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: YVN52

Calculation Name: 1YZF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YZF

Chain ID: A

ChEMBL ID:

UniProt ID: Q839J6

Base Structure: X-ray

Registration Date: 2023-09-22

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2189603.54898
FMO2-HF: Nuclear repulsion 2114800.087199
FMO2-HF: Total energy -74803.461781
FMO2-MP2: Total energy -75023.570194


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-14.892-9.98213.398-4.733-13.574-0.049
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / q_NPA : -0.004
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].
3A3LYS10.8430.9022.783-2.8360.9530.405-2.076-2.117-0.009
4A4ILE00.005-0.0025.2160.0190.117-0.001-0.007-0.0890.000
5A5VAL00.003-0.0067.9340.3470.3470.0000.0000.0000.000
6A6LEU00.002-0.00110.965-0.075-0.0750.0000.0000.0000.000
7A7PHE00.012-0.00213.7980.0340.0340.0000.0000.0000.000
8A8GLY00.0690.01916.918-0.023-0.0230.0000.0000.0000.000
9A9ASP-1-0.836-0.91620.1640.0310.0310.0000.0000.0000.000
10A10SER00.018-0.01521.9880.0150.0150.0000.0000.0000.000
11A11ILE0-0.0080.01521.8140.0130.0130.0000.0000.0000.000
12A12THR00.0000.01516.9250.0070.0070.0000.0000.0000.000
13A13ALA00.0100.01618.1680.0310.0310.0000.0000.0000.000
14A14GLY00.0480.03419.3590.0260.0260.0000.0000.0000.000
15A15TYR0-0.050-0.04620.4300.0100.0100.0000.0000.0000.000
16A16LEU0-0.0170.00422.480-0.002-0.0020.0000.0000.0000.000
17A17ASP-1-0.877-0.93426.1010.0470.0470.0000.0000.0000.000
18A18GLU-1-0.968-0.96323.8270.0910.0910.0000.0000.0000.000
19A19ALA00.012-0.00524.3810.0020.0020.0000.0000.0000.000
20A20VAL0-0.009-0.02319.4510.0040.0040.0000.0000.0000.000
21A21SER00.0130.00819.2220.0050.0050.0000.0000.0000.000
22A22PRO0-0.0110.00214.6040.0160.0160.0000.0000.0000.000
23A23VAL00.0020.00414.3890.0470.0470.0000.0000.0000.000
24A24LEU00.0600.04215.0770.0060.0060.0000.0000.0000.000
25A25VAL00.009-0.0099.5420.0040.0040.0000.0000.0000.000
26A26ASP-1-0.839-0.92410.8940.6030.6030.0000.0000.0000.000
27A27LEU0-0.054-0.02312.290-0.023-0.0230.0000.0000.0000.000
28A28VAL00.0400.0189.948-0.038-0.0380.0000.0000.0000.000
29A29LYS10.8560.9286.750-1.165-1.1650.0000.0000.0000.000
30A30ARG10.9340.9799.366-0.266-0.2660.0000.0000.0000.000
31A31ASP-1-0.869-0.94612.211-0.002-0.0020.0000.0000.0000.000
32A32ILE0-0.024-0.0167.884-0.063-0.0630.0000.0000.0000.000
33A33ALA0-0.016-0.0108.910-0.081-0.0810.0000.0000.0000.000
34A34ALA0-0.023-0.00710.338-0.043-0.0430.0000.0000.0000.000
35A35MET0-0.096-0.03513.130-0.011-0.0110.0000.0000.0000.000
36A36GLY0-0.0100.00412.497-0.013-0.0130.0000.0000.0000.000
37A37LEU0-0.029-0.0109.459-0.018-0.0180.0000.0000.0000.000
38A38GLU-1-0.834-0.8965.058-1.178-1.066-0.001-0.003-0.1080.000
39A39GLU-1-0.941-0.9742.466-6.548-4.2882.327-1.414-3.174-0.014
40A40VAL0-0.005-0.0082.186-3.596-2.5384.338-2.025-3.370-0.021
41A41ALA00.0120.0012.3093.1991.6086.249-0.156-4.503-0.006
42A42VAL0-0.018-0.0103.756-1.305-2.1210.0810.948-0.2130.001
43A43ILE0-0.006-0.0037.3220.2020.2020.0000.0000.0000.000
44A44ASN00.002-0.01210.169-0.192-0.1920.0000.0000.0000.000
45A45ALA00.0080.01713.7420.0040.0040.0000.0000.0000.000
46A46GLY00.0280.01016.020-0.049-0.0490.0000.0000.0000.000
47A47MET0-0.031-0.01218.8960.0200.0200.0000.0000.0000.000
48A48PRO00.014-0.00722.313-0.015-0.0150.0000.0000.0000.000
49A49GLY00.0030.01025.211-0.003-0.0030.0000.0000.0000.000
50A50ASP-1-0.741-0.85623.6090.0240.0240.0000.0000.0000.000
51A51THR0-0.081-0.05826.635-0.005-0.0050.0000.0000.0000.000
52A52THR00.016-0.04225.4600.0010.0010.0000.0000.0000.000
53A53GLU-1-0.855-0.90626.465-0.012-0.0120.0000.0000.0000.000
54A54ASP-1-0.841-0.90327.0420.0100.0100.0000.0000.0000.000
55A55GLY00.0650.03223.2170.0030.0030.0000.0000.0000.000
56A56LEU0-0.031-0.02522.849-0.004-0.0040.0000.0000.0000.000
57A57LYS10.7650.88224.481-0.001-0.0010.0000.0000.0000.000
58A58ARG10.7310.84818.973-0.055-0.0550.0000.0000.0000.000
59A59LEU00.0250.03519.4290.0090.0090.0000.0000.0000.000
60A60ASN00.0320.00218.380-0.028-0.0280.0000.0000.0000.000
61A61LYS10.8680.91917.820-0.126-0.1260.0000.0000.0000.000
62A62GLU-1-0.847-0.92616.2820.1210.1210.0000.0000.0000.000
63A63VAL00.0150.02314.3900.0270.0270.0000.0000.0000.000
64A64LEU00.0150.01013.518-0.060-0.0600.0000.0000.0000.000
65A65ILE0-0.022-0.01013.773-0.079-0.0790.0000.0000.0000.000
66A66GLU-1-0.838-0.8979.2680.3690.3690.0000.0000.0000.000
67A67LYS10.8110.9098.9550.3330.3330.0000.0000.0000.000
68A68PRO00.0110.0158.676-0.320-0.3200.0000.0000.0000.000
69A69ASP-1-0.849-0.9246.361-3.000-3.0000.0000.0000.0000.000
70A70GLU-1-0.826-0.9369.412-0.581-0.5810.0000.0000.0000.000
71A71VAL0-0.017-0.00510.6600.0450.0450.0000.0000.0000.000
72A72VAL0-0.0090.00012.780-0.004-0.0040.0000.0000.0000.000
73A73ILE0-0.013-0.00615.2560.0390.0390.0000.0000.0000.000
74A74PHE0-0.016-0.02218.689-0.005-0.0050.0000.0000.0000.000
75A75PHE00.0380.02520.5120.0150.0150.0000.0000.0000.000
76A76GLY00.0510.00124.191-0.008-0.0080.0000.0000.0000.000
77A77ALA00.0050.01127.0680.0000.0000.0000.0000.0000.000
78A78ASN0-0.053-0.03327.3310.0010.0010.0000.0000.0000.000
79A79ASP-1-0.731-0.84828.361-0.015-0.0150.0000.0000.0000.000
80A80ALA00.0210.00831.388-0.002-0.0020.0000.0000.0000.000
81A81SER0-0.051-0.02333.5360.0000.0000.0000.0000.0000.000
82A82LEU0-0.015-0.02735.501-0.001-0.0010.0000.0000.0000.000
83A83ASP-1-0.884-0.92737.3970.0080.0080.0000.0000.0000.000
84A84ARG10.7500.87530.250-0.014-0.0140.0000.0000.0000.000
85A85ASN00.003-0.00335.098-0.002-0.0020.0000.0000.0000.000
86A86ILE00.0030.01631.599-0.003-0.0030.0000.0000.0000.000
87A87THR00.0300.00634.822-0.001-0.0010.0000.0000.0000.000
88A88VAL00.0360.00234.792-0.002-0.0020.0000.0000.0000.000
89A89ALA0-0.005-0.00634.101-0.004-0.0040.0000.0000.0000.000
90A90THR00.0790.05032.541-0.003-0.0030.0000.0000.0000.000
91A91PHE00.0340.03027.266-0.004-0.0040.0000.0000.0000.000
92A92ARG10.8360.89429.3220.0510.0510.0000.0000.0000.000
93A93GLU-1-0.945-0.96929.648-0.052-0.0520.0000.0000.0000.000
94A94ASN00.026-0.00327.572-0.009-0.0090.0000.0000.0000.000
95A95LEU0-0.009-0.00524.171-0.008-0.0080.0000.0000.0000.000
96A96GLU-1-0.846-0.91324.835-0.116-0.1160.0000.0000.0000.000
97A97THR0-0.003-0.00725.962-0.012-0.0120.0000.0000.0000.000
98A98MET0-0.055-0.02021.546-0.010-0.0100.0000.0000.0000.000
99A99ILE0-0.019-0.01121.143-0.022-0.0220.0000.0000.0000.000
100A100HIS0-0.113-0.04521.699-0.025-0.0250.0000.0000.0000.000
101A101GLU-1-0.892-0.93921.708-0.124-0.1240.0000.0000.0000.000
102A102ILE0-0.064-0.02216.013-0.022-0.0220.0000.0000.0000.000
103A103GLY00.0400.02617.392-0.059-0.0590.0000.0000.0000.000
104A104SER00.0350.00918.177-0.017-0.0170.0000.0000.0000.000
105A105GLU-1-0.869-0.92116.056-0.358-0.3580.0000.0000.0000.000
106A106LYS10.7980.87413.2820.3970.3970.0000.0000.0000.000
107A107VAL0-0.030-0.00114.300-0.011-0.0110.0000.0000.0000.000
108A108ILE00.0090.01613.7280.0020.0020.0000.0000.0000.000
109A109LEU0-0.0180.00117.3980.0200.0200.0000.0000.0000.000
110A110ILE0-0.012-0.00217.810-0.001-0.0010.0000.0000.0000.000
111A111THR0-0.068-0.03321.7650.0070.0070.0000.0000.0000.000
112A112PRO00.0490.01324.8720.0060.0060.0000.0000.0000.000
113A113PRO00.0040.01726.023-0.004-0.0040.0000.0000.0000.000
114A114TYR0-0.033-0.03727.734-0.002-0.0020.0000.0000.0000.000
115A115ALA00.0220.01230.4910.0040.0040.0000.0000.0000.000
116A116ASP-1-0.758-0.86033.0060.0020.0020.0000.0000.0000.000
117A117SER0-0.043-0.04236.4250.0010.0010.0000.0000.0000.000
118A118GLY0-0.034-0.00138.8140.0000.0000.0000.0000.0000.000
119A119ARG10.7850.88235.471-0.012-0.0120.0000.0000.0000.000
120A120ARG10.7550.87634.610-0.013-0.0130.0000.0000.0000.000
121A121PRO00.0380.02238.253-0.002-0.0020.0000.0000.0000.000
122A122GLU-1-0.777-0.84436.4150.0090.0090.0000.0000.0000.000
123A123ARG10.8460.90031.285-0.014-0.0140.0000.0000.0000.000
124A124PRO00.0450.03437.030-0.001-0.0010.0000.0000.0000.000
125A125GLN00.0650.03835.608-0.004-0.0040.0000.0000.0000.000
126A126THR0-0.042-0.03137.153-0.002-0.0020.0000.0000.0000.000
127A127ARG10.8790.94435.2910.0120.0120.0000.0000.0000.000
128A128ILE00.0410.02431.651-0.003-0.0030.0000.0000.0000.000
129A129LYS10.9300.96432.8760.0170.0170.0000.0000.0000.000
130A130GLU-1-0.910-0.95434.383-0.028-0.0280.0000.0000.0000.000
131A131LEU0-0.024-0.00830.650-0.005-0.0050.0000.0000.0000.000
132A132VAL0-0.012-0.00429.563-0.006-0.0060.0000.0000.0000.000
133A133LYS10.8720.93030.0400.0390.0390.0000.0000.0000.000
134A134VAL0-0.029-0.00829.872-0.006-0.0060.0000.0000.0000.000
135A135ALA00.0420.02026.143-0.007-0.0070.0000.0000.0000.000
136A136GLN0-0.061-0.04626.953-0.009-0.0090.0000.0000.0000.000
137A137GLU-1-0.796-0.86328.554-0.062-0.0620.0000.0000.0000.000
138A138VAL0-0.0020.00325.622-0.006-0.0060.0000.0000.0000.000
139A139GLY00.023-0.00224.560-0.011-0.0110.0000.0000.0000.000
140A140ALA0-0.012-0.01125.404-0.012-0.0120.0000.0000.0000.000
141A141ALA0-0.026-0.00228.001-0.005-0.0050.0000.0000.0000.000
142A142HIS10.7900.86924.0690.1250.1250.0000.0000.0000.000
143A143ASN0-0.074-0.02824.010-0.014-0.0140.0000.0000.0000.000
144A144LEU0-0.0050.02120.213-0.017-0.0170.0000.0000.0000.000
145A145PRO0-0.017-0.01417.7360.0210.0210.0000.0000.0000.000
146A146VAL00.0170.01120.5420.0020.0020.0000.0000.0000.000
147A147ILE0-0.0070.00617.6200.0040.0040.0000.0000.0000.000
148A148ASP-1-0.808-0.91622.231-0.041-0.0410.0000.0000.0000.000
149A149LEU00.0340.01222.9250.0040.0040.0000.0000.0000.000
150A150TYR00.017-0.01325.4180.0050.0050.0000.0000.0000.000
151A151LYS10.9360.98529.0380.0470.0470.0000.0000.0000.000
152A152ALA0-0.039-0.02526.2360.0030.0030.0000.0000.0000.000
153A153MET00.0040.02327.1840.0020.0020.0000.0000.0000.000
154A154THR0-0.024-0.03329.5120.0020.0020.0000.0000.0000.000
155A155VAL0-0.098-0.03630.9670.0000.0000.0000.0000.0000.000
156A156TYR0-0.0180.00130.852-0.001-0.0010.0000.0000.0000.000
157A157PRO00.002-0.00732.9790.0010.0010.0000.0000.0000.000
158A158GLY00.0160.01834.6290.0010.0010.0000.0000.0000.000
159A159THR00.007-0.00832.1330.0020.0020.0000.0000.0000.000
160A160ASP-1-0.852-0.94732.2000.0070.0070.0000.0000.0000.000
161A161GLU-1-0.922-0.94632.2240.0150.0150.0000.0000.0000.000
162A162PHE0-0.055-0.01527.6740.0030.0030.0000.0000.0000.000
163A163LEU0-0.064-0.01828.2210.0050.0050.0000.0000.0000.000
164A164GLN00.007-0.01128.938-0.001-0.0010.0000.0000.0000.000
165A165ALA00.037-0.00131.628-0.005-0.0050.0000.0000.0000.000
166A166ASP-1-0.775-0.86832.4000.0290.0290.0000.0000.0000.000
167A167GLY0-0.009-0.00734.205-0.003-0.0030.0000.0000.0000.000
168A168LEU0-0.047-0.04030.123-0.005-0.0050.0000.0000.0000.000
169A169HIS0-0.036-0.03126.6090.0030.0030.0000.0000.0000.000
170A170PHE00.0180.00323.628-0.007-0.0070.0000.0000.0000.000
171A171SER00.033-0.00326.3640.0100.0100.0000.0000.0000.000
172A172GLN0-0.036-0.03923.8640.0050.0050.0000.0000.0000.000
173A173VAL00.0310.01824.0030.0030.0030.0000.0000.0000.000
174A174GLY00.0230.02024.969-0.006-0.0060.0000.0000.0000.000
175A175TYR0-0.056-0.05019.762-0.007-0.0070.0000.0000.0000.000
176A176GLU-1-0.878-0.92520.1840.0450.0450.0000.0000.0000.000
177A177LEU0-0.036-0.00820.708-0.009-0.0090.0000.0000.0000.000
178A178LEU0-0.014-0.01218.782-0.012-0.0120.0000.0000.0000.000
179A179GLY00.0280.00216.577-0.009-0.0090.0000.0000.0000.000
180A180ALA00.0360.01916.302-0.016-0.0160.0000.0000.0000.000
181A181LEU0-0.069-0.04118.207-0.026-0.0260.0000.0000.0000.000
182A182ILE00.0240.01013.286-0.027-0.0270.0000.0000.0000.000
183A183VAL00.006-0.00112.626-0.047-0.0470.0000.0000.0000.000
184A184ARG10.7720.86714.2500.0760.0760.0000.0000.0000.000
185A185GLU-1-0.818-0.89615.933-0.173-0.1730.0000.0000.0000.000
186A186ILE00.0140.0088.875-0.033-0.0330.0000.0000.0000.000
187A187LYS10.9310.97511.4680.0450.0450.0000.0000.0000.000
188A188GLY0-0.033-0.00912.774-0.031-0.0310.0000.0000.0000.000
189A189ARG10.8170.91611.0730.5080.5080.0000.0000.0000.000
190A190LEU0-0.049-0.0066.803-0.217-0.2170.0000.0000.0000.000
191A191LYS10.8100.8766.2100.9960.9960.0000.0000.0000.000
192A192PRO00.016-0.0049.717-0.027-0.0270.0000.0000.0000.000
193A193LYS10.9360.9866.4850.4470.4470.0000.0000.0000.000
194A194GLN0-0.029-0.02210.3620.0360.0360.0000.0000.0000.000
195A195ALA00.0070.01111.700-0.021-0.0210.0000.0000.0000.000