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: MN1LZ

Calculation Name: 2GS5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GS5

Chain ID: A

ChEMBL ID:

UniProt ID: Q6NEA9

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2009956.944239
FMO2-HF: Nuclear repulsion 1936056.559625
FMO2-HF: Total energy -73900.384614
FMO2-MP2: Total energy -74113.221241


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-12.803-8.40314.152-4.694-13.8540
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.031
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].
3A3ALA00.0550.0392.815-1.6180.2570.055-0.708-1.2210.001
4A4ASP-1-0.752-0.8664.7861.1411.299-0.001-0.009-0.1480.000
5A5ARG10.9410.9585.6210.2990.2990.0000.0000.0000.000
6A6LEU0-0.086-0.0312.877-0.176-0.6893.790-0.636-2.6410.004
7A7PHE0-0.018-0.0136.9010.2050.2050.0000.0000.0000.000
8A8ASN0-0.044-0.00810.364-0.219-0.2190.0000.0000.0000.000
9A9ALA0-0.026-0.01212.138-0.112-0.1120.0000.0000.0000.000
10A10MET0-0.038-0.0097.604-0.116-0.1160.0000.0000.0000.000
11A11GLU-1-0.899-0.95411.6000.5370.5370.0000.0000.0000.000
12A12ARG10.8670.9189.9070.1400.1400.0000.0000.0000.000
13A13ASN0-0.068-0.03912.276-0.129-0.1290.0000.0000.0000.000
14A14GLU-1-0.875-0.94914.2590.1080.1080.0000.0000.0000.000
15A15PRO0-0.030-0.01215.2920.0320.0320.0000.0000.0000.000
16A16ALA00.0190.00417.385-0.023-0.0230.0000.0000.0000.000
17A17PRO00.0390.01219.8640.0200.0200.0000.0000.0000.000
18A18GLY0-0.049-0.02321.1680.0190.0190.0000.0000.0000.000
19A19MET0-0.037-0.00215.3800.0580.0580.0000.0000.0000.000
20A20VAL0-0.038-0.03113.560-0.068-0.0680.0000.0000.0000.000
21A21LEU00.0210.02611.9530.1090.1090.0000.0000.0000.000
22A22VAL0-0.032-0.0278.066-0.062-0.0620.0000.0000.0000.000
23A23ALA00.0570.0377.702-0.003-0.0030.0000.0000.0000.000
24A24ALA00.0460.0162.5850.3870.8700.160-0.205-0.438-0.001
25A25PRO0-0.049-0.0392.309-1.612-1.2512.553-1.191-1.7220.005
26A26SER0-0.024-0.0163.735-0.518-0.3190.000-0.054-0.1440.000
27A27MET0-0.0140.0245.6140.3200.3200.0000.0000.0000.000
28A28GLU-1-0.917-0.9717.843-0.705-0.7050.0000.0000.0000.000
29A29SER0-0.056-0.01011.2510.1040.1040.0000.0000.0000.000
30A30GLU-1-0.897-0.97113.867-0.258-0.2580.0000.0000.0000.000
31A31ASP-1-0.925-0.95516.483-0.215-0.2150.0000.0000.0000.000
32A32PHE0-0.052-0.03712.3460.0570.0570.0000.0000.0000.000
33A33ALA00.0290.04510.5110.0090.0090.0000.0000.0000.000
34A34ARG10.8070.9027.7430.4150.4150.0000.0000.0000.000
35A35SER00.0160.00410.7720.1240.1240.0000.0000.0000.000
36A36VAL0-0.013-0.01611.2780.0940.0940.0000.0000.0000.000
37A37ILE00.0030.00513.645-0.011-0.0110.0000.0000.0000.000
38A38LEU0-0.0100.00915.6980.0380.0380.0000.0000.0000.000
39A39ILE00.0150.01716.422-0.045-0.0450.0000.0000.0000.000
40A40ILE0-0.049-0.05519.7800.0320.0320.0000.0000.0000.000
41A41GLU-1-0.825-0.90722.9530.0310.0310.0000.0000.0000.000
42A42HIS0-0.0210.00420.177-0.026-0.0260.0000.0000.0000.000
43A43SER0-0.040-0.03223.6240.0100.0100.0000.0000.0000.000
44A44GLU-1-0.998-1.00325.182-0.056-0.0560.0000.0000.0000.000
45A45TYR0-0.0070.01127.158-0.012-0.0120.0000.0000.0000.000
46A46ALA00.0100.00023.652-0.018-0.0180.0000.0000.0000.000
47A47THR0-0.027-0.01418.9360.0150.0150.0000.0000.0000.000
48A48PHE00.0120.01021.192-0.027-0.0270.0000.0000.0000.000
49A49GLY00.012-0.01319.0990.0340.0340.0000.0000.0000.000
50A50VAL0-0.039-0.00620.111-0.027-0.0270.0000.0000.0000.000
51A51ASN00.025-0.00416.1290.0880.0880.0000.0000.0000.000
52A52LEU0-0.026-0.02317.3100.0000.0000.0000.0000.0000.000
53A53ALA0-0.034-0.02215.5820.0160.0160.0000.0000.0000.000
54A54SER00.0070.01417.577-0.005-0.0050.0000.0000.0000.000
55A55ARG10.8500.92219.860-0.042-0.0420.0000.0000.0000.000
56A56SER00.013-0.00823.544-0.019-0.0190.0000.0000.0000.000
57A57ASP-1-0.866-0.93026.1520.0040.0040.0000.0000.0000.000
58A58VAL0-0.031-0.00629.4450.0000.0000.0000.0000.0000.000
59A59ALA0-0.008-0.00431.0970.0080.0080.0000.0000.0000.000
60A60VAL00.0590.01131.749-0.005-0.0050.0000.0000.0000.000
61A61PHE0-0.029-0.02134.060-0.003-0.0030.0000.0000.0000.000
62A62ASN0-0.020-0.01936.2290.0000.0000.0000.0000.0000.000
63A63VAL0-0.048-0.00933.583-0.005-0.0050.0000.0000.0000.000
64A64ILE00.0140.01633.593-0.002-0.0020.0000.0000.0000.000
65A65PRO0-0.0040.00137.5450.0070.0070.0000.0000.0000.000
66A66GLU-1-0.847-0.93039.5390.0280.0280.0000.0000.0000.000
67A67TRP00.0620.01635.5550.0110.0110.0000.0000.0000.000
68A68VAL0-0.055-0.01936.1500.0080.0080.0000.0000.0000.000
69A69PRO0-0.009-0.01436.5830.0070.0070.0000.0000.0000.000
70A70CYS0-0.051-0.01935.3900.0070.0070.0000.0000.0000.000
71A71VAL0-0.0610.00430.8340.0090.0090.0000.0000.0000.000
72A72THR00.0050.00428.604-0.001-0.0010.0000.0000.0000.000
73A73LYS10.9270.97930.399-0.100-0.1000.0000.0000.0000.000
74A74PRO0-0.010-0.01727.1360.0130.0130.0000.0000.0000.000
75A75GLN00.004-0.01129.352-0.003-0.0030.0000.0000.0000.000
76A76ALA0-0.022-0.01328.581-0.009-0.0090.0000.0000.0000.000
77A77LEU00.0240.01728.3310.0110.0110.0000.0000.0000.000
78A78TYR00.0170.01521.859-0.004-0.0040.0000.0000.0000.000
79A79ILE00.0060.00421.385-0.003-0.0030.0000.0000.0000.000
80A80GLY00.0020.00020.8460.0050.0050.0000.0000.0000.000
81A81GLY00.0330.01619.708-0.001-0.0010.0000.0000.0000.000
82A82PRO00.0360.02919.1340.0200.0200.0000.0000.0000.000
83A83LEU0-0.0010.02422.0450.0010.0010.0000.0000.0000.000
84A84ASN00.006-0.01324.6710.0110.0110.0000.0000.0000.000
85A85GLN00.0520.00923.3490.0150.0150.0000.0000.0000.000
86A86GLN0-0.056-0.01827.7680.0030.0030.0000.0000.0000.000
87A87SER0-0.039-0.01029.5270.0040.0040.0000.0000.0000.000
88A88VAL00.001-0.00928.923-0.002-0.0020.0000.0000.0000.000
89A89VAL00.0330.02826.2740.0020.0020.0000.0000.0000.000
90A90GLY00.0430.02028.3410.0030.0030.0000.0000.0000.000
91A91VAL00.0060.01324.2700.0020.0020.0000.0000.0000.000
92A92GLY0-0.001-0.00727.5050.0010.0010.0000.0000.0000.000
93A93VAL0-0.035-0.01026.2070.0160.0160.0000.0000.0000.000
94A94THR00.0420.01328.831-0.005-0.0050.0000.0000.0000.000
95A95ALA00.0000.00831.6720.0140.0140.0000.0000.0000.000
96A96GLN0-0.001-0.03132.9190.0020.0020.0000.0000.0000.000
97A97GLY0-0.012-0.00935.881-0.008-0.0080.0000.0000.0000.000
98A98VAL0-0.0330.00835.087-0.005-0.0050.0000.0000.0000.000
99A99ASP-1-0.874-0.94234.8040.1260.1260.0000.0000.0000.000
100A100ALA00.016-0.01332.545-0.007-0.0070.0000.0000.0000.000
101A101ALA0-0.0150.00634.591-0.007-0.0070.0000.0000.0000.000
102A102ARG10.8640.93536.147-0.096-0.0960.0000.0000.0000.000
103A103VAL0-0.016-0.00837.116-0.003-0.0030.0000.0000.0000.000
104A104ASP-1-0.863-0.91837.3360.0570.0570.0000.0000.0000.000
105A105ASN0-0.058-0.03837.555-0.005-0.0050.0000.0000.0000.000
106A106LEU0-0.046-0.02033.2710.0040.0040.0000.0000.0000.000
107A107THR00.0360.02929.873-0.003-0.0030.0000.0000.0000.000
108A108ARG10.9180.95326.314-0.160-0.1600.0000.0000.0000.000
109A109LEU00.0100.03123.829-0.005-0.0050.0000.0000.0000.000
110A110ALA00.020-0.00422.7610.0030.0030.0000.0000.0000.000
111A111ASN0-0.031-0.02122.584-0.012-0.0120.0000.0000.0000.000
112A112ARG10.8870.94226.139-0.196-0.1960.0000.0000.0000.000
113A113LEU0-0.0020.02621.702-0.014-0.0140.0000.0000.0000.000
114A114VAL00.001-0.00326.210-0.005-0.0050.0000.0000.0000.000
115A115MET00.0400.03027.195-0.001-0.0010.0000.0000.0000.000
116A116VAL0-0.031-0.02629.4780.0020.0020.0000.0000.0000.000
117A117ASN00.0130.00132.685-0.011-0.0110.0000.0000.0000.000
118A118LEU0-0.007-0.01731.9070.0020.0020.0000.0000.0000.000
119A119GLY0-0.0040.00435.973-0.004-0.0040.0000.0000.0000.000
120A120ALA0-0.050-0.01638.535-0.001-0.0010.0000.0000.0000.000
121A121ASP-1-0.824-0.90840.2840.0410.0410.0000.0000.0000.000
122A122PRO00.006-0.01239.5040.0060.0060.0000.0000.0000.000
123A123GLU-1-0.948-0.98940.4780.0540.0540.0000.0000.0000.000
124A124GLU-1-0.920-0.94440.9360.0620.0620.0000.0000.0000.000
125A125ILE00.008-0.00935.7890.0070.0070.0000.0000.0000.000
126A126LYS10.9420.97436.445-0.086-0.0860.0000.0000.0000.000
127A127PRO0-0.077-0.03637.8260.0090.0090.0000.0000.0000.000
128A128LEU0-0.0100.00337.0570.0080.0080.0000.0000.0000.000
129A129VAL00.0240.01232.5150.0100.0100.0000.0000.0000.000
130A130SER0-0.057-0.03730.355-0.004-0.0040.0000.0000.0000.000
131A131GLY0-0.063-0.03529.7790.0030.0030.0000.0000.0000.000
132A132MET00.0290.00929.3490.0000.0000.0000.0000.0000.000
133A133ARG10.8420.94023.596-0.150-0.1500.0000.0000.0000.000
134A134LEU00.0330.01427.930-0.001-0.0010.0000.0000.0000.000
135A135PHE00.002-0.01022.1140.0060.0060.0000.0000.0000.000
136A136ALA00.0250.02025.958-0.002-0.0020.0000.0000.0000.000
137A137GLY00.0430.02224.866-0.008-0.0080.0000.0000.0000.000
138A138HIS0-0.085-0.04622.1860.0220.0220.0000.0000.0000.000
139A139ALA00.0020.00117.805-0.025-0.0250.0000.0000.0000.000
140A140GLU-1-0.857-0.94819.925-0.079-0.0790.0000.0000.0000.000
141A141TRP0-0.088-0.04913.8960.0290.0290.0000.0000.0000.000
142A142ALA00.0420.01319.5470.0320.0320.0000.0000.0000.000
143A143PRO00.0780.02520.782-0.015-0.0150.0000.0000.0000.000
144A144GLY0-0.031-0.01120.372-0.016-0.0160.0000.0000.0000.000
145A145GLN0-0.073-0.04215.5610.0050.0050.0000.0000.0000.000
146A146LEU00.0300.01513.553-0.060-0.0600.0000.0000.0000.000
147A147ALA00.002-0.00513.893-0.048-0.0480.0000.0000.0000.000
148A148GLN0-0.008-0.00114.111-0.065-0.0650.0000.0000.0000.000
149A149GLU-1-0.744-0.85311.168-0.650-0.6500.0000.0000.0000.000
150A150ILE0-0.045-0.0309.652-0.262-0.2620.0000.0000.0000.000
151A151GLU-1-0.968-0.9759.403-0.525-0.5250.0000.0000.0000.000
152A152ASN0-0.133-0.0729.383-0.054-0.0540.0000.0000.0000.000
153A153GLY0-0.0140.0035.642-0.529-0.5290.0000.0000.0000.000
154A154ASP-1-0.860-0.9224.547-3.172-3.161-0.001-0.0160.0070.000
155A155TRP0-0.041-0.0526.6450.2900.2900.0000.0000.0000.000
156A156PHE0-0.032-0.0095.9250.1510.1510.0000.0000.0000.000
157A157VAL00.0410.0277.981-0.017-0.0170.0000.0000.0000.000
158A158ALA0-0.0020.00411.0740.1920.1920.0000.0000.0000.000
159A159PRO00.0160.01212.941-0.128-0.1280.0000.0000.0000.000
160A160ALA00.0310.03016.0330.0650.0650.0000.0000.0000.000
161A161LEU0-0.044-0.03717.986-0.017-0.0170.0000.0000.0000.000
162A162PRO00.0380.00020.388-0.020-0.0200.0000.0000.0000.000
163A163SER00.0000.00620.155-0.021-0.0210.0000.0000.0000.000
164A164ASP-1-0.749-0.83717.4420.5050.5050.0000.0000.0000.000
165A165VAL00.0070.01219.893-0.028-0.0280.0000.0000.0000.000
166A166THR0-0.075-0.05122.987-0.024-0.0240.0000.0000.0000.000
167A167ALA00.0290.03621.324-0.011-0.0110.0000.0000.0000.000
168A168PRO00.0230.00423.473-0.026-0.0260.0000.0000.0000.000
169A169GLY00.0310.00623.7230.0100.0100.0000.0000.0000.000
170A170SER0-0.041-0.01123.848-0.014-0.0140.0000.0000.0000.000
171A171VAL0-0.033-0.01318.9500.0040.0040.0000.0000.0000.000
172A172ASP-1-0.769-0.84214.5660.3410.3410.0000.0000.0000.000
173A173VAL00.025-0.00316.0370.0800.0800.0000.0000.0000.000
174A174TRP00.024-0.0036.4520.1090.1090.0000.0000.0000.000
175A175GLY0-0.015-0.01211.4230.2210.2210.0000.0000.0000.000
176A176ASP-1-0.844-0.93012.3940.6680.6680.0000.0000.0000.000
177A177VAL0-0.030-0.01411.2470.0910.0910.0000.0000.0000.000
178A178MET0-0.0070.0064.5630.1140.207-0.001-0.003-0.0890.000
179A179ARG10.7670.8519.502-0.380-0.3800.0000.0000.0000.000
180A180ARG10.7200.83812.135-0.732-0.7320.0000.0000.0000.000
181A181GLN0-0.057-0.0168.549-0.112-0.1120.0000.0000.0000.000
182A182PRO00.0390.0138.702-0.007-0.0070.0000.0000.0000.000
183A183MET0-0.0130.0137.3630.8200.8200.0000.0000.0000.000
184A184PRO0-0.013-0.0182.543-1.312-0.8561.681-0.443-1.6940.003
185A185LEU00.0580.0173.111-0.1450.0681.850-0.332-1.730-0.001
186A186PRO00.0600.0255.444-0.853-0.811-0.001-0.007-0.0340.000
187A187LEU0-0.086-0.0335.751-0.569-0.5690.0000.0000.0000.000
188A188TYR0-0.017-0.0142.616-4.152-3.1304.067-1.090-4.000-0.011
189A189SER0-0.084-0.0206.380-0.337-0.3370.0000.0000.0000.000
190A190THR0-0.001-0.0299.406-0.152-0.1520.0000.0000.0000.000
191A191PHE00.0030.00212.4590.0650.0650.0000.0000.0000.000
192A192PRO00.0310.01416.207-0.045-0.0450.0000.0000.0000.000
193A193VAL0-0.0280.00417.783-0.010-0.0100.0000.0000.0000.000