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: 94YQ2

Calculation Name: 1AIP-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AIP

Chain ID: C

ChEMBL ID:

UniProt ID: P43895

Base Structure: X-ray

Registration Date: 2023-06-21

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2044444.138329
FMO2-HF: Nuclear repulsion 1965718.068398
FMO2-HF: Total energy -78726.069931
FMO2-MP2: Total energy -78954.012728


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:SER)


Summations of interaction energy for fragment #1(C:2:SER)
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.
-13.589-11.42510.638-5.268-7.5340.034
Interaction energy analysis for fragmet #1(C:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.080 / q_NPA : 0.031
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].
3C4MET0-0.040-0.0322.292-7.346-4.8163.515-2.558-3.4860.025
4C5GLU-1-0.904-0.9901.789-5.321-6.7147.115-2.426-3.2960.009
5C6LEU00.0480.0713.722-0.6980.1910.009-0.274-0.6250.000
6C7ILE00.0820.0295.0910.4790.617-0.001-0.010-0.1270.000
7C8LYS10.8730.9406.0480.2440.2440.0000.0000.0000.000
8C9LYS10.9520.9917.0150.7860.7860.0000.0000.0000.000
9C10LEU00.0590.0368.7210.1420.1420.0000.0000.0000.000
10C11ARG10.7830.87510.4130.2570.2570.0000.0000.0000.000
11C12GLU-1-0.988-0.98111.451-0.258-0.2580.0000.0000.0000.000
12C13ALA00.0420.05412.8550.0400.0400.0000.0000.0000.000
13C14THR0-0.069-0.06214.5050.0690.0690.0000.0000.0000.000
14C15GLY00.0070.02016.0720.0380.0380.0000.0000.0000.000
15C16ALA00.0610.02616.5620.0290.0290.0000.0000.0000.000
16C17GLY00.0780.01917.0060.0090.0090.0000.0000.0000.000
17C18MET00.0140.01012.0050.0180.0180.0000.0000.0000.000
18C19MET0-0.001-0.01113.6610.0130.0130.0000.0000.0000.000
19C20ASP-1-0.834-0.91815.425-0.062-0.0620.0000.0000.0000.000
20C21VAL0-0.0460.00511.457-0.030-0.0300.0000.0000.0000.000
21C22LYS10.9550.97310.415-0.433-0.4330.0000.0000.0000.000
22C23ARG10.9200.94212.346-0.037-0.0370.0000.0000.0000.000
23C24ALA00.0490.03114.726-0.005-0.0050.0000.0000.0000.000
24C25LEU00.0320.0038.632-0.030-0.0300.0000.0000.0000.000
25C26GLU-1-1.001-1.00712.2510.1030.1030.0000.0000.0000.000
26C27ASP-1-0.962-1.00513.841-0.105-0.1050.0000.0000.0000.000
27C28ALA0-0.039-0.00715.1840.0190.0190.0000.0000.0000.000
28C29GLY00.0050.01713.379-0.047-0.0470.0000.0000.0000.000
29C30TRP0-0.019-0.0147.1350.1310.1310.0000.0000.0000.000
30C31ASP-1-0.840-0.9378.365-0.988-0.9880.0000.0000.0000.000
31C32GLU-1-0.879-0.9428.368-1.345-1.3450.0000.0000.0000.000
32C33GLU-1-0.870-0.92211.879-0.473-0.4730.0000.0000.0000.000
33C34LYS10.8090.89313.1180.5620.5620.0000.0000.0000.000
34C35ALA00.0980.05112.7560.0560.0560.0000.0000.0000.000
35C36VAL0-0.042-0.01313.4390.0760.0760.0000.0000.0000.000
36C37GLN00.0050.00515.7810.0600.0600.0000.0000.0000.000
37C38LEU00.1080.04517.4320.0380.0380.0000.0000.0000.000
38C39LEU0-0.126-0.05914.4330.0390.0390.0000.0000.0000.000
39C40ARG10.8910.93917.8450.2970.2970.0000.0000.0000.000
40C41GLU-1-0.936-0.95821.337-0.132-0.1320.0000.0000.0000.000
41C42ARG10.8260.92117.9580.1600.1600.0000.0000.0000.000
42C43GLY0-0.040-0.03922.7510.0180.0180.0000.0000.0000.000
43C44ALA00.0820.04224.0420.0130.0130.0000.0000.0000.000
44C45MET0-0.0020.00625.6130.0140.0140.0000.0000.0000.000
45C46LYS10.8790.95522.0000.0970.0970.0000.0000.0000.000
46C47ALA00.0460.02827.9740.0080.0080.0000.0000.0000.000
47C48ALA00.0270.01229.8990.0060.0060.0000.0000.0000.000
48C49LYS10.8530.93530.6160.0490.0490.0000.0000.0000.000
49C50LYS10.8840.91729.4210.0550.0550.0000.0000.0000.000
50C51ALA00.0420.04534.2110.0020.0020.0000.0000.0000.000
51C52ASP-1-0.863-0.93036.271-0.036-0.0360.0000.0000.0000.000
52C53ARG10.7300.87032.2290.0370.0370.0000.0000.0000.000
53C54GLU-1-0.813-0.90138.434-0.029-0.0290.0000.0000.0000.000
54C55ALA00.002-0.01637.3790.0000.0000.0000.0000.0000.000
55C56ARG10.7720.87939.4130.0270.0270.0000.0000.0000.000
56C57GLU-1-0.851-0.90938.092-0.032-0.0320.0000.0000.0000.000
57C58GLY0-0.001-0.00537.192-0.002-0.0020.0000.0000.0000.000
58C59ILE0-0.039-0.02336.4650.0020.0020.0000.0000.0000.000
59C60ILE0-0.038-0.01539.661-0.001-0.0010.0000.0000.0000.000
60C61GLY00.0140.00838.7700.0000.0000.0000.0000.0000.000
61C62HIS0-0.008-0.02739.5660.0020.0020.0000.0000.0000.000
62C63TYR00.0330.00038.930-0.004-0.0040.0000.0000.0000.000
63C64ILE0-0.026-0.00241.2420.0030.0030.0000.0000.0000.000
64C65HIS00.0530.03141.846-0.002-0.0020.0000.0000.0000.000
65C66HIS00.0410.01042.3020.0040.0040.0000.0000.0000.000
66C67ASN0-0.0090.01044.2470.0020.0020.0000.0000.0000.000
67C68GLN0-0.004-0.02447.0530.0030.0030.0000.0000.0000.000
68C69ARG10.9160.97048.5990.0360.0360.0000.0000.0000.000
69C70VAL00.0200.01845.4790.0010.0010.0000.0000.0000.000
70C71GLY0-0.0160.00045.578-0.001-0.0010.0000.0000.0000.000
71C72VAL0-0.032-0.01741.7500.0010.0010.0000.0000.0000.000
72C73LEU0-0.021-0.01243.5370.0000.0000.0000.0000.0000.000
73C74VAL00.0140.00238.9890.0000.0000.0000.0000.0000.000
74C75GLU-1-0.836-0.88841.024-0.037-0.0370.0000.0000.0000.000
75C76LEU0-0.0080.00233.781-0.001-0.0010.0000.0000.0000.000
76C77ASN00.0240.00738.2240.0020.0020.0000.0000.0000.000
77C78CYS0-0.0250.00533.997-0.004-0.0040.0000.0000.0000.000
78C79GLU-1-0.805-0.91434.290-0.036-0.0360.0000.0000.0000.000
79C80THR0-0.078-0.06133.1380.0040.0040.0000.0000.0000.000
80C81ASP-1-0.826-0.92035.198-0.036-0.0360.0000.0000.0000.000
81C82PHE0-0.028-0.02731.789-0.002-0.0020.0000.0000.0000.000
82C83VAL0-0.018-0.00529.778-0.005-0.0050.0000.0000.0000.000
83C84ALA00.0250.02631.722-0.005-0.0050.0000.0000.0000.000
84C85ARG10.9090.94633.2140.0350.0350.0000.0000.0000.000
85C86ASN0-0.031-0.01726.005-0.007-0.0070.0000.0000.0000.000
86C87GLU-1-0.904-0.96025.591-0.110-0.1100.0000.0000.0000.000
87C88LEU00.0240.01123.131-0.003-0.0030.0000.0000.0000.000
88C89PHE0-0.0140.01727.548-0.001-0.0010.0000.0000.0000.000
89C90GLN0-0.022-0.02330.9120.0000.0000.0000.0000.0000.000
90C91ASN00.0010.00226.9350.0070.0070.0000.0000.0000.000
91C92LEU00.0140.02029.6800.0010.0010.0000.0000.0000.000
92C93ALA00.0420.01231.0290.0020.0020.0000.0000.0000.000
93C94LYN0-0.0050.01233.3000.0030.0030.0000.0000.0000.000
94C95ASP-1-0.919-0.97529.840-0.096-0.0960.0000.0000.0000.000
95C96LEU0-0.042-0.02633.4620.0020.0020.0000.0000.0000.000
96C97ALA00.0000.00635.5600.0030.0030.0000.0000.0000.000
97C98MET0-0.025-0.02234.8760.0010.0010.0000.0000.0000.000
98C99HIS00.014-0.00435.391-0.002-0.0020.0000.0000.0000.000
99C100ILE0-0.0030.00137.3570.0020.0020.0000.0000.0000.000
100C101ALA0-0.023-0.01240.7160.0030.0030.0000.0000.0000.000
101C102MET0-0.044-0.01639.3730.0030.0030.0000.0000.0000.000
102C103MET0-0.006-0.01737.0830.0030.0030.0000.0000.0000.000
103C104ASN0-0.078-0.02441.4490.0020.0020.0000.0000.0000.000
104C105PRO0-0.0190.01041.3700.0010.0010.0000.0000.0000.000
105C106ARG10.9090.95443.9810.0380.0380.0000.0000.0000.000
106C107TYR00.007-0.01545.1700.0020.0020.0000.0000.0000.000
107C108VAL0-0.0260.00140.639-0.004-0.0040.0000.0000.0000.000
108C109SER00.019-0.03041.013-0.003-0.0030.0000.0000.0000.000
109C110ALA00.0240.01042.0840.0020.0020.0000.0000.0000.000
110C111GLU-1-0.876-0.93442.226-0.045-0.0450.0000.0000.0000.000
111C112GLU-1-0.888-0.94145.430-0.040-0.0400.0000.0000.0000.000
112C113ILE0-0.047-0.03546.4770.0020.0020.0000.0000.0000.000
113C114PRO00.0090.01249.4510.0000.0000.0000.0000.0000.000
114C115ALA00.0910.02350.6940.0000.0000.0000.0000.0000.000
115C116GLU-1-0.893-0.96051.724-0.026-0.0260.0000.0000.0000.000
116C117GLU-1-0.968-0.98253.462-0.031-0.0310.0000.0000.0000.000
117C118LEU00.0170.02248.0310.0000.0000.0000.0000.0000.000
118C119GLU-1-0.843-0.93151.862-0.033-0.0330.0000.0000.0000.000
119C120LYS10.7960.90153.4760.0310.0310.0000.0000.0000.000
120C121GLU-1-0.842-0.98651.589-0.035-0.0350.0000.0000.0000.000
121C122ARG10.9441.00550.1480.0330.0330.0000.0000.0000.000
122C123GLN0-0.012-0.00752.8700.0000.0000.0000.0000.0000.000
123C124ILE0-0.0580.01855.8380.0010.0010.0000.0000.0000.000
124C125TYR0-0.102-0.07349.161-0.001-0.0010.0000.0000.0000.000
125C126ILE00.0010.00353.1680.0000.0000.0000.0000.0000.000
126C127GLN0-0.017-0.00855.4810.0010.0010.0000.0000.0000.000
127C128ALA0-0.001-0.02256.3760.0010.0010.0000.0000.0000.000
128C129ALA00.0320.03154.4700.0000.0000.0000.0000.0000.000
129C130LEU00.0060.00756.4490.0000.0000.0000.0000.0000.000
130C131ASN0-0.093-0.03859.3990.0010.0010.0000.0000.0000.000
131C132GLU-1-0.942-0.95955.324-0.033-0.0330.0000.0000.0000.000
132C133GLY0-0.0170.00159.0870.0000.0000.0000.0000.0000.000
133C134LYS10.8470.93453.3800.0330.0330.0000.0000.0000.000
134C135PRO0-0.026-0.00655.1630.0010.0010.0000.0000.0000.000
135C136GLN00.0900.01655.970-0.001-0.0010.0000.0000.0000.000
136C137GLN00.0970.03852.8790.0000.0000.0000.0000.0000.000
137C138ILE0-0.092-0.03650.438-0.002-0.0020.0000.0000.0000.000
138C139ALA00.010-0.02151.067-0.002-0.0020.0000.0000.0000.000
139C140GLU-1-0.880-0.93751.095-0.032-0.0320.0000.0000.0000.000
140C141LYS10.9170.96545.6430.0410.0410.0000.0000.0000.000
141C142ILE00.0080.00747.081-0.002-0.0020.0000.0000.0000.000
142C143ALA00.0640.03047.856-0.002-0.0020.0000.0000.0000.000
143C144GLU-1-0.856-0.92444.396-0.046-0.0460.0000.0000.0000.000
144C145GLY0-0.0080.00443.304-0.002-0.0020.0000.0000.0000.000
145C146ARG10.8770.95044.3240.0410.0410.0000.0000.0000.000
146C147LEU00.0420.00846.499-0.001-0.0010.0000.0000.0000.000
147C148LYS10.8250.89837.2790.0690.0690.0000.0000.0000.000
148C149LYS10.8920.94342.2390.0480.0480.0000.0000.0000.000
149C150TYR00.0580.02943.313-0.001-0.0010.0000.0000.0000.000
150C151LEU00.016-0.00142.4500.0000.0000.0000.0000.0000.000
151C152GLU-1-0.855-0.90438.119-0.074-0.0740.0000.0000.0000.000
152C153GLU-1-0.932-0.96840.568-0.052-0.0520.0000.0000.0000.000
153C154VAL00.0180.02543.3100.0000.0000.0000.0000.0000.000
154C155VAL0-0.0310.00840.5030.0010.0010.0000.0000.0000.000
155C156LEU00.0270.01837.607-0.003-0.0030.0000.0000.0000.000
156C157LEU00.0080.00335.809-0.005-0.0050.0000.0000.0000.000
157C158GLU-1-0.838-0.92735.821-0.073-0.0730.0000.0000.0000.000
158C159GLN0-0.0030.00637.376-0.004-0.0040.0000.0000.0000.000
159C160PRO0-0.0140.00933.991-0.004-0.0040.0000.0000.0000.000
160C161PHE00.019-0.01528.8100.0050.0050.0000.0000.0000.000
161C162VAL00.0350.00632.519-0.003-0.0030.0000.0000.0000.000
162C163LYS10.8470.93529.4800.1010.1010.0000.0000.0000.000
163C164ASP-1-0.890-0.96826.037-0.161-0.1610.0000.0000.0000.000
164C165ASP-1-0.929-0.93329.282-0.107-0.1070.0000.0000.0000.000
165C166LYS10.9080.96423.5930.1830.1830.0000.0000.0000.000
166C167VAL0-0.048-0.01826.049-0.002-0.0020.0000.0000.0000.000
167C168LYS10.8830.95429.2670.0840.0840.0000.0000.0000.000
168C169VAL00.0460.02031.127-0.006-0.0060.0000.0000.0000.000
169C170LYS10.8220.89831.7510.0680.0680.0000.0000.0000.000
170C171GLU-1-0.908-0.95327.670-0.124-0.1240.0000.0000.0000.000
171C172LEU0-0.0060.01827.150-0.008-0.0080.0000.0000.0000.000
172C173ILE00.018-0.00127.996-0.003-0.0030.0000.0000.0000.000
173C174GLN0-0.027-0.02028.314-0.006-0.0060.0000.0000.0000.000
174C175GLN0-0.002-0.00621.3800.0030.0030.0000.0000.0000.000
175C176ALA0-0.006-0.00724.467-0.006-0.0060.0000.0000.0000.000
176C177ILE00.0130.00826.0640.0010.0010.0000.0000.0000.000
177C178ALA0-0.071-0.02723.3550.0060.0060.0000.0000.0000.000
178C179LYS10.8730.94519.9130.1920.1920.0000.0000.0000.000
179C180ILE0-0.0360.00923.0650.0050.0050.0000.0000.0000.000
180C181GLY0-0.054-0.03226.2210.0080.0080.0000.0000.0000.000
181C182GLU-1-0.806-0.88627.991-0.037-0.0370.0000.0000.0000.000
182C183ASN0-0.046-0.02831.369-0.011-0.0110.0000.0000.0000.000
183C184ILE0-0.003-0.00230.3050.0010.0010.0000.0000.0000.000
184C185VAL0-0.021-0.00834.155-0.002-0.0020.0000.0000.0000.000
185C186VAL00.0150.01136.7280.0000.0000.0000.0000.0000.000
186C187ARG10.8650.92539.1870.0410.0410.0000.0000.0000.000
187C188ARG10.8920.92642.7200.0360.0360.0000.0000.0000.000
188C189PHE00.0390.02042.469-0.002-0.0020.0000.0000.0000.000
189C190CYS0-0.064-0.02644.4580.0030.0030.0000.0000.0000.000
190C191ARG10.9060.97144.7960.0440.0440.0000.0000.0000.000
191C192PHE0-0.037-0.00647.4160.0020.0020.0000.0000.0000.000
192C193GLU-1-0.854-0.93249.108-0.043-0.0430.0000.0000.0000.000
193C194LEU0-0.052-0.05550.6230.0020.0020.0000.0000.0000.000
194C195GLY0-0.051-0.01953.6010.0000.0000.0000.0000.0000.000
195C196ALA00.0190.02152.7320.0010.0010.0000.0000.0000.000