FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: QL7LY

Calculation Name: 1H0H-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide | guanylate-o'-phosphoric acid mono-(2-amino-5,6-dimercapto-4-oxo-3,5,6,7,8a,9,10,10a-octahydro-4h-8-oxa-1,3,9,10-tetraaza-anthracen-7-ylmethyl) ester | iron/sulfur cluster | 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid | selenocysteine | calcium ion | tungsten ion | unknown atom or ion

Ligand 3-letter code: MGD | 2MD | SF4 | EPE | SEC | CA | W | UNX

Ligand of Interest (LOI):

PDB ID: 1H0H

Chain ID: B

ChEMBL ID:

UniProt ID: Q934F5

Base Structure: X-ray

Registration Date: 2025-10-05

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
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 -2544252.911646
FMO2-HF: Nuclear repulsion 2456168.260364
FMO2-HF: Total energy -88084.651282
FMO2-MP2: Total energy -88326.624081


3D Structure
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:1:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-324.103-313.88315.431-12.759-12.889-0.061
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.926
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].
3A3GLY00.0630.0383.8252.2143.476-0.017-0.577-0.6670.000
96A96ASP-1-0.915-0.9464.795-54.018-53.863-0.001-0.028-0.1260.000
97A97ALA0-0.0010.0012.758-19.233-16.6300.364-1.298-1.668-0.013
98A98THR0-0.089-0.0962.161-33.374-30.6707.075-5.770-4.008-0.051
99A99GLY00.0460.0142.795-10.439-8.3950.666-1.521-1.189-0.015
100A100CYS0-0.102-0.0283.3897.5187.4360.0270.066-0.0110.000
165A165ASP-1-0.834-0.8963.418-74.394-73.5040.006-0.472-0.424-0.003
166A166LEU0-0.017-0.0024.0406.2386.8120.003-0.172-0.4050.000
167A167SER00.0480.0205.7663.5023.643-0.001-0.009-0.1300.000
196A196ARG10.9160.9602.10837.54137.4707.309-2.978-4.2610.021
4A4PHE0-0.035-0.0407.1760.9930.9930.0000.0000.0000.000
5A5PHE00.0420.03210.8940.4710.4710.0000.0000.0000.000
6A6VAL0-0.015-0.01814.0180.5250.5250.0000.0000.0000.000
7A7ASP-1-0.739-0.82817.114-13.234-13.2340.0000.0000.0000.000
8A8THR0-0.034-0.05320.4690.6560.6560.0000.0000.0000.000
9A9THR0-0.048-0.04923.2040.6220.6220.0000.0000.0000.000
10A10ARG10.8750.94521.97713.72913.7290.0000.0000.0000.000
11A11CYS0-0.0400.00723.6990.0090.0090.0000.0000.0000.000
12A12THR00.0310.00425.3120.2770.2770.0000.0000.0000.000
13A13ALA00.0460.01827.2230.3030.3030.0000.0000.0000.000
14A14CYS0-0.059-0.02126.5540.0250.0250.0000.0000.0000.000
15A15ARG10.8760.93925.62410.37810.3780.0000.0000.0000.000
16A16GLY00.0520.03824.893-0.058-0.0580.0000.0000.0000.000
17A17CYS-1-0.849-0.89719.863-14.446-14.4460.0000.0000.0000.000
18A18GLN00.049-0.01121.058-0.467-0.4670.0000.0000.0000.000
19A19VAL0-0.036-0.01623.172-0.015-0.0150.0000.0000.0000.000
20A20ALA00.0020.00021.2010.0090.0090.0000.0000.0000.000
21A21CYS0-0.008-0.00118.852-0.674-0.6740.0000.0000.0000.000
22A22LYS10.8500.94220.20811.31511.3150.0000.0000.0000.000
23A23GLN0-0.019-0.01523.335-0.369-0.3690.0000.0000.0000.000
24A24TRP0-0.037-0.04516.9500.4740.4740.0000.0000.0000.000
25A25HIS10.7890.85915.97616.88816.8880.0000.0000.0000.000
26A26GLY00.0170.03121.1750.2400.2400.0000.0000.0000.000
27A27ASN0-0.063-0.02521.5190.3420.3420.0000.0000.0000.000
28A28PRO00.0070.01325.3290.1970.1970.0000.0000.0000.000
29A29ALA0-0.012-0.01628.401-0.254-0.2540.0000.0000.0000.000
30A30THR00.013-0.00129.036-0.104-0.1040.0000.0000.0000.000
31A31PRO0-0.012-0.01631.9090.0500.0500.0000.0000.0000.000
32A32THR0-0.040-0.01132.397-0.198-0.1980.0000.0000.0000.000
33A33GLU-1-0.898-0.93835.433-7.479-7.4790.0000.0000.0000.000
34A34ASN0-0.047-0.02937.000-0.169-0.1690.0000.0000.0000.000
35A35THR00.0300.01337.1100.1660.1660.0000.0000.0000.000
36A36GLY00.0130.01439.6780.1060.1060.0000.0000.0000.000
37A37PHE00.0030.00834.619-0.075-0.0750.0000.0000.0000.000
38A38HIS00.0420.01634.030-0.101-0.1010.0000.0000.0000.000
39A39GLN00.0340.02928.943-0.220-0.2200.0000.0000.0000.000
40A40ASN00.030-0.01430.2240.1660.1660.0000.0000.0000.000
41A41PRO0-0.034-0.01727.629-0.223-0.2230.0000.0000.0000.000
42A42PRO00.0270.01829.168-0.212-0.2120.0000.0000.0000.000
43A43ASP-1-0.728-0.84425.687-11.741-11.7410.0000.0000.0000.000
44A44PHE0-0.0200.01019.5410.0880.0880.0000.0000.0000.000
45A45ASN00.0310.01124.3950.1590.1590.0000.0000.0000.000
46A46PHE00.0360.02723.546-0.410-0.4100.0000.0000.0000.000
47A47HIS00.0360.01523.360-0.606-0.6060.0000.0000.0000.000
48A48THR0-0.084-0.07423.6310.0180.0180.0000.0000.0000.000
49A49TYR00.0490.02017.900-0.156-0.1560.0000.0000.0000.000
50A50LYS10.7600.84917.16415.98515.9850.0000.0000.0000.000
51A51LEU0-0.035-0.00720.3070.5600.5600.0000.0000.0000.000
52A52VAL0-0.038-0.02723.012-0.308-0.3080.0000.0000.0000.000
53A53ARG10.7840.88622.81512.72712.7270.0000.0000.0000.000
54A54MET0-0.098-0.05926.748-0.181-0.1810.0000.0000.0000.000
55A55HIS0-0.0010.00527.9310.4800.4800.0000.0000.0000.000
56A56GLU-1-0.946-0.96831.620-8.367-8.3670.0000.0000.0000.000
57A57GLN0-0.036-0.03031.4050.2360.2360.0000.0000.0000.000
58A58GLU-1-0.934-0.96235.259-7.399-7.3990.0000.0000.0000.000
59A59ILE0-0.050-0.03632.842-0.125-0.1250.0000.0000.0000.000
60A60ASP-1-0.918-0.95937.037-8.294-8.2940.0000.0000.0000.000
61A61GLY0-0.038-0.00839.7010.1560.1560.0000.0000.0000.000
62A62ARG10.8870.93439.3767.6367.6360.0000.0000.0000.000
63A63ILE00.0020.01437.628-0.122-0.1220.0000.0000.0000.000
64A64ASP-1-0.847-0.92832.820-9.699-9.6990.0000.0000.0000.000
65A65TRP0-0.024-0.03032.6770.1140.1140.0000.0000.0000.000
66A66LEU0-0.035-0.00128.315-0.319-0.3190.0000.0000.0000.000
67A67PHE00.012-0.00726.415-0.024-0.0240.0000.0000.0000.000
68A68PHE00.015-0.00319.515-0.336-0.3360.0000.0000.0000.000
69A69PRO0-0.018-0.00419.8780.1880.1880.0000.0000.0000.000
70A70ASP-1-0.705-0.83019.173-15.446-15.4460.0000.0000.0000.000
71A71GLN00.047-0.02513.7670.8150.8150.0000.0000.0000.000
72A72CYS-1-0.791-0.78613.107-20.494-20.4940.0000.0000.0000.000
73A73ARG10.8800.92112.61115.68215.6820.0000.0000.0000.000
74A74HIS0-0.012-0.1277.802-3.050-3.0500.0000.0000.0000.000
75A75CYS0-0.018-0.0028.062-1.823-1.8230.0000.0000.0000.000
76A76ILE00.0110.0036.431-1.657-1.6570.0000.0000.0000.000
77A77ALA00.0090.0048.051-1.375-1.3750.0000.0000.0000.000
78A78PRO0-0.013-0.0019.5901.5391.5390.0000.0000.0000.000
79A79PRO00.0480.03112.3780.4870.4870.0000.0000.0000.000
80A80CYS0-0.0090.00915.2950.2600.2600.0000.0000.0000.000
81A81LYS10.8180.87812.35419.53219.5320.0000.0000.0000.000
82A82ALA0-0.0010.00115.5820.5940.5940.0000.0000.0000.000
83A83THR0-0.031-0.01717.1580.8660.8660.0000.0000.0000.000
84A84ALA00.0380.00918.5790.5520.5520.0000.0000.0000.000
85A85ASP-1-0.794-0.88716.077-17.232-17.2320.0000.0000.0000.000
86A86MET0-0.086-0.03119.6420.4370.4370.0000.0000.0000.000
87A87GLU-1-0.854-0.91122.703-10.685-10.6850.0000.0000.0000.000
88A88ASP-1-0.783-0.88221.706-13.665-13.6650.0000.0000.0000.000
89A89GLU-1-0.935-0.95417.692-16.038-16.0380.0000.0000.0000.000
90A90SER0-0.172-0.11716.837-1.152-1.1520.0000.0000.0000.000
91A91ALA00.0350.02418.614-0.092-0.0920.0000.0000.0000.000
92A92ILE0-0.0070.00113.669-0.183-0.1830.0000.0000.0000.000
93A93ILE0-0.0070.00110.968-0.117-0.1170.0000.0000.0000.000
94A94HIS00.001-0.0126.909-0.282-0.2820.0000.0000.0000.000
95A95ASP-1-0.831-0.8846.145-41.851-41.8510.0000.0000.0000.000
101A101VAL00.0280.0317.0651.2181.2180.0000.0000.0000.000
102A102LEU00.027-0.00210.0021.6371.6370.0000.0000.0000.000
103A103PHE00.0490.01112.4680.6820.6820.0000.0000.0000.000
104A104THR0-0.027-0.02016.1070.2130.2130.0000.0000.0000.000
105A105PRO00.014-0.01218.4850.4960.4960.0000.0000.0000.000
106A106LYS10.9230.96320.54014.94314.9430.0000.0000.0000.000
107A107THR00.0330.01619.7140.4910.4910.0000.0000.0000.000
108A108LYS10.8550.91822.44610.62610.6260.0000.0000.0000.000
109A109ASP-1-0.944-0.97425.464-10.914-10.9140.0000.0000.0000.000
110A110LEU0-0.0310.01421.4650.0750.0750.0000.0000.0000.000
111A111GLU-1-0.974-0.99226.148-9.376-9.3760.0000.0000.0000.000
112A112ASP-1-0.833-0.88126.895-10.580-10.5800.0000.0000.0000.000
113A113TYR0-0.003-0.02724.647-0.552-0.5520.0000.0000.0000.000
114A114GLU-1-0.925-0.96424.718-9.974-9.9740.0000.0000.0000.000
115A115SER0-0.026-0.03324.811-0.167-0.1670.0000.0000.0000.000
116A116VAL0-0.030-0.01719.554-0.493-0.4930.0000.0000.0000.000
117A117ILE0-0.063-0.03620.480-0.653-0.6530.0000.0000.0000.000
118A118SER0-0.034-0.03421.846-0.343-0.3430.0000.0000.0000.000
119A119ALA00.0080.02119.924-0.027-0.0270.0000.0000.0000.000
120A120CYS0-0.103-0.03116.672-0.896-0.8960.0000.0000.0000.000
121A121PRO00.0300.00417.2940.4600.4600.0000.0000.0000.000
122A122TYR0-0.055-0.07615.467-0.141-0.1410.0000.0000.0000.000
123A123ASP-1-0.820-0.87619.630-11.840-11.8400.0000.0000.0000.000
124A124VAL00.000-0.00716.8190.0610.0610.0000.0000.0000.000
125A125PRO0-0.041-0.02117.9090.0980.0980.0000.0000.0000.000
126A126ARG10.7520.84320.19212.76712.7670.0000.0000.0000.000
127A127LYS10.9000.95823.3209.7829.7820.0000.0000.0000.000
128A128VAL0-0.055-0.00625.8300.2150.2150.0000.0000.0000.000
129A129ALA0-0.0020.00027.9220.1470.1470.0000.0000.0000.000
130A130GLU-1-0.892-0.96731.646-9.383-9.3830.0000.0000.0000.000
131A131SER0-0.074-0.04029.2450.0200.0200.0000.0000.0000.000
132A132ASN00.038-0.00327.0370.1310.1310.0000.0000.0000.000
133A133GLN0-0.0370.00423.485-0.523-0.5230.0000.0000.0000.000
134A134MET0-0.0100.00221.2710.2670.2670.0000.0000.0000.000
135A135ALA0-0.041-0.01019.355-0.532-0.5320.0000.0000.0000.000
136A136LYS10.7970.84712.06721.42921.4290.0000.0000.0000.000
137A137CYS-1-0.865-0.80513.569-21.751-21.7510.0000.0000.0000.000
138A138ASP-1-0.726-0.84112.994-20.549-20.5490.0000.0000.0000.000
139A139MET00.008-0.0335.787-3.039-3.0390.0000.0000.0000.000
140A140CYS0-0.062-0.02110.572-0.098-0.0980.0000.0000.0000.000
141A141ILE00.0710.0338.246-0.827-0.8270.0000.0000.0000.000
142A142ASP-1-0.750-0.84610.620-20.752-20.7520.0000.0000.0000.000
143A143ARG10.8020.90313.08818.28118.2810.0000.0000.0000.000
144A144ILE0-0.040-0.0116.438-0.551-0.5510.0000.0000.0000.000
145A145THR0-0.044-0.0338.505-2.294-2.2940.0000.0000.0000.000
146A146ASN0-0.092-0.04610.2261.7571.7570.0000.0000.0000.000
147A147GLY00.0020.00611.9271.4861.4860.0000.0000.0000.000
148A148LEU0-0.058-0.01812.9081.2161.2160.0000.0000.0000.000
149A149ARG11.0021.00112.04517.07817.0780.0000.0000.0000.000
150A150PRO00.0800.04710.7211.9421.9420.0000.0000.0000.000
151A151ALA00.0080.00313.4380.9410.9410.0000.0000.0000.000
152A152CYS0-0.012-0.00515.6170.3680.3680.0000.0000.0000.000
153A153VAL00.0230.00313.0940.6830.6830.0000.0000.0000.000
154A154THR0-0.120-0.06916.3650.4100.4100.0000.0000.0000.000
155A155SER0-0.031-0.02918.3520.8700.8700.0000.0000.0000.000
156A156CYS0-0.0490.02119.8640.7680.7680.0000.0000.0000.000
157A157PRO00.0170.00921.640-0.242-0.2420.0000.0000.0000.000
158A158THR0-0.011-0.02923.8790.0950.0950.0000.0000.0000.000
159A159GLY00.0430.02920.1220.1240.1240.0000.0000.0000.000
160A160ALA0-0.0090.00420.224-0.263-0.2630.0000.0000.0000.000
161A161MET00.0270.03115.315-0.267-0.2670.0000.0000.0000.000
162A162ASN0-0.062-0.03514.6770.4730.4730.0000.0000.0000.000
163A163PHE00.037-0.0217.117-0.656-0.6560.0000.0000.0000.000
164A164GLY00.0350.0208.3582.7272.7270.0000.0000.0000.000
168A168GLU-1-0.941-0.9678.094-28.861-28.8610.0000.0000.0000.000
169A169MET0-0.063-0.0189.2663.9703.9700.0000.0000.0000.000
170A170GLU-1-0.802-0.9087.819-28.084-28.0840.0000.0000.0000.000
171A171ALA0-0.0170.00111.3412.3342.3340.0000.0000.0000.000
172A172MET0-0.033-0.01513.6511.7301.7300.0000.0000.0000.000
173A173ALA00.0110.00414.2671.4971.4970.0000.0000.0000.000
174A174SER0-0.003-0.01615.0511.5141.5140.0000.0000.0000.000
175A175ALA0-0.042-0.01717.4771.0741.0740.0000.0000.0000.000
176A176ARG10.8040.87719.05713.98213.9820.0000.0000.0000.000
177A177LEU0-0.0020.00219.9010.7820.7820.0000.0000.0000.000
178A178ALA0-0.032-0.02821.5870.7420.7420.0000.0000.0000.000
179A179GLU-1-0.914-0.94123.467-12.159-12.1590.0000.0000.0000.000
180A180ILE0-0.008-0.00524.2640.5850.5850.0000.0000.0000.000
181A181LYS10.7810.87924.49911.90811.9080.0000.0000.0000.000
182A182ALA0-0.027-0.00827.2540.2870.2870.0000.0000.0000.000
183A183ALA0-0.027-0.01030.5840.3120.3120.0000.0000.0000.000
184A184TYR0-0.0080.00028.3130.1940.1940.0000.0000.0000.000
185A185SER00.0530.01528.523-0.341-0.3410.0000.0000.0000.000
186A186ASP-1-0.898-0.92928.871-9.940-9.9400.0000.0000.0000.000
187A187ALA0-0.031-0.00324.741-0.227-0.2270.0000.0000.0000.000
188A188LYS10.9070.95121.52213.24713.2470.0000.0000.0000.000
189A189LEU00.0420.02315.384-0.021-0.0210.0000.0000.0000.000
190A190CYS0-0.085-0.05117.4630.9100.9100.0000.0000.0000.000
191A191ASP-1-0.732-0.85415.717-16.241-16.2410.0000.0000.0000.000
192A192PRO0-0.026-0.02013.217-0.908-0.9080.0000.0000.0000.000
193A193ASP-1-0.891-0.93511.489-20.011-20.0110.0000.0000.0000.000
194A194ASP-1-0.912-0.94311.177-19.292-19.2920.0000.0000.0000.000
195A195VAL0-0.077-0.04210.371-1.076-1.0760.0000.0000.0000.000
197A197VAL0-0.074-0.0318.044-1.117-1.1170.0000.0000.0000.000
198A198ILE00.0450.0319.9111.8521.8520.0000.0000.0000.000
199A199PHE00.011-0.00513.4710.3600.3600.0000.0000.0000.000
200A200LEU0-0.0020.01017.1660.1090.1090.0000.0000.0000.000
201A201THR0-0.0080.00919.8850.1480.1480.0000.0000.0000.000
202A202ALA00.0250.00623.454-0.040-0.0400.0000.0000.0000.000
203A203HIS10.9190.96126.60710.61110.6110.0000.0000.0000.000
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