LEU00.0050.00441.4080.3500.3500.0000.0000.0000.000
196A231ASN0-0.029-0.02037.6500.3380.3380.0000.0000.0000.000
197A232HIS00.0360.00940.4420.0620.0620.0000.0000.0000.000
198A233ILE0-0.040-0.01142.1590.2260.2260.0000.0000.0000.000
199A234TYR0-0.008-0.06545.1720.1140.1140.0000.0000.0000.000
200A235GLY00.0040.00643.0440.1640.1640.0000.0000.0000.000
201A236GLU-1-0.812-0.89536.570-16.817-16.8170.0000.0000.0000.000
202A237THR00.0170.00639.9550.1520.1520.0000.0000.0000.000
203A238LEU00.0380.01342.2610.2700.2700.0000.0000.0000.000
204A239ALA0-0.006-0.00844.5630.3300.3300.0000.0000.0000.000
205A240ARG10.7600.86742.70414.66614.6660.0000.0000.0000.000
206A241GLN00.0640.03145.8780.5070.5070.0000.0000.0000.000
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