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: 4G3GN

Calculation Name: 6SWC-A-Other547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-guanylate ester | [(2~{r},3~{r},4~{r},5~{r})-5-(4-acetamido-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate | n(4)-acetylcytidine-5'-monophosphate | 6n-dimethyladenosine-5'-monophoshate | 5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate) | n6-methyladenosine-5'-monophosphate | pseudouridine-5'-monophosphate | 5-methylcytidine-5'-monophosphate | 5-methyluridine 5'-monophosphate | [(2~{r},3~{s},4~{r},5~{s})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate | 3-methyluridine-5'-monophoshate | 4-thiouridine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | 2'-o-methyladenosine 5'-(dihydrogen phosphate)

Ligand 3-letter code: GNP | LHH | 4AC | MA6 | 5HM | 6MZ | PSU | 5MC | 5MU | B8H | UR3 | 4SU | H2U | OMC | A2M

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6SWC

Chain ID: A

ChEMBL ID:

UniProt ID: Q9V138

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 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1999954.364035
FMO2-HF: Nuclear repulsion 1925159.272735
FMO2-HF: Total energy -74795.0913
FMO2-MP2: Total energy -75016.761431


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:11:LYS)


Summations of interaction energy for fragment #1(A:11:LYS)
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.
383.979388.0492.126-1.88-4.316-0.007
Interaction energy analysis for fragmet #1(A:11:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.780 / q_NPA : 1.867
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].
3A13LYS10.9810.9902.264107.239110.8092.126-1.785-3.912-0.007
4A14TRP00.0130.0094.04111.61512.1150.000-0.095-0.4040.000
5A15LYS10.9180.9485.12074.69974.6990.0000.0000.0000.000
6A16LEU00.0160.0195.8544.0784.0780.0000.0000.0000.000
7A17LYS10.7680.8837.96768.34168.3410.0000.0000.0000.000
8A18GLN00.0140.02311.0442.7912.7910.0000.0000.0000.000
9A19TRP00.001-0.02112.549-0.004-0.0040.0000.0000.0000.000
10A20TYR00.0170.01716.6232.0422.0420.0000.0000.0000.000
11A21VAL00.0360.01219.963-0.504-0.5040.0000.0000.0000.000
12A22ILE0-0.037-0.00821.6900.3060.3060.0000.0000.0000.000
13A23TYR00.0110.02324.9300.3780.3780.0000.0000.0000.000
14A24ALA0-0.0310.00228.747-0.117-0.1170.0000.0000.0000.000
15A25PRO0-0.030-0.02531.3750.1540.1540.0000.0000.0000.000
16A26ASP-1-0.834-0.91434.285-17.139-17.1390.0000.0000.0000.000
17A27PHE0-0.060-0.04237.3050.1930.1930.0000.0000.0000.000
18A28PHE0-0.060-0.04435.7610.3620.3620.0000.0000.0000.000
19A29GLY00.0290.03237.1200.0380.0380.0000.0000.0000.000
20A30GLY00.000-0.00133.540-0.387-0.3870.0000.0000.0000.000
21A31VAL00.0090.01031.6250.1020.1020.0000.0000.0000.000
22A32GLU-1-0.873-0.94726.501-20.896-20.8960.0000.0000.0000.000
23A33VAL0-0.076-0.03925.9590.3250.3250.0000.0000.0000.000
24A34GLY00.0090.00522.670-0.761-0.7610.0000.0000.0000.000
25A35LEU00.0350.02318.4870.0270.0270.0000.0000.0000.000
26A36THR0-0.042-0.03917.222-0.328-0.3280.0000.0000.0000.000
27A37PRO0-0.0220.01912.1650.0470.0470.0000.0000.0000.000
28A38ALA0-0.031-0.02113.4710.3130.3130.0000.0000.0000.000
29A39ASP-1-0.833-0.8969.955-61.040-61.0400.0000.0000.0000.000
30A40ASP-1-0.762-0.88013.028-38.669-38.6690.0000.0000.0000.000
31A41PRO00.0420.00915.959-0.169-0.1690.0000.0000.0000.000
32A42GLU-1-0.855-0.91918.811-27.018-27.0180.0000.0000.0000.000
33A43LYS10.8030.89512.23543.44443.4440.0000.0000.0000.000
34A44VAL0-0.118-0.07118.299-0.362-0.3620.0000.0000.0000.000
35A45LEU00.0910.04920.6120.9290.9290.0000.0000.0000.000
36A46ASN00.0210.00123.2630.7440.7440.0000.0000.0000.000
37A47ARG10.8240.91415.45435.24735.2470.0000.0000.0000.000
38A48VAL0-0.033-0.02423.2111.0451.0450.0000.0000.0000.000
39A49VAL00.0400.03023.948-0.907-0.9070.0000.0000.0000.000
40A50GLU-1-0.875-0.93525.516-19.305-19.3050.0000.0000.0000.000
41A51VAL00.0900.05226.945-0.594-0.5940.0000.0000.0000.000
42A52THR0-0.064-0.04829.5250.7920.7920.0000.0000.0000.000
43A53LEU00.0330.00332.648-0.140-0.1400.0000.0000.0000.000
44A54LYS10.9170.96534.31917.34117.3410.0000.0000.0000.000
45A55ASP-1-0.865-0.93829.809-19.906-19.9060.0000.0000.0000.000
46A56ILE0-0.0160.00132.400-0.242-0.2420.0000.0000.0000.000
47A57THR0-0.035-0.02134.8960.5330.5330.0000.0000.0000.000
48A58GLY0-0.0060.00536.7800.3840.3840.0000.0000.0000.000
49A59ASP-1-0.831-0.91338.014-14.479-14.4790.0000.0000.0000.000
50A60PHE0-0.015-0.03538.378-0.256-0.2560.0000.0000.0000.000
51A61LEU0-0.015-0.00239.940-0.187-0.1870.0000.0000.0000.000
52A62LYS10.8690.95040.07114.11014.1100.0000.0000.0000.000
53A63GLY00.0560.03936.244-0.371-0.3710.0000.0000.0000.000
54A64HIS0-0.084-0.03635.499-0.287-0.2870.0000.0000.0000.000
55A65VAL0-0.012-0.01937.2280.0680.0680.0000.0000.0000.000
56A66LYS10.8790.95731.21418.64418.6440.0000.0000.0000.000
57A67LEU00.0460.02332.7750.5370.5370.0000.0000.0000.000
58A68TYR0-0.130-0.09229.327-0.202-0.2020.0000.0000.0000.000
59A69PHE00.0610.02828.9400.7500.7500.0000.0000.0000.000
60A70GLN0-0.025-0.01427.285-1.101-1.1010.0000.0000.0000.000
61A71VAL00.0070.00623.7450.6710.6710.0000.0000.0000.000
62A72TYR0-0.028-0.01327.0950.1170.1170.0000.0000.0000.000
63A73ASP-1-0.823-0.91127.959-21.398-21.3980.0000.0000.0000.000
64A74VAL0-0.018-0.01322.157-0.419-0.4190.0000.0000.0000.000
65A75LYS10.9541.00025.12319.45019.4500.0000.0000.0000.000
66A76GLY00.0190.01223.7070.2910.2910.0000.0000.0000.000
67A77GLN0-0.020-0.02719.1780.3570.3570.0000.0000.0000.000
68A78ASN0-0.004-0.00222.8250.5470.5470.0000.0000.0000.000
69A79ALA00.0060.00623.5250.1020.1020.0000.0000.0000.000
70A80TYR00.0430.02125.6300.3370.3370.0000.0000.0000.000
71A81THR0-0.029-0.04527.567-0.146-0.1460.0000.0000.0000.000
72A82LYS10.9280.97430.17817.74017.7400.0000.0000.0000.000
73A83PHE00.0030.00232.161-0.410-0.4100.0000.0000.0000.000
74A84LYS10.9550.98129.99520.14920.1490.0000.0000.0000.000
75A85GLY0-0.002-0.02234.0950.3250.3250.0000.0000.0000.000
76A86MET0-0.0020.02635.045-0.356-0.3560.0000.0000.0000.000
77A87LYS10.8780.93031.80119.10719.1070.0000.0000.0000.000
78A88LEU00.0690.05236.130-0.225-0.2250.0000.0000.0000.000
79A89ALA00.0050.00835.606-0.447-0.4470.0000.0000.0000.000
80A90ARG10.9470.95233.52918.18618.1860.0000.0000.0000.000
81A91SER00.0190.00936.9460.2840.2840.0000.0000.0000.000
82A92TYR00.0940.04938.7120.4280.4280.0000.0000.0000.000
83A93ILE00.0460.00940.6320.3570.3570.0000.0000.0000.000
84A94ARG10.9030.95838.49115.69615.6960.0000.0000.0000.000
85A95SER00.0350.01743.1370.2280.2280.0000.0000.0000.000
86A96LEU0-0.038-0.00145.3540.3360.3360.0000.0000.0000.000
87A97VAL00.0000.00546.9380.3500.3500.0000.0000.0000.000
88A98ARG10.9330.97247.18012.73912.7390.0000.0000.0000.000
89A99ARG11.0340.99751.27211.29711.2970.0000.0000.0000.000
90A100ARG10.9080.94554.37610.26210.2620.0000.0000.0000.000
91A101THR00.0120.01053.0710.1230.1230.0000.0000.0000.000
92A102THR0-0.007-0.01555.029-0.005-0.0050.0000.0000.0000.000
93A103ARG10.8760.93346.02013.20213.2020.0000.0000.0000.000
94A104ILE00.0510.02952.1100.0950.0950.0000.0000.0000.000
95A105ASP-1-0.767-0.85147.275-13.697-13.6970.0000.0000.0000.000
96A106GLY00.0530.03349.2220.3140.3140.0000.0000.0000.000
97A107ILE0-0.038-0.01845.238-0.340-0.3400.0000.0000.0000.000
98A108PHE00.0420.02347.5130.2240.2240.0000.0000.0000.000
99A109ASN00.0050.01345.822-0.684-0.6840.0000.0000.0000.000
100A110ILE00.0330.01646.7820.3090.3090.0000.0000.0000.000
101A111THR00.0590.02547.010-0.472-0.4720.0000.0000.0000.000
102A112THR0-0.0060.00146.3320.0450.0450.0000.0000.0000.000
103A113LYS10.9210.94948.81811.80211.8020.0000.0000.0000.000
104A114ASP-1-0.831-0.91245.439-13.790-13.7900.0000.0000.0000.000
105A115GLY00.0700.04746.611-0.117-0.1170.0000.0000.0000.000
106A116TYR0-0.103-0.05939.383-0.051-0.0510.0000.0000.0000.000
107A117LYS10.9830.99742.81014.64014.6400.0000.0000.0000.000
108A118LEU00.006-0.00542.070-0.544-0.5440.0000.0000.0000.000
109A119ARG10.8480.91642.14914.98614.9860.0000.0000.0000.000
110A120VAL00.0370.02442.468-0.407-0.4070.0000.0000.0000.000
111A121MET0-0.059-0.03941.0300.0640.0640.0000.0000.0000.000
112A122ALA00.0410.02744.850-0.220-0.2200.0000.0000.0000.000
113A123MET0-0.055-0.01445.510-0.036-0.0360.0000.0000.0000.000
114A124VAL00.0720.03348.8510.0260.0260.0000.0000.0000.000
115A125ILE0-0.035-0.01248.572-0.036-0.0360.0000.0000.0000.000
116A126ALA00.0560.04053.1500.1510.1510.0000.0000.0000.000
117A127ALA00.0350.00956.031-0.147-0.1470.0000.0000.0000.000
118A128ARG10.9400.96758.5119.8499.8490.0000.0000.0000.000
119A129ARG10.9310.98158.37910.34610.3460.0000.0000.0000.000
120A130ILE00.0410.03358.8320.1480.1480.0000.0000.0000.000
121A131GLN00.0640.03361.757-0.097-0.0970.0000.0000.0000.000
122A132THR00.0720.01559.654-0.019-0.0190.0000.0000.0000.000
123A133SER0-0.0070.00061.424-0.150-0.1500.0000.0000.0000.000
124A134GLN00.0530.01462.973-0.035-0.0350.0000.0000.0000.000
125A135GLU-1-0.892-0.93656.514-11.347-11.3470.0000.0000.0000.000
126A136ARG10.9330.95658.45410.05210.0520.0000.0000.0000.000
127A137ALA00.0320.02759.587-0.075-0.0750.0000.0000.0000.000
128A138ILE00.0220.01456.279-0.061-0.0610.0000.0000.0000.000
129A139ARG10.8200.88653.32511.48611.4860.0000.0000.0000.000
130A140LYS10.8750.92655.93110.06310.0630.0000.0000.0000.000
131A141ILE00.0710.03757.915-0.053-0.0530.0000.0000.0000.000
132A142MET0-0.081-0.03551.169-0.085-0.0850.0000.0000.0000.000
133A143GLN00.0010.00753.959-0.127-0.1270.0000.0000.0000.000
134A144GLU-1-0.847-0.90655.007-10.509-10.5090.0000.0000.0000.000
135A145ILE00.0250.00254.627-0.013-0.0130.0000.0000.0000.000
136A146ILE0-0.062-0.02249.307-0.192-0.1920.0000.0000.0000.000
137A147TYR0-0.020-0.03051.762-0.108-0.1080.0000.0000.0000.000
138A148LYS10.8920.94754.24911.16711.1670.0000.0000.0000.000
139A149LYS10.8180.91251.36512.08912.0890.0000.0000.0000.000
140A150ALA0-0.043-0.02550.360-0.192-0.1920.0000.0000.0000.000
141A151GLU-1-0.886-0.91951.581-11.863-11.8630.0000.0000.0000.000
142A152GLU-1-0.857-0.92954.164-11.510-11.5100.0000.0000.0000.000
143A153LEU0-0.0020.00949.297-0.096-0.0960.0000.0000.0000.000
144A154ASN0-0.019-0.02646.7750.0420.0420.0000.0000.0000.000
145A155PHE00.0150.01138.224-0.092-0.0920.0000.0000.0000.000
146A156LYS10.9480.96142.08313.60213.6020.0000.0000.0000.000
147A157ASP-1-0.919-0.94943.121-13.293-13.2930.0000.0000.0000.000
148A158PHE00.0140.00545.243-0.061-0.0610.0000.0000.0000.000
149A159VAL0-0.026-0.02439.5460.0100.0100.0000.0000.0000.000
150A160LEU00.0200.02941.588-0.149-0.1490.0000.0000.0000.000
151A161GLU-1-0.837-0.94943.291-12.557-12.5570.0000.0000.0000.000
152A162ALA0-0.035-0.01544.0230.1260.1260.0000.0000.0000.000
153A163VAL0-0.065-0.03438.8880.0330.0330.0000.0000.0000.000
154A164ASN0-0.0100.00742.310-0.046-0.0460.0000.0000.0000.000
155A165GLY00.0080.00844.2710.1070.1070.0000.0000.0000.000
156A166LYS10.9120.94946.97112.66712.6670.0000.0000.0000.000
157A167ILE00.0770.04348.0210.2370.2370.0000.0000.0000.000
158A168ALA0-0.035-0.01448.8970.2000.2000.0000.0000.0000.000
159A169ALA0-0.016-0.02050.9330.1990.1990.0000.0000.0000.000
160A170GLU-1-0.851-0.90053.840-11.287-11.2870.0000.0000.0000.000
161A171ILE00.0350.00651.2640.1870.1870.0000.0000.0000.000
162A172ALA0-0.067-0.04354.4820.1950.1950.0000.0000.0000.000
163A173LYS10.9110.97256.35610.52010.5200.0000.0000.0000.000
164A174GLU-1-0.834-0.93559.519-10.320-10.3200.0000.0000.0000.000
165A175ALA0-0.009-0.00657.7370.1320.1320.0000.0000.0000.000
166A176LYS10.9460.97459.67510.39810.3980.0000.0000.0000.000
167A177LYS10.9050.96161.1249.7169.7160.0000.0000.0000.000
168A178ILE0-0.0280.00761.5040.1420.1420.0000.0000.0000.000
169A179TYR00.033-0.00361.0080.0920.0920.0000.0000.0000.000
170A180PRO00.0000.01061.210-0.171-0.1710.0000.0000.0000.000
171A181LEU0-0.019-0.00155.304-0.070-0.0700.0000.0000.0000.000
172A182LYS10.9150.95052.54011.79011.7900.0000.0000.0000.000
173A183LYS10.8780.93647.08712.93912.9390.0000.0000.0000.000
174A184ALA00.0710.04950.847-0.034-0.0340.0000.0000.0000.000
175A185GLU-1-0.887-0.96545.164-13.341-13.3410.0000.0000.0000.000
176A186ILE00.0540.02643.3020.0810.0810.0000.0000.0000.000
177A187ARG10.7830.85441.54913.80813.8080.0000.0000.0000.000
178A188LYS10.8980.92436.09316.35416.3540.0000.0000.0000.000
179A189ILE00.0470.03439.2820.4200.4200.0000.0000.0000.000
180A190LYS10.8910.94937.43216.01316.0130.0000.0000.0000.000
181A191VAL00.0780.04936.3320.5100.5100.0000.0000.0000.000
182A192LEU0-0.120-0.08237.987-0.329-0.3290.0000.0000.0000.000
183A193GLY0-0.021-0.01339.113-0.200-0.2000.0000.0000.0000.000
184A194GLU-1-0.766-0.85837.144-16.627-16.6270.0000.0000.0000.000
185A195PRO0-0.026-0.00640.3300.1790.1790.0000.0000.0000.000
186A196GLU-1-0.936-0.96541.563-14.277-14.2770.0000.0000.0000.000
187A197VAL0-0.065-0.02542.859-0.008-0.0080.0000.0000.0000.000
188A198ALA-1-0.925-0.95839.938-16.163-16.1630.0000.0000.0000.000