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: 2NYMR

Calculation Name: 2NN6-I-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN6

Chain ID: I

ChEMBL ID:

UniProt ID: Q9Y3B2

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1591860.245359
FMO2-HF: Nuclear repulsion 1521232.748024
FMO2-HF: Total energy -70627.497334
FMO2-MP2: Total energy -70828.853441


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(I:6:ARG)


Summations of interaction energy for fragment #1(I:6:ARG)
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.
-15.125-11.3290.194-1.558-2.432-0.003
Interaction energy analysis for fragmet #1(I:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.993 / q_NPA : 0.989
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].
3I8CYS0-0.0070.0143.877-1.852-0.294-0.017-0.781-0.7600.000
4I9ILE00.0140.0086.8101.4351.4350.0000.0000.0000.000
5I10PRO0-0.013-0.01710.5090.0000.0000.0000.0000.0000.000
6I11GLY0-0.010-0.01013.1451.1971.1970.0000.0000.0000.000
7I12GLU-1-0.897-0.9288.201-26.220-26.2200.0000.0000.0000.000
8I13ARG10.8690.93111.68816.91316.9130.0000.0000.0000.000
9I14LEU0-0.052-0.0197.186-1.097-1.0970.0000.0000.0000.000
10I15CYS00.0050.01711.2660.4500.4500.0000.0000.0000.000
11I16ASN0-0.048-0.07914.094-0.252-0.2520.0000.0000.0000.000
12I17LEU00.0040.00717.469-0.314-0.3140.0000.0000.0000.000
13I18GLU-1-0.883-0.92619.951-13.396-13.3960.0000.0000.0000.000
14I19GLU-1-0.914-0.94313.731-20.952-20.9520.0000.0000.0000.000
15I20GLY00.0860.03316.830-0.049-0.0490.0000.0000.0000.000
16I21SER0-0.019-0.00217.3880.3100.3100.0000.0000.0000.000
17I22PRO00.002-0.00514.183-0.810-0.8100.0000.0000.0000.000
18I23GLY00.0410.01414.4460.9870.9870.0000.0000.0000.000
19I24SER0-0.062-0.04812.2361.1151.1150.0000.0000.0000.000
20I25GLY00.015-0.00312.616-1.038-1.0380.0000.0000.0000.000
21I26THR00.0270.02913.484-0.488-0.4880.0000.0000.0000.000
22I27TYR00.0540.04015.4681.2211.2210.0000.0000.0000.000
23I28THR00.000-0.00716.477-0.576-0.5760.0000.0000.0000.000
24I29ARG10.8870.94719.09912.56012.5600.0000.0000.0000.000
25I30HIS00.005-0.00821.347-0.482-0.4820.0000.0000.0000.000
26I31GLY00.0840.06121.8640.0900.0900.0000.0000.0000.000
27I32TYR00.0230.00616.969-0.221-0.2210.0000.0000.0000.000
28I33ILE00.0020.00112.7270.4830.4830.0000.0000.0000.000
29I34PHE0-0.041-0.04013.612-0.700-0.7000.0000.0000.0000.000
30I35SER00.0280.02010.628-0.460-0.4600.0000.0000.0000.000
31I36SER0-0.065-0.05012.5440.5530.5530.0000.0000.0000.000
32I37LEU0-0.0010.00412.6670.5600.5600.0000.0000.0000.000
33I38ALA00.0100.00411.193-0.565-0.5650.0000.0000.0000.000
34I39GLY00.0320.0249.3691.0571.0570.0000.0000.0000.000
35I40CYS0-0.056-0.0303.377-2.488-2.0570.016-0.171-0.2770.000
36I41LEU00.0130.0162.8682.7413.7470.182-0.329-0.858-0.001
37I42MET0-0.042-0.0203.652-6.037-5.2360.013-0.277-0.537-0.002
38I43LYS10.9570.9786.33530.62730.6270.0000.0000.0000.000
39I44SER0-0.0020.0038.884-0.323-0.3230.0000.0000.0000.000
40I45SER0-0.001-0.01512.102-0.862-0.8620.0000.0000.0000.000
41I46GLU-1-0.901-0.93614.738-14.421-14.4210.0000.0000.0000.000
42I47ASN0-0.053-0.03418.414-0.305-0.3050.0000.0000.0000.000
43I48GLY00.003-0.01720.9110.7130.7130.0000.0000.0000.000
44I49ALA0-0.066-0.02520.0940.1230.1230.0000.0000.0000.000
45I50LEU00.0340.04017.928-0.184-0.1840.0000.0000.0000.000
46I51PRO0-0.027-0.00412.741-0.143-0.1430.0000.0000.0000.000
47I52VAL00.0090.01613.6020.7190.7190.0000.0000.0000.000
48I53VAL0-0.004-0.0119.589-1.885-1.8850.0000.0000.0000.000
49I54SER0-0.014-0.0239.4052.0442.0440.0000.0000.0000.000
50I55VAL00.0090.0118.223-2.467-2.4670.0000.0000.0000.000
51I56VAL0-0.022-0.0165.6421.7941.7940.0000.0000.0000.000
52I57ARG10.9020.9548.65915.80115.8010.0000.0000.0000.000
53I58GLU-1-0.806-0.91211.029-18.012-18.0120.0000.0000.0000.000
54I59THR0-0.077-0.02712.1570.9910.9910.0000.0000.0000.000
55I60GLU-1-0.892-0.94913.235-17.308-17.3080.0000.0000.0000.000
56I61SER0-0.058-0.02415.5900.6630.6630.0000.0000.0000.000
57I62GLN0-0.0130.00017.3890.7980.7980.0000.0000.0000.000
58I63LEU0-0.043-0.04920.9620.3740.3740.0000.0000.0000.000
59I64LEU00.0680.04021.8030.0550.0550.0000.0000.0000.000
60I65PRO0-0.108-0.05525.9490.0950.0950.0000.0000.0000.000
61I66ASP-1-0.785-0.90529.665-8.959-8.9590.0000.0000.0000.000
62I67VAL0-0.010-0.01231.2730.2000.2000.0000.0000.0000.000
63I68GLY0-0.0130.00234.6680.2660.2660.0000.0000.0000.000
64I69ALA0-0.0020.01632.4850.0780.0780.0000.0000.0000.000
65I70ILE00.0140.00134.4010.2170.2170.0000.0000.0000.000
66I71VAL0-0.074-0.04433.427-0.319-0.3190.0000.0000.0000.000
67I72THR0-0.0040.00433.2530.2560.2560.0000.0000.0000.000
68I73CYS0-0.022-0.03335.025-0.171-0.1710.0000.0000.0000.000
69I74LYN0-0.037-0.01337.5930.1240.1240.0000.0000.0000.000
70I75VAL00.0260.02139.630-0.042-0.0420.0000.0000.0000.000
71I76SER0-0.031-0.01241.329-0.074-0.0740.0000.0000.0000.000
72I77SER0-0.020-0.01643.6550.1210.1210.0000.0000.0000.000
73I78ILE00.0120.00847.009-0.063-0.0630.0000.0000.0000.000
74I79ASN00.0270.03449.9410.2000.2000.0000.0000.0000.000
75I80SER00.003-0.05352.438-0.092-0.0920.0000.0000.0000.000
76I81ARG10.8870.94453.8145.3785.3780.0000.0000.0000.000
77I82PHE00.0150.00549.091-0.034-0.0340.0000.0000.0000.000
78I83ALA00.0030.01946.7760.0490.0490.0000.0000.0000.000
79I84LYS10.9460.97641.2927.0217.0210.0000.0000.0000.000
80I85VAL00.000-0.00539.8240.0840.0840.0000.0000.0000.000
81I86HIS00.0040.00635.982-0.167-0.1670.0000.0000.0000.000
82I87ILE00.0060.00232.8350.1120.1120.0000.0000.0000.000
83I88LEU0-0.0210.00230.716-0.109-0.1090.0000.0000.0000.000
84I89TYR00.0260.02127.459-0.155-0.1550.0000.0000.0000.000
85I90VAL00.0330.00729.4720.3060.3060.0000.0000.0000.000
86I91GLY00.0410.02829.412-0.320-0.3200.0000.0000.0000.000
87I92SER0-0.024-0.03128.3140.0790.0790.0000.0000.0000.000
88I93MET00.0270.02822.101-0.184-0.1840.0000.0000.0000.000
89I94PRO0-0.026-0.00523.869-0.346-0.3460.0000.0000.0000.000
90I95LEU00.0850.04221.6850.4570.4570.0000.0000.0000.000
91I96LYS10.9050.95724.25610.51910.5190.0000.0000.0000.000
92I97ASN00.028-0.00626.3790.5970.5970.0000.0000.0000.000
93I98SER0-0.022-0.00326.2640.3090.3090.0000.0000.0000.000
94I99PHE00.0360.02028.5370.1450.1450.0000.0000.0000.000
95I100ARG10.9240.95631.3808.4138.4130.0000.0000.0000.000
96I101GLY00.0150.01533.2550.0760.0760.0000.0000.0000.000
97I102THR0-0.065-0.04335.1140.3090.3090.0000.0000.0000.000
98I103ILE00.0020.01036.164-0.030-0.0300.0000.0000.0000.000
99I104ARG10.8140.90839.4617.3477.3470.0000.0000.0000.000
100I105LYS10.8900.95942.9636.6436.6430.0000.0000.0000.000
101I106GLU-1-0.841-0.93245.689-6.329-6.3290.0000.0000.0000.000
102I107ASP-1-0.801-0.91449.449-5.604-5.6040.0000.0000.0000.000
103I108VAL00.0080.01051.459-0.009-0.0090.0000.0000.0000.000
104I109ARG10.8860.94746.6776.2676.2670.0000.0000.0000.000
105I110ALA0-0.0070.00747.369-0.156-0.1560.0000.0000.0000.000
106I111THR00.0270.02348.989-0.129-0.1290.0000.0000.0000.000
107I112GLU-1-0.813-0.92450.006-6.047-6.0470.0000.0000.0000.000
108I113LYS10.8500.93852.2295.6435.6430.0000.0000.0000.000
109I114ASP-1-0.808-0.89655.341-5.520-5.5200.0000.0000.0000.000
110I115LYS10.8220.88555.6075.4495.4490.0000.0000.0000.000
111I116VAL00.0180.02555.6680.0800.0800.0000.0000.0000.000
112I117GLU-1-0.777-0.85555.190-5.293-5.2930.0000.0000.0000.000
113I118ILE00.0520.02850.077-0.043-0.0430.0000.0000.0000.000
114I119TYR00.0170.00752.091-0.082-0.0820.0000.0000.0000.000
115I120LYS10.8120.90254.3065.1425.1420.0000.0000.0000.000
116I121SER00.0060.01250.6630.0140.0140.0000.0000.0000.000
117I122PHE00.036-0.01147.036-0.089-0.0890.0000.0000.0000.000
118I123ARG10.8250.90848.0715.7375.7370.0000.0000.0000.000
119I124PRO0-0.032-0.01846.525-0.112-0.1120.0000.0000.0000.000
120I125GLY00.0210.00145.113-0.054-0.0540.0000.0000.0000.000
121I126ASP-1-0.763-0.86544.201-6.464-6.4640.0000.0000.0000.000
122I127ILE00.0360.01238.720-0.127-0.1270.0000.0000.0000.000
123I128VAL0-0.025-0.00940.5000.1490.1490.0000.0000.0000.000
124I129LEU00.0030.01539.030-0.259-0.2590.0000.0000.0000.000
125I130ALA00.041-0.00438.9350.2240.2240.0000.0000.0000.000
126I131LYS10.8300.89438.2547.0777.0770.0000.0000.0000.000
127I132VAL0-0.024-0.00734.9670.2370.2370.0000.0000.0000.000
128I133ILE0-0.024-0.01138.3150.1010.1010.0000.0000.0000.000
129I134SER00.002-0.02239.549-0.139-0.1390.0000.0000.0000.000
130I135LEU00.0000.03034.5320.1650.1650.0000.0000.0000.000
131I136GLY00.0380.01538.7390.0320.0320.0000.0000.0000.000
132I137ASP-1-0.868-0.95335.108-8.133-8.1330.0000.0000.0000.000
133I138ALA0-0.0110.00438.422-0.022-0.0220.0000.0000.0000.000
134I139GLN0-0.028-0.01041.2030.1040.1040.0000.0000.0000.000
135I140SER0-0.027-0.00936.9180.0460.0460.0000.0000.0000.000
136I141ASN00.011-0.01738.358-0.005-0.0050.0000.0000.0000.000
137I142TYR00.0260.03132.548-0.080-0.0800.0000.0000.0000.000
138I143LEU00.0440.02338.6280.1180.1180.0000.0000.0000.000
139I144LEU00.0360.01437.949-0.150-0.1500.0000.0000.0000.000
140I145THR00.001-0.00541.8210.2750.2750.0000.0000.0000.000
141I146THR0-0.033-0.04542.897-0.174-0.1740.0000.0000.0000.000
142I147ALA0-0.071-0.00845.3590.0780.0780.0000.0000.0000.000
143I148GLU-1-0.729-0.86943.173-7.087-7.0870.0000.0000.0000.000
144I149ASN0-0.039-0.02247.0950.1080.1080.0000.0000.0000.000
145I150GLU-1-0.940-0.95041.631-7.165-7.1650.0000.0000.0000.000
146I151LEU0-0.062-0.00640.759-0.135-0.1350.0000.0000.0000.000
147I152GLY00.0030.00443.8180.1980.1980.0000.0000.0000.000
148I153VAL0-0.061-0.03143.787-0.191-0.1910.0000.0000.0000.000
149I154VAL00.014-0.00441.0100.0900.0900.0000.0000.0000.000
150I155VAL0-0.0200.00441.702-0.099-0.0990.0000.0000.0000.000
151I156ALA00.0140.00544.7020.0910.0910.0000.0000.0000.000
152I157HIS0-0.043-0.02744.692-0.121-0.1210.0000.0000.0000.000
153I158SER00.0530.01449.7520.0900.0900.0000.0000.0000.000
154I159GLU-1-0.838-0.89753.090-5.272-5.2720.0000.0000.0000.000
155I160SER0-0.011-0.01255.3470.0300.0300.0000.0000.0000.000
156I161GLY0-0.010-0.00150.919-0.021-0.0210.0000.0000.0000.000
157I162ILE0-0.063-0.02749.908-0.127-0.1270.0000.0000.0000.000
158I163GLN00.0260.01446.065-0.065-0.0650.0000.0000.0000.000
159I164MET0-0.059-0.02349.1810.1830.1830.0000.0000.0000.000
160I165VAL00.0240.01849.288-0.142-0.1420.0000.0000.0000.000
161I166PRO00.0260.00148.9910.1130.1130.0000.0000.0000.000
162I167ILE0-0.026-0.00851.9530.0110.0110.0000.0000.0000.000
163I168SER0-0.014-0.00654.8010.0590.0590.0000.0000.0000.000
164I169TRP0-0.024-0.02853.267-0.082-0.0820.0000.0000.0000.000
165I170CYS0-0.040-0.01552.827-0.099-0.0990.0000.0000.0000.000
166I171GLU-1-0.872-0.92954.337-5.187-5.1870.0000.0000.0000.000
167I172MET0-0.0070.00148.245-0.056-0.0560.0000.0000.0000.000
168I173GLN00.0500.01253.5330.1360.1360.0000.0000.0000.000
169I174CYS0-0.088-0.01453.884-0.098-0.0980.0000.0000.0000.000
170I175PRO00.003-0.00953.8700.0980.0980.0000.0000.0000.000
171I176LYS10.9230.97656.0775.5505.5500.0000.0000.0000.000
172I177THR00.0220.00357.5870.1270.1270.0000.0000.0000.000
173I178HIS00.005-0.00958.982-0.052-0.0520.0000.0000.0000.000
174I179THR00.006-0.02256.7310.0270.0270.0000.0000.0000.000
175I180LYS10.9400.98857.6684.8924.8920.0000.0000.0000.000
176I181GLU-1-0.806-0.88052.863-5.747-5.7470.0000.0000.0000.000
177I182PHE0-0.018-0.00955.437-0.052-0.0520.0000.0000.0000.000
178I183ARG10.7460.83748.1086.0816.0810.0000.0000.0000.000
179I184LYS10.8440.92848.3086.2846.2840.0000.0000.0000.000
180I185VAL0-0.018-0.00546.764-0.216-0.2160.0000.0000.0000.000