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: 6YN3Z

Calculation Name: 2NYI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NYI

Chain ID: A

ChEMBL ID:

UniProt ID: J3QW32

Base Structure: X-ray

Registration Date: 2023-09-21

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1519054.916734
FMO2-HF: Nuclear repulsion 1452990.667294
FMO2-HF: Total energy -66064.24944
FMO2-MP2: Total energy -66258.004297


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:2:GLU)


Summations of interaction energy for fragment #1(A:2:GLU)
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.
-91.597-104.68744.474-17.853-13.5320.193
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.803 / q_NPA : -0.884
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].
3A4GLN0-0.078-0.0451.775-8.041-12.88715.891-5.728-5.3170.047
4A5SER00.0310.0005.453-4.695-4.6950.0000.0000.0000.000
5A6PHE0-0.033-0.0278.7052.3832.3830.0000.0000.0000.000
6A7VAL00.0090.01611.814-1.041-1.0410.0000.0000.0000.000
7A8VAL00.003-0.00415.4320.2480.2480.0000.0000.0000.000
8A9SER0-0.039-0.02417.966-0.523-0.5230.0000.0000.0000.000
9A10VAL00.002-0.00921.7430.1110.1110.0000.0000.0000.000
10A11ALA00.0240.01524.658-0.189-0.1890.0000.0000.0000.000
11A12GLY00.0140.00428.4260.1010.1010.0000.0000.0000.000
12A13SER00.0130.00631.741-0.037-0.0370.0000.0000.0000.000
13A14ASP-1-0.853-0.93833.6969.4679.4670.0000.0000.0000.000
14A15ARG10.7570.86029.858-10.234-10.2340.0000.0000.0000.000
15A16VAL00.0320.01133.3290.2660.2660.0000.0000.0000.000
16A17GLY00.0110.00730.826-0.027-0.0270.0000.0000.0000.000
17A18ILE00.0230.04127.3450.3680.3680.0000.0000.0000.000
18A19VAL00.0830.02924.7920.4560.4560.0000.0000.0000.000
19A20HIS0-0.0320.00724.6140.6180.6180.0000.0000.0000.000
20A21ASP-1-0.773-0.89024.58610.96510.9650.0000.0000.0000.000
21A22PHE00.0290.00819.1380.5130.5130.0000.0000.0000.000
22A23SER0-0.005-0.02520.4270.8750.8750.0000.0000.0000.000
23A24TRP0-0.057-0.02619.9130.6480.6480.0000.0000.0000.000
24A25ALA00.0220.01120.0860.3970.3970.0000.0000.0000.000
25A26LEU00.005-0.00115.4330.7830.7830.0000.0000.0000.000
26A27LYS10.9680.98415.415-12.576-12.5760.0000.0000.0000.000
27A28ASN0-0.070-0.03016.422-0.003-0.0030.0000.0000.0000.000
28A29ILE0-0.049-0.01613.5500.1120.1120.0000.0000.0000.000
29A30SER0-0.067-0.03411.1231.2891.2890.0000.0000.0000.000
30A31ALA0-0.0180.00710.9411.7021.7020.0000.0000.0000.000
31A32ASN0-0.015-0.02112.153-2.286-2.2860.0000.0000.0000.000
32A33VAL00.0110.00413.5701.0411.0410.0000.0000.0000.000
33A34GLU-1-0.873-0.90611.16824.23424.2340.0000.0000.0000.000
34A35SER00.004-0.00914.781-0.894-0.8940.0000.0000.0000.000
35A36SER0-0.032-0.02218.0950.2420.2420.0000.0000.0000.000
36A37ARG10.8660.91420.963-12.606-12.6060.0000.0000.0000.000
37A38MET0-0.019-0.00724.2440.3030.3030.0000.0000.0000.000
38A39ALA00.0420.02527.005-0.241-0.2410.0000.0000.0000.000
39A40CYS0-0.049-0.02230.6260.2860.2860.0000.0000.0000.000
40A41LEU00.0570.02533.634-0.186-0.1860.0000.0000.0000.000
41A42GLY00.0070.00636.8690.0630.0630.0000.0000.0000.000
42A43GLY0-0.025-0.00738.097-0.217-0.2170.0000.0000.0000.000
43A44ASP-1-0.901-0.92733.8899.0489.0480.0000.0000.0000.000
44A45PHE00.008-0.01826.5000.0650.0650.0000.0000.0000.000
45A46ALA00.020-0.00528.2760.1490.1490.0000.0000.0000.000
46A47MET0-0.043-0.01022.546-0.114-0.1140.0000.0000.0000.000
47A48ILE00.0120.00820.1180.4010.4010.0000.0000.0000.000
48A49VAL0-0.020-0.02217.252-0.260-0.2600.0000.0000.0000.000
49A50LEU0-0.0050.02413.8940.7160.7160.0000.0000.0000.000
50A51VAL00.010-0.00412.647-0.617-0.6170.0000.0000.0000.000
51A52SER0-0.004-0.0088.9342.9212.9210.0000.0000.0000.000
52A53LEU00.0370.0078.113-2.009-2.0090.0000.0000.0000.000
53A54ASN0-0.0170.0074.1046.8176.9670.000-0.068-0.0830.000
54A55ALA00.0160.0034.915-1.508-1.340-0.001-0.010-0.1570.000
55A56LYS10.8430.8931.762-146.686-155.29828.585-12.045-7.9280.146
56A57ASP-1-0.836-0.9266.21425.73025.7300.0000.0000.0000.000
57A58GLY00.0760.0479.817-0.488-0.4880.0000.0000.0000.000
58A59LYS10.8530.90612.491-24.335-24.3350.0000.0000.0000.000
59A60LEU00.0080.02111.847-1.291-1.2910.0000.0000.0000.000
60A61ILE00.0460.02011.842-0.978-0.9780.0000.0000.0000.000
61A62GLN0-0.034-0.02715.547-0.276-0.2760.0000.0000.0000.000
62A63SER0-0.016-0.02218.074-1.100-1.1000.0000.0000.0000.000
63A64ALA0-0.036-0.01517.691-0.857-0.8570.0000.0000.0000.000
64A65LEU00.0050.00418.931-0.737-0.7370.0000.0000.0000.000
65A66GLU-1-0.842-0.92021.49812.99412.9940.0000.0000.0000.000
66A67SER0-0.092-0.04522.870-0.617-0.6170.0000.0000.0000.000
67A68ALA0-0.048-0.01623.609-0.410-0.4100.0000.0000.0000.000
68A69LEU0-0.061-0.01624.861-0.403-0.4030.0000.0000.0000.000
69A70PRO00.0340.01827.2760.0230.0230.0000.0000.0000.000
70A71GLY0-0.013-0.01629.236-0.353-0.3530.0000.0000.0000.000
71A72PHE0-0.0270.00127.890-0.193-0.1930.0000.0000.0000.000
72A73GLN0-0.0170.00326.4390.3120.3120.0000.0000.0000.000
73A74ILE00.0100.00221.6620.2280.2280.0000.0000.0000.000
74A75SER0-0.046-0.00520.5310.1270.1270.0000.0000.0000.000
75A76THR00.0470.00314.4490.3510.3510.0000.0000.0000.000
76A77ARG10.8830.94014.069-19.564-19.5640.0000.0000.0000.000
77A78ARG10.8480.9284.773-46.301-46.251-0.001-0.002-0.0470.000
78A79ALA00.0030.00110.194-2.160-2.1600.0000.0000.0000.000
79A80SER0-0.010-0.01210.6511.9681.9680.0000.0000.0000.000
80A81SER00.0300.01710.361-0.553-0.5530.0000.0000.0000.000
81A82VAL00.0170.00111.746-0.186-0.1860.0000.0000.0000.000
82A83ALA00.0320.01714.334-0.985-0.9850.0000.0000.0000.000
83A84GLU-1-0.831-0.88313.03521.98721.9870.0000.0000.0000.000
84A85ARG10.7540.84214.509-20.109-20.1090.0000.0000.0000.000
85A86HIS00.0000.00918.8230.2110.2110.0000.0000.0000.000
86A87VAL00.0090.01620.383-0.503-0.5030.0000.0000.0000.000
87A88SER00.0060.00723.8220.3600.3600.0000.0000.0000.000
88A89PRO00.0390.02425.3740.0760.0760.0000.0000.0000.000
89A90ASP-1-0.859-0.91626.69610.01210.0120.0000.0000.0000.000
90A91THR0-0.077-0.05626.726-0.369-0.3690.0000.0000.0000.000
91A92ARG10.8370.92228.394-10.184-10.1840.0000.0000.0000.000
92A93GLU-1-0.803-0.88527.01211.67911.6790.0000.0000.0000.000
93A94TYR0-0.054-0.06330.358-0.217-0.2170.0000.0000.0000.000
94A95GLU-1-0.809-0.86832.7689.6549.6540.0000.0000.0000.000
95A96LEU0-0.028-0.02035.343-0.181-0.1810.0000.0000.0000.000
96A97TYR0-0.074-0.06036.3130.0730.0730.0000.0000.0000.000
97A98VAL00.0160.00440.582-0.087-0.0870.0000.0000.0000.000
98A99GLU-1-0.784-0.85943.5636.7976.7970.0000.0000.0000.000
99A100GLY00.0820.04346.720-0.081-0.0810.0000.0000.0000.000
100A101PRO0-0.030-0.02249.9580.0240.0240.0000.0000.0000.000
101A102ASP-1-0.860-0.94748.0536.8116.8110.0000.0000.0000.000
102A103SER0-0.052-0.03848.828-0.156-0.1560.0000.0000.0000.000
103A104GLU-1-0.965-0.98447.8536.6146.6140.0000.0000.0000.000
104A105GLY00.0070.00646.2270.1470.1470.0000.0000.0000.000
105A106ILE00.0150.03044.2590.1310.1310.0000.0000.0000.000
106A107VAL00.0470.01539.5360.1400.1400.0000.0000.0000.000
107A108GLU-1-0.946-0.95340.5577.6587.6580.0000.0000.0000.000
108A109ALA00.0610.03941.4380.1600.1600.0000.0000.0000.000
109A110VAL00.0380.01239.2310.0970.0970.0000.0000.0000.000
110A111THR0-0.041-0.04736.5960.2200.2200.0000.0000.0000.000
111A112ALA0-0.006-0.00737.1730.2360.2360.0000.0000.0000.000
112A113VAL0-0.056-0.02539.2820.0700.0700.0000.0000.0000.000
113A114LEU00.0230.01334.8940.0940.0940.0000.0000.0000.000
114A115ALA00.0040.00434.3950.1810.1810.0000.0000.0000.000
115A116LYS10.8610.92735.424-7.497-7.4970.0000.0000.0000.000
116A117LYS10.7760.87736.753-7.939-7.9390.0000.0000.0000.000
117A118GLY0-0.035-0.01232.7110.1420.1420.0000.0000.0000.000
118A119ALA0-0.036-0.00531.0810.3700.3700.0000.0000.0000.000
119A120ASN0-0.024-0.01125.967-0.041-0.0410.0000.0000.0000.000
120A121ILE00.0180.00929.093-0.229-0.2290.0000.0000.0000.000
121A122VAL0-0.099-0.03925.1750.4980.4980.0000.0000.0000.000
122A123GLU-1-0.792-0.89027.33311.60811.6080.0000.0000.0000.000
123A124LEU0-0.032-0.01430.080-0.209-0.2090.0000.0000.0000.000
124A125GLU-1-0.971-0.96333.3858.9908.9900.0000.0000.0000.000
125A126THR00.009-0.01236.023-0.090-0.0900.0000.0000.0000.000
126A127GLU-1-0.886-0.92339.7707.3387.3380.0000.0000.0000.000
127A128THR0-0.004-0.00442.810-0.059-0.0590.0000.0000.0000.000
128A129LEU0-0.024-0.00646.017-0.036-0.0360.0000.0000.0000.000
129A130PRO0-0.034-0.01649.105-0.108-0.1080.0000.0000.0000.000
130A131ALA00.0290.03052.6790.0100.0100.0000.0000.0000.000
131A132PRO0-0.067-0.04155.452-0.036-0.0360.0000.0000.0000.000
132A133PHE0-0.040-0.02057.949-0.117-0.1170.0000.0000.0000.000
133A134ALA00.005-0.00758.7510.0810.0810.0000.0000.0000.000
134A135GLY0-0.005-0.01258.966-0.061-0.0610.0000.0000.0000.000
135A136PHE0-0.0080.00353.316-0.009-0.0090.0000.0000.0000.000
136A137THR00.0080.00649.851-0.054-0.0540.0000.0000.0000.000
137A138LEU0-0.0370.00748.685-0.039-0.0390.0000.0000.0000.000
138A139PHE00.0380.00942.3630.1130.1130.0000.0000.0000.000
139A140ARG10.7650.84042.959-7.009-7.0090.0000.0000.0000.000
140A141MET0-0.037-0.01937.1330.1000.1000.0000.0000.0000.000
141A142GLY00.0440.03837.665-0.137-0.1370.0000.0000.0000.000
142A143SER0-0.057-0.05733.5140.1940.1940.0000.0000.0000.000
143A144ARG10.8210.90827.751-10.850-10.8500.0000.0000.0000.000
144A145VAL00.0280.00930.9260.3010.3010.0000.0000.0000.000
145A146ALA00.006-0.00628.0420.0390.0390.0000.0000.0000.000
146A147PHE00.0280.00830.0180.1030.1030.0000.0000.0000.000
147A148PRO0-0.016-0.01730.3440.0400.0400.0000.0000.0000.000
148A149PHE00.0730.03732.157-0.283-0.2830.0000.0000.0000.000
149A150PRO0-0.069-0.03434.750-0.272-0.2720.0000.0000.0000.000
150A151LEU00.0020.00834.531-0.233-0.2330.0000.0000.0000.000
151A152TYR0-0.009-0.00237.948-0.225-0.2250.0000.0000.0000.000
152A153GLN00.0470.01739.146-0.110-0.1100.0000.0000.0000.000
153A154GLU-1-0.844-0.89640.4317.7227.7220.0000.0000.0000.000
154A155VAL0-0.025-0.00837.252-0.070-0.0700.0000.0000.0000.000
155A156VAL00.0770.03940.705-0.091-0.0910.0000.0000.0000.000
156A157THR0-0.046-0.03243.377-0.192-0.1920.0000.0000.0000.000
157A158ALA0-0.066-0.02742.586-0.141-0.1410.0000.0000.0000.000
158A159LEU00.0270.00440.186-0.056-0.0560.0000.0000.0000.000
159A160SER00.0150.00644.441-0.140-0.1400.0000.0000.0000.000
160A161ARG10.8090.89347.673-6.545-6.5450.0000.0000.0000.000
161A162VAL0-0.002-0.00144.355-0.111-0.1110.0000.0000.0000.000
162A163GLU-1-0.851-0.92247.3526.6666.6660.0000.0000.0000.000
163A164GLU-1-0.948-0.97549.5185.7565.7560.0000.0000.0000.000
164A165GLU-1-0.998-0.99350.1766.3356.3350.0000.0000.0000.000
165A166PHE0-0.055-0.03748.454-0.026-0.0260.0000.0000.0000.000
166A167GLY0-0.0330.00751.398-0.037-0.0370.0000.0000.0000.000
167A168VAL0-0.111-0.05547.214-0.013-0.0130.0000.0000.0000.000
168A169ASP-1-0.866-0.92448.4006.2946.2940.0000.0000.0000.000
169A170ILE0-0.077-0.06642.5740.1880.1880.0000.0000.0000.000
170A171ASP-1-0.889-0.91642.1287.1337.1330.0000.0000.0000.000
171A172LEU0-0.054-0.05136.9730.2370.2370.0000.0000.0000.000
172A173GLU-1-0.905-0.93938.3457.5897.5890.0000.0000.0000.000
173A174GLU-1-0.894-0.93534.1889.3189.3180.0000.0000.0000.000
174A175VAL0-0.039-0.02029.808-0.101-0.1010.0000.0000.0000.000
175A176VAL0-0.078-0.03131.0740.3150.3150.0000.0000.0000.000