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: MVMZZ

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2042690.058693
FMO2-HF: Nuclear repulsion 1963961.304632
FMO2-HF: Total energy -78728.754061
FMO2-MP2: Total energy -78956.400595


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.
-11.904-6.5653.886-3.62-5.6030.013
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 : 0.051 / q_NPA : 0.019
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].
3C4MET0-0.009-0.0142.542-7.184-3.3970.951-2.049-2.6890.019
4C5GLU-1-0.798-0.9292.019-5.107-4.3662.926-1.411-2.255-0.006
5C6LEU00.0640.0593.589-0.2960.3820.010-0.151-0.5370.000
6C7ILE00.0750.0415.1410.6280.761-0.001-0.009-0.1220.000
7C8LYS10.7520.8706.4560.6720.6720.0000.0000.0000.000
8C9LYS10.8810.9467.0520.9220.9220.0000.0000.0000.000
9C10LEU00.0500.0358.7620.1880.1880.0000.0000.0000.000
10C11ARG10.8090.89410.4500.3630.3630.0000.0000.0000.000
11C12GLU-1-0.896-0.93211.434-0.434-0.4340.0000.0000.0000.000
12C13ALA00.0380.04512.8800.0600.0600.0000.0000.0000.000
13C14THR0-0.032-0.04614.5710.0820.0820.0000.0000.0000.000
14C15GLY0-0.0170.00316.0840.0450.0450.0000.0000.0000.000
15C16ALA00.0740.03116.5940.0360.0360.0000.0000.0000.000
16C17GLY00.0460.00516.8140.0020.0020.0000.0000.0000.000
17C18MET00.0250.02211.4910.0110.0110.0000.0000.0000.000
18C19MET00.017-0.00113.982-0.003-0.0030.0000.0000.0000.000
19C20ASP-1-0.812-0.89315.707-0.103-0.1030.0000.0000.0000.000
20C21VAL0-0.0240.00211.628-0.031-0.0310.0000.0000.0000.000
21C22LYS10.8120.89310.907-0.256-0.2560.0000.0000.0000.000
22C23ARG10.8820.92712.5660.0130.0130.0000.0000.0000.000
23C24ALA00.0740.03814.9110.0000.0000.0000.0000.0000.000
24C25LEU00.0350.0038.783-0.026-0.0260.0000.0000.0000.000
25C26GLU-1-0.897-0.93312.1980.1300.1300.0000.0000.0000.000
26C27ASP-1-0.856-0.93413.841-0.134-0.1340.0000.0000.0000.000
27C28ALA0-0.028-0.00315.1390.0280.0280.0000.0000.0000.000
28C29GLY00.0190.02513.348-0.050-0.0500.0000.0000.0000.000
29C30TRP0-0.010-0.0137.1100.0860.0860.0000.0000.0000.000
30C31ASP-1-0.863-0.9478.329-0.923-0.9230.0000.0000.0000.000
31C32GLU-1-0.868-0.9538.545-1.466-1.4660.0000.0000.0000.000
32C33GLU-1-0.880-0.92311.825-0.456-0.4560.0000.0000.0000.000
33C34LYS10.8140.90713.2760.5790.5790.0000.0000.0000.000
34C35ALA00.0830.03712.7170.0520.0520.0000.0000.0000.000
35C36VAL0-0.044-0.01213.4210.0740.0740.0000.0000.0000.000
36C37GLN00.0060.00515.8380.0590.0590.0000.0000.0000.000
37C38LEU00.0860.05117.5960.0400.0400.0000.0000.0000.000
38C39LEU0-0.092-0.04914.4770.0380.0380.0000.0000.0000.000
39C40ARG10.9190.95917.1800.3510.3510.0000.0000.0000.000
40C41GLU-1-0.937-0.96421.392-0.146-0.1460.0000.0000.0000.000
41C42ARG10.7560.86018.7030.1840.1840.0000.0000.0000.000
42C43GLY0-0.048-0.03222.7920.0180.0180.0000.0000.0000.000
43C44ALA00.0670.03324.0930.0140.0140.0000.0000.0000.000
44C45MET0-0.0030.00125.7930.0160.0160.0000.0000.0000.000
45C46LYS10.8540.91722.0020.1280.1280.0000.0000.0000.000
46C47ALA00.0380.02628.0240.0100.0100.0000.0000.0000.000
47C48ALA00.0210.00729.9460.0070.0070.0000.0000.0000.000
48C49LYS10.8580.93331.0020.0650.0650.0000.0000.0000.000
49C50LYS10.7380.85430.6430.0700.0700.0000.0000.0000.000
50C51ALA00.0460.03834.2550.0020.0020.0000.0000.0000.000
51C52ASP-1-0.873-0.93436.317-0.046-0.0460.0000.0000.0000.000
52C53ARG10.7380.85433.1720.0500.0500.0000.0000.0000.000
53C54GLU-1-0.818-0.89338.439-0.037-0.0370.0000.0000.0000.000
54C55ALA0-0.006-0.01937.422-0.001-0.0010.0000.0000.0000.000
55C56ARG10.7960.88339.3460.0360.0360.0000.0000.0000.000
56C57GLU-1-0.876-0.91937.974-0.041-0.0410.0000.0000.0000.000
57C58GLY00.008-0.00337.126-0.002-0.0020.0000.0000.0000.000
58C59ILE0-0.044-0.02435.9750.0020.0020.0000.0000.0000.000
59C60ILE0-0.034-0.01639.676-0.001-0.0010.0000.0000.0000.000
60C61GLY00.0070.00738.789-0.001-0.0010.0000.0000.0000.000
61C62HIS0-0.014-0.03639.5810.0020.0020.0000.0000.0000.000
62C63TYR00.0370.00838.494-0.004-0.0040.0000.0000.0000.000
63C64ILE0-0.023-0.00741.2550.0030.0030.0000.0000.0000.000
64C65HIS00.0560.03241.870-0.002-0.0020.0000.0000.0000.000
65C66HIS00.0340.00942.4620.0040.0040.0000.0000.0000.000
66C67ASN0-0.013-0.01144.2510.0020.0020.0000.0000.0000.000
67C68GLN0-0.022-0.01947.0560.0030.0030.0000.0000.0000.000
68C69ARG10.9320.98348.6610.0400.0400.0000.0000.0000.000
69C70VAL00.0060.00945.7350.0010.0010.0000.0000.0000.000
70C71GLY0-0.0120.00745.596-0.001-0.0010.0000.0000.0000.000
71C72VAL0-0.022-0.00941.7930.0010.0010.0000.0000.0000.000
72C73LEU0-0.032-0.01943.553-0.001-0.0010.0000.0000.0000.000
73C74VAL00.0180.00239.0340.0000.0000.0000.0000.0000.000
74C75GLU-1-0.824-0.87341.045-0.046-0.0460.0000.0000.0000.000
75C76LEU0-0.0060.00433.775-0.001-0.0010.0000.0000.0000.000
76C77ASN00.021-0.00738.2460.0020.0020.0000.0000.0000.000
77C78CYS0-0.0210.00333.822-0.005-0.0050.0000.0000.0000.000
78C79GLU-1-0.734-0.84333.991-0.050-0.0500.0000.0000.0000.000
79C80THR0-0.044-0.05533.0680.0040.0040.0000.0000.0000.000
80C81ASP-1-0.777-0.89635.034-0.048-0.0480.0000.0000.0000.000
81C82PHE0-0.027-0.01931.684-0.002-0.0020.0000.0000.0000.000
82C83VAL0-0.0040.00529.469-0.005-0.0050.0000.0000.0000.000
83C84ALA00.0330.03231.573-0.005-0.0050.0000.0000.0000.000
84C85ARG10.8610.92233.1680.0440.0440.0000.0000.0000.000
85C86ASN0-0.044-0.02125.847-0.009-0.0090.0000.0000.0000.000
86C87GLU-1-0.860-0.94726.190-0.129-0.1290.0000.0000.0000.000
87C88LEU00.0460.02223.082-0.004-0.0040.0000.0000.0000.000
88C89PHE0-0.0200.00827.561-0.001-0.0010.0000.0000.0000.000
89C90GLN0-0.026-0.03230.9290.0030.0030.0000.0000.0000.000
90C91ASN0-0.027-0.00827.3550.0080.0080.0000.0000.0000.000
91C92LEU00.0000.01029.6010.0020.0020.0000.0000.0000.000
92C93ALA00.0330.01131.0500.0030.0030.0000.0000.0000.000
93C94LYN0-0.0040.01733.3980.0040.0040.0000.0000.0000.000
94C95ASP-1-0.797-0.90329.954-0.111-0.1110.0000.0000.0000.000
95C96LEU0-0.033-0.02133.4810.0020.0020.0000.0000.0000.000
96C97ALA0-0.0020.00335.5850.0040.0040.0000.0000.0000.000
97C98MET0-0.022-0.02034.4170.0020.0020.0000.0000.0000.000
98C99HIS00.0340.00535.351-0.002-0.0020.0000.0000.0000.000
99C100ILE0-0.0040.00137.3820.0030.0030.0000.0000.0000.000
100C101ALA0-0.015-0.00740.7430.0040.0040.0000.0000.0000.000
101C102MET0-0.033-0.00739.3300.0040.0040.0000.0000.0000.000
102C103MET0-0.008-0.01936.8390.0030.0030.0000.0000.0000.000
103C104ASN0-0.054-0.00341.4800.0030.0030.0000.0000.0000.000
104C105PRO0-0.0230.00441.2320.0020.0020.0000.0000.0000.000
105C106ARG10.8760.93844.0160.0440.0440.0000.0000.0000.000
106C107TYR00.012-0.01345.2900.0020.0020.0000.0000.0000.000
107C108VAL0-0.023-0.01040.693-0.004-0.0040.0000.0000.0000.000
108C109SER0-0.039-0.07041.054-0.003-0.0030.0000.0000.0000.000
109C110ALA00.0430.01342.1140.0020.0020.0000.0000.0000.000
110C111GLU-1-0.837-0.88942.565-0.053-0.0530.0000.0000.0000.000
111C112GLU-1-0.877-0.92645.475-0.047-0.0470.0000.0000.0000.000
112C113ILE0-0.065-0.03746.5650.0020.0020.0000.0000.0000.000
113C114PRO00.0250.00949.4980.0000.0000.0000.0000.0000.000
114C115ALA00.0790.02550.7520.0000.0000.0000.0000.0000.000
115C116GLU-1-0.917-0.96351.777-0.030-0.0300.0000.0000.0000.000
116C117GLU-1-0.938-0.96653.554-0.037-0.0370.0000.0000.0000.000
117C118LEU00.0180.00147.9610.0000.0000.0000.0000.0000.000
118C119GLU-1-0.724-0.81851.914-0.037-0.0370.0000.0000.0000.000
119C120LYS10.8010.89853.5310.0360.0360.0000.0000.0000.000
120C121GLU-1-0.867-0.93751.840-0.038-0.0380.0000.0000.0000.000
121C122ARG10.8670.91650.1130.0370.0370.0000.0000.0000.000
122C123GLN0-0.019-0.02052.9260.0000.0000.0000.0000.0000.000
123C124ILE0-0.0210.00155.9530.0010.0010.0000.0000.0000.000
124C125TYR0-0.110-0.08749.519-0.001-0.0010.0000.0000.0000.000
125C126ILE0-0.008-0.00553.0050.0000.0000.0000.0000.0000.000
126C127GLN0-0.045-0.01455.4770.0010.0010.0000.0000.0000.000
127C128ALA00.003-0.01256.3840.0010.0010.0000.0000.0000.000
128C129ALA00.0340.02654.3680.0000.0000.0000.0000.0000.000
129C130LEU00.0040.01656.3990.0010.0010.0000.0000.0000.000
130C131ASN0-0.073-0.04359.3490.0010.0010.0000.0000.0000.000
131C132GLU-1-0.876-0.89755.580-0.035-0.0350.0000.0000.0000.000
132C133GLY0-0.0050.00259.0410.0000.0000.0000.0000.0000.000
133C134LYS10.7710.86554.1260.0340.0340.0000.0000.0000.000
134C135PRO0-0.012-0.00355.4170.0010.0010.0000.0000.0000.000
135C136GLN00.0660.00255.921-0.001-0.0010.0000.0000.0000.000
136C137GLN00.0730.02452.8000.0000.0000.0000.0000.0000.000
137C138ILE0-0.078-0.03050.726-0.002-0.0020.0000.0000.0000.000
138C139ALA00.017-0.01051.018-0.002-0.0020.0000.0000.0000.000
139C140GLU-1-0.871-0.91751.236-0.035-0.0350.0000.0000.0000.000
140C141LYS10.8060.87846.1640.0450.0450.0000.0000.0000.000
141C142ILE00.0230.01447.029-0.002-0.0020.0000.0000.0000.000
142C143ALA00.0590.03347.858-0.002-0.0020.0000.0000.0000.000
143C144GLU-1-0.781-0.85944.491-0.050-0.0500.0000.0000.0000.000
144C145GLY00.0100.01443.344-0.002-0.0020.0000.0000.0000.000
145C146ARG10.8670.94744.3530.0450.0450.0000.0000.0000.000
146C147LEU00.023-0.00446.622-0.001-0.0010.0000.0000.0000.000
147C148LYS10.8400.91037.2020.0780.0780.0000.0000.0000.000
148C149LYS10.7990.87742.2890.0540.0540.0000.0000.0000.000
149C150TYR00.0480.02143.363-0.001-0.0010.0000.0000.0000.000
150C151LEU00.006-0.00142.5930.0000.0000.0000.0000.0000.000
151C152GLU-1-0.837-0.89738.175-0.083-0.0830.0000.0000.0000.000
152C153GLU-1-0.835-0.89940.611-0.058-0.0580.0000.0000.0000.000
153C154VAL00.0070.00843.3520.0000.0000.0000.0000.0000.000
154C155VAL0-0.0210.01740.9060.0010.0010.0000.0000.0000.000
155C156LEU00.0230.01937.765-0.004-0.0040.0000.0000.0000.000
156C157LEU00.003-0.00735.533-0.005-0.0050.0000.0000.0000.000
157C158GLU-1-0.807-0.88835.865-0.085-0.0850.0000.0000.0000.000
158C159GLN00.0470.03337.422-0.004-0.0040.0000.0000.0000.000
159C160PRO0-0.0090.00934.035-0.005-0.0050.0000.0000.0000.000
160C161PHE00.003-0.02028.6140.0050.0050.0000.0000.0000.000
161C162VAL00.0430.00832.552-0.004-0.0040.0000.0000.0000.000
162C163LYS10.7350.86529.2600.1190.1190.0000.0000.0000.000
163C164ASP-1-0.898-0.97126.180-0.178-0.1780.0000.0000.0000.000
164C165ASP-1-0.955-0.94629.314-0.116-0.1160.0000.0000.0000.000
165C166LYS10.9200.96823.4020.2040.2040.0000.0000.0000.000
166C167VAL0-0.051-0.02125.953-0.003-0.0030.0000.0000.0000.000
167C168LYS10.8230.89829.3100.0930.0930.0000.0000.0000.000
168C169VAL00.0250.00631.170-0.007-0.0070.0000.0000.0000.000
169C170LYS10.8010.88231.7900.0780.0780.0000.0000.0000.000
170C171GLU-1-0.864-0.92627.892-0.137-0.1370.0000.0000.0000.000
171C172LEU00.0000.01526.931-0.010-0.0100.0000.0000.0000.000
172C173ILE00.014-0.00128.032-0.004-0.0040.0000.0000.0000.000
173C174GLN0-0.025-0.01728.415-0.008-0.0080.0000.0000.0000.000
174C175GLN0-0.045-0.02521.784-0.017-0.0170.0000.0000.0000.000
175C176ALA00.0340.01424.503-0.009-0.0090.0000.0000.0000.000
176C177ILE00.0030.00126.0950.0000.0000.0000.0000.0000.000
177C178ALA0-0.061-0.02023.4600.0040.0040.0000.0000.0000.000
178C179LYS10.8400.93619.1760.2330.2330.0000.0000.0000.000
179C180ILE0-0.052-0.00823.0960.0040.0040.0000.0000.0000.000
180C181GLY0-0.0020.00126.1050.0080.0080.0000.0000.0000.000
181C182GLU-1-0.811-0.88327.823-0.051-0.0510.0000.0000.0000.000
182C183ASN0-0.066-0.04631.351-0.011-0.0110.0000.0000.0000.000
183C184ILE00.004-0.00130.2760.0010.0010.0000.0000.0000.000
184C185VAL0-0.032-0.01234.188-0.002-0.0020.0000.0000.0000.000
185C186VAL00.0320.01436.7660.0000.0000.0000.0000.0000.000
186C187ARG10.8590.93739.2190.0500.0500.0000.0000.0000.000
187C188ARG10.8810.91742.7520.0440.0440.0000.0000.0000.000
188C189PHE00.0330.01242.432-0.002-0.0020.0000.0000.0000.000
189C190CYS0-0.061-0.02744.4860.0030.0030.0000.0000.0000.000
190C191ARG10.8110.89044.8790.0500.0500.0000.0000.0000.000
191C192PHE0-0.026-0.00247.4400.0020.0020.0000.0000.0000.000
192C193GLU-1-0.789-0.86948.498-0.049-0.0490.0000.0000.0000.000
193C194LEU0-0.032-0.04850.6430.0020.0020.0000.0000.0000.000
194C195GLY0-0.047-0.01853.6180.0000.0000.0000.0000.0000.000
195C196ALA00.0150.01852.5200.0010.0010.0000.0000.0000.000