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: M9V3Z

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 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 362
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5818522.195626
FMO2-HF: Nuclear repulsion 5680317.521035
FMO2-HF: Total energy -138204.674591
FMO2-MP2: Total energy -138604.793622


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.
-4.368-0.990.121-1.574-1.9240
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 : 0.016 / q_NPA : 0.003
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].
3C9PRO00.0030.0033.316-3.591-0.9400.037-1.351-1.3370.001
4C10ASP-1-0.858-0.9266.007-1.078-1.0780.0000.0000.0000.000
5C11SER0-0.016-0.0107.8640.2460.2460.0000.0000.0000.000
6C12GLY00.005-0.0067.9650.2530.2530.0000.0000.0000.000
7C13ALA0-0.100-0.0557.062-0.197-0.1970.0000.0000.0000.000
8C14VAL00.0150.0069.1000.0660.0660.0000.0000.0000.000
9C15PHE0-0.015-0.0207.9580.0850.0850.0000.0000.0000.000
10C16THR0-0.042-0.01812.641-0.018-0.0180.0000.0000.0000.000
11C17PHE00.0210.01414.0380.0330.0330.0000.0000.0000.000
12C18GLY00.0600.03618.196-0.015-0.0150.0000.0000.0000.000
13C19LYS10.8990.94420.641-0.019-0.0190.0000.0000.0000.000
14C20SER00.0260.01417.842-0.008-0.0080.0000.0000.0000.000
15C21LYS10.7940.86820.963-0.028-0.0280.0000.0000.0000.000
16C22PHE0-0.0060.00315.048-0.001-0.0010.0000.0000.0000.000
17C23ALA00.0230.01018.3460.0010.0010.0000.0000.0000.000
18C24GLU-1-0.933-0.95217.8390.1650.1650.0000.0000.0000.000
19C25ASN0-0.004-0.00214.647-0.004-0.0040.0000.0000.0000.000
20C26ASN0-0.106-0.06012.9010.0280.0280.0000.0000.0000.000
21C27PRO00.0540.0069.317-0.045-0.0450.0000.0000.0000.000
22C28GLY00.0350.04412.343-0.028-0.0280.0000.0000.0000.000
23C29LYS10.8630.9154.380-0.513-0.437-0.001-0.004-0.0710.000
24C30PHE0-0.038-0.0068.8570.0960.0960.0000.0000.0000.000
25C31TRP00.0670.0253.057-0.899-0.2480.085-0.219-0.516-0.001
26C32PHE00.0210.0119.5050.1300.1300.0000.0000.0000.000
27C33LYS10.9310.9497.6790.7500.7500.0000.0000.0000.000
28C34ASN0-0.0050.00310.020-0.004-0.0040.0000.0000.0000.000
29C35ASP-1-0.704-0.85611.926-0.256-0.2560.0000.0000.0000.000
30C36VAL00.0110.01612.454-0.142-0.1420.0000.0000.0000.000
31C37PRO00.0150.00813.4380.0760.0760.0000.0000.0000.000
32C38VAL0-0.039-0.02216.675-0.026-0.0260.0000.0000.0000.000
33C39HIS00.0320.01420.0000.0080.0080.0000.0000.0000.000
34C40LEU0-0.032-0.00917.199-0.006-0.0060.0000.0000.0000.000
35C41SER00.0360.00421.3600.0100.0100.0000.0000.0000.000
36C42CYS0-0.039-0.02322.449-0.001-0.0010.0000.0000.0000.000
37C43GLY00.1010.06925.054-0.001-0.0010.0000.0000.0000.000
38C44ASP-1-0.759-0.85627.535-0.010-0.0100.0000.0000.0000.000
39C45GLU-1-0.842-0.90627.4250.0180.0180.0000.0000.0000.000
40C46HIS0-0.013-0.00625.0450.0140.0140.0000.0000.0000.000
41C47SER00.0420.02721.400-0.006-0.0060.0000.0000.0000.000
42C48ALA00.0170.00422.5680.0050.0050.0000.0000.0000.000
43C49VAL0-0.029-0.02116.709-0.013-0.0130.0000.0000.0000.000
44C50VAL00.0460.03420.0890.0060.0060.0000.0000.0000.000
45C51THR0-0.030-0.03416.355-0.009-0.0090.0000.0000.0000.000
46C52GLY00.0510.02618.0390.0290.0290.0000.0000.0000.000
47C53ASN0-0.151-0.07016.4280.0400.0400.0000.0000.0000.000
48C54ASN0-0.023-0.00720.1060.0350.0350.0000.0000.0000.000
49C55LYS10.8640.94816.9320.3300.3300.0000.0000.0000.000
50C56LEU00.0460.02621.200-0.013-0.0130.0000.0000.0000.000
51C57TYR0-0.046-0.03216.2390.0210.0210.0000.0000.0000.000
52C58MET00.0120.02420.194-0.008-0.0080.0000.0000.0000.000
53C59PHE0-0.021-0.02218.2660.0120.0120.0000.0000.0000.000
54C60GLY00.0850.04921.834-0.008-0.0080.0000.0000.0000.000
55C61SER0-0.087-0.07523.9080.0070.0070.0000.0000.0000.000
56C62ASN00.013-0.01927.520-0.015-0.0150.0000.0000.0000.000
57C63ASN00.0060.01129.4000.0030.0030.0000.0000.0000.000
58C64TRP00.0190.00432.7570.0010.0010.0000.0000.0000.000
59C65GLY00.0470.03331.746-0.003-0.0030.0000.0000.0000.000
60C66GLN00.018-0.00229.157-0.001-0.0010.0000.0000.0000.000
61C67LEU0-0.042-0.01024.401-0.009-0.0090.0000.0000.0000.000
62C68GLY00.0110.01627.051-0.008-0.0080.0000.0000.0000.000
63C69LEU0-0.065-0.04924.257-0.003-0.0030.0000.0000.0000.000
64C70GLY00.0040.00528.3210.0040.0040.0000.0000.0000.000
65C71SER0-0.075-0.03529.6290.0060.0060.0000.0000.0000.000
66C72LYS10.8870.91531.835-0.004-0.0040.0000.0000.0000.000
67C73SER0-0.0070.00929.4250.0030.0030.0000.0000.0000.000
68C74ALA00.0230.00827.034-0.005-0.0050.0000.0000.0000.000
69C75ILE0-0.016-0.00622.0990.0030.0030.0000.0000.0000.000
70C76SER00.0110.01220.954-0.004-0.0040.0000.0000.0000.000
71C77LYS10.9480.96916.572-0.019-0.0190.0000.0000.0000.000
72C78PRO00.0080.01314.565-0.010-0.0100.0000.0000.0000.000
73C79THR0-0.077-0.04117.5840.0170.0170.0000.0000.0000.000
74C80CYM-1-0.763-0.81519.156-0.130-0.1300.0000.0000.0000.000
75C81VAL00.0500.02820.8480.0200.0200.0000.0000.0000.000
76C82LYS10.9340.93921.9190.0270.0270.0000.0000.0000.000
77C83ALA00.0210.00725.685-0.004-0.0040.0000.0000.0000.000
78C84LEU00.0480.02626.8420.0000.0000.0000.0000.0000.000
79C85LYS10.7380.83320.9030.1180.1180.0000.0000.0000.000
80C86PRO0-0.042-0.01726.307-0.009-0.0090.0000.0000.0000.000
81C87GLU-1-0.815-0.85828.740-0.089-0.0890.0000.0000.0000.000
82C88LYS10.9190.96226.2650.1490.1490.0000.0000.0000.000
83C89VAL00.004-0.00124.8270.0050.0050.0000.0000.0000.000
84C90LYS10.8150.90825.2380.1640.1640.0000.0000.0000.000
85C91LEU00.0030.01426.050-0.011-0.0110.0000.0000.0000.000
86C92ALA0-0.002-0.01625.6170.0080.0080.0000.0000.0000.000
87C93ALA00.0120.02127.437-0.006-0.0060.0000.0000.0000.000
88C94CYS0-0.084-0.01826.8690.0020.0020.0000.0000.0000.000
89C95GLY00.1340.07429.2340.0000.0000.0000.0000.0000.000
90C96ARG10.8140.89431.1890.0160.0160.0000.0000.0000.000
91C97ASN0-0.049-0.02932.5170.0010.0010.0000.0000.0000.000
92C98HIS00.0100.01633.1690.0050.0050.0000.0000.0000.000
93C99THR0-0.024-0.03327.815-0.004-0.0040.0000.0000.0000.000
94C100LEU0-0.0040.01930.9970.0030.0030.0000.0000.0000.000
95C101VAL00.004-0.01327.969-0.008-0.0080.0000.0000.0000.000
96C102SER00.0290.03729.9270.0050.0050.0000.0000.0000.000
97C103THR0-0.012-0.02929.586-0.011-0.0110.0000.0000.0000.000
98C104GLU-1-0.858-0.95228.869-0.158-0.1580.0000.0000.0000.000
99C105GLY0-0.040-0.01831.6690.0030.0030.0000.0000.0000.000
100C106GLY00.0080.00034.4600.0060.0060.0000.0000.0000.000
101C107ASN0-0.052-0.00734.5800.0080.0080.0000.0000.0000.000
102C108VAL00.0390.01033.965-0.008-0.0080.0000.0000.0000.000
103C109TYR0-0.093-0.07132.2210.0080.0080.0000.0000.0000.000
104C110ALA00.0340.01733.535-0.004-0.0040.0000.0000.0000.000
105C111THR0-0.026-0.00530.4740.0040.0040.0000.0000.0000.000
106C112GLY00.0040.00333.558-0.003-0.0030.0000.0000.0000.000
107C113GLY00.0450.00334.4980.0020.0020.0000.0000.0000.000
108C114ASN0-0.032-0.04737.457-0.006-0.0060.0000.0000.0000.000
109C115ASN00.0050.01140.589-0.001-0.0010.0000.0000.0000.000
110C116GLU-1-0.854-0.92742.620-0.016-0.0160.0000.0000.0000.000
111C117GLY00.0160.00243.375-0.001-0.0010.0000.0000.0000.000
112C118GLN00.0370.01137.820-0.002-0.0020.0000.0000.0000.000
113C119LEU0-0.048-0.00636.165-0.005-0.0050.0000.0000.0000.000
114C120GLY0-0.039-0.01338.927-0.003-0.0030.0000.0000.0000.000
115C121LEU0-0.010-0.02538.799-0.001-0.0010.0000.0000.0000.000
116C122GLY0-0.018-0.00742.7550.0010.0010.0000.0000.0000.000
117C123ASP-1-0.804-0.85943.921-0.022-0.0220.0000.0000.0000.000
118C124THR00.026-0.00744.318-0.002-0.0020.0000.0000.0000.000
119C125GLU-1-0.965-0.96143.291-0.011-0.0110.0000.0000.0000.000
120C126GLU-1-0.864-0.90837.770-0.008-0.0080.0000.0000.0000.000
121C127ARG10.7830.86236.5770.0250.0250.0000.0000.0000.000
122C128ASN00.0210.00333.271-0.003-0.0030.0000.0000.0000.000
123C129THR0-0.034-0.01232.0710.0000.0000.0000.0000.0000.000
124C130PHE00.0320.00727.7340.0000.0000.0000.0000.0000.000
125C131HIS0-0.026-0.01133.0320.0020.0020.0000.0000.0000.000
126C132VAL00.008-0.00236.530-0.002-0.0020.0000.0000.0000.000
127C133ILE00.0050.01037.5980.0040.0040.0000.0000.0000.000
128C134SER0-0.027-0.02839.919-0.003-0.0030.0000.0000.0000.000
129C135PHE0-0.0170.00242.410-0.001-0.0010.0000.0000.0000.000
130C136PHE0-0.015-0.00538.793-0.001-0.0010.0000.0000.0000.000
131C137THR00.0510.02540.3630.0000.0000.0000.0000.0000.000
132C138SER00.0340.01238.541-0.002-0.0020.0000.0000.0000.000
133C139GLU-1-0.841-0.89739.577-0.066-0.0660.0000.0000.0000.000
134C140HIS00.0290.01739.677-0.003-0.0030.0000.0000.0000.000
135C141LYS10.8650.93936.4350.0800.0800.0000.0000.0000.000
136C142ILE0-0.0030.00633.3690.0010.0010.0000.0000.0000.000
137C143LYS10.9090.96732.9400.0960.0960.0000.0000.0000.000
138C144GLN00.0270.00330.582-0.006-0.0060.0000.0000.0000.000
139C145LEU0-0.0110.00530.5330.0070.0070.0000.0000.0000.000
140C146SER00.021-0.00831.355-0.002-0.0020.0000.0000.0000.000
141C147ALA0-0.003-0.00932.3370.0030.0030.0000.0000.0000.000
142C148GLY00.1150.08532.945-0.001-0.0010.0000.0000.0000.000
143C149SER0-0.037-0.04135.3250.0020.0020.0000.0000.0000.000
144C150ASN0-0.0020.00037.3590.0010.0010.0000.0000.0000.000
145C151THR00.0480.03837.9000.0000.0000.0000.0000.0000.000
146C152SER0-0.021-0.03236.702-0.002-0.0020.0000.0000.0000.000
147C153ALA00.0310.02236.3580.0020.0020.0000.0000.0000.000
148C154ALA0-0.013-0.01135.771-0.005-0.0050.0000.0000.0000.000
149C155LEU0-0.0090.01135.5510.0050.0050.0000.0000.0000.000
150C156THR0-0.076-0.05036.138-0.005-0.0050.0000.0000.0000.000
151C157GLU-1-0.877-0.97133.621-0.116-0.1160.0000.0000.0000.000
152C158ASP-1-0.890-0.90237.785-0.072-0.0720.0000.0000.0000.000
153C159GLY00.0170.02040.2110.0040.0040.0000.0000.0000.000
154C160ARG10.7300.82241.4070.0690.0690.0000.0000.0000.000
155C161LEU00.0440.02239.269-0.004-0.0040.0000.0000.0000.000
156C162PHE0-0.008-0.01340.7400.0050.0050.0000.0000.0000.000
157C163MET00.0050.00539.454-0.003-0.0030.0000.0000.0000.000
158C164TRP0-0.027-0.02537.5490.0010.0010.0000.0000.0000.000
159C165GLY00.0300.01941.387-0.002-0.0020.0000.0000.0000.000
160C166ASP-1-0.784-0.89542.466-0.022-0.0220.0000.0000.0000.000
161C167ASN0-0.042-0.03943.987-0.004-0.0040.0000.0000.0000.000
162C168SER0-0.016-0.03046.1570.0010.0010.0000.0000.0000.000
163C169GLU-1-0.795-0.90045.732-0.019-0.0190.0000.0000.0000.000
164C170GLY0-0.040-0.01147.368-0.001-0.0010.0000.0000.0000.000
165C171GLN00.0810.04141.813-0.002-0.0020.0000.0000.0000.000
166C172ILE0-0.042-0.01841.462-0.003-0.0030.0000.0000.0000.000
167C173GLY00.0170.01743.814-0.001-0.0010.0000.0000.0000.000
168C174LEU0-0.043-0.02446.4660.0000.0000.0000.0000.0000.000
169C175LYS10.9140.94649.2210.0330.0330.0000.0000.0000.000
170C176ASN00.010-0.00651.9260.0000.0000.0000.0000.0000.000
171C177VAL0-0.0380.00550.5520.0010.0010.0000.0000.0000.000
172C178SER00.0580.04450.790-0.001-0.0010.0000.0000.0000.000
173C179ASN0-0.017-0.02446.6720.0010.0010.0000.0000.0000.000
174C180VAL0-0.0300.00645.6280.0000.0000.0000.0000.0000.000
175C181CYS00.0300.03944.886-0.001-0.0010.0000.0000.0000.000
176C182VAL0-0.002-0.00144.487-0.001-0.0010.0000.0000.0000.000
177C183PRO0-0.023-0.00641.5120.0010.0010.0000.0000.0000.000
178C184GLN0-0.0020.01444.0420.0010.0010.0000.0000.0000.000
179C185GLN0-0.035-0.02445.143-0.004-0.0040.0000.0000.0000.000
180C186VAL00.0030.01044.3000.0030.0030.0000.0000.0000.000
181C187THR0-0.027-0.03145.470-0.003-0.0030.0000.0000.0000.000
182C188ILE00.0200.01245.7990.0020.0020.0000.0000.0000.000
183C189GLY0-0.028-0.00449.2760.0010.0010.0000.0000.0000.000
184C190LYS10.7740.85946.2440.0500.0500.0000.0000.0000.000
185C191PRO00.0020.01142.9110.0000.0000.0000.0000.0000.000
186C192VAL0-0.004-0.00238.9510.0000.0000.0000.0000.0000.000
187C193SER0-0.046-0.03936.997-0.004-0.0040.0000.0000.0000.000
188C194TRP00.0300.01528.792-0.011-0.0110.0000.0000.0000.000
189C195ILE0-0.009-0.00634.6190.0060.0060.0000.0000.0000.000
190C196SER0-0.0280.00232.648-0.004-0.0040.0000.0000.0000.000
191C197CYS0-0.027-0.02234.3000.0030.0030.0000.0000.0000.000
192C198GLY00.0720.04034.179-0.002-0.0020.0000.0000.0000.000
193C199TYR0-0.141-0.10631.6150.0000.0000.0000.0000.0000.000
194C200TYR00.0480.00636.9460.0010.0010.0000.0000.0000.000
195C201HIS0-0.0040.00137.4510.0030.0030.0000.0000.0000.000
196C202SER0-0.005-0.00838.552-0.003-0.0030.0000.0000.0000.000
197C203ALA00.0030.00538.0900.0020.0020.0000.0000.0000.000
198C204PHE0-0.016-0.02038.087-0.004-0.0040.0000.0000.0000.000
199C205VAL00.0170.01836.7820.0030.0030.0000.0000.0000.000
200C206THR00.022-0.00439.538-0.003-0.0030.0000.0000.0000.000
201C207THR00.007-0.01740.168-0.002-0.0020.0000.0000.0000.000
202C208ASP-1-0.897-0.90541.612-0.059-0.0590.0000.0000.0000.000
203C209GLY0-0.0030.00940.7730.0020.0020.0000.0000.0000.000
204C210GLU-1-0.771-0.84141.827-0.047-0.0470.0000.0000.0000.000
205C211LEU00.0210.01139.046-0.003-0.0030.0000.0000.0000.000
206C212TYR0-0.050-0.05442.1630.0040.0040.0000.0000.0000.000
207C213VAL0-0.013-0.00641.348-0.003-0.0030.0000.0000.0000.000
208C214PHE0-0.028-0.02341.9290.0010.0010.0000.0000.0000.000
209C215GLY00.0210.00943.125-0.002-0.0020.0000.0000.0000.000
210C216GLU-1-0.808-0.89443.531-0.018-0.0180.0000.0000.0000.000
211C217PRO0-0.054-0.01744.895-0.001-0.0010.0000.0000.0000.000
212C218GLU-1-0.882-0.94545.325-0.014-0.0140.0000.0000.0000.000
213C219ASN0-0.061-0.06642.486-0.001-0.0010.0000.0000.0000.000
214C220GLY00.0340.02343.204-0.001-0.0010.0000.0000.0000.000
215C221LYS10.8000.87939.8960.0220.0220.0000.0000.0000.000
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