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: 66VZZ

Calculation Name: 3VZI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VZI

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0J9

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 OptAll
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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2498561.124683
FMO2-HF: Nuclear repulsion 2410856.42537
FMO2-HF: Total energy -87704.699313
FMO2-MP2: Total energy -87959.097495


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:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-1.6471.5812.48-1.837-3.8690
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.009
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].
3A2SER0-0.073-0.0523.8520.4202.093-0.024-0.830-0.8200.002
4A3TYR0-0.027-0.0286.6570.2490.2490.0000.0000.0000.000
5A4GLY00.0230.0319.485-0.153-0.1530.0000.0000.0000.000
6A5VAL0-0.045-0.03012.528-0.034-0.0340.0000.0000.0000.000
7A6ARG00.0650.00715.165-0.035-0.0350.0000.0000.0000.000
8A7LEU0-0.046-0.02218.862-0.026-0.0260.0000.0000.0000.000
9A8HIS00.0610.04020.8840.0010.0010.0000.0000.0000.000
10A9VAL00.002-0.01623.212-0.016-0.0160.0000.0000.0000.000
11A10TRP0-0.012-0.00426.1160.0010.0010.0000.0000.0000.000
12A11GLY00.0360.00629.898-0.008-0.0080.0000.0000.0000.000
13A12GLU-1-0.809-0.87632.8840.0980.0980.0000.0000.0000.000
14A13ARG10.7750.84935.605-0.090-0.0900.0000.0000.0000.000
15A14ALA0-0.0010.00831.8760.0020.0020.0000.0000.0000.000
16A15LEU0-0.023-0.00832.703-0.004-0.0040.0000.0000.0000.000
17A16PHE00.0540.03027.892-0.005-0.0050.0000.0000.0000.000
18A17THR0-0.037-0.02831.0380.0010.0010.0000.0000.0000.000
19A18ARG10.9010.94731.695-0.125-0.1250.0000.0000.0000.000
20A19PRO0-0.043-0.00929.987-0.009-0.0090.0000.0000.0000.000
21A20GLU-1-0.789-0.89733.1420.0990.0990.0000.0000.0000.000
22A21MET0-0.024-0.00435.611-0.003-0.0030.0000.0000.0000.000
23A22LYS10.9290.97634.933-0.038-0.0380.0000.0000.0000.000
24A23VAL0-0.030-0.02738.308-0.007-0.0070.0000.0000.0000.000
25A24GLU-1-0.913-0.95141.3710.0560.0560.0000.0000.0000.000
26A25ARG10.8410.91836.433-0.059-0.0590.0000.0000.0000.000
27A26VAL00.0320.01437.6150.0020.0020.0000.0000.0000.000
28A27SER0-0.032-0.02433.5040.0000.0000.0000.0000.0000.000
29A28TYR0-0.049-0.04030.1000.0020.0020.0000.0000.0000.000
30A29ASP-1-0.815-0.90632.7120.1440.1440.0000.0000.0000.000
31A30ILE0-0.019-0.00827.0500.0050.0050.0000.0000.0000.000
32A31ILE0-0.0310.00124.668-0.011-0.0110.0000.0000.0000.000
33A32THR00.000-0.00324.7350.0160.0160.0000.0000.0000.000
34A33PRO00.0340.01219.6570.0030.0030.0000.0000.0000.000
35A34SER00.0300.02520.1410.0030.0030.0000.0000.0000.000
36A35ALA0-0.057-0.01621.369-0.013-0.0130.0000.0000.0000.000
37A36ALA00.010-0.00120.696-0.004-0.0040.0000.0000.0000.000
38A37ARG10.7710.83615.575-0.128-0.1280.0000.0000.0000.000
39A38GLY00.0150.01118.075-0.011-0.0110.0000.0000.0000.000
40A39ILE0-0.041-0.02620.601-0.019-0.0190.0000.0000.0000.000
41A40LEU00.0040.00615.387-0.003-0.0030.0000.0000.0000.000
42A41GLU-1-0.852-0.92315.7030.0830.0830.0000.0000.0000.000
43A42ALA0-0.031-0.00217.335-0.026-0.0260.0000.0000.0000.000
44A43ILE00.0140.01318.163-0.017-0.0170.0000.0000.0000.000
45A44HIS0-0.028-0.04812.202-0.041-0.0410.0000.0000.0000.000
46A45TRP00.0940.06512.6150.0260.0260.0000.0000.0000.000
47A46LYS10.9170.94912.7470.1450.1450.0000.0000.0000.000
48A47PRO00.0600.02512.074-0.005-0.0050.0000.0000.0000.000
49A48ALA00.0170.0478.587-0.069-0.0690.0000.0000.0000.000
50A49ILE0-0.025-0.0116.941-0.205-0.2050.0000.0000.0000.000
51A50ARG10.8960.9508.487-0.220-0.2200.0000.0000.0000.000
52A51TRP0-0.015-0.0189.8960.1400.1400.0000.0000.0000.000
53A52VAL0-0.022-0.01610.749-0.071-0.0710.0000.0000.0000.000
54A53VAL00.0060.00013.1160.0770.0770.0000.0000.0000.000
55A54ASP-1-0.811-0.88713.4040.9600.9600.0000.0000.0000.000
56A55SER0-0.024-0.02116.364-0.036-0.0360.0000.0000.0000.000
57A56ILE0-0.011-0.00719.9790.0010.0010.0000.0000.0000.000
58A57GLN00.0020.01422.9200.0040.0040.0000.0000.0000.000
59A58VAL0-0.014-0.02525.573-0.014-0.0140.0000.0000.0000.000
60A59LEU0-0.016-0.00828.0820.0030.0030.0000.0000.0000.000
61A60LYS10.8660.93131.266-0.158-0.1580.0000.0000.0000.000
62A61PRO00.0150.00734.2650.0040.0040.0000.0000.0000.000
63A62ILE00.0250.02933.107-0.005-0.0050.0000.0000.0000.000
64A63CYS0-0.049-0.01436.381-0.009-0.0090.0000.0000.0000.000
65A64PHE00.014-0.00836.5460.0010.0010.0000.0000.0000.000
66A65GLU-1-0.729-0.83740.3960.0860.0860.0000.0000.0000.000
67A66SER0-0.042-0.01842.0450.0000.0000.0000.0000.0000.000
68A67ILE0-0.032-0.01841.672-0.003-0.0030.0000.0000.0000.000
69A68ARG10.7890.85244.334-0.048-0.0480.0000.0000.0000.000
70A69ARG10.8420.94238.203-0.065-0.0650.0000.0000.0000.000
71A70ASN0-0.018-0.04644.8370.0010.0010.0000.0000.0000.000
72A71GLU-1-0.899-0.93346.7750.0330.0330.0000.0000.0000.000
73A72VAL0-0.0180.00549.400-0.002-0.0020.0000.0000.0000.000
74A73GLY00.0210.01252.2010.0000.0000.0000.0000.0000.000
75A74SER0-0.011-0.01555.7630.0020.0020.0000.0000.0000.000
76A75LYS10.8590.92958.521-0.022-0.0220.0000.0000.0000.000
77A76LEU00.0430.05553.309-0.001-0.0010.0000.0000.0000.000
78A77SER00.0380.00657.3670.0020.0020.0000.0000.0000.000
79A78ALA00.0730.02759.106-0.002-0.0020.0000.0000.0000.000
80A79ALA00.0220.00860.801-0.002-0.0020.0000.0000.0000.000
81A80SER0-0.051-0.03361.142-0.001-0.0010.0000.0000.0000.000
82A81ILE00.0430.03158.393-0.002-0.0020.0000.0000.0000.000
83A82SER00.0070.00562.322-0.002-0.0020.0000.0000.0000.000
84A83LYS10.9520.96065.597-0.024-0.0240.0000.0000.0000.000
85A84ALA00.0320.01763.847-0.001-0.0010.0000.0000.0000.000
86A85ILE0-0.001-0.00163.076-0.001-0.0010.0000.0000.0000.000
87A86LYS10.8810.94466.779-0.025-0.0250.0000.0000.0000.000
88A87ALA0-0.0100.01069.080-0.001-0.0010.0000.0000.0000.000
89A88GLY00.0340.02468.732-0.001-0.0010.0000.0000.0000.000
90A89ARG10.7920.87965.214-0.017-0.0170.0000.0000.0000.000
91A90THR00.0580.00662.0210.0010.0010.0000.0000.0000.000
92A91ASP-1-0.746-0.83961.4580.0150.0150.0000.0000.0000.000
93A92GLU-1-0.869-0.94160.3360.0200.0200.0000.0000.0000.000
94A93LEU0-0.0080.00259.4380.0010.0010.0000.0000.0000.000
95A94VAL00.0260.01556.1210.0010.0010.0000.0000.0000.000
96A95LYS10.9040.93455.638-0.014-0.0140.0000.0000.0000.000
97A96TYR0-0.014-0.01455.0100.0000.0000.0000.0000.0000.000
98A97VAL00.0400.02652.3790.0020.0020.0000.0000.0000.000
99A98GLU-1-0.907-0.93651.1890.0160.0160.0000.0000.0000.000
100A99GLU-1-0.834-0.93150.1610.0300.0300.0000.0000.0000.000
101A100ASP-1-0.883-0.90950.1150.0430.0430.0000.0000.0000.000
102A101ARG10.8660.91646.859-0.020-0.0200.0000.0000.0000.000
103A102GLN00.0460.02145.7030.0030.0030.0000.0000.0000.000
104A103GLN0-0.0050.02245.4910.0040.0040.0000.0000.0000.000
105A104ARG10.8330.91140.396-0.036-0.0360.0000.0000.0000.000
106A105ALA00.0310.01342.1970.0040.0040.0000.0000.0000.000
107A106ALA00.0080.01039.5650.0000.0000.0000.0000.0000.000
108A107THR00.0080.00340.140-0.003-0.0030.0000.0000.0000.000
109A108VAL0-0.0140.00737.3720.0040.0040.0000.0000.0000.000
110A109LEU00.0330.01732.772-0.001-0.0010.0000.0000.0000.000
111A110ARG10.7110.81636.716-0.108-0.1080.0000.0000.0000.000
112A111GLU-1-0.896-0.93936.1910.1290.1290.0000.0000.0000.000
113A112VAL00.0100.02231.2330.0070.0070.0000.0000.0000.000
114A113GLY00.029-0.01130.045-0.004-0.0040.0000.0000.0000.000
115A114TYR00.017-0.00625.802-0.005-0.0050.0000.0000.0000.000
116A115ILE00.0180.01922.118-0.005-0.0050.0000.0000.0000.000
117A116ILE0-0.027-0.00918.6050.0110.0110.0000.0000.0000.000
118A117ALA00.0400.02617.8320.0150.0150.0000.0000.0000.000
119A118ALA0-0.0010.00414.549-0.019-0.0190.0000.0000.0000.000
120A119HIS10.8190.8857.926-1.060-1.0600.0000.0000.0000.000
121A120PHE00.005-0.0035.810-0.081-0.0810.0000.0000.0000.000
122A121GLU-1-0.793-0.8755.1410.8961.063-0.001-0.017-0.1480.000
123A122MET0-0.042-0.0192.449-0.0600.6742.282-0.830-2.185-0.001
124A123THR0-0.019-0.0274.410-0.287-0.212-0.001-0.009-0.0650.000
125A124ASP-1-0.829-0.9066.724-1.297-1.2970.0000.0000.0000.000
126A125LYS10.8080.8869.0710.7570.7570.0000.0000.0000.000
127A126ALA0-0.033-0.0096.5850.2600.2600.0000.0000.0000.000
128A127GLY00.0180.0148.655-0.172-0.1720.0000.0000.0000.000
129A128PRO00.016-0.0128.732-0.132-0.1320.0000.0000.0000.000
130A129ASP-1-0.906-0.9419.669-0.636-0.6360.0000.0000.0000.000
131A130ASP-1-0.847-0.8918.267-0.211-0.2110.0000.0000.0000.000
132A131ASN00.013-0.0015.1100.0950.0950.0000.0000.0000.000
133A132VAL00.1110.0432.711-1.208-0.6290.224-0.151-0.651-0.001
134A133GLY00.0320.0235.423-0.439-0.4390.0000.0000.0000.000
135A134LYS10.8050.8828.8760.0550.0550.0000.0000.0000.000
136A135HIS0-0.008-0.0117.898-0.035-0.0350.0000.0000.0000.000
137A136LEU00.0670.0428.992-0.090-0.0900.0000.0000.0000.000
138A137ASP-1-0.811-0.88110.7350.2690.2690.0000.0000.0000.000
139A138ILE0-0.067-0.03213.194-0.082-0.0820.0000.0000.0000.000
140A139PHE00.0420.01913.500-0.043-0.0430.0000.0000.0000.000
141A140ASN00.0210.00313.762-0.069-0.0690.0000.0000.0000.000
142A141ARG10.7870.88316.204-0.252-0.2520.0000.0000.0000.000
143A142ARG10.8540.91717.303-0.152-0.1520.0000.0000.0000.000
144A143ALA00.0690.03418.880-0.021-0.0210.0000.0000.0000.000
145A144ARG10.8880.93717.305-0.456-0.4560.0000.0000.0000.000
146A145ARG10.8220.90021.575-0.211-0.2110.0000.0000.0000.000
147A146GLY00.0220.03824.658-0.019-0.0190.0000.0000.0000.000
148A147GLN0-0.034-0.01122.890-0.019-0.0190.0000.0000.0000.000
149A148CYS0-0.086-0.05221.5450.0210.0210.0000.0000.0000.000
150A149PHE0-0.0330.00120.624-0.020-0.0200.0000.0000.0000.000
151A150GLN00.005-0.00122.537-0.026-0.0260.0000.0000.0000.000
152A151ALA00.0460.01724.5960.0170.0170.0000.0000.0000.000
153A152PRO00.0590.04923.576-0.008-0.0080.0000.0000.0000.000
154A153CYS0-0.081-0.04225.503-0.010-0.0100.0000.0000.0000.000
155A154LEU00.0170.01727.0910.0110.0110.0000.0000.0000.000
156A155GLY00.0260.01628.326-0.003-0.0030.0000.0000.0000.000
157A156THR0-0.034-0.04529.636-0.009-0.0090.0000.0000.0000.000
158A157ARG10.9790.96931.088-0.033-0.0330.0000.0000.0000.000
159A158GLU-1-0.919-0.92632.1250.0580.0580.0000.0000.0000.000
160A159PHE00.014-0.00333.088-0.003-0.0030.0000.0000.0000.000
161A160PRO00.0270.02330.6390.0060.0060.0000.0000.0000.000
162A161ALA0-0.006-0.00326.8460.0040.0040.0000.0000.0000.000
163A162SER0-0.027-0.00728.286-0.008-0.0080.0000.0000.0000.000
164A163PHE0-0.020-0.02722.9830.0110.0110.0000.0000.0000.000
165A164ALA00.0000.00024.513-0.015-0.0150.0000.0000.0000.000
166A165LEU0-0.052-0.01917.4570.0100.0100.0000.0000.0000.000
167A166LEU0-0.046-0.01320.930-0.034-0.0340.0000.0000.0000.000
168A167GLY0-0.022-0.00720.5590.0180.0180.0000.0000.0000.000
169A168ASP-1-0.857-0.90517.0560.8570.8570.0000.0000.0000.000
170A169ASP-1-0.979-0.98519.4840.5370.5370.0000.0000.0000.000
171A170ASP-1-0.805-0.90522.5820.3200.3200.0000.0000.0000.000
172A171THR0-0.112-0.05022.2820.0170.0170.0000.0000.0000.000
173A172PRO00.0110.01324.898-0.011-0.0110.0000.0000.0000.000
174A173PRO0-0.009-0.01428.653-0.002-0.0020.0000.0000.0000.000
175A174ALA00.0160.02130.647-0.021-0.0210.0000.0000.0000.000
176A175SER0-0.015-0.02232.418-0.008-0.0080.0000.0000.0000.000
177A176ASP-1-0.847-0.91135.5800.1580.1580.0000.0000.0000.000
178A177PRO00.011-0.00536.9180.0060.0060.0000.0000.0000.000
179A178ALA0-0.052-0.02438.057-0.003-0.0030.0000.0000.0000.000
180A179LEU0-0.053-0.03732.3700.0020.0020.0000.0000.0000.000
181A180SER00.0220.01933.4420.0100.0100.0000.0000.0000.000
182A181GLY00.0180.00534.130-0.012-0.0120.0000.0000.0000.000
183A182GLU-1-0.837-0.90931.0640.2760.2760.0000.0000.0000.000
184A183ARG10.8010.88332.638-0.201-0.2010.0000.0000.0000.000
185A184ASP-1-0.789-0.86432.2650.1970.1970.0000.0000.0000.000
186A185LEU0-0.011-0.00629.883-0.010-0.0100.0000.0000.0000.000
187A186GLY0-0.0090.00532.652-0.011-0.0110.0000.0000.0000.000
188A187TRP0-0.069-0.03527.2180.0130.0130.0000.0000.0000.000
189A188MET0-0.0090.00126.601-0.009-0.0090.0000.0000.0000.000
190A189LEU0-0.0040.00025.1720.0070.0070.0000.0000.0000.000
191A190HIS0-0.011-0.01318.379-0.027-0.0270.0000.0000.0000.000
192A191ASP-1-0.738-0.85318.0270.1870.1870.0000.0000.0000.000
193A192ILE0-0.022-0.01820.580-0.007-0.0070.0000.0000.0000.000
194A193ASP-1-0.812-0.87319.0500.0440.0440.0000.0000.0000.000
195A194PHE00.036-0.00114.954-0.016-0.0160.0000.0000.0000.000
196A195ALA0-0.062-0.02217.048-0.051-0.0510.0000.0000.0000.000
197A196ASP-1-0.804-0.87018.655-0.023-0.0230.0000.0000.0000.000
198A197GLY0-0.0130.00021.108-0.006-0.0060.0000.0000.0000.000
199A198MET0-0.093-0.05822.2490.0070.0070.0000.0000.0000.000
200A199THR0-0.050-0.06024.1910.0170.0170.0000.0000.0000.000
201A200PRO0-0.045-0.01423.7740.0090.0090.0000.0000.0000.000
202A201ARG10.8720.91719.954-0.117-0.1170.0000.0000.0000.000
203A202PHE00.0190.00124.2730.0020.0020.0000.0000.0000.000
204A203PHE00.0500.01123.6440.0080.0080.0000.0000.0000.000
205A204ARG10.8350.89225.788-0.191-0.1910.0000.0000.0000.000
206A205ALA00.0060.02026.8010.0210.0210.0000.0000.0000.000
207A206ARG10.8620.90526.585-0.320-0.3200.0000.0000.0000.000
208A207MET0-0.0380.01027.3520.0210.0210.0000.0000.0000.000
209A208VAL0-0.006-0.00928.235-0.014-0.0140.0000.0000.0000.000
210A209ASP-1-0.830-0.89928.7870.2700.2700.0000.0000.0000.000
211A210GLY00.0320.00729.8940.0090.0090.0000.0000.0000.000
212A211LEU00.0090.01922.4290.0030.0030.0000.0000.0000.000
213A212VAL0-0.024-0.01424.558-0.014-0.0140.0000.0000.0000.000
214A213ALA00.0120.00321.3640.0270.0270.0000.0000.0000.000
215A214VAL0-0.019-0.01918.353-0.053-0.0530.0000.0000.0000.000
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