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: R9KG8

Calculation Name: 5D1Q-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D1Q

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2327874.001565
FMO2-HF: Nuclear repulsion 2241474.88207
FMO2-HF: Total energy -86399.119494
FMO2-MP2: Total energy -86651.210463


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:1:GLU)


Summations of interaction energy for fragment #1(C:1:GLU)
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.
2.14.2960.192-1.059-1.3290.001
Interaction energy analysis for fragmet #1(C:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.945 / q_NPA : -0.989
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].
3C3GLN0-0.044-0.0082.886-4.187-2.0720.194-1.009-1.3000.001
4C4LEU00.0010.0006.125-1.147-1.1470.0000.0000.0000.000
5C5VAL0-0.001-0.0069.793-0.155-0.1550.0000.0000.0000.000
6C6GLU-1-0.765-0.87512.30816.73216.7320.0000.0000.0000.000
7C7SER0-0.045-0.02715.776-0.357-0.3570.0000.0000.0000.000
8C8GLY00.0520.01518.973-0.095-0.0950.0000.0000.0000.000
9C9GLY00.0180.01921.847-0.365-0.3650.0000.0000.0000.000
10C10GLY0-0.019-0.01623.512-0.125-0.1250.0000.0000.0000.000
11C11LEU0-0.049-0.02426.9440.0020.0020.0000.0000.0000.000
12C12VAL0-0.0030.00530.478-0.130-0.1300.0000.0000.0000.000
13C13GLN00.0380.01033.178-0.188-0.1880.0000.0000.0000.000
14C14PRO00.002-0.01535.8410.1420.1420.0000.0000.0000.000
15C15GLY0-0.028-0.00837.153-0.163-0.1630.0000.0000.0000.000
16C16GLY0-0.024-0.00435.247-0.022-0.0220.0000.0000.0000.000
17C17SER0-0.009-0.04432.178-0.031-0.0310.0000.0000.0000.000
18C18LEU0-0.063-0.02025.348-0.117-0.1170.0000.0000.0000.000
19C19THR0-0.009-0.02325.0450.0100.0100.0000.0000.0000.000
20C20LEU0-0.044-0.00321.0240.1810.1810.0000.0000.0000.000
21C21SER0-0.037-0.02819.6940.0240.0240.0000.0000.0000.000
22C22CYS0-0.055-0.03014.126-0.023-0.0230.0000.0000.0000.000
23C23ALA00.0250.02713.595-0.160-0.1600.0000.0000.0000.000
24C24ALA00.003-0.00810.4630.6680.6680.0000.0000.0000.000
25C25SER00.003-0.0186.714-1.502-1.5020.0000.0000.0000.000
26C26GLY00.0500.0224.5241.1051.071-0.001-0.0440.0790.000
27C27LEU0-0.034-0.0144.9554.0074.122-0.001-0.006-0.1080.000
28C28ILE00.0250.0147.737-1.621-1.6210.0000.0000.0000.000
29C29PHE00.0610.04511.360-1.068-1.0680.0000.0000.0000.000
30C30SER0-0.027-0.02713.419-0.699-0.6990.0000.0000.0000.000
31C31ASP-1-0.912-0.94914.67817.35717.3570.0000.0000.0000.000
32C32SER0-0.033-0.01712.1080.1350.1350.0000.0000.0000.000
33C33THR0-0.023-0.00614.436-1.009-1.0090.0000.0000.0000.000
34C34MET00.0050.02713.3131.2131.2130.0000.0000.0000.000
35C35HIS0-0.007-0.02816.841-1.743-1.7430.0000.0000.0000.000
36C36TRP00.0110.01817.4700.5900.5900.0000.0000.0000.000
37C37VAL0-0.013-0.00518.636-0.627-0.6270.0000.0000.0000.000
38C38ARG10.7650.86719.960-9.888-9.8880.0000.0000.0000.000
39C39GLN00.0100.00920.9550.4330.4330.0000.0000.0000.000
40C40ALA00.0400.03323.674-0.021-0.0210.0000.0000.0000.000
41C41SER00.007-0.02126.3560.2590.2590.0000.0000.0000.000
42C42GLY00.0130.01626.688-0.314-0.3140.0000.0000.0000.000
43C43ARG10.8910.95326.880-9.411-9.4110.0000.0000.0000.000
44C44GLY00.0460.02025.1940.3400.3400.0000.0000.0000.000
45C45LEU00.0010.00619.430-0.124-0.1240.0000.0000.0000.000
46C46GLU-1-0.831-0.90223.2709.6789.6780.0000.0000.0000.000
47C47TRP00.0010.00121.060-0.142-0.1420.0000.0000.0000.000
48C48VAL0-0.006-0.01022.941-0.553-0.5530.0000.0000.0000.000
49C49ALA00.002-0.00823.023-0.539-0.5390.0000.0000.0000.000
50C50ARG10.8010.88120.817-11.833-11.8330.0000.0000.0000.000
51C51ILE0-0.037-0.01820.278-0.732-0.7320.0000.0000.0000.000
52C52ARG10.7970.87819.983-11.427-11.4270.0000.0000.0000.000
53C52SER00.0960.05519.232-0.340-0.3400.0000.0000.0000.000
54C52LYS10.9510.95620.754-12.039-12.0390.0000.0000.0000.000
55C52ALA0-0.0100.00622.565-0.532-0.5320.0000.0000.0000.000
56C52ASN0-0.056-0.03723.645-0.051-0.0510.0000.0000.0000.000
57C52ASN00.007-0.00121.715-0.103-0.1030.0000.0000.0000.000
58C52TYR00.0360.01622.5260.1870.1870.0000.0000.0000.000
59C52ALA00.0670.03522.125-0.054-0.0540.0000.0000.0000.000
60C52THR0-0.002-0.00823.881-0.341-0.3410.0000.0000.0000.000
61C52SER0-0.024-0.01827.687-0.032-0.0320.0000.0000.0000.000
62C52SER0-0.006-0.01131.031-0.205-0.2050.0000.0000.0000.000
63C53ASP-1-0.783-0.86526.44511.13711.1370.0000.0000.0000.000
64C54LYS10.9150.98327.970-9.331-9.3310.0000.0000.0000.000
65C55SER0-0.0010.01729.195-0.063-0.0630.0000.0000.0000.000
66C56ALA00.0330.02825.8270.3100.3100.0000.0000.0000.000
67C57THR0-0.0070.00224.6990.3760.3760.0000.0000.0000.000
68C58ALA0-0.033-0.01826.049-0.358-0.3580.0000.0000.0000.000
69C59TYR00.0210.01726.3200.3370.3370.0000.0000.0000.000
70C60LEU00.0080.02527.521-0.324-0.3240.0000.0000.0000.000
71C61ALA00.004-0.01429.271-0.202-0.2020.0000.0000.0000.000
72C62SER0-0.0020.00231.378-0.149-0.1490.0000.0000.0000.000
73C63VAL00.0310.02028.171-0.158-0.1580.0000.0000.0000.000
74C64LYS10.9660.98431.666-8.728-8.7280.0000.0000.0000.000
75C65GLY0-0.014-0.00533.254-0.208-0.2080.0000.0000.0000.000
76C66ARG10.7000.84032.409-8.873-8.8730.0000.0000.0000.000
77C67PHE00.0470.02526.9830.0600.0600.0000.0000.0000.000
78C68THR0-0.067-0.04128.229-0.247-0.2470.0000.0000.0000.000
79C69ILE0-0.0040.00920.8060.0820.0820.0000.0000.0000.000
80C70SER0-0.032-0.02323.393-0.180-0.1800.0000.0000.0000.000
81C71ARG10.7830.86517.110-15.171-15.1710.0000.0000.0000.000
82C72ASP-1-0.777-0.84319.81812.53712.5370.0000.0000.0000.000
83C73ASP-1-0.848-0.93317.97515.38715.3870.0000.0000.0000.000
84C74SER0-0.100-0.06118.1940.3550.3550.0000.0000.0000.000
85C75LYS10.8510.90017.746-13.269-13.2690.0000.0000.0000.000
86C76ASP-1-0.863-0.91113.11819.82519.8250.0000.0000.0000.000
87C77THR0-0.012-0.00914.3920.2670.2670.0000.0000.0000.000
88C78THR0-0.052-0.03616.340-0.596-0.5960.0000.0000.0000.000
89C79PHE00.000-0.01718.7580.1030.1030.0000.0000.0000.000
90C80LEU0-0.018-0.01621.645-0.063-0.0630.0000.0000.0000.000
91C81GLU-1-0.780-0.84023.9599.5699.5690.0000.0000.0000.000
92C82MET0-0.063-0.03025.7850.0810.0810.0000.0000.0000.000
93C82SER00.0530.00829.098-0.252-0.2520.0000.0000.0000.000
94C82SER00.000-0.00932.932-0.089-0.0890.0000.0000.0000.000
95C82LEU0-0.0130.01529.797-0.041-0.0410.0000.0000.0000.000
96C83LYS10.8600.91633.469-8.500-8.5000.0000.0000.0000.000
97C84ILE00.0440.02733.3170.2100.2100.0000.0000.0000.000
98C85GLU-1-0.838-0.91332.8908.3188.3180.0000.0000.0000.000
99C86ASP-1-0.767-0.85229.5339.2719.2710.0000.0000.0000.000
100C87THR0-0.034-0.00928.2360.3650.3650.0000.0000.0000.000
101C88ALA0-0.040-0.01724.789-0.071-0.0710.0000.0000.0000.000
102C89VAL0-0.0010.01419.438-0.032-0.0320.0000.0000.0000.000
103C90TYR00.001-0.03920.580-0.095-0.0950.0000.0000.0000.000
104C91TYR00.014-0.00815.1690.3010.3010.0000.0000.0000.000
105C93ILE0-0.017-0.01413.2950.8190.8190.0000.0000.0000.000
106C94ALA00.0260.00611.234-0.725-0.7250.0000.0000.0000.000
107C95SER0-0.035-0.02512.4860.4550.4550.0000.0000.0000.000
108C96SER0-0.035-0.0079.6010.4560.4560.0000.0000.0000.000
109C97THR0-0.012-0.00811.858-0.586-0.5860.0000.0000.0000.000
110C98THR0-0.019-0.01010.093-1.049-1.0490.0000.0000.0000.000
111C99GLY00.0440.00913.270-0.437-0.4370.0000.0000.0000.000
112C100TRP0-0.0040.00316.791-0.213-0.2130.0000.0000.0000.000
113C100TYR0-0.036-0.01519.969-0.764-0.7640.0000.0000.0000.000
114C100VAL00.0060.00619.4830.7930.7930.0000.0000.0000.000
115C100ARG10.7470.85012.989-20.705-20.7050.0000.0000.0000.000
116C100GLU-1-0.782-0.89317.62813.64613.6460.0000.0000.0000.000
117C100ASP-1-0.838-0.89315.94415.83515.8350.0000.0000.0000.000
118C100PHE0-0.016-0.01215.4130.2100.2100.0000.0000.0000.000
119C101ASP-1-0.748-0.85810.67721.76921.7690.0000.0000.0000.000
120C102TYR00.0250.0116.3862.5682.5680.0000.0000.0000.000
121C103TRP0-0.034-0.0329.295-2.824-2.8240.0000.0000.0000.000
122C104GLY00.0430.0479.1281.8561.8560.0000.0000.0000.000
123C105HIS0-0.062-0.04411.0640.2200.2200.0000.0000.0000.000
124C106GLY00.0090.00813.608-0.376-0.3760.0000.0000.0000.000
125C107THR0-0.032-0.00417.034-0.544-0.5440.0000.0000.0000.000
126C108LEU0-0.026-0.01719.498-0.192-0.1920.0000.0000.0000.000
127C109VAL00.0450.02623.062-0.109-0.1090.0000.0000.0000.000
128C110THR0-0.064-0.04726.027-0.126-0.1260.0000.0000.0000.000
129C111VAL00.0330.02929.579-0.073-0.0730.0000.0000.0000.000
130C112SER00.013-0.00132.913-0.194-0.1940.0000.0000.0000.000
131C113SER00.0590.03136.0620.0380.0380.0000.0000.0000.000
132C114ALA0-0.085-0.03637.696-0.025-0.0250.0000.0000.0000.000
133C119SER00.004-0.00639.360-0.033-0.0330.0000.0000.0000.000
134C120THR0-0.021-0.01236.1640.0260.0260.0000.0000.0000.000
135C121LYS10.8370.92338.267-6.890-6.8900.0000.0000.0000.000
136C122GLY00.0440.02438.6550.1880.1880.0000.0000.0000.000
137C123PRO0-0.071-0.02238.376-0.131-0.1310.0000.0000.0000.000
138C124SER00.023-0.00640.955-0.117-0.1170.0000.0000.0000.000
139C125VAL0-0.0100.00641.8430.0520.0520.0000.0000.0000.000
140C126PHE0-0.005-0.00744.483-0.169-0.1690.0000.0000.0000.000
141C127PRO00.0210.01545.8560.1410.1410.0000.0000.0000.000
142C128LEU0-0.052-0.02144.035-0.066-0.0660.0000.0000.0000.000
143C129ALA00.0480.01647.9960.0630.0630.0000.0000.0000.000
144C130PRO00.0080.00350.3850.0330.0330.0000.0000.0000.000
145C131SER0-0.027-0.00951.472-0.127-0.1270.0000.0000.0000.000
146C132SER00.011-0.00253.363-0.019-0.0190.0000.0000.0000.000
147C133LYS10.9120.96855.851-5.447-5.4470.0000.0000.0000.000
148C134SER00.0930.04754.5370.0810.0810.0000.0000.0000.000
149C135THR0-0.009-0.00855.6060.0280.0280.0000.0000.0000.000
150C136SER0-0.052-0.03051.9270.0170.0170.0000.0000.0000.000
151C137GLY00.0320.02351.5420.0710.0710.0000.0000.0000.000
152C138GLY00.0110.02152.269-0.050-0.0500.0000.0000.0000.000
153C139THR0-0.022-0.02046.7000.0220.0220.0000.0000.0000.000
154C140ALA00.0090.01349.080-0.052-0.0520.0000.0000.0000.000
155C141ALA00.010-0.00445.4320.1420.1420.0000.0000.0000.000
156C142LEU00.0080.01845.036-0.161-0.1610.0000.0000.0000.000
157C143GLY00.0370.00243.4260.1820.1820.0000.0000.0000.000
158C144CYS0-0.078-0.00640.6110.0250.0250.0000.0000.0000.000
159C145LEU00.0210.02341.6340.1730.1730.0000.0000.0000.000
160C146VAL0-0.003-0.01237.731-0.098-0.0980.0000.0000.0000.000
161C147LYS10.9080.91839.696-6.373-6.3730.0000.0000.0000.000
162C148ASP-1-0.809-0.86441.3676.5276.5270.0000.0000.0000.000
163C149TYR0-0.055-0.05133.605-0.191-0.1910.0000.0000.0000.000
164C150PHE00.0680.03733.9260.1180.1180.0000.0000.0000.000
165C151PRO00.0360.03031.436-0.168-0.1680.0000.0000.0000.000
166C152GLU-1-0.781-0.87429.5858.7638.7630.0000.0000.0000.000
167C153PRO0-0.016-0.00627.7270.0960.0960.0000.0000.0000.000
168C154VAL0-0.012-0.01230.127-0.263-0.2630.0000.0000.0000.000
169C155THR0-0.056-0.03230.8820.3110.3110.0000.0000.0000.000
170C156VAL00.009-0.00732.870-0.250-0.2500.0000.0000.0000.000
171C157SER0-0.037-0.01734.2540.1910.1910.0000.0000.0000.000
172C158TRP00.0540.01236.293-0.283-0.2830.0000.0000.0000.000
173C159ASN00.008-0.00939.3530.1060.1060.0000.0000.0000.000
174C160SER0-0.020-0.00739.0870.0420.0420.0000.0000.0000.000
175C161GLY00.0420.02436.2820.1890.1890.0000.0000.0000.000
176C162ALA0-0.037-0.00436.7740.1170.1170.0000.0000.0000.000
177C163LEU0-0.0180.00038.904-0.071-0.0710.0000.0000.0000.000
178C164THR00.0260.00333.9670.0640.0640.0000.0000.0000.000
179C165SER00.0130.00336.3840.0640.0640.0000.0000.0000.000
180C166GLY00.0430.01837.478-0.192-0.1920.0000.0000.0000.000
181C167VAL0-0.028-0.01035.974-0.152-0.1520.0000.0000.0000.000
182C168HIS0-0.0140.00034.9900.2840.2840.0000.0000.0000.000
183C169THR00.0030.00133.383-0.315-0.3150.0000.0000.0000.000
184C170PHE0-0.0040.01233.2780.2450.2450.0000.0000.0000.000
185C171PRO00.0270.00630.8660.0260.0260.0000.0000.0000.000
186C172ALA0-0.0040.00232.462-0.261-0.2610.0000.0000.0000.000
187C173VAL0-0.007-0.00633.8270.1400.1400.0000.0000.0000.000
188C174LEU0-0.023-0.01433.921-0.141-0.1410.0000.0000.0000.000
189C175GLN0-0.044-0.02936.658-0.197-0.1970.0000.0000.0000.000
190C176SER00.0310.00540.1570.0850.0850.0000.0000.0000.000
191C177SER0-0.007-0.00242.385-0.006-0.0060.0000.0000.0000.000
192C178GLY00.0350.02339.005-0.032-0.0320.0000.0000.0000.000
193C179LEU0-0.036-0.01338.3300.1380.1380.0000.0000.0000.000
194C180TYR00.0300.01631.483-0.055-0.0550.0000.0000.0000.000
195C181SER0-0.002-0.00737.394-0.249-0.2490.0000.0000.0000.000
196C182LEU0-0.0040.02133.7250.0970.0970.0000.0000.0000.000
197C183SER0-0.007-0.01437.549-0.244-0.2440.0000.0000.0000.000
198C184SER00.0080.00636.9420.1680.1680.0000.0000.0000.000
199C185VAL00.0210.00038.880-0.230-0.2300.0000.0000.0000.000
200C186VAL00.0240.01239.6300.1950.1950.0000.0000.0000.000
201C187THR0-0.017-0.00141.799-0.151-0.1510.0000.0000.0000.000
202C188VAL00.0170.00743.5660.1080.1080.0000.0000.0000.000
203C189PRO00.0460.00946.289-0.102-0.1020.0000.0000.0000.000
204C190SER00.0110.00449.375-0.049-0.0490.0000.0000.0000.000
205C191SER0-0.023-0.01352.473-0.058-0.0580.0000.0000.0000.000
206C192SER0-0.029-0.01950.115-0.055-0.0550.0000.0000.0000.000
207C193LEU0-0.0070.00550.8290.0890.0890.0000.0000.0000.000
208C194GLY00.0180.01952.721-0.006-0.0060.0000.0000.0000.000
209C195THR0-0.015-0.01352.071-0.044-0.0440.0000.0000.0000.000
210C196GLN00.0160.01646.8640.0370.0370.0000.0000.0000.000
211C197THR00.0300.02348.840-0.100-0.1000.0000.0000.0000.000
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