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: MZ8MZ

Calculation Name: 7OTC-F-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: F

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 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1797484.308584
FMO2-HF: Nuclear repulsion 1727414.658486
FMO2-HF: Total energy -70069.650097
FMO2-MP2: Total energy -70274.223534


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:ALA)


Summations of interaction energy for fragment #1(A:2: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.
-16.074-6.33.715-6.083-7.404-0.042
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.906
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].
3A4LEU00.1100.0613.3817.89210.912-0.003-1.427-1.589-0.006
4A5HIS0-0.040-0.0012.3037.2488.2610.815-0.595-1.233-0.003
5A6ASP-1-0.846-0.9194.297-46.842-46.789-0.001-0.030-0.0210.000
93A94GLU-1-0.888-0.9612.128-52.297-51.4882.131-1.185-1.755-0.005
94A95ARG10.9660.9853.21020.80522.1030.040-0.622-0.716-0.007
96A97TRP00.0590.0052.4260.0960.9520.680-0.683-0.853-0.005
97A98GLU-1-0.916-0.9463.023-72.897-70.1920.054-1.527-1.232-0.016
98A99PHE0-0.029-0.0214.4526.5796.599-0.001-0.014-0.0050.000
6A7TYR00.0340.0205.9093.6413.6410.0000.0000.0000.000
7A8TYR0-0.033-0.0347.4772.9572.9570.0000.0000.0000.000
8A9LYS10.8320.8895.36639.96739.9670.0000.0000.0000.000
9A10ASP-1-0.837-0.9029.890-23.587-23.5870.0000.0000.0000.000
10A11GLU0-0.007-0.02711.8262.0162.0160.0000.0000.0000.000
11A12VAL00.0210.02512.1461.4391.4390.0000.0000.0000.000
12A13VAL0-0.042-0.02712.0351.4011.4010.0000.0000.0000.000
13A14LYS10.8450.92013.92820.46320.4630.0000.0000.0000.000
14A15LYS10.8860.94517.08915.67115.6710.0000.0000.0000.000
15A16LEU00.0360.00616.4950.7130.7130.0000.0000.0000.000
16A17MET0-0.054-0.01219.1010.5700.5700.0000.0000.0000.000
17A18THR0-0.081-0.05120.9390.6810.6810.0000.0000.0000.000
18A19GLU-1-0.813-0.88721.611-13.414-13.4140.0000.0000.0000.000
19A20PHE0-0.035-0.02021.5330.3470.3470.0000.0000.0000.000
20A21ASN0-0.028-0.00325.1250.3990.3990.0000.0000.0000.000
21A22TYR0-0.019-0.00520.6500.0460.0460.0000.0000.0000.000
22A23ASN00.0390.00724.1620.0590.0590.0000.0000.0000.000
23A24SER00.000-0.00321.479-0.053-0.0530.0000.0000.0000.000
24A25VAL00.0710.02615.668-0.215-0.2150.0000.0000.0000.000
25A26MET0-0.039-0.02415.994-0.935-0.9350.0000.0000.0000.000
26A27GLN0-0.0100.00716.971-0.236-0.2360.0000.0000.0000.000
27A28VAL0-0.0150.00815.2860.2490.2490.0000.0000.0000.000
28A29PRO0-0.0100.01115.678-0.900-0.9000.0000.0000.0000.000
29A30ARG10.9670.98310.74219.47719.4770.0000.0000.0000.000
30A31VAL00.0470.0229.3191.2651.2650.0000.0000.0000.000
31A32GLU-1-0.856-0.90610.566-20.882-20.8820.0000.0000.0000.000
32A33LYS10.7790.85011.26816.62116.6210.0000.0000.0000.000
33A34ILE00.0200.03110.1710.7850.7850.0000.0000.0000.000
34A35THR0-0.054-0.03912.849-0.108-0.1080.0000.0000.0000.000
35A36LEU00.0340.03413.5910.3960.3960.0000.0000.0000.000
36A37ASN0-0.076-0.05617.5320.5510.5510.0000.0000.0000.000
37A38MET00.0600.03921.3580.2740.2740.0000.0000.0000.000
38A39GLY00.0130.01223.8720.2050.2050.0000.0000.0000.000
39A40VAL00.0390.00627.3870.0680.0680.0000.0000.0000.000
40A41GLY00.0040.02429.3190.2160.2160.0000.0000.0000.000
41A42GLU-1-0.881-0.96932.727-9.471-9.4710.0000.0000.0000.000
42A43ALA00.0150.01732.1970.2010.2010.0000.0000.0000.000
43A44ILE0-0.079-0.04734.2490.1580.1580.0000.0000.0000.000
44A45ALA0-0.0210.00137.6220.2110.2110.0000.0000.0000.000
45A46ASP-1-0.787-0.89835.866-8.760-8.7600.0000.0000.0000.000
46A47LYS10.8180.89734.2428.4568.4560.0000.0000.0000.000
47A48LYS10.9540.98631.5439.6059.6050.0000.0000.0000.000
48A49LEU00.0250.02030.802-0.253-0.2530.0000.0000.0000.000
49A50LEU0-0.056-0.03427.989-0.361-0.3610.0000.0000.0000.000
50A51ASP-1-0.888-0.95427.182-10.975-10.9750.0000.0000.0000.000
51A52ASN0-0.016-0.01526.033-0.773-0.7730.0000.0000.0000.000
52A53ALA00.0520.03024.964-0.513-0.5130.0000.0000.0000.000
53A54ALA0-0.038-0.03822.931-0.654-0.6540.0000.0000.0000.000
54A55ALA0-0.025-0.01221.365-0.845-0.8450.0000.0000.0000.000
55A56ASP-1-0.822-0.91120.519-13.921-13.9210.0000.0000.0000.000
56A57LEU0-0.060-0.04618.553-0.993-0.9930.0000.0000.0000.000
57A58ALA0-0.056-0.02316.975-1.199-1.1990.0000.0000.0000.000
58A59ALA0-0.0190.01216.479-0.833-0.8330.0000.0000.0000.000
59A60ILE00.0000.00714.963-1.391-1.3910.0000.0000.0000.000
60A61SER0-0.075-0.04312.279-2.173-2.1730.0000.0000.0000.000
61A62GLY00.0710.05111.8011.1631.1630.0000.0000.0000.000
62A63GLN0-0.098-0.07312.226-0.485-0.4850.0000.0000.0000.000
63A64LYS11.0051.00014.49117.23517.2350.0000.0000.0000.000
64A65PRO0-0.0040.01718.066-0.346-0.3460.0000.0000.0000.000
65A66LEU0-0.032-0.02119.5050.7050.7050.0000.0000.0000.000
66A67ILE00.0410.01922.4950.1200.1200.0000.0000.0000.000
67A68THR0-0.023-0.01525.0760.4320.4320.0000.0000.0000.000
68A69LYS10.8950.94027.40610.55410.5540.0000.0000.0000.000
69A70ALA00.0400.02231.033-0.085-0.0850.0000.0000.0000.000
70A71ARG10.9460.98232.2609.4909.4900.0000.0000.0000.000
71A72LYS10.9320.95434.3568.4868.4860.0000.0000.0000.000
72A73SER00.0320.01537.660-0.166-0.1660.0000.0000.0000.000
73A74VAL0-0.026-0.00937.8130.0780.0780.0000.0000.0000.000
74A75ALA00.0400.01940.810-0.033-0.0330.0000.0000.0000.000
75A76GLY00.0260.00442.9100.0770.0770.0000.0000.0000.000
76A77PHE00.0280.00836.952-0.042-0.0420.0000.0000.0000.000
77A78LYS10.9280.97939.7766.9756.9750.0000.0000.0000.000
78A79ILE00.0600.04935.901-0.055-0.0550.0000.0000.0000.000
79A80ARG10.9490.95439.0757.7677.7670.0000.0000.0000.000
80A81GLN00.0270.00637.096-0.429-0.4290.0000.0000.0000.000
81A82GLY00.0590.03134.9780.1500.1500.0000.0000.0000.000
82A83TYR00.0140.00534.340-0.155-0.1550.0000.0000.0000.000
83A84PRO0-0.015-0.01630.301-0.156-0.1560.0000.0000.0000.000
84A85ILE0-0.0040.00230.4080.2700.2700.0000.0000.0000.000
85A86GLY00.0330.01527.2100.0480.0480.0000.0000.0000.000
86A87CYS0-0.0340.01622.3790.1170.1170.0000.0000.0000.000
87A88LYS10.9730.98720.10114.47214.4720.0000.0000.0000.000
88A89VAL00.0550.03314.7780.0810.0810.0000.0000.0000.000
89A90THR0-0.070-0.04015.0370.6040.6040.0000.0000.0000.000
90A91LEU00.0280.0349.464-0.149-0.1490.0000.0000.0000.000
91A92ARG10.9640.9589.57922.33422.3340.0000.0000.0000.000
92A93GLY00.0550.0296.437-1.201-1.2010.0000.0000.0000.000
95A96MET0-0.061-0.0055.7931.8301.8300.0000.0000.0000.000
99A100PHE00.001-0.0057.5783.1583.1580.0000.0000.0000.000
100A101GLU-1-0.902-0.9694.975-36.817-36.8170.0000.0000.0000.000
101A102ARG10.8970.9767.52135.16935.1690.0000.0000.0000.000
102A103LEU0-0.036-0.0129.9212.9892.9890.0000.0000.0000.000
103A104ILE0-0.021-0.02311.7012.0682.0680.0000.0000.0000.000
104A105THR0-0.019-0.02610.5711.8301.8300.0000.0000.0000.000
105A106ILE00.000-0.00112.4441.6221.6220.0000.0000.0000.000
106A107ALA0-0.0040.00714.4321.3571.3570.0000.0000.0000.000
107A108VAL0-0.029-0.03015.9971.3031.3030.0000.0000.0000.000
108A109PRO00.005-0.00316.8421.1161.1160.0000.0000.0000.000
109A110ARG10.8470.93918.76216.20516.2050.0000.0000.0000.000
110A111ILE0-0.075-0.01320.5820.5970.5970.0000.0000.0000.000
111A112ARG10.9700.97222.98811.45811.4580.0000.0000.0000.000
112A113ASP-1-0.940-0.98026.769-10.899-10.8990.0000.0000.0000.000
113A114PHE00.0260.03121.1830.0450.0450.0000.0000.0000.000
114A115ARG10.9710.97626.38011.35211.3520.0000.0000.0000.000
115A116GLY00.0010.01423.3700.1480.1480.0000.0000.0000.000
116A117LEU0-0.0180.00519.0070.3340.3340.0000.0000.0000.000
117A118SER0-0.060-0.03523.1420.4700.4700.0000.0000.0000.000
118A119ALA00.0570.02023.272-0.376-0.3760.0000.0000.0000.000
119A120LYS10.9810.97424.30311.09211.0920.0000.0000.0000.000
120A121SER0-0.055-0.01623.3660.3580.3580.0000.0000.0000.000
121A122PHE00.019-0.00420.054-0.649-0.6490.0000.0000.0000.000
122A123ASP-1-0.842-0.92323.296-12.903-12.9030.0000.0000.0000.000
123A124GLY00.0330.02526.0970.4390.4390.0000.0000.0000.000
124A125ARG10.8410.93023.12311.77811.7780.0000.0000.0000.000
125A126GLY00.0500.02021.632-0.227-0.2270.0000.0000.0000.000
126A127ASN0-0.054-0.02218.903-1.571-1.5710.0000.0000.0000.000
127A128TYR00.0110.01917.5990.3780.3780.0000.0000.0000.000
128A129SER00.0060.00918.971-0.685-0.6850.0000.0000.0000.000
129A130MET0-0.0070.02019.4840.4840.4840.0000.0000.0000.000
130A131GLY00.1190.06321.573-0.363-0.3630.0000.0000.0000.000
131A132VAL0-0.048-0.02120.6460.3860.3860.0000.0000.0000.000
132A133ARG10.8840.92523.06712.23712.2370.0000.0000.0000.000
133A134GLU-1-0.844-0.92024.348-12.321-12.3210.0000.0000.0000.000
134A135GLN00.001-0.01220.789-1.119-1.1190.0000.0000.0000.000
135A136ILE00.0680.02520.725-0.706-0.7060.0000.0000.0000.000
136A137ILE0-0.024-0.01018.585-0.254-0.2540.0000.0000.0000.000
137A138PHE0-0.011-0.01214.282-0.873-0.8730.0000.0000.0000.000
138A139PRO0-0.009-0.00715.2870.7070.7070.0000.0000.0000.000
139A140GLU-1-0.820-0.89812.506-22.796-22.7960.0000.0000.0000.000
140A141ILE0-0.066-0.02216.5180.4720.4720.0000.0000.0000.000
141A142ASP-1-0.872-0.94020.157-12.582-12.5820.0000.0000.0000.000
142A143TYR0-0.019-0.01323.0860.1610.1610.0000.0000.0000.000
143A144ASP-1-0.910-0.95325.717-10.268-10.2680.0000.0000.0000.000
144A145LYS10.8250.91025.96511.00111.0010.0000.0000.0000.000
145A146VAL00.0060.02025.0510.1240.1240.0000.0000.0000.000
146A147ASP-1-0.885-0.93927.129-10.362-10.3620.0000.0000.0000.000
147A148ARG10.8840.94129.06010.27610.2760.0000.0000.0000.000
148A149VAL00.0220.02727.041-0.398-0.3980.0000.0000.0000.000
149A150ARG10.8960.93625.32011.69211.6920.0000.0000.0000.000
150A151GLY00.0350.03124.158-0.543-0.5430.0000.0000.0000.000
151A152LEU0-0.032-0.02118.7560.2610.2610.0000.0000.0000.000
152A153ASP-1-0.837-0.92521.707-12.868-12.8680.0000.0000.0000.000
153A154ILE0-0.027-0.01415.500-0.793-0.7930.0000.0000.0000.000
154A155THR0-0.065-0.04817.3780.6230.6230.0000.0000.0000.000
155A156ILE00.0220.00313.117-1.078-1.0780.0000.0000.0000.000
156A157THR0-0.023-0.00515.2040.9130.9130.0000.0000.0000.000
157A158THR00.035-0.00614.576-1.783-1.7830.0000.0000.0000.000
158A159THR0-0.032-0.01016.0250.7640.7640.0000.0000.0000.000
159A160ALA0-0.0340.00218.1270.5690.5690.0000.0000.0000.000
160A161LYS10.8610.92220.15412.15312.1530.0000.0000.0000.000
161A162SER0-0.052-0.06623.5050.6850.6850.0000.0000.0000.000
162A163ASP-1-0.827-0.91122.935-12.302-12.3020.0000.0000.0000.000
163A164GLU-1-0.861-0.89523.178-11.709-11.7090.0000.0000.0000.000
164A165GLU-1-0.749-0.87820.704-13.269-13.2690.0000.0000.0000.000
165A166GLY00.0060.00118.690-0.911-0.9110.0000.0000.0000.000
166A167ARG10.8500.90618.51211.20011.2000.0000.0000.0000.000
167A168ALA00.0240.02219.791-0.380-0.3800.0000.0000.0000.000
168A169LEU0-0.028-0.00212.620-0.733-0.7330.0000.0000.0000.000
169A170LEU0-0.022-0.02214.389-1.158-1.1580.0000.0000.0000.000
170A171ALA00.0080.00716.024-0.604-0.6040.0000.0000.0000.000
171A172ALA0-0.025-0.00715.368-0.004-0.0040.0000.0000.0000.000
172A173PHE0-0.065-0.0638.087-2.086-2.0860.0000.0000.0000.000
173A174ASP-1-0.917-0.93513.436-18.176-18.1760.0000.0000.0000.000
174A175PHE0-0.0090.00714.7120.2110.2110.0000.0000.0000.000
175A176PRO00.0400.02316.8261.0031.0030.0000.0000.0000.000
176A177PHE0-0.007-0.03120.0080.6140.6140.0000.0000.0000.000
177A178ARG0-0.049-0.00922.8430.7570.7570.0000.0000.0000.000