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: G7821

Calculation Name: 7OTC-d-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: d

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 205
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2382473.176695
FMO2-HF: Nuclear repulsion 2301577.489726
FMO2-HF: Total energy -80895.686969
FMO2-MP2: Total energy -81134.700235


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.
278.214278.473.566-1.614-2.208-0.005
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 : 0.902 / q_NPA : 0.940
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].
3A4TYR00.0260.0173.890-2.920-1.513-0.017-0.752-0.6380.001
67A68LEU0-0.010-0.0122.151-1.253-2.4043.583-0.862-1.570-0.006
4A5LEU00.001-0.0205.4072.6692.6690.0000.0000.0000.000
5A6GLY00.0590.0568.1062.8452.8450.0000.0000.0000.000
6A7PRO00.0300.00411.0320.2960.2960.0000.0000.0000.000
7A8LYS10.9340.95710.31028.03228.0320.0000.0000.0000.000
8A9LEU00.0830.04515.141-0.052-0.0520.0000.0000.0000.000
9A10LYS10.9380.97115.99317.53117.5310.0000.0000.0000.000
10A11LEU0-0.040-0.01312.2450.0930.0930.0000.0000.0000.000
11A12SER00.1140.05116.4860.2070.2070.0000.0000.0000.000
12A13ARG10.8450.90719.82213.63113.6310.0000.0000.0000.000
13A14ARG10.8630.93717.94115.24615.2460.0000.0000.0000.000
14A15GLU-1-0.733-0.86917.211-17.592-17.5920.0000.0000.0000.000
15A16GLY0-0.0020.02620.9680.4140.4140.0000.0000.0000.000
16A17THR00.0350.01522.6450.3310.3310.0000.0000.0000.000
17A18ASP-1-0.850-0.93621.932-14.803-14.8030.0000.0000.0000.000
18A19LEU0-0.025-0.01416.696-0.369-0.3690.0000.0000.0000.000
19A20PHE00.0430.01518.431-1.084-1.0840.0000.0000.0000.000
20A21LEU0-0.066-0.03613.431-0.970-0.9700.0000.0000.0000.000
21A22LYS10.8480.91517.23816.44016.4400.0000.0000.0000.000
22A23SER00.0550.01220.0420.2450.2450.0000.0000.0000.000
23A24GLY00.0780.05122.2220.2770.2770.0000.0000.0000.000
24A25VAL0-0.0070.00525.0800.4020.4020.0000.0000.0000.000
25A26ARG10.9290.96627.00411.14411.1440.0000.0000.0000.000
26A27ALA00.0660.04427.186-0.412-0.4120.0000.0000.0000.000
27A28ILE0-0.004-0.01622.564-0.137-0.1370.0000.0000.0000.000
28A29ASP-1-0.873-0.93526.451-10.584-10.5840.0000.0000.0000.000
29A30THR00.0150.00928.989-0.006-0.0060.0000.0000.0000.000
30A31LYS10.8750.94522.56012.93312.9330.0000.0000.0000.000
31A32CYS0-0.106-0.06323.705-0.609-0.6090.0000.0000.0000.000
32A33LYS11.0391.05125.7799.9519.9510.0000.0000.0000.000
33A34ILE00.0250.00023.908-0.419-0.4190.0000.0000.0000.000
34A35GLU-1-0.785-0.88826.224-10.714-10.7140.0000.0000.0000.000
35A36GLN0-0.0180.00027.2850.2310.2310.0000.0000.0000.000
36A37ALA00.0320.04123.623-0.555-0.5550.0000.0000.0000.000
37A38PRO0-0.091-0.05419.3970.1640.1640.0000.0000.0000.000
38A39GLY0-0.003-0.00722.179-0.135-0.1350.0000.0000.0000.000
39A40GLN00.0540.03123.530-0.017-0.0170.0000.0000.0000.000
40A41HIS00.0750.03126.6540.0510.0510.0000.0000.0000.000
41A42GLY0-0.0280.00026.3470.1590.1590.0000.0000.0000.000
42A43ALA00.0830.03927.0130.0310.0310.0000.0000.0000.000
43A44ARG10.8560.92629.6499.8139.8130.0000.0000.0000.000
44A45LYS10.8930.93028.05110.36210.3620.0000.0000.0000.000
45A46PRO00.0270.02327.4100.3020.3020.0000.0000.0000.000
46A47ARG10.9950.99529.3009.4079.4070.0000.0000.0000.000
47A48LEU0-0.069-0.01723.773-0.099-0.0990.0000.0000.0000.000
48A49SER00.0370.01526.7700.1980.1980.0000.0000.0000.000
49A50ASP-1-0.749-0.87526.834-11.138-11.1380.0000.0000.0000.000
50A51TYR00.0210.00319.380-0.547-0.5470.0000.0000.0000.000
51A52GLY0-0.007-0.01322.632-0.710-0.7100.0000.0000.0000.000
52A53VAL00.015-0.01122.329-0.696-0.6960.0000.0000.0000.000
53A54GLN00.0550.03522.529-0.776-0.7760.0000.0000.0000.000
54A55LEU0-0.022-0.00316.161-0.961-0.9610.0000.0000.0000.000
55A56ARG10.7750.86716.77215.03415.0340.0000.0000.0000.000
56A57GLU-1-0.689-0.82818.880-14.371-14.3710.0000.0000.0000.000
57A58LYS10.8950.93013.47319.60219.6020.0000.0000.0000.000
58A59GLN0-0.086-0.06111.721-1.598-1.5980.0000.0000.0000.000
59A60LYS10.8570.93214.53112.31312.3130.0000.0000.0000.000
60A61VAL00.0470.03515.729-0.823-0.8230.0000.0000.0000.000
61A62ARG10.8270.8998.31126.85426.8540.0000.0000.0000.000
62A63ARG10.7670.87811.34418.70318.7030.0000.0000.0000.000
63A64ILE00.0350.03313.002-0.809-0.8090.0000.0000.0000.000
64A65TYR0-0.020-0.03412.994-0.599-0.5990.0000.0000.0000.000
65A66GLY0-0.050-0.00910.131-1.379-1.3790.0000.0000.0000.000
66A67VAL0-0.005-0.0017.153-5.125-5.1250.0000.0000.0000.000
68A69GLU-1-0.734-0.8206.355-20.846-20.8460.0000.0000.0000.000
69A70ARG10.9680.9846.74826.78326.7830.0000.0000.0000.000
70A71GLN0-0.0100.0006.6643.2573.2570.0000.0000.0000.000
71A72PHE00.0690.0278.5631.5721.5720.0000.0000.0000.000
72A73ARG11.0281.01311.32519.48419.4840.0000.0000.0000.000
73A74ASN0-0.029-0.02810.7922.1452.1450.0000.0000.0000.000
74A75TYR00.0650.01911.055-0.040-0.0400.0000.0000.0000.000
75A76TYR00.0530.03014.5850.7290.7290.0000.0000.0000.000
76A77LYS10.9130.96014.56918.67318.6730.0000.0000.0000.000
77A78GLU-1-0.794-0.86417.202-13.592-13.5920.0000.0000.0000.000
78A79ALA0-0.021-0.01818.6020.7120.7120.0000.0000.0000.000
79A80ALA00.0080.00620.5540.5840.5840.0000.0000.0000.000
80A81ARG10.8110.89321.28613.31513.3150.0000.0000.0000.000
81A82LEU0-0.058-0.02821.6610.4600.4600.0000.0000.0000.000
82A83LYS10.9720.98824.7489.6919.6910.0000.0000.0000.000
83A84GLY00.0160.00827.618-0.147-0.1470.0000.0000.0000.000
84A85ASN0-0.006-0.00626.9290.1000.1000.0000.0000.0000.000
85A86THR00.0320.01121.667-0.188-0.1880.0000.0000.0000.000
86A87GLY00.0300.01221.953-0.699-0.6990.0000.0000.0000.000
87A88GLU-1-0.787-0.90322.028-11.732-11.7320.0000.0000.0000.000
88A89ASN0-0.044-0.01522.207-0.162-0.1620.0000.0000.0000.000
89A90LEU0-0.025-0.02015.597-0.722-0.7220.0000.0000.0000.000
90A91LEU00.001-0.01217.892-0.995-0.9950.0000.0000.0000.000
91A92ALA00.0190.01419.480-0.359-0.3590.0000.0000.0000.000
92A93LEU0-0.024-0.00215.827-0.375-0.3750.0000.0000.0000.000
93A94LEU0-0.091-0.04413.333-1.305-1.3050.0000.0000.0000.000
94A95GLU-1-0.739-0.83615.750-15.685-15.6850.0000.0000.0000.000
95A96GLY00.0630.04418.2200.1330.1330.0000.0000.0000.000
96A97ARG10.7560.8849.23525.22325.2230.0000.0000.0000.000
97A98LEU00.0450.03214.0080.3950.3950.0000.0000.0000.000
98A99ASP-1-0.796-0.89710.291-27.807-27.8070.0000.0000.0000.000
99A100ASN0-0.088-0.04813.9450.2850.2850.0000.0000.0000.000
100A101VAL00.0820.04216.4970.6890.6890.0000.0000.0000.000
101A102VAL00.009-0.00317.1490.6130.6130.0000.0000.0000.000
102A103TYR0-0.046-0.03017.6640.2960.2960.0000.0000.0000.000
103A104ARG10.8490.92519.42314.26414.2640.0000.0000.0000.000
104A105MET00.0080.01921.9410.4630.4630.0000.0000.0000.000
105A106GLY00.0380.02822.7610.5180.5180.0000.0000.0000.000
106A107PHE0-0.006-0.00221.064-0.017-0.0170.0000.0000.0000.000
107A108GLY0-0.034-0.02618.888-0.378-0.3780.0000.0000.0000.000
108A109ALA00.0390.02119.8600.4030.4030.0000.0000.0000.000
109A110THR0-0.021-0.03616.783-0.373-0.3730.0000.0000.0000.000
110A111ARG10.9970.98913.38217.71017.7100.0000.0000.0000.000
111A112ALA0-0.117-0.05212.697-1.866-1.8660.0000.0000.0000.000
112A113GLU-1-0.775-0.87013.546-19.073-19.0730.0000.0000.0000.000
113A114ALA00.0560.04815.320-0.027-0.0270.0000.0000.0000.000
114A115ARG10.8110.9095.41836.56636.5660.0000.0000.0000.000
115A116GLN0-0.0210.01311.6140.1970.1970.0000.0000.0000.000
116A117LEU0-0.0030.01213.6110.2740.2740.0000.0000.0000.000
117A118VAL00.0420.02612.2910.4600.4600.0000.0000.0000.000
118A119SER0-0.074-0.0649.8290.1130.1130.0000.0000.0000.000
119A120HIS0-0.025-0.03111.7761.1721.1720.0000.0000.0000.000
120A121LYS10.9110.95414.75920.53020.5300.0000.0000.0000.000
121A122ALA0-0.020-0.00816.8921.1081.1080.0000.0000.0000.000
122A123ILE00.0220.01617.4810.7510.7510.0000.0000.0000.000
123A124MET0-0.031-0.01919.299-0.289-0.2890.0000.0000.0000.000
124A125VAL00.0360.01319.7860.1220.1220.0000.0000.0000.000
125A126ASN0-0.001-0.01522.3020.0700.0700.0000.0000.0000.000
126A127GLY00.0410.02525.5550.2510.2510.0000.0000.0000.000
127A128ARG10.9540.98321.93112.43712.4370.0000.0000.0000.000
128A129VAL0-0.031-0.01218.384-0.418-0.4180.0000.0000.0000.000
129A130VAL00.0190.01716.022-0.427-0.4270.0000.0000.0000.000
130A131ASN0-0.006-0.00311.1301.2141.2140.0000.0000.0000.000
131A132ILE0-0.012-0.0069.817-2.600-2.6000.0000.0000.0000.000
132A133ALA0-0.001-0.0128.1680.9320.9320.0000.0000.0000.000
133A134SER0-0.040-0.0319.023-0.084-0.0840.0000.0000.0000.000
134A135TYR00.0150.01510.8270.3990.3990.0000.0000.0000.000
135A136GLN0-0.028-0.03014.2150.5450.5450.0000.0000.0000.000
136A137VAL0-0.037-0.01516.9720.2900.2900.0000.0000.0000.000
137A138SER00.0070.01020.1190.1230.1230.0000.0000.0000.000
138A139PRO0-0.045-0.03823.4160.0110.0110.0000.0000.0000.000
139A140ASN0-0.0080.00026.5910.1910.1910.0000.0000.0000.000
140A141ASP-1-0.834-0.87823.005-12.642-12.6420.0000.0000.0000.000
141A142VAL0-0.0080.00325.868-0.041-0.0410.0000.0000.0000.000
142A143VAL0-0.046-0.03220.801-0.482-0.4820.0000.0000.0000.000
143A144SER00.0260.00923.2850.4540.4540.0000.0000.0000.000
144A145ILE0-0.0060.00721.680-0.643-0.6430.0000.0000.0000.000
145A146ARG10.9440.97021.42114.12014.1200.0000.0000.0000.000
146A147GLU-1-0.861-0.93724.637-10.158-10.1580.0000.0000.0000.000
147A148LYS10.9650.97023.80712.93412.9340.0000.0000.0000.000
148A149ALA0-0.0020.00422.355-0.003-0.0030.0000.0000.0000.000
149A150LYS10.8840.95024.33611.05511.0550.0000.0000.0000.000
150A151LYS10.9040.96027.51310.64310.6430.0000.0000.0000.000
151A152GLN00.0070.01820.813-0.543-0.5430.0000.0000.0000.000
152A153SER00.041-0.00425.7030.1220.1220.0000.0000.0000.000
153A154ARG10.8370.91016.68717.52617.5260.0000.0000.0000.000
154A155VAL00.0050.01422.753-0.211-0.2110.0000.0000.0000.000
155A156LYS10.9980.99123.96610.63910.6390.0000.0000.0000.000
156A157ALA00.0470.03025.6230.1100.1100.0000.0000.0000.000
157A158ALA0-0.070-0.02423.162-0.103-0.1030.0000.0000.0000.000
158A159LEU00.0130.00325.178-0.018-0.0180.0000.0000.0000.000
159A160GLU-1-0.840-0.92428.096-10.585-10.5850.0000.0000.0000.000
160A161LEU0-0.052-0.04724.367-0.033-0.0330.0000.0000.0000.000
161A162ALA0-0.067-0.02126.352-0.265-0.2650.0000.0000.0000.000
162A163GLU-1-0.899-0.93727.589-9.505-9.5050.0000.0000.0000.000
163A164GLN0-0.073-0.02628.109-0.170-0.1700.0000.0000.0000.000
164A165ARG10.7500.88722.74313.28613.2860.0000.0000.0000.000
165A166GLU-1-0.904-0.95028.799-10.461-10.4610.0000.0000.0000.000
166A167LYS10.9420.98127.9469.9729.9720.0000.0000.0000.000
167A168PRO0-0.013-0.01325.4650.1220.1220.0000.0000.0000.000
168A169THR00.023-0.00628.1260.0220.0220.0000.0000.0000.000
169A170TRP0-0.058-0.03322.8200.1440.1440.0000.0000.0000.000
170A171LEU0-0.043-0.02023.391-0.318-0.3180.0000.0000.0000.000
171A172GLU-1-0.789-0.88327.776-9.832-9.8320.0000.0000.0000.000
172A173VAL0-0.022-0.03327.045-0.373-0.3730.0000.0000.0000.000
173A174ASP-1-0.793-0.89229.774-9.073-9.0730.0000.0000.0000.000
174A175ALA00.013-0.01529.961-0.300-0.3000.0000.0000.0000.000
175A176GLY00.0100.01831.023-0.072-0.0720.0000.0000.0000.000
176A177LYS10.9050.96430.5879.3579.3570.0000.0000.0000.000
177A178MET0-0.072-0.04326.475-0.550-0.5500.0000.0000.0000.000
178A179GLU-1-0.885-0.96726.620-11.054-11.0540.0000.0000.0000.000
179A180GLY00.0620.02326.4840.1740.1740.0000.0000.0000.000
180A181THR0-0.0100.00426.148-0.263-0.2630.0000.0000.0000.000
181A182PHE0-0.020-0.02321.749-0.100-0.1000.0000.0000.0000.000
182A183LYS10.9140.96325.9449.5919.5910.0000.0000.0000.000
183A184ARG10.8280.87727.27110.34510.3450.0000.0000.0000.000
184A185LYS10.9870.99123.35112.16512.1650.0000.0000.0000.000
185A186PRO00.0120.01623.0910.4040.4040.0000.0000.0000.000
186A187GLU-1-0.775-0.86925.669-10.577-10.5770.0000.0000.0000.000
187A188ARG10.7700.85424.96011.90711.9070.0000.0000.0000.000
188A189SER0-0.004-0.01126.933-0.046-0.0460.0000.0000.0000.000
189A190ASP-1-0.796-0.87727.982-10.149-10.1490.0000.0000.0000.000
190A191LEU0-0.118-0.05022.367-0.427-0.4270.0000.0000.0000.000
191A192SER00.0240.00824.6320.3460.3460.0000.0000.0000.000
192A193ALA00.0410.01526.128-0.203-0.2030.0000.0000.0000.000
193A194ASP-1-0.903-0.94324.418-12.669-12.6690.0000.0000.0000.000
194A195ILE0-0.121-0.05719.919-0.515-0.5150.0000.0000.0000.000
195A196ASN00.0280.01323.6600.7080.7080.0000.0000.0000.000
196A197GLU-1-0.822-0.89522.301-12.257-12.2570.0000.0000.0000.000
197A198HIS00.0470.01223.229-0.246-0.2460.0000.0000.0000.000
198A199LEU0-0.011-0.00323.528-0.069-0.0690.0000.0000.0000.000
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