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: LZ319

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1582342.414902
FMO2-HF: Nuclear repulsion 1510205.854635
FMO2-HF: Total energy -72136.560267
FMO2-MP2: Total energy -72336.416075


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.
-14.058-17.80422.484-7.979-10.7560.019
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 : -0.035 / q_NPA : -0.027
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].
3A15ALA0-0.013-0.0013.649-0.2871.9360.006-1.256-0.9720.000
4A16ILE0-0.049-0.0245.7150.8490.8490.0000.0000.0000.000
5A17LYS10.9190.9817.473-0.942-0.9420.0000.0000.0000.000
6A18MET0-0.026-0.0049.9430.1970.1970.0000.0000.0000.000
7A19PHE0-0.025-0.02312.543-0.133-0.1330.0000.0000.0000.000
8A20VAL00.0200.00516.0770.0340.0340.0000.0000.0000.000
9A21GLY00.003-0.00318.313-0.047-0.0470.0000.0000.0000.000
10A22GLN00.002-0.01721.908-0.011-0.0110.0000.0000.0000.000
11A23VAL00.0280.02421.440-0.007-0.0070.0000.0000.0000.000
12A24PRO00.0430.01824.584-0.008-0.0080.0000.0000.0000.000
13A25ARG10.9270.94627.563-0.190-0.1900.0000.0000.0000.000
14A26THR0-0.018-0.01429.5970.0010.0010.0000.0000.0000.000
15A27TRP00.0130.01822.366-0.004-0.0040.0000.0000.0000.000
16A28SER0-0.054-0.03026.1710.0070.0070.0000.0000.0000.000
17A29GLU-1-0.718-0.88721.9890.2350.2350.0000.0000.0000.000
18A30LYS10.9530.98421.426-0.085-0.0850.0000.0000.0000.000
19A31ASP-1-0.784-0.88022.5160.1460.1460.0000.0000.0000.000
20A32LEU0-0.029-0.02819.6050.0160.0160.0000.0000.0000.000
21A33ARG10.8230.91315.443-0.118-0.1180.0000.0000.0000.000
22A34GLU-1-0.867-0.93517.4670.1130.1130.0000.0000.0000.000
23A35LEU0-0.085-0.02718.316-0.005-0.0050.0000.0000.0000.000
24A36PHE00.002-0.04113.9290.0300.0300.0000.0000.0000.000
25A37GLU-1-0.842-0.92513.5210.1440.1440.0000.0000.0000.000
26A38GLN0-0.073-0.01814.458-0.077-0.0770.0000.0000.0000.000
27A39TYR0-0.043-0.02311.852-0.034-0.0340.0000.0000.0000.000
28A40GLY00.0180.0039.0390.0260.0260.0000.0000.0000.000
29A41ALA00.0050.0199.1000.0280.0280.0000.0000.0000.000
30A42VAL00.0250.0009.7170.1500.1500.0000.0000.0000.000
31A43TYR0-0.039-0.00611.462-0.106-0.1060.0000.0000.0000.000
32A44GLU-1-0.961-0.98812.9830.3240.3240.0000.0000.0000.000
33A45ILE00.0070.01215.2960.0940.0940.0000.0000.0000.000
34A46ASN0-0.009-0.00518.004-0.063-0.0630.0000.0000.0000.000
35A47VAL00.0140.01320.3040.0380.0380.0000.0000.0000.000
36A48LEU0-0.0180.00620.509-0.019-0.0190.0000.0000.0000.000
37A49ARG10.8170.88024.228-0.228-0.2280.0000.0000.0000.000
38A50ASP-1-0.903-0.93527.8870.1850.1850.0000.0000.0000.000
39A51ARG10.9600.95631.090-0.163-0.1630.0000.0000.0000.000
40A52SER0-0.025-0.00633.751-0.010-0.0100.0000.0000.0000.000
41A53GLN00.0200.01036.415-0.010-0.0100.0000.0000.0000.000
42A54ASN0-0.0280.01537.2660.0070.0070.0000.0000.0000.000
43A55PRO0-0.010-0.01336.349-0.004-0.0040.0000.0000.0000.000
44A56PRO00.027-0.01432.2690.0060.0060.0000.0000.0000.000
45A57GLN0-0.0130.00631.9770.0010.0010.0000.0000.0000.000
46A58SER00.0440.03726.9410.0170.0170.0000.0000.0000.000
47A59LYS10.9330.94426.441-0.252-0.2520.0000.0000.0000.000
48A60GLY00.0190.01226.6360.0050.0050.0000.0000.0000.000
49A61CYS0-0.048-0.01321.7120.0130.0130.0000.0000.0000.000
50A62CYS0-0.034-0.01319.232-0.017-0.0170.0000.0000.0000.000
51A63PHE0-0.026-0.02615.8010.0540.0540.0000.0000.0000.000
52A64VAL00.0480.03112.728-0.079-0.0790.0000.0000.0000.000
53A65THR0-0.008-0.00810.1090.2150.2150.0000.0000.0000.000
54A66PHE00.0250.0157.491-0.169-0.1690.0000.0000.0000.000
55A67TYR00.0550.0066.9520.2590.2590.0000.0000.0000.000
56A68THR00.0010.0131.828-0.173-0.8044.169-1.788-1.7490.004
57A69ARG10.9820.9791.876-3.751-9.55815.683-4.056-5.8190.003
58A70LYS10.8470.9222.385-6.968-6.6712.616-0.779-2.1340.011
59A71ALA00.0450.0294.184-1.582-1.4100.010-0.100-0.0820.001
60A72ALA00.0070.0046.373-0.431-0.4310.0000.0000.0000.000
61A73LEU0-0.009-0.0047.068-0.502-0.5020.0000.0000.0000.000
62A74GLU-1-0.819-0.9078.242-0.152-0.1520.0000.0000.0000.000
63A75ALA00.0050.00510.335-0.196-0.1960.0000.0000.0000.000
64A76GLN0-0.053-0.04511.643-0.064-0.0640.0000.0000.0000.000
65A77ASN0-0.015-0.01811.370-0.139-0.1390.0000.0000.0000.000
66A78ALA00.0080.01914.435-0.084-0.0840.0000.0000.0000.000
67A79LEU0-0.040-0.02015.624-0.065-0.0650.0000.0000.0000.000
68A80HIS00.0540.04516.406-0.024-0.0240.0000.0000.0000.000
69A81ASN0-0.039-0.03618.295-0.047-0.0470.0000.0000.0000.000
70A82MET0-0.0080.01819.363-0.044-0.0440.0000.0000.0000.000
71A83LYS10.9490.97521.091-0.243-0.2430.0000.0000.0000.000
72A84VAL00.0020.00623.1160.0240.0240.0000.0000.0000.000
73A85LEU0-0.037-0.01222.516-0.017-0.0170.0000.0000.0000.000
74A86PRO00.021-0.00926.470-0.006-0.0060.0000.0000.0000.000
75A87GLY00.0210.02029.9140.0040.0040.0000.0000.0000.000
76A88MET0-0.075-0.01126.8690.0030.0030.0000.0000.0000.000
77A89HIS0-0.033-0.02630.117-0.014-0.0140.0000.0000.0000.000
78A90HIS00.0160.00227.0680.0040.0040.0000.0000.0000.000
79A91PRO00.0200.03123.3180.0020.0020.0000.0000.0000.000
80A92ILE00.0350.00818.7970.0150.0150.0000.0000.0000.000
81A93GLN0-0.077-0.03119.6240.0350.0350.0000.0000.0000.000
82A94MET0-0.0070.00813.4810.0350.0350.0000.0000.0000.000
83A95LYS10.8780.94313.534-0.681-0.6810.0000.0000.0000.000
84A96PRO00.0570.02910.172-0.028-0.0280.0000.0000.0000.000
85A97ALA00.002-0.00912.153-0.178-0.1780.0000.0000.0000.000
86A98ASP-1-0.838-0.94114.2130.6620.6620.0000.0000.0000.000
87A99SER0-0.002-0.01514.870-0.019-0.0190.0000.0000.0000.000
88A100GLU-1-0.841-0.90910.3851.4721.4720.0000.0000.0000.000
89A101LYS10.8010.92512.263-0.586-0.5860.0000.0000.0000.000
90A102ASN00.0700.03811.283-0.130-0.1300.0000.0000.0000.000
91A103ASN0-0.031-0.02414.183-0.175-0.1750.0000.0000.0000.000
92A104ALA00.0870.05116.6140.0030.0030.0000.0000.0000.000
93A105VAL00.024-0.00119.178-0.042-0.0420.0000.0000.0000.000
94A106GLU-1-0.975-0.99921.2800.3660.3660.0000.0000.0000.000
95A107ASP-1-0.883-0.91321.8470.3150.3150.0000.0000.0000.000
96A108ARG10.6970.83118.180-0.435-0.4350.0000.0000.0000.000
97A109LYS10.9330.98223.367-0.278-0.2780.0000.0000.0000.000
98A110LEU00.0020.00226.329-0.004-0.0040.0000.0000.0000.000
99A111PHE00.0110.00629.863-0.002-0.0020.0000.0000.0000.000
100A112ILE0-0.013-0.00332.365-0.006-0.0060.0000.0000.0000.000
101A113GLY00.032-0.00135.6320.0000.0000.0000.0000.0000.000
102A114MET0-0.032-0.00639.222-0.004-0.0040.0000.0000.0000.000
103A115ILE00.0380.01937.914-0.004-0.0040.0000.0000.0000.000
104A116SER00.0720.01241.7030.0000.0000.0000.0000.0000.000
105A117LYS10.9330.94342.870-0.073-0.0730.0000.0000.0000.000
106A118LYS10.9040.95044.341-0.049-0.0490.0000.0000.0000.000
107A119CYS0-0.0490.00139.614-0.003-0.0030.0000.0000.0000.000
108A120THR0-0.0330.01137.6090.0060.0060.0000.0000.0000.000
109A121GLU-1-0.865-0.96831.3190.1240.1240.0000.0000.0000.000
110A122ASN00.027-0.01533.9790.0040.0040.0000.0000.0000.000
111A123ASP-1-0.762-0.88335.1650.0650.0650.0000.0000.0000.000
112A124ILE00.000-0.00233.078-0.001-0.0010.0000.0000.0000.000
113A125ARG10.8830.93626.739-0.130-0.1300.0000.0000.0000.000
114A126VAL00.0120.00331.6610.0000.0000.0000.0000.0000.000
115A127MET0-0.059-0.02634.141-0.003-0.0030.0000.0000.0000.000
116A128PHE00.008-0.00830.4590.0000.0000.0000.0000.0000.000
117A129SER00.0020.00628.8390.0040.0040.0000.0000.0000.000
118A130SER0-0.0030.00228.4670.0010.0010.0000.0000.0000.000
119A131PHE0-0.026-0.00728.503-0.003-0.0030.0000.0000.0000.000
120A132GLY00.009-0.02124.5730.0120.0120.0000.0000.0000.000
121A133GLN0-0.008-0.00220.133-0.008-0.0080.0000.0000.0000.000
122A134ILE0-0.008-0.01123.1220.0240.0240.0000.0000.0000.000
123A135GLU-1-0.858-0.93019.6060.3530.3530.0000.0000.0000.000
124A136GLU-1-0.977-0.99323.0640.2260.2260.0000.0000.0000.000
125A137CYS0-0.065-0.01826.194-0.003-0.0030.0000.0000.0000.000
126A138ARG11.0261.02229.888-0.148-0.1480.0000.0000.0000.000
127A139ILE0-0.014-0.00432.5250.0010.0010.0000.0000.0000.000
128A140LEU0-0.006-0.00434.6730.0010.0010.0000.0000.0000.000
129A141ARG10.8980.94437.740-0.099-0.0990.0000.0000.0000.000
130A142GLY0-0.032-0.01540.7920.0050.0050.0000.0000.0000.000
131A143PRO00.0150.00143.1550.0020.0020.0000.0000.0000.000
132A144ASP-1-0.859-0.92144.9760.0730.0730.0000.0000.0000.000
133A145GLY0-0.0120.00143.055-0.003-0.0030.0000.0000.0000.000
134A146LEU00.0150.00143.4320.0010.0010.0000.0000.0000.000
135A147SER00.0280.02341.6070.0060.0060.0000.0000.0000.000
136A148ARG10.9180.94541.007-0.105-0.1050.0000.0000.0000.000
137A149GLY00.0020.00042.2860.0000.0000.0000.0000.0000.000
138A150CYS0-0.066-0.01537.9410.0010.0010.0000.0000.0000.000
139A151ALA00.008-0.00334.290-0.001-0.0010.0000.0000.0000.000
140A152PHE00.0050.00829.8850.0050.0050.0000.0000.0000.000
141A153VAL00.0200.00128.078-0.003-0.0030.0000.0000.0000.000
142A154THR00.0110.01622.5700.0090.0090.0000.0000.0000.000
143A155PHE00.0500.02223.330-0.010-0.0100.0000.0000.0000.000
144A156THR00.0740.01118.0070.0240.0240.0000.0000.0000.000
145A157THR00.0240.00117.4950.0430.0430.0000.0000.0000.000
146A158ARG10.9820.98819.915-0.278-0.2780.0000.0000.0000.000
147A159ALA0-0.006-0.00621.740-0.023-0.0230.0000.0000.0000.000
148A160MET0-0.0620.04122.070-0.017-0.0170.0000.0000.0000.000
149A161ALA00.0460.03124.729-0.016-0.0160.0000.0000.0000.000
150A162GLN0-0.019-0.02326.391-0.008-0.0080.0000.0000.0000.000
151A163THR0-0.022-0.01627.006-0.017-0.0170.0000.0000.0000.000
152A164ALA00.0170.01529.158-0.011-0.0110.0000.0000.0000.000
153A165ILE0-0.024-0.01030.387-0.009-0.0090.0000.0000.0000.000
154A166LYS10.8920.94832.525-0.095-0.0950.0000.0000.0000.000
155A167ALA00.0050.00733.841-0.007-0.0070.0000.0000.0000.000
156A168MET00.0220.00834.595-0.007-0.0070.0000.0000.0000.000
157A169HIS0-0.0100.01636.4850.0010.0010.0000.0000.0000.000
158A170GLN0-0.081-0.05338.035-0.005-0.0050.0000.0000.0000.000
159A171ALA00.0220.03039.920-0.005-0.0050.0000.0000.0000.000
160A172GLN00.006-0.00241.029-0.003-0.0030.0000.0000.0000.000
161A173THR00.004-0.00143.7170.0050.0050.0000.0000.0000.000
162A174MET0-0.0300.02241.771-0.001-0.0010.0000.0000.0000.000
163A175GLU-1-0.819-0.93245.7310.0510.0510.0000.0000.0000.000
164A176GLY0-0.023-0.01647.7850.0030.0030.0000.0000.0000.000
165A177CYS0-0.111-0.03545.6640.0030.0030.0000.0000.0000.000
166A178SER00.0220.01048.248-0.002-0.0020.0000.0000.0000.000
167A179SER0-0.013-0.01946.218-0.001-0.0010.0000.0000.0000.000
168A180PRO00.0210.01644.0380.0010.0010.0000.0000.0000.000
169A181MET00.0070.01338.4980.0050.0050.0000.0000.0000.000
170A182VAL0-0.0040.00437.5850.0000.0000.0000.0000.0000.000
171A183VAL0-0.012-0.01333.0720.0050.0050.0000.0000.0000.000
172A184LYS10.9760.98833.282-0.135-0.1350.0000.0000.0000.000
173A185PHE00.005-0.01225.9470.0040.0040.0000.0000.0000.000
174A186ALA0-0.049-0.03029.227-0.010-0.0100.0000.0000.0000.000
175A187ASP-1-0.947-0.95629.9140.1740.1740.0000.0000.0000.000