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: V2111

Calculation Name: 2Z9O-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z9O

Chain ID: A

ChEMBL ID:

UniProt ID: P03856

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 225
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2791241.532612
FMO2-HF: Nuclear repulsion 2699534.466805
FMO2-HF: Total energy -91707.065807
FMO2-MP2: Total energy -91975.716696


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:20:ACE )


Summations of interaction energy for fragment #1(A:20:ACE )
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.
1.0631.6854.221-2.747-2.095-0.01
Interaction energy analysis for fragmet #1(A:20:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / 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].
3A22ASN 00.0080.0163.8480.9841.795-0.005-0.364-0.4420.000
4A23ASP -1-0.704-0.8625.0260.0010.0860.000-0.004-0.0810.000
5A24LEU 00.000-0.0037.0650.1140.1140.0000.0000.0000.000
6A25THR 0-0.031-0.0368.6360.0450.0450.0000.0000.0000.000
7A26GLU -1-0.904-0.9384.0240.4630.6520.003-0.090-0.1020.000
8A27ALA 0-0.0040.0138.7600.1050.1050.0000.0000.0000.000
9A28ALA 00.0480.02011.7700.0240.0240.0000.0000.0000.000
10A29TYR 0-0.043-0.05410.9810.0590.0590.0000.0000.0000.000
11A30SER 0-0.011-0.01413.0780.0270.0270.0000.0000.0000.000
12A31LEU 0-0.101-0.00814.5160.0090.0090.0000.0000.0000.000
13A32SER 00.0430.00517.8950.0000.0000.0000.0000.0000.000
14A33ARG 10.9500.96621.2360.0050.0050.0000.0000.0000.000
15A34ASP -1-0.834-0.96322.586-0.018-0.0180.0000.0000.0000.000
16A35GLN 0-0.045-0.01620.839-0.005-0.0050.0000.0000.0000.000
17A36LYS 10.8630.97116.5480.0100.0100.0000.0000.0000.000
18A37ARG 10.8600.98120.5820.0240.0240.0000.0000.0000.000
19A38MET 0-0.030-0.00423.928-0.006-0.0060.0000.0000.0000.000
20A39LEU 00.001-0.01517.850-0.005-0.0050.0000.0000.0000.000
21A40TYR 00.0300.02722.160-0.014-0.0140.0000.0000.0000.000
22A41LEU 00.0750.02923.382-0.004-0.0040.0000.0000.0000.000
23A42PHE 0-0.028-0.00723.350-0.002-0.0020.0000.0000.0000.000
24A43VAL 00.008-0.01120.210-0.008-0.0080.0000.0000.0000.000
25A44ASP -1-1.057-1.00923.363-0.090-0.0900.0000.0000.0000.000
26A45GLN 00.007-0.02726.3670.0060.0060.0000.0000.0000.000
27A46ILE 0-0.0890.00723.4720.0010.0010.0000.0000.0000.000
28A47ARG 10.8930.92823.9950.1190.1190.0000.0000.0000.000
29A48NME 00.0370.03527.7680.0070.0070.0000.0000.0000.000
30A56ACE 0-0.024-0.02625.261-0.003-0.0030.0000.0000.0000.000
31A57ASP -1-0.890-0.95425.996-0.053-0.0530.0000.0000.0000.000
32A58GLY 0-0.016-0.00627.4230.0000.0000.0000.0000.0000.000
33A59ILE 0-0.062-0.02127.8890.0010.0010.0000.0000.0000.000
34A60CYS 00.0260.02028.593-0.004-0.0040.0000.0000.0000.000
35A61GLU -1-0.818-0.89230.680-0.025-0.0250.0000.0000.0000.000
36A62ILE 0-0.043-0.03428.340-0.003-0.0030.0000.0000.0000.000
37A63HIS 00.0030.00431.6010.0080.0080.0000.0000.0000.000
38A64VAL 0-0.0020.00133.561-0.001-0.0010.0000.0000.0000.000
39A65ALA 00.0190.01334.739-0.001-0.0010.0000.0000.0000.000
40A66LYS 10.9711.00031.9640.0540.0540.0000.0000.0000.000
41A67TYR 00.009-0.01127.662-0.003-0.0030.0000.0000.0000.000
42A68ALA 0-0.014-0.04031.9760.0000.0000.0000.0000.0000.000
43A69GLU -1-0.869-0.92834.795-0.042-0.0420.0000.0000.0000.000
44A70ILE 0-0.0210.01628.524-0.002-0.0020.0000.0000.0000.000
45A71PHE 0-0.104-0.06725.950-0.004-0.0040.0000.0000.0000.000
46A72GLY 0-0.0040.01731.4540.0040.0040.0000.0000.0000.000
47A73LEU 0-0.011-0.01532.7100.0030.0030.0000.0000.0000.000
48A74THR 00.0420.02736.314-0.001-0.0010.0000.0000.0000.000
49A75SER 00.065-0.00237.160-0.001-0.0010.0000.0000.0000.000
50A76ALA 0-0.029-0.00237.8220.0010.0010.0000.0000.0000.000
51A77GLU -1-0.818-0.92135.520-0.009-0.0090.0000.0000.0000.000
52A78ALA 00.0360.03133.2970.0010.0010.0000.0000.0000.000
53A79SER 0-0.056-0.03233.1680.0010.0010.0000.0000.0000.000
54A80LYS 10.9440.96733.667-0.002-0.0020.0000.0000.0000.000
55A81ASP -1-0.853-0.92229.855-0.007-0.0070.0000.0000.0000.000
56A82ILE 00.0190.02129.4890.0020.0020.0000.0000.0000.000
57A83ARG 10.8950.94529.6540.0010.0010.0000.0000.0000.000
58A84GLN 00.003-0.01329.2740.0030.0030.0000.0000.0000.000
59A85ALA 00.0520.04425.7120.0040.0040.0000.0000.0000.000
60A86LEU 00.0720.02625.7580.0040.0040.0000.0000.0000.000
61A87LYS 10.9090.95426.629-0.018-0.0180.0000.0000.0000.000
62A88SER 0-0.001-0.01424.2850.0070.0070.0000.0000.0000.000
63A89PHE 0-0.069-0.03819.4970.0080.0080.0000.0000.0000.000
64A90ALA 0-0.083-0.04223.117-0.001-0.0010.0000.0000.0000.000
65A91GLY 00.013-0.01422.8960.0020.0020.0000.0000.0000.000
66A92LYS 10.8940.98618.487-0.058-0.0580.0000.0000.0000.000
67A93GLU -1-0.877-0.97616.5220.0800.0800.0000.0000.0000.000
68A94VAL 0-0.096-0.02011.7660.0140.0140.0000.0000.0000.000
69A95VAL 00.0220.00210.250-0.011-0.0110.0000.0000.0000.000
70A96PHE 0-0.040-0.0149.031-0.010-0.0100.0000.0000.0000.000
71A97TYR 00.014-0.0176.8760.1180.1180.0000.0000.0000.000
72A98ARG 10.8190.8988.959-0.081-0.0810.0000.0000.0000.000
73A99PRO 0-0.0640.0019.2830.0690.0690.0000.0000.0000.000
74A100GLU -1-0.788-0.89311.029-0.001-0.0010.0000.0000.0000.000
75A101GLU -1-0.971-1.00714.5790.0440.0440.0000.0000.0000.000
76A102ASP -1-1.070-1.01512.6910.2850.2850.0000.0000.0000.000
77A103ALA 00.0330.00315.791-0.022-0.0220.0000.0000.0000.000
78A104GLY 0-0.0010.01517.863-0.001-0.0010.0000.0000.0000.000
79A105ASP -1-0.994-0.97616.5930.2520.2520.0000.0000.0000.000
80A106GLU -1-1.025-1.03416.5940.1710.1710.0000.0000.0000.000
81A107LYS 10.9160.9699.615-0.638-0.6380.0000.0000.0000.000
82A108GLY 00.0940.04313.288-0.022-0.0220.0000.0000.0000.000
83A109TYR 0-0.103-0.05412.0840.0250.0250.0000.0000.0000.000
84A110GLU -1-0.781-0.90013.208-0.068-0.0680.0000.0000.0000.000
85A111SER 0-0.061-0.01813.553-0.011-0.0110.0000.0000.0000.000
86A112PHE 00.0360.01414.686-0.016-0.0160.0000.0000.0000.000
87A113PRO 00.0380.04917.1320.0020.0020.0000.0000.0000.000
88A114TRP 00.017-0.01114.766-0.019-0.0190.0000.0000.0000.000
89A115PHE 0-0.050-0.04019.900-0.011-0.0110.0000.0000.0000.000
90A116ILE 00.0300.04923.5920.0080.0080.0000.0000.0000.000
91A117LYS 10.9660.97925.5750.0230.0230.0000.0000.0000.000
92A118ARG 10.9510.98425.793-0.009-0.0090.0000.0000.0000.000
93A119ALA 0-0.029-0.01829.4440.0040.0040.0000.0000.0000.000
94A120HIS 10.9080.97132.8270.0040.0040.0000.0000.0000.000
95A121SER 00.0070.00235.2170.0010.0010.0000.0000.0000.000
96A122PRO 0-0.0130.00538.980-0.002-0.0020.0000.0000.0000.000
97A123SER 00.0600.04140.847-0.001-0.0010.0000.0000.0000.000
98A124ARG 10.9590.97036.4490.0160.0160.0000.0000.0000.000
99A125GLY 0-0.001-0.01540.298-0.002-0.0020.0000.0000.0000.000
100A126LEU 00.0010.00935.904-0.002-0.0020.0000.0000.0000.000
101A127TYR 0-0.066-0.04432.2610.0050.0050.0000.0000.0000.000
102A128SER 00.011-0.02132.576-0.002-0.0020.0000.0000.0000.000
103A129VAL 0-0.041-0.03427.0670.0050.0050.0000.0000.0000.000
104A130HIS 0-0.0200.00228.072-0.006-0.0060.0000.0000.0000.000
105A131ILE 00.0940.03122.0540.0050.0050.0000.0000.0000.000
106A132ASN 00.0350.02920.8010.0060.0060.0000.0000.0000.000
107A133PRO 00.036-0.01721.624-0.011-0.0110.0000.0000.0000.000
108A134TYR 00.0150.00018.489-0.010-0.0100.0000.0000.0000.000
109A135LEU 00.0610.02915.539-0.022-0.0220.0000.0000.0000.000
110A136ILE 0-0.0020.02517.568-0.027-0.0270.0000.0000.0000.000
111A137PRO 0-0.026-0.01517.801-0.015-0.0150.0000.0000.0000.000
112A138PHE 00.0330.02011.726-0.038-0.0380.0000.0000.0000.000
113A139PHE 00.002-0.00415.683-0.023-0.0230.0000.0000.0000.000
114A140ILE 00.0330.02817.773-0.015-0.0150.0000.0000.0000.000
115A141GLY 00.0140.00814.842-0.011-0.0110.0000.0000.0000.000
116A142LEU 0-0.010-0.01814.402-0.016-0.0160.0000.0000.0000.000
117A143GLN 00.0180.03916.4190.0090.0090.0000.0000.0000.000
118A144ASN 0-0.019-0.02116.1360.0330.0330.0000.0000.0000.000
119A145ARG 10.8780.9089.8840.5840.5840.0000.0000.0000.000
120A146PHE 0-0.069-0.05216.4400.0260.0260.0000.0000.0000.000
121A147THR 0-0.0050.01919.4330.0240.0240.0000.0000.0000.000
122A148GLN 0-0.0130.00616.3740.0090.0090.0000.0000.0000.000
123A149PHE 0-0.030-0.02313.7810.0180.0180.0000.0000.0000.000
124A150ARG 10.8050.89517.6930.0830.0830.0000.0000.0000.000
125A151LEU 00.0470.02615.3320.0180.0180.0000.0000.0000.000
126A152SER 00.008-0.01918.6120.0170.0170.0000.0000.0000.000
127A153GLU -1-0.911-0.93921.543-0.042-0.0420.0000.0000.0000.000
128A154THR 0-0.017-0.00916.9660.0010.0010.0000.0000.0000.000
129A155LYS 10.8620.93719.776-0.018-0.0180.0000.0000.0000.000
130A156GLU -1-0.821-0.90417.9460.0350.0350.0000.0000.0000.000
131A157ILE 0-0.042-0.02912.7270.0120.0120.0000.0000.0000.000
132A158THR 00.0440.00212.5930.0010.0010.0000.0000.0000.000
133A159ASN 00.0780.04311.2440.1100.1100.0000.0000.0000.000
134A160PRO 00.1220.0396.103-0.113-0.1130.0000.0000.0000.000
135A161TYR 00.001-0.0136.751-0.115-0.1150.0000.0000.0000.000
136A162ALA 0-0.058-0.0268.589-0.135-0.1350.0000.0000.0000.000
137A163MET 0-0.0650.0018.656-0.057-0.0570.0000.0000.0000.000
138A164ARG 10.8930.9462.7840.257-0.4523.083-1.295-1.078-0.003
139A165LEU 00.023-0.0018.203-0.085-0.0850.0000.0000.0000.000
140A166TYR 0-0.009-0.03211.305-0.039-0.0390.0000.0000.0000.000
141A167GLU -1-0.798-0.88510.514-0.472-0.4720.0000.0000.0000.000
142A168SER 0-0.0280.00310.529-0.015-0.0150.0000.0000.0000.000
143A169LEU 0-0.031-0.02312.9190.0100.0100.0000.0000.0000.000
144A170CYS 0-0.0150.00715.8740.0060.0060.0000.0000.0000.000
145A171GLN 00.0040.01014.907-0.018-0.0180.0000.0000.0000.000
146A172TYR 0-0.052-0.03415.3210.0020.0020.0000.0000.0000.000
147A173ARG 10.8940.96519.9360.1210.1210.0000.0000.0000.000
148A174LYS 10.9530.99722.2690.0470.0470.0000.0000.0000.000
149A175PRO 00.0060.00025.8280.0020.0020.0000.0000.0000.000
150A176ASP -1-0.822-0.91928.010-0.051-0.0510.0000.0000.0000.000
151A177GLY 0-0.063-0.02925.2960.0050.0050.0000.0000.0000.000
152A178SER 0-0.017-0.02525.2990.0080.0080.0000.0000.0000.000
153A179GLY 0-0.002-0.00523.643-0.009-0.0090.0000.0000.0000.000
154A180ILE 0-0.0190.00523.5190.0090.0090.0000.0000.0000.000
155A181VAL 00.0170.01918.174-0.008-0.0080.0000.0000.0000.000
156A182SER 0-0.030-0.01420.4960.0180.0180.0000.0000.0000.000
157A183LEU 00.0080.01714.512-0.012-0.0120.0000.0000.0000.000
158A184LYS 10.9340.94516.9940.0200.0200.0000.0000.0000.000
159A185ILE 00.0780.03515.549-0.003-0.0030.0000.0000.0000.000
160A186ASP -1-0.846-0.92514.3090.1140.1140.0000.0000.0000.000
161A187TRP 0-0.050-0.02511.8590.0110.0110.0000.0000.0000.000
162A188ILE 0-0.020-0.02211.226-0.022-0.0220.0000.0000.0000.000
163A189ILE 0-0.025-0.0169.6660.0300.0300.0000.0000.0000.000
164A190GLU -1-0.851-0.9008.9680.2420.2420.0000.0000.0000.000
165A191ARG 10.9110.9746.7640.4850.4850.0000.0000.0000.000
166A192TYR 0-0.064-0.0535.522-0.208-0.2080.0000.0000.0000.000
167A193GLN 00.008-0.0162.813-1.066-0.8201.140-0.994-0.392-0.007
168A194LEU 0-0.053-0.0165.8370.2630.2630.0000.0000.0000.000
169A195PRO 00.0100.0158.814-0.029-0.0290.0000.0000.0000.000
170A196GLN 00.1250.05111.416-0.096-0.0960.0000.0000.0000.000
171A197SER 00.0420.01814.244-0.031-0.0310.0000.0000.0000.000
172A198TYR 0-0.061-0.03912.906-0.053-0.0530.0000.0000.0000.000
173A199GLN 00.040-0.01015.011-0.026-0.0260.0000.0000.0000.000
174A200ARG 10.8920.98216.893-0.179-0.1790.0000.0000.0000.000
175A201MET 00.007-0.01919.5840.0030.0030.0000.0000.0000.000
176A202PRO 0-0.029-0.02820.4510.0040.0040.0000.0000.0000.000
177A203ASP -1-0.856-0.92618.4540.1830.1830.0000.0000.0000.000
178A204PHE 00.0490.01514.5140.0080.0080.0000.0000.0000.000
179A205ARG 10.7840.86317.126-0.089-0.0890.0000.0000.0000.000
180A206ARG 10.9941.00619.521-0.156-0.1560.0000.0000.0000.000
181A207ARG 10.8810.94515.736-0.222-0.2220.0000.0000.0000.000
182A208PHE 00.0530.03110.2100.0150.0150.0000.0000.0000.000
183A209LEU 0-0.013-0.01014.854-0.022-0.0220.0000.0000.0000.000
184A210GLN 0-0.0070.00217.267-0.009-0.0090.0000.0000.0000.000
185A211VAL 00.0200.01615.381-0.013-0.0130.0000.0000.0000.000
186A212CYS 00.0240.02012.529-0.004-0.0040.0000.0000.0000.000
187A213VAL 00.0380.03715.775-0.026-0.0260.0000.0000.0000.000
188A214ASN 0-0.055-0.03218.553-0.020-0.0200.0000.0000.0000.000
189A215GLU -1-0.878-0.94215.9760.1260.1260.0000.0000.0000.000
190A216ILE 0-0.082-0.05614.637-0.015-0.0150.0000.0000.0000.000
191A217ASN 0-0.002-0.01118.403-0.024-0.0240.0000.0000.0000.000
192A218SER 00.0200.01521.115-0.009-0.0090.0000.0000.0000.000
193A219ARG 10.8430.93618.227-0.085-0.0850.0000.0000.0000.000
194A220THR 00.0450.06517.110-0.015-0.0150.0000.0000.0000.000
195A221PRO 00.0290.01620.1090.0100.0100.0000.0000.0000.000
196A222MET 0-0.0080.00918.1840.0020.0020.0000.0000.0000.000
197A223ARG 10.9190.96422.0210.0050.0050.0000.0000.0000.000
198A224LEU 0-0.074-0.03618.029-0.007-0.0070.0000.0000.0000.000
199A225SER 00.0500.03422.2750.0080.0080.0000.0000.0000.000
200A226TYR 00.003-0.02621.223-0.004-0.0040.0000.0000.0000.000
201A227ILE 00.0410.03423.2340.0040.0040.0000.0000.0000.000
202A228GLU -1-0.803-0.87022.7890.0720.0720.0000.0000.0000.000
203A229LYS 10.9880.99823.940-0.001-0.0010.0000.0000.0000.000
204A230LYS 10.9260.95424.959-0.045-0.0450.0000.0000.0000.000
205A231LYS 10.9701.00226.978-0.014-0.0140.0000.0000.0000.000
206A232GLY 00.0670.03228.8220.0010.0010.0000.0000.0000.000
207A233ARG 10.9110.94130.188-0.038-0.0380.0000.0000.0000.000
208A234GLN 00.0860.05521.8740.0040.0040.0000.0000.0000.000
209A235THR 0-0.010-0.04123.159-0.011-0.0110.0000.0000.0000.000
210A236THR 0-0.0170.02021.9170.0040.0040.0000.0000.0000.000
211A237HIS 0-0.0070.00120.0120.0020.0020.0000.0000.0000.000
212A238ILE 00.0170.02818.1760.0060.0060.0000.0000.0000.000
213A239VAL 0-0.024-0.01719.793-0.012-0.0120.0000.0000.0000.000
214A240PHE 00.0700.02416.2810.0080.0080.0000.0000.0000.000
215A241SER 0-0.007-0.02821.337-0.010-0.0100.0000.0000.0000.000
216A242PHE 00.0310.00019.0770.0120.0120.0000.0000.0000.000
217A243ARG 10.9180.94823.2500.0010.0010.0000.0000.0000.000
218A244ASP -1-0.773-0.88524.689-0.040-0.0400.0000.0000.0000.000
219A245ILE 0-0.006-0.02325.5800.0030.0030.0000.0000.0000.000
220A246THR 0-0.085-0.04026.7530.0030.0030.0000.0000.0000.000
221A247SER 0-0.0060.00229.2370.0010.0010.0000.0000.0000.000
222A248MET 0-0.0550.00528.9150.0000.0000.0000.0000.0000.000
223A249THR 0-0.020-0.01932.1760.0000.0000.0000.0000.0000.000
224A250THR 0-0.046-0.02833.6890.0020.0020.0000.0000.0000.000
225A251GLY -1-0.930-0.94530.5470.0080.0080.0000.0000.0000.000