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: 7M2GK

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 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 362
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5826950.134306
FMO2-HF: Nuclear repulsion 5688745.152554
FMO2-HF: Total energy -138204.981752
FMO2-MP2: Total energy -138605.098415


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.
-3.17-0.2030.042-1.381-1.6270.002
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 : 0.034 / q_NPA : 0.014
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].
3C9PRO0-0.029-0.0143.413-3.108-0.6420.025-1.253-1.2370.002
4C10ASP-1-0.829-0.9006.169-0.996-0.9960.0000.0000.0000.000
5C11SER0-0.018-0.0288.0670.2460.2460.0000.0000.0000.000
6C12GLY0-0.005-0.0108.6080.2110.2110.0000.0000.0000.000
7C13ALA0-0.097-0.0527.270-0.264-0.2640.0000.0000.0000.000
8C14VAL00.0170.0159.3480.0960.0960.0000.0000.0000.000
9C15PHE0-0.012-0.0168.6120.0170.0170.0000.0000.0000.000
10C16THR0-0.047-0.03112.923-0.002-0.0020.0000.0000.0000.000
11C17PHE00.0330.02914.3280.0200.0200.0000.0000.0000.000
12C18GLY00.0860.04618.542-0.007-0.0070.0000.0000.0000.000
13C19LYS10.9020.94520.8150.0270.0270.0000.0000.0000.000
14C20SER00.007-0.00117.8910.0020.0020.0000.0000.0000.000
15C21LYS10.7730.86921.0060.0360.0360.0000.0000.0000.000
16C22PHE0-0.018-0.00715.2330.0010.0010.0000.0000.0000.000
17C23ALA00.0360.02318.9780.0080.0080.0000.0000.0000.000
18C24GLU-1-0.932-0.95317.7970.0590.0590.0000.0000.0000.000
19C25ASN0-0.009-0.01214.5820.0140.0140.0000.0000.0000.000
20C26ASN0-0.089-0.05012.7010.0210.0210.0000.0000.0000.000
21C27PRO00.014-0.0099.475-0.024-0.0240.0000.0000.0000.000
22C28GLY00.0330.04212.429-0.011-0.0110.0000.0000.0000.000
23C29LYS10.8170.8995.0390.1090.1090.0000.0000.0000.000
24C30PHE0-0.030-0.0069.1330.0550.0550.0000.0000.0000.000
25C31TRP00.0520.0173.456-0.510-0.0090.017-0.128-0.3900.000
26C32PHE00.0180.0109.8310.1330.1330.0000.0000.0000.000
27C33LYS10.9390.9617.5840.5160.5160.0000.0000.0000.000
28C34ASN0-0.004-0.0099.9310.0370.0370.0000.0000.0000.000
29C35ASP-1-0.700-0.82011.735-0.289-0.2890.0000.0000.0000.000
30C36VAL00.0300.02612.204-0.136-0.1360.0000.0000.0000.000
31C37PRO00.002-0.00513.6160.0740.0740.0000.0000.0000.000
32C38VAL0-0.045-0.01616.842-0.019-0.0190.0000.0000.0000.000
33C39HIS00.0390.01720.3230.0110.0110.0000.0000.0000.000
34C40LEU0-0.032-0.01417.508-0.019-0.0190.0000.0000.0000.000
35C41SER00.0360.00221.6670.0160.0160.0000.0000.0000.000
36C42CYS0-0.0270.01122.616-0.007-0.0070.0000.0000.0000.000
37C43GLY00.1010.07625.2330.0010.0010.0000.0000.0000.000
38C44ASP-1-0.753-0.84427.839-0.047-0.0470.0000.0000.0000.000
39C45GLU-1-0.797-0.88428.321-0.032-0.0320.0000.0000.0000.000
40C46HIS0-0.0240.00225.2760.0090.0090.0000.0000.0000.000
41C47SER00.023-0.01521.3720.0020.0020.0000.0000.0000.000
42C48ALA00.0050.00222.6360.0040.0040.0000.0000.0000.000
43C49VAL0-0.022-0.01417.070-0.013-0.0130.0000.0000.0000.000
44C50VAL00.0370.03320.4650.0060.0060.0000.0000.0000.000
45C51THR0-0.009-0.04016.349-0.010-0.0100.0000.0000.0000.000
46C52GLY00.0520.03017.9330.0320.0320.0000.0000.0000.000
47C53ASN0-0.129-0.08416.3260.0560.0560.0000.0000.0000.000
48C54ASN0-0.0250.00019.9320.0350.0350.0000.0000.0000.000
49C55LYS10.8380.93316.5770.3650.3650.0000.0000.0000.000
50C56LEU00.0550.02621.852-0.011-0.0110.0000.0000.0000.000
51C57TYR0-0.078-0.04016.2100.0160.0160.0000.0000.0000.000
52C58MET00.0140.01820.553-0.007-0.0070.0000.0000.0000.000
53C59PHE0-0.031-0.03118.2930.0010.0010.0000.0000.0000.000
54C60GLY00.0840.04922.060-0.003-0.0030.0000.0000.0000.000
55C61SER0-0.078-0.07423.9950.0080.0080.0000.0000.0000.000
56C62ASN0-0.010-0.03527.740-0.012-0.0120.0000.0000.0000.000
57C63ASN00.0080.01529.9320.0050.0050.0000.0000.0000.000
58C64TRP0-0.004-0.01133.0890.0030.0030.0000.0000.0000.000
59C65GLY00.0630.04032.387-0.001-0.0010.0000.0000.0000.000
60C66GLN00.016-0.00229.3500.0010.0010.0000.0000.0000.000
61C67LEU0-0.025-0.00524.939-0.009-0.0090.0000.0000.0000.000
62C68GLY00.0230.01627.433-0.008-0.0080.0000.0000.0000.000
63C69LEU0-0.077-0.04924.242-0.001-0.0010.0000.0000.0000.000
64C70GLY00.0230.01428.2470.0050.0050.0000.0000.0000.000
65C71SER0-0.079-0.03929.7310.0060.0060.0000.0000.0000.000
66C72LYS10.8970.92631.7060.0250.0250.0000.0000.0000.000
67C73SER0-0.0210.00129.3090.0020.0020.0000.0000.0000.000
68C74ALA00.0300.01327.128-0.007-0.0070.0000.0000.0000.000
69C75ILE0-0.029-0.01022.1870.0020.0020.0000.0000.0000.000
70C76SER00.0170.01921.271-0.008-0.0080.0000.0000.0000.000
71C77LYS10.9300.95616.7520.0780.0780.0000.0000.0000.000
72C78PRO00.0290.02114.5420.0020.0020.0000.0000.0000.000
73C79THR0-0.049-0.02417.5970.0200.0200.0000.0000.0000.000
74C80CYM-1-0.772-0.82719.128-0.163-0.1630.0000.0000.0000.000
75C81VAL00.0760.03820.7840.0220.0220.0000.0000.0000.000
76C82LYS10.9070.92521.5340.0830.0830.0000.0000.0000.000
77C83ALA00.0230.01325.585-0.001-0.0010.0000.0000.0000.000
78C84LEU00.0350.02126.5970.0030.0030.0000.0000.0000.000
79C85LYS10.7620.84820.9450.1480.1480.0000.0000.0000.000
80C86PRO0-0.042-0.02026.256-0.006-0.0060.0000.0000.0000.000
81C87GLU-1-0.769-0.85128.414-0.102-0.1020.0000.0000.0000.000
82C88LYS10.8880.94825.8390.1460.1460.0000.0000.0000.000
83C89VAL00.0150.01325.2170.0060.0060.0000.0000.0000.000
84C90LYS10.8000.89225.5170.1640.1640.0000.0000.0000.000
85C91LEU00.0030.01525.985-0.014-0.0140.0000.0000.0000.000
86C92ALA00.010-0.01526.0310.0070.0070.0000.0000.0000.000
87C93ALA00.0170.02527.719-0.006-0.0060.0000.0000.0000.000
88C94CYS0-0.071-0.01927.342-0.001-0.0010.0000.0000.0000.000
89C95GLY00.1220.07229.6860.0000.0000.0000.0000.0000.000
90C96ARG10.7890.86931.4480.0410.0410.0000.0000.0000.000
91C97ASN0-0.042-0.02133.042-0.001-0.0010.0000.0000.0000.000
92C98HIS0-0.0030.00333.2580.0030.0030.0000.0000.0000.000
93C99THR0-0.010-0.02427.983-0.006-0.0060.0000.0000.0000.000
94C100LEU0-0.0070.01831.0850.0050.0050.0000.0000.0000.000
95C101VAL00.002-0.01328.100-0.010-0.0100.0000.0000.0000.000
96C102SER00.0330.03030.0390.0060.0060.0000.0000.0000.000
97C103THR0-0.008-0.02929.729-0.011-0.0110.0000.0000.0000.000
98C104GLU-1-0.854-0.93828.538-0.156-0.1560.0000.0000.0000.000
99C105GLY0-0.029-0.00731.5590.0040.0040.0000.0000.0000.000
100C106GLY00.009-0.00334.4020.0070.0070.0000.0000.0000.000
101C107ASN0-0.054-0.01334.6090.0080.0080.0000.0000.0000.000
102C108VAL00.0220.00834.246-0.009-0.0090.0000.0000.0000.000
103C109TYR0-0.093-0.06132.3880.0080.0080.0000.0000.0000.000
104C110ALA00.0200.01133.611-0.005-0.0050.0000.0000.0000.000
105C111THR0-0.036-0.00930.5650.0050.0050.0000.0000.0000.000
106C112GLY00.017-0.00233.490-0.004-0.0040.0000.0000.0000.000
107C113GLY00.0460.01534.8030.0040.0040.0000.0000.0000.000
108C114ASN0-0.039-0.02637.927-0.006-0.0060.0000.0000.0000.000
109C115ASN00.0090.02340.901-0.001-0.0010.0000.0000.0000.000
110C116GLU-1-0.843-0.92543.015-0.033-0.0330.0000.0000.0000.000
111C117GLY00.0230.00743.7210.0000.0000.0000.0000.0000.000
112C118GLN00.0270.00437.9980.0000.0000.0000.0000.0000.000
113C119LEU0-0.042-0.00936.258-0.005-0.0050.0000.0000.0000.000
114C120GLY0-0.041-0.01639.065-0.003-0.0030.0000.0000.0000.000
115C121LEU00.001-0.02238.8440.0000.0000.0000.0000.0000.000
116C122GLY00.0010.00542.8120.0020.0020.0000.0000.0000.000
117C123ASP-1-0.798-0.86343.997-0.038-0.0380.0000.0000.0000.000
118C124THR00.036-0.00244.402-0.002-0.0020.0000.0000.0000.000
119C125GLU-1-0.957-0.96043.454-0.029-0.0290.0000.0000.0000.000
120C126GLU-1-0.861-0.91737.746-0.035-0.0350.0000.0000.0000.000
121C127ARG10.7670.84436.6680.0430.0430.0000.0000.0000.000
122C128ASN00.0170.00633.465-0.004-0.0040.0000.0000.0000.000
123C129THR0-0.052-0.02532.259-0.002-0.0020.0000.0000.0000.000
124C130PHE00.0450.01227.7000.0010.0010.0000.0000.0000.000
125C131HIS0-0.0010.01733.0720.0030.0030.0000.0000.0000.000
126C132VAL00.010-0.00336.407-0.003-0.0030.0000.0000.0000.000
127C133ILE00.0020.00237.3420.0040.0040.0000.0000.0000.000
128C134SER0-0.027-0.02339.838-0.002-0.0020.0000.0000.0000.000
129C135PHE00.0050.01542.4760.0010.0010.0000.0000.0000.000
130C136PHE0-0.030-0.01338.830-0.001-0.0010.0000.0000.0000.000
131C137THR00.0470.01940.1180.0010.0010.0000.0000.0000.000
132C138SER00.0260.01838.448-0.002-0.0020.0000.0000.0000.000
133C139GLU-1-0.849-0.88739.483-0.069-0.0690.0000.0000.0000.000
134C140HIS00.0380.01939.458-0.004-0.0040.0000.0000.0000.000
135C141LYS10.8690.92736.2390.0800.0800.0000.0000.0000.000
136C142ILE0-0.026-0.00933.4870.0000.0000.0000.0000.0000.000
137C143LYS10.9020.97332.9920.0990.0990.0000.0000.0000.000
138C144GLN00.0170.00330.658-0.004-0.0040.0000.0000.0000.000
139C145LEU0-0.016-0.00730.4320.0070.0070.0000.0000.0000.000
140C146SER00.0180.00131.683-0.003-0.0030.0000.0000.0000.000
141C147ALA0-0.001-0.00632.5060.0030.0030.0000.0000.0000.000
142C148GLY00.0980.06233.596-0.002-0.0020.0000.0000.0000.000
143C149SER0-0.033-0.02935.4810.0010.0010.0000.0000.0000.000
144C150ASN00.0110.01537.7030.0010.0010.0000.0000.0000.000
145C151THR00.0450.04138.1400.0000.0000.0000.0000.0000.000
146C152SER0-0.004-0.03036.720-0.004-0.0040.0000.0000.0000.000
147C153ALA00.0160.02136.4240.0040.0040.0000.0000.0000.000
148C154ALA0-0.009-0.00835.769-0.006-0.0060.0000.0000.0000.000
149C155LEU0-0.0030.02035.7120.0050.0050.0000.0000.0000.000
150C156THR0-0.086-0.05436.298-0.005-0.0050.0000.0000.0000.000
151C157GLU-1-0.840-0.95033.819-0.116-0.1160.0000.0000.0000.000
152C158ASP-1-0.882-0.90238.030-0.074-0.0740.0000.0000.0000.000
153C159GLY00.0320.01940.5980.0040.0040.0000.0000.0000.000
154C160ARG10.7090.80541.6320.0720.0720.0000.0000.0000.000
155C161LEU00.0370.02139.481-0.005-0.0050.0000.0000.0000.000
156C162PHE0-0.003-0.01840.7730.0050.0050.0000.0000.0000.000
157C163MET0-0.0060.00039.537-0.004-0.0040.0000.0000.0000.000
158C164TRP0-0.020-0.01937.5140.0020.0020.0000.0000.0000.000
159C165GLY00.0300.01741.294-0.003-0.0030.0000.0000.0000.000
160C166ASP-1-0.774-0.89342.622-0.037-0.0370.0000.0000.0000.000
161C167ASN0-0.034-0.02944.009-0.005-0.0050.0000.0000.0000.000
162C168SER0-0.014-0.02046.1410.0010.0010.0000.0000.0000.000
163C169GLU-1-0.797-0.90046.270-0.030-0.0300.0000.0000.0000.000
164C170GLY0-0.024-0.01447.743-0.001-0.0010.0000.0000.0000.000
165C171GLN00.0440.03142.130-0.001-0.0010.0000.0000.0000.000
166C172ILE0-0.049-0.01741.429-0.004-0.0040.0000.0000.0000.000
167C173GLY00.0360.01743.852-0.001-0.0010.0000.0000.0000.000
168C174LEU0-0.047-0.02346.6270.0010.0010.0000.0000.0000.000
169C175LYS10.9080.94349.3920.0410.0410.0000.0000.0000.000
170C176ASN00.0110.00152.1470.0000.0000.0000.0000.0000.000
171C177VAL0-0.047-0.00350.8080.0010.0010.0000.0000.0000.000
172C178SER00.0450.01950.746-0.001-0.0010.0000.0000.0000.000
173C179ASN0-0.019-0.01346.5400.0010.0010.0000.0000.0000.000
174C180VAL0-0.024-0.00445.6120.0010.0010.0000.0000.0000.000
175C181CYS00.0030.02245.064-0.002-0.0020.0000.0000.0000.000
176C182VAL0-0.0100.00244.578-0.001-0.0010.0000.0000.0000.000
177C183PRO0-0.036-0.01441.4720.0010.0010.0000.0000.0000.000
178C184GLN00.0070.02344.0360.0020.0020.0000.0000.0000.000
179C185GLN0-0.023-0.02145.130-0.004-0.0040.0000.0000.0000.000
180C186VAL0-0.0070.00244.3240.0030.0030.0000.0000.0000.000
181C187THR0-0.030-0.03245.461-0.002-0.0020.0000.0000.0000.000
182C188ILE00.0170.00845.9620.0020.0020.0000.0000.0000.000
183C189GLY0-0.0180.00549.6130.0010.0010.0000.0000.0000.000
184C190LYS10.7720.86446.5720.0540.0540.0000.0000.0000.000
185C191PRO00.0010.00543.4620.0000.0000.0000.0000.0000.000
186C192VAL00.0030.00839.0830.0000.0000.0000.0000.0000.000
187C193SER0-0.051-0.04637.543-0.004-0.0040.0000.0000.0000.000
188C194TRP00.0290.00728.906-0.010-0.0100.0000.0000.0000.000
189C195ILE0-0.022-0.02534.7870.0070.0070.0000.0000.0000.000
190C196SER0-0.0290.00133.429-0.006-0.0060.0000.0000.0000.000
191C197CYS00.002-0.00534.9530.0050.0050.0000.0000.0000.000
192C198GLY00.0620.03034.349-0.005-0.0050.0000.0000.0000.000
193C199TYR0-0.156-0.11131.6980.0000.0000.0000.0000.0000.000
194C200TYR00.0520.00637.0520.0010.0010.0000.0000.0000.000
195C201HIS0-0.015-0.00737.8730.0040.0040.0000.0000.0000.000
196C202SER00.005-0.00938.746-0.005-0.0050.0000.0000.0000.000
197C203ALA00.0120.01238.1820.0030.0030.0000.0000.0000.000
198C204PHE0-0.024-0.01938.228-0.004-0.0040.0000.0000.0000.000
199C205VAL00.0280.02637.0880.0030.0030.0000.0000.0000.000
200C206THR00.019-0.00539.919-0.003-0.0030.0000.0000.0000.000
201C207THR00.002-0.01140.472-0.003-0.0030.0000.0000.0000.000
202C208ASP-1-0.860-0.88141.876-0.061-0.0610.0000.0000.0000.000
203C209GLY00.0490.03041.0200.0020.0020.0000.0000.0000.000
204C210GLU-1-0.795-0.86042.080-0.052-0.0520.0000.0000.0000.000
205C211LEU00.0280.01639.173-0.003-0.0030.0000.0000.0000.000
206C212TYR0-0.058-0.05542.2650.0050.0050.0000.0000.0000.000
207C213VAL00.002-0.00141.409-0.003-0.0030.0000.0000.0000.000
208C214PHE0-0.028-0.01641.9300.0020.0020.0000.0000.0000.000
209C215GLY00.0310.01143.309-0.003-0.0030.0000.0000.0000.000
210C216GLU-1-0.822-0.88644.136-0.034-0.0340.0000.0000.0000.000
211C217PRO0-0.040-0.02645.061-0.002-0.0020.0000.0000.0000.000
212C218GLU-1-0.869-0.94145.712-0.028-0.0280.0000.0000.0000.000
213C219ASN0-0.079-0.06242.753-0.001-0.0010.0000.0000.0000.000
214C220GLY00.0630.03443.395-0.001-0.0010.0000.0000.0000.000
215C221LYS10.7510.86540.1240.0380.0380.0000.0000.0000.000
216C222LEU0-0.031-0.00440.980-0.003-0.0030.0000.0000.0000.000
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