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: 4N4JN

Calculation Name: 3MH9-C-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MH9

Chain ID: C

ChEMBL ID:

UniProt ID: P9WK45

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2079029.009879
FMO2-HF: Nuclear repulsion 2004456.312555
FMO2-HF: Total energy -74572.697324
FMO2-MP2: Total energy -74794.039606


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:33:ACE )


Summations of interaction energy for fragment #1(C:33:ACE )
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.
1.2182.7410.042-0.575-0.989-0.001
Interaction energy analysis for fragmet #1(C:33:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / 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].
3C35GLY 00.0320.0363.8190.9751.826-0.006-0.369-0.476-0.001
4C36GLY 00.0150.0105.8570.0820.0820.0000.0000.0000.000
5C37PRO 00.008-0.0075.4220.1690.1690.0000.0000.0000.000
6C38LEU 0-0.014-0.0043.303-0.417-0.1860.023-0.099-0.1560.000
7C39PRO 00.0120.0206.678-0.035-0.0350.0000.0000.0000.000
8C40ASP -1-0.876-0.9449.9930.4030.4030.0000.0000.0000.000
9C41ALA 0-0.014-0.02411.696-0.044-0.0440.0000.0000.0000.000
10C42LYS 10.9560.97213.034-0.240-0.2400.0000.0000.0000.000
11C43PRO 00.0950.04615.508-0.019-0.0190.0000.0000.0000.000
12C44LEU 00.0650.04411.819-0.020-0.0200.0000.0000.0000.000
13C45VAL 00.0070.00115.469-0.022-0.0220.0000.0000.0000.000
14C46GLU -1-0.965-0.95717.6830.0850.0850.0000.0000.0000.000
15C47GLU -1-0.942-0.98917.9060.0560.0560.0000.0000.0000.000
16C48ALA 00.0350.01117.942-0.013-0.0130.0000.0000.0000.000
17C49THR 0-0.062-0.03620.023-0.011-0.0110.0000.0000.0000.000
18C50ALA 0-0.023-0.01522.868-0.007-0.0070.0000.0000.0000.000
19C51GLN 00.0000.00222.046-0.009-0.0090.0000.0000.0000.000
20C52THR 0-0.040-0.03522.263-0.008-0.0080.0000.0000.0000.000
21C53LYS 10.8740.94124.919-0.041-0.0410.0000.0000.0000.000
22C54ALA 0-0.0180.00927.733-0.002-0.0020.0000.0000.0000.000
23C55LEU 0-0.0380.00524.775-0.006-0.0060.0000.0000.0000.000
24C56LYS 10.8710.93028.4890.0100.0100.0000.0000.0000.000
25C57SER 0-0.031-0.04130.1490.0010.0010.0000.0000.0000.000
26C58ALA 00.0170.00825.841-0.001-0.0010.0000.0000.0000.000
27C59HIS 0-0.037-0.01425.496-0.002-0.0020.0000.0000.0000.000
28C60MET 0-0.019-0.01425.0040.0000.0000.0000.0000.0000.000
29C61VAL 00.0220.00723.155-0.001-0.0010.0000.0000.0000.000
30C62LEU 0-0.028-0.00823.5060.0010.0010.0000.0000.0000.000
31C63THR 00.022-0.00522.434-0.007-0.0070.0000.0000.0000.000
32C64VAL 0-0.020-0.00524.2560.0070.0070.0000.0000.0000.000
33C65ASN 0-0.043-0.01020.674-0.006-0.0060.0000.0000.0000.000
34C66GLY 00.0260.01824.2200.0080.0080.0000.0000.0000.000
35C67LYS 10.8660.93626.761-0.007-0.0070.0000.0000.0000.000
36C68ILE 00.0750.03426.2720.0050.0050.0000.0000.0000.000
37C69PRO 0-0.066-0.06830.328-0.003-0.0030.0000.0000.0000.000
38C70GLY 00.0720.04033.9130.0020.0020.0000.0000.0000.000
39C71LEU 00.0020.01629.795-0.001-0.0010.0000.0000.0000.000
40C72SER 0-0.020-0.01633.6010.0000.0000.0000.0000.0000.000
41C73LEU 00.0100.01130.174-0.002-0.0020.0000.0000.0000.000
42C74LYS 10.8720.94629.4710.0250.0250.0000.0000.0000.000
43C75THR 00.016-0.00726.822-0.003-0.0030.0000.0000.0000.000
44C76LEU 0-0.0170.00628.1830.0030.0030.0000.0000.0000.000
45C77SER 0-0.036-0.00127.941-0.005-0.0050.0000.0000.0000.000
46C78GLY 00.0760.02329.0840.0030.0030.0000.0000.0000.000
47C79ASP -1-0.896-0.87029.540-0.045-0.0450.0000.0000.0000.000
48C80LEU 00.0310.01630.3580.0030.0030.0000.0000.0000.000
49C81THR 0-0.014-0.02131.789-0.001-0.0010.0000.0000.0000.000
50C82THR 00.0750.02533.1550.0030.0030.0000.0000.0000.000
51C83ASN 0-0.0400.02735.7220.0000.0000.0000.0000.0000.000
52C84PRO 00.043-0.00338.8000.0000.0000.0000.0000.0000.000
53C85THR 00.014-0.01836.745-0.001-0.0010.0000.0000.0000.000
54C86ALA 0-0.040-0.00337.0330.0000.0000.0000.0000.0000.000
55C87ALA 00.003-0.00834.624-0.001-0.0010.0000.0000.0000.000
56C88THR 0-0.010-0.00134.8800.0010.0010.0000.0000.0000.000
57C89GLY 00.0630.02733.571-0.003-0.0030.0000.0000.0000.000
58C90ASN 0-0.0350.01231.8660.0010.0010.0000.0000.0000.000
59C91TRP 00.041-0.00432.629-0.001-0.0010.0000.0000.0000.000
60C92LYS 10.8580.92831.6500.0350.0350.0000.0000.0000.000
61C93LEU 0-0.023-0.01432.9800.0020.0020.0000.0000.0000.000
62C94THR 00.0080.00034.360-0.002-0.0020.0000.0000.0000.000
63C95LEU 0-0.014-0.01036.5790.0030.0030.0000.0000.0000.000
64C96GLY 00.0140.01240.172-0.001-0.0010.0000.0000.0000.000
65C97GLY 0-0.011-0.01039.0510.0000.0000.0000.0000.0000.000
66C98SER 0-0.040-0.02639.833-0.001-0.0010.0000.0000.0000.000
67C99ASP -1-0.820-0.90534.305-0.023-0.0230.0000.0000.0000.000
68C100ILE 0-0.032-0.02937.3040.0000.0000.0000.0000.0000.000
69C101ASP -1-0.806-0.87535.374-0.034-0.0340.0000.0000.0000.000
70C102ALA 0-0.052-0.02937.1220.0020.0020.0000.0000.0000.000
71C103ASP -1-0.854-0.92137.106-0.033-0.0330.0000.0000.0000.000
72C104PHE 0-0.049-0.04133.3560.0030.0030.0000.0000.0000.000
73C105VAL 00.000-0.01338.146-0.002-0.0020.0000.0000.0000.000
74C106VAL 0-0.029-0.00338.1670.0020.0020.0000.0000.0000.000
75C107PHE 00.020-0.01840.018-0.001-0.0010.0000.0000.0000.000
76C108ASP -1-0.892-0.93942.722-0.007-0.0070.0000.0000.0000.000
77C109GLY 0-0.013-0.01043.0850.0010.0010.0000.0000.0000.000
78C110ILE 0-0.0340.00544.0460.0010.0010.0000.0000.0000.000
79C111LEU 00.0100.00339.404-0.002-0.0020.0000.0000.0000.000
80C112TYR 00.0090.00142.3890.0000.0000.0000.0000.0000.000
81C113ALA 00.0470.00841.242-0.001-0.0010.0000.0000.0000.000
82C114THR 0-0.051-0.01141.9930.0000.0000.0000.0000.0000.000
83C115LEU 00.0100.02043.2600.0000.0000.0000.0000.0000.000
84C116THR 00.008-0.00445.4880.0000.0000.0000.0000.0000.000
85C117PRO 00.0460.00443.6840.0000.0000.0000.0000.0000.000
86C118ASN 0-0.021-0.01043.5450.0000.0000.0000.0000.0000.000
87C119GLN 0-0.029-0.00645.5010.0020.0020.0000.0000.0000.000
88C120TRP 0-0.014-0.00740.5940.0010.0010.0000.0000.0000.000
89C121SER 0-0.020-0.00546.4470.0010.0010.0000.0000.0000.000
90C122ASP -1-0.907-0.95646.439-0.008-0.0080.0000.0000.0000.000
91C123PHE 0-0.061-0.04644.4680.0000.0000.0000.0000.0000.000
92C124GLY 00.0420.03346.1450.0010.0010.0000.0000.0000.000
93C125PRO 00.021-0.00745.354-0.001-0.0010.0000.0000.0000.000
94C126ALA 00.0540.01739.8060.0000.0000.0000.0000.0000.000
95C127ALA 0-0.053-0.03040.3540.0010.0010.0000.0000.0000.000
96C128ASP -1-0.913-0.94041.3610.0030.0030.0000.0000.0000.000
97C129ILE 0-0.097-0.03738.0960.0000.0000.0000.0000.0000.000
98C130TYR 0-0.082-0.08231.3200.0010.0010.0000.0000.0000.000
99C131ASP -1-0.811-0.89937.117-0.003-0.0030.0000.0000.0000.000
100C132PRO 00.0200.00333.8140.0020.0020.0000.0000.0000.000
101C133ALA 0-0.020-0.01932.8340.0000.0000.0000.0000.0000.000
102C134GLN 0-0.059-0.02632.9480.0040.0040.0000.0000.0000.000
103C135VAL 00.0220.01327.1670.0040.0040.0000.0000.0000.000
104C136LEU 0-0.020-0.02027.1610.0020.0020.0000.0000.0000.000
105C137ASN 00.0260.03929.8630.0030.0030.0000.0000.0000.000
106C138PRO 00.0020.00130.0030.0030.0030.0000.0000.0000.000
107C139ASP -1-0.903-0.96230.1140.0260.0260.0000.0000.0000.000
108C140THR 0-0.043-0.02431.4470.0030.0030.0000.0000.0000.000
109C141GLY 00.0240.02128.9000.0010.0010.0000.0000.0000.000
110C142LEU 0-0.012-0.04322.7250.0060.0060.0000.0000.0000.000
111C143ALA 00.0030.00523.8650.0070.0070.0000.0000.0000.000
112C144ASN 00.0410.02125.2670.0110.0110.0000.0000.0000.000
113C145VAL 0-0.034-0.01421.7090.0080.0080.0000.0000.0000.000
114C146LEU 0-0.017-0.01218.7800.0110.0110.0000.0000.0000.000
115C147ALA 0-0.014-0.00521.8760.0110.0110.0000.0000.0000.000
116C148ASN 0-0.094-0.03724.2510.0060.0060.0000.0000.0000.000
117C149PHE 0-0.0160.00215.2520.0020.0020.0000.0000.0000.000
118C150ALA 00.0100.00020.2600.0090.0090.0000.0000.0000.000
119C151ASP -1-0.949-0.99418.1630.1830.1830.0000.0000.0000.000
120C152ALA 0-0.0180.00515.0450.0290.0290.0000.0000.0000.000
121C153LYS 10.9590.9739.655-0.704-0.7040.0000.0000.0000.000
122C154ALA 00.0080.0107.610-0.020-0.0200.0000.0000.0000.000
123C155GLU -1-0.896-0.9356.8990.9460.9460.0000.0000.0000.000
124C156GLY 0-0.053-0.0393.2700.7020.9890.024-0.069-0.2410.000
125C157ARG 10.7200.8464.0130.1270.2810.001-0.038-0.1160.000
126C158ASP -1-0.772-0.8615.524-0.721-0.7210.0000.0000.0000.000
127C159THR 0-0.022-0.0098.7090.1040.1040.0000.0000.0000.000
128C160ILE 00.0100.01111.7870.0250.0250.0000.0000.0000.000
129C161ASN 0-0.009-0.01214.8480.0080.0080.0000.0000.0000.000
130C162GLY 00.0080.00516.6910.0140.0140.0000.0000.0000.000
131C163GLN 00.0160.02415.1530.0060.0060.0000.0000.0000.000
132C164ASN 00.0140.01910.212-0.104-0.1040.0000.0000.0000.000
133C165THR 0-0.034-0.02310.2760.1020.1020.0000.0000.0000.000
134C166ILE 00.0210.0027.261-0.098-0.0980.0000.0000.0000.000
135C167ARG 10.8860.9575.312-0.182-0.1820.0000.0000.0000.000
136C168ILE 0-0.008-0.0178.4680.1880.1880.0000.0000.0000.000
137C169SER 0-0.020-0.01811.193-0.082-0.0820.0000.0000.0000.000
138C170GLY 00.0820.02013.2750.0160.0160.0000.0000.0000.000
139C171LYS 10.8500.93316.827-0.195-0.1950.0000.0000.0000.000
140C172VAL 00.0480.04120.479-0.001-0.0010.0000.0000.0000.000
141C173SER 00.0200.02123.051-0.005-0.0050.0000.0000.0000.000
142C174ALA 00.0480.00626.676-0.004-0.0040.0000.0000.0000.000
143C175GLN 0-0.025-0.01029.059-0.005-0.0050.0000.0000.0000.000
144C176ALA 00.0540.02426.727-0.005-0.0050.0000.0000.0000.000
145C177VAL 0-0.0020.00125.221-0.005-0.0050.0000.0000.0000.000
146C178ASN 0-0.016-0.02027.772-0.006-0.0060.0000.0000.0000.000
147C179GLN 0-0.037-0.01130.955-0.002-0.0020.0000.0000.0000.000
148C180ILE 00.0300.04326.174-0.004-0.0040.0000.0000.0000.000
149C181ALA 0-0.015-0.00528.854-0.006-0.0060.0000.0000.0000.000
150C182PRO 00.0650.03730.7180.0020.0020.0000.0000.0000.000
151C183PRO 0-0.014-0.01332.6870.0020.0020.0000.0000.0000.000
152C184PHE 0-0.0030.00225.1410.0010.0010.0000.0000.0000.000
153C185ASN 0-0.027-0.01630.8040.0020.0020.0000.0000.0000.000
154C186ALA 0-0.0160.00728.6130.0020.0020.0000.0000.0000.000
155C187THR 00.008-0.00830.4550.0000.0000.0000.0000.0000.000
156C188GLN 0-0.014-0.00326.4100.0000.0000.0000.0000.0000.000
157C189PRO 0-0.039-0.02724.600-0.002-0.0020.0000.0000.0000.000
158C190VAL 00.0090.00322.6620.0010.0010.0000.0000.0000.000
159C191PRO 0-0.0170.00719.2080.0090.0090.0000.0000.0000.000
160C192ALA 00.0390.01518.203-0.020-0.0200.0000.0000.0000.000
161C193THR 0-0.022-0.00812.3880.0450.0450.0000.0000.0000.000
162C194VAL 0-0.008-0.00414.069-0.038-0.0380.0000.0000.0000.000
163C195TRP 0-0.032-0.02810.4510.0650.0650.0000.0000.0000.000
164C196ILE 0-0.003-0.00112.476-0.017-0.0170.0000.0000.0000.000
165C197GLN 0-0.027-0.01112.672-0.006-0.0060.0000.0000.0000.000
166C198GLU -1-0.769-0.8719.021-0.227-0.2270.0000.0000.0000.000
167C199THR 0-0.046-0.02812.4630.0290.0290.0000.0000.0000.000
168C200GLY 0-0.002-0.01315.6100.0060.0060.0000.0000.0000.000
169C201ASP -1-0.869-0.94019.324-0.012-0.0120.0000.0000.0000.000
170C202HIS 10.7820.90315.4990.0010.0010.0000.0000.0000.000
171C203GLN 00.0650.02717.9740.0170.0170.0000.0000.0000.000
172C204LEU 00.0260.01617.240-0.002-0.0020.0000.0000.0000.000
173C205ALA 00.000-0.00915.389-0.010-0.0100.0000.0000.0000.000
174C206GLN 00.0030.01314.905-0.023-0.0230.0000.0000.0000.000
175C207ALA 00.0180.01916.6480.0210.0210.0000.0000.0000.000
176C208GLN 0-0.007-0.00116.6280.0070.0070.0000.0000.0000.000
177C209LEU 0-0.029-0.01018.9670.0200.0200.0000.0000.0000.000
178C210ASP -1-0.852-0.93519.3840.0630.0630.0000.0000.0000.000
179C211ARG 10.8450.91921.529-0.025-0.0250.0000.0000.0000.000
180C212GLY 00.0280.01823.054-0.001-0.0010.0000.0000.0000.000
181C213SER 0-0.035-0.02722.222-0.008-0.0080.0000.0000.0000.000
182C214GLY 00.0360.02520.695-0.008-0.0080.0000.0000.0000.000
183C215ASN 0-0.066-0.02721.701-0.016-0.0160.0000.0000.0000.000
184C216SER 00.0090.00721.1470.0060.0060.0000.0000.0000.000
185C217VAL 00.0170.01522.991-0.009-0.0090.0000.0000.0000.000
186C218GLN 00.0160.00417.5070.0190.0190.0000.0000.0000.000
187C219MET 00.0180.01020.855-0.004-0.0040.0000.0000.0000.000
188C220THR 0-0.023-0.02718.4880.0060.0060.0000.0000.0000.000
189C221LEU 0-0.040-0.01920.1560.0020.0020.0000.0000.0000.000
190C222SER 00.002-0.00720.690-0.014-0.0140.0000.0000.0000.000
191C223LYS 10.9050.96022.9370.0650.0650.0000.0000.0000.000
192C224TRP 00.0620.01619.310-0.001-0.0010.0000.0000.0000.000
193C225GLY 00.0020.00625.994-0.002-0.0020.0000.0000.0000.000
194C226GLH 0-0.122-0.09629.252-0.002-0.0020.0000.0000.0000.000
195C227LYS 10.9610.98130.9960.0340.0340.0000.0000.0000.000
196C228VAL 00.0290.02133.007-0.003-0.0030.0000.0000.0000.000
197C229GLN 0-0.052-0.02535.5200.0020.0020.0000.0000.0000.000
198C230VAL 00.0220.00837.886-0.001-0.0010.0000.0000.0000.000
199C231THR 0-0.036-0.01040.4850.0010.0010.0000.0000.0000.000
200C232LYS 10.9600.98343.9990.0090.0090.0000.0000.0000.000
201C233PRO 00.0170.02243.893-0.001-0.0010.0000.0000.0000.000
202C234PRO 0-0.007-0.00446.4320.0010.0010.0000.0000.0000.000
203C235VAL 00.0370.02449.7170.0000.0000.0000.0000.0000.000
204C236SER 0-0.029-0.01651.9610.0000.0000.0000.0000.0000.000
205C237LYS 10.9560.94955.2510.0120.0120.0000.0000.0000.000
206C238LEU 0-0.0180.00758.5090.0000.0000.0000.0000.0000.000
207C239NME 00.0420.03554.8530.0010.0010.0000.0000.0000.000