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

tag_button

FMODB ID: 1VYYZ

Calculation Name: 7OTC-g-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: g

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 156
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1419728.300484
FMO2-HF: Nuclear repulsion 1358538.72746
FMO2-HF: Total energy -61189.573024
FMO2-MP2: Total energy -61369.318031


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:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
211.924219.0313.515-4.957-5.664-0.049
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.907
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].
3A4ARG11.0111.0243.32334.81937.726-0.010-1.370-1.527-0.005
4A5ARG11.0161.0072.83958.48959.9510.053-0.400-1.114-0.002
5A6VAL00.0290.0132.238-37.896-35.4913.472-3.134-2.744-0.042
6A7ILE00.012-0.0013.6303.4423.7750.000-0.053-0.2790.000
7A8GLY00.0520.0295.8770.4050.4050.0000.0000.0000.000
8A9GLN0-0.029-0.0228.636-0.398-0.3980.0000.0000.0000.000
9A10ARG10.9800.9879.33226.27726.2770.0000.0000.0000.000
10A11LYS10.9470.97612.19022.27822.2780.0000.0000.0000.000
11A12ILE0-0.035-0.02615.627-0.580-0.5800.0000.0000.0000.000
12A13LEU00.0350.02618.5100.1350.1350.0000.0000.0000.000
13A14PRO00.0230.00922.084-0.114-0.1140.0000.0000.0000.000
14A15ASP-1-0.809-0.92924.351-10.439-10.4390.0000.0000.0000.000
15A16PRO0-0.033-0.01627.1190.1960.1960.0000.0000.0000.000
16A17LYS10.8120.92629.94110.59010.5900.0000.0000.0000.000
17A18PHE00.0340.00931.0880.2750.2750.0000.0000.0000.000
18A19GLY00.0080.02629.2680.0060.0060.0000.0000.0000.000
19A20SER00.0410.02026.721-0.297-0.2970.0000.0000.0000.000
20A21GLU-1-0.885-0.96221.084-13.249-13.2490.0000.0000.0000.000
21A22LEU0-0.050-0.01222.083-0.706-0.7060.0000.0000.0000.000
22A23LEU00.0990.04823.668-0.316-0.3160.0000.0000.0000.000
23A24ALA00.0460.03322.539-0.078-0.0780.0000.0000.0000.000
24A25LYS10.8520.91715.41218.12718.1270.0000.0000.0000.000
25A26PHE00.0410.00320.631-0.509-0.5090.0000.0000.0000.000
26A27VAL00.0270.02423.304-0.078-0.0780.0000.0000.0000.000
27A28ASN0-0.039-0.03519.2320.3390.3390.0000.0000.0000.000
28A29ILE0-0.091-0.04217.775-0.605-0.6050.0000.0000.0000.000
29A30LEU00.0200.01520.6570.0990.0990.0000.0000.0000.000
30A31MET0-0.077-0.01819.9490.4650.4650.0000.0000.0000.000
31A32VAL00.000-0.00122.202-0.580-0.5800.0000.0000.0000.000
32A33ASP-1-0.869-0.94423.442-11.414-11.4140.0000.0000.0000.000
33A34GLY00.0250.01822.6860.3340.3340.0000.0000.0000.000
34A35LYS10.8460.92423.59411.26611.2660.0000.0000.0000.000
35A36LYS10.9890.98722.54413.09713.0970.0000.0000.0000.000
36A37SER00.0280.00826.1840.0320.0320.0000.0000.0000.000
37A38THR00.0360.02929.7750.1650.1650.0000.0000.0000.000
38A39ALA00.0260.03026.9460.2470.2470.0000.0000.0000.000
39A40GLU-1-0.863-0.95526.948-11.144-11.1440.0000.0000.0000.000
40A41SER0-0.031-0.01730.0340.2740.2740.0000.0000.0000.000
41A42ILE0-0.012-0.01331.4890.1840.1840.0000.0000.0000.000
42A43VAL0-0.013-0.01128.4480.1480.1480.0000.0000.0000.000
43A44TYR00.0240.01631.339-0.049-0.0490.0000.0000.0000.000
44A45SER00.0230.00434.1930.1910.1910.0000.0000.0000.000
45A46ALA0-0.043-0.02933.1380.2060.2060.0000.0000.0000.000
46A47LEU00.0220.02832.1480.1160.1160.0000.0000.0000.000
47A48GLU-1-0.878-0.93835.510-7.806-7.8060.0000.0000.0000.000
48A49THR0-0.042-0.04338.4730.2080.2080.0000.0000.0000.000
49A50LEU0-0.001-0.00336.4620.2110.2110.0000.0000.0000.000
50A51ALA00.0210.04139.0710.1510.1510.0000.0000.0000.000
51A52GLN0-0.064-0.03840.5720.1580.1580.0000.0000.0000.000
52A53ARG10.9020.96039.2367.9717.9710.0000.0000.0000.000
53A54SER0-0.003-0.00840.3310.0490.0490.0000.0000.0000.000
54A55GLY00.0620.03141.7700.1710.1710.0000.0000.0000.000
55A56LYS10.8420.90541.2527.0207.0200.0000.0000.0000.000
56A57SER0-0.0110.00037.785-0.130-0.1300.0000.0000.0000.000
57A58GLU-1-0.868-0.95033.795-9.548-9.5480.0000.0000.0000.000
58A59LEU00.005-0.00133.116-0.199-0.1990.0000.0000.0000.000
59A60GLU-1-0.956-0.98033.125-8.674-8.6740.0000.0000.0000.000
60A61ALA00.0620.04934.741-0.151-0.1510.0000.0000.0000.000
61A62PHE0-0.027-0.03126.731-0.360-0.3600.0000.0000.0000.000
62A63GLU-1-0.940-0.96729.385-10.991-10.9910.0000.0000.0000.000
63A64VAL00.0880.03130.649-0.289-0.2890.0000.0000.0000.000
64A65ALA0-0.025-0.00332.268-0.121-0.1210.0000.0000.0000.000
65A66LEU0-0.060-0.03324.553-0.494-0.4940.0000.0000.0000.000
66A67GLU-1-0.997-1.01127.546-10.311-10.3110.0000.0000.0000.000
67A68ASN00.0020.01228.760-0.543-0.5430.0000.0000.0000.000
68A69VAL00.0090.00226.568-0.107-0.1070.0000.0000.0000.000
69A70ARG10.8740.94323.58611.20511.2050.0000.0000.0000.000
70A71PRO0-0.023-0.00220.9330.2600.2600.0000.0000.0000.000
71A72THR00.008-0.01122.116-0.445-0.4450.0000.0000.0000.000
72A73VAL00.0290.02921.344-0.402-0.4020.0000.0000.0000.000
73A74GLU-1-0.895-0.98216.650-17.329-17.3290.0000.0000.0000.000
74A75VAL0-0.014-0.00719.1430.6440.6440.0000.0000.0000.000
75A76LYS10.8700.97413.53917.73317.7330.0000.0000.0000.000
76A77SER0-0.012-0.03317.2320.2530.2530.0000.0000.0000.000
77A78ARG10.8660.94114.56917.67717.6770.0000.0000.0000.000
78A79ARG10.9961.02717.29415.96815.9680.0000.0000.0000.000
79A80VAL0-0.053-0.03617.886-0.809-0.8090.0000.0000.0000.000
80A81GLY00.012-0.00820.1860.0170.0170.0000.0000.0000.000
81A82GLY00.0100.01322.5620.4190.4190.0000.0000.0000.000
82A83SER00.0350.01924.0740.1540.1540.0000.0000.0000.000
83A84THR0-0.025-0.02121.285-0.597-0.5970.0000.0000.0000.000
84A85TYR00.0310.00621.2240.3270.3270.0000.0000.0000.000
85A86GLN00.0530.04820.755-1.118-1.1180.0000.0000.0000.000
86A87VAL00.0290.01819.1150.3720.3720.0000.0000.0000.000
87A88PRO0-0.0240.00619.583-0.756-0.7560.0000.0000.0000.000
88A89VAL00.0020.00315.952-0.028-0.0280.0000.0000.0000.000
89A90GLU-1-0.861-0.92818.952-13.207-13.2070.0000.0000.0000.000
90A91VAL0-0.089-0.04615.911-1.437-1.4370.0000.0000.0000.000
91A92ARG11.0020.9959.30626.40226.4020.0000.0000.0000.000
92A93PRO00.0890.01717.049-0.567-0.5670.0000.0000.0000.000
93A94VAL0-0.011-0.00213.8330.0660.0660.0000.0000.0000.000
94A95ARG10.9060.94812.34120.91420.9140.0000.0000.0000.000
95A96ARG10.8840.94315.83513.45313.4530.0000.0000.0000.000
96A97ASN00.1090.04219.5830.5040.5040.0000.0000.0000.000
97A98ALA0-0.035-0.01916.3140.2090.2090.0000.0000.0000.000
98A99LEU0-0.060-0.02217.844-0.003-0.0030.0000.0000.0000.000
99A100ALA00.0510.02919.2220.4100.4100.0000.0000.0000.000
100A101MET00.0280.03319.4990.2960.2960.0000.0000.0000.000
101A102ARG10.9310.96515.56117.10317.1030.0000.0000.0000.000
102A103TRP00.029-0.00621.6130.1370.1370.0000.0000.0000.000
103A104ILE00.0670.04124.2300.3980.3980.0000.0000.0000.000
104A105VAL0-0.0100.00723.6590.4250.4250.0000.0000.0000.000
105A106GLU-1-0.946-0.98924.652-10.872-10.8720.0000.0000.0000.000
106A107ALA00.0190.01226.5590.4030.4030.0000.0000.0000.000
107A108ALA00.0690.04129.4960.3880.3880.0000.0000.0000.000
108A109ARG10.8550.91527.77310.50510.5050.0000.0000.0000.000
109A110LYS10.8890.94329.80910.07210.0720.0000.0000.0000.000
110A111ARG10.7990.89732.4388.7588.7580.0000.0000.0000.000
111A112GLY0-0.0040.00235.2010.2190.2190.0000.0000.0000.000
112A113ASP-1-0.811-0.90537.178-7.563-7.5630.0000.0000.0000.000
113A114LYS10.9771.00339.0096.9066.9060.0000.0000.0000.000
114A115SER00.005-0.01038.394-0.080-0.0800.0000.0000.0000.000
115A116MET0-0.023-0.01530.797-0.127-0.1270.0000.0000.0000.000
116A117ALA00.0790.03033.890-0.215-0.2150.0000.0000.0000.000
117A118LEU0-0.0020.02035.497-0.060-0.0600.0000.0000.0000.000
118A119ARG10.8800.93533.6268.7488.7480.0000.0000.0000.000
119A120LEU0-0.025-0.01829.362-0.140-0.1400.0000.0000.0000.000
120A121ALA00.0530.02533.315-0.097-0.0970.0000.0000.0000.000
121A122ASN0-0.046-0.01736.2770.1190.1190.0000.0000.0000.000
122A123GLU-1-0.820-0.91331.991-9.384-9.3840.0000.0000.0000.000
123A124LEU0-0.020-0.00331.121-0.106-0.1060.0000.0000.0000.000
124A125SER0-0.033-0.00833.8220.0940.0940.0000.0000.0000.000
125A126ASP-1-0.749-0.87735.423-8.762-8.7620.0000.0000.0000.000
126A127ALA0-0.018-0.01432.2850.0150.0150.0000.0000.0000.000
127A128ALA00.0280.03034.289-0.043-0.0430.0000.0000.0000.000
128A129GLU-1-0.919-0.95836.439-7.752-7.7520.0000.0000.0000.000
129A130ASN0-0.031-0.02335.1620.1100.1100.0000.0000.0000.000
130A131LYS10.9580.98536.6277.8517.8510.0000.0000.0000.000
131A132GLY00.0300.01635.2180.0850.0850.0000.0000.0000.000
132A133THR0-0.030-0.02632.135-0.206-0.2060.0000.0000.0000.000
133A134ALA0-0.0050.00029.710-0.301-0.3010.0000.0000.0000.000
134A135VAL00.0800.04729.860-0.368-0.3680.0000.0000.0000.000
135A136LYS10.9170.97031.4259.5789.5780.0000.0000.0000.000
136A137LYS10.8390.92426.87910.60610.6060.0000.0000.0000.000
137A138ARG10.8340.94126.50311.07111.0710.0000.0000.0000.000
138A139GLU-1-0.868-0.94028.867-9.056-9.0560.0000.0000.0000.000
139A140ASP-1-0.882-0.92629.242-9.764-9.7640.0000.0000.0000.000
140A141VAL0-0.051-0.04224.346-0.145-0.1450.0000.0000.0000.000
141A142HIS00.0660.03626.896-0.503-0.5030.0000.0000.0000.000
142A143ARG10.9230.94528.9969.2369.2360.0000.0000.0000.000
143A144MET0-0.0200.00123.7660.0110.0110.0000.0000.0000.000
144A145ALA00.002-0.00425.516-0.167-0.1670.0000.0000.0000.000
145A146GLU-1-0.866-0.92226.819-10.207-10.2070.0000.0000.0000.000
146A147ALA00.0140.01629.8360.0430.0430.0000.0000.0000.000
147A148ASN0-0.019-0.02324.5690.1480.1480.0000.0000.0000.000
148A149LYS10.8600.91426.33910.38110.3810.0000.0000.0000.000
149A150ALA0-0.0040.01028.5190.0150.0150.0000.0000.0000.000
150A151PHE0-0.041-0.03724.663-0.084-0.0840.0000.0000.0000.000
151A152ALA0-0.018-0.00823.841-0.488-0.4880.0000.0000.0000.000
152A153HIS00.0380.03224.640-0.280-0.2800.0000.0000.0000.000
153A154TYR0-0.040-0.00624.2350.2300.2300.0000.0000.0000.000
154A155ARG10.9520.95522.13611.63011.6300.0000.0000.0000.000
155A156TRP0-0.098-0.06714.515-0.988-0.9880.0000.0000.0000.000
156A157LEU-1-0.838-0.89219.171-16.153-16.1530.0000.0000.0000.000