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: GY5N1

Calculation Name: 1P9Q-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P9Q

Chain ID: C

ChEMBL ID:

UniProt ID: O29759

Base Structure: X-ray

Registration Date: 2023-09-27

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 OptAll
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 233
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2580647.963722
FMO2-HF: Nuclear repulsion 2488747.481525
FMO2-HF: Total energy -91900.482196
FMO2-MP2: Total energy -92171.008993


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:2:VAL)


Summations of interaction energy for fragment #1(C:2:VAL)
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.
-17.277-8.6099.272-4.069-13.871-0.031
Interaction energy analysis for fragmet #1(C:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.001
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].
3C4LEU00.0570.0052.916-1.9870.4130.323-1.270-1.452-0.002
4C5ASP-1-0.852-0.8844.8811.1461.276-0.001-0.005-0.1230.000
5C6LYS10.8090.8893.241-2.859-2.3000.035-0.108-0.4860.000
6C7ALA0-0.0080.0202.453-0.9320.2381.280-0.795-1.657-0.001
7C8VAL0-0.039-0.0163.3250.469-0.0910.0950.706-0.2410.000
8C9ILE00.0100.0086.349-0.246-0.2460.0000.0000.0000.000
9C10ALA0-0.0160.0079.2050.0670.0670.0000.0000.0000.000
10C11ARG10.7810.85210.7050.2500.2500.0000.0000.0000.000
11C12LEU00.007-0.00214.2780.0270.0270.0000.0000.0000.000
12C13ARG10.8080.91517.5610.1770.1770.0000.0000.0000.000
13C14LYS10.8960.94420.5920.2680.2680.0000.0000.0000.000
14C15GLY00.0160.00522.7630.0010.0010.0000.0000.0000.000
15C16GLY0-0.009-0.00126.0830.0070.0070.0000.0000.0000.000
16C17GLU-1-0.857-0.90822.622-0.178-0.1780.0000.0000.0000.000
17C18GLU-1-0.783-0.86419.103-0.228-0.2280.0000.0000.0000.000
18C19PHE00.0350.00416.276-0.001-0.0010.0000.0000.0000.000
19C20GLU-1-0.744-0.86012.633-0.316-0.3160.0000.0000.0000.000
20C21VAL00.0400.0248.5190.0000.0000.0000.0000.0000.000
21C22LEU00.0010.0045.5910.1250.1250.0000.0000.0000.000
22C23VAL00.0280.0113.407-0.780-0.4250.017-0.092-0.2800.000
23C24ASP-1-0.750-0.8782.183-3.333-0.8043.958-2.469-4.019-0.007
24C25PRO0-0.023-0.0142.9531.4320.2860.1261.494-0.4740.000
25C26TYR0-0.100-0.0786.0560.0990.0990.0000.0000.0000.000
26C27LEU00.0280.0144.6060.0500.162-0.001-0.005-0.1060.000
27C28ALA00.0430.0196.8210.1370.1370.0000.0000.0000.000
28C29ARG10.7870.8768.4200.4320.4320.0000.0000.0000.000
29C30ASP-1-0.794-0.88510.498-0.329-0.3290.0000.0000.0000.000
30C31LEU00.0430.02410.4990.0760.0760.0000.0000.0000.000
31C32LYS10.7660.87312.3940.4710.4710.0000.0000.0000.000
32C33GLU-1-0.894-0.93114.698-0.202-0.2020.0000.0000.0000.000
33C34GLY0-0.031-0.00615.9620.0450.0450.0000.0000.0000.000
34C35LYS10.7160.85513.8500.3480.3480.0000.0000.0000.000
35C36GLU-1-0.790-0.87414.676-0.584-0.5840.0000.0000.0000.000
36C37VAL0-0.051-0.0288.5230.0170.0170.0000.0000.0000.000
37C38ASN0-0.025-0.0258.3770.0500.0500.0000.0000.0000.000
38C39PHE00.009-0.0227.423-0.395-0.3950.0000.0000.0000.000
39C40GLU-1-0.909-0.9456.802-1.229-1.2290.0000.0000.0000.000
40C41ASP-1-0.879-0.9254.161-1.891-1.7340.000-0.035-0.1210.000
41C42LEU0-0.083-0.0332.582-5.235-3.5701.017-1.056-1.626-0.013
42C43LEU0-0.005-0.0073.239-1.386-0.0990.148-0.654-0.782-0.005
43C44ALA0-0.0060.0022.276-2.382-1.1762.099-1.084-2.220-0.003
44C45ALA0-0.030-0.0272.8732.0980.9020.1761.304-0.2840.000
45C46GLU-1-0.935-0.9476.636-0.854-0.8540.0000.0000.0000.000
46C47GLU-1-0.848-0.9249.199-0.345-0.3450.0000.0000.0000.000
47C48VAL0-0.007-0.00610.362-0.094-0.0940.0000.0000.0000.000
48C49PHE0-0.028-0.0079.5120.0930.0930.0000.0000.0000.000
49C50LYS10.8040.88914.5600.2320.2320.0000.0000.0000.000
50C51ASP-1-0.791-0.89615.974-0.204-0.2040.0000.0000.0000.000
51C52ALA00.0120.00910.6480.0110.0110.0000.0000.0000.000
52C53LYS10.7550.87112.4640.2680.2680.0000.0000.0000.000
53C54LYS10.7920.86813.9220.2060.2060.0000.0000.0000.000
54C55GLY00.0170.02313.8040.0150.0150.0000.0000.0000.000
55C56GLU-1-0.901-0.94014.862-0.197-0.1970.0000.0000.0000.000
56C57ARG10.8650.91113.7530.3510.3510.0000.0000.0000.000
57C58ALA0-0.0090.00016.2570.0450.0450.0000.0000.0000.000
58C59SER00.0040.00118.299-0.013-0.0130.0000.0000.0000.000
59C60VAL00.0710.01719.843-0.011-0.0110.0000.0000.0000.000
60C61ASP-1-0.847-0.91421.235-0.203-0.2030.0000.0000.0000.000
61C62GLU-1-0.822-0.89321.350-0.208-0.2080.0000.0000.0000.000
62C63LEU00.0030.00216.8010.0030.0030.0000.0000.0000.000
63C64ARG10.8230.89020.8940.2390.2390.0000.0000.0000.000
64C65LYS10.8250.91823.8560.2050.2050.0000.0000.0000.000
65C66ILE0-0.060-0.02321.6880.0140.0140.0000.0000.0000.000
66C67PHE0-0.040-0.05517.8600.0010.0010.0000.0000.0000.000
67C68GLY0-0.0130.01522.111-0.002-0.0020.0000.0000.0000.000
68C69THR0-0.044-0.04419.5380.0100.0100.0000.0000.0000.000
69C70ASP-1-0.836-0.92819.426-0.288-0.2880.0000.0000.0000.000
70C71ASP-1-0.824-0.88615.787-0.581-0.5810.0000.0000.0000.000
71C72VAL00.0360.00510.942-0.006-0.0060.0000.0000.0000.000
72C73PHE00.0260.0119.305-0.105-0.1050.0000.0000.0000.000
73C74GLU-1-0.897-0.92712.703-0.370-0.3700.0000.0000.0000.000
74C75ILE0-0.036-0.01914.4300.0130.0130.0000.0000.0000.000
75C76ALA00.0120.0079.5230.0190.0190.0000.0000.0000.000
76C77ARG10.8140.88011.6480.6050.6050.0000.0000.0000.000
77C78LYS10.8120.88813.1800.3830.3830.0000.0000.0000.000
78C79ILE0-0.031-0.01512.4830.0500.0500.0000.0000.0000.000
79C80ILE00.0170.0168.3400.0420.0420.0000.0000.0000.000
80C81LEU0-0.0240.00812.3370.0680.0680.0000.0000.0000.000
81C82GLU-1-0.848-0.91815.681-0.282-0.2820.0000.0000.0000.000
82C83GLY0-0.0010.02216.0620.0400.0400.0000.0000.0000.000
83C84GLU-1-0.938-0.95714.595-0.228-0.2280.0000.0000.0000.000
84C85VAL00.0630.0048.963-0.053-0.0530.0000.0000.0000.000
85C86GLN0-0.108-0.04910.8450.0690.0690.0000.0000.0000.000
86C87ILE0-0.022-0.0118.8790.0430.0430.0000.0000.0000.000
87C88THR00.018-0.01010.2760.0120.0120.0000.0000.0000.000
88C89ALA00.006-0.01412.502-0.014-0.0140.0000.0000.0000.000
89C90GLU-1-0.792-0.85613.4070.1410.1410.0000.0000.0000.000
90C91GLN00.1280.0737.056-0.112-0.1120.0000.0000.0000.000
91C92ARG10.9410.97612.3550.0920.0920.0000.0000.0000.000
92C93ARG10.8320.88414.905-0.121-0.1210.0000.0000.0000.000
93C94GLU-1-0.854-0.91311.5550.2130.2130.0000.0000.0000.000
94C95MET00.0090.00310.941-0.025-0.0250.0000.0000.0000.000
95C96LEU0-0.017-0.00815.246-0.016-0.0160.0000.0000.0000.000
96C97GLU-1-0.830-0.89518.7740.0240.0240.0000.0000.0000.000
97C98ALA00.0220.00816.975-0.002-0.0020.0000.0000.0000.000
98C99LYS10.7780.89417.9680.1470.1470.0000.0000.0000.000
99C100ARG10.9090.94620.111-0.001-0.0010.0000.0000.0000.000
100C101LYS10.8740.92022.542-0.031-0.0310.0000.0000.0000.000
101C102GLN00.0180.01418.008-0.009-0.0090.0000.0000.0000.000
102C103ILE00.0100.00223.049-0.001-0.0010.0000.0000.0000.000
103C104ILE0-0.0090.00625.7980.0010.0010.0000.0000.0000.000
104C105ASN0-0.036-0.02225.5390.0050.0050.0000.0000.0000.000
105C106PHE0-0.0010.01726.1370.0030.0030.0000.0000.0000.000
106C107ILE00.004-0.01128.3250.0010.0010.0000.0000.0000.000
107C108SER0-0.070-0.02331.1670.0030.0030.0000.0000.0000.000
108C109ARG10.9490.97326.5500.0120.0120.0000.0000.0000.000
109C110ASN0-0.023-0.02229.6120.0030.0030.0000.0000.0000.000
110C111THR0-0.099-0.07833.579-0.003-0.0030.0000.0000.0000.000
111C112ILE00.0060.00236.3560.0040.0040.0000.0000.0000.000
112C113ASP-1-0.780-0.90739.721-0.013-0.0130.0000.0000.0000.000
113C114PRO0-0.080-0.03842.4520.0010.0010.0000.0000.0000.000
114C115ARG10.8430.90745.7290.0090.0090.0000.0000.0000.000
115C116THR0-0.015-0.01645.8780.0010.0010.0000.0000.0000.000
116C117ASN0-0.0270.01045.3410.0000.0000.0000.0000.0000.000
117C118ALA00.0870.03342.2320.0020.0020.0000.0000.0000.000
118C119PRO00.0200.03936.955-0.003-0.0030.0000.0000.0000.000
119C120HIS00.0140.00436.5940.0050.0050.0000.0000.0000.000
120C121PRO00.0510.03535.728-0.001-0.0010.0000.0000.0000.000
121C122PRO00.0720.01330.477-0.002-0.0020.0000.0000.0000.000
122C123SER00.0210.01132.335-0.003-0.0030.0000.0000.0000.000
123C124ARG10.7650.87834.0200.0070.0070.0000.0000.0000.000
124C125ILE00.0080.00030.950-0.003-0.0030.0000.0000.0000.000
125C126GLU-1-0.831-0.93327.7370.0090.0090.0000.0000.0000.000
126C127ARG10.9430.96831.068-0.006-0.0060.0000.0000.0000.000
127C128ALA0-0.0110.00034.029-0.002-0.0020.0000.0000.0000.000
128C129LEU0-0.015-0.01927.881-0.005-0.0050.0000.0000.0000.000
129C130GLU-1-0.903-0.94130.7620.0040.0040.0000.0000.0000.000
130C131GLU-1-0.814-0.88332.481-0.008-0.0080.0000.0000.0000.000
131C132ALA0-0.032-0.01734.470-0.001-0.0010.0000.0000.0000.000
132C133LYS10.8800.94131.7970.0230.0230.0000.0000.0000.000
133C134VAL0-0.033-0.00928.747-0.005-0.0050.0000.0000.0000.000
134C135HIS00.0230.01522.8240.0120.0120.0000.0000.0000.000
135C136ILE0-0.024-0.02421.782-0.001-0.0010.0000.0000.0000.000
136C137ASP-1-0.860-0.92119.455-0.178-0.1780.0000.0000.0000.000
137C138ILE00.006-0.00214.5940.0010.0010.0000.0000.0000.000
138C139PHE00.002-0.00112.257-0.014-0.0140.0000.0000.0000.000
139C140LYS10.9140.96716.7850.1590.1590.0000.0000.0000.000
140C141SER00.0580.00119.6620.0140.0140.0000.0000.0000.000
141C142VAL00.0270.01820.6720.0130.0130.0000.0000.0000.000
142C143GLU-1-0.815-0.90223.125-0.119-0.1190.0000.0000.0000.000
143C144ALA0-0.030-0.00123.0020.0060.0060.0000.0000.0000.000
144C145GLN0-0.028-0.02921.4430.0110.0110.0000.0000.0000.000
145C146VAL0-0.009-0.00326.5430.0100.0100.0000.0000.0000.000
146C147LYS10.9670.97428.6610.0950.0950.0000.0000.0000.000
147C148ASP-1-0.804-0.88430.104-0.074-0.0740.0000.0000.0000.000
148C149ILE00.0410.03026.3490.0070.0070.0000.0000.0000.000
149C150VAL00.005-0.00430.9510.0070.0070.0000.0000.0000.000
150C151LYS10.7780.87834.0280.0760.0760.0000.0000.0000.000
151C152ALA00.0060.01632.9310.0020.0020.0000.0000.0000.000
152C153LEU00.021-0.00232.1910.0040.0040.0000.0000.0000.000
153C154LYS10.7960.91935.9100.0420.0420.0000.0000.0000.000
154C155PRO0-0.010-0.00738.6270.0020.0020.0000.0000.0000.000
155C156ILE0-0.0120.00536.6610.0020.0020.0000.0000.0000.000
156C157LEU0-0.022-0.01236.0290.0040.0040.0000.0000.0000.000
157C158PRO0-0.0140.01039.834-0.004-0.0040.0000.0000.0000.000
158C159LEU00.0180.00734.7010.0020.0020.0000.0000.0000.000
159C160LYS10.8600.92639.2930.0250.0250.0000.0000.0000.000
160C161PHE00.0440.01732.3760.0010.0010.0000.0000.0000.000
161C162GLU-1-0.832-0.90537.527-0.023-0.0230.0000.0000.0000.000
162C163GLU-1-0.781-0.83137.025-0.046-0.0460.0000.0000.0000.000
163C164MET0-0.039-0.01839.5710.0020.0020.0000.0000.0000.000
164C165GLU-1-0.767-0.84541.261-0.034-0.0340.0000.0000.0000.000
165C166ILE0-0.012-0.02042.5780.0020.0020.0000.0000.0000.000
166C167ALA00.0130.02144.7390.0000.0000.0000.0000.0000.000
167C168ILE00.008-0.01043.6600.0020.0020.0000.0000.0000.000
168C169LYS10.8560.91847.1210.0020.0020.0000.0000.0000.000
169C170ILE00.0020.00844.5830.0020.0020.0000.0000.0000.000
170C171PRO00.0330.01148.086-0.001-0.0010.0000.0000.0000.000
171C172PRO00.0430.01349.4070.0010.0010.0000.0000.0000.000
172C173GLU-1-0.855-0.92449.1510.0090.0090.0000.0000.0000.000
173C174HIS0-0.035-0.01846.2440.0030.0030.0000.0000.0000.000
174C175THR0-0.040-0.01944.6650.0010.0010.0000.0000.0000.000
175C176GLY00.0170.01042.598-0.001-0.0010.0000.0000.0000.000
176C177ARG10.7990.88140.052-0.024-0.0240.0000.0000.0000.000
177C178ALA00.0310.01440.1860.0010.0010.0000.0000.0000.000
178C179ILE00.0160.01239.684-0.001-0.0010.0000.0000.0000.000
179C180SER0-0.013-0.00636.419-0.003-0.0030.0000.0000.0000.000
180C181ALA00.0290.01335.377-0.001-0.0010.0000.0000.0000.000
181C182LEU0-0.001-0.01235.494-0.002-0.0020.0000.0000.0000.000
182C183TYR0-0.058-0.06634.004-0.003-0.0030.0000.0000.0000.000
183C184ASN0-0.076-0.03329.6660.0000.0000.0000.0000.0000.000
184C185PHE0-0.047-0.01731.2510.0000.0000.0000.0000.0000.000
185C186GLY00.0310.03332.643-0.004-0.0040.0000.0000.0000.000
186C187GLY00.019-0.01333.4910.0030.0030.0000.0000.0000.000
187C188VAL0-0.0030.00036.0540.0000.0000.0000.0000.0000.000
188C189THR00.0080.00737.839-0.005-0.0050.0000.0000.0000.000
189C190ARG10.7980.86040.5820.0330.0330.0000.0000.0000.000
190C191GLU-1-0.831-0.88639.449-0.023-0.0230.0000.0000.0000.000
191C192GLU-1-0.891-0.93643.882-0.016-0.0160.0000.0000.0000.000
192C193TRP00.013-0.00743.6320.0020.0020.0000.0000.0000.000
193C194GLN0-0.067-0.03848.379-0.001-0.0010.0000.0000.0000.000
194C195ARG10.9480.96552.1140.0070.0070.0000.0000.0000.000
195C196ASP-1-0.783-0.85454.041-0.001-0.0010.0000.0000.0000.000
196C197GLY00.0290.01951.7650.0010.0010.0000.0000.0000.000
197C198SER0-0.099-0.07150.2900.0010.0010.0000.0000.0000.000
198C199TRP00.0570.00641.2640.0000.0000.0000.0000.0000.000
199C200ILE0-0.018-0.00247.5060.0010.0010.0000.0000.0000.000
200C201CYS0-0.0080.01541.938-0.001-0.0010.0000.0000.0000.000
201C202VAL0-0.033-0.02443.6680.0010.0010.0000.0000.0000.000
202C203MET00.0100.04837.780-0.003-0.0030.0000.0000.0000.000
203C204ARG10.7640.83238.1940.0430.0430.0000.0000.0000.000
204C205ILE00.0190.01736.517-0.001-0.0010.0000.0000.0000.000
205C206PRO00.0600.02433.3780.0000.0000.0000.0000.0000.000
206C207SER0-0.054-0.08136.5970.0030.0030.0000.0000.0000.000
207C208GLY00.0000.01036.6330.0030.0030.0000.0000.0000.000
208C209MET00.0180.01433.1880.0030.0030.0000.0000.0000.000
209C210TYR0-0.004-0.01436.7750.0020.0020.0000.0000.0000.000
210C211GLY00.0010.00339.9480.0010.0010.0000.0000.0000.000
211C212ASP-1-0.830-0.92535.1870.0070.0070.0000.0000.0000.000
212C213LEU0-0.021-0.00338.0370.0020.0020.0000.0000.0000.000
213C214MET0-0.034-0.01739.6970.0000.0000.0000.0000.0000.000
214C215ASP-1-0.866-0.92740.3590.0150.0150.0000.0000.0000.000
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216C217LEU0-0.009-0.02040.2140.0010.0010.0000.0000.0000.000
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