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: ZV3YN

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1961708.670604
FMO2-HF: Nuclear repulsion 1888327.533735
FMO2-HF: Total energy -73381.13687
FMO2-MP2: Total energy -73593.10075


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.
-18.911-11.5973.859-4.6-6.5720.038
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 : -0.854 / q_NPA : -0.947
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].
3A8MET00.0120.0113.727-6.809-5.165-0.005-0.725-0.9130.003
4A9ARG10.9030.9592.398-72.187-67.9273.817-3.368-4.7080.037
5A10ASP-1-0.817-0.9043.40436.07437.1560.049-0.467-0.664-0.002
6A11ALA00.0440.0215.095-4.555-4.490-0.001-0.004-0.0600.000
7A12ILE0-0.016-0.0017.463-3.848-3.8480.0000.0000.0000.000
8A13VAL00.0010.0047.192-3.244-3.2440.0000.0000.0000.000
9A14ASP-1-0.790-0.8679.09623.16323.1630.0000.0000.0000.000
10A15THR00.0030.00211.140-2.695-2.6950.0000.0000.0000.000
11A16ALA0-0.026-0.01212.353-1.729-1.7290.0000.0000.0000.000
12A17VAL0-0.016-0.01113.281-1.743-1.7430.0000.0000.0000.000
13A18GLU-1-0.811-0.89315.02116.03816.0380.0000.0000.0000.000
14A19LEU00.0140.01516.655-1.095-1.0950.0000.0000.0000.000
15A20ALA0-0.0030.01517.985-0.925-0.9250.0000.0000.0000.000
16A21ALA0-0.041-0.01619.152-0.868-0.8680.0000.0000.0000.000
17A22HIS0-0.039-0.02819.930-0.633-0.6330.0000.0000.0000.000
18A23THR00.0010.00222.398-0.568-0.5680.0000.0000.0000.000
19A24SER0-0.047-0.02923.324-0.193-0.1930.0000.0000.0000.000
20A25TRP00.0980.03415.0850.2900.2900.0000.0000.0000.000
21A26GLU-1-0.870-0.91520.71712.65612.6560.0000.0000.0000.000
22A27ALA00.0340.01022.8500.2810.2810.0000.0000.0000.000
23A28VAL00.0120.03116.708-0.018-0.0180.0000.0000.0000.000
24A29ARG10.7910.89519.316-12.873-12.8730.0000.0000.0000.000
25A30LEU00.029-0.00413.5670.1390.1390.0000.0000.0000.000
26A31TYR00.0420.01416.2920.7390.7390.0000.0000.0000.000
27A32ASP-1-0.830-0.90418.99914.23614.2360.0000.0000.0000.000
28A33ILE0-0.012-0.01612.657-0.046-0.0460.0000.0000.0000.000
29A34ALA0-0.0110.00015.1950.5510.5510.0000.0000.0000.000
30A35ALA00.0130.00916.202-0.088-0.0880.0000.0000.0000.000
31A36ARG10.7650.85915.006-17.881-17.8810.0000.0000.0000.000
32A37LEU0-0.038-0.02611.1150.0600.0600.0000.0000.0000.000
33A38ALA0-0.044-0.00915.0530.3080.3080.0000.0000.0000.000
34A39VAL0-0.0180.00712.7020.0160.0160.0000.0000.0000.000
35A40SER0-0.028-0.05615.920-0.728-0.7280.0000.0000.0000.000
36A41LEU00.002-0.02515.4961.1061.1060.0000.0000.0000.000
37A42ASP-1-0.907-0.96315.05218.13118.1310.0000.0000.0000.000
38A43GLU-1-0.801-0.87211.97622.03422.0340.0000.0000.0000.000
39A44ILE0-0.0040.00210.8223.0263.0260.0000.0000.0000.000
40A45ARG10.8300.90810.482-16.608-16.6080.0000.0000.0000.000
41A46LEU0-0.0380.0039.671-0.084-0.0840.0000.0000.0000.000
42A47TYR0-0.044-0.0124.3094.0164.279-0.001-0.036-0.2270.000
43A48PHE0-0.005-0.0156.6061.9961.9960.0000.0000.0000.000
44A49ARG10.8330.90410.338-22.912-22.9120.0000.0000.0000.000
45A50GLU-1-0.877-0.93513.36415.78415.7840.0000.0000.0000.000
46A51LYS10.8290.90113.712-14.188-14.1880.0000.0000.0000.000
47A52ASP-1-0.833-0.94314.73717.61717.6170.0000.0000.0000.000
48A53GLU-1-0.786-0.88110.42325.68925.6890.0000.0000.0000.000
49A54LEU0-0.013-0.0069.9902.4342.4340.0000.0000.0000.000
50A55ILE0-0.048-0.01711.3700.3700.3700.0000.0000.0000.000
51A56ASP-1-0.848-0.92312.13920.72120.7210.0000.0000.0000.000
52A57ALA00.0170.0187.2280.7720.7720.0000.0000.0000.000
53A58TRP0-0.023-0.0148.6731.2271.2270.0000.0000.0000.000
54A59PHE0-0.016-0.02010.905-1.233-1.2330.0000.0000.0000.000
55A60ASP-1-0.781-0.8628.84827.55527.5550.0000.0000.0000.000
56A61ARG10.7190.8286.609-29.630-29.6300.0000.0000.0000.000
57A62ALA00.0000.0129.253-1.100-1.1000.0000.0000.0000.000
58A63ASP-1-0.821-0.91312.58819.16519.1650.0000.0000.0000.000
59A64SER0-0.074-0.0408.944-0.561-0.5610.0000.0000.0000.000
60A65ARG10.8370.88410.848-18.861-18.8610.0000.0000.0000.000
61A66MET0-0.0110.00913.050-1.456-1.4560.0000.0000.0000.000
62A67LEU0-0.004-0.00511.829-0.965-0.9650.0000.0000.0000.000
63A68LYS10.7920.87111.374-22.569-22.5690.0000.0000.0000.000
64A69GLU-1-0.796-0.87114.58014.59814.5980.0000.0000.0000.000
65A70ALA00.0020.01617.978-0.786-0.7860.0000.0000.0000.000
66A71GLU-1-0.856-0.91115.05018.87918.8790.0000.0000.0000.000
67A72SER0-0.055-0.02619.143-0.577-0.5770.0000.0000.0000.000
68A73ALA00.033-0.00620.400-0.429-0.4290.0000.0000.0000.000
69A74GLY00.0410.02623.888-0.328-0.3280.0000.0000.0000.000
70A75PHE0-0.002-0.00322.434-0.340-0.3400.0000.0000.0000.000
71A76LEU0-0.038-0.03523.999-0.260-0.2600.0000.0000.0000.000
72A77ASP-1-0.909-0.94626.83310.03410.0340.0000.0000.0000.000
73A78LEU0-0.076-0.01125.735-0.301-0.3010.0000.0000.0000.000
74A79VAL00.0300.00829.604-0.014-0.0140.0000.0000.0000.000
75A80ALA00.0400.01129.6950.2960.2960.0000.0000.0000.000
76A81SER00.011-0.00429.3840.3350.3350.0000.0000.0000.000
77A82GLU-1-0.923-0.96729.2799.8599.8590.0000.0000.0000.000
78A83ARG10.8380.92825.818-10.408-10.4080.0000.0000.0000.000
79A84ILE00.0480.01524.7320.4800.4800.0000.0000.0000.000
80A85HIS0-0.078-0.05125.1920.3940.3940.0000.0000.0000.000
81A86HIS00.0040.00821.6230.4280.4280.0000.0000.0000.000
82A87LEU00.0220.01319.4960.4840.4840.0000.0000.0000.000
83A88ILE00.0420.01020.1370.6280.6280.0000.0000.0000.000
84A89MET0-0.029-0.01521.5570.1200.1200.0000.0000.0000.000
85A90ILE0-0.0040.00916.9190.2540.2540.0000.0000.0000.000
86A91TRP0-0.011-0.01816.3050.1440.1440.0000.0000.0000.000
87A92LEU0-0.002-0.02017.3840.4030.4030.0000.0000.0000.000
88A93ASP-1-0.801-0.86719.45213.21713.2170.0000.0000.0000.000
89A94ALA0-0.040-0.01613.7380.2130.2130.0000.0000.0000.000
90A95LEU00.0220.01614.8890.4890.4890.0000.0000.0000.000
91A96ALA0-0.080-0.03516.685-0.314-0.3140.0000.0000.0000.000
92A97VAL00.0100.00714.465-0.629-0.6290.0000.0000.0000.000
93A98GLN00.012-0.00116.594-0.743-0.7430.0000.0000.0000.000
94A99ARG10.8710.94618.410-11.507-11.5070.0000.0000.0000.000
95A100LYS10.7990.90621.170-13.060-13.0600.0000.0000.0000.000
96A101VAL00.0260.01617.280-0.353-0.3530.0000.0000.0000.000
97A102THR00.0650.02917.7890.3360.3360.0000.0000.0000.000
98A103ARG10.8120.88119.244-11.453-11.4530.0000.0000.0000.000
99A104GLN0-0.014-0.02021.9910.0290.0290.0000.0000.0000.000
100A105MET00.0030.01614.326-0.191-0.1910.0000.0000.0000.000
101A106ILE0-0.023-0.00220.002-0.048-0.0480.0000.0000.0000.000
102A107MET0-0.061-0.04022.448-0.613-0.6130.0000.0000.0000.000
103A108SER0-0.0060.00822.174-0.311-0.3110.0000.0000.0000.000
104A109LYS10.8970.96917.723-16.897-16.8970.0000.0000.0000.000
105A110LEU00.0070.00424.109-0.088-0.0880.0000.0000.0000.000
106A111GLU-1-0.931-0.97327.8039.3879.3870.0000.0000.0000.000
107A112PHE00.0560.04129.466-0.097-0.0970.0000.0000.0000.000
108A113GLY00.002-0.00229.5030.0840.0840.0000.0000.0000.000
109A114HIS00.0150.00222.7760.3400.3400.0000.0000.0000.000
110A115ILE00.0050.01324.6620.5850.5850.0000.0000.0000.000
111A116HIS00.004-0.00519.675-0.286-0.2860.0000.0000.0000.000
112A117ILE00.0220.00818.7910.5870.5870.0000.0000.0000.000
113A118GLN0-0.055-0.04321.0320.1210.1210.0000.0000.0000.000
114A119ILE00.0120.01323.1530.1040.1040.0000.0000.0000.000
115A120PRO00.0190.00918.146-0.022-0.0220.0000.0000.0000.000
116A121ALA00.0180.01219.6950.4700.4700.0000.0000.0000.000
117A122VAL00.0120.00820.682-0.049-0.0490.0000.0000.0000.000
118A123MET00.0030.01820.414-0.394-0.3940.0000.0000.0000.000
119A124ARG10.7480.83312.022-23.217-23.2170.0000.0000.0000.000
120A125VAL0-0.0040.01119.136-0.047-0.0470.0000.0000.0000.000
121A126SER0-0.016-0.01722.207-0.403-0.4030.0000.0000.0000.000
122A127ARG10.9750.98716.807-18.508-18.5080.0000.0000.0000.000
123A128THR0-0.019-0.02319.0750.2980.2980.0000.0000.0000.000
124A129VAL0-0.017-0.01520.511-0.254-0.2540.0000.0000.0000.000
125A130GLN0-0.046-0.03724.1120.1220.1220.0000.0000.0000.000
126A131TRP00.0320.01417.755-0.086-0.0860.0000.0000.0000.000
127A132VAL00.009-0.00321.164-0.179-0.1790.0000.0000.0000.000
128A133ARG10.7750.87823.037-10.600-10.6000.0000.0000.0000.000
129A134GLU-1-0.927-0.95623.67512.53712.5370.0000.0000.0000.000
130A135ALA00.0010.00821.094-0.255-0.2550.0000.0000.0000.000
131A136ALA0-0.0020.00523.000-0.045-0.0450.0000.0000.0000.000
132A137GLN0-0.046-0.01526.173-0.768-0.7680.0000.0000.0000.000
133A138ARG10.8320.91522.681-12.521-12.5210.0000.0000.0000.000
134A146ALA00.0450.02432.6800.0480.0480.0000.0000.0000.000
135A147LEU0-0.014-0.02532.002-0.180-0.1800.0000.0000.0000.000
136A148GLU-1-0.838-0.91932.7319.3689.3680.0000.0000.0000.000
137A149GLU-1-0.783-0.86329.61511.13011.1300.0000.0000.0000.000
138A150SER00.0320.03630.7690.3000.3000.0000.0000.0000.000
139A151THR00.0290.02032.6970.1010.1010.0000.0000.0000.000
140A152LEU00.0180.00927.2640.0360.0360.0000.0000.0000.000
141A153THR00.028-0.00427.2890.4380.4380.0000.0000.0000.000
142A154THR0-0.041-0.03128.6580.1510.1510.0000.0000.0000.000
143A155ILE0-0.002-0.00529.7630.0440.0440.0000.0000.0000.000
144A156TYR00.0000.01920.350-0.115-0.1150.0000.0000.0000.000
145A157LEU00.0250.01225.2320.2320.2320.0000.0000.0000.000
146A158MET0-0.027-0.01427.358-0.035-0.0350.0000.0000.0000.000
147A159THR0-0.015-0.02526.499-0.171-0.1710.0000.0000.0000.000
148A160PHE00.0340.02020.1720.0780.0780.0000.0000.0000.000
149A161PHE00.027-0.02025.2180.1430.1430.0000.0000.0000.000
150A162PHE0-0.050-0.01227.583-0.235-0.2350.0000.0000.0000.000
151A163TRP00.0600.01419.906-0.130-0.1300.0000.0000.0000.000
152A164MET0-0.054-0.01123.052-0.073-0.0730.0000.0000.0000.000
153A165ARG10.8970.94325.621-10.110-10.1100.0000.0000.0000.000
154A166ASP-1-0.702-0.77428.0309.7539.7530.0000.0000.0000.000
155A167GLU-1-0.817-0.89128.07711.14911.1490.0000.0000.0000.000
156A168SER0-0.060-0.03729.823-0.085-0.0850.0000.0000.0000.000
157A169GLU-1-0.762-0.86528.5399.7709.7700.0000.0000.0000.000
158A170ASN0-0.068-0.04924.405-0.378-0.3780.0000.0000.0000.000
159A171SER00.0200.02925.8070.3370.3370.0000.0000.0000.000
160A172ARG10.8910.92427.649-9.426-9.4260.0000.0000.0000.000
161A173HIS0-0.033-0.02530.711-0.399-0.3990.0000.0000.0000.000
162A174THR0-0.004-0.03526.066-0.088-0.0880.0000.0000.0000.000
163A175ARG10.7700.85123.363-12.115-12.1150.0000.0000.0000.000
164A176GLN00.0500.03329.279-0.321-0.3210.0000.0000.0000.000
165A177PHE00.0090.00230.914-0.240-0.2400.0000.0000.0000.000
166A178LEU00.0370.02826.416-0.217-0.2170.0000.0000.0000.000
167A179LYS10.9370.97829.962-10.072-10.0720.0000.0000.0000.000
168A180ARG10.9100.95132.548-8.225-8.2250.0000.0000.0000.000
169A181HIS0-0.020-0.01133.086-0.339-0.3390.0000.0000.0000.000
170A182LEU00.0030.00328.581-0.128-0.1280.0000.0000.0000.000
171A183THR0-0.031-0.01933.270-0.095-0.0950.0000.0000.0000.000
172A184MET0-0.039-0.02636.265-0.257-0.2570.0000.0000.0000.000
173A185ALA00.0080.01335.355-0.169-0.1690.0000.0000.0000.000
174A186ALA0-0.016-0.00135.409-0.142-0.1420.0000.0000.0000.000
175A187TRP0-0.058-0.03037.348-0.144-0.1440.0000.0000.0000.000
176A188LEU0-0.066-0.02539.660-0.275-0.2750.0000.0000.0000.000