FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 6Y18Z

Calculation Name: 1H2T-C-Xray372

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate

ligand 3-letter code: GDP

PDB ID: 1H2T

Chain ID: C

ChEMBL ID:

UniProt ID: Q09161

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 703
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -17817435.372836
FMO2-HF: Nuclear repulsion 17528903.088075
FMO2-HF: Total energy -288532.284761
FMO2-MP2: Total energy -289364.845126


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(C:29:ASP)


Summations of interaction energy for fragment #1(C:29:ASP)
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.
-93.25-92.08816.396-9.32-8.2380.073
Interaction energy analysis for fragmet #1(C:29:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.877 / q_NPA : -0.934
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].
3C31LEU00.023-0.0023.816-10.441-8.0500.014-1.097-1.3080.006
4C32GLU-1-0.820-0.8972.22529.39131.7111.456-1.471-2.304-0.012
5C33SER00.0400.0183.938-7.060-6.5750.001-0.159-0.3280.000
6C34LEU0-0.0110.0015.911-4.482-4.4820.0000.0000.0000.000
7C35ILE00.0270.0147.486-3.026-3.0260.0000.0000.0000.000
8C36CYS0-0.034-0.0127.106-2.864-2.8640.0000.0000.0000.000
9C37LYS10.9320.9757.885-36.010-36.0100.0000.0000.0000.000
10C38VAL0-0.0020.01611.733-1.785-1.7850.0000.0000.0000.000
11C39GLY00.019-0.00214.084-0.430-0.4300.0000.0000.0000.000
12C40GLU-1-0.978-0.97213.70520.86920.8690.0000.0000.0000.000
13C41LYS10.9230.95515.844-19.358-19.3580.0000.0000.0000.000
14C42SER00.0290.00617.9350.7340.7340.0000.0000.0000.000
15C43ALA0-0.0050.01219.982-0.678-0.6780.0000.0000.0000.000
16C44CYS0-0.029-0.00920.881-0.749-0.7490.0000.0000.0000.000
17C45SER00.031-0.00822.4210.2900.2900.0000.0000.0000.000
18C46LEU00.0330.01719.2400.7360.7360.0000.0000.0000.000
19C47GLU-1-0.794-0.89220.33913.07213.0720.0000.0000.0000.000
20C48SER00.0210.01621.6680.1350.1350.0000.0000.0000.000
21C49ASN0-0.077-0.05216.9811.1311.1310.0000.0000.0000.000
22C50LEU0-0.026-0.00916.6981.0181.0180.0000.0000.0000.000
23C51GLU-1-0.776-0.88217.39514.54214.5420.0000.0000.0000.000
24C52GLY0-0.028-0.01417.8730.2160.2160.0000.0000.0000.000
25C53LEU0-0.042-0.02210.5221.1601.1600.0000.0000.0000.000
26C54ALA00.026-0.00513.9010.9510.9510.0000.0000.0000.000
27C55GLY0-0.0030.00516.0950.0760.0760.0000.0000.0000.000
28C56VAL0-0.022-0.01611.0720.3080.3080.0000.0000.0000.000
29C57LEU0-0.010-0.0179.3391.3251.3250.0000.0000.0000.000
30C58GLU-1-0.848-0.91812.51115.11715.1170.0000.0000.0000.000
31C59ALA0-0.007-0.00514.834-0.420-0.4200.0000.0000.0000.000
32C60ASP-1-0.866-0.94010.26728.94728.9470.0000.0000.0000.000
33C61LEU0-0.067-0.02212.1450.6710.6710.0000.0000.0000.000
34C62PRO0-0.048-0.03014.184-0.165-0.1650.0000.0000.0000.000
35C63ASN00.0010.00512.319-1.422-1.4220.0000.0000.0000.000
36C64TYR0-0.045-0.0248.3802.8402.8400.0000.0000.0000.000
37C65LYS10.8910.93510.054-14.611-14.6110.0000.0000.0000.000
38C66SER0-0.014-0.00811.7750.1280.1280.0000.0000.0000.000
39C67LYS10.8940.9211.866-84.167-88.32514.927-6.582-4.1880.079
40C68ILE00.0360.0147.7720.9150.9150.0000.0000.0000.000
41C69LEU00.0190.0219.351-0.651-0.6510.0000.0000.0000.000
42C70ARG10.8660.9294.441-31.969-31.907-0.001-0.002-0.0590.000
43C71LEU0-0.055-0.0084.332-0.350-0.288-0.001-0.009-0.0510.000
44C72LEU00.0260.0148.408-0.764-0.7640.0000.0000.0000.000
45C73CYS0-0.020-0.00711.730-1.255-1.2550.0000.0000.0000.000
46C74THR0-0.072-0.0479.818-0.800-0.8000.0000.0000.0000.000
47C75VAL0-0.015-0.00310.064-0.643-0.6430.0000.0000.0000.000
48C76ALA0-0.0010.00412.693-0.881-0.8810.0000.0000.0000.000
49C77ARG10.8570.91714.003-16.948-16.9480.0000.0000.0000.000
50C78LEU0-0.037-0.02612.289-0.441-0.4410.0000.0000.0000.000
51C79LEU0-0.021-0.00812.3940.1420.1420.0000.0000.0000.000
52C80PRO00.0280.02416.081-0.164-0.1640.0000.0000.0000.000
53C81GLU-1-0.781-0.86918.56114.72014.7200.0000.0000.0000.000
54C82LYS10.8420.92013.743-19.477-19.4770.0000.0000.0000.000
55C83LEU00.0010.01318.3890.3860.3860.0000.0000.0000.000
56C84THR0-0.021-0.02219.9450.3280.3280.0000.0000.0000.000
57C85ILE0-0.0040.01516.732-0.020-0.0200.0000.0000.0000.000
58C86TYR0-0.025-0.04912.1190.2550.2550.0000.0000.0000.000
59C87THR0-0.030-0.02516.7720.3390.3390.0000.0000.0000.000
60C88THR00.0500.00119.817-0.403-0.4030.0000.0000.0000.000
61C89LEU0-0.037-0.00412.732-0.012-0.0120.0000.0000.0000.000
62C90VAL0-0.005-0.00616.1380.1450.1450.0000.0000.0000.000
63C91GLY00.0310.00817.980-0.274-0.2740.0000.0000.0000.000
64C92LEU00.0070.00219.212-0.270-0.2700.0000.0000.0000.000
65C93LEU0-0.020-0.00513.9440.0490.0490.0000.0000.0000.000
66C94ASN0-0.028-0.01118.644-0.132-0.1320.0000.0000.0000.000
67C95ALA0-0.0110.00121.395-0.402-0.4020.0000.0000.0000.000
68C96ARG10.7810.88719.677-15.107-15.1070.0000.0000.0000.000
69C97ASN0-0.019-0.01619.444-0.529-0.5290.0000.0000.0000.000
70C98TYR00.0760.02821.2570.3360.3360.0000.0000.0000.000
71C99ASN0-0.015-0.01722.191-0.356-0.3560.0000.0000.0000.000
72C100PHE00.0290.01013.6570.2110.2110.0000.0000.0000.000
73C101GLY00.0310.01518.7490.3250.3250.0000.0000.0000.000
74C102GLY0-0.019-0.01120.683-0.147-0.1470.0000.0000.0000.000
75C103GLU-1-0.805-0.88118.37214.78314.7830.0000.0000.0000.000
76C104PHE0-0.006-0.01814.5430.1310.1310.0000.0000.0000.000
77C105VAL00.0390.01017.978-0.025-0.0250.0000.0000.0000.000
78C106GLU-1-0.854-0.89521.25812.00412.0040.0000.0000.0000.000
79C107ALA0-0.041-0.03516.831-0.158-0.1580.0000.0000.0000.000
80C108MET0-0.0170.00717.9490.3110.3110.0000.0000.0000.000
81C109ILE00.0050.01119.733-0.253-0.2530.0000.0000.0000.000
82C110ARG10.8470.89519.274-13.295-13.2950.0000.0000.0000.000
83C111GLN0-0.0110.00416.725-0.232-0.2320.0000.0000.0000.000
84C112LEU00.0150.02119.963-0.147-0.1470.0000.0000.0000.000
85C113LYS10.9520.97122.984-10.169-10.1690.0000.0000.0000.000
86C114GLU-1-0.878-0.95521.48411.15311.1530.0000.0000.0000.000
87C115SER0-0.026-0.01521.0220.0720.0720.0000.0000.0000.000
88C116LEU0-0.045-0.02123.024-0.230-0.2300.0000.0000.0000.000
89C117LYS10.9140.98025.892-10.458-10.4580.0000.0000.0000.000
90C118ALA0-0.030-0.00623.775-0.245-0.2450.0000.0000.0000.000
91C119ASN00.0100.00425.823-0.070-0.0700.0000.0000.0000.000
92C120ASN0-0.027-0.01522.4970.2620.2620.0000.0000.0000.000
93C121TYR00.0650.01024.2610.3100.3100.0000.0000.0000.000
94C122ASN00.004-0.00924.786-0.206-0.2060.0000.0000.0000.000
95C123GLU-1-0.836-0.90418.57214.69614.6960.0000.0000.0000.000
96C124ALA00.0130.00721.7130.2560.2560.0000.0000.0000.000
97C125VAL0-0.0140.00123.909-0.049-0.0490.0000.0000.0000.000
98C126TYR00.0140.00220.3570.0290.0290.0000.0000.0000.000
99C127LEU00.0230.02018.1610.1900.1900.0000.0000.0000.000
100C128VAL00.0070.00421.602-0.060-0.0600.0000.0000.0000.000
101C129ARG10.8070.88724.013-10.894-10.8940.0000.0000.0000.000
102C130PHE00.0220.00016.812-0.007-0.0070.0000.0000.0000.000
103C131LEU0-0.022-0.01821.9460.0280.0280.0000.0000.0000.000
104C132SER00.017-0.01323.923-0.367-0.3670.0000.0000.0000.000
105C133ASP-1-0.735-0.83423.76211.34411.3440.0000.0000.0000.000
106C134LEU00.0130.00220.2090.0490.0490.0000.0000.0000.000
107C135VAL0-0.050-0.01324.205-0.070-0.0700.0000.0000.0000.000
108C136ASN0-0.047-0.04627.158-0.448-0.4480.0000.0000.0000.000
109C137CYS0-0.074-0.01623.5390.1200.1200.0000.0000.0000.000
110C138HIS00.0540.02825.4690.1910.1910.0000.0000.0000.000
111C139VAL0-0.0240.00121.8220.1390.1390.0000.0000.0000.000
112C140ILE0-0.046-0.03123.756-0.032-0.0320.0000.0000.0000.000
113C141ALA00.0530.03327.266-0.159-0.1590.0000.0000.0000.000
114C142ALA00.0680.02331.056-0.005-0.0050.0000.0000.0000.000
115C143PRO00.004-0.01932.978-0.044-0.0440.0000.0000.0000.000
116C144SER00.0070.02230.615-0.059-0.0590.0000.0000.0000.000
117C145MET00.0210.02328.3360.0990.0990.0000.0000.0000.000
118C146VAL0-0.022-0.00831.473-0.072-0.0720.0000.0000.0000.000
119C147ALA00.0170.01034.517-0.139-0.1390.0000.0000.0000.000
120C148MET0-0.0090.00327.3000.0040.0040.0000.0000.0000.000
121C149PHE00.011-0.01829.851-0.066-0.0660.0000.0000.0000.000
122C150GLU-1-0.922-0.95034.2657.2337.2330.0000.0000.0000.000
123C151ASN0-0.026-0.01634.5520.0050.0050.0000.0000.0000.000
124C152PHE0-0.0280.00128.7740.0160.0160.0000.0000.0000.000
125C153VAL00.0410.01635.038-0.093-0.0930.0000.0000.0000.000
126C154SER0-0.069-0.02238.204-0.187-0.1870.0000.0000.0000.000
127C155VAL00.0470.02435.401-0.140-0.1400.0000.0000.0000.000
128C156THR0-0.118-0.07538.818-0.153-0.1530.0000.0000.0000.000
129C157GLN0-0.018-0.03141.426-0.168-0.1680.0000.0000.0000.000
130C158GLU-1-0.781-0.83738.3047.6137.6130.0000.0000.0000.000
131C159GLU-1-0.912-0.95643.0956.0996.0990.0000.0000.0000.000
132C160ASP-1-0.922-0.95644.7926.3456.3450.0000.0000.0000.000
133C161VAL0-0.047-0.01240.2350.1350.1350.0000.0000.0000.000
134C162PRO00.007-0.00839.028-0.096-0.0960.0000.0000.0000.000
135C163GLN00.0470.02440.122-0.071-0.0710.0000.0000.0000.000
136C164VAL0-0.0020.00036.4020.1020.1020.0000.0000.0000.000
137C165ARG10.7310.84334.487-7.887-7.8870.0000.0000.0000.000
138C166ARG10.7990.89535.799-6.786-6.7860.0000.0000.0000.000
139C167ASP-1-0.779-0.84837.0667.5897.5890.0000.0000.0000.000
140C168TRP0-0.0030.00927.3330.1110.1110.0000.0000.0000.000
141C169TYR00.0710.02231.6320.2980.2980.0000.0000.0000.000
142C170VAL00.0280.01933.8250.0620.0620.0000.0000.0000.000
143C171TYR00.000-0.01329.364-0.017-0.0170.0000.0000.0000.000
144C172ALA0-0.0140.00329.3880.1840.1840.0000.0000.0000.000
145C173PHE00.0380.02130.3780.1760.1760.0000.0000.0000.000
146C174LEU00.0420.01332.5680.1150.1150.0000.0000.0000.000
147C175SER0-0.037-0.02229.8740.1770.1770.0000.0000.0000.000
148C176SER00.009-0.01828.8540.4400.4400.0000.0000.0000.000
149C177LEU0-0.034-0.00429.8570.0890.0890.0000.0000.0000.000
150C178PRO0-0.0220.00630.706-0.066-0.0660.0000.0000.0000.000
151C179TRP00.0120.00525.524-0.066-0.0660.0000.0000.0000.000
152C180VAL00.0400.03729.3010.0100.0100.0000.0000.0000.000
153C181GLY00.0170.01131.124-0.187-0.1870.0000.0000.0000.000
154C182LYS10.8620.93534.741-8.199-8.1990.0000.0000.0000.000
155C183GLU-1-0.802-0.88431.9638.4338.4330.0000.0000.0000.000
156C184LEU0-0.017-0.02732.113-0.154-0.1540.0000.0000.0000.000
157C185TYR0-0.042-0.06035.703-0.189-0.1890.0000.0000.0000.000
158C186GLU-1-0.907-0.97237.8367.6797.6790.0000.0000.0000.000
159C187LYS10.8100.90935.667-8.308-8.3080.0000.0000.0000.000
160C188LYS10.8490.91538.007-7.421-7.4210.0000.0000.0000.000
161C189ASP-1-0.802-0.88140.4906.7996.7990.0000.0000.0000.000
162C190ALA0-0.009-0.00142.464-0.076-0.0760.0000.0000.0000.000
163C191GLU-1-0.796-0.90240.5616.8976.8970.0000.0000.0000.000
164C192MET0-0.029-0.01636.3610.0760.0760.0000.0000.0000.000
165C193ASP-1-0.757-0.84740.8316.7276.7270.0000.0000.0000.000
166C194ARG10.8400.91843.877-6.761-6.7610.0000.0000.0000.000
167C195ILE00.0150.02138.161-0.064-0.0640.0000.0000.0000.000
168C196PHE00.0330.02138.6730.0270.0270.0000.0000.0000.000
169C197ALA00.0130.02542.733-0.060-0.0600.0000.0000.0000.000
170C198ASN0-0.027-0.02243.213-0.145-0.1450.0000.0000.0000.000
171C199THR0-0.013-0.02239.6300.0590.0590.0000.0000.0000.000
172C200GLU-1-0.859-0.91742.3596.3406.3400.0000.0000.0000.000
173C201SER0-0.067-0.03845.203-0.098-0.0980.0000.0000.0000.000
174C202TYR00.006-0.04540.449-0.115-0.1150.0000.0000.0000.000
175C203LEU0-0.002-0.01840.396-0.017-0.0170.0000.0000.0000.000
176C204LYS10.8120.89844.381-6.227-6.2270.0000.0000.0000.000
177C205ARG10.8970.96045.240-6.629-6.6290.0000.0000.0000.000
178C206ARG10.6750.81440.206-7.367-7.3670.0000.0000.0000.000
179C207GLN00.0090.00745.700-0.175-0.1750.0000.0000.0000.000
180C208LYS10.8350.87044.275-6.534-6.5340.0000.0000.0000.000
181C209THR00.0130.00146.5440.0060.0060.0000.0000.0000.000
182C210HIS00.028-0.00641.300-0.150-0.1500.0000.0000.0000.000
183C211VAL0-0.0060.00243.5690.0710.0710.0000.0000.0000.000
184C212PRO00.0070.00344.6390.0860.0860.0000.0000.0000.000
185C213MET0-0.064-0.00342.9400.0460.0460.0000.0000.0000.000
186C214LEU0-0.029-0.03338.8320.1240.1240.0000.0000.0000.000
187C215GLN0-0.053-0.01740.9970.0780.0780.0000.0000.0000.000
188C216VAL00.0220.00839.792-0.058-0.0580.0000.0000.0000.000
189C217TRP0-0.022-0.01442.190-0.010-0.0100.0000.0000.0000.000
190C218THR00.014-0.00246.5050.0110.0110.0000.0000.0000.000
191C219ALA0-0.0010.01149.524-0.069-0.0690.0000.0000.0000.000
192C220ASP-1-0.837-0.90749.0176.0856.0850.0000.0000.0000.000
193C221LYS10.8290.90850.050-5.944-5.9440.0000.0000.0000.000
194C222PRO0-0.012-0.00947.510-0.030-0.0300.0000.0000.0000.000
195C223HIS0-0.004-0.03144.4360.0840.0840.0000.0000.0000.000
196C224PRO00.0420.03346.1910.0220.0220.0000.0000.0000.000
197C225GLN0-0.028-0.00842.1200.3210.3210.0000.0000.0000.000
198C226GLU-1-0.783-0.87741.7087.0187.0180.0000.0000.0000.000
199C227GLU-1-0.683-0.79640.4477.7247.7240.0000.0000.0000.000
200C228TYR0-0.003-0.02434.2060.1160.1160.0000.0000.0000.000
201C229LEU0-0.038-0.01236.5290.0910.0910.0000.0000.0000.000
202C230ASP-1-0.825-0.88538.9566.8326.8320.0000.0000.0000.000
203C231CYS0-0.067-0.03238.7810.0110.0110.0000.0000.0000.000
204C232LEU00.0250.01333.925-0.002-0.0020.0000.0000.0000.000
205C233TRP00.010-0.00237.7120.0730.0730.0000.0000.0000.000
206C234ALA00.0300.01740.438-0.068-0.0680.0000.0000.0000.000
207C235GLN0-0.014-0.01536.5180.0960.0960.0000.0000.0000.000
208C236ILE0-0.022-0.01334.9260.0380.0380.0000.0000.0000.000
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