Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: LZ639

Calculation Name: 5D1Z-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D1Z

Chain ID: C

ChEMBL ID:

UniProt ID: Q2FZF0

Base Structure: X-ray

Registration Date: 2023-06-26

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2119432.454532
FMO2-HF: Nuclear repulsion 2038247.514559
FMO2-HF: Total energy -81184.939973
FMO2-MP2: Total energy -81423.227885


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:ASP)


Summations of interaction energy for fragment #1(C:2:ASP)
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.
-54.2-45.8123.018-4.637-6.7690.036
Interaction energy analysis for fragmet #1(C:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.889 / q_NPA : -0.957
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].
3C4GLN0-0.0170.0032.394-1.9240.2080.968-1.231-1.8690.004
4C5LEU00.011-0.0085.392-3.939-3.884-0.001-0.002-0.0520.000
5C6THR0-0.020-0.0078.608-0.236-0.2360.0000.0000.0000.000
6C7GLN00.004-0.02311.7710.5550.5550.0000.0000.0000.000
7C8SER0-0.0290.01914.945-0.245-0.2450.0000.0000.0000.000
8C9PRO00.0740.01518.325-0.041-0.0410.0000.0000.0000.000
9C10SER00.0270.01617.1340.4400.4400.0000.0000.0000.000
10C11PHE0-0.0090.00419.1450.2630.2630.0000.0000.0000.000
11C12LEU0-0.005-0.00122.703-0.055-0.0550.0000.0000.0000.000
12C13SER0-0.020-0.01925.574-0.095-0.0950.0000.0000.0000.000
13C14ALA0-0.021-0.00129.240-0.111-0.1110.0000.0000.0000.000
14C15SER0-0.037-0.04031.430-0.029-0.0290.0000.0000.0000.000
15C16VAL0-0.014-0.02333.8940.1840.1840.0000.0000.0000.000
16C17ALA0-0.056-0.02835.270-0.227-0.2270.0000.0000.0000.000
17C18ASP-1-0.794-0.85332.5349.0429.0420.0000.0000.0000.000
18C19ARG10.9370.96429.472-9.941-9.9410.0000.0000.0000.000
19C20VAL00.0200.01525.6280.0880.0880.0000.0000.0000.000
20C21THR0-0.076-0.05923.599-0.066-0.0660.0000.0000.0000.000
21C22ILE00.0050.02918.6950.0360.0360.0000.0000.0000.000
22C23THR0-0.021-0.02417.657-0.289-0.2890.0000.0000.0000.000
23C24CYS0-0.035-0.02112.8930.1410.1410.0000.0000.0000.000
24C25ARG10.8580.92813.544-16.322-16.3220.0000.0000.0000.000
25C26ALA00.0280.0219.4061.5401.5400.0000.0000.0000.000
26C27SER00.013-0.0046.943-0.449-0.4490.0000.0000.0000.000
27C28GLN0-0.024-0.0096.888-1.871-1.8710.0000.0000.0000.000
28C29ALA00.0120.00810.314-0.534-0.5340.0000.0000.0000.000
29C30VAL00.000-0.0029.1171.6911.6910.0000.0000.0000.000
30C31ARG10.9530.97711.988-19.573-19.5730.0000.0000.0000.000
31C32SER00.0800.02215.7050.0410.0410.0000.0000.0000.000
32C33SER0-0.052-0.00812.520-0.935-0.9350.0000.0000.0000.000
33C34LEU0-0.009-0.02011.9742.0752.0750.0000.0000.0000.000
34C35ALA00.0080.00813.831-1.496-1.4960.0000.0000.0000.000
35C36TRP00.0120.00015.1191.1281.1280.0000.0000.0000.000
36C37TYR0-0.012-0.02714.169-1.066-1.0660.0000.0000.0000.000
37C38GLN00.0250.00018.240-0.175-0.1750.0000.0000.0000.000
38C39GLN0-0.040-0.01518.0750.5430.5430.0000.0000.0000.000
39C40LYS10.9020.94420.787-11.530-11.5300.0000.0000.0000.000
40C41PRO00.039-0.00123.4590.4580.4580.0000.0000.0000.000
41C42GLY00.0070.00723.989-0.398-0.3980.0000.0000.0000.000
42C43LYS10.8750.94823.627-11.898-11.8980.0000.0000.0000.000
43C44ALA00.0520.02720.2030.5250.5250.0000.0000.0000.000
44C45PRO0-0.001-0.00615.981-0.542-0.5420.0000.0000.0000.000
45C46GLN0-0.027-0.00119.059-0.639-0.6390.0000.0000.0000.000
46C47LEU0-0.0050.00118.1390.3420.3420.0000.0000.0000.000
47C48LEU0-0.0120.00120.412-0.743-0.7430.0000.0000.0000.000
48C49ILE0-0.014-0.01320.160-0.548-0.5480.0000.0000.0000.000
49C50TYR00.0560.03118.1931.2541.2540.0000.0000.0000.000
50C51SER0-0.014-0.02318.071-0.415-0.4150.0000.0000.0000.000
51C52ALA00.0000.01217.644-0.478-0.4780.0000.0000.0000.000
52C53SER0-0.035-0.03418.858-0.177-0.1770.0000.0000.0000.000
53C54THR00.0120.02922.340-0.588-0.5880.0000.0000.0000.000
54C55LEU0-0.0060.00323.1400.5420.5420.0000.0000.0000.000
55C56GLU-1-0.839-0.90023.49212.83312.8330.0000.0000.0000.000
56C57ASN0-0.074-0.06825.571-0.828-0.8280.0000.0000.0000.000
57C58GLY0-0.018-0.01228.1890.2070.2070.0000.0000.0000.000
58C59VAL0-0.0230.01425.230-0.088-0.0880.0000.0000.0000.000
59C60SER00.005-0.00328.641-0.249-0.2490.0000.0000.0000.000
60C61SER00.026-0.00829.4580.3240.3240.0000.0000.0000.000
61C62ARG10.7720.87430.467-10.051-10.0510.0000.0000.0000.000
62C63PHE00.0160.01725.0160.1140.1140.0000.0000.0000.000
63C64SER0-0.035-0.01826.027-0.199-0.1990.0000.0000.0000.000
64C65GLY00.0800.02122.1620.4270.4270.0000.0000.0000.000
65C66SER0-0.089-0.04220.362-0.224-0.2240.0000.0000.0000.000
66C67GLY00.0000.03519.2680.1860.1860.0000.0000.0000.000
67C68PRO00.001-0.00118.379-0.531-0.5310.0000.0000.0000.000
68C69GLY0-0.012-0.02916.795-0.655-0.6550.0000.0000.0000.000
69C70THR0-0.014-0.00513.5730.7560.7560.0000.0000.0000.000
70C71GLU-1-0.837-0.91114.48016.09916.0990.0000.0000.0000.000
71C72PHE00.0140.02313.975-0.792-0.7920.0000.0000.0000.000
72C73THR00.016-0.01018.0820.2590.2590.0000.0000.0000.000
73C74LEU00.0140.03520.368-0.199-0.1990.0000.0000.0000.000
74C75THR0-0.064-0.03721.968-0.368-0.3680.0000.0000.0000.000
75C76ILE00.0590.03925.2530.0440.0440.0000.0000.0000.000
76C77SER0-0.060-0.04228.035-0.194-0.1940.0000.0000.0000.000
77C78SER00.0360.00931.547-0.289-0.2890.0000.0000.0000.000
78C79LEU0-0.053-0.00328.8810.0680.0680.0000.0000.0000.000
79C80GLN00.0350.01731.946-0.442-0.4420.0000.0000.0000.000
80C81PRO00.0340.00531.8660.3140.3140.0000.0000.0000.000
81C82GLU-1-0.818-0.89330.8689.8329.8320.0000.0000.0000.000
82C83ASP-1-0.800-0.88227.79911.11111.1110.0000.0000.0000.000
83C84VAL0-0.0050.02226.3480.5970.5970.0000.0000.0000.000
84C85GLY0-0.0020.00523.8760.1350.1350.0000.0000.0000.000
85C86THR0-0.035-0.01317.523-0.328-0.3280.0000.0000.0000.000
86C87TYR0-0.019-0.01019.0390.0870.0870.0000.0000.0000.000
87C88TYR0-0.042-0.01413.5660.4950.4950.0000.0000.0000.000
88C90GLN00.0120.0139.627-0.611-0.6110.0000.0000.0000.000
89C91GLN00.0390.0205.030-6.944-6.9440.0000.0000.0000.000
90C92LEU0-0.040-0.0348.6692.2832.2830.0000.0000.0000.000
91C93ASN0-0.031-0.0098.846-3.685-3.6850.0000.0000.0000.000
92C94THR00.001-0.0085.197-2.835-2.8350.0000.0000.0000.000
93C95TYR0-0.0160.0155.9522.4582.4580.0000.0000.0000.000
94C96PRO00.0470.0252.622-6.484-2.3371.638-2.396-3.3900.024
95C97PHE0-0.007-0.0124.4852.4442.556-0.001-0.011-0.1000.000
96C98THR0-0.005-0.0043.076-7.149-5.2070.414-0.997-1.3580.008
97C99PHE00.021-0.0065.828-5.917-5.9170.0000.0000.0000.000
98C100GLY00.0200.0177.8902.5572.5570.0000.0000.0000.000
99C101PRO0-0.032-0.02110.500-0.232-0.2320.0000.0000.0000.000
100C102GLY00.0060.00412.317-0.761-0.7610.0000.0000.0000.000
101C103THR0-0.036-0.02815.637-0.067-0.0670.0000.0000.0000.000
102C104LYS10.8230.87418.884-13.387-13.3870.0000.0000.0000.000
103C105VAL0-0.005-0.00421.836-0.263-0.2630.0000.0000.0000.000
104C106GLU-1-0.822-0.85625.0299.9969.9960.0000.0000.0000.000
105C107ILE00.0230.00728.304-0.086-0.0860.0000.0000.0000.000
106C108LYS10.9761.00231.573-9.032-9.0320.0000.0000.0000.000
107C109ARG10.8560.91534.266-8.216-8.2160.0000.0000.0000.000
108C110THR00.0240.00037.8590.0400.0400.0000.0000.0000.000
109C111VAL0-0.0160.00440.4650.1220.1220.0000.0000.0000.000
110C112ALA0-0.0030.01541.389-0.196-0.1960.0000.0000.0000.000
111C113ALA00.0390.01142.2260.1450.1450.0000.0000.0000.000
112C114PRO0-0.0030.01741.5330.0220.0220.0000.0000.0000.000
113C115SER0-0.026-0.02443.389-0.136-0.1360.0000.0000.0000.000
114C116VAL00.0100.00244.6560.1210.1210.0000.0000.0000.000
115C117PHE0-0.023-0.01145.304-0.208-0.2080.0000.0000.0000.000
116C118ILE0-0.0020.00545.7120.1720.1720.0000.0000.0000.000
117C119PHE0-0.010-0.01444.624-0.135-0.1350.0000.0000.0000.000
118C120PRO0-0.0020.00547.5140.0920.0920.0000.0000.0000.000
119C121PRO0-0.022-0.01648.1870.0640.0640.0000.0000.0000.000
120C122SER00.0050.01648.713-0.124-0.1240.0000.0000.0000.000
121C123ASP-1-0.912-0.95450.3615.9215.9210.0000.0000.0000.000
122C124GLU-1-0.985-0.99149.1696.3756.3750.0000.0000.0000.000
123C125GLN0-0.158-0.11647.2350.2010.2010.0000.0000.0000.000
124C126LEU00.1250.12541.4510.1080.1080.0000.0000.0000.000
125C127LYS10.9330.95742.295-7.252-7.2520.0000.0000.0000.000
126C128SER00.035-0.01945.748-0.024-0.0240.0000.0000.0000.000
127C129GLY00.025-0.10545.436-0.125-0.1250.0000.0000.0000.000
128C130THR0-0.0180.08441.6530.0540.0540.0000.0000.0000.000
129C131ALA00.0500.02945.0510.0410.0410.0000.0000.0000.000
130C132SER0-0.0230.00642.7280.1150.1150.0000.0000.0000.000
131C133VAL0-0.0010.01144.689-0.100-0.1000.0000.0000.0000.000
132C134VAL00.0210.01641.0680.1040.1040.0000.0000.0000.000
133C135CYS0-0.046-0.03342.023-0.076-0.0760.0000.0000.0000.000
134C136LEU00.0020.01939.7810.2140.2140.0000.0000.0000.000
135C137LEU0-0.002-0.01039.727-0.211-0.2110.0000.0000.0000.000
136C138ASN0-0.011-0.01739.6540.2560.2560.0000.0000.0000.000
137C139ASN00.0240.02139.0620.3450.3450.0000.0000.0000.000
138C140PHE0-0.044-0.00136.447-0.193-0.1930.0000.0000.0000.000
139C141TYR00.0280.00332.8910.1260.1260.0000.0000.0000.000
140C142PRO0-0.012-0.01735.070-0.281-0.2810.0000.0000.0000.000
141C143ARG10.9780.98727.251-11.020-11.0200.0000.0000.0000.000
142C144GLU-1-0.919-0.95634.1389.2519.2510.0000.0000.0000.000
143C145ALA0-0.021-0.00635.802-0.298-0.2980.0000.0000.0000.000
144C146LYS10.9380.96637.655-7.890-7.8900.0000.0000.0000.000
145C147VAL00.0360.01539.730-0.223-0.2230.0000.0000.0000.000
146C148GLN0-0.019-0.00141.6640.1560.1560.0000.0000.0000.000
147C149TRP00.0350.00941.652-0.249-0.2490.0000.0000.0000.000
148C150LYS10.8120.88245.966-6.399-6.3990.0000.0000.0000.000
149C151VAL00.0320.02349.6230.0120.0120.0000.0000.0000.000
150C152ASP-1-0.815-0.89752.2125.6015.6010.0000.0000.0000.000
151C153ASN0-0.033-0.01253.7570.0110.0110.0000.0000.0000.000
152C154ALA00.0260.01852.069-0.017-0.0170.0000.0000.0000.000
153C155LEU00.003-0.01246.1870.0650.0650.0000.0000.0000.000
154C156GLN00.0340.02945.248-0.051-0.0510.0000.0000.0000.000
155C157SER0-0.023-0.02242.3000.1370.1370.0000.0000.0000.000
156C158GLY00.0270.01639.734-0.057-0.0570.0000.0000.0000.000
157C159ASN0-0.027-0.01240.0330.0830.0830.0000.0000.0000.000
158C160SER00.0250.01339.483-0.122-0.1220.0000.0000.0000.000
159C161GLN0-0.055-0.01533.7270.1850.1850.0000.0000.0000.000
160C162GLU-1-0.929-0.96834.0788.6528.6520.0000.0000.0000.000
161C163SER0-0.014-0.00931.5060.4090.4090.0000.0000.0000.000
162C164VAL00.0020.00330.144-0.253-0.2530.0000.0000.0000.000
163C165THR00.0020.00730.3000.3420.3420.0000.0000.0000.000
164C166GLU-1-0.853-0.91425.18812.53812.5380.0000.0000.0000.000
165C167GLN0-0.026-0.02228.9070.0280.0280.0000.0000.0000.000
166C168ASP-1-0.796-0.87830.5859.2289.2280.0000.0000.0000.000
167C169SER0-0.031-0.02530.7290.2360.2360.0000.0000.0000.000
168C170LYS10.8310.89532.681-8.424-8.4240.0000.0000.0000.000
169C171ASP-1-0.826-0.91136.4138.0438.0430.0000.0000.0000.000
170C172SER00.0050.00634.083-0.070-0.0700.0000.0000.0000.000
171C173THR0-0.062-0.03935.1220.0670.0670.0000.0000.0000.000
172C174TYR0-0.049-0.05329.8960.3900.3900.0000.0000.0000.000
173C175SER00.011-0.00734.646-0.252-0.2520.0000.0000.0000.000
174C176LEU0-0.042-0.01534.8530.2920.2920.0000.0000.0000.000
175C177SER00.0140.00636.022-0.345-0.3450.0000.0000.0000.000
176C178SER00.0500.01236.6060.1990.1990.0000.0000.0000.000
177C179THR00.0110.00538.277-0.280-0.2800.0000.0000.0000.000
178C180LEU0-0.0020.00239.8570.1560.1560.0000.0000.0000.000
179C181THR0-0.034-0.02140.109-0.078-0.0780.0000.0000.0000.000
180C182LEU00.0140.00043.023-0.011-0.0110.0000.0000.0000.000
181C183SER0-0.024-0.01046.315-0.016-0.0160.0000.0000.0000.000
182C184LYS10.8970.91748.257-5.976-5.9760.0000.0000.0000.000
183C185ALA0-0.040-0.01651.381-0.120-0.1200.0000.0000.0000.000
184C186ASP-1-0.810-0.88749.1936.3716.3710.0000.0000.0000.000
185C187TYR0-0.007-0.00450.373-0.070-0.0700.0000.0000.0000.000
186C188GLU-1-0.813-0.90052.2935.5945.5940.0000.0000.0000.000
187C189LYS10.8760.95555.553-5.625-5.6250.0000.0000.0000.000
188C190HIS0-0.025-0.02354.539-0.043-0.0430.0000.0000.0000.000
189C191LYS10.8340.91856.261-5.353-5.3530.0000.0000.0000.000
190C192VAL00.0020.00355.3210.0160.0160.0000.0000.0000.000
191C193TYR00.0090.00049.8230.1030.1030.0000.0000.0000.000
192C194ALA0-0.005-0.00650.7160.0030.0030.0000.0000.0000.000
193C196GLU-1-0.869-0.91547.3686.4526.4520.0000.0000.0000.000
194C197VAL00.0430.02442.7860.1880.1880.0000.0000.0000.000
195C198THR0-0.050-0.03043.129-0.188-0.1880.0000.0000.0000.000
196C199HIS00.011-0.01639.078-0.020-0.0200.0000.0000.0000.000
197C200GLN00.0280.00938.6550.0030.0030.0000.0000.0000.000
198C201GLY00.0130.00643.010-0.122-0.1220.0000.0000.0000.000
199C202LEU0-0.061-0.02444.933-0.125-0.1250.0000.0000.0000.000
200C203SER00.0290.01747.5270.0450.0450.0000.0000.0000.000
201C204SER0-0.044-0.02950.188-0.125-0.1250.0000.0000.0000.000
202C205PRO00.0040.00748.1400.0240.0240.0000.0000.0000.000
203C206VAL00.0090.02247.438-0.150-0.1500.0000.0000.0000.000
204C207THR00.021-0.00548.5790.1530.1530.0000.0000.0000.000
205C208LYS10.9150.96749.128-6.414-6.4140.0000.0000.0000.000
206C209SER0-0.012-0.02350.4810.0950.0950.0000.0000.0000.000
207C210PHE0-0.0050.01749.862-0.050-0.0500.0000.0000.0000.000
208C211ASN0-0.020-0.05354.8660.1060.1060.0000.0000.0000.000
209C212ARG10.8870.93956.035-5.543-5.5430.0000.0000.0000.000
210C213GLY00.0250.02457.987-0.082-0.0820.0000.0000.0000.000
211C214GLU-1-0.901-0.91758.7375.2175.2170.0000.0000.0000.000