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: 7GQ6K

Calculation Name: 2Z9O-A-Xray372

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: 2023-06-19

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2772317.876824
FMO2-HF: Nuclear repulsion 2680930.243714
FMO2-HF: Total energy -91387.633111
FMO2-MP2: Total energy -91654.90604


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:21:SER)


Summations of interaction energy for fragment #1(A:21:SER)
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.
-16.763-9.5011.329-4.005-4.585-0.015
Interaction energy analysis for fragmet #1(A:21:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.011
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].
3A23ASP-1-0.734-0.8793.821-5.705-3.223-0.016-1.192-1.2740.006
4A24LEU0-0.006-0.0125.6401.2091.2090.0000.0000.0000.000
5A25THR0-0.013-0.0325.2810.7790.7790.0000.0000.0000.000
6A26GLU-1-0.845-0.9042.744-12.963-9.7330.443-1.964-1.709-0.022
7A27ALA0-0.0030.0136.9960.0090.0090.0000.0000.0000.000
8A28ALA00.0420.01610.1550.1130.1130.0000.0000.0000.000
9A29TYR0-0.036-0.0487.874-0.231-0.2310.0000.0000.0000.000
10A30SER00.0060.00411.527-0.027-0.0270.0000.0000.0000.000
11A31LEU0-0.107-0.02413.257-0.029-0.0290.0000.0000.0000.000
12A32SER00.0540.02416.2000.0600.0600.0000.0000.0000.000
13A33ARG10.8800.91619.014-0.123-0.1230.0000.0000.0000.000
14A34ASP-1-0.768-0.88320.1340.0890.0890.0000.0000.0000.000
15A35GLN0-0.0350.00419.358-0.003-0.0030.0000.0000.0000.000
16A36LYS10.7730.88714.447-0.216-0.2160.0000.0000.0000.000
17A37ARG10.8970.97217.772-0.123-0.1230.0000.0000.0000.000
18A38MET0-0.029-0.00820.732-0.008-0.0080.0000.0000.0000.000
19A39LEU0-0.017-0.02415.1290.0040.0040.0000.0000.0000.000
20A40TYR0-0.035-0.00518.1970.0150.0150.0000.0000.0000.000
21A41LEU00.0900.03519.672-0.008-0.0080.0000.0000.0000.000
22A42PHE0-0.013-0.01720.258-0.001-0.0010.0000.0000.0000.000
23A43VAL00.003-0.00816.405-0.013-0.0130.0000.0000.0000.000
24A44ASP-1-0.998-0.97419.5370.1730.1730.0000.0000.0000.000
25A45GLN0-0.021-0.03522.227-0.005-0.0050.0000.0000.0000.000
26A46ILE0-0.0760.01519.125-0.011-0.0110.0000.0000.0000.000
27A47ARG10.9160.93619.178-0.195-0.1950.0000.0000.0000.000
28A57ASP-1-0.880-0.93923.376-0.088-0.0880.0000.0000.0000.000
29A58GLY0-0.049-0.04624.934-0.027-0.0270.0000.0000.0000.000
30A59ILE0-0.058-0.02225.578-0.002-0.0020.0000.0000.0000.000
31A60CYS00.0130.01725.9120.0170.0170.0000.0000.0000.000
32A61GLU-1-0.814-0.87828.047-0.069-0.0690.0000.0000.0000.000
33A62ILE0-0.050-0.03926.2620.0090.0090.0000.0000.0000.000
34A63HIS00.0230.01828.7940.0010.0010.0000.0000.0000.000
35A64VAL0-0.002-0.00530.2610.0100.0100.0000.0000.0000.000
36A65ALA00.0280.02131.4180.0090.0090.0000.0000.0000.000
37A66LYS10.9170.95527.651-0.096-0.0960.0000.0000.0000.000
38A67TYR00.018-0.00324.4450.0160.0160.0000.0000.0000.000
39A68ALA0-0.027-0.04628.4890.0110.0110.0000.0000.0000.000
40A69GLU-1-0.822-0.88830.4920.1010.1010.0000.0000.0000.000
41A70ILE0-0.0300.00824.6170.0090.0090.0000.0000.0000.000
42A71PHE0-0.072-0.05822.2430.0240.0240.0000.0000.0000.000
43A72GLY0-0.0060.01327.743-0.003-0.0030.0000.0000.0000.000
44A73LEU0-0.013-0.01129.489-0.003-0.0030.0000.0000.0000.000
45A74THR00.014-0.01832.916-0.008-0.0080.0000.0000.0000.000
46A75SER00.0600.00034.046-0.001-0.0010.0000.0000.0000.000
47A76ALA0-0.0180.00434.998-0.006-0.0060.0000.0000.0000.000
48A77GLU-1-0.811-0.88532.8110.0520.0520.0000.0000.0000.000
49A78ALA00.0370.02730.415-0.004-0.0040.0000.0000.0000.000
50A79SER0-0.038-0.01430.511-0.010-0.0100.0000.0000.0000.000
51A80LYS10.8460.92230.865-0.038-0.0380.0000.0000.0000.000
52A81ASP-1-0.812-0.90927.4020.0420.0420.0000.0000.0000.000
53A82ILE00.0410.03526.238-0.015-0.0150.0000.0000.0000.000
54A83ARG10.9000.95427.5970.0030.0030.0000.0000.0000.000
55A84GLN00.006-0.01027.621-0.024-0.0240.0000.0000.0000.000
56A85ALA00.0310.03223.526-0.017-0.0170.0000.0000.0000.000
57A86LEU00.0820.03924.165-0.023-0.0230.0000.0000.0000.000
58A87LYS10.9590.98725.2820.0560.0560.0000.0000.0000.000
59A88SER0-0.016-0.02023.328-0.016-0.0160.0000.0000.0000.000
60A89PHE0-0.053-0.03717.689-0.015-0.0150.0000.0000.0000.000
61A90ALA0-0.072-0.04322.105-0.027-0.0270.0000.0000.0000.000
62A91GLY00.008-0.01522.132-0.008-0.0080.0000.0000.0000.000
63A92LYS10.8870.98017.5970.2140.2140.0000.0000.0000.000
64A93GLU-1-0.839-0.92216.033-0.579-0.5790.0000.0000.0000.000
65A94VAL0-0.102-0.02810.4950.0010.0010.0000.0000.0000.000
66A95VAL00.0210.01110.5450.0670.0670.0000.0000.0000.000
67A96PHE0-0.023-0.0078.229-0.363-0.3630.0000.0000.0000.000
68A97TYR0-0.005-0.0276.9000.7010.7010.0000.0000.0000.000
69A98ARG10.8380.8868.4460.9720.9720.0000.0000.0000.000
70A99PRO0-0.052-0.0019.1140.0670.0670.0000.0000.0000.000
71A100GLU-1-0.830-0.91911.393-1.015-1.0150.0000.0000.0000.000
72A101GLU-1-0.988-1.00714.534-0.610-0.6100.0000.0000.0000.000
73A102ASP-1-1.011-0.98713.262-0.817-0.8170.0000.0000.0000.000
74A103ALA00.0510.01416.2160.0510.0510.0000.0000.0000.000
75A104GLY0-0.0070.01118.7600.0160.0160.0000.0000.0000.000
76A105ASP-1-0.995-0.98017.885-0.370-0.3700.0000.0000.0000.000
77A106GLU-1-1.025-1.03617.624-0.459-0.4590.0000.0000.0000.000
78A107LYS10.8960.96910.4191.2111.2110.0000.0000.0000.000
79A108GLY00.0700.03713.6570.0470.0470.0000.0000.0000.000
80A109TYR0-0.093-0.06112.120-0.232-0.2320.0000.0000.0000.000
81A110GLU-1-0.763-0.86512.870-0.788-0.7880.0000.0000.0000.000
82A111SER0-0.073-0.05312.918-0.203-0.2030.0000.0000.0000.000
83A112PHE00.0210.00813.8420.1490.1490.0000.0000.0000.000
84A113PRO00.0460.05116.221-0.013-0.0130.0000.0000.0000.000
85A114TRP00.034-0.00812.7880.0160.0160.0000.0000.0000.000
86A115PHE0-0.049-0.03518.5680.0250.0250.0000.0000.0000.000
87A116ILE00.0270.03722.233-0.006-0.0060.0000.0000.0000.000
88A117LYS10.9770.98424.3510.1250.1250.0000.0000.0000.000
89A118ARG10.8980.95524.4690.1600.1600.0000.0000.0000.000
90A119ALA0-0.024-0.00828.091-0.002-0.0020.0000.0000.0000.000
91A120HIS10.8890.95731.4180.0470.0470.0000.0000.0000.000
92A121SER00.0350.02133.580-0.006-0.0060.0000.0000.0000.000
93A122PRO0-0.016-0.01337.2810.0040.0040.0000.0000.0000.000
94A123SER00.0520.04138.9970.0030.0030.0000.0000.0000.000
95A124ARG10.9500.96834.5030.0540.0540.0000.0000.0000.000
96A125GLY0-0.007-0.01938.0890.0010.0010.0000.0000.0000.000
97A126LEU00.0150.01733.7700.0040.0040.0000.0000.0000.000
98A127TYR0-0.077-0.05730.091-0.011-0.0110.0000.0000.0000.000
99A128SER0-0.002-0.03730.4340.0070.0070.0000.0000.0000.000
100A129VAL0-0.040-0.03624.993-0.008-0.0080.0000.0000.0000.000
101A130HIS0-0.0070.00626.2840.0140.0140.0000.0000.0000.000
102A131ILE00.0520.01720.076-0.021-0.0210.0000.0000.0000.000
103A132ASN00.0010.00118.9790.0170.0170.0000.0000.0000.000
104A133PRO00.0740.02119.738-0.008-0.0080.0000.0000.0000.000
105A134TYR00.0250.00916.9980.0130.0130.0000.0000.0000.000
106A135LEU00.0240.01314.145-0.048-0.0480.0000.0000.0000.000
107A136ILE00.0060.01915.0480.0180.0180.0000.0000.0000.000
108A137PRO0-0.002-0.00514.9450.0710.0710.0000.0000.0000.000
109A138PHE00.0330.0179.2500.0050.0050.0000.0000.0000.000
110A139PHE0-0.011-0.00811.7530.1790.1790.0000.0000.0000.000
111A140ILE00.0310.02513.2350.1300.1300.0000.0000.0000.000
112A141GLY00.0060.00010.1780.0950.0950.0000.0000.0000.000
113A142LEU00.000-0.02310.2800.2910.2910.0000.0000.0000.000
114A143GLN00.0450.06912.1990.0620.0620.0000.0000.0000.000
115A144ASN0-0.0050.00011.044-0.051-0.0510.0000.0000.0000.000
116A145ARG10.8180.8734.357-4.339-4.257-0.001-0.014-0.0660.000
117A146PHE0-0.045-0.04911.817-0.033-0.0330.0000.0000.0000.000
118A147THR0-0.024-0.00215.086-0.070-0.0700.0000.0000.0000.000
119A148GLN0-0.0180.00612.423-0.024-0.0240.0000.0000.0000.000
120A149PHE00.002-0.0249.244-0.010-0.0100.0000.0000.0000.000
121A150ARG10.7740.85813.772-0.442-0.4420.0000.0000.0000.000
122A151LEU00.0450.02311.549-0.070-0.0700.0000.0000.0000.000
123A152SER00.024-0.01114.910-0.054-0.0540.0000.0000.0000.000
124A153GLU-1-0.907-0.91618.0340.2730.2730.0000.0000.0000.000
125A154THR00.0060.00614.2090.0460.0460.0000.0000.0000.000
126A155LYS10.9090.96717.319-0.164-0.1640.0000.0000.0000.000
127A156GLU-1-0.831-0.92616.2830.1010.1010.0000.0000.0000.000
128A157ILE0-0.033-0.02711.6550.0240.0240.0000.0000.0000.000
129A158THR00.0370.00712.2030.0030.0030.0000.0000.0000.000
130A159ASN00.0420.01911.648-0.126-0.1260.0000.0000.0000.000
131A160PRO00.0990.0376.6290.2960.2960.0000.0000.0000.000
132A161TYR0-0.011-0.0056.7920.2690.2690.0000.0000.0000.000
133A162ALA0-0.028-0.0159.2810.2380.2380.0000.0000.0000.000
134A163MET0-0.0390.0097.1560.1560.1560.0000.0000.0000.000
135A164ARG10.8780.9232.1362.8414.1290.904-0.829-1.3630.001
136A165LEU0-0.0110.0047.0380.1270.1270.0000.0000.0000.000
137A166TYR00.008-0.02810.709-0.041-0.0410.0000.0000.0000.000
138A167GLU-1-0.743-0.8176.4893.5843.5840.0000.0000.0000.000
139A168SER0-0.016-0.0049.233-0.089-0.0890.0000.0000.0000.000
140A169LEU0-0.035-0.02611.066-0.178-0.1780.0000.0000.0000.000
141A170CYS0-0.0430.00412.895-0.141-0.1410.0000.0000.0000.000
142A171GLN00.0090.00312.104-0.003-0.0030.0000.0000.0000.000
143A172TYR0-0.054-0.02914.067-0.059-0.0590.0000.0000.0000.000
144A173ARG10.8790.95216.382-0.745-0.7450.0000.0000.0000.000
145A174LYS10.8580.92419.474-0.329-0.3290.0000.0000.0000.000
146A175PRO00.0270.01722.8450.0060.0060.0000.0000.0000.000
147A176ASP-1-0.757-0.87724.7920.2950.2950.0000.0000.0000.000
148A177GLY0-0.048-0.01522.291-0.008-0.0080.0000.0000.0000.000
149A178SER0-0.041-0.03322.986-0.018-0.0180.0000.0000.0000.000
150A179GLY00.0200.01321.6960.0190.0190.0000.0000.0000.000
151A180ILE0-0.0250.00122.456-0.008-0.0080.0000.0000.0000.000
152A181VAL00.0170.02317.0060.0020.0020.0000.0000.0000.000
153A182SER0-0.024-0.01120.144-0.025-0.0250.0000.0000.0000.000
154A183LEU00.0200.02314.0940.0160.0160.0000.0000.0000.000
155A184LYS10.8870.92717.284-0.390-0.3900.0000.0000.0000.000
156A185ILE00.0750.03616.5720.0620.0620.0000.0000.0000.000
157A186ASP-1-0.835-0.92616.1170.3600.3600.0000.0000.0000.000
158A187TRP0-0.009-0.01011.0650.0040.0040.0000.0000.0000.000
159A188ILE0-0.041-0.02112.1860.1250.1250.0000.0000.0000.000
160A189ILE0-0.050-0.03011.4780.1180.1180.0000.0000.0000.000
161A190GLU-1-0.792-0.8559.9990.8360.8360.0000.0000.0000.000
162A191ARG10.8830.9457.163-0.947-0.9470.0000.0000.0000.000
163A192TYR0-0.048-0.0636.6280.4270.4270.0000.0000.0000.000
164A193GLN0-0.006-0.0184.9900.8281.008-0.001-0.006-0.1730.000
165A194LEU0-0.044-0.0118.928-0.277-0.2770.0000.0000.0000.000
166A195PRO00.0140.02211.813-0.032-0.0320.0000.0000.0000.000
167A196GLN00.1140.04614.3660.0570.0570.0000.0000.0000.000
168A197SER00.0370.01417.2690.0330.0330.0000.0000.0000.000
169A198TYR0-0.044-0.03815.072-0.002-0.0020.0000.0000.0000.000
170A199GLN00.0750.01618.2820.0440.0440.0000.0000.0000.000
171A200ARG10.8620.94520.008-0.052-0.0520.0000.0000.0000.000
172A201MET00.010-0.01622.116-0.006-0.0060.0000.0000.0000.000
173A202PRO0-0.023-0.02222.9600.0120.0120.0000.0000.0000.000
174A203ASP-1-0.782-0.86021.2490.0530.0530.0000.0000.0000.000
175A204PHE00.0610.02616.198-0.001-0.0010.0000.0000.0000.000
176A205ARG10.8140.87919.177-0.147-0.1470.0000.0000.0000.000
177A206ARG10.9360.96921.128-0.036-0.0360.0000.0000.0000.000
178A207ARG10.8360.92818.023-0.055-0.0550.0000.0000.0000.000
179A208PHE00.0690.02911.687-0.018-0.0180.0000.0000.0000.000
180A209LEU0-0.009-0.00316.5310.0050.0050.0000.0000.0000.000
181A210GLN00.0070.00618.4210.0070.0070.0000.0000.0000.000
182A211VAL00.0090.00916.5930.0110.0110.0000.0000.0000.000
183A212CYS00.0190.01513.370-0.014-0.0140.0000.0000.0000.000
184A213VAL00.0620.04515.9690.0240.0240.0000.0000.0000.000
185A214ASN0-0.053-0.03718.3910.0210.0210.0000.0000.0000.000
186A215GLU-1-0.815-0.88715.5790.1060.1060.0000.0000.0000.000
187A216ILE0-0.062-0.03013.4800.0170.0170.0000.0000.0000.000
188A217ASN0-0.028-0.01817.149-0.002-0.0020.0000.0000.0000.000
189A218SER00.0060.00919.972-0.024-0.0240.0000.0000.0000.000
190A219ARG10.7760.87816.777-0.135-0.1350.0000.0000.0000.000
191A220THR00.0250.02214.8050.0070.0070.0000.0000.0000.000
192A221PRO00.0280.01917.585-0.039-0.0390.0000.0000.0000.000
193A222MET0-0.0090.00715.683-0.014-0.0140.0000.0000.0000.000
194A223ARG10.8900.95219.925-0.302-0.3020.0000.0000.0000.000
195A224LEU0-0.067-0.02317.2310.0210.0210.0000.0000.0000.000
196A225SER00.0690.04321.384-0.032-0.0320.0000.0000.0000.000
197A226TYR00.007-0.01921.3370.0350.0350.0000.0000.0000.000
198A227ILE00.0410.03023.411-0.030-0.0300.0000.0000.0000.000
199A228GLU-1-0.767-0.84024.4520.2180.2180.0000.0000.0000.000
200A229LYS10.9780.99125.071-0.282-0.2820.0000.0000.0000.000
201A230LYS10.8750.93126.118-0.170-0.1700.0000.0000.0000.000
202A231LYS10.9771.00528.413-0.185-0.1850.0000.0000.0000.000
203A232GLY00.0720.03730.137-0.006-0.0060.0000.0000.0000.000
204A233ARG10.9160.94532.168-0.119-0.1190.0000.0000.0000.000
205A234GLN00.0790.05124.446-0.006-0.0060.0000.0000.0000.000
206A235THR0-0.031-0.05924.268-0.001-0.0010.0000.0000.0000.000
207A236THR0-0.013-0.00423.7760.0080.0080.0000.0000.0000.000
208A237HIS0-0.014-0.00521.0820.0260.0260.0000.0000.0000.000
209A238ILE00.0170.02319.200-0.045-0.0450.0000.0000.0000.000
210A239VAL0-0.037-0.02220.2330.0450.0450.0000.0000.0000.000
211A240PHE00.0670.02516.954-0.033-0.0330.0000.0000.0000.000
212A241SER00.002-0.02421.052-0.007-0.0070.0000.0000.0000.000
213A242PHE00.026-0.00418.138-0.027-0.0270.0000.0000.0000.000
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