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: Q19VY

Calculation Name: 1HYQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HYQ

Chain ID: A

ChEMBL ID:

UniProt ID: O29562

Base Structure: X-ray

Registration Date: 2023-06-21

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2615155.102404
FMO2-HF: Nuclear repulsion 2531642.658638
FMO2-HF: Total energy -83512.443766
FMO2-MP2: Total energy -83759.705812


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:2:VAL)


Summations of interaction energy for fragment #1(A:2:VAL)
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.
-19.098-10.14.648-5.55-8.097-0.059
Interaction energy analysis for fragmet #1(A:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : 0.003
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].
3A4THR00.0240.0193.4740.1731.8660.016-0.563-1.1460.004
4A5ILE0-0.004-0.0036.267-0.594-0.5940.0000.0000.0000.000
5A6THR0-0.006-0.0159.7190.0350.0350.0000.0000.0000.000
6A7VAL0-0.030-0.00512.887-0.068-0.0680.0000.0000.0000.000
7A8ALA00.020-0.01515.743-0.003-0.0030.0000.0000.0000.000
8A9SER0-0.030-0.02119.025-0.020-0.0200.0000.0000.0000.000
9A10GLY00.0270.02122.7070.0050.0050.0000.0000.0000.000
10A11LYS10.9580.98226.037-0.071-0.0710.0000.0000.0000.000
11A12GLY00.0890.02826.5570.0070.0070.0000.0000.0000.000
12A13GLY0-0.0240.00327.3730.0000.0000.0000.0000.0000.000
13A14THR00.0310.01624.429-0.008-0.0080.0000.0000.0000.000
14A15GLY00.016-0.00325.071-0.008-0.0080.0000.0000.0000.000
15A16LYS10.8910.96318.956-0.213-0.2130.0000.0000.0000.000
16A17THR00.0630.04419.5200.0010.0010.0000.0000.0000.000
17A18THR0-0.047-0.01819.700-0.005-0.0050.0000.0000.0000.000
18A19ILE0-0.031-0.01817.604-0.014-0.0140.0000.0000.0000.000
19A20THR00.0240.00214.179-0.011-0.0110.0000.0000.0000.000
20A21ALA00.0500.02715.225-0.008-0.0080.0000.0000.0000.000
21A22ASN0-0.041-0.03716.702-0.038-0.0380.0000.0000.0000.000
22A23LEU00.0220.03512.891-0.028-0.0280.0000.0000.0000.000
23A24GLY00.0840.03412.261-0.032-0.0320.0000.0000.0000.000
24A25VAL0-0.003-0.02013.245-0.059-0.0590.0000.0000.0000.000
25A26ALA0-0.071-0.04315.824-0.029-0.0290.0000.0000.0000.000
26A27LEU00.017-0.0059.546-0.016-0.0160.0000.0000.0000.000
27A28ALA00.0390.03111.905-0.067-0.0670.0000.0000.0000.000
28A29GLN0-0.074-0.03213.016-0.033-0.0330.0000.0000.0000.000
29A30LEU0-0.120-0.05012.7580.0080.0080.0000.0000.0000.000
30A31GLY0-0.038-0.02212.844-0.014-0.0140.0000.0000.0000.000
31A32HIS0-0.037-0.0077.786-0.192-0.1920.0000.0000.0000.000
32A33ASP-1-0.779-0.8776.620-0.800-0.8000.0000.0000.0000.000
33A34VAL0-0.010-0.0256.548-0.231-0.2310.0000.0000.0000.000
34A35THR00.046-0.0047.702-0.042-0.0420.0000.0000.0000.000
35A36ILE0-0.052-0.0149.0250.2290.2290.0000.0000.0000.000
36A37VAL00.0260.01210.564-0.059-0.0590.0000.0000.0000.000
37A38ASP-1-0.862-0.95313.2070.1860.1860.0000.0000.0000.000
38A39ALA0-0.020-0.01616.041-0.016-0.0160.0000.0000.0000.000
39A40ASP-1-0.911-0.96117.8570.1410.1410.0000.0000.0000.000
40A41ILE0-0.0280.00521.030-0.016-0.0160.0000.0000.0000.000
41A42THR0-0.020-0.00823.783-0.015-0.0150.0000.0000.0000.000
42A43MET00.000-0.00625.791-0.003-0.0030.0000.0000.0000.000
43A44ALA0-0.074-0.03726.9640.0010.0010.0000.0000.0000.000
44A45ASN00.0410.01221.411-0.007-0.0070.0000.0000.0000.000
45A46LEU00.032-0.00816.076-0.017-0.0170.0000.0000.0000.000
46A47GLU-1-0.892-0.94020.4680.0520.0520.0000.0000.0000.000
47A48LEU00.0040.01622.620-0.012-0.0120.0000.0000.0000.000
48A49ILE0-0.047-0.03221.664-0.011-0.0110.0000.0000.0000.000
49A50LEU0-0.082-0.04617.016-0.011-0.0110.0000.0000.0000.000
50A51GLY0-0.010-0.00921.610-0.013-0.0130.0000.0000.0000.000
51A52MET0-0.093-0.03618.337-0.014-0.0140.0000.0000.0000.000
52A53GLU-1-0.956-0.97223.7620.0010.0010.0000.0000.0000.000
53A54GLY00.007-0.00124.5350.0030.0030.0000.0000.0000.000
54A55LEU0-0.0060.00119.661-0.007-0.0070.0000.0000.0000.000
55A56PRO0-0.067-0.03523.4730.0090.0090.0000.0000.0000.000
56A57VAL00.0300.02920.2940.0070.0070.0000.0000.0000.000
57A58THR00.0150.00219.4950.0100.0100.0000.0000.0000.000
58A59LEU00.0560.00914.322-0.009-0.0090.0000.0000.0000.000
59A60GLN0-0.041-0.01318.322-0.008-0.0080.0000.0000.0000.000
60A61ASN00.0070.02321.707-0.006-0.0060.0000.0000.0000.000
61A62VAL00.0080.01916.388-0.005-0.0050.0000.0000.0000.000
62A63LEU0-0.089-0.05017.863-0.003-0.0030.0000.0000.0000.000
63A64ALA0-0.065-0.01920.475-0.005-0.0050.0000.0000.0000.000
64A65GLY0-0.044-0.01522.367-0.009-0.0090.0000.0000.0000.000
65A66GLU-1-0.946-0.98523.4460.0480.0480.0000.0000.0000.000
66A67ALA0-0.017-0.00721.396-0.008-0.0080.0000.0000.0000.000
67A68ARG10.8810.94118.0240.0640.0640.0000.0000.0000.000
68A69ILE00.0670.03011.2550.0010.0010.0000.0000.0000.000
69A70ASP-1-0.893-0.95614.668-0.097-0.0970.0000.0000.0000.000
70A71GLU-1-0.934-0.97315.635-0.016-0.0160.0000.0000.0000.000
71A72ALA0-0.033-0.00416.1690.0060.0060.0000.0000.0000.000
72A73ILE0-0.009-0.00711.0600.0340.0340.0000.0000.0000.000
73A74TYR0-0.026-0.01414.959-0.042-0.0420.0000.0000.0000.000
74A75VAL00.001-0.00215.558-0.003-0.0030.0000.0000.0000.000
75A76GLY00.0500.01616.4630.0210.0210.0000.0000.0000.000
76A77PRO0-0.041-0.03718.269-0.025-0.0250.0000.0000.0000.000
77A78GLY0-0.036-0.03517.607-0.001-0.0010.0000.0000.0000.000
78A79GLY00.0090.02315.662-0.024-0.0240.0000.0000.0000.000
79A80VAL0-0.0400.01612.394-0.038-0.0380.0000.0000.0000.000
80A81LYS10.8830.9608.8280.6020.6020.0000.0000.0000.000
81A82VAL0-0.028-0.02512.7020.0640.0640.0000.0000.0000.000
82A83VAL00.0210.01311.966-0.025-0.0250.0000.0000.0000.000
83A84PRO00.0040.02214.8260.0510.0510.0000.0000.0000.000
84A85ALA00.0980.03417.4130.0000.0000.0000.0000.0000.000
85A86GLY00.0000.01118.430-0.012-0.0120.0000.0000.0000.000
86A87VAL0-0.048-0.02921.566-0.015-0.0150.0000.0000.0000.000
87A88SER00.0250.01421.2260.0210.0210.0000.0000.0000.000
88A89LEU00.1270.03715.953-0.007-0.0070.0000.0000.0000.000
89A90GLU-1-0.972-0.98719.8370.1450.1450.0000.0000.0000.000
90A91GLY0-0.013-0.01422.773-0.009-0.0090.0000.0000.0000.000
91A92LEU00.0420.01617.973-0.010-0.0100.0000.0000.0000.000
92A93ARG10.9830.98419.178-0.234-0.2340.0000.0000.0000.000
93A94LYS10.8540.92920.924-0.131-0.1310.0000.0000.0000.000
94A95ALA0-0.068-0.03123.262-0.012-0.0120.0000.0000.0000.000
95A96ASN00.0270.00721.651-0.006-0.0060.0000.0000.0000.000
96A97PRO0-0.021-0.00519.5470.0170.0170.0000.0000.0000.000
97A98GLU-1-0.884-0.92717.7280.1580.1580.0000.0000.0000.000
98A99LYS10.9760.99616.759-0.084-0.0840.0000.0000.0000.000
99A100LEU0-0.029-0.02015.3340.0130.0130.0000.0000.0000.000
100A101GLU-1-0.922-0.95912.3090.4320.4320.0000.0000.0000.000
101A102ASP-1-0.869-0.93311.7990.3050.3050.0000.0000.0000.000
102A103VAL0-0.042-0.02611.594-0.006-0.0060.0000.0000.0000.000
103A104LEU0-0.003-0.0189.4840.0100.0100.0000.0000.0000.000
104A105THR0-0.0140.0057.6950.3680.3680.0000.0000.0000.000
105A106GLN0-0.002-0.0117.045-0.070-0.0700.0000.0000.0000.000
106A107ILE0-0.019-0.0117.218-0.214-0.2140.0000.0000.0000.000
107A108MET0-0.044-0.0193.485-0.572-0.1410.011-0.105-0.3360.000
108A109GLU-1-0.955-0.9702.867-4.692-3.2210.167-0.736-0.903-0.008
109A110SER0-0.124-0.0555.224-0.616-0.563-0.001-0.001-0.0510.000
110A111THR0-0.105-0.0314.4161.0281.133-0.001-0.012-0.0920.000
111A112ASP-1-0.835-0.9082.477-9.114-6.0021.046-1.612-2.546-0.014
112A113ILE0-0.039-0.0352.317-4.163-2.4153.412-2.411-2.750-0.041
113A114LEU00.0430.0284.614-0.281-0.083-0.001-0.013-0.1840.000
114A115LEU0-0.044-0.0296.307-0.080-0.0800.0000.0000.0000.000
115A116LEU00.0490.0149.862-0.075-0.0750.0000.0000.0000.000
116A117ASP-1-0.810-0.90112.3950.1480.1480.0000.0000.0000.000
117A118ALA0-0.007-0.00815.950-0.009-0.0090.0000.0000.0000.000
118A119PRO0-0.0010.00017.780-0.025-0.0250.0000.0000.0000.000
119A120ALA0-0.016-0.01021.4840.0030.0030.0000.0000.0000.000
120A121GLY00.0460.03023.7350.0010.0010.0000.0000.0000.000
121A122LEU0-0.028-0.03023.0800.0140.0140.0000.0000.0000.000
122A123GLU-1-0.918-0.94023.8690.1530.1530.0000.0000.0000.000
123A124ARG10.9730.97523.526-0.141-0.1410.0000.0000.0000.000
124A125SER00.0760.01420.9880.0210.0210.0000.0000.0000.000
125A126ALA00.0540.04119.3310.0330.0330.0000.0000.0000.000
126A127VAL0-0.010-0.01218.6830.0320.0320.0000.0000.0000.000
127A128ILE0-0.055-0.01916.8150.0170.0170.0000.0000.0000.000
128A129ALA00.0470.02214.9610.0480.0480.0000.0000.0000.000
129A130ILE0-0.0320.00013.8920.0800.0800.0000.0000.0000.000
130A131ALA0-0.023-0.00814.1440.0330.0330.0000.0000.0000.000
131A132ALA0-0.0220.00511.7720.0130.0130.0000.0000.0000.000
132A133ALA0-0.0190.0119.3620.2150.2150.0000.0000.0000.000
133A134GLN00.0100.0014.136-0.500-0.313-0.001-0.097-0.0890.000
134A135GLU-1-0.876-0.9467.4130.1880.1880.0000.0000.0000.000
135A136LEU00.0020.00211.0720.0590.0590.0000.0000.0000.000
136A137LEU0-0.0030.00713.904-0.049-0.0490.0000.0000.0000.000
137A138LEU0-0.025-0.01015.5790.0040.0040.0000.0000.0000.000
138A139VAL00.0060.00619.325-0.021-0.0210.0000.0000.0000.000
139A140VAL0-0.002-0.00721.7430.0020.0020.0000.0000.0000.000
140A141ASN0-0.039-0.01825.386-0.004-0.0040.0000.0000.0000.000
141A142PRO00.0220.00028.5830.0030.0030.0000.0000.0000.000
142A143GLU-1-0.911-0.94030.9070.0550.0550.0000.0000.0000.000
143A144ILE00.0880.02231.8130.0050.0050.0000.0000.0000.000
144A145SER0-0.0070.01532.4870.0050.0050.0000.0000.0000.000
145A146SER00.0040.00028.3490.0060.0060.0000.0000.0000.000
146A147ILE00.0770.03128.1050.0090.0090.0000.0000.0000.000
147A148THR0-0.070-0.02828.3110.0050.0050.0000.0000.0000.000
148A149ASP-1-0.951-0.97728.3940.1000.1000.0000.0000.0000.000
149A150GLY00.021-0.00325.0450.0110.0110.0000.0000.0000.000
150A151LEU00.0350.02524.3370.0130.0130.0000.0000.0000.000
151A152LYS10.9350.96525.678-0.089-0.0890.0000.0000.0000.000
152A153THR00.0200.01320.8360.0090.0090.0000.0000.0000.000
153A154LYS10.8980.97120.922-0.099-0.0990.0000.0000.0000.000
154A155ILE00.0090.00221.3640.0110.0110.0000.0000.0000.000
155A156VAL0-0.044-0.02320.5630.0040.0040.0000.0000.0000.000
156A157ALA00.0510.01817.4650.0120.0120.0000.0000.0000.000
157A158GLU-1-0.884-0.94918.3720.1560.1560.0000.0000.0000.000
158A159ARG10.8190.91420.480-0.145-0.1450.0000.0000.0000.000
159A160LEU0-0.062-0.04317.482-0.011-0.0110.0000.0000.0000.000
160A161GLY0-0.0040.02516.7610.0110.0110.0000.0000.0000.000
161A162THR0-0.041-0.01112.9900.0000.0000.0000.0000.0000.000
162A163LYS10.9310.95812.262-0.243-0.2430.0000.0000.0000.000
163A164VAL00.002-0.00313.5130.0320.0320.0000.0000.0000.000
164A165LEU0-0.0060.01210.560-0.029-0.0290.0000.0000.0000.000
165A166GLY00.008-0.00713.791-0.036-0.0360.0000.0000.0000.000
166A167VAL0-0.040-0.03117.2380.0190.0190.0000.0000.0000.000
167A168VAL0-0.010-0.00418.206-0.018-0.0180.0000.0000.0000.000
168A169VAL00.006-0.00120.9700.0050.0050.0000.0000.0000.000
169A170ASN0-0.014-0.04223.959-0.015-0.0150.0000.0000.0000.000
170A171ARG10.8890.95025.634-0.057-0.0570.0000.0000.0000.000
171A172ILE00.0240.04127.9350.0000.0000.0000.0000.0000.000
172A173THR00.000-0.01230.579-0.004-0.0040.0000.0000.0000.000
173A174THR00.012-0.03430.6790.0020.0020.0000.0000.0000.000
174A175LEU0-0.0110.00632.884-0.001-0.0010.0000.0000.0000.000
175A176GLY00.0640.03135.576-0.001-0.0010.0000.0000.0000.000
176A177ILE0-0.0150.00530.0470.0020.0020.0000.0000.0000.000
177A178GLU-1-0.876-0.92830.8750.0200.0200.0000.0000.0000.000
178A179MET0-0.018-0.02031.4480.0030.0030.0000.0000.0000.000
179A180ALA00.0500.03431.2430.0030.0030.0000.0000.0000.000
180A181LYS10.9100.96323.885-0.029-0.0290.0000.0000.0000.000
181A182ASN00.0190.00728.1830.0060.0060.0000.0000.0000.000
182A183GLU-1-0.959-0.97330.0790.0450.0450.0000.0000.0000.000
183A184ILE0-0.012-0.02326.3100.0040.0040.0000.0000.0000.000
184A185GLU-1-0.869-0.95024.0810.0600.0600.0000.0000.0000.000
185A186ALA0-0.019-0.00226.7110.0040.0040.0000.0000.0000.000
186A187ILE0-0.059-0.01929.6510.0020.0020.0000.0000.0000.000
187A188LEU0-0.050-0.03624.2540.0040.0040.0000.0000.0000.000
188A189GLU-1-0.995-0.98624.6220.0960.0960.0000.0000.0000.000
189A190ALA00.004-0.00320.7560.0100.0100.0000.0000.0000.000
190A191LYS10.9110.95718.021-0.064-0.0640.0000.0000.0000.000
191A192VAL0-0.0080.00020.0340.0120.0120.0000.0000.0000.000
192A193ILE0-0.090-0.04815.247-0.012-0.0120.0000.0000.0000.000
193A194GLY00.0420.01819.107-0.010-0.0100.0000.0000.0000.000
194A195LEU0-0.0160.00120.9970.0090.0090.0000.0000.0000.000
195A196ILE00.0130.00521.115-0.008-0.0080.0000.0000.0000.000
196A197PRO0-0.011-0.00825.1440.0040.0040.0000.0000.0000.000
197A198GLU-1-0.905-0.96328.6200.0360.0360.0000.0000.0000.000
198A199ASP-1-0.788-0.92229.0910.0020.0020.0000.0000.0000.000
199A200PRO0-0.041-0.02330.7610.0020.0020.0000.0000.0000.000
200A201GLU-1-0.749-0.86629.729-0.001-0.0010.0000.0000.0000.000
201A202VAL00.0110.00126.095-0.002-0.0020.0000.0000.0000.000
202A203ARG10.9520.97727.774-0.017-0.0170.0000.0000.0000.000
203A204ARG10.8470.91730.424-0.005-0.0050.0000.0000.0000.000
204A205ALA00.0090.01226.169-0.002-0.0020.0000.0000.0000.000
205A206ALA0-0.0040.00326.780-0.001-0.0010.0000.0000.0000.000
206A207ALA0-0.050-0.02927.7530.0000.0000.0000.0000.0000.000
207A208TYR0-0.076-0.05030.177-0.001-0.0010.0000.0000.0000.000
208A209GLY00.0530.06626.510-0.004-0.0040.0000.0000.0000.000
209A210LYS10.9620.98424.9730.0310.0310.0000.0000.0000.000
210A211PRO00.0600.03720.7240.0040.0040.0000.0000.0000.000
211A212VAL00.0370.02523.156-0.009-0.0090.0000.0000.0000.000
212A213VAL00.0020.00919.300-0.004-0.0040.0000.0000.0000.000
213A214LEU0-0.019-0.00620.632-0.009-0.0090.0000.0000.0000.000
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