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: Q199Y

Calculation Name: 3C9B-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C9B

Chain ID: B

ChEMBL ID:

UniProt ID: P53853

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2455067.25047
FMO2-HF: Nuclear repulsion 2370870.211807
FMO2-HF: Total energy -84197.038664
FMO2-MP2: Total energy -84445.392133


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(B:17:GLY)


Summations of interaction energy for fragment #1(B:17:GLY)
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.
-8.082-7.3675.753-2.276-4.1910.01
Interaction energy analysis for fragmet #1(B:17:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.016
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].
3B19ALA00.0120.0053.511-0.2311.6110.015-0.865-0.9930.002
4B20LYS10.9600.9812.480-8.251-9.6745.738-1.326-2.9880.008
5B21CYS00.0090.0054.513-1.214-0.9180.000-0.085-0.2100.000
6B22GLU-1-0.932-0.9686.367-0.101-0.1010.0000.0000.0000.000
7B23GLU-1-0.940-0.9618.3091.6701.6700.0000.0000.0000.000
8B24GLU-1-0.962-0.9877.814-0.245-0.2450.0000.0000.0000.000
9B25VAL0-0.0170.00310.622-0.037-0.0370.0000.0000.0000.000
10B26ASP-1-0.874-0.92612.6540.1800.1800.0000.0000.0000.000
11B27ALA0-0.079-0.04313.712-0.014-0.0140.0000.0000.0000.000
12B28ILE0-0.003-0.01413.048-0.023-0.0230.0000.0000.0000.000
13B29GLU-1-0.891-0.95616.384-0.051-0.0510.0000.0000.0000.000
14B30ARG10.8760.94818.529-0.103-0.1030.0000.0000.0000.000
15B31GLU-1-0.950-0.96718.3360.0080.0080.0000.0000.0000.000
16B32VAL0-0.015-0.00820.192-0.007-0.0070.0000.0000.0000.000
17B33GLU-1-0.948-0.97622.5910.0140.0140.0000.0000.0000.000
18B34LEU0-0.004-0.01523.695-0.002-0.0020.0000.0000.0000.000
19B35TYR0-0.050-0.01324.607-0.006-0.0060.0000.0000.0000.000
20B36ARG10.9210.95726.1650.0000.0000.0000.0000.0000.000
21B37LEU00.0000.00428.173-0.002-0.0020.0000.0000.0000.000
22B38ASN00.025-0.00128.207-0.001-0.0010.0000.0000.0000.000
23B39LYS10.8820.95430.0020.0080.0080.0000.0000.0000.000
24B40MET0-0.006-0.00732.690-0.003-0.0030.0000.0000.0000.000
25B41LYS10.9411.00034.424-0.024-0.0240.0000.0000.0000.000
26B42PRO0-0.007-0.01035.7240.0000.0000.0000.0000.0000.000
27B43VAL00.0210.00037.571-0.001-0.0010.0000.0000.0000.000
28B44TYR00.0430.00635.668-0.002-0.0020.0000.0000.0000.000
29B45GLU-1-0.918-0.95540.4470.0160.0160.0000.0000.0000.000
30B46LYS10.8640.94441.483-0.008-0.0080.0000.0000.0000.000
31B47ARG10.7800.88641.495-0.007-0.0070.0000.0000.0000.000
32B48ASP-1-0.769-0.90743.4560.0100.0100.0000.0000.0000.000
33B49ALA00.0310.03446.1090.0000.0000.0000.0000.0000.000
34B50TYR0-0.028-0.01347.358-0.001-0.0010.0000.0000.0000.000
35B51ILE0-0.073-0.02945.7850.0000.0000.0000.0000.0000.000
36B52ASP-1-0.928-0.95849.5870.0100.0100.0000.0000.0000.000
37B53GLU-1-0.986-0.98652.0010.0040.0040.0000.0000.0000.000
38B54ILE0-0.097-0.04451.714-0.001-0.0010.0000.0000.0000.000
39B55ALA00.003-0.00154.7090.0010.0010.0000.0000.0000.000
40B56GLU-1-0.913-0.96256.3150.0050.0050.0000.0000.0000.000
41B57PHE00.0320.01447.4290.0000.0000.0000.0000.0000.000
42B58TRP00.0840.01144.5010.0000.0000.0000.0000.0000.000
43B59LYS10.9450.99950.995-0.006-0.0060.0000.0000.0000.000
44B60ILE0-0.021-0.01852.9520.0000.0000.0000.0000.0000.000
45B61VAL0-0.014-0.01246.862-0.001-0.0010.0000.0000.0000.000
46B62LEU0-0.044-0.03146.9620.0000.0000.0000.0000.0000.000
47B63SER0-0.055-0.02149.8740.0000.0000.0000.0000.0000.000
48B64GLN0-0.069-0.02449.4960.0000.0000.0000.0000.0000.000
49B65HIS0-0.045-0.00642.5710.0000.0000.0000.0000.0000.000
50B66VAL00.0100.00444.9710.0010.0010.0000.0000.0000.000
51B67SER0-0.004-0.00943.0180.0010.0010.0000.0000.0000.000
52B68PHE00.0440.00645.6480.0010.0010.0000.0000.0000.000
53B69ALA00.027-0.00146.7790.0010.0010.0000.0000.0000.000
54B70ASN0-0.047-0.01347.0130.0000.0000.0000.0000.0000.000
55B71TYR0-0.033-0.00741.5520.0020.0020.0000.0000.0000.000
56B72ILE0-0.0380.00247.4650.0020.0020.0000.0000.0000.000
57B73ARG10.9210.95650.473-0.014-0.0140.0000.0000.0000.000
58B74ALA00.0590.01954.1630.0000.0000.0000.0000.0000.000
59B75SER0-0.067-0.03757.0100.0000.0000.0000.0000.0000.000
60B76ASP-1-0.682-0.84953.0500.0150.0150.0000.0000.0000.000
61B77PHE00.0320.02052.7240.0000.0000.0000.0000.0000.000
62B78LYS10.9160.98256.309-0.011-0.0110.0000.0000.0000.000
63B79TYR0-0.033-0.02855.7220.0000.0000.0000.0000.0000.000
64B80ILE0-0.0080.00450.5340.0010.0010.0000.0000.0000.000
65B81ASP-1-0.906-0.95053.4570.0070.0070.0000.0000.0000.000
66B82THR0-0.116-0.07156.0640.0000.0000.0000.0000.0000.000
67B83ILE0-0.044-0.01049.3710.0010.0010.0000.0000.0000.000
68B84ASP-1-0.794-0.87052.8990.0110.0110.0000.0000.0000.000
69B85LYS10.9210.96746.619-0.018-0.0180.0000.0000.0000.000
70B86ILE0-0.012-0.00743.5460.0010.0010.0000.0000.0000.000
71B87LYS10.9330.96940.245-0.021-0.0210.0000.0000.0000.000
72B88VAL0-0.0020.01536.7190.0020.0020.0000.0000.0000.000
73B89GLU-1-0.969-0.97636.8190.0270.0270.0000.0000.0000.000
74B90TRP00.0380.00631.2240.0000.0000.0000.0000.0000.000
75B91LEU00.012-0.00231.6630.0000.0000.0000.0000.0000.000
76B92ALA00.0030.01926.8080.0030.0030.0000.0000.0000.000
77B93LEU0-0.073-0.04528.1750.0020.0020.0000.0000.0000.000
78B94GLU-1-0.969-0.97630.5990.0460.0460.0000.0000.0000.000
79B95SER0-0.035-0.01528.6020.0050.0050.0000.0000.0000.000
80B96GLU-1-0.877-0.96323.2920.1090.1090.0000.0000.0000.000
81B97MET0-0.088-0.03824.1560.0160.0160.0000.0000.0000.000
82B98TYR0-0.0510.00126.329-0.001-0.0010.0000.0000.0000.000
83B99ASP-1-0.723-0.83624.7020.0910.0910.0000.0000.0000.000
84B100THR00.010-0.01224.055-0.003-0.0030.0000.0000.0000.000
85B101ARG10.7870.86224.537-0.082-0.0820.0000.0000.0000.000
86B102ASP-1-0.778-0.88628.8740.0710.0710.0000.0000.0000.000
87B103PHE0-0.015-0.02431.077-0.004-0.0040.0000.0000.0000.000
88B104SER0-0.0130.00334.5590.0010.0010.0000.0000.0000.000
89B105ILE0-0.0010.00238.163-0.002-0.0020.0000.0000.0000.000
90B106THR0-0.036-0.03041.2120.0010.0010.0000.0000.0000.000
91B107PHE00.008-0.00144.230-0.002-0.0020.0000.0000.0000.000
92B108HIS10.7420.82447.771-0.013-0.0130.0000.0000.0000.000
93B109PHE00.0040.00050.131-0.001-0.0010.0000.0000.0000.000
94B110HIS00.0830.03254.1000.0010.0010.0000.0000.0000.000
95B111GLY00.0150.00857.3990.0000.0000.0000.0000.0000.000
96B112ILE0-0.072-0.04659.032-0.001-0.0010.0000.0000.0000.000
97B113GLU-1-0.891-0.94862.3290.0100.0100.0000.0000.0000.000
98B114GLY0-0.026-0.01365.2940.0000.0000.0000.0000.0000.000
99B115ASP-1-0.776-0.84762.7750.0120.0120.0000.0000.0000.000
100B116PHE0-0.041-0.03154.2780.0010.0010.0000.0000.0000.000
101B117LYS11.0081.01357.626-0.018-0.0180.0000.0000.0000.000
102B118GLU-1-0.853-0.88756.3490.0160.0160.0000.0000.0000.000
103B119GLN0-0.041-0.02153.3090.0020.0020.0000.0000.0000.000
104B120GLN00.029-0.00647.773-0.002-0.0020.0000.0000.0000.000
105B121VAL0-0.024-0.00846.6810.0010.0010.0000.0000.0000.000
106B122THR00.0280.01441.665-0.002-0.0020.0000.0000.0000.000
107B123LYS10.7790.91241.022-0.034-0.0340.0000.0000.0000.000
108B124VAL00.0520.02536.151-0.001-0.0010.0000.0000.0000.000
109B125PHE0-0.020-0.00335.2250.0000.0000.0000.0000.0000.000
110B126GLN00.0190.00231.1360.0050.0050.0000.0000.0000.000
111B127ILE00.0200.01726.084-0.002-0.0020.0000.0000.0000.000
112B128LYS10.8490.93428.404-0.072-0.0720.0000.0000.0000.000
113B129LYS10.9840.99120.723-0.152-0.1520.0000.0000.0000.000
114B130GLY00.0050.00226.4240.0050.0050.0000.0000.0000.000
115B131LYS10.7050.84627.614-0.065-0.0650.0000.0000.0000.000
116B132ASP-1-0.768-0.87226.1640.0860.0860.0000.0000.0000.000
117B133ASP-1-0.870-0.92124.4880.0690.0690.0000.0000.0000.000
118B134GLN0-0.153-0.10318.0130.0030.0030.0000.0000.0000.000
119B135GLU-1-0.808-0.88018.5170.1770.1770.0000.0000.0000.000
120B136ASP-1-0.922-0.95921.5060.0710.0710.0000.0000.0000.000
121B137GLY0-0.018-0.02123.9100.0010.0010.0000.0000.0000.000
122B138ILE0-0.045-0.02626.600-0.011-0.0110.0000.0000.0000.000
123B139LEU00.0340.01930.2900.0040.0040.0000.0000.0000.000
124B140THR0-0.110-0.05932.674-0.001-0.0010.0000.0000.0000.000
125B141SER0-0.021-0.04835.032-0.002-0.0020.0000.0000.0000.000
126B142GLU-1-0.946-0.96937.9010.0550.0550.0000.0000.0000.000
127B143PRO0-0.077-0.04740.625-0.003-0.0030.0000.0000.0000.000
128B144VAL00.0080.02044.2330.0010.0010.0000.0000.0000.000
129B145PRO0-0.046-0.03145.995-0.002-0.0020.0000.0000.0000.000
130B146ILE00.0130.01849.8060.0000.0000.0000.0000.0000.000
131B147GLU-1-0.957-0.98851.7980.0180.0180.0000.0000.0000.000
132B148TRP0-0.045-0.03752.043-0.001-0.0010.0000.0000.0000.000
133B149PRO00.0250.02156.4030.0000.0000.0000.0000.0000.000
134B150GLN00.0910.04859.6260.0000.0000.0000.0000.0000.000
135B151SER0-0.085-0.07862.2180.0000.0000.0000.0000.0000.000
136B152TYR0-0.119-0.10055.739-0.001-0.0010.0000.0000.0000.000
137B153ASP-1-0.812-0.90359.9500.0160.0160.0000.0000.0000.000
138B154SER0-0.116-0.06461.7250.0000.0000.0000.0000.0000.000
139B155ILE0-0.076-0.06357.2050.0000.0000.0000.0000.0000.000
140B156ASN00.1240.07356.8020.0020.0020.0000.0000.0000.000
141B157PRO0-0.046-0.01552.8760.0000.0000.0000.0000.0000.000
142B158ASP-1-0.802-0.89854.0280.0260.0260.0000.0000.0000.000
143B159LEU0-0.038-0.00856.6800.0000.0000.0000.0000.0000.000
144B160ILE0-0.097-0.03958.113-0.001-0.0010.0000.0000.0000.000
145B161LYS10.9760.99360.163-0.017-0.0170.0000.0000.0000.000
146B162ASP-1-0.887-0.93361.8270.0180.0180.0000.0000.0000.000
147B163LYS10.9190.95054.079-0.024-0.0240.0000.0000.0000.000
148B164ARG10.9370.95657.127-0.022-0.0220.0000.0000.0000.000
149B165SER00.0580.03759.901-0.001-0.0010.0000.0000.0000.000
150B166PRO00.0200.00862.2240.0000.0000.0000.0000.0000.000
151B167GLU-1-0.946-0.97862.2370.0130.0130.0000.0000.0000.000
152B168GLY00.0950.03961.4860.0000.0000.0000.0000.0000.000
153B169LYS10.9180.96157.091-0.018-0.0180.0000.0000.0000.000
154B170LYS10.8950.95057.020-0.012-0.0120.0000.0000.0000.000
155B171LYS10.9360.98758.205-0.013-0.0130.0000.0000.0000.000
156B172TYR00.0810.03350.4960.0000.0000.0000.0000.0000.000
157B173ARG10.9390.95752.578-0.017-0.0170.0000.0000.0000.000
158B174GLN0-0.055-0.03253.3450.0000.0000.0000.0000.0000.000
159B175GLY00.0920.06054.7190.0000.0000.0000.0000.0000.000
160B176MET0-0.037-0.01048.8440.0010.0010.0000.0000.0000.000
161B177LYS10.9150.94349.476-0.017-0.0170.0000.0000.0000.000
162B178THR0-0.055-0.00950.999-0.001-0.0010.0000.0000.0000.000
163B179ILE00.0720.03647.2810.0010.0010.0000.0000.0000.000
164B180PHE00.0360.00648.9280.0010.0010.0000.0000.0000.000
165B181GLY0-0.047-0.01749.5490.0010.0010.0000.0000.0000.000
166B182TRP0-0.041-0.01741.4200.0020.0020.0000.0000.0000.000
167B183PHE00.0590.02144.5200.0020.0020.0000.0000.0000.000
168B184ARG10.8400.90445.455-0.024-0.0240.0000.0000.0000.000
169B185TRP0-0.0370.01236.5650.0020.0020.0000.0000.0000.000
170B186THR0-0.0010.00039.4000.0020.0020.0000.0000.0000.000
171B187GLY00.1140.05937.1970.0030.0030.0000.0000.0000.000
172B188LEU0-0.052-0.03234.7570.0030.0030.0000.0000.0000.000
173B189LYS10.8930.94838.206-0.046-0.0460.0000.0000.0000.000
174B190PRO00.0900.03638.393-0.003-0.0030.0000.0000.0000.000
175B191GLY00.0140.01041.142-0.001-0.0010.0000.0000.0000.000
176B192LYS10.8300.90944.417-0.031-0.0310.0000.0000.0000.000
177B193GLU-1-0.800-0.88941.6810.0370.0370.0000.0000.0000.000
178B194PHE00.0040.00744.207-0.001-0.0010.0000.0000.0000.000
179B195PRO0-0.071-0.04944.0140.0010.0010.0000.0000.0000.000
180B196HIS00.0590.03540.6270.0000.0000.0000.0000.0000.000
181B197GLY00.0270.00341.471-0.001-0.0010.0000.0000.0000.000
182B198ASP-1-0.824-0.90935.7470.0310.0310.0000.0000.0000.000
183B199SER00.0100.00337.211-0.001-0.0010.0000.0000.0000.000
184B200LEU0-0.024-0.00738.551-0.002-0.0020.0000.0000.0000.000
185B201ALA0-0.001-0.00537.621-0.001-0.0010.0000.0000.0000.000
186B202SER00.0450.02134.8640.0000.0000.0000.0000.0000.000
187B203LEU00.0050.02536.650-0.002-0.0020.0000.0000.0000.000
188B204PHE0-0.022-0.01739.656-0.002-0.0020.0000.0000.0000.000
189B205SER00.0140.00634.678-0.003-0.0030.0000.0000.0000.000
190B206GLU-1-0.911-0.96132.5130.0160.0160.0000.0000.0000.000
191B207GLU-1-0.938-0.98136.0000.0000.0000.0000.0000.0000.000
192B208ILE0-0.040-0.01839.359-0.001-0.0010.0000.0000.0000.000
193B209TYR0-0.038-0.03738.640-0.001-0.0010.0000.0000.0000.000
194B210PRO00.0310.02636.871-0.001-0.0010.0000.0000.0000.000
195B211PHE0-0.038-0.03236.229-0.003-0.0030.0000.0000.0000.000
196B212CYS0-0.0010.03141.769-0.002-0.0020.0000.0000.0000.000
197B213VAL00.0630.01244.809-0.001-0.0010.0000.0000.0000.000
198B214LYS10.8730.94740.5130.0080.0080.0000.0000.0000.000
199B215TYR00.0670.03442.9130.0000.0000.0000.0000.0000.000
200B216TYR00.0400.02347.8000.0000.0000.0000.0000.0000.000
201B217ALA0-0.015-0.01549.3340.0000.0000.0000.0000.0000.000
202B218GLU-1-0.980-0.98848.114-0.005-0.0050.0000.0000.0000.000
203B219ALA00.0210.01451.2330.0000.0000.0000.0000.0000.000
204B220GLN0-0.068-0.00853.7250.0010.0010.0000.0000.0000.000
205B221ARG10.8980.95551.6730.0080.0080.0000.0000.0000.000