Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: VKQR1

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 OptH
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2578200.171272
FMO2-HF: Nuclear repulsion 2486303.000566
FMO2-HF: Total energy -91897.170706
FMO2-MP2: Total energy -92167.795881


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.
-26.341-18.61110.72-4.113-14.338-0.03
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 : 0.013 / q_NPA : 0.008
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].
3C4LEU00.0690.0212.881-2.1960.4130.441-1.349-1.702-0.002
4C5ASP-1-0.897-0.9454.7710.7130.855-0.001-0.006-0.1350.000
5C6LYS10.8290.9042.497-8.878-7.3840.703-0.697-1.5010.005
6C7ALA0-0.0310.0072.452-0.8980.1130.633-0.449-1.195-0.001
7C8VAL0-0.033-0.0073.5860.2520.2320.0440.162-0.1850.000
8C9ILE0-0.0190.0016.664-0.366-0.3660.0000.0000.0000.000
9C10ALA0-0.0320.0019.4790.1280.1280.0000.0000.0000.000
10C11ARG10.8410.88611.2080.3470.3470.0000.0000.0000.000
11C12LEU00.0340.00914.6650.0390.0390.0000.0000.0000.000
12C13ARG10.9350.99317.6210.2560.2560.0000.0000.0000.000
13C14LYS10.9190.95321.1030.3760.3760.0000.0000.0000.000
14C15GLY00.0140.00022.9350.0010.0010.0000.0000.0000.000
15C16GLY0-0.054-0.02926.1890.0080.0080.0000.0000.0000.000
16C17GLU-1-0.877-0.92022.403-0.263-0.2630.0000.0000.0000.000
17C18GLU-1-0.903-0.94119.052-0.335-0.3350.0000.0000.0000.000
18C19PHE00.0180.00216.197-0.004-0.0040.0000.0000.0000.000
19C20GLU-1-0.822-0.91812.615-0.502-0.5020.0000.0000.0000.000
20C21VAL00.0320.0328.420-0.006-0.0060.0000.0000.0000.000
21C22LEU00.0140.0055.5550.1940.1940.0000.0000.0000.000
22C23VAL00.005-0.0063.572-0.876-0.6200.005-0.052-0.2090.000
23C24ASP-1-0.776-0.8822.231-2.876-0.5663.346-2.190-3.466-0.008
24C25PRO0-0.008-0.0232.9701.2450.4200.1301.141-0.445-0.001
25C26TYR0-0.096-0.0636.0080.1070.1070.0000.0000.0000.000
26C27LEU00.0460.0364.6060.0370.147-0.001-0.004-0.1050.000
27C28ALA00.0260.0047.1080.1400.1400.0000.0000.0000.000
28C29ARG10.8260.9028.7200.4330.4330.0000.0000.0000.000
29C30ASP-1-0.873-0.93610.778-0.418-0.4180.0000.0000.0000.000
30C31LEU00.0210.01510.8580.1030.1030.0000.0000.0000.000
31C32LYS10.8520.93212.7510.6140.6140.0000.0000.0000.000
32C33GLU-1-0.902-0.93514.897-0.176-0.1760.0000.0000.0000.000
33C34GLY0-0.055-0.02216.0760.0620.0620.0000.0000.0000.000
34C35LYS10.8590.94314.3740.2990.2990.0000.0000.0000.000
35C36GLU-1-0.927-0.95714.871-0.617-0.6170.0000.0000.0000.000
36C37VAL0-0.017-0.0188.5500.0110.0110.0000.0000.0000.000
37C38ASN00.0300.0288.889-0.166-0.1660.0000.0000.0000.000
38C39PHE0-0.019-0.0457.508-0.419-0.4190.0000.0000.0000.000
39C40GLU-1-0.891-0.9356.558-1.851-1.8510.0000.0000.0000.000
40C41ASP-1-0.944-0.9604.005-2.358-2.1840.000-0.039-0.1350.000
41C42LEU0-0.097-0.0472.573-6.543-4.6590.967-1.193-1.658-0.014
42C43LEU0-0.013-0.0113.036-2.257-0.9370.182-0.711-0.791-0.007
43C44ALA0-0.007-0.0042.009-3.067-2.1794.083-2.480-2.4910.000
44C45ALA0-0.009-0.0222.6574.5810.9580.1883.754-0.320-0.002
45C46GLU-1-0.944-0.9606.390-1.332-1.3320.0000.0000.0000.000
46C47GLU-1-0.867-0.9489.100-0.504-0.5040.0000.0000.0000.000
47C48VAL0-0.0170.00310.602-0.125-0.1250.0000.0000.0000.000
48C49PHE0-0.009-0.0079.2100.1110.1110.0000.0000.0000.000
49C50LYS10.7900.87814.4700.3550.3550.0000.0000.0000.000
50C51ASP-1-0.872-0.94416.290-0.297-0.2970.0000.0000.0000.000
51C52ALA00.0110.00210.6270.0060.0060.0000.0000.0000.000
52C53LYS10.9190.95912.4330.3250.3250.0000.0000.0000.000
53C54LYS10.8910.94413.6120.2610.2610.0000.0000.0000.000
54C55GLY00.0120.02314.1080.0290.0290.0000.0000.0000.000
55C56GLU-1-0.976-0.98315.103-0.302-0.3020.0000.0000.0000.000
56C57ARG10.8950.94914.0860.4810.4810.0000.0000.0000.000
57C58ALA00.0000.00816.2610.0620.0620.0000.0000.0000.000
58C59SER00.0190.00618.104-0.022-0.0220.0000.0000.0000.000
59C60VAL00.0790.02419.813-0.009-0.0090.0000.0000.0000.000
60C61ASP-1-0.920-0.96021.370-0.271-0.2710.0000.0000.0000.000
61C62GLU-1-0.879-0.92722.354-0.323-0.3230.0000.0000.0000.000
62C63LEU0-0.008-0.00116.9470.0040.0040.0000.0000.0000.000
63C64ARG10.9770.98621.0670.3440.3440.0000.0000.0000.000
64C65LYS10.9120.97323.8660.2650.2650.0000.0000.0000.000
65C66ILE0-0.069-0.03122.1790.0180.0180.0000.0000.0000.000
66C67PHE0-0.031-0.04718.1820.0050.0050.0000.0000.0000.000
67C68GLY0-0.0010.02221.992-0.003-0.0030.0000.0000.0000.000
68C69THR0-0.017-0.01519.4440.0120.0120.0000.0000.0000.000
69C70ASP-1-0.946-0.98619.642-0.459-0.4590.0000.0000.0000.000
70C71ASP-1-0.836-0.89015.889-0.814-0.8140.0000.0000.0000.000
71C72VAL00.0630.01711.051-0.006-0.0060.0000.0000.0000.000
72C73PHE00.0350.0189.393-0.111-0.1110.0000.0000.0000.000
73C74GLU-1-0.943-0.98212.526-0.528-0.5280.0000.0000.0000.000
74C75ILE0-0.041-0.03014.7250.0250.0250.0000.0000.0000.000
75C76ALA00.0240.0089.7020.0300.0300.0000.0000.0000.000
76C77ARG10.9560.98211.7960.7580.7580.0000.0000.0000.000
77C78LYS10.8540.92313.2800.5170.5170.0000.0000.0000.000
78C79ILE0-0.023-0.00312.5870.0750.0750.0000.0000.0000.000
79C80ILE00.0140.0128.6040.0760.0760.0000.0000.0000.000
80C81LEU0-0.108-0.06412.7270.1010.1010.0000.0000.0000.000
81C82GLU-1-0.906-0.95715.981-0.351-0.3510.0000.0000.0000.000
82C83GLY0-0.0270.01216.2610.0530.0530.0000.0000.0000.000
83C84GLU-1-0.991-0.99514.864-0.286-0.2860.0000.0000.0000.000
84C85VAL00.0350.0029.407-0.064-0.0640.0000.0000.0000.000
85C86GLN0-0.047-0.02611.3060.1000.1000.0000.0000.0000.000
86C87ILE0-0.0180.0059.4660.0260.0260.0000.0000.0000.000
87C88THR00.0390.00410.0220.0370.0370.0000.0000.0000.000
88C89ALA00.006-0.01412.501-0.013-0.0130.0000.0000.0000.000
89C90GLU-1-0.816-0.89013.6870.2300.2300.0000.0000.0000.000
90C91GLN00.1300.0777.234-0.183-0.1830.0000.0000.0000.000
91C92ARG10.9570.97112.3590.1110.1110.0000.0000.0000.000
92C93ARG10.8600.90515.047-0.201-0.2010.0000.0000.0000.000
93C94GLU-1-0.853-0.91612.4200.4030.4030.0000.0000.0000.000
94C95MET0-0.031-0.01011.935-0.011-0.0110.0000.0000.0000.000
95C96LEU0-0.026-0.00315.361-0.020-0.0200.0000.0000.0000.000
96C97GLU-1-0.952-0.96918.8750.0890.0890.0000.0000.0000.000
97C98ALA0-0.005-0.01016.973-0.004-0.0040.0000.0000.0000.000
98C99LYS10.7950.88917.9290.1490.1490.0000.0000.0000.000
99C100ARG10.9860.99220.147-0.017-0.0170.0000.0000.0000.000
100C101LYS10.9920.98321.986-0.108-0.1080.0000.0000.0000.000
101C102GLN0-0.026-0.00818.093-0.023-0.0230.0000.0000.0000.000
102C103ILE00.0260.02023.444-0.006-0.0060.0000.0000.0000.000
103C104ILE00.0070.01425.869-0.003-0.0030.0000.0000.0000.000
104C105ASN0-0.035-0.02825.0590.0000.0000.0000.0000.0000.000
105C106PHE0-0.0110.00126.6260.0010.0010.0000.0000.0000.000
106C107ILE00.023-0.00428.488-0.002-0.0020.0000.0000.0000.000
107C108SER0-0.076-0.01931.3580.0010.0010.0000.0000.0000.000
108C109ARG10.9950.99126.201-0.007-0.0070.0000.0000.0000.000
109C110ASN0-0.059-0.02830.499-0.005-0.0050.0000.0000.0000.000
110C111THR0-0.094-0.05033.902-0.005-0.0050.0000.0000.0000.000
111C112ILE00.014-0.01236.7110.0050.0050.0000.0000.0000.000
112C113ASP-1-0.861-0.97440.083-0.005-0.0050.0000.0000.0000.000
113C114PRO0-0.059-0.03642.6700.0020.0020.0000.0000.0000.000
114C115ARG10.8970.94645.9840.0030.0030.0000.0000.0000.000
115C116THR0-0.015-0.02246.4380.0000.0000.0000.0000.0000.000
116C117ASN0-0.0230.01345.4810.0000.0000.0000.0000.0000.000
117C118ALA00.0550.02242.5010.0030.0030.0000.0000.0000.000
118C119PRO00.0350.08237.343-0.004-0.0040.0000.0000.0000.000
119C120HIS00.0270.02236.8170.0070.0070.0000.0000.0000.000
120C121PRO00.0510.03335.9170.0000.0000.0000.0000.0000.000
121C122PRO00.1130.02130.634-0.003-0.0030.0000.0000.0000.000
122C123SER00.0190.01932.648-0.005-0.0050.0000.0000.0000.000
123C124ARG10.9100.97334.160-0.008-0.0080.0000.0000.0000.000
124C125ILE00.007-0.00531.369-0.005-0.0050.0000.0000.0000.000
125C126GLU-1-0.894-0.96728.6590.0360.0360.0000.0000.0000.000
126C127ARG10.9800.99131.666-0.025-0.0250.0000.0000.0000.000
127C128ALA0-0.022-0.00934.626-0.003-0.0030.0000.0000.0000.000
128C129LEU0-0.004-0.01128.177-0.007-0.0070.0000.0000.0000.000
129C130GLU-1-0.933-0.95930.7130.0220.0220.0000.0000.0000.000
130C131GLU-1-0.942-0.97732.489-0.002-0.0020.0000.0000.0000.000
131C132ALA0-0.042-0.01134.473-0.002-0.0020.0000.0000.0000.000
132C133LYS10.8690.93331.6990.0250.0250.0000.0000.0000.000
133C134VAL0-0.032-0.00928.593-0.008-0.0080.0000.0000.0000.000
134C135HIS0-0.0120.00223.3950.0180.0180.0000.0000.0000.000
135C136ILE0-0.015-0.01621.626-0.003-0.0030.0000.0000.0000.000
136C137ASP-1-0.856-0.93319.917-0.212-0.2120.0000.0000.0000.000
137C138ILE0-0.017-0.01715.0760.0060.0060.0000.0000.0000.000
138C139PHE00.008-0.00312.526-0.018-0.0180.0000.0000.0000.000
139C140LYS10.9851.01517.0970.1690.1690.0000.0000.0000.000
140C141SER00.0820.03720.1430.0270.0270.0000.0000.0000.000
141C142VAL00.0470.01220.9890.0120.0120.0000.0000.0000.000
142C143GLU-1-0.899-0.97322.862-0.120-0.1200.0000.0000.0000.000
143C144ALA0-0.041-0.00723.5370.0060.0060.0000.0000.0000.000
144C145GLN0-0.025-0.02321.6800.0150.0150.0000.0000.0000.000
145C146VAL0-0.022-0.00726.6640.0130.0130.0000.0000.0000.000
146C147LYS10.9600.96328.8510.1030.1030.0000.0000.0000.000
147C148ASP-1-0.928-0.95829.879-0.098-0.0980.0000.0000.0000.000
148C149ILE00.0480.02026.5080.0080.0080.0000.0000.0000.000
149C150VAL00.0720.03831.0300.0080.0080.0000.0000.0000.000
150C151LYS10.8040.90833.9850.0800.0800.0000.0000.0000.000
151C152ALA00.0140.01333.244-0.001-0.0010.0000.0000.0000.000
152C153LEU00.0120.00632.7270.0040.0040.0000.0000.0000.000
153C154LYS10.8460.93636.4030.0460.0460.0000.0000.0000.000
154C155PRO0-0.012-0.01738.8750.0030.0030.0000.0000.0000.000
155C156ILE00.0370.03637.1240.0020.0020.0000.0000.0000.000
156C157LEU0-0.046-0.01236.3220.0050.0050.0000.0000.0000.000
157C158PRO0-0.0320.00339.685-0.004-0.0040.0000.0000.0000.000
158C159LEU00.0440.00135.1800.0020.0020.0000.0000.0000.000
159C160LYS10.8760.94839.3610.0260.0260.0000.0000.0000.000
160C161PHE00.014-0.00132.4100.0010.0010.0000.0000.0000.000
161C162GLU-1-0.916-0.95737.742-0.022-0.0220.0000.0000.0000.000
162C163GLU-1-0.772-0.84536.630-0.047-0.0470.0000.0000.0000.000
163C164MET0-0.055-0.01939.3980.0010.0010.0000.0000.0000.000
164C165GLU-1-0.812-0.89441.162-0.034-0.0340.0000.0000.0000.000
165C166ILE0-0.021-0.01942.2890.0010.0010.0000.0000.0000.000
166C167ALA0-0.0170.00044.6600.0000.0000.0000.0000.0000.000
167C168ILE00.0360.00243.5710.0030.0030.0000.0000.0000.000
168C169LYS10.9700.98846.942-0.004-0.0040.0000.0000.0000.000
169C170ILE0-0.029-0.02744.8470.0020.0020.0000.0000.0000.000
170C171PRO00.0150.01348.433-0.002-0.0020.0000.0000.0000.000
171C172PRO00.030-0.00349.7450.0010.0010.0000.0000.0000.000
172C173GLU-1-0.872-0.94549.9860.0190.0190.0000.0000.0000.000
173C174HIS00.018-0.00346.5330.0040.0040.0000.0000.0000.000
174C175THR0-0.050-0.00945.2690.0010.0010.0000.0000.0000.000
175C176GLY00.0310.01843.663-0.001-0.0010.0000.0000.0000.000
176C177ARG10.8420.89139.936-0.045-0.0450.0000.0000.0000.000
177C178ALA00.0050.00240.8460.0020.0020.0000.0000.0000.000
178C179ILE00.0300.02340.051-0.001-0.0010.0000.0000.0000.000
179C180SER0-0.0040.00736.379-0.003-0.0030.0000.0000.0000.000
180C181ALA00.0410.01035.750-0.001-0.0010.0000.0000.0000.000
181C182LEU00.0160.00335.694-0.001-0.0010.0000.0000.0000.000
182C183TYR0-0.063-0.09134.583-0.002-0.0020.0000.0000.0000.000
183C184ASN0-0.065-0.02230.535-0.005-0.0050.0000.0000.0000.000
184C185PHE0-0.070-0.02631.4470.0000.0000.0000.0000.0000.000
185C186GLY00.0330.03132.553-0.004-0.0040.0000.0000.0000.000
186C187GLY00.029-0.00633.4160.0020.0020.0000.0000.0000.000
187C188VAL0-0.043-0.00436.110-0.001-0.0010.0000.0000.0000.000
188C189THR0-0.012-0.02238.104-0.006-0.0060.0000.0000.0000.000
189C190ARG10.9210.94040.7550.0310.0310.0000.0000.0000.000
190C191GLU-1-0.816-0.85539.654-0.019-0.0190.0000.0000.0000.000
191C192GLU-1-0.888-0.95043.979-0.014-0.0140.0000.0000.0000.000
192C193TRP0-0.012-0.01044.0280.0020.0020.0000.0000.0000.000
193C194GLN0-0.080-0.03948.654-0.001-0.0010.0000.0000.0000.000
194C195ARG10.9440.96152.3340.0030.0030.0000.0000.0000.000
195C196ASP-1-0.897-0.95955.2820.0050.0050.0000.0000.0000.000
196C197GLY00.0350.03351.8320.0020.0020.0000.0000.0000.000
197C198SER0-0.057-0.00950.5510.0010.0010.0000.0000.0000.000
198C199TRP00.0660.00441.636-0.001-0.0010.0000.0000.0000.000
199C200ILE0-0.0190.00247.5200.0020.0020.0000.0000.0000.000
200C201CYS00.0020.01941.740-0.001-0.0010.0000.0000.0000.000
201C202VAL0-0.049-0.02043.1930.0010.0010.0000.0000.0000.000
202C203MET0-0.0070.03337.781-0.003-0.0030.0000.0000.0000.000
203C204ARG10.8060.88537.7340.0450.0450.0000.0000.0000.000
204C205ILE00.0010.00136.410-0.001-0.0010.0000.0000.0000.000
205C206PRO00.0720.03933.183-0.002-0.0020.0000.0000.0000.000
206C207SER00.020-0.05136.4010.0050.0050.0000.0000.0000.000
207C208GLY0-0.0170.00936.6160.0040.0040.0000.0000.0000.000
208C209MET0-0.0150.00032.5770.0050.0050.0000.0000.0000.000
209C210TYR0-0.015-0.01536.7790.0040.0040.0000.0000.0000.000
210C211GLY0-0.012-0.01740.2520.0010.0010.0000.0000.0000.000
211C212ASP-1-0.806-0.89835.3480.0310.0310.0000.0000.0000.000
212C213LEU0-0.057-0.02238.1830.0020.0020.0000.0000.0000.000
213C214MET0-0.045-0.03839.7120.0010.0010.0000.0000.0000.000
214C215ASP-1-0.870-0.92140.0030.0340.0340.0000.0000.0000.000
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