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: 9M4G2

Calculation Name: 4JHP-C-Xray372

Preferred Name: Phosphodiesterase 6D

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4JHP

Chain ID: C

ChEMBL ID: CHEMBL3860

UniProt ID: O43924

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptH
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 362
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5812997.803907
FMO2-HF: Nuclear repulsion 5674794.25945
FMO2-HF: Total energy -138203.544458
FMO2-MP2: Total energy -138603.527977


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:7:LEU)


Summations of interaction energy for fragment #1(C:7:LEU)
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.
-4.599-1.4110.094-1.461-1.8210.001
Interaction energy analysis for fragmet #1(C:7:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.007
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].
3C9PRO00.0000.0043.451-3.384-0.9630.023-1.231-1.2130.002
4C10ASP-1-0.860-0.9306.143-1.046-1.0460.0000.0000.0000.000
5C11SER0-0.011-0.0067.9450.2320.2320.0000.0000.0000.000
6C12GLY00.009-0.0057.9070.2500.2500.0000.0000.0000.000
7C13ALA0-0.105-0.0607.100-0.200-0.2000.0000.0000.0000.000
8C14VAL00.0150.0099.1350.0630.0630.0000.0000.0000.000
9C15PHE0-0.018-0.0217.8480.0900.0900.0000.0000.0000.000
10C16THR0-0.042-0.01812.733-0.019-0.0190.0000.0000.0000.000
11C17PHE00.0170.01314.1940.0340.0340.0000.0000.0000.000
12C18GLY00.0650.03718.311-0.015-0.0150.0000.0000.0000.000
13C19LYS10.8990.94220.786-0.029-0.0290.0000.0000.0000.000
14C20SER00.0340.01917.773-0.007-0.0070.0000.0000.0000.000
15C21LYS10.8550.91820.917-0.037-0.0370.0000.0000.0000.000
16C22PHE0-0.0050.00815.012-0.003-0.0030.0000.0000.0000.000
17C23ALA00.0230.01218.276-0.001-0.0010.0000.0000.0000.000
18C24GLU-1-0.947-0.95917.8880.1760.1760.0000.0000.0000.000
19C25ASN00.0200.01114.801-0.004-0.0040.0000.0000.0000.000
20C26ASN0-0.109-0.06312.9430.0060.0060.0000.0000.0000.000
21C27PRO00.0530.0019.333-0.044-0.0440.0000.0000.0000.000
22C28GLY00.0360.04312.361-0.029-0.0290.0000.0000.0000.000
23C29LYS10.9160.9574.276-0.771-0.674-0.001-0.008-0.0880.000
24C30PHE0-0.043-0.0108.7750.1010.1010.0000.0000.0000.000
25C31TRP00.0680.0263.144-0.957-0.2870.072-0.222-0.520-0.001
26C32PHE00.0300.0179.4970.1300.1300.0000.0000.0000.000
27C33LYS10.9260.9547.7520.7850.7850.0000.0000.0000.000
28C34ASN0-0.036-0.01910.029-0.009-0.0090.0000.0000.0000.000
29C35ASP-1-0.732-0.87411.917-0.277-0.2770.0000.0000.0000.000
30C36VAL0-0.0110.00112.439-0.148-0.1480.0000.0000.0000.000
31C37PRO0-0.0020.00013.4230.0780.0780.0000.0000.0000.000
32C38VAL0-0.036-0.01716.675-0.026-0.0260.0000.0000.0000.000
33C39HIS00.0480.02619.9960.0080.0080.0000.0000.0000.000
34C40LEU0-0.035-0.01517.147-0.005-0.0050.0000.0000.0000.000
35C41SER00.0530.02321.4070.0090.0090.0000.0000.0000.000
36C42CYS0-0.053-0.02922.5160.0000.0000.0000.0000.0000.000
37C43GLY00.0860.06325.141-0.001-0.0010.0000.0000.0000.000
38C44ASP-1-0.828-0.89427.640-0.006-0.0060.0000.0000.0000.000
39C45GLU-1-0.926-0.98327.3640.0200.0200.0000.0000.0000.000
40C46HIS0-0.065-0.03324.9710.0130.0130.0000.0000.0000.000
41C47SER00.0340.01921.301-0.006-0.0060.0000.0000.0000.000
42C48ALA00.0190.00722.5470.0050.0050.0000.0000.0000.000
43C49VAL0-0.024-0.01816.678-0.012-0.0120.0000.0000.0000.000
44C50VAL00.0320.02820.0790.0060.0060.0000.0000.0000.000
45C51THR0-0.028-0.03216.524-0.008-0.0080.0000.0000.0000.000
46C52GLY00.0340.01818.0160.0300.0300.0000.0000.0000.000
47C53ASN0-0.129-0.06216.4830.0310.0310.0000.0000.0000.000
48C54ASN0-0.038-0.01520.0940.0300.0300.0000.0000.0000.000
49C55LYS10.9470.98717.7640.2660.2660.0000.0000.0000.000
50C56LEU00.0500.03021.205-0.013-0.0130.0000.0000.0000.000
51C57TYR0-0.030-0.02416.6000.0180.0180.0000.0000.0000.000
52C58MET00.0080.02020.190-0.008-0.0080.0000.0000.0000.000
53C59PHE0-0.025-0.02218.1600.0120.0120.0000.0000.0000.000
54C60GLY00.0940.05421.816-0.008-0.0080.0000.0000.0000.000
55C61SER0-0.057-0.04923.8630.0070.0070.0000.0000.0000.000
56C62ASN00.020-0.01427.539-0.015-0.0150.0000.0000.0000.000
57C63ASN0-0.011-0.00629.3820.0020.0020.0000.0000.0000.000
58C64TRP00.0140.01032.7130.0010.0010.0000.0000.0000.000
59C65GLY00.0340.02931.734-0.003-0.0030.0000.0000.0000.000
60C66GLN00.0810.03229.166-0.003-0.0030.0000.0000.0000.000
61C67LEU0-0.048-0.00124.435-0.009-0.0090.0000.0000.0000.000
62C68GLY00.0100.01727.044-0.008-0.0080.0000.0000.0000.000
63C69LEU0-0.064-0.04924.307-0.003-0.0030.0000.0000.0000.000
64C70GLY00.0060.00828.3170.0040.0040.0000.0000.0000.000
65C71SER0-0.071-0.03229.6610.0060.0060.0000.0000.0000.000
66C72LYS10.9400.96231.825-0.008-0.0080.0000.0000.0000.000
67C73SER0-0.0080.00729.5850.0030.0030.0000.0000.0000.000
68C74ALA00.0220.00926.965-0.005-0.0050.0000.0000.0000.000
69C75ILE0-0.014-0.00222.0270.0040.0040.0000.0000.0000.000
70C76SER00.0000.00520.922-0.005-0.0050.0000.0000.0000.000
71C77LYS10.9730.97616.512-0.051-0.0510.0000.0000.0000.000
72C78PRO0-0.0010.01214.502-0.011-0.0110.0000.0000.0000.000
73C79THR0-0.074-0.03417.5770.0160.0160.0000.0000.0000.000
74C80CYM-1-0.819-0.87719.175-0.139-0.1390.0000.0000.0000.000
75C81VAL00.0400.02720.8510.0210.0210.0000.0000.0000.000
76C82LYS10.9170.93222.5320.0190.0190.0000.0000.0000.000
77C83ALA00.0270.00925.695-0.005-0.0050.0000.0000.0000.000
78C84LEU00.0480.02626.8850.0000.0000.0000.0000.0000.000
79C85LYS10.7870.88320.7620.1150.1150.0000.0000.0000.000
80C86PRO0-0.040-0.01626.322-0.010-0.0100.0000.0000.0000.000
81C87GLU-1-0.917-0.93828.754-0.088-0.0880.0000.0000.0000.000
82C88LYS10.9240.95826.1870.1530.1530.0000.0000.0000.000
83C89VAL00.0060.00124.8250.0050.0050.0000.0000.0000.000
84C90LYS10.8890.95025.2450.1710.1710.0000.0000.0000.000
85C91LEU00.0030.01526.050-0.011-0.0110.0000.0000.0000.000
86C92ALA00.000-0.01525.6460.0080.0080.0000.0000.0000.000
87C93ALA00.0050.01627.489-0.005-0.0050.0000.0000.0000.000
88C94CYS0-0.090-0.02826.6840.0020.0020.0000.0000.0000.000
89C95GLY00.1280.07029.2490.0000.0000.0000.0000.0000.000
90C96ARG10.8970.94531.2110.0130.0130.0000.0000.0000.000
91C97ASN0-0.035-0.02632.4390.0010.0010.0000.0000.0000.000
92C98HIS00.0100.01833.1260.0050.0050.0000.0000.0000.000
93C99THR0-0.017-0.03827.822-0.003-0.0030.0000.0000.0000.000
94C100LEU0-0.0080.01330.9770.0030.0030.0000.0000.0000.000
95C101VAL00.014-0.00627.741-0.008-0.0080.0000.0000.0000.000
96C102SER00.0240.03529.9210.0050.0050.0000.0000.0000.000
97C103THR0-0.007-0.02629.588-0.010-0.0100.0000.0000.0000.000
98C104GLU-1-0.936-0.98929.293-0.150-0.1500.0000.0000.0000.000
99C105GLY0-0.043-0.01531.6550.0030.0030.0000.0000.0000.000
100C106GLY00.0110.00034.4630.0060.0060.0000.0000.0000.000
101C107ASN0-0.0110.02834.6310.0080.0080.0000.0000.0000.000
102C108VAL00.0370.00733.970-0.008-0.0080.0000.0000.0000.000
103C109TYR0-0.027-0.01732.1980.0050.0050.0000.0000.0000.000
104C110ALA00.0350.01633.531-0.004-0.0040.0000.0000.0000.000
105C111THR0-0.024-0.00630.4730.0040.0040.0000.0000.0000.000
106C112GLY00.0040.00533.547-0.003-0.0030.0000.0000.0000.000
107C113GLY00.0470.00134.4850.0020.0020.0000.0000.0000.000
108C114ASN0-0.037-0.04937.441-0.006-0.0060.0000.0000.0000.000
109C115ASN00.0070.00840.5740.0000.0000.0000.0000.0000.000
110C116GLU-1-0.878-0.93042.535-0.015-0.0150.0000.0000.0000.000
111C117GLY00.0410.02043.383-0.002-0.0020.0000.0000.0000.000
112C118GLN00.018-0.00437.787-0.002-0.0020.0000.0000.0000.000
113C119LEU0-0.052-0.01036.124-0.005-0.0050.0000.0000.0000.000
114C120GLY0-0.036-0.00938.917-0.003-0.0030.0000.0000.0000.000
115C121LEU0-0.016-0.03038.756-0.001-0.0010.0000.0000.0000.000
116C122GLY0-0.019-0.00442.7500.0010.0010.0000.0000.0000.000
117C123ASP-1-0.809-0.88243.892-0.021-0.0210.0000.0000.0000.000
118C124THR00.032-0.00144.325-0.002-0.0020.0000.0000.0000.000
119C125GLU-1-0.959-0.95643.244-0.010-0.0100.0000.0000.0000.000
120C126GLU-1-0.907-0.95437.947-0.007-0.0070.0000.0000.0000.000
121C127ARG10.7840.88136.5420.0240.0240.0000.0000.0000.000
122C128ASN00.0160.00033.167-0.003-0.0030.0000.0000.0000.000
123C129THR0-0.022-0.00432.0690.0000.0000.0000.0000.0000.000
124C130PHE00.0360.00427.7540.0000.0000.0000.0000.0000.000
125C131HIS0-0.032-0.01433.0310.0020.0020.0000.0000.0000.000
126C132VAL00.001-0.00436.529-0.003-0.0030.0000.0000.0000.000
127C133ILE00.0130.01037.3890.0040.0040.0000.0000.0000.000
128C134SER0-0.028-0.02939.918-0.003-0.0030.0000.0000.0000.000
129C135PHE0-0.0130.00542.469-0.001-0.0010.0000.0000.0000.000
130C136PHE0-0.037-0.00938.813-0.001-0.0010.0000.0000.0000.000
131C137THR00.0680.03540.3680.0000.0000.0000.0000.0000.000
132C138SER00.008-0.00638.523-0.002-0.0020.0000.0000.0000.000
133C139GLU-1-0.947-0.97539.563-0.064-0.0640.0000.0000.0000.000
134C140HIS00.0300.01439.644-0.004-0.0040.0000.0000.0000.000
135C141LYS10.9440.98636.4520.0820.0820.0000.0000.0000.000
136C142ILE00.0050.00833.4230.0010.0010.0000.0000.0000.000
137C143LYS10.9250.96432.7350.0980.0980.0000.0000.0000.000
138C144GLN00.0360.00530.702-0.007-0.0070.0000.0000.0000.000
139C145LEU0-0.017-0.00430.5050.0070.0070.0000.0000.0000.000
140C146SER00.0150.00131.393-0.002-0.0020.0000.0000.0000.000
141C147ALA00.013-0.00632.4790.0030.0030.0000.0000.0000.000
142C148GLY00.1170.08833.018-0.001-0.0010.0000.0000.0000.000
143C149SER0-0.048-0.04635.4040.0030.0030.0000.0000.0000.000
144C150ASN0-0.0110.00037.4090.0010.0010.0000.0000.0000.000
145C151THR00.0510.04237.9870.0000.0000.0000.0000.0000.000
146C152SER0-0.013-0.03436.779-0.002-0.0020.0000.0000.0000.000
147C153ALA00.0310.02436.4120.0020.0020.0000.0000.0000.000
148C154ALA0-0.011-0.00935.817-0.005-0.0050.0000.0000.0000.000
149C155LEU0-0.0130.01235.4680.0050.0050.0000.0000.0000.000
150C156THR0-0.098-0.05236.146-0.006-0.0060.0000.0000.0000.000
151C157GLU-1-0.910-0.98633.690-0.118-0.1180.0000.0000.0000.000
152C158ASP-1-0.918-0.95537.766-0.072-0.0720.0000.0000.0000.000
153C159GLY00.0050.01840.1840.0040.0040.0000.0000.0000.000
154C160ARG10.8420.92641.3950.0680.0680.0000.0000.0000.000
155C161LEU00.0570.02939.257-0.004-0.0040.0000.0000.0000.000
156C162PHE0-0.017-0.01840.7660.0050.0050.0000.0000.0000.000
157C163MET00.0080.00739.490-0.003-0.0030.0000.0000.0000.000
158C164TRP0-0.038-0.03037.6260.0000.0000.0000.0000.0000.000
159C165GLY00.0300.02041.459-0.002-0.0020.0000.0000.0000.000
160C166ASP-1-0.784-0.91942.546-0.020-0.0200.0000.0000.0000.000
161C167ASN0-0.066-0.05244.064-0.004-0.0040.0000.0000.0000.000
162C168SER0-0.009-0.00546.3420.0000.0000.0000.0000.0000.000
163C169GLU-1-0.863-0.94045.639-0.017-0.0170.0000.0000.0000.000
164C170GLY0-0.046-0.02047.434-0.001-0.0010.0000.0000.0000.000
165C171GLN00.0980.04741.827-0.002-0.0020.0000.0000.0000.000
166C172ILE0-0.035-0.02041.543-0.003-0.0030.0000.0000.0000.000
167C173GLY00.0140.01443.870-0.002-0.0020.0000.0000.0000.000
168C174LEU0-0.037-0.02146.5950.0000.0000.0000.0000.0000.000
169C175LYS10.9230.94949.2720.0320.0320.0000.0000.0000.000
170C176ASN00.006-0.01151.9870.0010.0010.0000.0000.0000.000
171C177VAL0-0.0400.00850.6440.0020.0020.0000.0000.0000.000
172C178SER00.0650.04250.862-0.001-0.0010.0000.0000.0000.000
173C179ASN0-0.003-0.00546.6870.0010.0010.0000.0000.0000.000
174C180VAL0-0.0280.00745.5760.0000.0000.0000.0000.0000.000
175C181CYS00.0100.02144.8720.0000.0000.0000.0000.0000.000
176C182VAL00.0100.00444.454-0.001-0.0010.0000.0000.0000.000
177C183PRO0-0.030-0.00841.5750.0010.0010.0000.0000.0000.000
178C184GLN0-0.0010.01244.0350.0010.0010.0000.0000.0000.000
179C185GLN0-0.042-0.02545.186-0.004-0.0040.0000.0000.0000.000
180C186VAL00.0040.01144.3490.0030.0030.0000.0000.0000.000
181C187THR0-0.023-0.02545.488-0.003-0.0030.0000.0000.0000.000
182C188ILE00.0260.01045.8590.0020.0020.0000.0000.0000.000
183C189GLY0-0.031-0.00849.3040.0010.0010.0000.0000.0000.000
184C190LYS10.7960.88946.2210.0500.0500.0000.0000.0000.000
185C191PRO00.0070.01642.9110.0000.0000.0000.0000.0000.000
186C192VAL00.0030.00038.9160.0000.0000.0000.0000.0000.000
187C193SER0-0.032-0.03336.903-0.004-0.0040.0000.0000.0000.000
188C194TRP00.0310.02129.018-0.011-0.0110.0000.0000.0000.000
189C195ILE0-0.008-0.00134.6300.0060.0060.0000.0000.0000.000
190C196SER0-0.039-0.00732.699-0.004-0.0040.0000.0000.0000.000
191C197CYS0-0.019-0.02034.3560.0030.0030.0000.0000.0000.000
192C198GLY00.0700.04234.239-0.002-0.0020.0000.0000.0000.000
193C199TYR0-0.146-0.11731.7600.0000.0000.0000.0000.0000.000
194C200TYR00.0410.00037.0270.0010.0010.0000.0000.0000.000
195C201HIS0-0.014-0.00537.3760.0030.0030.0000.0000.0000.000
196C202SER0-0.009-0.00738.601-0.003-0.0030.0000.0000.0000.000
197C203ALA00.0170.01338.1360.0020.0020.0000.0000.0000.000
198C204PHE0-0.026-0.02338.109-0.004-0.0040.0000.0000.0000.000
199C205VAL00.0180.02136.6970.0030.0030.0000.0000.0000.000
200C206THR00.015-0.01639.529-0.003-0.0030.0000.0000.0000.000
201C207THR0-0.001-0.02240.135-0.002-0.0020.0000.0000.0000.000
202C208ASP-1-0.901-0.91541.576-0.060-0.0600.0000.0000.0000.000
203C209GLY0-0.0010.01040.7370.0020.0020.0000.0000.0000.000
204C210GLU-1-0.781-0.85741.791-0.047-0.0470.0000.0000.0000.000
205C211LEU00.0160.01038.958-0.003-0.0030.0000.0000.0000.000
206C212TYR0-0.056-0.04542.1690.0050.0050.0000.0000.0000.000
207C213VAL0-0.004-0.00541.263-0.002-0.0020.0000.0000.0000.000
208C214PHE0-0.040-0.02742.0330.0010.0010.0000.0000.0000.000
209C215GLY00.0160.00543.173-0.002-0.0020.0000.0000.0000.000
210C216GLU-1-0.803-0.90043.691-0.017-0.0170.0000.0000.0000.000
211C217PRO0-0.051-0.01844.956-0.002-0.0020.0000.0000.0000.000
212C218GLU-1-0.888-0.94245.271-0.013-0.0130.0000.0000.0000.000
213C219ASN0-0.045-0.05942.248-0.001-0.0010.0000.0000.0000.000
214C220GLY00.0330.02143.258-0.001-0.0010.0000.0000.0000.000
215C221LYS10.8080.88739.9790.0210.0210.0000.0000.0000.000
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