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: MV18Z

Calculation Name: 2GHP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GHP

Chain ID: A

ChEMBL ID:

UniProt ID: P49960

Base Structure: X-ray

Registration Date: 2023-09-19

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2829498.963137
FMO2-HF: Nuclear repulsion 2734985.003423
FMO2-HF: Total energy -94513.959714
FMO2-MP2: Total energy -94788.74131


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:41:THR)


Summations of interaction energy for fragment #1(A:41:THR)
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.
-8.513-4.1746.416-2.824-7.928-0.023
Interaction energy analysis for fragmet #1(A:41:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.001
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].
3A43VAL0-0.014-0.0073.8051.4002.951-0.022-0.704-0.8250.003
4A44LEU0-0.0120.0006.471-0.369-0.3690.0000.0000.0000.000
5A45VAL0-0.017-0.01510.2070.0170.0170.0000.0000.0000.000
6A46LYS10.9840.98012.931-0.293-0.2930.0000.0000.0000.000
7A47ASN0-0.012-0.02816.330-0.028-0.0280.0000.0000.0000.000
8A48LEU00.0360.02715.483-0.030-0.0300.0000.0000.0000.000
9A49PRO00.0790.04719.5730.0200.0200.0000.0000.0000.000
10A50LYS11.0351.00722.5140.0060.0060.0000.0000.0000.000
11A51SER0-0.027-0.00624.566-0.013-0.0130.0000.0000.0000.000
12A52TYR0-0.018-0.02918.836-0.012-0.0120.0000.0000.0000.000
13A53ASN00.0720.02520.3760.0040.0040.0000.0000.0000.000
14A54GLN00.1180.03715.5740.0390.0390.0000.0000.0000.000
15A55ASN00.0230.02416.270-0.082-0.0820.0000.0000.0000.000
16A56LYS10.9220.96318.2280.1760.1760.0000.0000.0000.000
17A57VAL00.0270.02013.8510.0110.0110.0000.0000.0000.000
18A58TYR00.0400.01812.3300.0360.0360.0000.0000.0000.000
19A59LYS10.8920.93414.5530.3430.3430.0000.0000.0000.000
20A60TYR0-0.030-0.00415.1440.0020.0020.0000.0000.0000.000
21A61PHE00.0410.00411.0180.0400.0400.0000.0000.0000.000
22A62LYS10.9591.00811.6480.4290.4290.0000.0000.0000.000
23A63HIS0-0.033-0.03112.760-0.050-0.0500.0000.0000.0000.000
24A64CYS0-0.094-0.0209.2610.1800.1800.0000.0000.0000.000
25A65GLY00.0600.0348.487-0.038-0.0380.0000.0000.0000.000
26A66PRO0-0.006-0.0038.2380.0130.0130.0000.0000.0000.000
27A67ILE0-0.051-0.0287.168-0.811-0.8110.0000.0000.0000.000
28A68ILE0-0.014-0.0044.4290.3860.469-0.001-0.003-0.0780.000
29A69HIS00.0350.0297.4270.6370.6370.0000.0000.0000.000
30A70VAL0-0.065-0.0438.888-0.208-0.2080.0000.0000.0000.000
31A71ASP-1-0.827-0.89911.434-0.374-0.3740.0000.0000.0000.000
32A72VAL0-0.057-0.03113.8400.0260.0260.0000.0000.0000.000
33A73ALA00.0130.01516.8360.0150.0150.0000.0000.0000.000
34A74ASP-1-0.813-0.88419.156-0.047-0.0470.0000.0000.0000.000
35A75SER0-0.0100.00021.9250.0210.0210.0000.0000.0000.000
36A76LEU00.0920.03922.838-0.020-0.0200.0000.0000.0000.000
37A77LYS10.9530.97625.517-0.099-0.0990.0000.0000.0000.000
38A78LYS10.8790.92825.819-0.011-0.0110.0000.0000.0000.000
39A79ASN0-0.026-0.01026.192-0.013-0.0130.0000.0000.0000.000
40A80PHE0-0.033-0.00419.738-0.001-0.0010.0000.0000.0000.000
41A81ARG10.8120.89319.4540.1220.1220.0000.0000.0000.000
42A82PHE00.0370.01415.5610.0160.0160.0000.0000.0000.000
43A83ALA0-0.021-0.02613.661-0.059-0.0590.0000.0000.0000.000
44A84ARG10.8000.8967.5210.4210.4210.0000.0000.0000.000
45A85ILE0-0.022-0.0117.662-0.083-0.0830.0000.0000.0000.000
46A86GLU-1-0.804-0.8903.927-1.965-1.6670.000-0.047-0.2500.000
47A87PHE00.005-0.0013.1240.9741.6760.033-0.156-0.5790.000
48A88ALA00.0200.0122.248-11.301-9.2981.305-1.648-1.660-0.021
49A89ARG10.8950.9383.4311.4141.9370.016-0.141-0.3970.000
50A90TYR00.0700.0192.133-2.913-1.8254.496-2.253-3.331-0.003
51A91ASP-1-0.811-0.9092.9271.060-1.2840.1212.455-0.231-0.001
52A92GLY00.0170.0145.2810.2240.2240.0000.0000.0000.000
53A93ALA00.000-0.0092.7730.0930.4690.469-0.318-0.528-0.001
54A94LEU0-0.011-0.0054.6780.6250.684-0.001-0.009-0.0490.000
55A95ALA00.0620.0336.7820.1320.1320.0000.0000.0000.000
56A96ALA0-0.017-0.0117.6810.1310.1310.0000.0000.0000.000
57A97ILE00.0290.0156.3230.0980.0980.0000.0000.0000.000
58A98THR0-0.057-0.0269.8270.0310.0310.0000.0000.0000.000
59A99LYS10.8980.94412.3410.3750.3750.0000.0000.0000.000
60A100THR00.0020.00613.143-0.022-0.0220.0000.0000.0000.000
61A101HIS10.8250.87414.861-0.207-0.2070.0000.0000.0000.000
62A102LYS10.9691.00217.3140.0860.0860.0000.0000.0000.000
63A103VAL00.0370.02119.3560.0090.0090.0000.0000.0000.000
64A104VAL0-0.036-0.01118.301-0.035-0.0350.0000.0000.0000.000
65A105GLY0-0.018-0.01621.7070.0160.0160.0000.0000.0000.000
66A106GLN00.002-0.00625.1590.0070.0070.0000.0000.0000.000
67A107ASN0-0.048-0.01622.3810.0060.0060.0000.0000.0000.000
68A108GLU-1-0.802-0.86620.5700.0970.0970.0000.0000.0000.000
69A109ILE0-0.031-0.00914.9400.0170.0170.0000.0000.0000.000
70A110ILE00.0080.01014.4220.0280.0280.0000.0000.0000.000
71A111VAL0-0.039-0.0239.383-0.032-0.0320.0000.0000.0000.000
72A112SER0-0.015-0.0069.7880.0650.0650.0000.0000.0000.000
73A113HIS00.0740.0294.8040.9180.9180.0000.0000.0000.000
74A114LEU0-0.028-0.0106.291-0.510-0.5100.0000.0000.0000.000
75A115THR0-0.010-0.0116.3090.9800.9800.0000.0000.0000.000
76A116GLU-1-0.829-0.9108.1960.7420.7420.0000.0000.0000.000
77A117CYS0-0.042-0.01210.351-0.261-0.2610.0000.0000.0000.000
78A118THR0-0.011-0.01510.500-0.041-0.0410.0000.0000.0000.000
79A119LEU00.0110.01912.7780.0140.0140.0000.0000.0000.000
80A120TRP00.0000.00315.987-0.054-0.0540.0000.0000.0000.000
81A121MET0-0.038-0.01417.9830.0050.0050.0000.0000.0000.000
82A122THR0-0.017-0.02921.562-0.023-0.0230.0000.0000.0000.000
83A123ASN0-0.015-0.00124.464-0.002-0.0020.0000.0000.0000.000
84A124PHE00.0060.01423.2580.0000.0000.0000.0000.0000.000
85A125PRO00.0490.03028.871-0.005-0.0050.0000.0000.0000.000
86A126PRO00.0270.00630.100-0.004-0.0040.0000.0000.0000.000
87A127SER00.0200.02230.465-0.006-0.0060.0000.0000.0000.000
88A128TYR0-0.0080.00527.327-0.004-0.0040.0000.0000.0000.000
89A129THR00.016-0.00826.306-0.010-0.0100.0000.0000.0000.000
90A130GLN00.047-0.00518.7910.0230.0230.0000.0000.0000.000
91A131ARG10.8960.96523.5310.0430.0430.0000.0000.0000.000
92A132ASN00.0880.06426.0650.0010.0010.0000.0000.0000.000
93A133ILE00.0500.02721.3580.0130.0130.0000.0000.0000.000
94A134ARG10.8320.90618.6830.0120.0120.0000.0000.0000.000
95A135ASP-1-0.868-0.95423.7910.0360.0360.0000.0000.0000.000
96A136LEU00.0540.04625.4530.0080.0080.0000.0000.0000.000
97A137LEU00.001-0.01019.7600.0130.0130.0000.0000.0000.000
98A138GLN0-0.058-0.02624.1410.0020.0020.0000.0000.0000.000
99A139ASP-1-0.884-0.92626.3370.0830.0830.0000.0000.0000.000
100A140ILE0-0.092-0.03524.0060.0030.0030.0000.0000.0000.000
101A141ASN0-0.107-0.07026.4290.0120.0120.0000.0000.0000.000
102A142VAL00.0310.02220.2490.0200.0200.0000.0000.0000.000
103A143VAL0-0.025-0.01618.570-0.032-0.0320.0000.0000.0000.000
104A144ALA00.0320.02218.2250.0440.0440.0000.0000.0000.000
105A145LEU0-0.063-0.03811.801-0.075-0.0750.0000.0000.0000.000
106A146SER0-0.003-0.01012.267-0.049-0.0490.0000.0000.0000.000
107A147ILE00.0280.00815.2610.0820.0820.0000.0000.0000.000
108A148ARG10.8460.92510.996-0.304-0.3040.0000.0000.0000.000
109A149LEU00.002-0.00916.7260.0460.0460.0000.0000.0000.000
110A150PRO00.0390.03118.417-0.021-0.0210.0000.0000.0000.000
111A158ARG10.8930.94727.010-0.078-0.0780.0000.0000.0000.000
112A159ARG10.8780.93823.8680.0040.0040.0000.0000.0000.000
113A160PHE00.0180.00717.9340.0170.0170.0000.0000.0000.000
114A161ALA0-0.030-0.01019.297-0.026-0.0260.0000.0000.0000.000
115A162TYR0-0.036-0.02913.8300.0120.0120.0000.0000.0000.000
116A163ILE0-0.014-0.01515.566-0.078-0.0780.0000.0000.0000.000
117A164ASP-1-0.795-0.84710.0440.7590.7590.0000.0000.0000.000
118A165VAL00.0260.00813.432-0.128-0.1280.0000.0000.0000.000
119A166THR0-0.044-0.03413.5150.0790.0790.0000.0000.0000.000
120A167SER0-0.082-0.06414.8950.0530.0530.0000.0000.0000.000
121A168LYS10.9460.94312.021-1.314-1.3140.0000.0000.0000.000
122A169GLU-1-0.891-0.93615.7290.3780.3780.0000.0000.0000.000
123A170ASP-1-0.820-0.89217.9400.3550.3550.0000.0000.0000.000
124A171ALA0-0.004-0.00715.673-0.039-0.0390.0000.0000.0000.000
125A172ARG10.9530.97717.825-0.493-0.4930.0000.0000.0000.000
126A173TYR00.0410.01620.442-0.048-0.0480.0000.0000.0000.000
127A174CYS0-0.0050.00120.392-0.044-0.0440.0000.0000.0000.000
128A175VAL0-0.040-0.02820.042-0.032-0.0320.0000.0000.0000.000
129A176GLU-1-0.983-0.99322.8510.2480.2480.0000.0000.0000.000
130A177LYS10.8970.96525.802-0.199-0.1990.0000.0000.0000.000
131A178LEU0-0.0040.00123.598-0.020-0.0200.0000.0000.0000.000
132A179ASN00.0000.00225.531-0.009-0.0090.0000.0000.0000.000
133A180GLY00.0090.00127.339-0.004-0.0040.0000.0000.0000.000
134A181LEU0-0.0090.00229.445-0.014-0.0140.0000.0000.0000.000
135A182LYS10.9420.96531.526-0.092-0.0920.0000.0000.0000.000
136A183ILE00.0100.00529.487-0.004-0.0040.0000.0000.0000.000
137A184GLU-1-0.879-0.96533.7710.0370.0370.0000.0000.0000.000
138A185GLY0-0.0130.00136.708-0.004-0.0040.0000.0000.0000.000
139A186TYR0-0.0230.00231.961-0.001-0.0010.0000.0000.0000.000
140A187THR0-0.040-0.01631.4760.0030.0030.0000.0000.0000.000
141A188LEU00.0180.01625.9170.0010.0010.0000.0000.0000.000
142A189VAL00.0160.00724.6580.0120.0120.0000.0000.0000.000
143A190THR0-0.029-0.03120.763-0.005-0.0050.0000.0000.0000.000
144A191LYS10.9080.97420.090-0.274-0.2740.0000.0000.0000.000
145A192VAL00.0170.00315.1890.0020.0020.0000.0000.0000.000
146A193SER0-0.092-0.06412.8580.0100.0100.0000.0000.0000.000
147A194ASN00.0080.00114.6580.1110.1110.0000.0000.0000.000
148A195PRO00.0250.02310.053-0.044-0.0440.0000.0000.0000.000
149A196LEU00.0160.00510.912-0.138-0.1380.0000.0000.0000.000
150A206THR00.029-0.00219.802-0.005-0.0050.0000.0000.0000.000
151A207LEU00.0210.00320.9110.0180.0180.0000.0000.0000.000
152A208GLU-1-0.809-0.87822.3640.2990.2990.0000.0000.0000.000
153A209GLY00.0120.00321.2900.0340.0340.0000.0000.0000.000
154A210ARG10.7550.84118.594-0.220-0.2200.0000.0000.0000.000
155A211GLU-1-0.853-0.90722.3310.1330.1330.0000.0000.0000.000
156A212ILE00.0080.01626.1410.0100.0100.0000.0000.0000.000
157A213MET00.0050.00628.662-0.009-0.0090.0000.0000.0000.000
158A214ILE00.0030.00531.6860.0030.0030.0000.0000.0000.000
159A215ARG10.9380.93734.701-0.117-0.1170.0000.0000.0000.000
160A216ASN00.0160.00238.234-0.003-0.0030.0000.0000.0000.000
161A217LEU00.0210.03537.020-0.004-0.0040.0000.0000.0000.000
162A218SER00.014-0.03141.3560.0000.0000.0000.0000.0000.000
163A219THR00.015-0.01943.4990.0020.0020.0000.0000.0000.000
164A220GLU-1-0.882-0.92344.6560.0370.0370.0000.0000.0000.000
165A221LEU0-0.0110.00540.220-0.001-0.0010.0000.0000.0000.000
166A222LEU0-0.085-0.01639.2580.0030.0030.0000.0000.0000.000
167A223ASP-1-0.807-0.92139.2660.0280.0280.0000.0000.0000.000
168A224GLU-1-0.797-0.89833.3790.0500.0500.0000.0000.0000.000
169A225ASN00.007-0.00634.7000.0030.0030.0000.0000.0000.000
170A226LEU00.0550.04135.1950.0010.0010.0000.0000.0000.000
171A227LEU0-0.036-0.01533.4740.0050.0050.0000.0000.0000.000
172A228ARG10.8750.91728.421-0.036-0.0360.0000.0000.0000.000
173A229GLU-1-0.918-0.95630.6100.0210.0210.0000.0000.0000.000
174A230SER0-0.069-0.03731.7910.0010.0010.0000.0000.0000.000
175A231PHE0-0.047-0.04128.2560.0090.0090.0000.0000.0000.000
176A232GLU-1-0.884-0.93626.3670.0360.0360.0000.0000.0000.000
177A233GLY0-0.033-0.01025.173-0.002-0.0020.0000.0000.0000.000
178A234PHE0-0.042-0.03623.8550.0050.0050.0000.0000.0000.000
179A235GLY0-0.009-0.00920.8320.0320.0320.0000.0000.0000.000
180A236SER0-0.009-0.03119.288-0.006-0.0060.0000.0000.0000.000
181A237ILE0-0.031-0.01422.0780.0260.0260.0000.0000.0000.000
182A238GLU-1-0.838-0.89121.6030.1570.1570.0000.0000.0000.000
183A239LYS10.8940.93124.720-0.097-0.0970.0000.0000.0000.000
184A240ILE00.0210.02428.2930.0120.0120.0000.0000.0000.000
185A241ASN0-0.045-0.02431.364-0.011-0.0110.0000.0000.0000.000
186A242ILE00.0750.04033.8410.0060.0060.0000.0000.0000.000
187A243PRO0-0.045-0.01636.956-0.004-0.0040.0000.0000.0000.000
188A244ALA00.0380.01439.658-0.002-0.0020.0000.0000.0000.000
189A245GLY00.0030.01742.7730.0020.0020.0000.0000.0000.000
190A246GLN00.0470.00440.1100.0030.0030.0000.0000.0000.000
191A247LYS10.8650.95944.555-0.040-0.0400.0000.0000.0000.000
192A248GLU-1-0.846-0.92748.7300.0400.0400.0000.0000.0000.000
193A249HIS0-0.0080.01047.6650.0010.0010.0000.0000.0000.000
194A250SER0-0.059-0.05046.0260.0040.0040.0000.0000.0000.000
195A251PHE00.0310.00147.298-0.003-0.0030.0000.0000.0000.000
196A252ASN0-0.036-0.02246.3410.0010.0010.0000.0000.0000.000
197A253ASN00.008-0.00143.7020.0050.0050.0000.0000.0000.000
198A254CYS0-0.0450.00142.2920.0030.0030.0000.0000.0000.000
199A255CYS0-0.041-0.02637.5000.0050.0050.0000.0000.0000.000
200A256ALA00.0500.02435.027-0.005-0.0050.0000.0000.0000.000
201A257PHE0-0.022-0.01931.3510.0050.0050.0000.0000.0000.000
202A258MET0-0.0060.01527.360-0.008-0.0080.0000.0000.0000.000
203A259VAL0-0.0060.00723.7550.0160.0160.0000.0000.0000.000
204A260PHE00.0340.01121.503-0.015-0.0150.0000.0000.0000.000
205A261GLU-1-0.812-0.89518.0920.1250.1250.0000.0000.0000.000
206A262ASN0-0.033-0.00715.6870.0510.0510.0000.0000.0000.000
207A263LYS10.9550.96315.617-0.595-0.5950.0000.0000.0000.000
208A264ASP-1-0.731-0.80914.9700.5100.5100.0000.0000.0000.000
209A265SER0-0.026-0.03118.087-0.043-0.0430.0000.0000.0000.000
210A266ALA00.0220.02320.636-0.023-0.0230.0000.0000.0000.000
211A267GLU-1-0.911-0.97720.6790.2770.2770.0000.0000.0000.000
212A268ARG10.7930.91017.294-0.262-0.2620.0000.0000.0000.000
213A269ALA00.0500.02923.798-0.019-0.0190.0000.0000.0000.000
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