FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 2N62R

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 OptH
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
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1955200.842761
FMO2-HF: Nuclear repulsion 1881822.256291
FMO2-HF: Total energy -73378.58647
FMO2-MP2: Total energy -73590.800361


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.
-7.6020.600999999999981.088-4.067-5.2220.017
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 : -0.880 / q_NPA : -0.958
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].
3A8MET00.0110.0053.831-6.152-4.379-0.010-0.766-0.9970.003
4A9ARG10.9690.9852.673-65.681-61.3920.848-2.286-2.8510.024
5A10ASP-1-0.878-0.9612.97842.54144.6110.251-1.011-1.309-0.010
6A11ALA00.0660.0324.976-4.424-4.353-0.001-0.004-0.0650.000
7A12ILE0-0.0270.0217.592-3.478-3.4780.0000.0000.0000.000
8A13VAL0-0.0020.0027.375-2.971-2.9710.0000.0000.0000.000
9A14ASP-1-0.813-0.8949.00523.92223.9220.0000.0000.0000.000
10A15THR0-0.021-0.01211.026-2.674-2.6740.0000.0000.0000.000
11A16ALA0-0.033-0.03512.442-1.747-1.7470.0000.0000.0000.000
12A17VAL0-0.026-0.01113.134-1.750-1.7500.0000.0000.0000.000
13A18GLU-1-0.923-0.97614.39316.74616.7460.0000.0000.0000.000
14A19LEU0-0.014-0.00416.904-1.012-1.0120.0000.0000.0000.000
15A20ALA00.0220.01318.138-0.896-0.8960.0000.0000.0000.000
16A21ALA0-0.058-0.02219.410-0.895-0.8950.0000.0000.0000.000
17A22HIS0-0.027-0.01920.687-0.412-0.4120.0000.0000.0000.000
18A23THR0-0.0140.00722.483-0.537-0.5370.0000.0000.0000.000
19A24SER0-0.009-0.02723.365-0.322-0.3220.0000.0000.0000.000
20A25TRP00.1320.06715.5680.1920.1920.0000.0000.0000.000
21A26GLU-1-0.943-0.95221.27611.66211.6620.0000.0000.0000.000
22A27ALA00.0570.03123.8190.1000.1000.0000.0000.0000.000
23A28VAL0-0.0010.00517.1710.0380.0380.0000.0000.0000.000
24A29ARG10.8220.89920.186-12.956-12.9560.0000.0000.0000.000
25A30LEU00.0810.02514.6500.0770.0770.0000.0000.0000.000
26A31TYR00.0270.01017.2370.5880.5880.0000.0000.0000.000
27A32ASP-1-0.832-0.91219.53813.61813.6180.0000.0000.0000.000
28A33ILE0-0.052-0.01213.1810.0090.0090.0000.0000.0000.000
29A34ALA00.0270.00415.5360.5100.5100.0000.0000.0000.000
30A35ALA0-0.0100.00516.539-0.117-0.1170.0000.0000.0000.000
31A36ARG10.8460.91215.881-16.677-16.6770.0000.0000.0000.000
32A37LEU0-0.036-0.02511.7680.0150.0150.0000.0000.0000.000
33A38ALA0-0.060-0.00515.2540.2680.2680.0000.0000.0000.000
34A39VAL0-0.0040.00512.8520.1560.1560.0000.0000.0000.000
35A40SER00.0040.00116.021-0.617-0.6170.0000.0000.0000.000
36A41LEU00.020-0.00815.6821.0271.0270.0000.0000.0000.000
37A42ASP-1-0.917-0.96616.09416.72016.7200.0000.0000.0000.000
38A43GLU-1-0.893-0.96312.29022.53922.5390.0000.0000.0000.000
39A44ILE0-0.021-0.00811.5162.2332.2330.0000.0000.0000.000
40A45ARG10.8800.92811.524-15.990-15.9900.0000.0000.0000.000
41A46LEU0-0.054-0.00710.4320.0520.0520.0000.0000.0000.000
42A47TYR0-0.050-0.0114.8720.6090.6090.0000.0000.0000.000
43A48PHE00.025-0.0087.0601.3021.3020.0000.0000.0000.000
44A49ARG10.9340.96711.199-20.917-20.9170.0000.0000.0000.000
45A50GLU-1-0.943-0.97714.21015.09815.0980.0000.0000.0000.000
46A51LYS10.8280.90614.470-13.582-13.5820.0000.0000.0000.000
47A52ASP-1-0.849-0.92815.31417.05017.0500.0000.0000.0000.000
48A53GLU-1-0.848-0.92111.22925.08025.0800.0000.0000.0000.000
49A54LEU0-0.013-0.00810.6332.0542.0540.0000.0000.0000.000
50A55ILE0-0.051-0.02611.8750.4390.4390.0000.0000.0000.000
51A56ASP-1-0.862-0.93411.06922.74522.7450.0000.0000.0000.000
52A57ALA0-0.003-0.0077.5800.7760.7760.0000.0000.0000.000
53A58TRP0-0.056-0.0229.0701.3381.3380.0000.0000.0000.000
54A59PHE0-0.050-0.04711.341-1.086-1.0860.0000.0000.0000.000
55A60ASP-1-0.799-0.8908.91328.46928.4690.0000.0000.0000.000
56A61ARG10.7830.9125.843-30.685-30.6850.0000.0000.0000.000
57A62ALA0-0.009-0.0109.439-0.852-0.8520.0000.0000.0000.000
58A63ASP-1-0.816-0.89712.64520.50720.5070.0000.0000.0000.000
59A64SER0-0.029-0.0079.336-0.788-0.7880.0000.0000.0000.000
60A65ARG10.9110.96111.170-20.296-20.2960.0000.0000.0000.000
61A66MET0-0.006-0.00313.053-1.507-1.5070.0000.0000.0000.000
62A67LEU00.0070.00311.390-0.980-0.9800.0000.0000.0000.000
63A68LYS10.8340.90810.463-24.632-24.6320.0000.0000.0000.000
64A69GLU-1-0.910-0.95914.26114.43514.4350.0000.0000.0000.000
65A70ALA0-0.012-0.00617.534-0.810-0.8100.0000.0000.0000.000
66A71GLU-1-0.877-0.92814.31120.22820.2280.0000.0000.0000.000
67A72SER0-0.044-0.01418.855-0.455-0.4550.0000.0000.0000.000
68A73ALA00.012-0.02020.060-0.425-0.4250.0000.0000.0000.000
69A74GLY00.0390.02223.161-0.409-0.4090.0000.0000.0000.000
70A75PHE00.0200.01221.961-0.474-0.4740.0000.0000.0000.000
71A76LEU0-0.060-0.05123.686-0.345-0.3450.0000.0000.0000.000
72A77ASP-1-0.909-0.94326.32910.14110.1410.0000.0000.0000.000
73A78LEU0-0.065-0.01525.390-0.362-0.3620.0000.0000.0000.000
74A79VAL00.0300.02029.210-0.029-0.0290.0000.0000.0000.000
75A80ALA00.0430.01429.9420.2970.2970.0000.0000.0000.000
76A81SER00.0190.00429.6210.3620.3620.0000.0000.0000.000
77A82GLU-1-0.963-1.00429.25010.11510.1150.0000.0000.0000.000
78A83ARG10.8720.95525.974-10.925-10.9250.0000.0000.0000.000
79A84ILE00.0650.03524.8880.5150.5150.0000.0000.0000.000
80A85HIS0-0.093-0.06325.1800.4070.4070.0000.0000.0000.000
81A86HIS00.0210.01821.3710.4170.4170.0000.0000.0000.000
82A87LEU00.0220.01119.5720.5270.5270.0000.0000.0000.000
83A88ILE00.0210.00820.3430.5860.5860.0000.0000.0000.000
84A89MET0-0.042-0.02521.3830.1580.1580.0000.0000.0000.000
85A90ILE0-0.0090.01816.5550.3030.3030.0000.0000.0000.000
86A91TRP0-0.020-0.02816.1200.0360.0360.0000.0000.0000.000
87A92LEU00.014-0.02817.4940.3690.3690.0000.0000.0000.000
88A93ASP-1-0.880-0.93919.23413.65513.6550.0000.0000.0000.000
89A94ALA0-0.035-0.01413.8410.3550.3550.0000.0000.0000.000
90A95LEU0-0.016-0.01115.0070.2880.2880.0000.0000.0000.000
91A96ALA0-0.076-0.03316.718-0.276-0.2760.0000.0000.0000.000
92A97VAL0-0.0170.00814.540-0.617-0.6170.0000.0000.0000.000
93A98GLN00.005-0.00216.584-1.146-1.1460.0000.0000.0000.000
94A99ARG10.8790.95718.530-11.537-11.5370.0000.0000.0000.000
95A100LYS10.8430.92521.279-12.815-12.8150.0000.0000.0000.000
96A101VAL00.0260.01817.188-0.365-0.3650.0000.0000.0000.000
97A102THR00.0710.03817.9390.2720.2720.0000.0000.0000.000
98A103ARG10.8980.94619.361-11.647-11.6470.0000.0000.0000.000
99A104GLN0-0.002-0.00722.0880.1290.1290.0000.0000.0000.000
100A105MET00.0100.01014.590-0.252-0.2520.0000.0000.0000.000
101A106ILE0-0.031-0.01320.2840.1700.1700.0000.0000.0000.000
102A107MET0-0.068-0.05222.740-0.507-0.5070.0000.0000.0000.000
103A108SER00.0160.02422.601-0.299-0.2990.0000.0000.0000.000
104A109LYS10.8840.97018.798-16.228-16.2280.0000.0000.0000.000
105A110LEU0-0.0050.02124.5450.0120.0120.0000.0000.0000.000
106A111GLU-1-0.888-0.96628.1729.1819.1810.0000.0000.0000.000
107A112PHE0-0.014-0.01029.815-0.010-0.0100.0000.0000.0000.000
108A113GLY0-0.001-0.00129.988-0.114-0.1140.0000.0000.0000.000
109A114HIS0-0.015-0.01024.0960.3800.3800.0000.0000.0000.000
110A115ILE00.0010.00225.6690.3830.3830.0000.0000.0000.000
111A116HIS00.0450.01119.781-0.374-0.3740.0000.0000.0000.000
112A117ILE00.0780.02419.9080.3420.3420.0000.0000.0000.000
113A118GLN0-0.035-0.02821.6830.1470.1470.0000.0000.0000.000
114A119ILE0-0.0350.00123.1010.0570.0570.0000.0000.0000.000
115A120PRO0-0.0090.00818.6890.0390.0390.0000.0000.0000.000
116A121ALA00.010-0.00419.9670.5010.5010.0000.0000.0000.000
117A122VAL00.0090.02220.9720.1260.1260.0000.0000.0000.000
118A123MET00.0250.00220.757-0.334-0.3340.0000.0000.0000.000
119A124ARG10.8390.91912.253-22.654-22.6540.0000.0000.0000.000
120A125VAL00.0010.03219.2850.1180.1180.0000.0000.0000.000
121A126SER00.0210.02222.147-0.307-0.3070.0000.0000.0000.000
122A127ARG10.9921.00816.117-19.145-19.1450.0000.0000.0000.000
123A128THR0-0.008-0.04918.8200.3270.3270.0000.0000.0000.000
124A129VAL0-0.004-0.00720.302-0.225-0.2250.0000.0000.0000.000
125A130GLN0-0.069-0.05823.4440.0280.0280.0000.0000.0000.000
126A131TRP0-0.0030.01117.057-0.220-0.2200.0000.0000.0000.000
127A132VAL00.019-0.01021.196-0.141-0.1410.0000.0000.0000.000
128A133ARG10.8610.92022.672-10.919-10.9190.0000.0000.0000.000
129A134GLU-1-0.931-0.97223.58212.69412.6940.0000.0000.0000.000
130A135ALA0-0.033-0.00321.074-0.206-0.2060.0000.0000.0000.000
131A136ALA0-0.023-0.00922.925-0.069-0.0690.0000.0000.0000.000
132A137GLN0-0.029-0.00326.175-0.846-0.8460.0000.0000.0000.000
133A138ARG10.8600.94322.175-12.993-12.9930.0000.0000.0000.000
134A146ALA00.0460.02432.2230.0700.0700.0000.0000.0000.000
135A147LEU0-0.005-0.01631.080-0.197-0.1970.0000.0000.0000.000
136A148GLU-1-0.881-0.91732.9369.1169.1160.0000.0000.0000.000
137A149GLU-1-0.860-0.94028.99411.20511.2050.0000.0000.0000.000
138A150SER00.0680.03330.7470.3120.3120.0000.0000.0000.000
139A151THR00.0010.03132.8450.0480.0480.0000.0000.0000.000
140A152LEU00.0580.01727.3120.0620.0620.0000.0000.0000.000
141A153THR00.0180.00827.5870.4520.4520.0000.0000.0000.000
142A154THR0-0.051-0.04128.9760.1730.1730.0000.0000.0000.000
143A155ILE0-0.019-0.01429.659-0.006-0.0060.0000.0000.0000.000
144A156TYR0-0.0070.01420.228-0.093-0.0930.0000.0000.0000.000
145A157LEU00.0350.01225.7890.2200.2200.0000.0000.0000.000
146A158MET0-0.012-0.01127.630-0.007-0.0070.0000.0000.0000.000
147A159THR0-0.015-0.03226.912-0.217-0.2170.0000.0000.0000.000
148A160PHE0-0.0050.02120.8700.0310.0310.0000.0000.0000.000
149A161PHE00.041-0.01225.5620.0870.0870.0000.0000.0000.000
150A162PHE0-0.057-0.01827.799-0.181-0.1810.0000.0000.0000.000
151A163TRP00.0650.01420.244-0.164-0.1640.0000.0000.0000.000
152A164MET0-0.051-0.00523.575-0.034-0.0340.0000.0000.0000.000
153A165ARG10.8790.93025.920-9.874-9.8740.0000.0000.0000.000
154A166ASP-1-0.749-0.84528.1929.8149.8140.0000.0000.0000.000
155A167GLU-1-0.882-0.95528.20610.91210.9120.0000.0000.0000.000
156A168SER0-0.073-0.02830.162-0.081-0.0810.0000.0000.0000.000
157A169GLU-1-0.732-0.85328.7669.7799.7790.0000.0000.0000.000
158A170ASN0-0.069-0.04624.537-0.385-0.3850.0000.0000.0000.000
159A171SER00.0480.02625.4280.4020.4020.0000.0000.0000.000
160A172ARG10.8770.91227.567-9.602-9.6020.0000.0000.0000.000
161A173HIS0-0.032-0.00930.597-0.300-0.3000.0000.0000.0000.000
162A174THR00.0180.00226.253-0.125-0.1250.0000.0000.0000.000
163A175ARG10.9180.97924.104-11.952-11.9520.0000.0000.0000.000
164A176GLN00.009-0.01129.291-0.307-0.3070.0000.0000.0000.000
165A177PHE00.0070.00630.768-0.214-0.2140.0000.0000.0000.000
166A178LEU00.0440.03026.509-0.196-0.1960.0000.0000.0000.000
167A179LYS10.9670.99330.560-10.056-10.0560.0000.0000.0000.000
168A180ARG10.9521.01532.608-8.404-8.4040.0000.0000.0000.000
169A181HIS0-0.017-0.00833.353-0.316-0.3160.0000.0000.0000.000
170A182LEU0-0.024-0.00828.802-0.111-0.1110.0000.0000.0000.000
171A183THR0-0.038-0.06233.516-0.049-0.0490.0000.0000.0000.000
172A184MET0-0.054-0.03436.409-0.233-0.2330.0000.0000.0000.000
173A185ALA0-0.006-0.00535.675-0.176-0.1760.0000.0000.0000.000
174A186ALA0-0.0200.00435.773-0.066-0.0660.0000.0000.0000.000
175A187TRP0-0.070-0.03737.536-0.191-0.1910.0000.0000.0000.000
176A188LEU0-0.0050.01940.249-0.215-0.2150.0000.0000.0000.000