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: 22RRR

Calculation Name: 2BHV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BHV

Chain ID: A

ChEMBL ID:

UniProt ID: O24883

Base Structure: X-ray

Registration Date: 2023-03-13

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1901451.740501
FMO2-HF: Nuclear repulsion 1827054.167735
FMO2-HF: Total energy -74397.572766
FMO2-MP2: Total energy -74614.867281


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:166:ASN)


Summations of interaction energy for fragment #1(A:166:ASN)
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.
-0.820.0960000000000024.491-2.045-3.3630.005
Interaction energy analysis for fragmet #1(A:166:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.068 / q_NPA : 0.024
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].
3A168LEU00.023-0.0043.829-5.546-3.3600.028-1.037-1.1770.006
4A169LEU0-0.0300.0011.9770.061-1.4634.465-0.983-1.958-0.001
5A170ARG10.8240.8964.9670.5360.642-0.001-0.008-0.0970.000
6A171THR00.0060.0047.3910.9750.9750.0000.0000.0000.000
7A172ILE0-0.0190.0069.616-0.286-0.2860.0000.0000.0000.000
8A173THR0-0.017-0.01412.7320.2300.2300.0000.0000.0000.000
9A174ALA00.0210.00213.917-0.143-0.1430.0000.0000.0000.000
10A175ASP-1-0.887-0.94916.8560.5110.5110.0000.0000.0000.000
11A176LYS10.9120.96615.503-0.280-0.2800.0000.0000.0000.000
12A177MET0-0.045-0.01818.762-0.009-0.0090.0000.0000.0000.000
13A178ILE0-0.012-0.01618.903-0.040-0.0400.0000.0000.0000.000
14A179PRO0-0.0060.02522.1840.0060.0060.0000.0000.0000.000
15A180ALA00.022-0.00325.500-0.014-0.0140.0000.0000.0000.000
16A181PHE00.0330.02927.7890.0020.0020.0000.0000.0000.000
17A182LEU0-0.020-0.01131.3430.0020.0020.0000.0000.0000.000
18A183ILE0-0.015-0.01031.711-0.010-0.0100.0000.0000.0000.000
19A184THR0-0.062-0.01635.174-0.006-0.0060.0000.0000.0000.000
20A185PRO00.0270.01936.5970.0070.0070.0000.0000.0000.000
21A186ILE00.0250.00734.4290.0050.0050.0000.0000.0000.000
22A187SER0-0.037-0.02538.968-0.001-0.0010.0000.0000.0000.000
23A188SER00.0680.03841.4950.0030.0030.0000.0000.0000.000
24A189GLN0-0.017-0.00743.0260.0040.0040.0000.0000.0000.000
25A190ILE0-0.029-0.01641.4690.0050.0050.0000.0000.0000.000
26A191ALA00.0360.04038.7330.0050.0050.0000.0000.0000.000
27A192GLY00.007-0.01038.019-0.007-0.0070.0000.0000.0000.000
28A193LYS10.9300.97333.118-0.109-0.1090.0000.0000.0000.000
29A194VAL00.0260.01831.573-0.011-0.0110.0000.0000.0000.000
30A195ILE0-0.003-0.01030.6180.0100.0100.0000.0000.0000.000
31A196ALA00.0380.03028.477-0.009-0.0090.0000.0000.0000.000
32A197GLN0-0.013-0.01227.9870.0010.0010.0000.0000.0000.000
33A198VAL00.0070.01121.9440.0020.0020.0000.0000.0000.000
34A199GLU-1-0.847-0.93525.3850.0430.0430.0000.0000.0000.000
35A200SER0-0.078-0.05522.805-0.019-0.0190.0000.0000.0000.000
36A201ASP-1-0.811-0.90018.418-0.104-0.1040.0000.0000.0000.000
37A202ILE0-0.050-0.01515.8300.0200.0200.0000.0000.0000.000
38A203PHE0-0.011-0.01713.086-0.018-0.0180.0000.0000.0000.000
39A204ALA0-0.021-0.0108.7020.1500.1500.0000.0000.0000.000
40A205HIS0-0.013-0.0038.517-0.153-0.1530.0000.0000.0000.000
41A206MET00.0200.0184.368-0.0140.134-0.001-0.017-0.1310.000
42A207GLY0-0.008-0.0027.302-0.377-0.3770.0000.0000.0000.000
43A208LYS10.9690.9628.4450.9050.9050.0000.0000.0000.000
44A209ALA00.0110.0209.8100.0760.0760.0000.0000.0000.000
45A210VAL00.0210.01211.4940.1070.1070.0000.0000.0000.000
46A211LEU0-0.067-0.01410.365-0.028-0.0280.0000.0000.0000.000
47A212ILE00.0050.00414.4070.0410.0410.0000.0000.0000.000
48A213PRO00.0350.02618.075-0.012-0.0120.0000.0000.0000.000
49A214LYS10.9831.01820.2740.0850.0850.0000.0000.0000.000
50A215GLY0-0.038-0.01423.404-0.016-0.0160.0000.0000.0000.000
51A216SER0-0.036-0.06222.3820.0000.0000.0000.0000.0000.000
52A217LYS10.9240.97424.744-0.038-0.0380.0000.0000.0000.000
53A218VAL00.0050.00824.3270.0110.0110.0000.0000.0000.000
54A219ILE0-0.020-0.01626.406-0.014-0.0140.0000.0000.0000.000
55A220GLY00.0490.01527.6420.0290.0290.0000.0000.0000.000
56A221TYR0-0.064-0.03129.692-0.025-0.0250.0000.0000.0000.000
57A222TYR00.0310.01232.0250.0180.0180.0000.0000.0000.000
58A223SER00.006-0.00734.580-0.009-0.0090.0000.0000.0000.000
59A224ASN00.0500.03336.8840.0030.0030.0000.0000.0000.000
60A225ASN0-0.044-0.01537.582-0.015-0.0150.0000.0000.0000.000
61A226ASN00.0490.00140.0800.0050.0050.0000.0000.0000.000
62A227LYS10.9510.98341.604-0.162-0.1620.0000.0000.0000.000
63A228MET0-0.052-0.02444.1700.0010.0010.0000.0000.0000.000
64A229GLY00.0570.05546.956-0.001-0.0010.0000.0000.0000.000
65A230GLU-1-1.010-0.99740.6570.1670.1670.0000.0000.0000.000
66A231TYR0-0.001-0.00538.020-0.004-0.0040.0000.0000.0000.000
67A232ARG10.9250.95634.942-0.225-0.2250.0000.0000.0000.000
68A233LEU0-0.060-0.01634.705-0.006-0.0060.0000.0000.0000.000
69A234ASP-1-0.859-0.91832.0280.2580.2580.0000.0000.0000.000
70A235ILE0-0.002-0.02129.586-0.016-0.0160.0000.0000.0000.000
71A236VAL00.0020.01026.5250.0260.0260.0000.0000.0000.000
72A237TRP00.008-0.02524.727-0.031-0.0310.0000.0000.0000.000
73A238SER0-0.027-0.00224.4900.0290.0290.0000.0000.0000.000
74A239ARG10.9890.98823.085-0.150-0.1500.0000.0000.0000.000
75A240ILE00.0270.02319.745-0.022-0.0220.0000.0000.0000.000
76A241ILE0-0.0260.00022.256-0.002-0.0020.0000.0000.0000.000
77A242THR00.0240.00819.249-0.008-0.0080.0000.0000.0000.000
78A243PRO00.0210.00522.7310.0020.0020.0000.0000.0000.000
79A244HIS00.0140.00222.2070.0120.0120.0000.0000.0000.000
80A245GLY0-0.0020.01624.135-0.003-0.0030.0000.0000.0000.000
81A246ILE0-0.061-0.02317.2190.0060.0060.0000.0000.0000.000
82A247ASN0-0.019-0.03121.4110.0310.0310.0000.0000.0000.000
83A248ILE00.0220.01116.9730.0110.0110.0000.0000.0000.000
84A249MET0-0.009-0.01119.434-0.009-0.0090.0000.0000.0000.000
85A250LEU0-0.027-0.01018.8710.0650.0650.0000.0000.0000.000
86A251THR0-0.033-0.04120.8820.0450.0450.0000.0000.0000.000
87A252ASN00.0060.00223.581-0.027-0.0270.0000.0000.0000.000
88A253ALA00.0520.03025.719-0.010-0.0100.0000.0000.0000.000
89A261TYR00.0220.00736.3270.0000.0000.0000.0000.0000.000
90A262ASN00.0600.01036.6850.0190.0190.0000.0000.0000.000
91A263GLY00.0320.02437.2150.0090.0090.0000.0000.0000.000
92A264LEU0-0.020-0.00932.4400.0110.0110.0000.0000.0000.000
93A265VAL00.0290.00932.2600.0180.0180.0000.0000.0000.000
94A266GLY00.0260.02032.1140.0190.0190.0000.0000.0000.000
95A267GLU-1-0.844-0.93331.7110.2850.2850.0000.0000.0000.000
96A268LEU0-0.107-0.04528.3580.0280.0280.0000.0000.0000.000
97A269ILE0-0.0070.00127.6470.0390.0390.0000.0000.0000.000
98A270GLU-1-0.898-0.93828.3510.3160.3160.0000.0000.0000.000
99A271ARG10.8910.93425.318-0.325-0.3250.0000.0000.0000.000
100A272ASN0-0.082-0.04123.8470.0670.0670.0000.0000.0000.000
101A273PHE0-0.008-0.00923.7210.0590.0590.0000.0000.0000.000
102A274GLN0-0.011-0.00225.6460.0240.0240.0000.0000.0000.000
103A275ARG10.8860.96120.192-0.578-0.5780.0000.0000.0000.000
104A276TYR0-0.004-0.02417.2280.0950.0950.0000.0000.0000.000
105A277GLY00.0630.04921.0050.0320.0320.0000.0000.0000.000
106A278VAL0-0.050-0.03721.516-0.017-0.0170.0000.0000.0000.000
107A279PRO00.0200.02624.2870.0020.0020.0000.0000.0000.000
108A280LEU00.0380.00325.572-0.011-0.0110.0000.0000.0000.000
109A281LEU00.0030.00719.3870.0280.0280.0000.0000.0000.000
110A282LEU0-0.040-0.02020.2510.0480.0480.0000.0000.0000.000
111A283SER00.0210.01623.134-0.039-0.0390.0000.0000.0000.000
112A284THR0-0.008-0.00825.865-0.007-0.0070.0000.0000.0000.000
113A285LEU00.0370.01426.037-0.009-0.0090.0000.0000.0000.000
114A286THR00.0110.00129.670-0.008-0.0080.0000.0000.0000.000
115A287ASN0-0.018-0.00429.8220.0030.0030.0000.0000.0000.000
116A288GLY00.0510.03231.932-0.013-0.0130.0000.0000.0000.000
117A289LEU0-0.010-0.01034.132-0.003-0.0030.0000.0000.0000.000
118A290LEU00.0300.00537.171-0.006-0.0060.0000.0000.0000.000
119A291ILE0-0.017-0.00539.1340.0020.0020.0000.0000.0000.000
120A292GLY0-0.038-0.00542.359-0.006-0.0060.0000.0000.0000.000
121A293ILE00.004-0.00845.1380.0050.0050.0000.0000.0000.000
122A294THR00.0070.01547.826-0.002-0.0020.0000.0000.0000.000
123A295SER00.021-0.00650.6900.0050.0050.0000.0000.0000.000
124A296ALA00.0220.01953.086-0.002-0.0020.0000.0000.0000.000
125A310PHE0-0.018-0.02668.9430.0000.0000.0000.0000.0000.000
126A311GLY00.0300.03370.0140.0010.0010.0000.0000.0000.000
127A312ASP-1-0.830-0.91865.8110.0590.0590.0000.0000.0000.000
128A313TYR0-0.063-0.05762.8310.0010.0010.0000.0000.0000.000
129A314LEU00.0200.01467.6440.0010.0010.0000.0000.0000.000
130A315LEU00.0300.01270.0110.0000.0000.0000.0000.0000.000
131A316MET00.0310.02463.3830.0000.0000.0000.0000.0000.000
132A317GLN00.023-0.00869.0330.0010.0010.0000.0000.0000.000
133A318LEU00.0280.00771.1420.0000.0000.0000.0000.0000.000
134A319MET0-0.0550.00370.3200.0000.0000.0000.0000.0000.000
135A320ARG10.8580.90965.311-0.069-0.0690.0000.0000.0000.000
136A321GLN0-0.013-0.02166.0260.0020.0020.0000.0000.0000.000
137A322SER00.0210.02870.380-0.001-0.0010.0000.0000.0000.000
138A323GLY00.0380.03174.142-0.001-0.0010.0000.0000.0000.000
139A324MET0-0.030-0.01766.3150.0020.0020.0000.0000.0000.000
140A325GLY00.0100.01870.075-0.001-0.0010.0000.0000.0000.000
141A326ILE00.0850.00969.1140.0020.0020.0000.0000.0000.000
142A327ASN00.0380.01065.8090.0010.0010.0000.0000.0000.000
143A328GLN0-0.022-0.01163.9790.0040.0040.0000.0000.0000.000
144A329VAL00.0190.02364.7270.0020.0020.0000.0000.0000.000
145A330VAL00.0280.02263.9250.0020.0020.0000.0000.0000.000
146A331ASN00.001-0.00960.8350.0030.0030.0000.0000.0000.000
147A332GLN0-0.0330.00258.9050.0040.0040.0000.0000.0000.000
148A333ILE00.0270.01360.0740.0030.0030.0000.0000.0000.000
149A334LEU0-0.009-0.01258.7960.0020.0020.0000.0000.0000.000
150A335ARG10.9540.96455.285-0.086-0.0860.0000.0000.0000.000
151A336ASP-1-0.891-0.96355.2510.0910.0910.0000.0000.0000.000
152A337LYS10.9100.96656.090-0.070-0.0700.0000.0000.0000.000
153A338SER0-0.088-0.02451.4990.0020.0020.0000.0000.0000.000
154A339LYS10.9440.98351.081-0.097-0.0970.0000.0000.0000.000
155A340ILE00.001-0.00850.7500.0050.0050.0000.0000.0000.000
156A341ALA00.0250.01646.9560.0000.0000.0000.0000.0000.000
157A342PRO0-0.0140.00547.338-0.003-0.0030.0000.0000.0000.000
158A343ILE0-0.009-0.00846.9740.0060.0060.0000.0000.0000.000
159A344VAL0-0.026-0.01942.173-0.003-0.0030.0000.0000.0000.000
160A345VAL00.000-0.01642.6410.0040.0040.0000.0000.0000.000
161A346ILE0-0.008-0.00136.613-0.002-0.0020.0000.0000.0000.000
162A347ARG10.9520.96739.329-0.073-0.0730.0000.0000.0000.000
163A348GLU-1-0.853-0.91037.5170.0790.0790.0000.0000.0000.000
164A349GLY0-0.026-0.02436.426-0.006-0.0060.0000.0000.0000.000
165A350SER0-0.078-0.04735.756-0.001-0.0010.0000.0000.0000.000
166A351ARG10.8690.92631.224-0.057-0.0570.0000.0000.0000.000
167A352VAL0-0.035-0.02028.4170.0060.0060.0000.0000.0000.000
168A353PHE00.0170.01125.280-0.010-0.0100.0000.0000.0000.000
169A354ILE0-0.012-0.00822.8800.0150.0150.0000.0000.0000.000
170A355SER00.0470.02121.807-0.001-0.0010.0000.0000.0000.000
171A356PRO0-0.019-0.00217.605-0.001-0.0010.0000.0000.0000.000
172A357ASN00.0210.01619.769-0.004-0.0040.0000.0000.0000.000
173A358THR0-0.013-0.01314.8610.0040.0040.0000.0000.0000.000
174A359ASP-1-0.826-0.90111.2441.6321.6320.0000.0000.0000.000
175A360ILE0-0.035-0.01813.3090.0390.0390.0000.0000.0000.000
176A361PHE0-0.032-0.0266.2690.1280.1280.0000.0000.0000.000
177A362PHE00.0380.01310.328-0.174-0.1740.0000.0000.0000.000
178A363PRO00.0820.0569.655-0.277-0.2770.0000.0000.0000.000
179A364ILE0-0.019-0.0267.949-0.131-0.1310.0000.0000.0000.000
180A365PRO0-0.0150.00111.5280.0790.0790.0000.0000.0000.000
181A366ARG10.9610.97615.3440.0050.0050.0000.0000.0000.000
182A367GLU-1-0.913-0.95317.5530.0540.0540.0000.0000.0000.000
183A368ASN0-0.046-0.02820.2950.0060.0060.0000.0000.0000.000
184A369GLU-1-0.877-0.92319.6030.1980.1980.0000.0000.0000.000
185A370VAL0-0.036-0.02714.220-0.013-0.0130.0000.0000.0000.000
186A371ILE00.0100.00815.9270.0010.0010.0000.0000.0000.000
187A372ALA0-0.024-0.00614.3510.0910.0910.0000.0000.0000.000
188A373GLU-1-0.916-0.95810.8131.8691.8690.0000.0000.0000.000
189A374PHE0-0.009-0.00512.8970.1270.1270.0000.0000.0000.000
190A375LEU0-0.004-0.0078.8410.0810.0810.0000.0000.0000.000
191A376LYS10.8850.96412.373-0.961-0.9610.0000.0000.0000.000