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: 94V72

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 OptH
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 -2827030.909017
FMO2-HF: Nuclear repulsion 2732518.089337
FMO2-HF: Total energy -94512.819681
FMO2-MP2: Total energy -94787.646332


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.
-13.289-9.82610.822-5.994-8.293-0.038
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 : -0.013 / q_NPA : -0.022
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].
3A43VAL0-0.017-0.0083.8050.8842.527-0.023-0.747-0.8740.003
4A44LEU0-0.014-0.0016.454-0.353-0.3530.0000.0000.0000.000
5A45VAL0-0.020-0.01610.191-0.020-0.0200.0000.0000.0000.000
6A46LYS10.9790.98112.914-0.296-0.2960.0000.0000.0000.000
7A47ASN00.000-0.02116.314-0.025-0.0250.0000.0000.0000.000
8A48LEU00.0390.03115.595-0.035-0.0350.0000.0000.0000.000
9A49PRO00.0710.04219.5540.0220.0220.0000.0000.0000.000
10A50LYS11.0210.99622.495-0.013-0.0130.0000.0000.0000.000
11A51SER0-0.025-0.00724.395-0.006-0.0060.0000.0000.0000.000
12A52TYR0-0.018-0.01418.569-0.014-0.0140.0000.0000.0000.000
13A53ASN00.0580.02619.9930.0160.0160.0000.0000.0000.000
14A54GLN00.1160.03415.480-0.005-0.0050.0000.0000.0000.000
15A55ASN00.0120.01515.843-0.107-0.1070.0000.0000.0000.000
16A56LYS10.9230.95617.7410.1420.1420.0000.0000.0000.000
17A57VAL00.0310.02013.4110.0050.0050.0000.0000.0000.000
18A58TYR00.0480.02212.1320.0100.0100.0000.0000.0000.000
19A59LYS10.9210.95214.2120.2870.2870.0000.0000.0000.000
20A60TYR0-0.0180.00014.994-0.003-0.0030.0000.0000.0000.000
21A61PHE00.0390.00011.0810.0420.0420.0000.0000.0000.000
22A62LYS10.9390.99211.6920.3990.3990.0000.0000.0000.000
23A63HIS0-0.026-0.02312.811-0.051-0.0510.0000.0000.0000.000
24A64CYS0-0.078-0.0139.2400.1810.1810.0000.0000.0000.000
25A65GLY00.0610.0358.467-0.069-0.0690.0000.0000.0000.000
26A66PRO0-0.001-0.0038.1430.0430.0430.0000.0000.0000.000
27A67ILE0-0.040-0.0216.735-0.906-0.9060.0000.0000.0000.000
28A68ILE0-0.008-0.0074.1780.3270.433-0.001-0.008-0.0970.000
29A69HIS00.0290.0267.2600.4780.4780.0000.0000.0000.000
30A70VAL0-0.071-0.0478.588-0.212-0.2120.0000.0000.0000.000
31A71ASP-1-0.859-0.91111.347-0.138-0.1380.0000.0000.0000.000
32A72VAL0-0.054-0.03113.6510.0220.0220.0000.0000.0000.000
33A73ALA00.0100.00916.6010.0120.0120.0000.0000.0000.000
34A74ASP-1-0.874-0.93019.1290.0020.0020.0000.0000.0000.000
35A75SER0-0.024-0.00621.9250.0240.0240.0000.0000.0000.000
36A76LEU00.0880.03822.838-0.020-0.0200.0000.0000.0000.000
37A77LYS10.9450.97625.517-0.122-0.1220.0000.0000.0000.000
38A78LYS10.9430.97226.014-0.051-0.0510.0000.0000.0000.000
39A79ASN0-0.037-0.01726.547-0.010-0.0100.0000.0000.0000.000
40A80PHE0-0.0280.00019.739-0.002-0.0020.0000.0000.0000.000
41A81ARG10.8230.89119.4510.0690.0690.0000.0000.0000.000
42A82PHE00.0430.02015.5160.0100.0100.0000.0000.0000.000
43A83ALA0-0.016-0.02513.345-0.061-0.0610.0000.0000.0000.000
44A84ARG10.8790.9447.494-0.162-0.1620.0000.0000.0000.000
45A85ILE0-0.033-0.0127.224-0.083-0.0830.0000.0000.0000.000
46A86GLU-1-0.828-0.8993.582-0.972-0.4610.007-0.124-0.3950.000
47A87PHE0-0.009-0.0043.2210.5731.5500.025-0.305-0.6970.000
48A88ALA00.0290.0251.792-13.706-15.9368.515-3.824-2.462-0.038
49A89ARG10.9450.9743.6761.9052.3980.007-0.121-0.3790.000
50A90TYR00.0540.0152.274-3.313-1.2941.786-1.211-2.594-0.003
51A91ASP-1-0.852-0.9433.316-0.676-1.1850.0540.667-0.2120.000
52A92GLY00.0300.0235.1500.2810.2810.0000.0000.0000.000
53A93ALA0-0.002-0.0112.7710.1360.5240.453-0.312-0.5280.000
54A94LEU0-0.017-0.0104.6650.6900.755-0.001-0.009-0.0550.000
55A95ALA00.0510.0336.7790.1650.1650.0000.0000.0000.000
56A96ALA0-0.011-0.0047.6980.1560.1560.0000.0000.0000.000
57A97ILE00.0180.0156.2070.1150.1150.0000.0000.0000.000
58A98THR0-0.051-0.0269.8170.0290.0290.0000.0000.0000.000
59A99LYS10.8750.93512.3270.3450.3450.0000.0000.0000.000
60A100THR00.0320.02613.168-0.014-0.0140.0000.0000.0000.000
61A101HIS10.8220.87614.848-0.206-0.2060.0000.0000.0000.000
62A102LYS10.9610.99717.2830.1180.1180.0000.0000.0000.000
63A103VAL00.0430.02419.3410.0130.0130.0000.0000.0000.000
64A104VAL0-0.031-0.01018.270-0.034-0.0340.0000.0000.0000.000
65A105GLY0-0.028-0.01921.6900.0180.0180.0000.0000.0000.000
66A106GLN0-0.003-0.00925.1410.0020.0020.0000.0000.0000.000
67A107ASN0-0.040-0.01022.3430.0100.0100.0000.0000.0000.000
68A108GLU-1-0.802-0.87120.4780.1030.1030.0000.0000.0000.000
69A109ILE0-0.046-0.01714.9810.0190.0190.0000.0000.0000.000
70A110ILE00.0170.01414.4180.0200.0200.0000.0000.0000.000
71A111VAL0-0.052-0.0389.383-0.019-0.0190.0000.0000.0000.000
72A112SER0-0.013-0.0059.7690.0420.0420.0000.0000.0000.000
73A113HIS00.0750.0325.1830.8160.8160.0000.0000.0000.000
74A114LEU0-0.015-0.0066.275-0.557-0.5570.0000.0000.0000.000
75A115THR0-0.037-0.0176.3090.9360.9360.0000.0000.0000.000
76A116GLU-1-0.879-0.9588.1960.7150.7150.0000.0000.0000.000
77A117CYS0-0.068-0.01910.339-0.257-0.2570.0000.0000.0000.000
78A118THR00.003-0.00810.449-0.027-0.0270.0000.0000.0000.000
79A119LEU00.0120.01912.769-0.004-0.0040.0000.0000.0000.000
80A120TRP00.0120.00815.980-0.032-0.0320.0000.0000.0000.000
81A121MET0-0.027-0.01317.976-0.001-0.0010.0000.0000.0000.000
82A122THR0-0.011-0.02721.549-0.019-0.0190.0000.0000.0000.000
83A123ASN0-0.0180.00324.458-0.002-0.0020.0000.0000.0000.000
84A124PHE0-0.0010.00523.379-0.001-0.0010.0000.0000.0000.000
85A125PRO00.0660.03628.866-0.005-0.0050.0000.0000.0000.000
86A126PRO00.019-0.00530.0960.0000.0000.0000.0000.0000.000
87A127SER0-0.0030.00230.492-0.003-0.0030.0000.0000.0000.000
88A128TYR00.0080.01527.092-0.007-0.0070.0000.0000.0000.000
89A129THR00.023-0.01326.516-0.004-0.0040.0000.0000.0000.000
90A130GLN00.048-0.00419.0570.0190.0190.0000.0000.0000.000
91A131ARG10.9060.96823.671-0.007-0.0070.0000.0000.0000.000
92A132ASN00.0980.07026.1470.0020.0020.0000.0000.0000.000
93A133ILE00.0500.02821.4110.0120.0120.0000.0000.0000.000
94A134ARG10.8500.91318.790-0.062-0.0620.0000.0000.0000.000
95A135ASP-1-0.886-0.95323.7860.0770.0770.0000.0000.0000.000
96A136LEU00.0420.03825.5310.0050.0050.0000.0000.0000.000
97A137LEU0-0.008-0.01519.7120.0120.0120.0000.0000.0000.000
98A138GLN0-0.057-0.02524.1340.0010.0010.0000.0000.0000.000
99A139ASP-1-0.890-0.92826.3310.1100.1100.0000.0000.0000.000
100A140ILE0-0.088-0.03723.9610.0000.0000.0000.0000.0000.000
101A141ASN0-0.077-0.05226.4210.0100.0100.0000.0000.0000.000
102A142VAL00.0200.01620.1960.0170.0170.0000.0000.0000.000
103A143VAL0-0.032-0.01918.376-0.027-0.0270.0000.0000.0000.000
104A144ALA00.0240.01818.2160.0470.0470.0000.0000.0000.000
105A145LEU0-0.069-0.04411.684-0.066-0.0660.0000.0000.0000.000
106A146SER0-0.050-0.03512.976-0.047-0.0470.0000.0000.0000.000
107A147ILE00.0560.02315.2580.0680.0680.0000.0000.0000.000
108A148ARG10.8720.96110.693-0.520-0.5200.0000.0000.0000.000
109A149LEU0-0.002-0.01316.9280.0360.0360.0000.0000.0000.000
110A150PRO00.0340.03218.825-0.026-0.0260.0000.0000.0000.000
111A158ARG10.9120.96626.769-0.093-0.0930.0000.0000.0000.000
112A159ARG10.9010.97023.846-0.048-0.0480.0000.0000.0000.000
113A160PHE00.0170.00717.9980.0150.0150.0000.0000.0000.000
114A161ALA0-0.027-0.01119.277-0.018-0.0180.0000.0000.0000.000
115A162TYR0-0.053-0.03913.8380.0110.0110.0000.0000.0000.000
116A163ILE0-0.012-0.01215.572-0.061-0.0610.0000.0000.0000.000
117A164ASP-1-0.799-0.8859.9951.0321.0320.0000.0000.0000.000
118A165VAL00.0320.00913.425-0.125-0.1250.0000.0000.0000.000
119A166THR0-0.051-0.04013.5070.1060.1060.0000.0000.0000.000
120A167SER00.0030.00014.9060.0380.0380.0000.0000.0000.000
121A168LYS11.0120.99312.636-1.187-1.1870.0000.0000.0000.000
122A169GLU-1-0.905-0.94015.7290.3710.3710.0000.0000.0000.000
123A170ASP-1-0.842-0.93218.2560.3380.3380.0000.0000.0000.000
124A171ALA0-0.028-0.01315.674-0.034-0.0340.0000.0000.0000.000
125A172ARG10.9470.96617.814-0.488-0.4880.0000.0000.0000.000
126A173TYR00.0580.03620.430-0.049-0.0490.0000.0000.0000.000
127A174CYS0-0.040-0.01420.202-0.047-0.0470.0000.0000.0000.000
128A175VAL0-0.006-0.01520.141-0.030-0.0300.0000.0000.0000.000
129A176GLU-1-0.978-0.99022.8410.2490.2490.0000.0000.0000.000
130A177LYS10.8880.95325.791-0.210-0.2100.0000.0000.0000.000
131A178LEU0-0.011-0.00123.597-0.021-0.0210.0000.0000.0000.000
132A179ASN0-0.0030.00425.551-0.015-0.0150.0000.0000.0000.000
133A180GLY00.0040.00027.330-0.006-0.0060.0000.0000.0000.000
134A181LEU0-0.0040.00429.822-0.014-0.0140.0000.0000.0000.000
135A182LYS10.9390.96331.518-0.099-0.0990.0000.0000.0000.000
136A183ILE00.0200.00429.614-0.004-0.0040.0000.0000.0000.000
137A184GLU-1-0.920-0.97333.7640.0580.0580.0000.0000.0000.000
138A185GLY0-0.020-0.00236.700-0.004-0.0040.0000.0000.0000.000
139A186TYR0-0.0140.00531.919-0.002-0.0020.0000.0000.0000.000
140A187THR0-0.037-0.01731.4260.0030.0030.0000.0000.0000.000
141A188LEU00.0020.00825.6590.0010.0010.0000.0000.0000.000
142A189VAL00.0320.01224.4590.0090.0090.0000.0000.0000.000
143A190THR0-0.018-0.02420.561-0.001-0.0010.0000.0000.0000.000
144A191LYS10.9170.97520.069-0.281-0.2810.0000.0000.0000.000
145A192VAL00.0130.00715.3180.0080.0080.0000.0000.0000.000
146A193SER0-0.097-0.07612.776-0.004-0.0040.0000.0000.0000.000
147A194ASN0-0.002-0.01714.6470.1030.1030.0000.0000.0000.000
148A195PRO00.0220.02410.209-0.038-0.0380.0000.0000.0000.000
149A196LEU00.009-0.00710.903-0.121-0.1210.0000.0000.0000.000
150A206THR00.0370.00519.954-0.007-0.0070.0000.0000.0000.000
151A207LEU00.021-0.00220.9040.0180.0180.0000.0000.0000.000
152A208GLU-1-0.866-0.91422.3850.2740.2740.0000.0000.0000.000
153A209GLY00.0290.00921.2810.0290.0290.0000.0000.0000.000
154A210ARG10.7930.86918.347-0.198-0.1980.0000.0000.0000.000
155A211GLU-1-0.885-0.94222.3240.1170.1170.0000.0000.0000.000
156A212ILE00.0100.01826.1350.0100.0100.0000.0000.0000.000
157A213MET00.001-0.00628.655-0.009-0.0090.0000.0000.0000.000
158A214ILE00.0000.00331.6400.0040.0040.0000.0000.0000.000
159A215ARG10.9620.95534.694-0.109-0.1090.0000.0000.0000.000
160A216ASN00.010-0.00938.227-0.002-0.0020.0000.0000.0000.000
161A217LEU00.0230.02837.021-0.003-0.0030.0000.0000.0000.000
162A218SER00.0490.01141.3500.0000.0000.0000.0000.0000.000
163A219THR0-0.001-0.02843.4940.0020.0020.0000.0000.0000.000
164A220GLU-1-0.914-0.95744.6520.0390.0390.0000.0000.0000.000
165A221LEU0-0.019-0.00240.211-0.001-0.0010.0000.0000.0000.000
166A222LEU0-0.087-0.01539.0670.0030.0030.0000.0000.0000.000
167A223ASP-1-0.839-0.92539.2800.0330.0330.0000.0000.0000.000
168A224GLU-1-0.832-0.93433.5460.0510.0510.0000.0000.0000.000
169A225ASN00.0390.00934.6970.0050.0050.0000.0000.0000.000
170A226LEU00.0290.02335.1930.0020.0020.0000.0000.0000.000
171A227LEU0-0.034-0.02333.4180.0060.0060.0000.0000.0000.000
172A228ARG10.8980.94828.234-0.041-0.0410.0000.0000.0000.000
173A229GLU-1-0.922-0.96130.6070.0340.0340.0000.0000.0000.000
174A230SER0-0.036-0.01831.7890.0040.0040.0000.0000.0000.000
175A231PHE0-0.059-0.05228.1510.0100.0100.0000.0000.0000.000
176A232GLU-1-0.891-0.94726.3680.0550.0550.0000.0000.0000.000
177A233GLY0-0.031-0.01025.1710.0010.0010.0000.0000.0000.000
178A234PHE0-0.045-0.03723.8400.0090.0090.0000.0000.0000.000
179A235GLY00.0080.00120.8140.0320.0320.0000.0000.0000.000
180A236SER00.0150.00619.868-0.010-0.0100.0000.0000.0000.000
181A237ILE0-0.0070.00322.0760.0220.0220.0000.0000.0000.000
182A238GLU-1-0.899-0.94921.4280.1250.1250.0000.0000.0000.000
183A239LYS10.9270.95824.461-0.093-0.0930.0000.0000.0000.000
184A240ILE00.0370.02328.0630.0110.0110.0000.0000.0000.000
185A241ASN0-0.081-0.04831.301-0.012-0.0120.0000.0000.0000.000
186A242ILE00.0730.04133.7550.0050.0050.0000.0000.0000.000
187A243PRO0-0.041-0.01136.981-0.004-0.0040.0000.0000.0000.000
188A244ALA00.0350.01239.612-0.002-0.0020.0000.0000.0000.000
189A245GLY0-0.0100.01142.6240.0010.0010.0000.0000.0000.000
190A246GLN00.0480.00440.2420.0030.0030.0000.0000.0000.000
191A247LYS10.8930.96744.319-0.041-0.0410.0000.0000.0000.000
192A248GLU-1-0.848-0.92948.7010.0390.0390.0000.0000.0000.000
193A249HIS0-0.0120.00847.5400.0010.0010.0000.0000.0000.000
194A250SER0-0.063-0.05445.9810.0040.0040.0000.0000.0000.000
195A251PHE00.0320.00047.282-0.002-0.0020.0000.0000.0000.000
196A252ASN0-0.040-0.01746.3470.0010.0010.0000.0000.0000.000
197A253ASN00.0170.00143.8670.0050.0050.0000.0000.0000.000
198A254CYS0-0.0360.00842.1940.0030.0030.0000.0000.0000.000
199A255CYS0-0.049-0.02137.4450.0040.0040.0000.0000.0000.000
200A256ALA00.0560.02234.965-0.005-0.0050.0000.0000.0000.000
201A257PHE0-0.039-0.02031.3330.0050.0050.0000.0000.0000.000
202A258MET0-0.0150.00827.369-0.007-0.0070.0000.0000.0000.000
203A259VAL00.0010.01223.7500.0150.0150.0000.0000.0000.000
204A260PHE00.0430.02321.429-0.012-0.0120.0000.0000.0000.000
205A261GLU-1-0.860-0.93217.9480.1250.1250.0000.0000.0000.000
206A262ASN0-0.051-0.03515.1950.0250.0250.0000.0000.0000.000
207A263LYS10.9600.98015.748-0.522-0.5220.0000.0000.0000.000
208A264ASP-1-0.741-0.80015.2500.5130.5130.0000.0000.0000.000
209A265SER0-0.008-0.00718.080-0.035-0.0350.0000.0000.0000.000
210A266ALA00.0140.02120.630-0.021-0.0210.0000.0000.0000.000
211A267GLU-1-0.931-0.98420.6270.2700.2700.0000.0000.0000.000
212A268ARG10.7920.90417.537-0.278-0.2780.0000.0000.0000.000
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