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: Z6G5N

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2322562.232176
FMO2-HF: Nuclear repulsion 2236164.951758
FMO2-HF: Total energy -86397.280418
FMO2-MP2: Total energy -86649.60445


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.
3.6436.1810.385-1.245-1.6760
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 : -0.969 / q_NPA : -0.999
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].
3C3GLN0-0.028-0.0112.935-4.388-1.9160.387-1.197-1.6620.000
4C4LEU0-0.010-0.0045.635-1.297-1.2970.0000.0000.0000.000
5C5VAL00.004-0.0019.401-0.490-0.4900.0000.0000.0000.000
6C6GLU-1-0.779-0.88511.79816.97716.9770.0000.0000.0000.000
7C7SER0-0.053-0.03315.315-0.362-0.3620.0000.0000.0000.000
8C8GLY00.0480.00918.366-0.092-0.0920.0000.0000.0000.000
9C9GLY00.0130.02421.599-0.395-0.3950.0000.0000.0000.000
10C10GLY00.010-0.00923.352-0.088-0.0880.0000.0000.0000.000
11C11LEU0-0.039-0.00726.620-0.004-0.0040.0000.0000.0000.000
12C12VAL0-0.005-0.00530.099-0.127-0.1270.0000.0000.0000.000
13C13GLN00.0320.00532.615-0.222-0.2220.0000.0000.0000.000
14C14PRO00.0280.00435.1630.1720.1720.0000.0000.0000.000
15C15GLY0-0.036-0.01936.770-0.177-0.1770.0000.0000.0000.000
16C16GLY0-0.0250.00034.678-0.054-0.0540.0000.0000.0000.000
17C17SER0-0.004-0.03231.826-0.027-0.0270.0000.0000.0000.000
18C18LEU0-0.066-0.02725.004-0.094-0.0940.0000.0000.0000.000
19C19THR00.0160.00124.269-0.026-0.0260.0000.0000.0000.000
20C20LEU0-0.0330.01020.5240.1560.1560.0000.0000.0000.000
21C21SER0-0.025-0.02219.262-0.021-0.0210.0000.0000.0000.000
22C22CYS0-0.045-0.02013.6860.0720.0720.0000.0000.0000.000
23C23ALA00.0240.01612.818-0.187-0.1870.0000.0000.0000.000
24C24ALA00.0010.00310.2391.1741.1740.0000.0000.0000.000
25C25SER00.0320.0076.471-1.439-1.4390.0000.0000.0000.000
26C26GLY00.0510.0224.3501.2231.144-0.001-0.0400.1210.000
27C27LEU0-0.038-0.0094.7634.2074.352-0.001-0.008-0.1350.000
28C28ILE00.0190.0147.508-1.239-1.2390.0000.0000.0000.000
29C29PHE00.0410.02711.050-1.342-1.3420.0000.0000.0000.000
30C30SER00.003-0.01012.858-0.701-0.7010.0000.0000.0000.000
31C31ASP-1-0.925-0.96714.44617.71817.7180.0000.0000.0000.000
32C32SER0-0.052-0.01212.2480.1360.1360.0000.0000.0000.000
33C33THR0-0.0250.00114.667-0.938-0.9380.0000.0000.0000.000
34C34MET0-0.0200.00412.8301.1951.1950.0000.0000.0000.000
35C35HIS0-0.005-0.03416.644-1.729-1.7290.0000.0000.0000.000
36C36TRP00.0400.02917.3610.5230.5230.0000.0000.0000.000
37C37VAL0-0.027-0.01418.660-0.693-0.6930.0000.0000.0000.000
38C38ARG10.7660.87819.775-9.930-9.9300.0000.0000.0000.000
39C39GLN00.0120.00820.9880.4100.4100.0000.0000.0000.000
40C40ALA00.0400.03423.680-0.007-0.0070.0000.0000.0000.000
41C41SER00.015-0.01625.9320.3170.3170.0000.0000.0000.000
42C42GLY00.0050.00926.561-0.320-0.3200.0000.0000.0000.000
43C43ARG10.9050.95826.858-9.479-9.4790.0000.0000.0000.000
44C44GLY00.0330.01225.7570.3510.3510.0000.0000.0000.000
45C45LEU00.0000.00720.025-0.122-0.1220.0000.0000.0000.000
46C46GLU-1-0.832-0.90923.6549.7139.7130.0000.0000.0000.000
47C47TRP00.0120.01221.334-0.055-0.0550.0000.0000.0000.000
48C48VAL0-0.024-0.00922.968-0.561-0.5610.0000.0000.0000.000
49C49ALA0-0.003-0.02322.985-0.540-0.5400.0000.0000.0000.000
50C50ARG10.8170.89320.907-11.744-11.7440.0000.0000.0000.000
51C51ILE0-0.027-0.01220.307-0.740-0.7400.0000.0000.0000.000
52C52ARG10.7990.87720.140-11.600-11.6000.0000.0000.0000.000
53C52SER00.0760.04119.071-0.367-0.3670.0000.0000.0000.000
54C52LYS10.9570.95620.780-11.896-11.8960.0000.0000.0000.000
55C52ALA0-0.0080.00322.268-0.497-0.4970.0000.0000.0000.000
56C52ASN0-0.028-0.01323.371-0.107-0.1070.0000.0000.0000.000
57C52ASN00.0100.00622.244-0.158-0.1580.0000.0000.0000.000
58C52TYR00.0330.00322.9000.1880.1880.0000.0000.0000.000
59C52ALA00.0710.03922.4100.0480.0480.0000.0000.0000.000
60C52THR00.0350.00824.110-0.299-0.2990.0000.0000.0000.000
61C52SER0-0.027-0.02827.758-0.010-0.0100.0000.0000.0000.000
62C52SER0-0.021-0.01831.012-0.340-0.3400.0000.0000.0000.000
63C53ASP-1-0.813-0.87926.70511.05211.0520.0000.0000.0000.000
64C54LYS10.9190.98727.815-9.318-9.3180.0000.0000.0000.000
65C55SER0-0.0020.01428.3250.0990.0990.0000.0000.0000.000
66C56ALA00.0550.04025.5830.2880.2880.0000.0000.0000.000
67C57THR00.0020.00424.6130.3830.3830.0000.0000.0000.000
68C58ALA0-0.037-0.01426.090-0.349-0.3490.0000.0000.0000.000
69C59TYR00.0130.01626.3730.3660.3660.0000.0000.0000.000
70C60LEU00.0280.03227.786-0.295-0.2950.0000.0000.0000.000
71C61ALA0-0.005-0.01929.481-0.201-0.2010.0000.0000.0000.000
72C62SER00.000-0.00531.705-0.144-0.1440.0000.0000.0000.000
73C63VAL00.0040.00728.193-0.187-0.1870.0000.0000.0000.000
74C64LYS10.9770.98931.573-8.810-8.8100.0000.0000.0000.000
75C65GLY0-0.026-0.01833.259-0.196-0.1960.0000.0000.0000.000
76C66ARG10.7330.86832.396-8.980-8.9800.0000.0000.0000.000
77C67PHE00.0180.00026.8390.0940.0940.0000.0000.0000.000
78C68THR0-0.015-0.00328.144-0.188-0.1880.0000.0000.0000.000
79C69ILE0-0.0220.00020.7940.1110.1110.0000.0000.0000.000
80C70SER0-0.026-0.02223.133-0.267-0.2670.0000.0000.0000.000
81C71ARG10.7950.88716.790-15.333-15.3330.0000.0000.0000.000
82C72ASP-1-0.807-0.86419.40012.69912.6990.0000.0000.0000.000
83C73ASP-1-0.841-0.93317.77415.58915.5890.0000.0000.0000.000
84C74SER0-0.092-0.05517.5870.4720.4720.0000.0000.0000.000
85C75LYS10.8590.90317.465-13.079-13.0790.0000.0000.0000.000
86C76ASP-1-0.866-0.91913.04920.20020.2000.0000.0000.0000.000
87C77THR00.0020.01314.1480.4490.4490.0000.0000.0000.000
88C78THR0-0.070-0.05716.101-0.617-0.6170.0000.0000.0000.000
89C79PHE0-0.004-0.02118.5780.1090.1090.0000.0000.0000.000
90C80LEU0-0.010-0.01421.626-0.045-0.0450.0000.0000.0000.000
91C81GLU-1-0.853-0.91023.7119.7189.7180.0000.0000.0000.000
92C82MET0-0.055-0.01625.811-0.147-0.1470.0000.0000.0000.000
93C82SER00.0590.01528.735-0.251-0.2510.0000.0000.0000.000
94C82SER0-0.005-0.00932.514-0.081-0.0810.0000.0000.0000.000
95C82LEU0-0.0360.00129.369-0.045-0.0450.0000.0000.0000.000
96C83LYS10.9580.99033.070-8.393-8.3930.0000.0000.0000.000
97C84ILE00.0310.01233.0190.2140.2140.0000.0000.0000.000
98C85GLU-1-0.879-0.95632.8888.2778.2770.0000.0000.0000.000
99C86ASP-1-0.781-0.85329.1109.3959.3950.0000.0000.0000.000
100C87THR0-0.0190.00127.9390.3740.3740.0000.0000.0000.000
101C88ALA0-0.039-0.01624.612-0.066-0.0660.0000.0000.0000.000
102C89VAL00.0060.01419.316-0.020-0.0200.0000.0000.0000.000
103C90TYR0-0.022-0.05220.326-0.107-0.1070.0000.0000.0000.000
104C91TYR0-0.013-0.01315.0750.2820.2820.0000.0000.0000.000
105C93ILE0-0.016-0.00413.1660.8310.8310.0000.0000.0000.000
106C94ALA00.0230.01010.812-0.840-0.8400.0000.0000.0000.000
107C95SER0-0.037-0.03212.4300.2940.2940.0000.0000.0000.000
108C96SER0-0.047-0.0189.9200.3850.3850.0000.0000.0000.000
109C97THR00.0210.01111.953-0.718-0.7180.0000.0000.0000.000
110C98THR0-0.032-0.00910.197-0.850-0.8500.0000.0000.0000.000
111C99GLY00.0410.00213.257-0.519-0.5190.0000.0000.0000.000
112C100TRP0-0.0080.00016.725-0.225-0.2250.0000.0000.0000.000
113C100TYR0-0.038-0.01719.892-0.773-0.7730.0000.0000.0000.000
114C100VAL00.0050.00519.4030.7780.7780.0000.0000.0000.000
115C100ARG10.7520.86813.006-20.731-20.7310.0000.0000.0000.000
116C100GLU-1-0.825-0.90617.33814.14014.1400.0000.0000.0000.000
117C100ASP-1-0.830-0.89115.93915.65615.6560.0000.0000.0000.000
118C100PHE0-0.024-0.01715.2410.3550.3550.0000.0000.0000.000
119C101ASP-1-0.741-0.85510.60021.76821.7680.0000.0000.0000.000
120C102TYR00.0300.0056.2272.1872.1870.0000.0000.0000.000
121C103TRP0-0.039-0.0319.745-2.530-2.5300.0000.0000.0000.000
122C104GLY00.0490.0389.5751.5621.5620.0000.0000.0000.000
123C105HIS0-0.046-0.03111.2040.0250.0250.0000.0000.0000.000
124C106GLY00.0190.01213.373-0.215-0.2150.0000.0000.0000.000
125C107THR0-0.027-0.00416.833-0.476-0.4760.0000.0000.0000.000
126C108LEU0-0.028-0.02119.150-0.164-0.1640.0000.0000.0000.000
127C109VAL00.0130.01222.690-0.141-0.1410.0000.0000.0000.000
128C110THR0-0.058-0.04325.704-0.147-0.1470.0000.0000.0000.000
129C111VAL00.0250.02329.209-0.079-0.0790.0000.0000.0000.000
130C112SER0-0.002-0.01732.409-0.190-0.1900.0000.0000.0000.000
131C113SER00.0580.03435.5350.0440.0440.0000.0000.0000.000
132C114ALA00.057-0.02437.637-0.129-0.1290.0000.0000.0000.000
133C119SER0-0.0890.07538.684-0.002-0.0020.0000.0000.0000.000
134C120THR0-0.074-0.10235.7080.0060.0060.0000.0000.0000.000
135C121LYS10.8450.91437.737-6.963-6.9630.0000.0000.0000.000
136C122GLY00.0220.01338.4970.1730.1730.0000.0000.0000.000
137C123PRO0-0.045-0.00538.172-0.102-0.1020.0000.0000.0000.000
138C124SER00.004-0.00940.770-0.132-0.1320.0000.0000.0000.000
139C125VAL0-0.0070.00141.4310.0860.0860.0000.0000.0000.000
140C126PHE00.0130.00443.991-0.128-0.1280.0000.0000.0000.000
141C127PRO00.0120.00045.6390.1260.1260.0000.0000.0000.000
142C128LEU0-0.023-0.02644.059-0.048-0.0480.0000.0000.0000.000
143C129ALA00.0140.00747.8550.0340.0340.0000.0000.0000.000
144C130PRO00.0100.00750.2340.0170.0170.0000.0000.0000.000
145C131SER0-0.044-0.02851.513-0.130-0.1300.0000.0000.0000.000
146C132SER00.0320.00853.662-0.020-0.0200.0000.0000.0000.000
147C133LYS10.9200.97355.891-5.456-5.4560.0000.0000.0000.000
148C134SER00.0750.03854.4320.0810.0810.0000.0000.0000.000
149C135THR00.0410.03455.2710.0420.0420.0000.0000.0000.000
150C136SER00.1110.04952.2340.0300.0300.0000.0000.0000.000
151C137GLY00.1800.27552.0630.0300.0300.0000.0000.0000.000
152C138GLY0-0.260-0.29352.337-0.089-0.0890.0000.0000.0000.000
153C139THR0-0.089-0.06847.0350.0020.0020.0000.0000.0000.000
154C140ALA0-0.0100.00048.959-0.048-0.0480.0000.0000.0000.000
155C141ALA00.009-0.00345.7170.1250.1250.0000.0000.0000.000
156C142LEU0-0.0070.01245.045-0.148-0.1480.0000.0000.0000.000
157C143GLY00.0570.01943.3080.1810.1810.0000.0000.0000.000
158C144CYS0-0.103-0.01540.412-0.011-0.0110.0000.0000.0000.000
159C145LEU00.0300.02641.4980.1730.1730.0000.0000.0000.000
160C146VAL0-0.026-0.02037.712-0.057-0.0570.0000.0000.0000.000
161C147LYS10.9030.91939.801-6.427-6.4270.0000.0000.0000.000
162C148ASP-1-0.813-0.87241.2066.6136.6130.0000.0000.0000.000
163C149TYR0-0.024-0.03433.301-0.193-0.1930.0000.0000.0000.000
164C150PHE00.0900.05233.6010.1370.1370.0000.0000.0000.000
165C151PRO00.0120.02531.099-0.192-0.1920.0000.0000.0000.000
166C152GLU-1-0.761-0.85429.3048.8178.8170.0000.0000.0000.000
167C153PRO0-0.033-0.01627.5680.0740.0740.0000.0000.0000.000
168C154VAL0-0.002-0.02229.964-0.281-0.2810.0000.0000.0000.000
169C155THR0-0.033-0.00930.2570.2400.2400.0000.0000.0000.000
170C156VAL00.005-0.00532.506-0.238-0.2380.0000.0000.0000.000
171C157SER0-0.028-0.00633.8610.2010.2010.0000.0000.0000.000
172C158TRP00.0490.01936.153-0.277-0.2770.0000.0000.0000.000
173C159ASN00.0280.00139.3210.0500.0500.0000.0000.0000.000
174C160SER0-0.039-0.02038.3820.0300.0300.0000.0000.0000.000
175C161GLY00.0270.00735.6230.1140.1140.0000.0000.0000.000
176C162ALA0-0.016-0.00336.3890.1090.1090.0000.0000.0000.000
177C163LEU0-0.0180.00238.7420.0100.0100.0000.0000.0000.000
178C164THR00.016-0.00133.9350.1420.1420.0000.0000.0000.000
179C165SER00.012-0.00536.4240.0580.0580.0000.0000.0000.000
180C166GLY0-0.010-0.00437.683-0.178-0.1780.0000.0000.0000.000
181C167VAL00.0340.02735.477-0.167-0.1670.0000.0000.0000.000
182C168HIS0-0.038-0.01434.7800.2920.2920.0000.0000.0000.000
183C169THR00.0230.00933.091-0.309-0.3090.0000.0000.0000.000
184C170PHE0-0.0130.01033.1920.2500.2500.0000.0000.0000.000
185C171PRO00.0170.00430.9980.0520.0520.0000.0000.0000.000
186C172ALA0-0.004-0.00532.564-0.265-0.2650.0000.0000.0000.000
187C173VAL0-0.009-0.00733.8970.1530.1530.0000.0000.0000.000
188C174LEU0-0.042-0.02433.878-0.148-0.1480.0000.0000.0000.000
189C175GLN0-0.048-0.03436.642-0.210-0.2100.0000.0000.0000.000
190C176SER00.0380.00539.9470.1000.1000.0000.0000.0000.000
191C177SER0-0.016-0.00842.404-0.008-0.0080.0000.0000.0000.000
192C178GLY00.0390.03138.736-0.019-0.0190.0000.0000.0000.000
193C179LEU0-0.046-0.01838.2180.1070.1070.0000.0000.0000.000
194C180TYR00.0350.01831.318-0.042-0.0420.0000.0000.0000.000
195C181SER00.000-0.00537.001-0.224-0.2240.0000.0000.0000.000
196C182LEU0-0.0130.01933.5240.0760.0760.0000.0000.0000.000
197C183SER0-0.001-0.01937.317-0.240-0.2400.0000.0000.0000.000
198C184SER00.0280.01836.5090.1250.1250.0000.0000.0000.000
199C185VAL00.011-0.00938.525-0.231-0.2310.0000.0000.0000.000
200C186VAL00.0230.00939.4490.1950.1950.0000.0000.0000.000
201C187THR0-0.021-0.00641.725-0.149-0.1490.0000.0000.0000.000
202C188VAL00.0160.01943.5910.1210.1210.0000.0000.0000.000
203C189PRO00.0560.00546.161-0.099-0.0990.0000.0000.0000.000
204C190SER0-0.008-0.00249.317-0.015-0.0150.0000.0000.0000.000
205C191SER00.0110.01052.431-0.063-0.0630.0000.0000.0000.000
206C192SER0-0.054-0.02350.123-0.060-0.0600.0000.0000.0000.000
207C193LEU00.0190.01550.7790.1090.1090.0000.0000.0000.000
208C194GLY00.0200.00752.7700.0220.0220.0000.0000.0000.000
209C195THR0-0.010-0.01051.969-0.043-0.0430.0000.0000.0000.000
210C196GLN0-0.024-0.00346.9040.0170.0170.0000.0000.0000.000
211C197THR00.0510.04348.528-0.077-0.0770.0000.0000.0000.000
212C198TYR0-0.009-0.01645.0130.1890.1890.0000.0000.0000.000
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