Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 6Y96Z

Calculation Name: 3NI7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NI7

Chain ID: A

ChEMBL ID:

UniProt ID: Q82XH4

Base Structure: X-ray

Registration Date: 2023-09-24

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1955029.287008
FMO2-HF: Nuclear repulsion 1881649.01971
FMO2-HF: Total energy -73380.267299
FMO2-MP2: Total energy -73592.357799


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:6:ASP)


Summations of interaction energy for fragment #1(A:6:ASP)
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.
-16.502-8.571.746-4.181-5.4960.028
Interaction energy analysis for fragmet #1(A:6:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.871 / q_NPA : -0.957
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].
3A8MET00.0140.0093.785-6.797-4.984-0.011-0.789-1.0120.003
4A9ARG10.9420.9752.728-68.260-63.7031.682-2.741-3.4990.029
5A10ASP-1-0.809-0.9053.23937.08038.4210.077-0.643-0.775-0.004
6A11ALA00.0320.0225.110-5.093-5.029-0.001-0.003-0.0600.000
7A12ILE0-0.0110.0077.678-3.919-3.9190.0000.0000.0000.000
8A13VAL0-0.0040.0107.487-3.305-3.3050.0000.0000.0000.000
9A14ASP-1-0.787-0.8748.97823.75523.7550.0000.0000.0000.000
10A15THR00.0000.00311.151-2.748-2.7480.0000.0000.0000.000
11A16ALA0-0.037-0.03112.589-1.819-1.8190.0000.0000.0000.000
12A17VAL0-0.035-0.01513.401-1.809-1.8090.0000.0000.0000.000
13A18GLU-1-0.821-0.89015.12416.34316.3430.0000.0000.0000.000
14A19LEU00.0090.01016.962-1.013-1.0130.0000.0000.0000.000
15A20ALA00.0110.00218.271-0.928-0.9280.0000.0000.0000.000
16A21ALA0-0.056-0.02119.534-0.931-0.9310.0000.0000.0000.000
17A22HIS0-0.034-0.01920.417-0.519-0.5190.0000.0000.0000.000
18A23THR0-0.0120.00222.693-0.561-0.5610.0000.0000.0000.000
19A24SER0-0.026-0.02223.515-0.305-0.3050.0000.0000.0000.000
20A25TRP00.1340.06515.4730.2490.2490.0000.0000.0000.000
21A26GLU-1-0.881-0.92221.40012.30812.3080.0000.0000.0000.000
22A27ALA00.0640.03023.6940.1020.1020.0000.0000.0000.000
23A28VAL0-0.013-0.00317.2350.0490.0490.0000.0000.0000.000
24A29ARG10.7970.90719.744-12.866-12.8660.0000.0000.0000.000
25A30LEU00.0520.01114.0310.1720.1720.0000.0000.0000.000
26A31TYR00.0400.01716.8360.6250.6250.0000.0000.0000.000
27A32ASP-1-0.818-0.90919.40114.06314.0630.0000.0000.0000.000
28A33ILE0-0.026-0.00513.1030.0500.0500.0000.0000.0000.000
29A34ALA00.0150.00015.5280.5380.5380.0000.0000.0000.000
30A35ALA0-0.0090.00816.536-0.124-0.1240.0000.0000.0000.000
31A36ARG10.7350.82615.384-17.548-17.5480.0000.0000.0000.000
32A37LEU0-0.033-0.02611.4830.0480.0480.0000.0000.0000.000
33A38ALA0-0.057-0.01315.2140.3200.3200.0000.0000.0000.000
34A39VAL0-0.021-0.00212.7480.2510.2510.0000.0000.0000.000
35A40SER0-0.030-0.04515.987-0.793-0.7930.0000.0000.0000.000
36A41LEU00.005-0.01615.6701.1751.1750.0000.0000.0000.000
37A42ASP-1-0.916-0.96315.72517.21517.2150.0000.0000.0000.000
38A43GLU-1-0.825-0.89412.15421.88421.8840.0000.0000.0000.000
39A44ILE0-0.022-0.01611.3192.5772.5770.0000.0000.0000.000
40A45ARG10.8670.92011.006-16.383-16.3830.0000.0000.0000.000
41A46LEU0-0.060-0.00510.1940.1700.1700.0000.0000.0000.000
42A47TYR0-0.050-0.0144.7513.4163.573-0.001-0.005-0.1500.000
43A48PHE00.025-0.0066.9841.4231.4230.0000.0000.0000.000
44A49ARG10.8520.91610.814-21.602-21.6020.0000.0000.0000.000
45A50GLU-1-0.901-0.94113.89815.57215.5720.0000.0000.0000.000
46A51LYS10.8350.90214.179-13.824-13.8240.0000.0000.0000.000
47A52ASP-1-0.853-0.94215.09017.27117.2710.0000.0000.0000.000
48A53GLU-1-0.800-0.88811.11825.03725.0370.0000.0000.0000.000
49A54LEU0-0.009-0.00610.2812.0962.0960.0000.0000.0000.000
50A55ILE0-0.056-0.02811.8520.4000.4000.0000.0000.0000.000
51A56ASP-1-0.844-0.91211.55521.86621.8660.0000.0000.0000.000
52A57ALA00.0210.0117.5830.6550.6550.0000.0000.0000.000
53A58TRP0-0.039-0.0219.1171.0591.0590.0000.0000.0000.000
54A59PHE0-0.036-0.03711.406-1.180-1.1800.0000.0000.0000.000
55A60ASP-1-0.797-0.8749.16927.32027.3200.0000.0000.0000.000
56A61ARG10.7140.8386.296-30.494-30.4940.0000.0000.0000.000
57A62ALA0-0.009-0.0019.441-0.947-0.9470.0000.0000.0000.000
58A63ASP-1-0.825-0.90512.69519.68319.6830.0000.0000.0000.000
59A64SER0-0.047-0.0279.344-0.428-0.4280.0000.0000.0000.000
60A65ARG10.8400.89111.247-19.021-19.0210.0000.0000.0000.000
61A66MET0-0.0150.00613.249-1.493-1.4930.0000.0000.0000.000
62A67LEU00.0120.00511.727-0.923-0.9230.0000.0000.0000.000
63A68LYS10.8390.91110.542-23.456-23.4560.0000.0000.0000.000
64A69GLU-1-0.809-0.89014.36214.61214.6120.0000.0000.0000.000
65A70ALA0-0.016-0.00217.604-0.802-0.8020.0000.0000.0000.000
66A71GLU-1-0.879-0.93114.48719.18819.1880.0000.0000.0000.000
67A72SER0-0.053-0.01918.995-0.437-0.4370.0000.0000.0000.000
68A73ALA00.017-0.01820.158-0.395-0.3950.0000.0000.0000.000
69A74GLY00.0440.02823.303-0.367-0.3670.0000.0000.0000.000
70A75PHE0-0.007-0.00222.085-0.434-0.4340.0000.0000.0000.000
71A76LEU0-0.059-0.04223.679-0.310-0.3100.0000.0000.0000.000
72A77ASP-1-0.908-0.94726.38710.13310.1330.0000.0000.0000.000
73A78LEU0-0.080-0.02125.572-0.333-0.3330.0000.0000.0000.000
74A79VAL00.0200.00529.333-0.037-0.0370.0000.0000.0000.000
75A80ALA00.0430.01330.0300.2910.2910.0000.0000.0000.000
76A81SER00.0230.00129.6950.3280.3280.0000.0000.0000.000
77A82GLU-1-0.926-0.97329.42310.05410.0540.0000.0000.0000.000
78A83ARG10.8730.95426.065-10.589-10.5890.0000.0000.0000.000
79A84ILE00.0630.03225.0030.5000.5000.0000.0000.0000.000
80A85HIS0-0.078-0.05125.2860.3670.3670.0000.0000.0000.000
81A86HIS00.0000.00921.5510.4310.4310.0000.0000.0000.000
82A87LEU00.0210.00919.5240.5190.5190.0000.0000.0000.000
83A88ILE00.0320.01120.3870.5660.5660.0000.0000.0000.000
84A89MET0-0.033-0.02021.3670.1810.1810.0000.0000.0000.000
85A90ILE0-0.0050.01716.7590.3020.3020.0000.0000.0000.000
86A91TRP00.002-0.00916.3670.0980.0980.0000.0000.0000.000
87A92LEU0-0.006-0.02817.5010.3820.3820.0000.0000.0000.000
88A93ASP-1-0.790-0.86419.23713.33413.3340.0000.0000.0000.000
89A94ALA0-0.019-0.00113.7730.3270.3270.0000.0000.0000.000
90A95LEU0-0.002-0.00515.0650.3040.3040.0000.0000.0000.000
91A96ALA0-0.086-0.03516.758-0.243-0.2430.0000.0000.0000.000
92A97VAL0-0.0040.01414.451-0.606-0.6060.0000.0000.0000.000
93A98GLN0-0.009-0.01716.902-1.044-1.0440.0000.0000.0000.000
94A99ARG10.8540.93018.611-11.429-11.4290.0000.0000.0000.000
95A100LYS10.8490.93221.350-12.902-12.9020.0000.0000.0000.000
96A101VAL00.0230.01217.540-0.343-0.3430.0000.0000.0000.000
97A102THR00.0560.02618.0600.2550.2550.0000.0000.0000.000
98A103ARG10.8370.89919.440-11.509-11.5090.0000.0000.0000.000
99A104GLN00.0050.00322.2840.0520.0520.0000.0000.0000.000
100A105MET00.0050.00314.772-0.237-0.2370.0000.0000.0000.000
101A106ILE0-0.034-0.01220.2190.1430.1430.0000.0000.0000.000
102A107MET0-0.067-0.04822.813-0.562-0.5620.0000.0000.0000.000
103A108SER00.0110.02422.458-0.292-0.2920.0000.0000.0000.000
104A109LYS10.9010.98018.403-16.564-16.5640.0000.0000.0000.000
105A110LEU0-0.005-0.01324.496-0.087-0.0870.0000.0000.0000.000
106A111GLU-1-0.892-0.94028.1409.2149.2140.0000.0000.0000.000
107A112PHE0-0.0010.00329.554-0.021-0.0210.0000.0000.0000.000
108A113GLY0-0.003-0.00529.893-0.095-0.0950.0000.0000.0000.000
109A114HIS0-0.019-0.01123.7260.4160.4160.0000.0000.0000.000
110A115ILE00.0140.01025.6580.3770.3770.0000.0000.0000.000
111A116HIS00.011-0.00419.885-0.354-0.3540.0000.0000.0000.000
112A117ILE00.0470.01119.6480.3590.3590.0000.0000.0000.000
113A118GLN0-0.026-0.02821.7540.1060.1060.0000.0000.0000.000
114A119ILE0-0.0140.00623.7020.0340.0340.0000.0000.0000.000
115A120PRO0-0.0030.00318.656-0.012-0.0120.0000.0000.0000.000
116A121ALA00.0110.00320.1520.4360.4360.0000.0000.0000.000
117A122VAL00.0160.02621.1530.0890.0890.0000.0000.0000.000
118A123MET00.0240.00420.987-0.347-0.3470.0000.0000.0000.000
119A124ARG10.7550.85012.282-22.884-22.8840.0000.0000.0000.000
120A125VAL0-0.0020.00919.5910.0630.0630.0000.0000.0000.000
121A126SER00.0080.01422.462-0.330-0.3300.0000.0000.0000.000
122A127ARG11.0031.00916.366-18.710-18.7100.0000.0000.0000.000
123A128THR00.000-0.02218.9260.2810.2810.0000.0000.0000.000
124A129VAL0-0.016-0.01520.637-0.252-0.2520.0000.0000.0000.000
125A130GLN0-0.078-0.06423.7730.0460.0460.0000.0000.0000.000
126A131TRP00.0080.00617.558-0.103-0.1030.0000.0000.0000.000
127A132VAL00.019-0.00521.307-0.159-0.1590.0000.0000.0000.000
128A133ARG10.8190.90722.942-10.762-10.7620.0000.0000.0000.000
129A134GLU-1-0.936-0.97123.86212.46712.4670.0000.0000.0000.000
130A135ALA0-0.036-0.00521.283-0.210-0.2100.0000.0000.0000.000
131A136ALA0-0.020-0.01123.240-0.073-0.0730.0000.0000.0000.000
132A137GLN0-0.032-0.00526.403-0.831-0.8310.0000.0000.0000.000
133A138ARG10.8590.94222.231-12.690-12.6900.0000.0000.0000.000
134A146ALA00.0390.01932.5660.0640.0640.0000.0000.0000.000
135A147LEU0-0.012-0.02131.885-0.194-0.1940.0000.0000.0000.000
136A148GLU-1-0.858-0.91433.3639.1329.1320.0000.0000.0000.000
137A149GLU-1-0.805-0.89329.56411.19311.1930.0000.0000.0000.000
138A150SER00.0520.03331.0000.3080.3080.0000.0000.0000.000
139A151THR00.0210.03932.9300.0670.0670.0000.0000.0000.000
140A152LEU00.0600.02027.3870.0680.0680.0000.0000.0000.000
141A153THR00.009-0.00827.7580.4370.4370.0000.0000.0000.000
142A154THR0-0.058-0.04528.9660.1800.1800.0000.0000.0000.000
143A155ILE0-0.016-0.01729.6000.0020.0020.0000.0000.0000.000
144A156TYR0-0.0240.00720.366-0.080-0.0800.0000.0000.0000.000
145A157LEU00.0270.00125.7800.2210.2210.0000.0000.0000.000
146A158MET0-0.006-0.00327.638-0.003-0.0030.0000.0000.0000.000
147A159THR0-0.021-0.02326.861-0.194-0.1940.0000.0000.0000.000
148A160PHE00.0210.02420.6950.0590.0590.0000.0000.0000.000
149A161PHE00.040-0.01125.5840.1150.1150.0000.0000.0000.000
150A162PHE0-0.050-0.01827.837-0.177-0.1770.0000.0000.0000.000
151A163TRP00.0630.01120.192-0.149-0.1490.0000.0000.0000.000
152A164MET0-0.0450.00023.392-0.028-0.0280.0000.0000.0000.000
153A165ARG10.8890.94625.977-9.965-9.9650.0000.0000.0000.000
154A166ASP-1-0.726-0.79828.1849.7819.7810.0000.0000.0000.000
155A167GLU-1-0.819-0.89828.25611.06811.0680.0000.0000.0000.000
156A168SER0-0.056-0.03130.221-0.066-0.0660.0000.0000.0000.000
157A169GLU-1-0.761-0.86628.7979.7359.7350.0000.0000.0000.000
158A170ASN0-0.044-0.03524.643-0.371-0.3710.0000.0000.0000.000
159A171SER00.0390.03125.7080.4010.4010.0000.0000.0000.000
160A172ARG10.8910.91827.593-9.554-9.5540.0000.0000.0000.000
161A173HIS0-0.036-0.01230.612-0.326-0.3260.0000.0000.0000.000
162A174THR0-0.006-0.03326.191-0.115-0.1150.0000.0000.0000.000
163A175ARG10.7810.87423.271-12.223-12.2230.0000.0000.0000.000
164A176GLN00.0360.02129.288-0.301-0.3010.0000.0000.0000.000
165A177PHE00.0140.00431.011-0.214-0.2140.0000.0000.0000.000
166A178LEU00.0350.01726.498-0.195-0.1950.0000.0000.0000.000
167A179LYS10.9480.97930.247-10.067-10.0670.0000.0000.0000.000
168A180ARG10.9190.96232.584-8.263-8.2630.0000.0000.0000.000
169A181HIS0-0.015-0.00333.304-0.346-0.3460.0000.0000.0000.000
170A182LEU0-0.021-0.00828.755-0.107-0.1070.0000.0000.0000.000
171A183THR0-0.027-0.02233.483-0.078-0.0780.0000.0000.0000.000
172A184MET0-0.049-0.03436.465-0.235-0.2350.0000.0000.0000.000
173A185ALA00.0160.01135.619-0.175-0.1750.0000.0000.0000.000
174A186ALA0-0.0080.02935.768-0.095-0.0950.0000.0000.0000.000
175A187TRP0-0.067-0.03337.609-0.165-0.1650.0000.0000.0000.000
176A188LEU0-0.049-0.03139.790-0.230-0.2300.0000.0000.0000.000