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: 8N9ZY

Calculation Name: 3DV8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DV8

Chain ID: A

ChEMBL ID:

UniProt ID: A5ZWV4

Base Structure: X-ray

Registration Date: 2023-09-27

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2587650.007813
FMO2-HF: Nuclear repulsion 2499004.309227
FMO2-HF: Total energy -88645.698586
FMO2-MP2: Total energy -88899.745217


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:4:GLU)


Summations of interaction energy for fragment #1(A:4:GLU)
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.
-9.926-0.603000000000016.921-6.391-9.8560.058
Interaction energy analysis for fragmet #1(A:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.910 / q_NPA : -0.962
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].
3A6TYR00.0320.0033.293-6.968-4.1060.052-1.372-1.5420.008
4A7PHE00.0390.0233.218-5.208-4.3000.056-0.263-0.7010.001
5A8PRO00.016-0.0024.7100.9320.961-0.001-0.008-0.0200.000
6A9LEU00.0270.0247.500-0.935-0.9350.0000.0000.0000.000
7A10TRP00.0350.0113.044-7.150-2.7681.410-1.545-4.2480.004
8A11ASN0-0.051-0.0495.5761.5941.5940.0000.0000.0000.000
9A12ASP-1-0.865-0.9188.35120.47720.4770.0000.0000.0000.000
10A13LEU0-0.077-0.0106.701-1.177-1.1770.0000.0000.0000.000
11A14ASN00.0220.01110.0921.5721.5720.0000.0000.0000.000
12A15THR00.046-0.0019.8782.3132.3130.0000.0000.0000.000
13A16ALA00.0110.0079.5872.3912.3910.0000.0000.0000.000
14A17GLN00.0250.00310.3391.3561.3560.0000.0000.0000.000
15A18LYS10.8630.9435.896-34.126-34.1260.0000.0000.0000.000
16A19LYS10.8120.8875.562-24.225-24.108-0.001-0.001-0.1150.000
17A20LEU00.0020.0167.5720.6740.6740.0000.0000.0000.000
18A21ILE00.0230.0055.603-1.385-1.3850.0000.0000.0000.000
19A22SER0-0.020-0.0151.886-20.882-20.6265.399-3.045-2.6100.045
20A23ASP-1-0.838-0.9004.67531.91331.946-0.001-0.016-0.0160.000
21A24ASN0-0.092-0.0587.921-5.233-5.2330.0000.0000.0000.000
22A25LEU0-0.0040.0173.676-3.016-2.7470.005-0.053-0.2210.000
23A26ILE0-0.0140.0108.209-1.014-1.0140.0000.0000.0000.000
24A27THR0-0.012-0.0189.0201.3771.3770.0000.0000.0000.000
25A28GLN00.001-0.00910.683-1.352-1.3520.0000.0000.0000.000
26A29HIS0-0.040-0.00813.133-0.494-0.4940.0000.0000.0000.000
27A30VAL00.001-0.00415.386-0.782-0.7820.0000.0000.0000.000
28A31LYS10.8860.93917.863-13.417-13.4170.0000.0000.0000.000
29A32LYS10.8950.94021.018-11.472-11.4720.0000.0000.0000.000
30A33GLY0-0.018-0.01122.712-0.400-0.4000.0000.0000.0000.000
31A34THR0-0.070-0.03421.294-0.387-0.3870.0000.0000.0000.000
32A35ILE00.0180.01222.1120.3880.3880.0000.0000.0000.000
33A36ILE0-0.040-0.03516.3880.1230.1230.0000.0000.0000.000
34A37HIS0-0.042-0.00919.5440.9480.9480.0000.0000.0000.000
35A38ASN0-0.005-0.00621.445-0.377-0.3770.0000.0000.0000.000
36A39GLY00.0410.01525.022-0.307-0.3070.0000.0000.0000.000
37A40ASN0-0.072-0.06524.9310.6410.6410.0000.0000.0000.000
38A41MET0-0.094-0.02626.799-0.147-0.1470.0000.0000.0000.000
39A42ASP-1-0.849-0.90521.53912.81212.8120.0000.0000.0000.000
40A43CYS0-0.062-0.04120.434-0.281-0.2810.0000.0000.0000.000
41A44THR00.0410.03216.4160.5110.5110.0000.0000.0000.000
42A45GLY00.0520.01014.1960.6150.6150.0000.0000.0000.000
43A46LEU0-0.0390.01611.347-0.801-0.8010.0000.0000.0000.000
44A47LEU0-0.013-0.00210.8221.3241.3240.0000.0000.0000.000
45A48LEU0-0.0170.0034.344-0.291-0.1570.001-0.039-0.0970.000
46A49VAL00.0250.0088.5240.8210.8210.0000.0000.0000.000
47A50LYS10.8300.9247.079-24.725-24.7250.0000.0000.0000.000
48A51SER0-0.070-0.0658.426-0.899-0.8990.0000.0000.0000.000
49A52GLY00.0210.00912.065-0.199-0.1990.0000.0000.0000.000
50A53GLN0-0.020-0.01615.390-0.002-0.0020.0000.0000.0000.000
51A54LEU0-0.0150.00014.606-0.311-0.3110.0000.0000.0000.000
52A55ARG10.7780.86318.715-10.687-10.6870.0000.0000.0000.000
53A56THR00.0060.00820.3530.1200.1200.0000.0000.0000.000
54A57TYR0-0.063-0.06322.759-0.413-0.4130.0000.0000.0000.000
55A58ILE00.0280.02626.5270.1710.1710.0000.0000.0000.000
56A59LEU00.0250.00529.426-0.153-0.1530.0000.0000.0000.000
57A60SER0-0.030-0.01032.3560.0060.0060.0000.0000.0000.000
58A61ASP-1-0.864-0.94535.9447.7017.7010.0000.0000.0000.000
59A62GLU-1-1.011-0.99837.9987.0877.0870.0000.0000.0000.000
60A63GLY0-0.035-0.02035.799-0.086-0.0860.0000.0000.0000.000
61A64ARG10.8240.92535.805-7.629-7.6290.0000.0000.0000.000
62A65GLU-1-0.758-0.86930.6919.7009.7000.0000.0000.0000.000
63A66ILE0-0.029-0.02731.117-0.279-0.2790.0000.0000.0000.000
64A67THR0-0.016-0.03325.2680.2050.2050.0000.0000.0000.000
65A68LEU0-0.050-0.01524.889-0.200-0.2000.0000.0000.0000.000
66A69TYR00.023-0.00519.013-0.053-0.0530.0000.0000.0000.000
67A70ARG10.6900.78720.768-11.389-11.3890.0000.0000.0000.000
68A71LEU0-0.054-0.00615.1630.1810.1810.0000.0000.0000.000
69A72PHE00.024-0.00515.710-0.465-0.4650.0000.0000.0000.000
70A73ASP-1-0.746-0.87211.78619.55219.5520.0000.0000.0000.000
71A74MET0-0.073-0.0478.879-0.253-0.2530.0000.0000.0000.000
72A75ASP-1-0.789-0.8549.94617.43017.4300.0000.0000.0000.000
73A76MET0-0.033-0.0058.7692.1682.1680.0000.0000.0000.000
74A77CYS0-0.040-0.01511.771-1.888-1.8880.0000.0000.0000.000
75A78LEU00.0460.01013.8090.7820.7820.0000.0000.0000.000
76A79LEU00.0370.00416.070-0.070-0.0700.0000.0000.0000.000
77A80SER00.0620.03515.275-0.674-0.6740.0000.0000.0000.000
78A81ALA0-0.030-0.00415.9410.0040.0040.0000.0000.0000.000
79A82SER00.041-0.02318.043-0.209-0.2090.0000.0000.0000.000
80A84ILE0-0.074-0.03417.085-0.434-0.4340.0000.0000.0000.000
81A85MET0-0.031-0.01419.396-0.039-0.0390.0000.0000.0000.000
82A86ARG10.9240.95623.520-11.700-11.7000.0000.0000.0000.000
83A87SER00.0190.00627.136-0.273-0.2730.0000.0000.0000.000
84A88ILE0-0.0210.01123.079-0.245-0.2450.0000.0000.0000.000
85A89GLN0-0.059-0.03726.548-0.209-0.2090.0000.0000.0000.000
86A90PHE00.0010.00525.000-0.348-0.3480.0000.0000.0000.000
87A91GLU-1-0.828-0.89726.64810.44110.4410.0000.0000.0000.000
88A92VAL0-0.025-0.01922.725-0.216-0.2160.0000.0000.0000.000
89A93THR00.0190.01024.5990.1860.1860.0000.0000.0000.000
90A94ILE0-0.036-0.02018.3970.0820.0820.0000.0000.0000.000
91A95GLU-1-0.782-0.86221.49311.21111.2110.0000.0000.0000.000
92A96ALA00.0120.01819.0260.2300.2300.0000.0000.0000.000
93A97GLU-1-0.729-0.84120.37411.14811.1480.0000.0000.0000.000
94A98LYS10.8000.89319.463-13.011-13.0110.0000.0000.0000.000
95A99ASP-1-0.819-0.89618.68513.64713.6470.0000.0000.0000.000
96A100THR0-0.022-0.02013.6480.1820.1820.0000.0000.0000.000
97A101ASP-1-0.829-0.87610.61620.84520.8450.0000.0000.0000.000
98A102LEU0-0.016-0.02410.1510.6900.6900.0000.0000.0000.000
99A103TRP00.0140.0074.4291.5801.9130.001-0.049-0.2860.000
100A104ILE00.0030.0018.175-1.219-1.2190.0000.0000.0000.000
101A105ILE0-0.0040.0076.8791.8831.8830.0000.0000.0000.000
102A106PRO00.0240.01010.083-1.789-1.7890.0000.0000.0000.000
103A107ALA00.0810.03313.8110.4480.4480.0000.0000.0000.000
104A108GLU-1-0.914-0.97016.25417.54317.5430.0000.0000.0000.000
105A109ILE00.0030.00611.514-0.339-0.3390.0000.0000.0000.000
106A110TYR0-0.014-0.02010.9110.6080.6080.0000.0000.0000.000
107A111LYS10.9400.96413.909-14.020-14.0200.0000.0000.0000.000
108A112GLY0-0.019-0.00817.082-0.706-0.7060.0000.0000.0000.000
109A113ILE00.007-0.00310.915-0.476-0.4760.0000.0000.0000.000
110A114MET0-0.042-0.01415.120-0.732-0.7320.0000.0000.0000.000
111A115LYS10.7810.88417.086-14.656-14.6560.0000.0000.0000.000
112A116ASP-1-0.829-0.90418.45414.02814.0280.0000.0000.0000.000
113A117SER0-0.0270.00114.414-0.475-0.4750.0000.0000.0000.000
114A118ALA00.0730.02917.496-0.002-0.0020.0000.0000.0000.000
115A119PRO00.0320.01514.319-0.127-0.1270.0000.0000.0000.000
116A120VAL00.0480.02511.7520.2530.2530.0000.0000.0000.000
117A121ALA0-0.0110.00914.181-0.062-0.0620.0000.0000.0000.000
118A122ASN0-0.004-0.02017.759-0.346-0.3460.0000.0000.0000.000
119A123TYR00.0300.00210.459-0.232-0.2320.0000.0000.0000.000
120A124THR00.004-0.01315.0380.2830.2830.0000.0000.0000.000
121A125ASN0-0.042-0.01716.354-0.389-0.3890.0000.0000.0000.000
122A126GLU-1-0.859-0.92616.60513.12613.1260.0000.0000.0000.000
123A127LEU0-0.0470.00413.243-0.248-0.2480.0000.0000.0000.000
124A128MET0-0.024-0.02716.908-0.625-0.6250.0000.0000.0000.000
125A129ALA00.0220.00920.329-0.546-0.5460.0000.0000.0000.000
126A130THR0-0.0090.01118.054-0.537-0.5370.0000.0000.0000.000
127A131ARG10.8380.92415.253-15.963-15.9630.0000.0000.0000.000
128A132PHE0-0.056-0.02721.555-0.572-0.5720.0000.0000.0000.000
129A133SER00.002-0.02923.853-0.587-0.5870.0000.0000.0000.000
130A134ASP-1-0.873-0.93821.06112.59012.5900.0000.0000.0000.000
131A135VAL00.008-0.01424.747-0.431-0.4310.0000.0000.0000.000
132A136MET0-0.047-0.01627.289-0.544-0.5440.0000.0000.0000.000
133A137TRP00.0570.03427.486-0.357-0.3570.0000.0000.0000.000
134A138LEU0-0.0120.00028.677-0.367-0.3670.0000.0000.0000.000
135A139ILE0-0.003-0.00430.584-0.342-0.3420.0000.0000.0000.000
136A140GLU-1-0.925-0.96632.6038.5878.5870.0000.0000.0000.000
137A141GLN0-0.049-0.00530.809-0.436-0.4360.0000.0000.0000.000
138A142ILE0-0.048-0.04033.045-0.262-0.2620.0000.0000.0000.000
139A143MET0-0.044-0.00636.330-0.283-0.2830.0000.0000.0000.000
140A144TRP0-0.0060.00137.221-0.320-0.3200.0000.0000.0000.000
141A145LYS10.8090.90636.100-7.958-7.9580.0000.0000.0000.000
142A146SER0-0.006-0.03239.2750.0370.0370.0000.0000.0000.000
143A147LEU00.033-0.00138.3800.1180.1180.0000.0000.0000.000
144A148ASP-1-0.729-0.84339.2777.1257.1250.0000.0000.0000.000
145A149LYS10.8710.92638.842-6.844-6.8440.0000.0000.0000.000
146A150ARG10.8800.93633.171-8.250-8.2500.0000.0000.0000.000
147A151VAL0-0.005-0.00134.6050.2330.2330.0000.0000.0000.000
148A152ALA0-0.021-0.01335.4330.1610.1610.0000.0000.0000.000
149A153SER00.0060.00231.5790.1180.1180.0000.0000.0000.000
150A154PHE00.0200.01928.5710.1000.1000.0000.0000.0000.000
151A155LEU0-0.036-0.02430.7690.1840.1840.0000.0000.0000.000
152A156LEU00.0030.01831.8920.0830.0830.0000.0000.0000.000
153A157GLU-1-0.872-0.90625.62511.00211.0020.0000.0000.0000.000
154A158GLU-1-0.780-0.89326.62510.91110.9110.0000.0000.0000.000
155A159THR0-0.092-0.05827.4960.1530.1530.0000.0000.0000.000
156A160SER0-0.054-0.02826.0500.0410.0410.0000.0000.0000.000
157A161ILE0-0.046-0.01122.0320.2900.2900.0000.0000.0000.000
158A162GLU-1-0.896-0.95123.24411.75211.7520.0000.0000.0000.000
159A163GLY0-0.0030.02025.752-0.003-0.0030.0000.0000.0000.000
160A164THR0-0.042-0.03126.915-0.384-0.3840.0000.0000.0000.000
161A165ASN0-0.003-0.00730.4270.1310.1310.0000.0000.0000.000
162A166GLU-1-0.846-0.90632.8687.8637.8630.0000.0000.0000.000
163A167LEU00.0610.03730.2930.2180.2180.0000.0000.0000.000
164A168LYS10.8620.91531.292-9.113-9.1130.0000.0000.0000.000
165A169ILE00.0610.03530.1210.1460.1460.0000.0000.0000.000
166A170THR0-0.037-0.02833.133-0.186-0.1860.0000.0000.0000.000
167A171HIS00.0580.02835.156-0.010-0.0100.0000.0000.0000.000
168A172GLU-1-0.810-0.91035.9387.7927.7920.0000.0000.0000.000
169A173THR00.0350.02730.2050.1380.1380.0000.0000.0000.000
170A174ILE00.0100.01332.0500.1280.1280.0000.0000.0000.000
171A175ALA0-0.073-0.04833.9490.0430.0430.0000.0000.0000.000
172A176ASN00.000-0.00131.747-0.294-0.2940.0000.0000.0000.000
173A177HIS00.0480.06926.0670.0830.0830.0000.0000.0000.000
174A178LEU0-0.025-0.01230.9420.0460.0460.0000.0000.0000.000
175A179GLY00.0810.06633.724-0.136-0.1360.0000.0000.0000.000
176A180SER0-0.081-0.04635.485-0.334-0.3340.0000.0000.0000.000
177A181HIS00.0830.03838.2430.1090.1090.0000.0000.0000.000
178A182ARG10.9390.95339.830-7.015-7.0150.0000.0000.0000.000
179A183GLU-1-0.845-0.90240.7756.4256.4250.0000.0000.0000.000
180A184VAL0-0.014-0.01542.421-0.124-0.1240.0000.0000.0000.000
181A185ILE00.0290.02837.811-0.071-0.0710.0000.0000.0000.000
182A186THR0-0.020-0.04640.958-0.046-0.0460.0000.0000.0000.000
183A187ARG10.8610.91843.179-6.375-6.3750.0000.0000.0000.000
184A188MET00.0060.02941.377-0.140-0.1400.0000.0000.0000.000
185A189LEU00.0230.01238.256-0.039-0.0390.0000.0000.0000.000
186A190ARG10.9310.95442.424-6.475-6.4750.0000.0000.0000.000
187A191TYR0-0.051-0.02445.512-0.065-0.0650.0000.0000.0000.000
188A192PHE00.0430.00539.098-0.057-0.0570.0000.0000.0000.000
189A193GLN0-0.0040.00744.3350.0640.0640.0000.0000.0000.000
190A194VAL0-0.056-0.02645.698-0.076-0.0760.0000.0000.0000.000
191A195GLU-1-0.853-0.90046.3876.0926.0920.0000.0000.0000.000
192A196GLY00.0090.00846.3770.0230.0230.0000.0000.0000.000
193A197LEU0-0.0140.00141.4570.0900.0900.0000.0000.0000.000
194A198VAL00.000-0.00739.0020.2050.2050.0000.0000.0000.000
195A199LYS10.9740.99140.979-7.307-7.3070.0000.0000.0000.000
196A200LEU0-0.030-0.01340.8830.1950.1950.0000.0000.0000.000
197A201SER0-0.038-0.02341.146-0.155-0.1550.0000.0000.0000.000
198A202ARG10.9650.95541.185-6.717-6.7170.0000.0000.0000.000
199A203GLY00.0190.02438.1330.0730.0730.0000.0000.0000.000
200A204LYS10.8110.90236.458-7.599-7.5990.0000.0000.0000.000
201A205ILE00.0230.02135.897-0.288-0.2880.0000.0000.0000.000
202A206THR0-0.049-0.02636.1120.1280.1280.0000.0000.0000.000
203A207ILE00.0430.01334.796-0.250-0.2500.0000.0000.0000.000
204A208LEU0-0.067-0.02437.7370.0340.0340.0000.0000.0000.000
205A209ASP-1-0.823-0.91740.8237.0397.0390.0000.0000.0000.000
206A210SER00.0660.01735.1670.0890.0890.0000.0000.0000.000
207A211LYS10.9670.99337.322-6.796-6.7960.0000.0000.0000.000
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209A213LEU00.0140.02136.877-0.056-0.0560.0000.0000.0000.000
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