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: 72J4K

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2041874.444865
FMO2-HF: Nuclear repulsion 1963144.240575
FMO2-HF: Total energy -78730.204291
FMO2-MP2: Total energy -78957.5237


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.
-12.972-6.6182.715-3.824-5.2460.022
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 : 0.067 / 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].
3C4MET0-0.0010.0042.395-7.378-3.6621.561-2.367-2.9100.022
4C5GLU-1-0.771-0.9082.324-5.984-3.9591.151-1.265-1.9110.000
5C6LEU00.0330.0433.890-0.2070.4060.003-0.192-0.4250.000
6C7ILE00.0070.0095.5580.5530.5530.0000.0000.0000.000
7C8LYS10.7440.8456.7580.6740.6740.0000.0000.0000.000
8C9LYS10.8520.9237.2690.9290.9290.0000.0000.0000.000
9C10LEU00.0770.0398.8610.2000.2000.0000.0000.0000.000
10C11ARG10.8680.95310.8120.3460.3460.0000.0000.0000.000
11C12GLU-1-0.848-0.89811.030-0.496-0.4960.0000.0000.0000.000
12C13ALA00.0510.04813.3430.0560.0560.0000.0000.0000.000
13C14THR0-0.022-0.05414.5660.0800.0800.0000.0000.0000.000
14C15GLY0-0.044-0.02416.4250.0400.0400.0000.0000.0000.000
15C16ALA00.0610.04817.3540.0330.0330.0000.0000.0000.000
16C17GLY00.0380.01117.5850.0050.0050.0000.0000.0000.000
17C18MET00.0260.00511.6520.0060.0060.0000.0000.0000.000
18C19MET00.0330.00214.0130.0070.0070.0000.0000.0000.000
19C20ASP-1-0.843-0.89515.999-0.088-0.0880.0000.0000.0000.000
20C21VAL0-0.0110.00511.694-0.016-0.0160.0000.0000.0000.000
21C22LYS10.7940.86511.336-0.234-0.2340.0000.0000.0000.000
22C23ARG10.8750.92712.9230.0240.0240.0000.0000.0000.000
23C24ALA00.0340.02115.125-0.006-0.0060.0000.0000.0000.000
24C25LEU00.0090.0038.928-0.035-0.0350.0000.0000.0000.000
25C26GLU-1-0.855-0.89812.4950.1160.1160.0000.0000.0000.000
26C27ASP-1-0.819-0.91114.396-0.108-0.1080.0000.0000.0000.000
27C28ALA00.0090.00815.8320.0200.0200.0000.0000.0000.000
28C29GLY0-0.0120.00613.333-0.022-0.0220.0000.0000.0000.000
29C30TRP0-0.027-0.0347.2720.0700.0700.0000.0000.0000.000
30C31ASP-1-0.827-0.9068.413-0.832-0.8320.0000.0000.0000.000
31C32GLU-1-0.861-0.9488.101-1.476-1.4760.0000.0000.0000.000
32C33GLU-1-0.894-0.94011.699-0.375-0.3750.0000.0000.0000.000
33C34LYS10.7970.89913.2820.5390.5390.0000.0000.0000.000
34C35ALA00.0180.02313.0940.0530.0530.0000.0000.0000.000
35C36VAL0-0.028-0.03113.8550.0550.0550.0000.0000.0000.000
36C37GLN00.0030.01816.3190.0520.0520.0000.0000.0000.000
37C38LEU00.0710.04618.0260.0290.0290.0000.0000.0000.000
38C39LEU0-0.050-0.04814.9290.0340.0340.0000.0000.0000.000
39C40ARG10.8830.95117.3690.3110.3110.0000.0000.0000.000
40C41GLU-1-0.900-0.94722.115-0.145-0.1450.0000.0000.0000.000
41C42ARG10.7650.84319.3710.1520.1520.0000.0000.0000.000
42C43GLY00.001-0.00123.1910.0140.0140.0000.0000.0000.000
43C44ALA00.0620.03224.4890.0120.0120.0000.0000.0000.000
44C45MET0-0.032-0.01426.0830.0150.0150.0000.0000.0000.000
45C46LYS10.8530.91222.1560.1210.1210.0000.0000.0000.000
46C47ALA00.0350.02128.0920.0080.0080.0000.0000.0000.000
47C48ALA00.0060.00130.3220.0070.0070.0000.0000.0000.000
48C49LYS10.8630.94031.0810.0620.0620.0000.0000.0000.000
49C50LYS10.7480.84931.0990.0670.0670.0000.0000.0000.000
50C51ALA00.0500.03934.1270.0020.0020.0000.0000.0000.000
51C52ASP-1-0.876-0.93136.580-0.046-0.0460.0000.0000.0000.000
52C53ARG10.7410.85133.8920.0480.0480.0000.0000.0000.000
53C54GLU-1-0.771-0.86038.638-0.039-0.0390.0000.0000.0000.000
54C55ALA0-0.020-0.00738.232-0.001-0.0010.0000.0000.0000.000
55C56ARG10.7420.83839.9860.0390.0390.0000.0000.0000.000
56C57GLU-1-0.862-0.90838.171-0.042-0.0420.0000.0000.0000.000
57C58GLY00.031-0.00537.433-0.002-0.0020.0000.0000.0000.000
58C59ILE0-0.054-0.01935.9510.0020.0020.0000.0000.0000.000
59C60ILE0-0.028-0.01239.680-0.001-0.0010.0000.0000.0000.000
60C61GLY00.0470.02838.890-0.001-0.0010.0000.0000.0000.000
61C62HIS0-0.027-0.02739.5820.0020.0020.0000.0000.0000.000
62C63TYR00.0470.00838.437-0.004-0.0040.0000.0000.0000.000
63C64ILE0-0.015-0.01041.4820.0030.0030.0000.0000.0000.000
64C65HIS00.0680.04741.618-0.003-0.0030.0000.0000.0000.000
65C66HIS0-0.012-0.02242.5600.0040.0040.0000.0000.0000.000
66C67ASN00.0100.00944.3620.0020.0020.0000.0000.0000.000
67C68GLN0-0.013-0.01847.3390.0030.0030.0000.0000.0000.000
68C69ARG10.8710.93948.9490.0390.0390.0000.0000.0000.000
69C70VAL00.0140.01445.5990.0010.0010.0000.0000.0000.000
70C71GLY0-0.0080.00345.550-0.001-0.0010.0000.0000.0000.000
71C72VAL0-0.028-0.00242.0550.0010.0010.0000.0000.0000.000
72C73LEU0-0.015-0.00443.7450.0000.0000.0000.0000.0000.000
73C74VAL00.014-0.00239.3240.0010.0010.0000.0000.0000.000
74C75GLU-1-0.822-0.86641.035-0.046-0.0460.0000.0000.0000.000
75C76LEU0-0.0030.00334.032-0.001-0.0010.0000.0000.0000.000
76C77ASN00.008-0.01138.3570.0020.0020.0000.0000.0000.000
77C78CYS0-0.045-0.02034.165-0.005-0.0050.0000.0000.0000.000
78C79GLU-1-0.730-0.83834.355-0.049-0.0490.0000.0000.0000.000
79C80THR0-0.058-0.06633.4900.0040.0040.0000.0000.0000.000
80C81ASP-1-0.761-0.88335.243-0.051-0.0510.0000.0000.0000.000
81C82PHE0-0.034-0.01831.655-0.003-0.0030.0000.0000.0000.000
82C83VAL0-0.0110.00429.752-0.006-0.0060.0000.0000.0000.000
83C84ALA00.0250.02231.825-0.005-0.0050.0000.0000.0000.000
84C85ARG10.8570.91333.4860.0480.0480.0000.0000.0000.000
85C86ASN0-0.037-0.00526.054-0.009-0.0090.0000.0000.0000.000
86C87GLU-1-0.848-0.93426.551-0.129-0.1290.0000.0000.0000.000
87C88LEU00.0440.01323.095-0.001-0.0010.0000.0000.0000.000
88C89PHE0-0.0110.00027.6010.0000.0000.0000.0000.0000.000
89C90GLN0-0.026-0.02931.0400.0040.0040.0000.0000.0000.000
90C91ASN0-0.045-0.02327.8840.0080.0080.0000.0000.0000.000
91C92LEU0-0.0010.00930.0270.0020.0020.0000.0000.0000.000
92C93ALA00.0260.01031.5770.0040.0040.0000.0000.0000.000
93C94LYN00.0020.01533.9970.0040.0040.0000.0000.0000.000
94C95ASP-1-0.779-0.88330.231-0.110-0.1100.0000.0000.0000.000
95C96LEU0-0.016-0.01133.8320.0020.0020.0000.0000.0000.000
96C97ALA00.0070.00836.1020.0040.0040.0000.0000.0000.000
97C98MET0-0.027-0.01934.0860.0020.0020.0000.0000.0000.000
98C99HIS00.015-0.00635.586-0.002-0.0020.0000.0000.0000.000
99C100ILE0-0.008-0.00737.6030.0030.0030.0000.0000.0000.000
100C101ALA0-0.021-0.01540.9940.0030.0030.0000.0000.0000.000
101C102MET0-0.042-0.01039.3150.0040.0040.0000.0000.0000.000
102C103MET00.008-0.00536.9000.0030.0030.0000.0000.0000.000
103C104ASN0-0.054-0.00641.7920.0030.0030.0000.0000.0000.000
104C105PRO0-0.0110.00841.6910.0020.0020.0000.0000.0000.000
105C106ARG10.8090.89544.4800.0420.0420.0000.0000.0000.000
106C107TYR00.0080.00145.5700.0020.0020.0000.0000.0000.000
107C108VAL0-0.013-0.01041.164-0.004-0.0040.0000.0000.0000.000
108C109SER0-0.041-0.07141.285-0.003-0.0030.0000.0000.0000.000
109C110ALA00.0290.00842.4300.0020.0020.0000.0000.0000.000
110C111GLU-1-0.863-0.91642.533-0.051-0.0510.0000.0000.0000.000
111C112GLU-1-0.855-0.91445.803-0.046-0.0460.0000.0000.0000.000
112C113ILE0-0.043-0.01446.6640.0020.0020.0000.0000.0000.000
113C114PRO00.0190.01149.6350.0000.0000.0000.0000.0000.000
114C115ALA00.0620.01650.9490.0000.0000.0000.0000.0000.000
115C116GLU-1-0.921-0.96351.992-0.029-0.0290.0000.0000.0000.000
116C117GLU-1-0.863-0.91253.560-0.036-0.0360.0000.0000.0000.000
117C118LEU00.0400.00747.9220.0000.0000.0000.0000.0000.000
118C119GLU-1-0.715-0.81251.976-0.035-0.0350.0000.0000.0000.000
119C120LYS10.8200.90453.7030.0350.0350.0000.0000.0000.000
120C121GLU-1-0.854-0.89051.700-0.036-0.0360.0000.0000.0000.000
121C122ARG10.8500.89350.1080.0350.0350.0000.0000.0000.000
122C123GLN0-0.018-0.03352.8630.0000.0000.0000.0000.0000.000
123C124ILE0-0.0160.00056.3150.0010.0010.0000.0000.0000.000
124C125TYR0-0.083-0.07849.747-0.001-0.0010.0000.0000.0000.000
125C126ILE00.0210.01253.5530.0000.0000.0000.0000.0000.000
126C127GLN0-0.027-0.01655.6910.0010.0010.0000.0000.0000.000
127C128ALA0-0.017-0.00155.9980.0010.0010.0000.0000.0000.000
128C129ALA00.0290.01354.2170.0000.0000.0000.0000.0000.000
129C130LEU0-0.020-0.00956.3240.0010.0010.0000.0000.0000.000
130C131ASN0-0.038-0.02059.4460.0010.0010.0000.0000.0000.000
131C132GLU-1-0.895-0.91055.737-0.034-0.0340.0000.0000.0000.000
132C133GLY0-0.0050.00959.3280.0000.0000.0000.0000.0000.000
133C134LYS10.7570.85054.2780.0320.0320.0000.0000.0000.000
134C135PRO00.0050.00555.7250.0010.0010.0000.0000.0000.000
135C136GLN00.049-0.00455.752-0.001-0.0010.0000.0000.0000.000
136C137GLN00.0700.03352.590-0.001-0.0010.0000.0000.0000.000
137C138ILE0-0.070-0.03350.946-0.002-0.0020.0000.0000.0000.000
138C139ALA00.0150.00351.243-0.002-0.0020.0000.0000.0000.000
139C140GLU-1-0.849-0.92251.160-0.034-0.0340.0000.0000.0000.000
140C141LYS10.8110.88346.4330.0400.0400.0000.0000.0000.000
141C142ILE0-0.0020.00647.136-0.003-0.0030.0000.0000.0000.000
142C143ALA0-0.0010.00548.512-0.002-0.0020.0000.0000.0000.000
143C144GLU-1-0.799-0.87645.172-0.045-0.0450.0000.0000.0000.000
144C145GLY00.0060.00943.830-0.003-0.0030.0000.0000.0000.000
145C146ARG10.8580.93344.6210.0420.0420.0000.0000.0000.000
146C147LEU00.0330.01046.602-0.001-0.0010.0000.0000.0000.000
147C148LYS10.8370.90637.2180.0730.0730.0000.0000.0000.000
148C149LYS10.7980.87342.3250.0510.0510.0000.0000.0000.000
149C150TYR00.0400.01743.620-0.001-0.0010.0000.0000.0000.000
150C151LEU00.0270.00142.7560.0000.0000.0000.0000.0000.000
151C152GLU-1-0.815-0.88138.261-0.076-0.0760.0000.0000.0000.000
152C153GLU-1-0.801-0.86940.587-0.056-0.0560.0000.0000.0000.000
153C154VAL0-0.028-0.00443.3580.0000.0000.0000.0000.0000.000
154C155VAL0-0.0130.01141.0850.0020.0020.0000.0000.0000.000
155C156LEU00.0140.01638.166-0.004-0.0040.0000.0000.0000.000
156C157LEU0-0.006-0.01735.618-0.005-0.0050.0000.0000.0000.000
157C158GLU-1-0.812-0.89636.033-0.080-0.0800.0000.0000.0000.000
158C159GLN00.0230.01437.253-0.005-0.0050.0000.0000.0000.000
159C160PRO0-0.0020.01134.144-0.004-0.0040.0000.0000.0000.000
160C161PHE00.008-0.01828.9420.0050.0050.0000.0000.0000.000
161C162VAL00.002-0.01032.708-0.003-0.0030.0000.0000.0000.000
162C163LYS10.7400.85829.1990.1190.1190.0000.0000.0000.000
163C164ASP-1-0.908-0.96426.205-0.170-0.1700.0000.0000.0000.000
164C165ASP-1-0.934-0.94929.271-0.109-0.1090.0000.0000.0000.000
165C166LYS10.9150.96123.1680.1980.1980.0000.0000.0000.000
166C167VAL0-0.038-0.00726.386-0.003-0.0030.0000.0000.0000.000
167C168LYS10.8050.89429.7540.0870.0870.0000.0000.0000.000
168C169VAL00.0140.00931.332-0.007-0.0070.0000.0000.0000.000
169C170LYS10.8170.88732.2580.0750.0750.0000.0000.0000.000
170C171GLU-1-0.859-0.92027.910-0.127-0.1270.0000.0000.0000.000
171C172LEU00.0050.01426.940-0.010-0.0100.0000.0000.0000.000
172C173ILE00.0320.01228.101-0.004-0.0040.0000.0000.0000.000
173C174GLN0-0.017-0.01328.686-0.005-0.0050.0000.0000.0000.000
174C175GLN0-0.040-0.02721.468-0.020-0.0200.0000.0000.0000.000
175C176ALA00.0360.02024.477-0.010-0.0100.0000.0000.0000.000
176C177ILE00.0070.00826.348-0.001-0.0010.0000.0000.0000.000
177C178ALA0-0.052-0.02123.5280.0040.0040.0000.0000.0000.000
178C179LYS10.7880.90819.2420.2200.2200.0000.0000.0000.000
179C180ILE0-0.0160.01123.2600.0010.0010.0000.0000.0000.000
180C181GLY0-0.036-0.00726.4400.0080.0080.0000.0000.0000.000
181C182GLU-1-0.770-0.86727.831-0.053-0.0530.0000.0000.0000.000
182C183ASN0-0.073-0.06331.179-0.010-0.0100.0000.0000.0000.000
183C184ILE0-0.009-0.00530.1430.0000.0000.0000.0000.0000.000
184C185VAL0-0.013-0.00234.298-0.001-0.0010.0000.0000.0000.000
185C186VAL00.0200.01337.0490.0010.0010.0000.0000.0000.000
186C187ARG10.8580.93339.3880.0490.0490.0000.0000.0000.000
187C188ARG10.8750.91042.9450.0440.0440.0000.0000.0000.000
188C189PHE00.0170.00242.801-0.003-0.0030.0000.0000.0000.000
189C190CYS0-0.052-0.01344.9650.0030.0030.0000.0000.0000.000
190C191ARG10.8280.89345.1100.0490.0490.0000.0000.0000.000
191C192PHE0-0.0090.00047.6560.0020.0020.0000.0000.0000.000
192C193GLU-1-0.755-0.86248.941-0.048-0.0480.0000.0000.0000.000
193C194LEU0-0.037-0.01650.9800.0020.0020.0000.0000.0000.000
194C195GLY0-0.008-0.00453.8950.0000.0000.0000.0000.0000.000
195C196ALA0-0.057-0.02452.0560.0010.0010.0000.0000.0000.000