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: N185Q

Calculation Name: 2OZV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OZV

Chain ID: A

ChEMBL ID:

UniProt ID: Q7D120

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2295162.925273
FMO2-HF: Nuclear repulsion 2215369.385744
FMO2-HF: Total energy -79793.539528
FMO2-MP2: Total energy -80022.962585


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:31:MET)


Summations of interaction energy for fragment #1(A:31: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.
-9.638-4.2844.404-2.28-7.474-0.006
Interaction energy analysis for fragmet #1(A:31:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.007
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].
3A33ALA00.0060.0023.393-1.1540.0330.008-0.339-0.8560.002
4A34MET00.0520.0343.5150.2240.8080.010-0.113-0.4800.000
5A35LEU0-0.008-0.0122.4220.5331.4071.423-0.417-1.881-0.001
6A36LEU0-0.0080.0065.6920.8230.8230.0000.0000.0000.000
7A37ALA00.0420.0187.9660.2950.2950.0000.0000.0000.000
8A38SER0-0.052-0.0238.6420.3210.3210.0000.0000.0000.000
9A39LEU0-0.012-0.0149.7920.2010.2010.0000.0000.0000.000
10A40VAL00.0100.02612.3360.1200.1200.0000.0000.0000.000
11A41ALA0-0.0040.00215.304-0.059-0.0590.0000.0000.0000.000
12A42ASP-1-0.828-0.91417.250-0.175-0.1750.0000.0000.0000.000
13A43ASP-1-0.873-0.92119.992-0.391-0.3910.0000.0000.0000.000
14A44ARG10.8790.92822.1410.1850.1850.0000.0000.0000.000
15A45ALA00.0100.00923.353-0.017-0.0170.0000.0000.0000.000
16A46CYS0-0.074-0.02821.4230.0090.0090.0000.0000.0000.000
17A47ARG10.9270.96422.8580.0880.0880.0000.0000.0000.000
18A48ILE0-0.005-0.01916.5330.0050.0050.0000.0000.0000.000
19A49ALA00.0260.02819.4100.0070.0070.0000.0000.0000.000
20A50ASP-1-0.815-0.92612.941-0.146-0.1460.0000.0000.0000.000
21A51LEU0-0.060-0.04816.2160.0310.0310.0000.0000.0000.000
22A52GLY00.0910.08414.3340.0420.0420.0000.0000.0000.000
23A53ALA0-0.036-0.05012.804-0.039-0.0390.0000.0000.0000.000
24A54GLY0-0.025-0.02811.2620.0610.0610.0000.0000.0000.000
25A55ALA00.0450.03211.789-0.039-0.0390.0000.0000.0000.000
26A56GLY00.0920.03312.876-0.050-0.0500.0000.0000.0000.000
27A57ALA0-0.017-0.0057.410-0.076-0.0760.0000.0000.0000.000
28A58ALA0-0.011-0.0028.667-0.244-0.2440.0000.0000.0000.000
29A59GLY00.0820.0269.491-0.101-0.1010.0000.0000.0000.000
30A60MET0-0.028-0.01111.3060.0030.0030.0000.0000.0000.000
31A61ALA00.0160.0128.392-0.036-0.0360.0000.0000.0000.000
32A62VAL0-0.058-0.02510.498-0.006-0.0060.0000.0000.0000.000
33A63ALA00.0190.01013.3280.0320.0320.0000.0000.0000.000
34A64ALA0-0.033-0.00112.6980.0400.0400.0000.0000.0000.000
35A65ARG10.8490.92412.2380.7980.7980.0000.0000.0000.000
36A66LEU0-0.039-0.01015.2010.0480.0480.0000.0000.0000.000
37A67GLU-1-0.905-0.96518.198-0.257-0.2570.0000.0000.0000.000
38A68LYS10.8460.91820.9600.2890.2890.0000.0000.0000.000
39A69ALA0-0.025-0.00318.7690.0250.0250.0000.0000.0000.000
40A70GLU-1-0.926-0.95720.787-0.136-0.1360.0000.0000.0000.000
41A71VAL0-0.025-0.01815.9650.0010.0010.0000.0000.0000.000
42A72THR00.0160.01719.3790.0130.0130.0000.0000.0000.000
43A73LEU0-0.025-0.01414.862-0.007-0.0070.0000.0000.0000.000
44A74TYR0-0.004-0.03318.0980.0070.0070.0000.0000.0000.000
45A75GLU-1-0.857-0.93316.3580.1540.1540.0000.0000.0000.000
46A76ARG10.9140.96019.989-0.211-0.2110.0000.0000.0000.000
47A77SER0-0.032-0.01921.877-0.015-0.0150.0000.0000.0000.000
48A78GLN00.1230.05622.7440.0040.0040.0000.0000.0000.000
49A79GLU-1-0.971-0.98022.3890.1660.1660.0000.0000.0000.000
50A80MET0-0.031-0.00615.5950.0200.0200.0000.0000.0000.000
51A81ALA00.0490.02418.844-0.015-0.0150.0000.0000.0000.000
52A82GLU-1-0.828-0.90220.786-0.008-0.0080.0000.0000.0000.000
53A83PHE0-0.034-0.01214.075-0.013-0.0130.0000.0000.0000.000
54A84ALA00.0210.00316.327-0.017-0.0170.0000.0000.0000.000
55A85ARG10.7860.86817.314-0.041-0.0410.0000.0000.0000.000
56A86ARG10.8220.87620.288-0.005-0.0050.0000.0000.0000.000
57A87SER0-0.028-0.00113.826-0.032-0.0320.0000.0000.0000.000
58A88LEU0-0.008-0.02116.178-0.047-0.0470.0000.0000.0000.000
59A89GLU-1-0.883-0.90018.203-0.064-0.0640.0000.0000.0000.000
60A90LEU0-0.044-0.01315.8510.0030.0030.0000.0000.0000.000
61A91PRO00.000-0.01619.322-0.024-0.0240.0000.0000.0000.000
62A92ASP-1-0.943-0.97114.566-0.388-0.3880.0000.0000.0000.000
63A93ASN0-0.033-0.01914.290-0.108-0.1080.0000.0000.0000.000
64A94ALA0-0.004-0.00817.0300.0030.0030.0000.0000.0000.000
65A95ALA0-0.050-0.01618.3540.0120.0120.0000.0000.0000.000
66A96PHE00.007-0.01413.8230.0030.0030.0000.0000.0000.000
67A97SER00.0320.02818.9280.0110.0110.0000.0000.0000.000
68A98ALA00.0060.00319.7860.0180.0180.0000.0000.0000.000
69A99ARG10.8010.91018.6820.3370.3370.0000.0000.0000.000
70A100ILE0-0.037-0.01415.893-0.013-0.0130.0000.0000.0000.000
71A101GLU-1-0.914-0.94720.057-0.048-0.0480.0000.0000.0000.000
72A102VAL0-0.041-0.00818.744-0.001-0.0010.0000.0000.0000.000
73A103LEU0-0.0040.00021.2360.0080.0080.0000.0000.0000.000
74A104GLU-1-0.869-0.94022.4060.0580.0580.0000.0000.0000.000
75A105ALA00.0220.00323.688-0.007-0.0070.0000.0000.0000.000
76A106ASP-1-0.853-0.91723.4550.1540.1540.0000.0000.0000.000
77A107VAL00.0310.01419.851-0.009-0.0090.0000.0000.0000.000
78A108THR0-0.076-0.02622.794-0.001-0.0010.0000.0000.0000.000
79A109LEU00.0060.01324.950-0.003-0.0030.0000.0000.0000.000
80A110ARG10.9370.95227.913-0.111-0.1110.0000.0000.0000.000
81A111ALA0-0.019-0.01730.584-0.004-0.0040.0000.0000.0000.000
82A112LYS11.0140.99832.736-0.031-0.0310.0000.0000.0000.000
83A113ALA00.0750.06232.487-0.003-0.0030.0000.0000.0000.000
84A114ARG10.9170.95726.800-0.047-0.0470.0000.0000.0000.000
85A115VAL00.0450.02029.866-0.004-0.0040.0000.0000.0000.000
86A116GLU-1-0.974-0.99331.8870.0270.0270.0000.0000.0000.000
87A117ALA0-0.042-0.01228.517-0.002-0.0020.0000.0000.0000.000
88A118GLY00.0380.02628.1410.0000.0000.0000.0000.0000.000
89A119LEU0-0.070-0.01323.510-0.008-0.0080.0000.0000.0000.000
90A120PRO0-0.011-0.00526.7310.0080.0080.0000.0000.0000.000
91A121ASP-1-0.891-0.95828.2310.0100.0100.0000.0000.0000.000
92A122GLU-1-1.064-1.03628.561-0.022-0.0220.0000.0000.0000.000
93A123HIS00.0410.02526.034-0.004-0.0040.0000.0000.0000.000
94A124PHE00.008-0.00822.390-0.013-0.0130.0000.0000.0000.000
95A125HIS00.0310.01722.9230.0060.0060.0000.0000.0000.000
96A126HIS0-0.026-0.03117.759-0.009-0.0090.0000.0000.0000.000
97A127VAL00.0000.00017.7190.0100.0100.0000.0000.0000.000
98A128ILE0-0.020-0.01212.2260.0000.0000.0000.0000.0000.000
99A129MET0-0.039-0.01512.9650.0630.0630.0000.0000.0000.000
100A130ASN0-0.005-0.0237.284-0.013-0.0130.0000.0000.0000.000
101A131PRO00.0120.02810.8660.0770.0770.0000.0000.0000.000
102A132PRO0-0.0050.01012.3650.1180.1180.0000.0000.0000.000
103A133TYR00.006-0.0128.0710.0690.0690.0000.0000.0000.000
104A155GLY00.0350.01619.8060.0130.0130.0000.0000.0000.000
105A156LEU0-0.011-0.01717.465-0.034-0.0340.0000.0000.0000.000
106A157PHE00.0230.00713.163-0.029-0.0290.0000.0000.0000.000
107A158GLU-1-0.775-0.87719.0210.1080.1080.0000.0000.0000.000
108A159ASP-1-0.865-0.94422.5400.1480.1480.0000.0000.0000.000
109A160TRP00.0410.01115.054-0.012-0.0120.0000.0000.0000.000
110A161ILE00.018-0.00117.384-0.031-0.0310.0000.0000.0000.000
111A162ARG10.7730.90620.855-0.147-0.1470.0000.0000.0000.000
112A163THR0-0.049-0.05322.705-0.019-0.0190.0000.0000.0000.000
113A164ALA00.0330.01719.857-0.017-0.0170.0000.0000.0000.000
114A165SER0-0.020-0.02221.915-0.024-0.0240.0000.0000.0000.000
115A166ALA0-0.063-0.03124.666-0.011-0.0110.0000.0000.0000.000
116A167ILE00.0620.04321.908-0.006-0.0060.0000.0000.0000.000
117A168MET0-0.0770.02919.848-0.021-0.0210.0000.0000.0000.000
118A169VAL0-0.007-0.00325.0720.0110.0110.0000.0000.0000.000
119A170SER0-0.011-0.02326.5110.0030.0030.0000.0000.0000.000
120A171GLY0-0.006-0.00526.391-0.009-0.0090.0000.0000.0000.000
121A172GLY00.0270.01623.655-0.013-0.0130.0000.0000.0000.000
122A173GLN0-0.042-0.03315.6350.0350.0350.0000.0000.0000.000
123A174LEU00.0000.00516.351-0.012-0.0120.0000.0000.0000.000
124A175SER00.007-0.01112.537-0.012-0.0120.0000.0000.0000.000
125A176LEU00.0130.00811.3900.0110.0110.0000.0000.0000.000
126A177ILE0-0.0120.0044.050-0.213-0.0530.000-0.028-0.1320.000
127A178SER00.004-0.0048.4670.0240.0240.0000.0000.0000.000
128A179ARG10.9260.9718.372-0.684-0.6840.0000.0000.0000.000
129A180PRO00.0720.0369.250-0.231-0.2310.0000.0000.0000.000
130A181GLN00.025-0.00312.323-0.034-0.0340.0000.0000.0000.000
131A182SER0-0.0140.00813.922-0.023-0.0230.0000.0000.0000.000
132A183VAL00.0180.01315.728-0.070-0.0700.0000.0000.0000.000
133A184ALA00.0210.00416.848-0.051-0.0510.0000.0000.0000.000
134A185GLU-1-0.865-0.93618.3370.3570.3570.0000.0000.0000.000
135A186ILE00.0110.00513.817-0.037-0.0370.0000.0000.0000.000
136A187ILE0-0.002-0.00518.308-0.043-0.0430.0000.0000.0000.000
137A188ALA0-0.025-0.01320.937-0.027-0.0270.0000.0000.0000.000
138A189ALA00.0060.02020.426-0.022-0.0220.0000.0000.0000.000
139A190CYS0-0.041-0.01019.731-0.029-0.0290.0000.0000.0000.000
140A191GLY00.0570.03622.615-0.021-0.0210.0000.0000.0000.000
141A192SER0-0.067-0.04626.222-0.003-0.0030.0000.0000.0000.000
142A193ARG10.7490.87224.517-0.116-0.1160.0000.0000.0000.000
143A194PHE00.019-0.00121.669-0.015-0.0150.0000.0000.0000.000
144A195GLY00.0510.03523.6870.0180.0180.0000.0000.0000.000
145A196GLY0-0.041-0.03522.505-0.016-0.0160.0000.0000.0000.000
146A197LEU00.0240.01618.592-0.015-0.0150.0000.0000.0000.000
147A198GLU-1-0.801-0.87916.515-0.087-0.0870.0000.0000.0000.000
148A199ILE0-0.005-0.00913.975-0.001-0.0010.0000.0000.0000.000
149A200THR00.0230.02410.740-0.063-0.0630.0000.0000.0000.000
150A201LEU00.0030.01110.2810.1120.1120.0000.0000.0000.000
151A202ILE00.0350.0224.236-0.608-0.2540.025-0.089-0.2890.001
152A203HIS0-0.003-0.0227.5010.3880.3880.0000.0000.0000.000
153A204PRO00.0020.0135.055-0.182-0.1820.0000.0000.0000.000
154A205ARG10.9200.9456.067-0.395-0.3950.0000.0000.0000.000
155A206PRO00.0150.0009.5030.1120.1120.0000.0000.0000.000
156A207GLY0-0.016-0.00313.068-0.007-0.0070.0000.0000.0000.000
157A208GLU-1-0.864-0.9179.5260.4190.4190.0000.0000.0000.000
158A209ASP-1-0.863-0.92311.8410.5600.5600.0000.0000.0000.000
159A210ALA0-0.070-0.0359.4380.1220.1220.0000.0000.0000.000
160A211VAL00.023-0.0044.505-0.1050.0280.001-0.021-0.1120.000
161A212ARG10.8230.8993.820-3.622-3.0410.057-0.102-0.5360.000
162A213MET0-0.046-0.0126.818-0.361-0.3610.0000.0000.0000.000
163A214LEU00.0540.0356.145-0.038-0.0380.0000.0000.0000.000
164A215VAL0-0.013-0.0149.6440.0350.0350.0000.0000.0000.000
165A216THR00.0590.04713.244-0.052-0.0520.0000.0000.0000.000
166A217ALA0-0.030-0.02115.6150.0390.0390.0000.0000.0000.000
167A218ILE00.0040.01519.334-0.021-0.0210.0000.0000.0000.000
168A219LYS10.9300.97022.5220.0250.0250.0000.0000.0000.000
169A220GLY00.000-0.00224.923-0.010-0.0100.0000.0000.0000.000
170A221SER0-0.054-0.01125.1410.0030.0030.0000.0000.0000.000
171A222ARG11.0060.98327.2730.0060.0060.0000.0000.0000.000
172A223ALA0-0.042-0.00125.5170.0070.0070.0000.0000.0000.000
173A224ARG10.9830.99325.347-0.038-0.0380.0000.0000.0000.000
174A225LEU00.0260.02120.297-0.013-0.0130.0000.0000.0000.000
175A226THR0-0.085-0.05020.454-0.011-0.0110.0000.0000.0000.000
176A227PHE00.0590.02416.1920.0050.0050.0000.0000.0000.000
177A228ARG10.8260.91515.0280.1060.1060.0000.0000.0000.000
178A229ALA00.005-0.00416.0790.0490.0490.0000.0000.0000.000
179A230PRO0-0.0030.00611.979-0.020-0.0200.0000.0000.0000.000
180A231LEU00.0260.0167.733-0.099-0.0990.0000.0000.0000.000
181A232ILE0-0.0030.0058.6180.3040.3040.0000.0000.0000.000
182A233MET0-0.021-0.0062.876-1.143-1.2672.710-0.549-2.037-0.003
183A234HIS10.8340.9144.6710.5860.652-0.001-0.001-0.0640.000
184A235GLU-1-0.831-0.9178.742-0.119-0.1190.0000.0000.0000.000
185A236THR00.006-0.02512.0530.0000.0000.0000.0000.0000.000
186A237GLY0-0.023-0.00413.881-0.017-0.0170.0000.0000.0000.000
187A238SER0-0.0200.00511.688-0.023-0.0230.0000.0000.0000.000
188A239HIS00.022-0.00510.757-0.035-0.0350.0000.0000.0000.000
189A240ALA00.0030.0159.445-0.145-0.1450.0000.0000.0000.000
190A241PHE0-0.018-0.0083.061-0.660-0.1420.066-0.111-0.4720.000
191A242THR00.0110.0087.9440.0530.0530.0000.0000.0000.000
192A243PRO00.0580.0169.697-0.175-0.1750.0000.0000.0000.000
193A244PHE00.0340.02511.455-0.095-0.0950.0000.0000.0000.000
194A245VAL00.0350.0014.940-0.105-0.1050.0000.0000.0000.000
195A246ASP-1-0.882-0.9447.294-1.936-1.9360.0000.0000.0000.000
196A247ASP-1-0.831-0.9058.963-1.025-1.0250.0000.0000.0000.000
197A248LEU0-0.071-0.0267.373-0.051-0.0510.0000.0000.0000.000
198A249ASN0-0.048-0.0333.094-2.812-1.7910.105-0.510-0.615-0.005
199A250ASN0-0.072-0.0425.734-0.052-0.0520.0000.0000.0000.000
200A251GLY00.0080.0238.7490.2460.2460.0000.0000.0000.000
201A252ARG10.7980.87710.6661.2061.2060.0000.0000.0000.000
202A253ALA0-0.021-0.00611.9390.1430.1430.0000.0000.0000.000
203A254ALA00.0010.00811.750-0.151-0.1510.0000.0000.0000.000
204A255TYR0-0.055-0.05911.0970.0560.0560.0000.0000.0000.000
205A256ALA00.0150.01513.0560.0350.0350.0000.0000.0000.000
206A257ARG10.8530.91116.5240.1050.1050.0000.0000.0000.000
207A258ASN0-0.035-0.04118.298-0.026-0.0260.0000.0000.0000.000
208A259VAL0-0.052-0.00821.044-0.004-0.0040.0000.0000.0000.000