FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8NN8Y

Calculation Name: 3HHP-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HHP

Chain ID: C

ChEMBL ID:

UniProt ID: P61889

Base Structure: X-ray

Registration Date: 2023-09-27

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 312
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4199605.130001
FMO2-HF: Nuclear repulsion 4086956.602555
FMO2-HF: Total energy -112648.527445
FMO2-MP2: Total energy -112979.787109


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:MET)


Summations of interaction energy for fragment #1(C:1:MET)
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.
-29.391-17.21321.642-10.818-23.001-0.054
Interaction energy analysis for fragmet #1(C:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.026
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].
3C3VAL00.002-0.0042.891-0.7281.9480.175-1.197-1.6530.001
4C4ALA00.0230.0164.9480.2210.262-0.001-0.004-0.0350.000
5C5VAL0-0.024-0.0208.6430.3380.3380.0000.0000.0000.000
6C6LEU00.0190.00411.335-0.022-0.0220.0000.0000.0000.000
7C7GLY00.007-0.01714.5710.0930.0930.0000.0000.0000.000
8C8ALA0-0.038-0.02314.7990.0430.0430.0000.0000.0000.000
9C9ALA0-0.0060.00816.5440.0100.0100.0000.0000.0000.000
10C10GLY00.0390.03219.9460.0350.0350.0000.0000.0000.000
11C11GLY0-0.008-0.01519.799-0.011-0.0110.0000.0000.0000.000
12C12ILE0-0.014-0.01216.6050.0090.0090.0000.0000.0000.000
13C13GLY00.0410.02815.4120.0160.0160.0000.0000.0000.000
14C14GLN0-0.023-0.02115.302-0.046-0.0460.0000.0000.0000.000
15C15ALA0-0.0050.00316.823-0.018-0.0180.0000.0000.0000.000
16C16LEU00.000-0.00210.8220.0120.0120.0000.0000.0000.000
17C17ALA00.0010.00512.066-0.027-0.0270.0000.0000.0000.000
18C18LEU00.0370.01812.835-0.077-0.0770.0000.0000.0000.000
19C19LEU0-0.0110.00713.5850.0070.0070.0000.0000.0000.000
20C20LEU00.0250.0047.0710.0560.0560.0000.0000.0000.000
21C21LYS10.8330.9229.2720.6440.6440.0000.0000.0000.000
22C22THR0-0.055-0.03911.3420.0360.0360.0000.0000.0000.000
23C23GLN0-0.044-0.01710.7500.1630.1630.0000.0000.0000.000
24C24LEU0-0.0060.0103.9470.2100.3790.000-0.022-0.1470.000
25C25PRO00.0150.0164.310-0.521-0.345-0.001-0.012-0.1630.000
26C26SER0-0.006-0.0015.267-1.000-1.0000.0000.0000.0000.000
27C27GLY0-0.013-0.0075.4860.7130.7130.0000.0000.0000.000
28C28SER0-0.050-0.0222.300-3.716-1.6460.821-1.351-1.539-0.002
29C29GLU-1-0.868-0.9253.196-0.743-0.1860.0150.002-0.5740.000
30C30LEU00.0050.0155.731-0.582-0.5820.0000.0000.0000.000
31C31SER0-0.065-0.0518.3190.2010.2010.0000.0000.0000.000
32C32LEU00.0040.00710.6490.1640.1640.0000.0000.0000.000
33C33TYR00.009-0.03713.523-0.014-0.0140.0000.0000.0000.000
34C34ASP-1-0.794-0.90816.052-0.218-0.2180.0000.0000.0000.000
35C35ILE00.0250.04519.367-0.017-0.0170.0000.0000.0000.000
36C36ALA0-0.0090.00122.7280.0150.0150.0000.0000.0000.000
37C37PRO00.0450.00622.660-0.033-0.0330.0000.0000.0000.000
38C38VAL00.0070.00322.399-0.015-0.0150.0000.0000.0000.000
39C39THR00.0050.01017.473-0.010-0.0100.0000.0000.0000.000
40C40PRO0-0.012-0.01118.822-0.049-0.0490.0000.0000.0000.000
41C41GLY00.0210.02020.014-0.023-0.0230.0000.0000.0000.000
42C42VAL00.0070.00117.4540.0030.0030.0000.0000.0000.000
43C43ALA00.0110.00515.747-0.020-0.0200.0000.0000.0000.000
44C44VAL0-0.032-0.01116.735-0.039-0.0390.0000.0000.0000.000
45C45ASP-1-0.895-0.92819.279-0.294-0.2940.0000.0000.0000.000
46C46LEU00.0450.01115.046-0.002-0.0020.0000.0000.0000.000
47C47SER0-0.111-0.08514.886-0.026-0.0260.0000.0000.0000.000
48C48HIS0-0.063-0.02815.9600.0310.0310.0000.0000.0000.000
49C49ILE00.0120.01915.6650.0570.0570.0000.0000.0000.000
50C50PRO0-0.0070.00115.272-0.079-0.0790.0000.0000.0000.000
51C51THR00.011-0.00911.5670.0270.0270.0000.0000.0000.000
52C52ALA00.0030.0089.823-0.123-0.1230.0000.0000.0000.000
53C53VAL0-0.0100.0026.790-0.161-0.1610.0000.0000.0000.000
54C54LYS10.8340.9117.5212.4672.4670.0000.0000.0000.000
55C55ILE00.0240.0138.782-0.342-0.3420.0000.0000.0000.000
56C56LYS10.9090.95311.5021.0861.0860.0000.0000.0000.000
57C57GLY00.0450.02013.701-0.073-0.0730.0000.0000.0000.000
58C58PHE0-0.019-0.01213.7000.0480.0480.0000.0000.0000.000
59C59SER00.000-0.02918.2630.0390.0390.0000.0000.0000.000
60C60GLY00.0280.03021.093-0.016-0.0160.0000.0000.0000.000
61C61GLU-1-0.918-0.96222.553-0.244-0.2440.0000.0000.0000.000
62C62ASP-1-0.796-0.86319.308-0.478-0.4780.0000.0000.0000.000
63C63ALA00.0310.01115.585-0.037-0.0370.0000.0000.0000.000
64C64THR0-0.026-0.04715.019-0.114-0.1140.0000.0000.0000.000
65C65PRO0-0.005-0.00114.244-0.121-0.1210.0000.0000.0000.000
66C66ALA0-0.027-0.02012.437-0.184-0.1840.0000.0000.0000.000
67C67LEU00.011-0.00110.423-0.324-0.3240.0000.0000.0000.000
68C68GLU-1-0.890-0.94110.082-1.264-1.2640.0000.0000.0000.000
69C69GLY00.0160.0118.599-0.270-0.2700.0000.0000.0000.000
70C70ALA0-0.054-0.0195.752-0.931-0.9310.0000.0000.0000.000
71C71ASP-1-0.795-0.8892.113-15.349-11.6767.142-4.653-6.162-0.054
72C72VAL0-0.026-0.0153.3201.1101.9830.440-0.237-1.0760.001
73C73VAL00.0210.0095.580-0.895-0.8950.0000.0000.0000.000
74C74LEU0-0.0090.0088.1260.2670.2670.0000.0000.0000.000
75C75ILE00.002-0.00510.713-0.156-0.1560.0000.0000.0000.000
76C76SER00.0390.01914.4560.0630.0630.0000.0000.0000.000
77C77ALA0-0.0190.00017.0770.0030.0030.0000.0000.0000.000
78C78GLY00.0270.02419.1620.0290.0290.0000.0000.0000.000
79C79VAL0-0.086-0.04422.817-0.017-0.0170.0000.0000.0000.000
80C80ALA00.0510.02626.0460.0170.0170.0000.0000.0000.000
81C81ARG10.8570.89528.4510.0140.0140.0000.0000.0000.000
82C82LYS10.9660.98528.4420.1100.1100.0000.0000.0000.000
83C83PRO00.028-0.00933.9970.0060.0060.0000.0000.0000.000
84C84GLY00.0120.02037.306-0.004-0.0040.0000.0000.0000.000
85C85MET0-0.0110.03231.0930.0000.0000.0000.0000.0000.000
86C86ASP-1-0.698-0.81536.357-0.007-0.0070.0000.0000.0000.000
87C87ARG10.8760.90733.873-0.022-0.0220.0000.0000.0000.000
88C88SER0-0.003-0.01632.8960.0000.0000.0000.0000.0000.000
89C89ASP-1-0.779-0.87433.064-0.043-0.0430.0000.0000.0000.000
90C90LEU0-0.044-0.03228.776-0.006-0.0060.0000.0000.0000.000
91C91PHE0-0.0100.00027.661-0.005-0.0050.0000.0000.0000.000
92C92ASN00.005-0.02128.178-0.005-0.0050.0000.0000.0000.000
93C93VAL00.0000.00427.305-0.010-0.0100.0000.0000.0000.000
94C94ASN00.0390.02124.413-0.031-0.0310.0000.0000.0000.000
95C95ALA00.0290.01823.689-0.007-0.0070.0000.0000.0000.000
96C96GLY00.0120.00124.623-0.006-0.0060.0000.0000.0000.000
97C97ILE0-0.036-0.01420.934-0.020-0.0200.0000.0000.0000.000
98C98VAL00.0210.00719.041-0.028-0.0280.0000.0000.0000.000
99C99LYS10.9080.95420.0800.0880.0880.0000.0000.0000.000
100C100ASN0-0.0050.00121.828-0.023-0.0230.0000.0000.0000.000
101C101LEU00.0150.00317.046-0.029-0.0290.0000.0000.0000.000
102C102VAL00.0280.01616.416-0.046-0.0460.0000.0000.0000.000
103C103GLN00.0330.02417.5850.0110.0110.0000.0000.0000.000
104C104GLN0-0.032-0.02117.459-0.067-0.0670.0000.0000.0000.000
105C105VAL00.0140.00012.382-0.066-0.0660.0000.0000.0000.000
106C106ALA0-0.024-0.01414.416-0.045-0.0450.0000.0000.0000.000
107C107LYS10.8310.92516.8610.4540.4540.0000.0000.0000.000
108C108THR0-0.033-0.01513.1150.0270.0270.0000.0000.0000.000
109C109CYS0-0.0240.0089.659-0.104-0.1040.0000.0000.0000.000
110C110PRO00.0280.01411.0570.0570.0570.0000.0000.0000.000
111C111LYS10.9080.9489.5540.4540.4540.0000.0000.0000.000
112C112ALA00.0340.0376.8590.0280.0280.0000.0000.0000.000
113C113CYS0-0.042-0.0046.5240.2310.2310.0000.0000.0000.000
114C114ILE0-0.001-0.0108.506-0.203-0.2030.0000.0000.0000.000
115C115GLY00.0450.01611.0670.1140.1140.0000.0000.0000.000
116C116ILE0-0.049-0.02112.158-0.119-0.1190.0000.0000.0000.000
117C117ILE0-0.009-0.01413.0620.0550.0550.0000.0000.0000.000
118C118THR0-0.034-0.03917.1460.0000.0000.0000.0000.0000.000
119C119ASN00.0200.03420.0960.0270.0270.0000.0000.0000.000
120C120PRO00.0090.00523.084-0.021-0.0210.0000.0000.0000.000
121C121VAL00.0500.01019.455-0.004-0.0040.0000.0000.0000.000
122C122ASN0-0.019-0.01422.0460.0260.0260.0000.0000.0000.000
123C123THR0-0.020-0.00824.7400.0010.0010.0000.0000.0000.000
124C124THR0-0.036-0.05321.140-0.001-0.0010.0000.0000.0000.000
125C125VAL00.0410.02418.058-0.017-0.0170.0000.0000.0000.000
126C126ALA00.0410.03420.390-0.005-0.0050.0000.0000.0000.000
127C127ILE0-0.043-0.01022.437-0.014-0.0140.0000.0000.0000.000
128C128ALA00.003-0.00617.734-0.021-0.0210.0000.0000.0000.000
129C129ALA00.0200.00219.562-0.018-0.0180.0000.0000.0000.000
130C130GLU-1-0.829-0.91120.530-0.012-0.0120.0000.0000.0000.000
131C131VAL0-0.050-0.02820.046-0.017-0.0170.0000.0000.0000.000
132C132LEU00.0060.00115.816-0.020-0.0200.0000.0000.0000.000
133C133LYS10.8250.93319.488-0.082-0.0820.0000.0000.0000.000
134C134LYS10.8120.89622.3390.0420.0420.0000.0000.0000.000
135C135ALA0-0.034-0.00420.289-0.010-0.0100.0000.0000.0000.000
136C136GLY0-0.0110.00321.129-0.020-0.0200.0000.0000.0000.000
137C137VAL0-0.040-0.02916.008-0.004-0.0040.0000.0000.0000.000
138C138TYR0-0.061-0.06015.9580.0220.0220.0000.0000.0000.000
139C139ASP-1-0.746-0.85812.4230.2760.2760.0000.0000.0000.000
140C140LYS10.8170.90114.476-0.138-0.1380.0000.0000.0000.000
141C141ASN0-0.038-0.00813.0060.0470.0470.0000.0000.0000.000
142C142LYS10.8780.9298.042-0.115-0.1150.0000.0000.0000.000
143C143LEU0-0.0420.00411.2950.0500.0500.0000.0000.0000.000
144C144PHE00.0140.0079.8820.0350.0350.0000.0000.0000.000
145C145GLY0-0.003-0.00314.592-0.079-0.0790.0000.0000.0000.000
146C146VAL0-0.014-0.00313.4450.0360.0360.0000.0000.0000.000
147C147THR00.039-0.01516.234-0.041-0.0410.0000.0000.0000.000
148C148THR00.0360.02315.477-0.039-0.0390.0000.0000.0000.000
149C149LEU0-0.023-0.02318.179-0.015-0.0150.0000.0000.0000.000
150C150ASP-1-0.753-0.86920.5600.1810.1810.0000.0000.0000.000
151C151ILE00.0140.05019.803-0.019-0.0190.0000.0000.0000.000
152C152ILE00.0160.01119.358-0.020-0.0200.0000.0000.0000.000
153C153ARG10.7890.89322.523-0.174-0.1740.0000.0000.0000.000
154C154SER00.039-0.00325.651-0.022-0.0220.0000.0000.0000.000
155C155ASN0-0.008-0.01822.238-0.026-0.0260.0000.0000.0000.000
156C156THR00.001-0.00825.582-0.013-0.0130.0000.0000.0000.000
157C157PHE0-0.027-0.02727.956-0.013-0.0130.0000.0000.0000.000
158C158VAL00.0180.01529.847-0.012-0.0120.0000.0000.0000.000
159C159ALA0-0.035-0.01729.359-0.007-0.0070.0000.0000.0000.000
160C160GLU-1-0.929-0.95831.4070.1090.1090.0000.0000.0000.000
161C161LEU0-0.054-0.02633.879-0.007-0.0070.0000.0000.0000.000
162C162LYS10.7810.87734.704-0.138-0.1380.0000.0000.0000.000
163C163GLY00.0080.02436.1040.0030.0030.0000.0000.0000.000
164C164LYS10.8380.92331.468-0.172-0.1720.0000.0000.0000.000
165C165GLN00.0390.01128.995-0.008-0.0080.0000.0000.0000.000
166C166PRO00.022-0.00726.6610.0150.0150.0000.0000.0000.000
167C167GLY0-0.043-0.00823.7830.0140.0140.0000.0000.0000.000
168C168GLU-1-0.941-0.96823.7300.3430.3430.0000.0000.0000.000
169C169VAL0-0.065-0.02525.826-0.006-0.0060.0000.0000.0000.000
170C170GLU-1-0.732-0.83620.3110.4900.4900.0000.0000.0000.000
171C171VAL0-0.044-0.02024.211-0.021-0.0210.0000.0000.0000.000
172C172PRO00.0430.02422.8900.0160.0160.0000.0000.0000.000
173C173VAL0-0.019-0.01222.757-0.034-0.0340.0000.0000.0000.000
174C174ILE00.0010.00222.7730.0340.0340.0000.0000.0000.000
175C175GLY00.0370.00824.963-0.020-0.0200.0000.0000.0000.000
176C176GLY00.000-0.01324.2210.0070.0070.0000.0000.0000.000
177C177HIS10.7770.87819.919-0.195-0.1950.0000.0000.0000.000
178C178SER0-0.045-0.03724.492-0.022-0.0220.0000.0000.0000.000
179C179GLY00.0660.05927.933-0.001-0.0010.0000.0000.0000.000
180C180VAL00.0360.00130.6770.0110.0110.0000.0000.0000.000
181C181THR00.004-0.02628.2860.0100.0100.0000.0000.0000.000
182C182ILE0-0.0660.00725.9860.0150.0150.0000.0000.0000.000
183C183LEU00.0360.02127.324-0.014-0.0140.0000.0000.0000.000
184C184PRO00.0060.00927.3810.0220.0220.0000.0000.0000.000
185C185LEU00.0000.00326.726-0.017-0.0170.0000.0000.0000.000
186C186LEU00.010-0.01029.2900.0110.0110.0000.0000.0000.000
187C187SER0-0.092-0.07831.5860.0020.0020.0000.0000.0000.000
188C188GLN0-0.057-0.05127.4670.0180.0180.0000.0000.0000.000
189C189VAL0-0.0290.00028.5240.0160.0160.0000.0000.0000.000
190C190PRO00.0320.02228.175-0.018-0.0180.0000.0000.0000.000
191C191GLY00.002-0.00331.223-0.002-0.0020.0000.0000.0000.000
192C192VAL0-0.037-0.02332.613-0.012-0.0120.0000.0000.0000.000
193C193SER0-0.001-0.00135.4310.0000.0000.0000.0000.0000.000
194C194PHE00.001-0.00433.066-0.006-0.0060.0000.0000.0000.000
195C195THR00.002-0.00838.798-0.003-0.0030.0000.0000.0000.000
196C196GLU-1-0.818-0.93040.3270.1160.1160.0000.0000.0000.000
197C197GLN0-0.045-0.02740.6640.0000.0000.0000.0000.0000.000
198C198GLU-1-0.767-0.86538.3150.1200.1200.0000.0000.0000.000
199C199VAL00.0320.01935.4250.0060.0060.0000.0000.0000.000
200C200ALA00.0200.02436.0350.0050.0050.0000.0000.0000.000
201C201ASP-1-0.825-0.90837.3470.0880.0880.0000.0000.0000.000
202C202LEU0-0.030-0.00432.6770.0000.0000.0000.0000.0000.000
203C203THR0-0.011-0.00932.5570.0080.0080.0000.0000.0000.000
204C204LYS10.8870.94232.929-0.081-0.0810.0000.0000.0000.000
205C205ARG10.8360.89132.446-0.109-0.1090.0000.0000.0000.000
206C206ILE00.005-0.01127.731-0.003-0.0030.0000.0000.0000.000
207C207GLN0-0.064-0.03929.053-0.008-0.0080.0000.0000.0000.000
208C208ASN0-0.043-0.03731.029-0.015-0.0150.0000.0000.0000.000
209C209ALA00.0580.04728.557-0.011-0.0110.0000.0000.0000.000
210C210GLY0-0.093-0.05328.2420.0050.0050.0000.0000.0000.000
211C211THR00.002-0.00428.927-0.009-0.0090.0000.0000.0000.000
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