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: VYV91

Calculation Name: 2G3Y-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate

Ligand 3-letter code: GDP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2G3Y

Chain ID: A

ChEMBL ID:

UniProt ID: P55040

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
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 172
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1824120.561147
FMO2-HF: Nuclear repulsion 1754477.851501
FMO2-HF: Total energy -69642.709645
FMO2-MP2: Total energy -69841.887845


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:73:ASN)


Summations of interaction energy for fragment #1(A:73:ASN)
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.
-163.808-159.0452.89-3.183-4.471-0.026
Interaction energy analysis for fragmet #1(A:73:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.916
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].
3A75TYR00.0540.0292.291-4.774-0.0402.891-3.173-4.452-0.026
4A76TYR0-0.008-0.0084.6720.2680.297-0.001-0.010-0.0190.000
5A77ARG10.8670.9116.53740.46140.4610.0000.0000.0000.000
6A78VAL0-0.006-0.0079.6291.1511.1510.0000.0000.0000.000
7A79VAL00.0250.02113.4520.5190.5190.0000.0000.0000.000
8A80LEU0-0.036-0.01016.0420.7390.7390.0000.0000.0000.000
9A81ILE00.0170.00219.5150.3380.3380.0000.0000.0000.000
10A82GLY00.0230.00422.4700.1470.1470.0000.0000.0000.000
11A83GLU-1-0.841-0.90326.255-10.146-10.1460.0000.0000.0000.000
12A84GLN0-0.002-0.00728.609-0.186-0.1860.0000.0000.0000.000
13A85GLY00.0150.01929.7260.2550.2550.0000.0000.0000.000
14A86VAL0-0.044-0.02126.9420.1950.1950.0000.0000.0000.000
15A87GLY00.002-0.00127.638-0.006-0.0060.0000.0000.0000.000
16A88LYS10.7740.88222.50512.21112.2110.0000.0000.0000.000
17A89SER00.1130.03122.378-0.207-0.2070.0000.0000.0000.000
18A90THR0-0.068-0.02623.195-0.139-0.1390.0000.0000.0000.000
19A91LEU0-0.014-0.01520.966-0.073-0.0730.0000.0000.0000.000
20A92ALA00.0240.01118.842-0.367-0.3670.0000.0000.0000.000
21A93ASN00.0450.02019.481-0.460-0.4600.0000.0000.0000.000
22A94ILE0-0.051-0.01521.8010.0240.0240.0000.0000.0000.000
23A95PHE0-0.032-0.01114.2270.0980.0980.0000.0000.0000.000
24A96ALA0-0.0040.00017.164-0.449-0.4490.0000.0000.0000.000
25A97GLY0-0.0180.00318.176-0.073-0.0730.0000.0000.0000.000
26A98VAL0-0.060-0.04021.1490.0290.0290.0000.0000.0000.000
27A99HIS10.7660.84413.99019.09319.0930.0000.0000.0000.000
28A100ASP-1-0.867-0.93119.089-13.158-13.1580.0000.0000.0000.000
29A101SER0-0.020-0.01918.561-0.489-0.4890.0000.0000.0000.000
30A102MET0-0.084-0.04819.6260.1330.1330.0000.0000.0000.000
31A103ASP-1-0.753-0.85513.342-20.508-20.5080.0000.0000.0000.000
32A104SER0-0.097-0.07313.8321.0401.0400.0000.0000.0000.000
33A105ASP-1-1.060-1.0168.723-24.749-24.7490.0000.0000.0000.000
34A106CYS-1-0.795-0.8288.562-26.830-26.8300.0000.0000.0000.000
35A107GLU-1-0.822-0.93610.911-17.406-17.4060.0000.0000.0000.000
36A108VAL0-0.0250.0089.9811.4881.4880.0000.0000.0000.000
37A109LEU0-0.073-0.03610.591-0.470-0.4700.0000.0000.0000.000
38A110GLY0-0.004-0.01314.3771.2711.2710.0000.0000.0000.000
39A111GLU-1-0.915-0.95117.124-14.404-14.4040.0000.0000.0000.000
40A112ASP-1-0.844-0.92518.120-14.832-14.8320.0000.0000.0000.000
41A113THR0-0.068-0.02712.616-0.978-0.9780.0000.0000.0000.000
42A114TYR0-0.033-0.03414.6820.8090.8090.0000.0000.0000.000
43A115GLU-1-0.934-0.9888.036-33.629-33.6290.0000.0000.0000.000
44A116ARG10.9010.93411.30320.37620.3760.0000.0000.0000.000
45A117THR00.0070.02010.608-1.657-1.6570.0000.0000.0000.000
46A118LEU00.004-0.00811.5392.5242.5240.0000.0000.0000.000
47A119MET0-0.0170.01212.723-1.798-1.7980.0000.0000.0000.000
48A120VAL00.0180.00714.0311.2221.2220.0000.0000.0000.000
49A121ASP-1-0.817-0.88215.505-18.009-18.0090.0000.0000.0000.000
50A122GLY0-0.0080.00417.6050.2490.2490.0000.0000.0000.000
51A123GLU-1-0.874-0.92810.437-28.776-28.7760.0000.0000.0000.000
52A124SER0-0.004-0.01210.3520.3620.3620.0000.0000.0000.000
53A125ALA0-0.0080.0018.571-2.669-2.6690.0000.0000.0000.000
54A126THR00.0150.0075.6011.9431.9430.0000.0000.0000.000
55A127ILE0-0.046-0.0357.229-3.601-3.6010.0000.0000.0000.000
56A128ILE00.0290.0207.1410.2220.2220.0000.0000.0000.000
57A129LEU0-0.063-0.02410.4050.6530.6530.0000.0000.0000.000
58A130LEU00.0310.01411.436-0.144-0.1440.0000.0000.0000.000
59A131ASP-1-0.826-0.91215.292-13.840-13.8400.0000.0000.0000.000
60A132MET00.0380.04515.0140.6860.6860.0000.0000.0000.000
61A133TRP0-0.043-0.01820.0490.1540.1540.0000.0000.0000.000
62A134GLU-1-0.785-0.89922.623-11.161-11.1610.0000.0000.0000.000
63A135ASN0-0.089-0.03722.5790.8910.8910.0000.0000.0000.000
64A136LYS10.8530.91821.05713.91413.9140.0000.0000.0000.000
65A137GLY00.0500.03221.9650.0650.0650.0000.0000.0000.000
66A138GLU-1-0.902-0.96122.640-11.069-11.0690.0000.0000.0000.000
67A139ASN0-0.009-0.01825.8870.4670.4670.0000.0000.0000.000
68A140GLU-1-0.830-0.90821.362-14.344-14.3440.0000.0000.0000.000
69A141TRP0-0.039-0.01922.261-0.233-0.2330.0000.0000.0000.000
70A142LEU0-0.029-0.03325.2650.3420.3420.0000.0000.0000.000
71A143HIS0-0.112-0.05828.3200.7670.7670.0000.0000.0000.000
72A144ASP-1-0.840-0.92824.634-11.735-11.7350.0000.0000.0000.000
73A145HIS10.7790.90925.12110.95210.9520.0000.0000.0000.000
74A146CYS0-0.023-0.00220.116-0.386-0.3860.0000.0000.0000.000
75A147MET0-0.0190.00318.0480.1390.1390.0000.0000.0000.000
76A148GLN00.022-0.00914.686-0.730-0.7300.0000.0000.0000.000
77A149VAL00.0140.01010.605-0.042-0.0420.0000.0000.0000.000
78A150GLY00.0310.01410.910-1.153-1.1530.0000.0000.0000.000
79A151ASP-1-0.832-0.8857.642-40.841-40.8410.0000.0000.0000.000
80A152ALA00.0140.00010.6121.3131.3130.0000.0000.0000.000
81A153TYR0-0.023-0.03114.259-0.267-0.2670.0000.0000.0000.000
82A154LEU0-0.029-0.01517.5470.6980.6980.0000.0000.0000.000
83A155ILE00.0090.01520.1940.2090.2090.0000.0000.0000.000
84A156VAL0-0.026-0.01622.9360.3800.3800.0000.0000.0000.000
85A157TYR00.0130.01025.5890.2130.2130.0000.0000.0000.000
86A158SER00.008-0.01529.384-0.249-0.2490.0000.0000.0000.000
87A159ILE0-0.012-0.00632.0360.2430.2430.0000.0000.0000.000
88A160THR0-0.046-0.02434.4540.1910.1910.0000.0000.0000.000
89A161ASP-1-0.828-0.89634.571-8.932-8.9320.0000.0000.0000.000
90A162ARG10.8740.92835.0127.9307.9300.0000.0000.0000.000
91A163ALA00.0310.02936.216-0.100-0.1000.0000.0000.0000.000
92A164SER0-0.009-0.02531.391-0.365-0.3650.0000.0000.0000.000
93A165PHE0-0.020-0.02131.220-0.368-0.3680.0000.0000.0000.000
94A166GLU-1-0.906-0.95432.108-8.713-8.7130.0000.0000.0000.000
95A167LYS10.8890.93829.96710.07010.0700.0000.0000.0000.000
96A168ALA00.0250.00227.943-0.357-0.3570.0000.0000.0000.000
97A169SER0-0.029-0.02327.913-0.376-0.3760.0000.0000.0000.000
98A170GLU-1-0.875-0.92329.675-10.203-10.2030.0000.0000.0000.000
99A171LEU00.0220.01025.428-0.186-0.1860.0000.0000.0000.000
100A172ARG10.8790.93622.11313.08713.0870.0000.0000.0000.000
101A173ILE0-0.033-0.01725.691-0.257-0.2570.0000.0000.0000.000
102A174GLN0-0.078-0.04126.994-0.294-0.2940.0000.0000.0000.000
103A175LEU00.0410.02819.562-0.035-0.0350.0000.0000.0000.000
104A176ARG10.8650.93422.53912.14512.1450.0000.0000.0000.000
105A177ARG10.9140.94724.42210.84510.8450.0000.0000.0000.000
106A178ALA00.0290.03120.4760.1260.1260.0000.0000.0000.000
107A179ARG10.9320.96120.32911.53111.5310.0000.0000.0000.000
108A180GLN00.0100.00815.924-0.786-0.7860.0000.0000.0000.000
109A181THR0-0.011-0.02815.908-0.884-0.8840.0000.0000.0000.000
110A182GLU-1-1.026-0.99517.670-13.906-13.9060.0000.0000.0000.000
111A183ASP-1-0.817-0.90716.706-17.303-17.3030.0000.0000.0000.000
112A184ILE0-0.0160.01013.092-0.956-0.9560.0000.0000.0000.000
113A185PRO0-0.042-0.02314.1021.3581.3580.0000.0000.0000.000
114A186ILE00.0250.02117.018-0.315-0.3150.0000.0000.0000.000
115A187ILE0-0.042-0.02818.9970.6600.6600.0000.0000.0000.000
116A188LEU00.0020.01221.911-0.008-0.0080.0000.0000.0000.000
117A189VAL00.009-0.01722.6470.1790.1790.0000.0000.0000.000
118A190GLY00.0520.02125.9160.2300.2300.0000.0000.0000.000
119A191ASN00.007-0.00227.3420.0950.0950.0000.0000.0000.000
120A192LYS10.8810.93329.19510.26910.2690.0000.0000.0000.000
121A193SER0-0.010-0.02631.1810.3860.3860.0000.0000.0000.000
122A194ASP-1-0.814-0.87833.121-9.385-9.3850.0000.0000.0000.000
123A195LEU0-0.0100.00535.1910.3530.3530.0000.0000.0000.000
124A196VAL00.019-0.00337.8720.1310.1310.0000.0000.0000.000
125A197ARG10.9120.93939.8077.3617.3610.0000.0000.0000.000
126A198CYS0-0.096-0.04939.6850.2850.2850.0000.0000.0000.000
127A199ARG10.7780.85434.8018.9568.9560.0000.0000.0000.000
128A200GLU-1-0.855-0.91438.685-7.874-7.8740.0000.0000.0000.000
129A201VAL0-0.0040.01034.7620.0730.0730.0000.0000.0000.000
130A202SER0-0.032-0.02437.134-0.134-0.1340.0000.0000.0000.000
131A203VAL00.0480.00333.638-0.160-0.1600.0000.0000.0000.000
132A204SER0-0.094-0.04334.616-0.171-0.1710.0000.0000.0000.000
133A205GLU-1-0.732-0.83035.954-8.436-8.4360.0000.0000.0000.000
134A206GLY00.0810.04632.690-0.140-0.1400.0000.0000.0000.000
135A207ARG10.9460.97531.0949.7849.7840.0000.0000.0000.000
136A208ALA00.004-0.00131.688-0.189-0.1890.0000.0000.0000.000
137A209CYS0-0.002-0.00131.630-0.004-0.0040.0000.0000.0000.000
138A210ALA0-0.007-0.00227.510-0.216-0.2160.0000.0000.0000.000
139A211VAL0-0.032-0.00928.241-0.277-0.2770.0000.0000.0000.000
140A212VAL0-0.043-0.01830.702-0.025-0.0250.0000.0000.0000.000
141A213PHE0-0.020-0.02228.5440.0600.0600.0000.0000.0000.000
142A214ASP-1-0.874-0.90924.545-13.393-13.3930.0000.0000.0000.000
143A215CYS0-0.0140.01323.518-0.612-0.6120.0000.0000.0000.000
144A216LYS10.9180.95721.67914.69914.6990.0000.0000.0000.000
145A217PHE0-0.008-0.01324.1670.0900.0900.0000.0000.0000.000
146A218ILE0-0.033-0.00823.7580.0590.0590.0000.0000.0000.000
147A219GLU-1-0.754-0.84427.082-9.669-9.6690.0000.0000.0000.000
148A220THR00.0500.01224.548-0.195-0.1950.0000.0000.0000.000
149A221SER0-0.088-0.05327.9670.3990.3990.0000.0000.0000.000
150A222ALA00.0420.01526.513-0.172-0.1720.0000.0000.0000.000
151A223ALA0-0.0190.00027.569-0.045-0.0450.0000.0000.0000.000
152A224VAL0-0.016-0.02230.9270.1660.1660.0000.0000.0000.000
153A225GLN0-0.013-0.00125.5620.2200.2200.0000.0000.0000.000
154A226HIS00.0290.02727.000-0.305-0.3050.0000.0000.0000.000
155A227ASN0-0.029-0.03825.891-0.157-0.1570.0000.0000.0000.000
156A228VAL00.0250.01621.389-0.508-0.5080.0000.0000.0000.000
157A229LYS10.8380.92019.09614.27814.2780.0000.0000.0000.000
158A230GLU-1-0.843-0.93219.688-13.743-13.7430.0000.0000.0000.000
159A231LEU0-0.029-0.00619.515-0.383-0.3830.0000.0000.0000.000
160A232PHE00.0490.01215.359-0.584-0.5840.0000.0000.0000.000
161A233GLU-1-0.817-0.90515.646-16.659-16.6590.0000.0000.0000.000
162A234GLY0-0.028-0.01117.197-0.473-0.4730.0000.0000.0000.000
163A235ILE0-0.024-0.01013.890-0.193-0.1930.0000.0000.0000.000
164A236VAL00.0250.01611.620-0.819-0.8190.0000.0000.0000.000
165A237ARG10.8370.88713.64215.46715.4670.0000.0000.0000.000
166A238GLN0-0.021-0.01016.1230.4560.4560.0000.0000.0000.000
167A239VAL00.0180.0059.9340.0350.0350.0000.0000.0000.000
168A240ARG10.7690.86311.59623.17023.1700.0000.0000.0000.000
169A241LEU0-0.053-0.02612.716-0.036-0.0360.0000.0000.0000.000
170A242ARG10.8290.91812.69519.24119.2410.0000.0000.0000.000
171A243ARG10.7520.8936.48439.51539.5150.0000.0000.0000.000
172A244ASP-2-1.867-1.91911.066-40.623-40.6230.0000.0000.0000.000