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: 94V32

Calculation Name: 3NNC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NNC

Chain ID: A

ChEMBL ID:

UniProt ID: Q92879

Base Structure: X-ray

Registration Date: 2023-09-19

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1585179.372667
FMO2-HF: Nuclear repulsion 1513041.458392
FMO2-HF: Total energy -72137.914275
FMO2-MP2: Total energy -72337.77839


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:13:SER)


Summations of interaction energy for fragment #1(A:13:SER)
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.
-12.433-12.12613.798-5.567-8.5380.014
Interaction energy analysis for fragmet #1(A:13:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.033
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].
3A15ALA0-0.005-0.0043.8470.1611.853-0.011-0.928-0.7530.000
4A16ILE0-0.043-0.0165.8880.7170.7170.0000.0000.0000.000
5A17LYS10.8150.9067.704-0.725-0.7250.0000.0000.0000.000
6A18MET0-0.0140.00510.2430.1440.1440.0000.0000.0000.000
7A19PHE0-0.016-0.02112.716-0.115-0.1150.0000.0000.0000.000
8A20VAL00.012-0.00616.1130.0290.0290.0000.0000.0000.000
9A21GLY00.0070.00418.469-0.043-0.0430.0000.0000.0000.000
10A22GLN0-0.001-0.01722.046-0.008-0.0080.0000.0000.0000.000
11A23VAL00.0220.02221.735-0.005-0.0050.0000.0000.0000.000
12A24PRO00.0370.01324.763-0.008-0.0080.0000.0000.0000.000
13A25ARG10.9080.93527.772-0.169-0.1690.0000.0000.0000.000
14A26THR0-0.007-0.00929.8050.0010.0010.0000.0000.0000.000
15A27TRP0-0.0100.00222.308-0.005-0.0050.0000.0000.0000.000
16A28SER0-0.038-0.03726.2010.0060.0060.0000.0000.0000.000
17A29GLU-1-0.708-0.85621.9660.2120.2120.0000.0000.0000.000
18A30LYS10.8790.94021.455-0.090-0.0900.0000.0000.0000.000
19A31ASP-1-0.782-0.85022.5410.1260.1260.0000.0000.0000.000
20A32LEU0-0.003-0.01519.6810.0110.0110.0000.0000.0000.000
21A33ARG10.8120.89515.360-0.101-0.1010.0000.0000.0000.000
22A34GLU-1-0.855-0.93617.4900.1110.1110.0000.0000.0000.000
23A35LEU0-0.075-0.02218.397-0.004-0.0040.0000.0000.0000.000
24A36PHE00.027-0.02713.9970.0260.0260.0000.0000.0000.000
25A37GLU-1-0.808-0.90213.5410.1430.1430.0000.0000.0000.000
26A38GLN0-0.104-0.03514.472-0.070-0.0700.0000.0000.0000.000
27A39TYR0-0.038-0.02011.851-0.026-0.0260.0000.0000.0000.000
28A40GLY00.0220.0059.0560.0390.0390.0000.0000.0000.000
29A41ALA00.0070.0199.1270.0150.0150.0000.0000.0000.000
30A42VAL00.0230.0029.7430.1510.1510.0000.0000.0000.000
31A43TYR0-0.0250.00511.388-0.097-0.0970.0000.0000.0000.000
32A44GLU-1-0.827-0.90713.0140.3770.3770.0000.0000.0000.000
33A45ILE00.0110.01315.3290.0810.0810.0000.0000.0000.000
34A46ASN0-0.071-0.02818.037-0.053-0.0530.0000.0000.0000.000
35A47VAL00.0320.01820.5690.0330.0330.0000.0000.0000.000
36A48LEU0-0.0100.01120.746-0.018-0.0180.0000.0000.0000.000
37A49ARG10.8030.85324.450-0.206-0.2060.0000.0000.0000.000
38A50ASP-1-0.839-0.89728.1160.1720.1720.0000.0000.0000.000
39A51ARG10.9540.95831.146-0.147-0.1470.0000.0000.0000.000
40A52SER0-0.017-0.00933.980-0.009-0.0090.0000.0000.0000.000
41A53GLN00.0020.00436.625-0.008-0.0080.0000.0000.0000.000
42A54ASN0-0.0220.01937.4990.0070.0070.0000.0000.0000.000
43A55PRO00.002-0.00836.609-0.004-0.0040.0000.0000.0000.000
44A56PRO00.026-0.01632.4540.0050.0050.0000.0000.0000.000
45A57GLN00.0170.02432.4040.0040.0040.0000.0000.0000.000
46A58SER00.0560.03727.1770.0150.0150.0000.0000.0000.000
47A59LYS10.8600.90526.721-0.214-0.2140.0000.0000.0000.000
48A60GLY00.0190.01826.8220.0050.0050.0000.0000.0000.000
49A61CYS0-0.057-0.01921.9720.0120.0120.0000.0000.0000.000
50A62CYS0-0.041-0.00819.537-0.019-0.0190.0000.0000.0000.000
51A63PHE00.003-0.01816.0850.0460.0460.0000.0000.0000.000
52A64VAL00.0350.02512.742-0.072-0.0720.0000.0000.0000.000
53A65THR0-0.033-0.02010.6390.1810.1810.0000.0000.0000.000
54A66PHE00.0300.0167.579-0.155-0.1550.0000.0000.0000.000
55A67TYR00.0440.0027.0320.1960.1960.0000.0000.0000.000
56A68THR0-0.0040.0071.7850.113-0.9664.788-1.914-1.7950.002
57A69ARG10.8770.9232.055-2.558-3.5666.382-1.581-3.793-0.001
58A70LYS10.8120.8912.385-7.536-7.0132.629-1.040-2.1120.012
59A71ALA00.0380.0244.165-1.697-1.5180.010-0.104-0.0850.001
60A72ALA00.0060.0046.367-0.491-0.4910.0000.0000.0000.000
61A73LEU0-0.0010.0007.068-0.503-0.5030.0000.0000.0000.000
62A74GLU-1-0.786-0.8718.113-0.133-0.1330.0000.0000.0000.000
63A75ALA00.0030.00310.315-0.197-0.1970.0000.0000.0000.000
64A76GLN0-0.064-0.05511.642-0.033-0.0330.0000.0000.0000.000
65A77ASN0-0.006-0.01511.500-0.105-0.1050.0000.0000.0000.000
66A78ALA0-0.0070.01014.414-0.082-0.0820.0000.0000.0000.000
67A79LEU0-0.028-0.01715.960-0.060-0.0600.0000.0000.0000.000
68A80HIS00.0460.04516.351-0.027-0.0270.0000.0000.0000.000
69A81ASN0-0.083-0.05918.346-0.052-0.0520.0000.0000.0000.000
70A82MET00.0200.02919.535-0.041-0.0410.0000.0000.0000.000
71A83LYS10.9400.97521.342-0.222-0.2220.0000.0000.0000.000
72A84VAL0-0.0030.00223.1160.0210.0210.0000.0000.0000.000
73A85LEU0-0.024-0.00322.603-0.015-0.0150.0000.0000.0000.000
74A86PRO00.032-0.00526.474-0.005-0.0050.0000.0000.0000.000
75A87GLY00.0170.01629.9350.0030.0030.0000.0000.0000.000
76A88MET0-0.071-0.00627.0670.0030.0030.0000.0000.0000.000
77A89HIS0-0.041-0.03430.251-0.013-0.0130.0000.0000.0000.000
78A90HIS00.0250.01027.0030.0040.0040.0000.0000.0000.000
79A91PRO00.0100.02323.3850.0030.0030.0000.0000.0000.000
80A92ILE00.0400.01318.8330.0130.0130.0000.0000.0000.000
81A93GLN0-0.059-0.02319.6720.0320.0320.0000.0000.0000.000
82A94MET00.0060.00613.5800.0310.0310.0000.0000.0000.000
83A95LYS10.8360.92213.605-0.591-0.5910.0000.0000.0000.000
84A96PRO00.0780.03210.089-0.027-0.0270.0000.0000.0000.000
85A97ALA00.000-0.00112.238-0.145-0.1450.0000.0000.0000.000
86A98ASP-1-0.785-0.89214.3120.5970.5970.0000.0000.0000.000
87A99SER00.0210.01114.932-0.015-0.0150.0000.0000.0000.000
88A100GLU-1-0.833-0.9039.2601.6031.6030.0000.0000.0000.000
89A101LYS10.8110.90512.317-0.455-0.4550.0000.0000.0000.000
90A102ASN00.0570.02411.139-0.187-0.1870.0000.0000.0000.000
91A103ASN0-0.003-0.00414.622-0.151-0.1510.0000.0000.0000.000
92A104ALA00.0530.03516.8010.0010.0010.0000.0000.0000.000
93A105VAL00.0350.00919.290-0.034-0.0340.0000.0000.0000.000
94A106GLU-1-0.919-0.97321.4350.3470.3470.0000.0000.0000.000
95A107ASP-1-0.852-0.89822.1290.2670.2670.0000.0000.0000.000
96A108ARG10.6680.79818.665-0.397-0.3970.0000.0000.0000.000
97A109LYS10.8290.91623.502-0.251-0.2510.0000.0000.0000.000
98A110LEU00.0080.00626.458-0.005-0.0050.0000.0000.0000.000
99A111PHE0-0.001-0.00229.981-0.002-0.0020.0000.0000.0000.000
100A112ILE0-0.007-0.00232.258-0.005-0.0050.0000.0000.0000.000
101A113GLY00.0310.00435.725-0.001-0.0010.0000.0000.0000.000
102A114MET0-0.032-0.01039.326-0.004-0.0040.0000.0000.0000.000
103A115ILE00.0370.02737.898-0.003-0.0030.0000.0000.0000.000
104A116SER00.0700.00741.756-0.001-0.0010.0000.0000.0000.000
105A117LYS10.9070.93542.901-0.069-0.0690.0000.0000.0000.000
106A118LYS10.8550.90744.361-0.047-0.0470.0000.0000.0000.000
107A119CYS0-0.0560.00639.678-0.002-0.0020.0000.0000.0000.000
108A120THR0-0.008-0.01337.9200.0060.0060.0000.0000.0000.000
109A121GLU-1-0.778-0.89231.4460.1210.1210.0000.0000.0000.000
110A122ASN00.005-0.00934.0480.0040.0040.0000.0000.0000.000
111A123ASP-1-0.760-0.88435.2050.0650.0650.0000.0000.0000.000
112A124ILE00.0050.00233.1140.0000.0000.0000.0000.0000.000
113A125ARG10.8670.91226.963-0.125-0.1250.0000.0000.0000.000
114A126VAL00.0240.00631.7240.0010.0010.0000.0000.0000.000
115A127MET0-0.054-0.01634.200-0.002-0.0020.0000.0000.0000.000
116A128PHE00.006-0.00630.6480.0000.0000.0000.0000.0000.000
117A129SER00.0090.00628.9050.0050.0050.0000.0000.0000.000
118A130SER0-0.0090.00328.5270.0020.0020.0000.0000.0000.000
119A131PHE0-0.029-0.01728.618-0.003-0.0030.0000.0000.0000.000
120A132GLY00.010-0.01624.7010.0120.0120.0000.0000.0000.000
121A133GLN0-0.0080.00420.483-0.013-0.0130.0000.0000.0000.000
122A134ILE0-0.001-0.00723.2260.0230.0230.0000.0000.0000.000
123A135GLU-1-0.809-0.88619.6210.3410.3410.0000.0000.0000.000
124A136GLU-1-0.911-0.94523.1180.2100.2100.0000.0000.0000.000
125A137CYS0-0.031-0.00426.208-0.003-0.0030.0000.0000.0000.000
126A138ARG10.8930.95229.907-0.136-0.1360.0000.0000.0000.000
127A139ILE00.007-0.00532.5640.0010.0010.0000.0000.0000.000
128A140LEU0-0.0040.01134.9660.0010.0010.0000.0000.0000.000
129A141ARG10.9040.94237.790-0.091-0.0910.0000.0000.0000.000
130A142GLY0-0.030-0.01240.7180.0040.0040.0000.0000.0000.000
131A143PRO00.0130.00242.9960.0020.0020.0000.0000.0000.000
132A144ASP-1-0.856-0.92144.8230.0680.0680.0000.0000.0000.000
133A145GLY0-0.0110.00342.964-0.003-0.0030.0000.0000.0000.000
134A146LEU00.0120.00343.4530.0010.0010.0000.0000.0000.000
135A147SER00.0240.02041.6820.0060.0060.0000.0000.0000.000
136A148ARG10.9430.95140.985-0.098-0.0980.0000.0000.0000.000
137A149GLY0-0.011-0.00442.3560.0000.0000.0000.0000.0000.000
138A150CYS0-0.059-0.02038.0580.0010.0010.0000.0000.0000.000
139A151ALA00.004-0.00734.334-0.001-0.0010.0000.0000.0000.000
140A152PHE00.0080.01230.0070.0040.0040.0000.0000.0000.000
141A153VAL00.017-0.00328.220-0.003-0.0030.0000.0000.0000.000
142A154THR00.0030.01922.7040.0040.0040.0000.0000.0000.000
143A155PHE00.0430.03023.537-0.007-0.0070.0000.0000.0000.000
144A156THR00.0710.02118.0960.0200.0200.0000.0000.0000.000
145A157THR00.0320.00717.6450.0420.0420.0000.0000.0000.000
146A158ARG10.8970.92820.012-0.271-0.2710.0000.0000.0000.000
147A159ALA0-0.008-0.00421.847-0.023-0.0230.0000.0000.0000.000
148A160MET0-0.0520.02821.994-0.021-0.0210.0000.0000.0000.000
149A161ALA00.0520.03424.828-0.016-0.0160.0000.0000.0000.000
150A162GLN0-0.019-0.02426.492-0.009-0.0090.0000.0000.0000.000
151A163THR0-0.023-0.02227.134-0.017-0.0170.0000.0000.0000.000
152A164ALA00.0170.01529.299-0.011-0.0110.0000.0000.0000.000
153A165ILE0-0.018-0.00630.402-0.009-0.0090.0000.0000.0000.000
154A166LYS10.8920.94632.646-0.096-0.0960.0000.0000.0000.000
155A167ALA00.0020.00834.001-0.007-0.0070.0000.0000.0000.000
156A168MET00.0170.00834.522-0.007-0.0070.0000.0000.0000.000
157A169HIS0-0.0070.00736.5530.0000.0000.0000.0000.0000.000
158A170GLN0-0.076-0.05038.126-0.005-0.0050.0000.0000.0000.000
159A171ALA00.0210.03140.006-0.005-0.0050.0000.0000.0000.000
160A172GLN00.004-0.00541.104-0.003-0.0030.0000.0000.0000.000
161A173THR0-0.001-0.00343.8120.0050.0050.0000.0000.0000.000
162A174MET0-0.0020.03541.600-0.001-0.0010.0000.0000.0000.000
163A175GLU-1-0.784-0.89645.8160.0490.0490.0000.0000.0000.000
164A176GLY0-0.013-0.01047.8310.0030.0030.0000.0000.0000.000
165A177CYS0-0.108-0.03045.9030.0030.0030.0000.0000.0000.000
166A178SER00.0380.01548.318-0.001-0.0010.0000.0000.0000.000
167A179SER0-0.041-0.02946.684-0.001-0.0010.0000.0000.0000.000
168A180PRO00.0200.01244.1970.0010.0010.0000.0000.0000.000
169A181MET00.0070.00938.4270.0050.0050.0000.0000.0000.000
170A182VAL0-0.0020.00937.8400.0000.0000.0000.0000.0000.000
171A183VAL0-0.011-0.00733.2120.0040.0040.0000.0000.0000.000
172A184LYS10.8430.92133.458-0.140-0.1400.0000.0000.0000.000
173A185PHE00.017-0.00826.0110.0030.0030.0000.0000.0000.000
174A186ALA0-0.031-0.02229.354-0.010-0.0100.0000.0000.0000.000
175A187ASP-1-0.840-0.89729.8810.1570.1570.0000.0000.0000.000