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: 2GRLR

Calculation Name: 7OTC-i-Other547

Preferred Name:

Target Type:

Ligand Name: argyrin b | adenosine-5'-triphosphate | guanosine-5'-diphosphate | n7-methyl-guanosine-5'-monophosphate | 1n-methylguanosine-5'-monophosphate | 2n-methylguanosine-5'-monophosphate | 6n-dimethyladenosine-5'-monophoshate | 2-methyladenosine-5'-monophosphate | 4n,o2'-methylcytidine-5'-monophosphate | n6-methyladenosine-5'-monophosphate | pseudouridine-5'-monophosphate | (1s)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-o-phosphono-d-ribitol | 5-methylcytidine-5'-monophosphate | 5-methyluridine 5'-monophosphate | o2'-methylguanosine-5'-monophosphate | 3-methyluridine-5'-monophoshate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (2s,3r)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid | (3r)-3-(methylsulfanyl)-l-aspartic acid | spermidine | 1,4-diaminobutane | magnesium ion | zinc ion

Ligand 3-letter code: 1I7 | ATP | GDP | G7M | 1MG | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | H2U | OMC | OMU | 4D4 | D2T | SPD | PUT | MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7OTC

Chain ID: i

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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 127
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1028087.403574
FMO2-HF: Nuclear repulsion 977649.61649
FMO2-HF: Total energy -50437.787084
FMO2-MP2: Total energy -50586.189816


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:4:ASN)


Summations of interaction energy for fragment #1(A:4:ASN)
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.
130.679132.718-0.014-0.893-1.132-0.001
Interaction energy analysis for fragmet #1(A:4:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / q_NPA : 0.917
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].
3A6TYR00.0560.0533.599-8.300-6.413-0.013-0.888-0.987-0.001
20A23PRO00.0820.0364.9953.2563.408-0.001-0.005-0.1450.000
4A7TYR00.007-0.0095.8104.4184.4180.0000.0000.0000.000
5A8GLY00.0680.0488.5701.9221.9220.0000.0000.0000.000
6A9THR0-0.080-0.05412.3500.7210.7210.0000.0000.0000.000
7A10GLY00.0480.03115.5280.3010.3010.0000.0000.0000.000
8A11ARG10.9070.94118.92815.56915.5690.0000.0000.0000.000
9A12ARG10.8560.95922.52511.61711.6170.0000.0000.0000.000
10A13LYS11.0030.98325.80910.31110.3110.0000.0000.0000.000
11A14SER00.0020.00328.0280.0640.0640.0000.0000.0000.000
12A15SER0-0.063-0.03324.1320.1050.1050.0000.0000.0000.000
13A16ALA0-0.017-0.02120.099-0.029-0.0290.0000.0000.0000.000
14A17ALA0-0.0020.00817.8270.1630.1630.0000.0000.0000.000
15A18ARG10.9630.97713.30221.53421.5340.0000.0000.0000.000
16A19VAL00.0130.00412.1170.7520.7520.0000.0000.0000.000
17A20PHE0-0.005-0.0047.614-1.665-1.6650.0000.0000.0000.000
18A21ILE00.0340.0258.1152.6452.6450.0000.0000.0000.000
19A22LYS10.8440.9065.35021.19521.1950.0000.0000.0000.000
21A24GLY0-0.042-0.0448.163-0.905-0.9050.0000.0000.0000.000
22A25ASN0-0.0020.00011.0140.0510.0510.0000.0000.0000.000
23A26GLY00.1020.06914.4361.1081.1080.0000.0000.0000.000
24A27LYS10.8230.94115.11717.59717.5970.0000.0000.0000.000
25A28ILE00.0690.01714.930-1.117-1.1170.0000.0000.0000.000
26A29VAL0-0.069-0.03214.3161.2961.2960.0000.0000.0000.000
27A30ILE00.0290.01016.030-1.002-1.0020.0000.0000.0000.000
28A31ASN0-0.050-0.02917.9620.0940.0940.0000.0000.0000.000
29A32GLN00.0340.02716.693-0.330-0.3300.0000.0000.0000.000
30A33ARG10.9751.01018.90212.97012.9700.0000.0000.0000.000
31A34SER00.0650.03020.193-0.726-0.7260.0000.0000.0000.000
32A35LEU00.022-0.00520.9390.4820.4820.0000.0000.0000.000
33A36GLU-1-0.820-0.89122.872-10.990-10.9900.0000.0000.0000.000
34A37GLN00.0350.02225.3740.2870.2870.0000.0000.0000.000
35A38TYR0-0.088-0.04823.9050.1960.1960.0000.0000.0000.000
36A39PHE0-0.046-0.04322.8180.3680.3680.0000.0000.0000.000
37A40GLY00.0870.04727.4960.0830.0830.0000.0000.0000.000
38A41ARG10.9500.97630.9919.9569.9560.0000.0000.0000.000
39A42GLU-1-0.739-0.87030.392-9.962-9.9620.0000.0000.0000.000
40A43THR00.005-0.01130.131-0.439-0.4390.0000.0000.0000.000
41A44ALA0-0.107-0.05728.292-0.341-0.3410.0000.0000.0000.000
42A45ARG10.8240.88626.05310.33010.3300.0000.0000.0000.000
43A46MET0-0.0050.01425.160-0.563-0.5630.0000.0000.0000.000
44A47VAL00.028-0.01025.401-0.356-0.3560.0000.0000.0000.000
45A48VAL0-0.089-0.04720.300-0.389-0.3890.0000.0000.0000.000
46A49ARG10.9710.98420.84412.18912.1890.0000.0000.0000.000
47A50GLN00.0240.02122.0240.1400.1400.0000.0000.0000.000
48A51PRO0-0.051-0.03419.2550.2790.2790.0000.0000.0000.000
49A52LEU0-0.022-0.02216.220-0.776-0.7760.0000.0000.0000.000
50A53GLU-1-0.878-0.93620.063-13.155-13.1550.0000.0000.0000.000
51A54LEU0-0.066-0.01721.3780.1460.1460.0000.0000.0000.000
52A55VAL00.0160.00216.185-0.254-0.2540.0000.0000.0000.000
53A56ASP-1-0.853-0.89719.070-14.827-14.8270.0000.0000.0000.000
54A57MET0-0.064-0.05711.108-0.475-0.4750.0000.0000.0000.000
55A58VAL0-0.0180.00215.369-1.000-1.0000.0000.0000.0000.000
56A59GLU-1-0.800-0.88917.255-16.465-16.4650.0000.0000.0000.000
57A60LYS10.8350.90113.14616.75616.7560.0000.0000.0000.000
58A61LEU00.0010.0029.781-2.336-2.3360.0000.0000.0000.000
59A62ASP-1-0.872-0.90210.357-21.357-21.3570.0000.0000.0000.000
60A63LEU0-0.030-0.00810.289-2.684-2.6840.0000.0000.0000.000
61A64TYR0-0.021-0.02210.6161.6531.6530.0000.0000.0000.000
62A65ILE0-0.029-0.01112.218-0.907-0.9070.0000.0000.0000.000
63A66THR00.0090.00514.7640.7990.7990.0000.0000.0000.000
64A67VAL0-0.044-0.02216.871-0.206-0.2060.0000.0000.0000.000
65A68LYS11.0161.00820.14713.12013.1200.0000.0000.0000.000
66A69GLY00.0360.02222.967-0.019-0.0190.0000.0000.0000.000
67A70GLY00.008-0.00926.219-0.213-0.2130.0000.0000.0000.000
68A71GLY00.0570.03028.7940.0300.0300.0000.0000.0000.000
69A72ILE00.0720.02528.718-0.396-0.3960.0000.0000.0000.000
70A73SER00.0270.01028.070-0.392-0.3920.0000.0000.0000.000
71A74GLY0-0.029-0.01427.870-0.185-0.1850.0000.0000.0000.000
72A75GLN00.0620.04924.262-0.893-0.8930.0000.0000.0000.000
73A76ALA00.0650.04123.416-0.554-0.5540.0000.0000.0000.000
74A77GLY0-0.002-0.00723.669-0.360-0.3600.0000.0000.0000.000
75A78ALA0-0.058-0.03021.657-0.203-0.2030.0000.0000.0000.000
76A79ILE00.0210.00318.970-0.789-0.7890.0000.0000.0000.000
77A80ARG10.9881.01318.72312.02212.0220.0000.0000.0000.000
78A81HIS0-0.026-0.00319.595-0.549-0.5490.0000.0000.0000.000
79A82GLY00.0380.00216.438-0.472-0.4720.0000.0000.0000.000
80A83ILE0-0.005-0.00814.417-1.456-1.4560.0000.0000.0000.000
81A84THR00.0040.01014.476-0.569-0.5690.0000.0000.0000.000
82A85ARG10.8900.93414.76718.81018.8100.0000.0000.0000.000
83A86ALA00.0270.01610.295-0.311-0.3110.0000.0000.0000.000
84A87LEU00.0130.0109.888-2.458-2.4580.0000.0000.0000.000
85A88MET0-0.114-0.05212.1851.1481.1480.0000.0000.0000.000
86A89GLU-1-0.937-0.9648.798-25.013-25.0130.0000.0000.0000.000
87A90TYR0-0.047-0.0238.012-4.407-4.4070.0000.0000.0000.000
88A91ASP-1-0.696-0.8429.505-18.817-18.8170.0000.0000.0000.000
89A92GLU-1-0.924-0.95812.097-22.720-22.7200.0000.0000.0000.000
90A93SER0-0.031-0.01915.3501.4451.4450.0000.0000.0000.000
91A94LEU00.0330.03117.5131.0911.0910.0000.0000.0000.000
92A95ARG10.7580.84915.82217.92817.9280.0000.0000.0000.000
93A96SER00.009-0.00521.1200.1950.1950.0000.0000.0000.000
94A97GLU-1-0.842-0.91323.026-11.505-11.5050.0000.0000.0000.000
95A98LEU00.0420.01818.2480.2820.2820.0000.0000.0000.000
96A99ARG10.8910.94122.27513.31513.3150.0000.0000.0000.000
97A100LYS10.9550.98624.19310.23410.2340.0000.0000.0000.000
98A101ALA00.0550.03224.7880.3880.3880.0000.0000.0000.000
99A102GLY0-0.0050.00325.7860.1880.1880.0000.0000.0000.000
100A103PHE00.000-0.00521.238-0.062-0.0620.0000.0000.0000.000
101A104VAL00.0260.00619.140-0.316-0.3160.0000.0000.0000.000
102A105THR0-0.092-0.04921.136-0.028-0.0280.0000.0000.0000.000
103A106ARG10.9100.95222.84112.23812.2380.0000.0000.0000.000
104A107ASP-1-0.776-0.86624.242-10.261-10.2610.0000.0000.0000.000
105A108ALA00.0310.02627.597-0.113-0.1130.0000.0000.0000.000
106A109ARG10.8240.90129.40410.33910.3390.0000.0000.0000.000
107A110GLN00.016-0.00129.502-0.321-0.3210.0000.0000.0000.000
108A111VAL0-0.050-0.03033.1350.2350.2350.0000.0000.0000.000
109A112GLU-1-0.809-0.88336.219-7.795-7.7950.0000.0000.0000.000
110A113ARG10.9750.98239.2707.5347.5340.0000.0000.0000.000
111A114LYS10.9050.94840.6056.8866.8860.0000.0000.0000.000
112A115LYS10.9060.95343.4667.3117.3110.0000.0000.0000.000
113A116VAL00.0950.04647.1040.0090.0090.0000.0000.0000.000
114A117GLY00.0630.03550.5420.0160.0160.0000.0000.0000.000
115A118LEU0-0.077-0.01948.1560.0600.0600.0000.0000.0000.000
116A119ARG10.9710.97350.0245.9055.9050.0000.0000.0000.000
117A120LYS10.9980.99044.5887.0867.0860.0000.0000.0000.000
118A121ALA00.0360.02143.222-0.070-0.0700.0000.0000.0000.000
119A122ARG10.8750.91742.5987.4397.4390.0000.0000.0000.000
120A123ARG10.9851.00147.0556.2516.2510.0000.0000.0000.000
121A124ARG11.0531.01849.8895.9545.9540.0000.0000.0000.000
122A125PRO0-0.054-0.03853.140-0.024-0.0240.0000.0000.0000.000
123A126GLN0-0.0040.00755.835-0.039-0.0390.0000.0000.0000.000
124A127PHE0-0.015-0.00358.448-0.014-0.0140.0000.0000.0000.000
125A128SER00.036-0.00361.804-0.004-0.0040.0000.0000.0000.000
126A129LYS10.9270.95565.4814.8704.8700.0000.0000.0000.000
127A130ARG00.1400.10867.223-0.119-0.1190.0000.0000.0000.000