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: 72VNK

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 OptAll
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 -2836441.287656
FMO2-HF: Nuclear repulsion 2741926.623819
FMO2-HF: Total energy -94514.663837
FMO2-MP2: Total energy -94789.534887


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.
-14.488-11.87711.559-4.511-9.654-0.041
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 : -0.002 / q_NPA : -0.014
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].
3A43VAL0-0.017-0.0053.8650.7432.088-0.015-0.584-0.7450.002
4A44LEU0-0.0090.0096.573-0.267-0.2670.0000.0000.0000.000
5A45VAL0-0.004-0.01110.293-0.023-0.0230.0000.0000.0000.000
6A46LYS10.9860.98013.056-0.301-0.3010.0000.0000.0000.000
7A47ASN0-0.004-0.00916.606-0.034-0.0340.0000.0000.0000.000
8A48LEU00.0480.03515.925-0.035-0.0350.0000.0000.0000.000
9A49PRO00.0430.03619.9100.0250.0250.0000.0000.0000.000
10A50LYS10.9630.96122.959-0.021-0.0210.0000.0000.0000.000
11A51SER00.0010.01524.571-0.008-0.0080.0000.0000.0000.000
12A52TYR0-0.008-0.02818.641-0.013-0.0130.0000.0000.0000.000
13A53ASN00.0640.02519.9150.0230.0230.0000.0000.0000.000
14A54GLN00.0720.03015.1050.0260.0260.0000.0000.0000.000
15A55ASN00.0380.02916.037-0.070-0.0700.0000.0000.0000.000
16A56LYS10.8780.93618.4430.1650.1650.0000.0000.0000.000
17A57VAL00.0240.02213.3790.0100.0100.0000.0000.0000.000
18A58TYR00.0570.02511.8290.0480.0480.0000.0000.0000.000
19A59LYS10.8770.92814.2780.3260.3260.0000.0000.0000.000
20A60TYR0-0.0120.00815.2490.0070.0070.0000.0000.0000.000
21A61PHE00.020-0.00210.6110.0390.0390.0000.0000.0000.000
22A62LYS10.9530.98911.0120.4390.4390.0000.0000.0000.000
23A63HIS0-0.032-0.02312.231-0.056-0.0560.0000.0000.0000.000
24A64CYS0-0.114-0.0219.1950.1890.1890.0000.0000.0000.000
25A65GLY00.0640.0278.226-0.033-0.0330.0000.0000.0000.000
26A66PRO00.003-0.0038.2090.0150.0150.0000.0000.0000.000
27A67ILE0-0.057-0.0236.541-0.998-0.9980.0000.0000.0000.000
28A68ILE00.0010.0124.2810.3840.493-0.001-0.007-0.1010.000
29A69HIS00.0370.0267.2030.5530.5530.0000.0000.0000.000
30A70VAL0-0.025-0.0298.580-0.217-0.2170.0000.0000.0000.000
31A71ASP-1-0.814-0.88911.192-0.102-0.1020.0000.0000.0000.000
32A72VAL0-0.065-0.05513.662-0.006-0.0060.0000.0000.0000.000
33A73ALA00.0200.02316.7540.0160.0160.0000.0000.0000.000
34A74ASP-1-0.796-0.86919.1390.0010.0010.0000.0000.0000.000
35A75SER00.004-0.00221.7870.0260.0260.0000.0000.0000.000
36A76LEU00.0740.02023.281-0.024-0.0240.0000.0000.0000.000
37A77LYS10.9590.98425.960-0.121-0.1210.0000.0000.0000.000
38A78LYS10.8830.94125.989-0.062-0.0620.0000.0000.0000.000
39A79ASN00.0340.01726.634-0.010-0.0100.0000.0000.0000.000
40A80PHE0-0.039-0.00420.182-0.008-0.0080.0000.0000.0000.000
41A81ARG10.7920.87719.5570.0680.0680.0000.0000.0000.000
42A82PHE00.0540.02015.7700.0100.0100.0000.0000.0000.000
43A83ALA0-0.043-0.03413.933-0.066-0.0660.0000.0000.0000.000
44A84ARG10.7730.8747.686-0.253-0.2530.0000.0000.0000.000
45A85ILE0-0.018-0.0087.258-0.093-0.0930.0000.0000.0000.000
46A86GLU-1-0.792-0.8793.937-0.759-0.4260.000-0.050-0.2830.000
47A87PHE00.006-0.0022.648-0.4530.7100.226-0.362-1.0260.000
48A88ALA00.0200.0081.851-15.307-16.5927.757-3.486-2.985-0.039
49A89ARG10.8730.9282.7381.8032.5300.243-0.246-0.7240.000
50A90TYR00.0640.0212.232-3.235-1.4212.760-1.586-2.988-0.003
51A91ASP-1-0.788-0.8902.8570.549-1.5390.1692.117-0.1980.000
52A92GLY00.0430.0285.5560.2700.2700.0000.0000.0000.000
53A93ALA00.001-0.0022.824-0.0410.3580.422-0.289-0.531-0.001
54A94LEU0-0.005-0.0044.7290.6250.671-0.001-0.009-0.0360.000
55A95ALA00.0590.0227.2510.1040.1040.0000.0000.0000.000
56A96ALA0-0.019-0.0117.5990.1350.1350.0000.0000.0000.000
57A97ILE00.0480.0176.8030.1260.1260.0000.0000.0000.000
58A98THR0-0.072-0.03910.0950.0470.0470.0000.0000.0000.000
59A99LYS10.8830.94112.6550.4290.4290.0000.0000.0000.000
60A100THR0-0.0020.00113.388-0.002-0.0020.0000.0000.0000.000
61A101HIS10.8430.89115.179-0.189-0.1890.0000.0000.0000.000
62A102LYS10.9701.00917.7090.0880.0880.0000.0000.0000.000
63A103VAL00.0460.02219.6850.0200.0200.0000.0000.0000.000
64A104VAL0-0.031-0.01618.641-0.037-0.0370.0000.0000.0000.000
65A105GLY0-0.011-0.01422.0400.0190.0190.0000.0000.0000.000
66A106GLN00.006-0.00225.6160.0050.0050.0000.0000.0000.000
67A107ASN0-0.047-0.01622.8360.0020.0020.0000.0000.0000.000
68A108GLU-1-0.806-0.87720.7790.0870.0870.0000.0000.0000.000
69A109ILE0-0.032-0.00215.3900.0190.0190.0000.0000.0000.000
70A110ILE00.003-0.00114.9750.0180.0180.0000.0000.0000.000
71A111VAL0-0.051-0.0329.802-0.021-0.0210.0000.0000.0000.000
72A112SER0-0.007-0.00210.0480.0510.0510.0000.0000.0000.000
73A113HIS00.0730.0264.7510.5830.631-0.001-0.009-0.0370.000
74A114LEU0-0.029-0.0166.457-0.455-0.4550.0000.0000.0000.000
75A115THR0-0.020-0.0296.8200.9850.9850.0000.0000.0000.000
76A116GLU-1-0.747-0.8548.6651.0591.0590.0000.0000.0000.000
77A117CYS0-0.084-0.02110.801-0.285-0.2850.0000.0000.0000.000
78A118THR0-0.003-0.02010.4560.0030.0030.0000.0000.0000.000
79A119LEU0-0.0110.00512.7170.0040.0040.0000.0000.0000.000
80A120TRP0-0.022-0.01315.574-0.039-0.0390.0000.0000.0000.000
81A121MET0-0.021-0.00517.868-0.008-0.0080.0000.0000.0000.000
82A122THR0-0.001-0.01921.503-0.018-0.0180.0000.0000.0000.000
83A123ASN00.0050.00024.403-0.007-0.0070.0000.0000.0000.000
84A124PHE00.0000.01422.881-0.001-0.0010.0000.0000.0000.000
85A125PRO00.0400.02828.461-0.005-0.0050.0000.0000.0000.000
86A126PRO00.006-0.00229.825-0.001-0.0010.0000.0000.0000.000
87A127SER00.0280.01930.037-0.004-0.0040.0000.0000.0000.000
88A128TYR0-0.060-0.02827.160-0.002-0.0020.0000.0000.0000.000
89A129THR00.011-0.00425.746-0.007-0.0070.0000.0000.0000.000
90A130GLN00.042-0.00918.3840.0260.0260.0000.0000.0000.000
91A131ARG10.8180.91923.191-0.021-0.0210.0000.0000.0000.000
92A132ASN00.1190.06226.0580.0050.0050.0000.0000.0000.000
93A133ILE00.0350.02221.0530.0140.0140.0000.0000.0000.000
94A134ARG10.8580.92318.487-0.078-0.0780.0000.0000.0000.000
95A135ASP-1-0.842-0.91723.4010.0790.0790.0000.0000.0000.000
96A136LEU00.0470.02725.5850.0070.0070.0000.0000.0000.000
97A137LEU0-0.004-0.01119.7400.0160.0160.0000.0000.0000.000
98A138GLN0-0.056-0.02124.0900.0010.0010.0000.0000.0000.000
99A139ASP-1-0.876-0.92626.2190.1160.1160.0000.0000.0000.000
100A140ILE0-0.072-0.02823.7700.0010.0010.0000.0000.0000.000
101A141ASN0-0.098-0.05926.5840.0080.0080.0000.0000.0000.000
102A142VAL00.0270.01820.2350.0160.0160.0000.0000.0000.000
103A143VAL0-0.033-0.02818.457-0.032-0.0320.0000.0000.0000.000
104A144ALA00.0540.02818.2810.0570.0570.0000.0000.0000.000
105A145LEU0-0.060-0.01711.775-0.079-0.0790.0000.0000.0000.000
106A146SER0-0.003-0.01111.999-0.052-0.0520.0000.0000.0000.000
107A147ILE00.0210.01215.0480.0950.0950.0000.0000.0000.000
108A148ARG10.8200.89310.661-0.617-0.6170.0000.0000.0000.000
109A149LEU00.0010.00216.4040.0470.0470.0000.0000.0000.000
110A150PRO00.0470.03618.624-0.030-0.0300.0000.0000.0000.000
111A158ARG10.8650.92227.111-0.118-0.1180.0000.0000.0000.000
112A159ARG10.8800.93923.802-0.046-0.0460.0000.0000.0000.000
113A160PHE00.0100.00617.8530.0140.0140.0000.0000.0000.000
114A161ALA0-0.030-0.01519.013-0.028-0.0280.0000.0000.0000.000
115A162TYR0-0.016-0.02613.338-0.001-0.0010.0000.0000.0000.000
116A163ILE0-0.023-0.02415.404-0.076-0.0760.0000.0000.0000.000
117A164ASP-1-0.760-0.8159.8801.1481.1480.0000.0000.0000.000
118A165VAL0-0.015-0.01813.298-0.157-0.1570.0000.0000.0000.000
119A166THR0-0.047-0.04413.7950.1030.1030.0000.0000.0000.000
120A167SER0-0.050-0.04814.9880.0180.0180.0000.0000.0000.000
121A168LYS10.8930.92112.463-1.306-1.3060.0000.0000.0000.000
122A169GLU-1-0.802-0.86915.9310.4270.4270.0000.0000.0000.000
123A170ASP-1-0.813-0.87317.7570.4040.4040.0000.0000.0000.000
124A171ALA0-0.006-0.01015.606-0.041-0.0410.0000.0000.0000.000
125A172ARG10.8070.87117.746-0.477-0.4770.0000.0000.0000.000
126A173TYR00.0140.01020.529-0.048-0.0480.0000.0000.0000.000
127A174CYS0-0.009-0.01820.312-0.042-0.0420.0000.0000.0000.000
128A175VAL0-0.029-0.01120.186-0.032-0.0320.0000.0000.0000.000
129A176GLU-1-0.914-0.95122.9320.3000.3000.0000.0000.0000.000
130A177LYS10.8940.96125.601-0.241-0.2410.0000.0000.0000.000
131A178LEU0-0.0100.00023.546-0.022-0.0220.0000.0000.0000.000
132A179ASN0-0.012-0.00825.299-0.006-0.0060.0000.0000.0000.000
133A180GLY00.0240.01027.156-0.003-0.0030.0000.0000.0000.000
134A181LEU0-0.027-0.00729.247-0.016-0.0160.0000.0000.0000.000
135A182LYS10.9450.97031.466-0.117-0.1170.0000.0000.0000.000
136A183ILE00.0050.00029.642-0.003-0.0030.0000.0000.0000.000
137A184GLU-1-0.851-0.94133.8720.0740.0740.0000.0000.0000.000
138A185GLY0-0.0020.01336.667-0.006-0.0060.0000.0000.0000.000
139A186TYR0-0.0030.00932.0360.0010.0010.0000.0000.0000.000
140A187THR0-0.036-0.03131.727-0.001-0.0010.0000.0000.0000.000
141A188LEU00.0080.01925.9520.0040.0040.0000.0000.0000.000
142A189VAL00.0240.02024.6910.0100.0100.0000.0000.0000.000
143A190THR0-0.026-0.03420.951-0.001-0.0010.0000.0000.0000.000
144A191LYS10.9090.97219.788-0.339-0.3390.0000.0000.0000.000
145A192VAL00.0210.01215.1260.0130.0130.0000.0000.0000.000
146A193SER0-0.094-0.06312.6060.0120.0120.0000.0000.0000.000
147A194ASN00.0290.01014.2790.1260.1260.0000.0000.0000.000
148A195PRO00.0170.01210.361-0.069-0.0690.0000.0000.0000.000
149A196LEU00.0080.00810.947-0.135-0.1350.0000.0000.0000.000
150A206THR00.0360.00319.832-0.005-0.0050.0000.0000.0000.000
151A207LEU00.0340.02221.2000.0140.0140.0000.0000.0000.000
152A208GLU-1-0.818-0.88822.5720.3190.3190.0000.0000.0000.000
153A209GLY00.0070.00021.3810.0380.0380.0000.0000.0000.000
154A210ARG10.7200.80918.245-0.256-0.2560.0000.0000.0000.000
155A211GLU-1-0.832-0.90022.1750.1570.1570.0000.0000.0000.000
156A212ILE0-0.013-0.00325.9820.0120.0120.0000.0000.0000.000
157A213MET00.0110.02928.535-0.011-0.0110.0000.0000.0000.000
158A214ILE00.0210.01331.5230.0050.0050.0000.0000.0000.000
159A215ARG10.9010.91034.553-0.144-0.1440.0000.0000.0000.000
160A216ASN00.0280.01338.231-0.003-0.0030.0000.0000.0000.000
161A217LEU00.0170.03637.040-0.004-0.0040.0000.0000.0000.000
162A218SER00.010-0.03741.4000.0000.0000.0000.0000.0000.000
163A219THR00.010-0.00843.6130.0020.0020.0000.0000.0000.000
164A220GLU-1-0.841-0.90545.0340.0490.0490.0000.0000.0000.000
165A221LEU0-0.0190.00040.231-0.001-0.0010.0000.0000.0000.000
166A222LEU0-0.061-0.01438.9150.0040.0040.0000.0000.0000.000
167A223ASP-1-0.783-0.90539.0100.0420.0420.0000.0000.0000.000
168A224GLU-1-0.798-0.88932.6040.0730.0730.0000.0000.0000.000
169A225ASN0-0.027-0.02034.3210.0020.0020.0000.0000.0000.000
170A226LEU00.0680.03934.7050.0030.0030.0000.0000.0000.000
171A227LEU0-0.031-0.01033.4320.0070.0070.0000.0000.0000.000
172A228ARG10.8740.91827.671-0.058-0.0580.0000.0000.0000.000
173A229GLU-1-0.907-0.94430.2260.0470.0470.0000.0000.0000.000
174A230SER0-0.064-0.03931.4820.0040.0040.0000.0000.0000.000
175A231PHE0-0.049-0.03428.1160.0120.0120.0000.0000.0000.000
176A232GLU-1-0.875-0.94125.9070.0720.0720.0000.0000.0000.000
177A233GLY0-0.032-0.01124.6770.0040.0040.0000.0000.0000.000
178A234PHE0-0.035-0.02823.7930.0070.0070.0000.0000.0000.000
179A235GLY0-0.034-0.02220.7740.0400.0400.0000.0000.0000.000
180A236SER0-0.005-0.03418.777-0.008-0.0080.0000.0000.0000.000
181A237ILE0-0.011-0.00121.7380.0260.0260.0000.0000.0000.000
182A238GLU-1-0.813-0.87121.2390.1880.1880.0000.0000.0000.000
183A239LYS10.8530.91024.051-0.115-0.1150.0000.0000.0000.000
184A240ILE00.0470.04727.7120.0150.0150.0000.0000.0000.000
185A241ASN0-0.018-0.02130.912-0.010-0.0100.0000.0000.0000.000
186A242ILE00.0730.04733.6120.0070.0070.0000.0000.0000.000
187A243PRO0-0.039-0.01336.837-0.004-0.0040.0000.0000.0000.000
188A244ALA00.0400.01639.482-0.003-0.0030.0000.0000.0000.000
189A245GLY00.0180.01942.6090.0020.0020.0000.0000.0000.000
190A246GLN00.037-0.00839.8960.0030.0030.0000.0000.0000.000
191A247LYS10.8380.94143.871-0.052-0.0520.0000.0000.0000.000
192A248GLU-1-0.884-0.93848.2310.0480.0480.0000.0000.0000.000
193A249HIS0-0.0170.00647.6580.0000.0000.0000.0000.0000.000
194A250SER0-0.054-0.04145.7470.0050.0050.0000.0000.0000.000
195A251PHE00.0310.00647.318-0.003-0.0030.0000.0000.0000.000
196A252ASN0-0.036-0.03246.6360.0020.0020.0000.0000.0000.000
197A253ASN00.0050.00843.2910.0060.0060.0000.0000.0000.000
198A254CYS0-0.0390.00742.3100.0020.0020.0000.0000.0000.000
199A255CYS0-0.051-0.03937.8090.0060.0060.0000.0000.0000.000
200A256ALA00.0420.01734.919-0.007-0.0070.0000.0000.0000.000
201A257PHE00.0020.00131.2870.0070.0070.0000.0000.0000.000
202A258MET0-0.028-0.00427.212-0.008-0.0080.0000.0000.0000.000
203A259VAL0-0.0120.00123.2910.0170.0170.0000.0000.0000.000
204A260PHE00.0290.00621.118-0.017-0.0170.0000.0000.0000.000
205A261GLU-1-0.812-0.88717.5710.1800.1800.0000.0000.0000.000
206A262ASN0-0.0230.00715.2940.0650.0650.0000.0000.0000.000
207A263LYS10.9380.95815.918-0.675-0.6750.0000.0000.0000.000
208A264ASP-1-0.723-0.80914.8320.6510.6510.0000.0000.0000.000
209A265SER0-0.015-0.02118.137-0.048-0.0480.0000.0000.0000.000
210A266ALA00.0110.02720.487-0.032-0.0320.0000.0000.0000.000
211A267GLU-1-0.905-0.97920.9020.3230.3230.0000.0000.0000.000
212A268ARG10.7900.89417.162-0.370-0.3700.0000.0000.0000.000
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