Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: MNJGZ

Calculation Name: 4B9X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4B9X

Chain ID: A

ChEMBL ID:

UniProt ID: Q99MV1

Base Structure: X-ray

Registration Date: 2023-09-23

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 196
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2132211.580491
FMO2-HF: Nuclear repulsion 2053513.365173
FMO2-HF: Total energy -78698.215318
FMO2-MP2: Total energy -78923.57827


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(A:697:LEU)


Summations of interaction energy for fragment #1(A:697: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.
-10.283-2.2453.496-3.161-8.373-0.001
Interaction energy analysis for fragmet #1(A:697:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.023
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].
3A699TRP00.009-0.0043.811-1.2711.471-0.024-1.347-1.3720.004
4A700THR00.0420.0196.292-0.004-0.0040.0000.0000.0000.000
5A701TRP00.0180.01910.0260.0620.0620.0000.0000.0000.000
6A702VAL00.005-0.01013.198-0.021-0.0210.0000.0000.0000.000
7A703GLU-1-0.905-0.93515.026-0.647-0.6470.0000.0000.0000.000
8A704PHE0-0.027-0.02418.2780.0420.0420.0000.0000.0000.000
9A705THR0-0.057-0.02122.038-0.007-0.0070.0000.0000.0000.000
10A706VAL00.009-0.02325.1350.0050.0050.0000.0000.0000.000
11A707ASP-1-0.865-0.92527.870-0.149-0.1490.0000.0000.0000.000
12A708GLU-1-0.804-0.86724.326-0.251-0.2510.0000.0000.0000.000
13A709THR0-0.039-0.02628.4300.0020.0020.0000.0000.0000.000
14A710VAL0-0.010-0.01724.716-0.002-0.0020.0000.0000.0000.000
15A711ASP-1-0.841-0.90628.108-0.124-0.1240.0000.0000.0000.000
16A712VAL0-0.015-0.00724.981-0.014-0.0140.0000.0000.0000.000
17A713VAL0-0.001-0.01025.2660.0160.0160.0000.0000.0000.000
18A714VAL00.0130.01225.245-0.013-0.0130.0000.0000.0000.000
19A715CYS0-0.0580.00121.3580.0100.0100.0000.0000.0000.000
20A716MET00.0230.00721.6670.0180.0180.0000.0000.0000.000
21A717MET0-0.037-0.03224.545-0.010-0.0100.0000.0000.0000.000
22A718TYR0-0.039-0.00421.9310.0180.0180.0000.0000.0000.000
23A719SER0-0.059-0.03728.3900.0090.0090.0000.0000.0000.000
24A720PRO00.0450.00329.746-0.007-0.0070.0000.0000.0000.000
25A721GLY0-0.008-0.00329.482-0.006-0.0060.0000.0000.0000.000
26A722GLU-1-0.895-0.92223.218-0.172-0.1720.0000.0000.0000.000
27A723PHE0-0.0030.00125.2430.0160.0160.0000.0000.0000.000
28A724TYR0-0.032-0.02818.868-0.022-0.0220.0000.0000.0000.000
29A725CYS0-0.0200.00221.9300.0260.0260.0000.0000.0000.000
30A726HIS00.0070.00218.953-0.010-0.0100.0000.0000.0000.000
31A727PHE00.046-0.00520.9400.0160.0160.0000.0000.0000.000
32A728LEU0-0.038-0.02221.882-0.007-0.0070.0000.0000.0000.000
33A729LYS10.8230.88520.4780.3140.3140.0000.0000.0000.000
34A730ASP-1-0.889-0.94919.887-0.285-0.2850.0000.0000.0000.000
35A731ASP-1-0.847-0.90820.349-0.176-0.1760.0000.0000.0000.000
36A732ALA0-0.0050.01718.9390.0060.0060.0000.0000.0000.000
37A733LEU00.015-0.00918.966-0.003-0.0030.0000.0000.0000.000
38A734GLU-1-0.935-0.95620.884-0.102-0.1020.0000.0000.0000.000
39A735LYS10.8170.87216.4900.2170.2170.0000.0000.0000.000
40A736LEU0-0.027-0.01015.057-0.004-0.0040.0000.0000.0000.000
41A737ASP-1-0.892-0.94216.766-0.094-0.0940.0000.0000.0000.000
42A738ASP-1-0.912-0.95517.681-0.061-0.0610.0000.0000.0000.000
43A739LEU0-0.090-0.04010.4500.0210.0210.0000.0000.0000.000
44A740ASN00.030-0.01214.1400.0190.0190.0000.0000.0000.000
45A741GLN0-0.0250.00315.7720.0260.0260.0000.0000.0000.000
46A742SER0-0.025-0.01813.5030.0280.0280.0000.0000.0000.000
47A743LEU0-0.040-0.0299.5180.0410.0410.0000.0000.0000.000
48A744ALA00.0260.03013.3850.0360.0360.0000.0000.0000.000
49A745ASP-1-0.907-0.95016.3990.0950.0950.0000.0000.0000.000
50A746TYR0-0.122-0.0917.7730.0570.0570.0000.0000.0000.000
51A747CYS0-0.079-0.03912.1430.0450.0450.0000.0000.0000.000
52A748ALA00.0100.02513.979-0.001-0.0010.0000.0000.0000.000
53A749GLN0-0.043-0.02414.5160.0370.0370.0000.0000.0000.000
54A750LYS10.9100.93616.669-0.222-0.2220.0000.0000.0000.000
55A751PRO00.0230.01114.3320.0310.0310.0000.0000.0000.000
56A752PRO00.0600.0289.9080.0290.0290.0000.0000.0000.000
57A753ASN0-0.061-0.01110.2990.0110.0110.0000.0000.0000.000
58A754GLY0-0.031-0.01710.9840.0850.0850.0000.0000.0000.000
59A755PHE00.0490.0275.1290.0600.0600.0000.0000.0000.000
60A756LYS10.8940.9448.659-0.665-0.6650.0000.0000.0000.000
61A757ALA00.0140.0048.1390.1350.1350.0000.0000.0000.000
62A758GLU-1-0.915-0.9628.1940.3120.3120.0000.0000.0000.000
63A759ILE00.018-0.0038.5380.0000.0000.0000.0000.0000.000
64A760GLY00.0110.0128.880-0.017-0.0170.0000.0000.0000.000
65A761ARG10.8760.9623.630-2.050-1.7340.007-0.049-0.2740.000
66A762PRO00.0220.0052.513-1.2500.0000.798-0.381-1.6680.002
67A763CYS0-0.087-0.0394.0260.2890.6380.005-0.085-0.2680.000
68A764CYS00.0030.0156.109-0.198-0.1980.0000.0000.0000.000
69A765ALA00.0290.0159.1120.0700.0700.0000.0000.0000.000
70A766PHE0-0.002-0.00112.235-0.029-0.0290.0000.0000.0000.000
71A767PHE00.0150.01415.753-0.001-0.0010.0000.0000.0000.000
72A768SER00.008-0.01518.2960.0010.0010.0000.0000.0000.000
73A769GLY0-0.047-0.02121.7100.0020.0020.0000.0000.0000.000
74A770ASP-1-0.823-0.89620.815-0.027-0.0270.0000.0000.0000.000
75A771GLY0-0.040-0.00121.2830.0040.0040.0000.0000.0000.000
76A772ASN0-0.034-0.02018.2330.0190.0190.0000.0000.0000.000
77A773TRP0-0.027-0.01312.6350.0120.0120.0000.0000.0000.000
78A774TYR0-0.030-0.02213.154-0.021-0.0210.0000.0000.0000.000
79A775ARG10.7370.8238.3260.5490.5490.0000.0000.0000.000
80A776ALA0-0.001-0.0098.379-0.003-0.0030.0000.0000.0000.000
81A777LEU00.0060.0147.0270.0050.0050.0000.0000.0000.000
82A778VAL0-0.033-0.0108.3470.0230.0230.0000.0000.0000.000
83A779LYS10.8740.92810.3670.0860.0860.0000.0000.0000.000
84A780GLU-1-0.873-0.94613.685-0.089-0.0890.0000.0000.0000.000
85A781ILE00.0030.00612.7380.0230.0230.0000.0000.0000.000
86A782LEU0-0.044-0.00916.469-0.018-0.0180.0000.0000.0000.000
87A783PRO0-0.002-0.01120.1010.0140.0140.0000.0000.0000.000
88A784SER0-0.028-0.01022.0750.0070.0070.0000.0000.0000.000
89A785GLY00.0180.01619.3070.0060.0060.0000.0000.0000.000
90A786ASN0-0.042-0.02618.0160.0310.0310.0000.0000.0000.000
91A787VAL0-0.013-0.01812.3950.0020.0020.0000.0000.0000.000
92A788LYS10.8990.96515.8960.0050.0050.0000.0000.0000.000
93A789VAL00.0120.00311.9220.0050.0050.0000.0000.0000.000
94A790HIS00.0020.00512.807-0.029-0.0290.0000.0000.0000.000
95A791PHE00.0670.02012.277-0.020-0.0200.0000.0000.0000.000
96A792VAL00.0100.0109.7320.0030.0030.0000.0000.0000.000
97A793ASP-1-0.736-0.83312.537-0.413-0.4130.0000.0000.0000.000
98A794TYR00.005-0.00814.9810.0190.0190.0000.0000.0000.000
99A795GLY00.0320.01616.6490.0140.0140.0000.0000.0000.000
100A796ASN0-0.068-0.03418.236-0.010-0.0100.0000.0000.0000.000
101A797VAL0-0.030-0.02917.009-0.014-0.0140.0000.0000.0000.000
102A798GLU-1-0.858-0.90717.332-0.039-0.0390.0000.0000.0000.000
103A799GLU-1-0.915-0.97017.6990.0320.0320.0000.0000.0000.000
104A800VAL00.0150.01714.862-0.001-0.0010.0000.0000.0000.000
105A801THR0-0.018-0.02817.4770.0080.0080.0000.0000.0000.000
106A802THR00.0360.00014.3010.0010.0010.0000.0000.0000.000
107A803ASP-1-0.929-0.95114.2960.2300.2300.0000.0000.0000.000
108A804GLN0-0.033-0.00315.736-0.004-0.0040.0000.0000.0000.000
109A805LEU00.0020.00110.583-0.019-0.0190.0000.0000.0000.000
110A806GLN0-0.009-0.0129.3760.0560.0560.0000.0000.0000.000
111A807ALA00.0130.0085.0130.0410.0410.0000.0000.0000.000
112A808ILE00.0330.0292.763-0.736-0.1580.285-0.152-0.710-0.001
113A809LEU0-0.016-0.0013.336-0.9870.0530.098-0.415-0.723-0.003
114A810PRO00.0570.0032.466-1.444-0.5730.853-0.298-1.4260.002
115A811GLN00.0190.0173.810-0.400-0.3510.0080.009-0.0670.000
116A812PHE0-0.005-0.0096.457-0.036-0.0360.0000.0000.0000.000
117A813LEU0-0.016-0.0142.517-1.342-0.4991.466-0.443-1.865-0.005
118A814LEU0-0.0330.0006.501-0.103-0.1030.0000.0000.0000.000
119A815LEU0-0.0110.0179.224-0.002-0.0020.0000.0000.0000.000
120A816PRO00.0650.04110.494-0.081-0.0810.0000.0000.0000.000
121A817PHE0-0.033-0.0236.3550.0580.0580.0000.0000.0000.000
122A818GLN00.039-0.01712.1370.0420.0420.0000.0000.0000.000
123A819GLY0-0.0090.01515.3610.0400.0400.0000.0000.0000.000
124A820MET0-0.055-0.00915.264-0.026-0.0260.0000.0000.0000.000
125A821GLN00.0230.01718.7030.0130.0130.0000.0000.0000.000
126A822CYS0-0.070-0.03720.703-0.015-0.0150.0000.0000.0000.000
127A823TRP0-0.063-0.03322.8080.0100.0100.0000.0000.0000.000
128A824LEU0-0.016-0.01127.683-0.003-0.0030.0000.0000.0000.000
129A825VAL00.0300.02230.0250.0010.0010.0000.0000.0000.000
130A826ASP-1-0.928-0.96832.292-0.118-0.1180.0000.0000.0000.000
131A827ILE0-0.034-0.03134.0630.0100.0100.0000.0000.0000.000
132A828GLN0-0.049-0.02635.079-0.007-0.0070.0000.0000.0000.000
133A829PRO0-0.005-0.01835.3040.0050.0050.0000.0000.0000.000
134A830PRO0-0.0030.01138.0690.0010.0010.0000.0000.0000.000
135A831ASN0-0.032-0.01241.5110.0040.0040.0000.0000.0000.000
136A832LYS10.9610.96138.4970.0670.0670.0000.0000.0000.000
137A833HIS00.0160.02034.215-0.006-0.0060.0000.0000.0000.000
138A834TRP00.0780.03331.5300.0080.0080.0000.0000.0000.000
139A835THR00.0340.01836.4050.0030.0030.0000.0000.0000.000
140A836LYS11.0040.97135.1640.0510.0510.0000.0000.0000.000
141A837GLU-1-0.928-0.95937.879-0.053-0.0530.0000.0000.0000.000
142A838ALA00.0210.01237.815-0.001-0.0010.0000.0000.0000.000
143A839THR0-0.003-0.01232.668-0.005-0.0050.0000.0000.0000.000
144A840ALA0-0.0070.00235.049-0.002-0.0020.0000.0000.0000.000
145A841ARG10.8740.88937.3580.0670.0670.0000.0000.0000.000
146A842PHE00.0120.01630.2240.0010.0010.0000.0000.0000.000
147A843GLN00.0280.00530.331-0.005-0.0050.0000.0000.0000.000
148A844ALA0-0.047-0.02434.3020.0000.0000.0000.0000.0000.000
149A845CYM-1-0.893-0.87537.187-0.071-0.0710.0000.0000.0000.000
150A846VAL00.0230.00931.337-0.003-0.0030.0000.0000.0000.000
151A847VAL0-0.018-0.00232.009-0.003-0.0030.0000.0000.0000.000
152A848GLY0-0.031-0.01131.5270.0040.0040.0000.0000.0000.000
153A849LEU0-0.017-0.00131.9450.0050.0050.0000.0000.0000.000
154A850LYS10.8780.94430.0380.1070.1070.0000.0000.0000.000
155A851LEU0-0.049-0.01130.8840.0050.0050.0000.0000.0000.000
156A852GLN00.0210.00530.607-0.006-0.0060.0000.0000.0000.000
157A853ALA00.001-0.00227.7070.0050.0050.0000.0000.0000.000
158A854ARG10.8820.93629.7510.1380.1380.0000.0000.0000.000
159A855VAL00.0100.00024.4830.0020.0020.0000.0000.0000.000
160A856VAL0-0.027-0.01327.6240.0010.0010.0000.0000.0000.000
161A857GLU-1-0.873-0.92427.064-0.184-0.1840.0000.0000.0000.000
162A858ILE00.0070.01621.319-0.005-0.0050.0000.0000.0000.000
163A859THR0-0.056-0.03321.3890.0040.0040.0000.0000.0000.000
164A860ALA00.0150.00316.632-0.020-0.0200.0000.0000.0000.000
165A861ASN0-0.081-0.04715.469-0.061-0.0610.0000.0000.0000.000
166A862GLY00.0990.05318.1590.0370.0370.0000.0000.0000.000
167A863VAL0-0.048-0.01320.282-0.009-0.0090.0000.0000.0000.000
168A864GLY00.0440.02623.2880.0140.0140.0000.0000.0000.000
169A865VAL0-0.031-0.04226.047-0.001-0.0010.0000.0000.0000.000
170A866GLU-1-0.832-0.89028.832-0.109-0.1090.0000.0000.0000.000
171A867LEU0-0.0030.00628.703-0.001-0.0010.0000.0000.0000.000
172A868THR0-0.004-0.02232.6510.0100.0100.0000.0000.0000.000
173A869ASP-1-0.811-0.87034.885-0.083-0.0830.0000.0000.0000.000
174A870LEU0-0.012-0.02036.1410.0040.0040.0000.0000.0000.000
175A871SER0-0.037-0.03438.7620.0040.0040.0000.0000.0000.000
176A872THR0-0.039-0.02040.1600.0060.0060.0000.0000.0000.000
177A873PRO00.005-0.01742.917-0.003-0.0030.0000.0000.0000.000
178A874TYR0-0.068-0.01545.311-0.001-0.0010.0000.0000.0000.000
179A875PRO00.006-0.00140.566-0.001-0.0010.0000.0000.0000.000
180A876LYS10.8330.89138.6060.0780.0780.0000.0000.0000.000
181A877ILE00.0220.01036.986-0.003-0.0030.0000.0000.0000.000
182A878ILE0-0.003-0.00334.4060.0050.0050.0000.0000.0000.000
183A879SER00.053-0.01535.5730.0080.0080.0000.0000.0000.000
184A880ASP-1-0.820-0.90937.350-0.082-0.0820.0000.0000.0000.000
185A881VAL0-0.082-0.03740.1420.0060.0060.0000.0000.0000.000
186A882LEU00.0200.01336.0660.0050.0050.0000.0000.0000.000
187A883ILE0-0.0160.00039.5800.0030.0030.0000.0000.0000.000
188A884ARG10.9000.95242.5650.0740.0740.0000.0000.0000.000
189A885GLU-1-0.885-0.93343.841-0.059-0.0590.0000.0000.0000.000
190A886GLN0-0.101-0.04645.3120.0020.0020.0000.0000.0000.000
191A887LEU00.0070.01640.8630.0010.0010.0000.0000.0000.000
192A888VAL0-0.054-0.02937.273-0.002-0.0020.0000.0000.0000.000
193A889LEU0-0.0240.00640.1840.0030.0030.0000.0000.0000.000
194A890ARG10.9480.95739.5370.0820.0820.0000.0000.0000.000
195A891CYS0-0.0250.00135.9440.0040.0040.0000.0000.0000.000
196A892GLY0-0.0110.00439.224-0.002-0.0020.0000.0000.0000.000