FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2026-04-18

All entries: 88827

Number of unique PDB entries: 32070

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FMODB ID: 246RR

Calculation Name: 2CL5-A-Xray547

Preferred Name: Catechol O-methyltransferase

Target Type: SINGLE PROTEIN

Ligand Name: s-adenosylmethionine | (3,4-dihydroxy-2-nitrophenyl)(phenyl)methanone | 2-(n-morpholino)-ethanesulfonic acid | (r,r)-2,3-butanediol

Ligand 3-letter code: SAM | BIE | MES | BU3

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CL5

Chain ID: A

ChEMBL ID: CHEMBL2372

UniProt ID: P22734

Base Structure: X-ray

Registration Date: 2025-10-03

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 214
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2640090.730321
FMO2-HF: Nuclear repulsion 2554478.884895
FMO2-HF: Total energy -85611.845426
FMO2-MP2: Total energy -85856.777523


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:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
-35.226-34.281-0.006-0.394-0.545-0.001
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.865 / q_NPA : 0.919
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].
3A4THR0-0.016-0.0153.827-0.944-0.203-0.005-0.276-0.460-0.001
6A7GLN0-0.035-0.0283.8821.4691.673-0.001-0.118-0.0850.000
4A5LYS10.8640.9216.63824.91424.9140.0000.0000.0000.000
5A6GLU-1-0.754-0.8659.301-30.196-30.1960.0000.0000.0000.000
7A8ARG10.7640.8587.26335.04035.0400.0000.0000.0000.000
8A9ILE00.0270.02211.1282.0022.0020.0000.0000.0000.000
9A10LEU00.0060.01011.6671.3941.3940.0000.0000.0000.000
10A11ARG10.8620.9047.69235.93235.9320.0000.0000.0000.000
11A12TYR0-0.0070.00413.6771.5371.5370.0000.0000.0000.000
12A13VAL00.0240.00616.6041.3041.3040.0000.0000.0000.000
13A14GLN0-0.023-0.02413.8520.0330.0330.0000.0000.0000.000
14A15GLN0-0.060-0.00617.3070.3870.3870.0000.0000.0000.000
15A16ASN0-0.098-0.06519.1671.3351.3350.0000.0000.0000.000
16A17ALA0-0.0220.01221.4980.7050.7050.0000.0000.0000.000
17A18LYS10.9330.95923.29010.96610.9660.0000.0000.0000.000
18A19PRO0-0.001-0.00522.927-0.037-0.0370.0000.0000.0000.000
19A20GLY0-0.0060.00324.7070.5380.5380.0000.0000.0000.000
20A21ASP-1-0.869-0.92926.412-10.633-10.6330.0000.0000.0000.000
21A22PRO00.021-0.00725.928-0.418-0.4180.0000.0000.0000.000
22A23GLN0-0.015-0.00426.426-0.269-0.2690.0000.0000.0000.000
23A24SER0-0.004-0.00426.156-0.278-0.2780.0000.0000.0000.000
24A25VAL00.008-0.01321.143-0.530-0.5300.0000.0000.0000.000
25A26LEU0-0.0230.00022.455-0.656-0.6560.0000.0000.0000.000
26A27GLU-1-0.823-0.90123.816-11.383-11.3830.0000.0000.0000.000
27A28ALA0-0.0130.01721.070-0.151-0.1510.0000.0000.0000.000
28A29ILE00.019-0.00118.728-0.717-0.7170.0000.0000.0000.000
29A30ASP-1-0.723-0.82220.347-13.605-13.6050.0000.0000.0000.000
30A31THR0-0.040-0.01522.8340.2640.2640.0000.0000.0000.000
31A32TYR0-0.040-0.04913.203-0.033-0.0330.0000.0000.0000.000
32A33CYS0-0.071-0.04018.767-0.604-0.6040.0000.0000.0000.000
33A34THR0-0.041-0.02819.8540.4000.4000.0000.0000.0000.000
34A35GLN0-0.054-0.03321.778-0.028-0.0280.0000.0000.0000.000
35A36LYS10.8480.93916.93715.29615.2960.0000.0000.0000.000
36A37GLU-1-0.742-0.82012.082-26.660-26.6600.0000.0000.0000.000
37A38TRP00.0110.02616.739-0.736-0.7360.0000.0000.0000.000
38A39ALA00.007-0.01716.082-1.547-1.5470.0000.0000.0000.000
39A40MET00.0060.02415.4270.9710.9710.0000.0000.0000.000
40A41ASN0-0.001-0.00718.291-0.406-0.4060.0000.0000.0000.000
41A42VAL00.0750.03621.2000.2920.2920.0000.0000.0000.000
42A43GLY00.0490.02424.1870.4540.4540.0000.0000.0000.000
43A44ASP-1-0.790-0.88125.527-10.262-10.2620.0000.0000.0000.000
44A45ALA0-0.030-0.00828.7470.3610.3610.0000.0000.0000.000
45A46LYS10.7650.87326.59812.25812.2580.0000.0000.0000.000
46A47GLY00.0380.01329.0430.1900.1900.0000.0000.0000.000
47A48GLN0-0.054-0.04929.7470.4860.4860.0000.0000.0000.000
48A49ILE0-0.018-0.00433.1990.3180.3180.0000.0000.0000.000
49A50MET00.0060.01926.9640.1060.1060.0000.0000.0000.000
50A51ASP-1-0.766-0.85431.265-10.294-10.2940.0000.0000.0000.000
51A52ALA0-0.062-0.02933.6990.2600.2600.0000.0000.0000.000
52A53VAL00.0220.01035.0510.2450.2450.0000.0000.0000.000
53A54ILE0-0.013-0.00932.0640.1530.1530.0000.0000.0000.000
54A55ARG10.9240.95435.6439.1109.1100.0000.0000.0000.000
55A56GLU-1-0.905-0.93438.781-7.536-7.5360.0000.0000.0000.000
56A57TYR00.000-0.01838.6250.1490.1490.0000.0000.0000.000
57A58SER0-0.062-0.01238.5710.0790.0790.0000.0000.0000.000
58A59PRO0-0.030-0.00335.0540.1030.1030.0000.0000.0000.000
59A60SER00.001-0.01736.502-0.087-0.0870.0000.0000.0000.000
60A61LEU0-0.038-0.01932.516-0.238-0.2380.0000.0000.0000.000
61A62VAL00.0040.00230.1240.1520.1520.0000.0000.0000.000
62A63LEU0-0.010-0.00227.708-0.213-0.2130.0000.0000.0000.000
63A64GLU-1-0.753-0.82723.200-13.443-13.4430.0000.0000.0000.000
64A65LEU0-0.048-0.02524.502-0.232-0.2320.0000.0000.0000.000
65A66GLY00.0360.01320.4820.1000.1000.0000.0000.0000.000
66A67ALA00.0220.02218.4750.3720.3720.0000.0000.0000.000
67A68TYR0-0.049-0.05913.0080.1880.1880.0000.0000.0000.000
68A69CYS0-0.010-0.00814.445-1.964-1.9640.0000.0000.0000.000
69A70GLY00.0350.00616.1670.2010.2010.0000.0000.0000.000
70A71TYR0-0.079-0.05619.5860.8710.8710.0000.0000.0000.000
71A72SER00.021-0.02221.6190.4100.4100.0000.0000.0000.000
72A73ALA00.0350.01322.4720.5900.5900.0000.0000.0000.000
73A74VAL0-0.005-0.01022.1530.5710.5710.0000.0000.0000.000
74A75ARG10.7240.83924.95011.80311.8030.0000.0000.0000.000
75A76MET00.0240.01026.8810.6500.6500.0000.0000.0000.000
76A77ALA00.0320.01127.2610.4300.4300.0000.0000.0000.000
77A78ARG10.7160.83028.56511.07711.0770.0000.0000.0000.000
78A79LEU0-0.061-0.02830.5950.3600.3600.0000.0000.0000.000
79A80LEU0-0.0320.01030.9590.3060.3060.0000.0000.0000.000
80A81GLN00.0520.02034.245-0.021-0.0210.0000.0000.0000.000
81A82PRO00.013-0.01636.178-0.246-0.2460.0000.0000.0000.000
82A83GLY0-0.025-0.00336.8190.1570.1570.0000.0000.0000.000
83A84ALA0-0.0160.01635.516-0.121-0.1210.0000.0000.0000.000
84A85ARG10.8510.91028.41810.55410.5540.0000.0000.0000.000
85A86LEU00.0160.02025.6390.1840.1840.0000.0000.0000.000
86A87LEU0-0.028-0.01227.023-0.313-0.3130.0000.0000.0000.000
87A88THR0-0.020-0.05321.825-0.016-0.0160.0000.0000.0000.000
88A89MET0-0.0380.00622.673-0.210-0.2100.0000.0000.0000.000
89A90GLU-1-0.766-0.88316.250-18.607-18.6070.0000.0000.0000.000
90A91MET00.0020.00117.2050.3650.3650.0000.0000.0000.000
91A92ASN0-0.026-0.00410.429-1.238-1.2380.0000.0000.0000.000
92A93PRO00.0490.01711.2630.3090.3090.0000.0000.0000.000
93A94ASP-1-0.885-0.9437.380-38.136-38.1360.0000.0000.0000.000
94A95TYR0-0.037-0.02210.0640.7900.7900.0000.0000.0000.000
95A96ALA00.0420.03712.8911.0911.0910.0000.0000.0000.000
96A97ALA00.0130.00611.2671.0131.0130.0000.0000.0000.000
97A98ILE0-0.039-0.0109.4780.4020.4020.0000.0000.0000.000
98A99THR00.0130.00713.1561.6211.6210.0000.0000.0000.000
99A100GLN0-0.024-0.02716.5101.1141.1140.0000.0000.0000.000
100A101GLN0-0.069-0.05111.2800.7620.7620.0000.0000.0000.000
101A102MET00.0170.02415.8770.9090.9090.0000.0000.0000.000
102A103LEU00.008-0.00218.4410.9230.9230.0000.0000.0000.000
103A104ASN00.0040.00319.2411.0651.0650.0000.0000.0000.000
104A105PHE0-0.0140.00419.1390.4550.4550.0000.0000.0000.000
105A106ALA00.014-0.00121.2240.6190.6190.0000.0000.0000.000
106A107GLY0-0.0020.00823.9970.6150.6150.0000.0000.0000.000
107A108LEU0-0.028-0.01424.9900.4890.4890.0000.0000.0000.000
108A109GLN0-0.014-0.01923.226-0.129-0.1290.0000.0000.0000.000
109A110ASP-1-0.844-0.90924.976-11.269-11.2690.0000.0000.0000.000
110A111LYS10.7920.91528.32410.25310.2530.0000.0000.0000.000
111A112VAL0-0.0030.00024.0430.1460.1460.0000.0000.0000.000
112A113THR0-0.023-0.00625.044-0.014-0.0140.0000.0000.0000.000
113A114ILE00.0160.01818.5800.0880.0880.0000.0000.0000.000
114A115LEU0-0.046-0.02222.088-0.029-0.0290.0000.0000.0000.000
115A116ASN0-0.018-0.01617.370-1.239-1.2390.0000.0000.0000.000
116A117GLY00.019-0.00519.7550.4570.4570.0000.0000.0000.000
117A118ALA00.0200.00820.867-0.224-0.2240.0000.0000.0000.000
118A119SER00.020-0.02422.4080.2160.2160.0000.0000.0000.000
119A120GLN0-0.003-0.01124.1090.4450.4450.0000.0000.0000.000
120A121ASP-1-0.882-0.94224.544-12.113-12.1130.0000.0000.0000.000
121A122LEU0-0.050-0.01922.8220.4020.4020.0000.0000.0000.000
122A123ILE00.0260.00927.3160.3340.3340.0000.0000.0000.000
123A124PRO00.011-0.00430.2960.3150.3150.0000.0000.0000.000
124A125GLN0-0.088-0.06127.0800.2790.2790.0000.0000.0000.000
125A126LEU0-0.0140.00629.2670.0930.0930.0000.0000.0000.000
126A127LYS10.8800.94032.4578.2308.2300.0000.0000.0000.000
127A128LYS10.8790.95134.5599.0989.0980.0000.0000.0000.000
128A129LYS10.8620.93726.84311.68711.6870.0000.0000.0000.000
129A130TYR0-0.001-0.01826.042-0.349-0.3490.0000.0000.0000.000
130A131ASP-1-0.894-0.92932.105-9.024-9.0240.0000.0000.0000.000
131A132VAL0-0.035-0.00732.7100.1400.1400.0000.0000.0000.000
132A133ASP-1-0.835-0.92635.863-7.671-7.6710.0000.0000.0000.000
133A134THR0-0.057-0.03238.222-0.074-0.0740.0000.0000.0000.000
134A135LEU00.0160.01432.931-0.120-0.1200.0000.0000.0000.000
135A136ASP-1-0.782-0.85136.247-8.106-8.1060.0000.0000.0000.000
136A137MET0-0.025-0.01531.8410.1910.1910.0000.0000.0000.000
137A138VAL00.001-0.00430.569-0.203-0.2030.0000.0000.0000.000
138A139PHE00.0070.00124.9550.2510.2510.0000.0000.0000.000
139A140LEU0-0.041-0.02827.387-0.309-0.3090.0000.0000.0000.000
140A141ASP-1-0.827-0.92923.646-13.300-13.3000.0000.0000.0000.000
141A142HIS0-0.021-0.01021.824-0.836-0.8360.0000.0000.0000.000
142A143TRP0-0.020-0.02316.596-0.004-0.0040.0000.0000.0000.000
143A144LYS10.8660.94023.16413.53013.5300.0000.0000.0000.000
144A145ASP-1-0.887-0.94625.432-12.007-12.0070.0000.0000.0000.000
145A146ARG10.8710.92924.69811.98511.9850.0000.0000.0000.000
146A147TYR0-0.0010.00026.1160.1790.1790.0000.0000.0000.000
147A148LEU00.0250.03430.2050.2550.2550.0000.0000.0000.000
148A149PRO0-0.028-0.01230.2770.2410.2410.0000.0000.0000.000
149A150ASP-1-0.712-0.83527.604-11.377-11.3770.0000.0000.0000.000
150A151THR0-0.002-0.01131.3190.1540.1540.0000.0000.0000.000
151A152LEU0-0.003-0.00334.2470.2330.2330.0000.0000.0000.000
152A153LEU0-0.072-0.02131.1020.2430.2430.0000.0000.0000.000
153A154LEU00.0420.01031.5480.1260.1260.0000.0000.0000.000
154A155GLU-1-0.814-0.88135.159-7.633-7.6330.0000.0000.0000.000
155A156LYS10.9180.96337.7348.4998.4990.0000.0000.0000.000
156A157CYS0-0.087-0.04435.6190.0950.0950.0000.0000.0000.000
157A158GLY00.0280.01837.9360.0310.0310.0000.0000.0000.000
158A159LEU0-0.036-0.02333.6380.0190.0190.0000.0000.0000.000
159A160LEU0-0.0210.00335.971-0.108-0.1080.0000.0000.0000.000
160A161ARG10.8650.90739.1717.9697.9690.0000.0000.0000.000
161A162LYS10.9330.97642.3056.5076.5070.0000.0000.0000.000
162A163GLY00.001-0.00643.4520.0440.0440.0000.0000.0000.000
163A164THR0-0.034-0.01737.238-0.029-0.0290.0000.0000.0000.000
164A165VAL0-0.023-0.01236.7150.0610.0610.0000.0000.0000.000
165A166LEU00.0100.01134.192-0.324-0.3240.0000.0000.0000.000
166A167LEU0-0.014-0.01431.6930.2440.2440.0000.0000.0000.000
167A168ALA00.0020.01330.457-0.388-0.3880.0000.0000.0000.000
168A169ASP-1-0.711-0.85926.536-11.484-11.4840.0000.0000.0000.000
169A170ASN0-0.012-0.02225.456-0.385-0.3850.0000.0000.0000.000
170A171VAL0-0.026-0.00528.9310.0950.0950.0000.0000.0000.000
171A172ILE0-0.097-0.03732.1000.3230.3230.0000.0000.0000.000
172A173VAL0-0.006-0.00427.7930.0390.0390.0000.0000.0000.000
173A174PRO0-0.023-0.03025.272-0.277-0.2770.0000.0000.0000.000
174A175GLY00.0220.03828.5000.2790.2790.0000.0000.0000.000
175A176THR0-0.018-0.01629.573-0.274-0.2740.0000.0000.0000.000
176A177PRO00.0080.00432.0980.2710.2710.0000.0000.0000.000
177A178ASP-1-0.845-0.92533.315-9.411-9.4110.0000.0000.0000.000
178A179PHE00.024-0.00533.2320.2160.2160.0000.0000.0000.000
179A180LEU0-0.023-0.00935.2760.2430.2430.0000.0000.0000.000
180A181ALA0-0.030-0.01637.5680.2480.2480.0000.0000.0000.000
181A182TYR0-0.048-0.02237.9100.2570.2570.0000.0000.0000.000
182A183VAL0-0.010-0.01237.5320.2000.2000.0000.0000.0000.000
183A184ARG10.8300.87439.1858.3178.3170.0000.0000.0000.000
184A185GLY0-0.0140.01142.7860.1960.1960.0000.0000.0000.000
185A186SER0-0.025-0.00543.2330.2010.2010.0000.0000.0000.000
186A187SER00.0180.00245.193-0.011-0.0110.0000.0000.0000.000
187A188SER0-0.042-0.01543.8650.0410.0410.0000.0000.0000.000
188A189PHE0-0.040-0.03238.856-0.216-0.2160.0000.0000.0000.000
189A190GLU-1-0.955-0.95443.462-6.778-6.7780.0000.0000.0000.000
190A191CYS0-0.019-0.00441.196-0.254-0.2540.0000.0000.0000.000
191A192THR0-0.061-0.03940.5580.2230.2230.0000.0000.0000.000
192A193HIS0-0.043-0.01335.786-0.205-0.2050.0000.0000.0000.000
193A194TYR0-0.004-0.01236.2380.2100.2100.0000.0000.0000.000
194A195SER00.0080.01135.635-0.393-0.3930.0000.0000.0000.000
195A196SER0-0.001-0.01833.1250.0720.0720.0000.0000.0000.000
196A197TYR0-0.030-0.03031.0330.2450.2450.0000.0000.0000.000
197A198LEU00.0380.01225.792-0.149-0.1490.0000.0000.0000.000
198A199GLU-1-0.793-0.89022.726-13.015-13.0150.0000.0000.0000.000
199A200TYR0-0.073-0.07721.549-0.509-0.5090.0000.0000.0000.000
200A201MET0-0.0360.00824.1700.2280.2280.0000.0000.0000.000
201A202LYS10.8750.93827.8069.8319.8310.0000.0000.0000.000
202A203VAL00.0210.02329.0050.3950.3950.0000.0000.0000.000
203A204VAL0-0.0040.00131.265-0.136-0.1360.0000.0000.0000.000
204A205ASP-1-0.728-0.86429.056-11.130-11.1300.0000.0000.0000.000
205A206GLY0-0.006-0.01632.1160.3110.3110.0000.0000.0000.000
206A207LEU00.0000.01730.113-0.245-0.2450.0000.0000.0000.000
207A208GLU-1-0.788-0.87333.391-8.092-8.0920.0000.0000.0000.000
208A209LYS10.8590.94135.0527.7087.7080.0000.0000.0000.000
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