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: 89NQY

Calculation Name: 3KV0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KV0

Chain ID: A

ChEMBL ID:

UniProt ID: Q01494

Base Structure: X-ray

Registration Date: 2023-09-22

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 195
LigandCharge MLY=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2319105.925562
FMO2-HF: Nuclear repulsion 2240767.886052
FMO2-HF: Total energy -78338.03951
FMO2-MP2: Total energy -78568.35413


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:14:THR)


Summations of interaction energy for fragment #1(A:14:THR)
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.
-60.499-57.3935.757-19.639-19.226-0.105
Interaction energy analysis for fragmet #1(A:14:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.057
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].
3A16LEU0-0.043-0.0042.333-5.862-2.7902.788-2.482-3.3790.024
4A17GLU-1-0.868-0.9312.119-25.148-19.7267.150-5.623-6.948-0.030
5A18THR0-0.101-0.0564.398-1.284-0.9150.001-0.078-0.2920.000
6A19PHE0-0.091-0.0486.624-0.320-0.3200.0000.0000.0000.000
7A20MLY10.9510.9808.696-0.756-0.7560.0000.0000.0000.000
8A21MLY10.9060.97011.8830.0300.0300.0000.0000.0000.000
9A22SER00.0570.0328.8490.1480.1480.0000.0000.0000.000
10A23PHE00.002-0.02810.6550.0090.0090.0000.0000.0000.000
11A24VAL0-0.011-0.0069.5540.0480.0480.0000.0000.0000.000
12A25ASP-1-0.883-0.93611.574-0.591-0.5910.0000.0000.0000.000
13A26VAL0-0.057-0.02214.3870.0770.0770.0000.0000.0000.000
14A27PRO0-0.019-0.00217.173-0.025-0.0250.0000.0000.0000.000
15A28ILE0-0.018-0.02519.5400.0250.0250.0000.0000.0000.000
16A29ASP-1-0.831-0.91522.677-0.165-0.1650.0000.0000.0000.000
17A30ALA0-0.031-0.04226.0340.0130.0130.0000.0000.0000.000
18A31GLU-1-0.891-0.94527.576-0.139-0.1390.0000.0000.0000.000
19A32MLY10.8100.92829.8440.1350.1350.0000.0000.0000.000
20A33GLY00.0010.00130.6540.0060.0060.0000.0000.0000.000
21A34ASN0-0.049-0.04125.426-0.012-0.0120.0000.0000.0000.000
22A35ALA00.0400.04625.8160.0010.0010.0000.0000.0000.000
23A36ILE00.0190.01021.389-0.017-0.0170.0000.0000.0000.000
24A37SER0-0.023-0.02321.8210.0280.0280.0000.0000.0000.000
25A38THR0-0.018-0.03921.971-0.004-0.0040.0000.0000.0000.000
26A39ALA00.0280.00822.2700.0120.0120.0000.0000.0000.000
27A40GLU-1-0.781-0.87417.614-0.095-0.0950.0000.0000.0000.000
28A41PHE00.0380.01617.3350.0100.0100.0000.0000.0000.000
29A42LEU0-0.042-0.02618.3350.0200.0200.0000.0000.0000.000
30A43GLU-1-0.900-0.95315.5580.0760.0760.0000.0000.0000.000
31A44ALA00.0160.01213.8960.0610.0610.0000.0000.0000.000
32A45ALA0-0.012-0.01014.1240.0430.0430.0000.0000.0000.000
33A46GLU-1-0.860-0.91716.0310.2390.2390.0000.0000.0000.000
34A47SER0-0.020-0.00510.9360.0990.0990.0000.0000.0000.000
35A48LEU00.0270.04611.6450.1350.1350.0000.0000.0000.000
36A49THR0-0.064-0.05812.7490.0560.0560.0000.0000.0000.000
37A50THR0-0.021-0.02810.9300.0780.0780.0000.0000.0000.000
38A51MET00.0390.0277.6650.1420.1420.0000.0000.0000.000
39A52PHE0-0.027-0.02311.663-0.026-0.0260.0000.0000.0000.000
40A53ASP-1-0.801-0.89313.7460.4760.4760.0000.0000.0000.000
41A54VAL0-0.0250.0108.892-0.030-0.0300.0000.0000.0000.000
42A55LEU0-0.034-0.01012.020-0.048-0.0480.0000.0000.0000.000
43A56GLY00.0390.00414.417-0.041-0.0410.0000.0000.0000.000
44A57SER0-0.064-0.02017.045-0.060-0.0600.0000.0000.0000.000
45A58ILE00.0320.00518.399-0.030-0.0300.0000.0000.0000.000
46A59ALA00.0010.01620.644-0.026-0.0260.0000.0000.0000.000
47A60PHE00.045-0.01218.491-0.037-0.0370.0000.0000.0000.000
48A61SER0-0.0160.00220.623-0.012-0.0120.0000.0000.0000.000
49A62PRO0-0.0210.00122.202-0.012-0.0120.0000.0000.0000.000
50A63VAL00.0050.00820.442-0.015-0.0150.0000.0000.0000.000
51A64MLY10.9070.97117.298-0.402-0.4020.0000.0000.0000.000
52A65THR0-0.040-0.03720.293-0.008-0.0080.0000.0000.0000.000
53A66ASP-1-0.918-0.96023.6960.0640.0640.0000.0000.0000.000
54A67MET0-0.0230.00418.467-0.011-0.0110.0000.0000.0000.000
55A68LEU00.0290.00318.715-0.018-0.0180.0000.0000.0000.000
56A69GLY00.0150.01522.255-0.011-0.0110.0000.0000.0000.000
57A70ASN0-0.060-0.04824.625-0.022-0.0220.0000.0000.0000.000
58A71VAL00.0370.01420.169-0.019-0.0190.0000.0000.0000.000
59A72GLU-1-0.864-0.91123.5900.0850.0850.0000.0000.0000.000
60A73MLY10.8290.92326.176-0.051-0.0510.0000.0000.0000.000
61A74ILE0-0.021-0.00624.644-0.008-0.0080.0000.0000.0000.000
62A75ARG10.8700.90421.006-0.133-0.1330.0000.0000.0000.000
63A76MLY10.9620.98526.950-0.060-0.0600.0000.0000.0000.000
64A77ARG10.8850.94330.5000.0030.0030.0000.0000.0000.000
65A78MET00.013-0.00625.439-0.007-0.0070.0000.0000.0000.000
66A79LEU0-0.024-0.01228.072-0.004-0.0040.0000.0000.0000.000
67A80ALA0-0.043-0.01331.171-0.002-0.0020.0000.0000.0000.000
68A81ALA0-0.029-0.00733.624-0.002-0.0020.0000.0000.0000.000
69A82PRO00.0520.04531.669-0.007-0.0070.0000.0000.0000.000
70A83LEU0-0.003-0.01431.792-0.007-0.0070.0000.0000.0000.000
71A84GLU-1-0.879-0.94134.013-0.024-0.0240.0000.0000.0000.000
72A85SER0-0.036-0.03430.316-0.003-0.0030.0000.0000.0000.000
73A86GLN00.0160.01928.418-0.002-0.0020.0000.0000.0000.000
74A87ASN0-0.013-0.00526.403-0.009-0.0090.0000.0000.0000.000
75A88ILE00.0210.00623.9130.0130.0130.0000.0000.0000.000
76A89GLN00.0320.00726.7600.0140.0140.0000.0000.0000.000
77A90ASP-1-0.811-0.89330.054-0.063-0.0630.0000.0000.0000.000
78A91LEU0-0.059-0.01027.9890.0090.0090.0000.0000.0000.000
79A92VAL0-0.023-0.01730.1520.0070.0070.0000.0000.0000.000
80A93ARG10.7810.85232.5840.0780.0780.0000.0000.0000.000
81A94ASN0-0.020-0.03334.8090.0040.0040.0000.0000.0000.000
82A95GLU-1-0.749-0.83734.2260.0080.0080.0000.0000.0000.000
83A96LEU0-0.021-0.02335.7180.0050.0050.0000.0000.0000.000
84A97MLY10.8570.98838.4960.0260.0260.0000.0000.0000.000
85A98THR00.015-0.02739.8530.0040.0040.0000.0000.0000.000
86A99MLY10.8990.94842.008-0.015-0.0150.0000.0000.0000.000
87A100SER0-0.032-0.01236.4190.0040.0040.0000.0000.0000.000
88A101HIS10.9150.95335.972-0.010-0.0100.0000.0000.0000.000
89A102THR0-0.017-0.00732.9630.0000.0000.0000.0000.0000.000
90A103ALA00.0270.01030.3380.0050.0050.0000.0000.0000.000
91A104THR00.027-0.00129.800-0.004-0.0040.0000.0000.0000.000
92A105GLU-1-0.926-0.96130.7780.0160.0160.0000.0000.0000.000
93A106GLY0-0.021-0.01828.8480.0020.0020.0000.0000.0000.000
94A107LEU00.0330.02224.9380.0040.0040.0000.0000.0000.000
95A108LEU0-0.008-0.00226.160-0.006-0.0060.0000.0000.0000.000
96A109TRP0-0.020-0.02927.135-0.007-0.0070.0000.0000.0000.000
97A110LEU00.0290.02420.3540.0050.0050.0000.0000.0000.000
98A111VAL00.0120.00622.104-0.003-0.0030.0000.0000.0000.000
99A112ARG10.9250.97422.6690.0030.0030.0000.0000.0000.000
100A113GLY00.0120.00922.024-0.002-0.0020.0000.0000.0000.000
101A114LEU0-0.0010.00016.9390.0080.0080.0000.0000.0000.000
102A115GLU-1-0.822-0.91418.280-0.112-0.1120.0000.0000.0000.000
103A116PHE0-0.048-0.02420.212-0.010-0.0100.0000.0000.0000.000
104A117THR00.0150.00214.6540.0100.0100.0000.0000.0000.000
105A118CYS00.0440.03115.425-0.027-0.0270.0000.0000.0000.000
106A119ILE0-0.0040.00816.476-0.044-0.0440.0000.0000.0000.000
107A120ALA0-0.022-0.00817.752-0.017-0.0170.0000.0000.0000.000
108A121LEU00.0390.01211.4690.0020.0020.0000.0000.0000.000
109A122SER00.013-0.00114.464-0.078-0.0780.0000.0000.0000.000
110A123MLY10.8160.92215.7840.0880.0880.0000.0000.0000.000
111A124ASN0-0.0120.00714.996-0.009-0.0090.0000.0000.0000.000
112A125ILE00.0430.02711.1110.0150.0150.0000.0000.0000.000
113A126GLY0-0.0300.00614.327-0.051-0.0510.0000.0000.0000.000
114A127SER0-0.080-0.04517.5210.0440.0440.0000.0000.0000.000
115A128THR00.026-0.00117.889-0.015-0.0150.0000.0000.0000.000
116A129GLU-1-0.793-0.86319.826-0.048-0.0480.0000.0000.0000.000
117A130GLU-1-0.702-0.83618.6750.0800.0800.0000.0000.0000.000
118A131LEU00.0210.00113.829-0.021-0.0210.0000.0000.0000.000
119A132ALA00.0220.01318.150-0.010-0.0100.0000.0000.0000.000
120A133ASP-1-0.867-0.93021.3660.0160.0160.0000.0000.0000.000
121A134SER0-0.034-0.02918.688-0.014-0.0140.0000.0000.0000.000
122A135PHE00.0240.00015.779-0.016-0.0160.0000.0000.0000.000
123A136ARG10.8570.89520.986-0.061-0.0610.0000.0000.0000.000
124A137GLY0-0.058-0.03924.125-0.003-0.0030.0000.0000.0000.000
125A138SER00.0340.00420.796-0.010-0.0100.0000.0000.0000.000
126A139TYR00.011-0.01223.471-0.001-0.0010.0000.0000.0000.000
127A140ARG10.8530.91525.4860.0240.0240.0000.0000.0000.000
128A141VAL0-0.005-0.00525.5130.0020.0020.0000.0000.0000.000
129A142THR00.0330.03623.1730.0010.0010.0000.0000.0000.000
130A143LEU00.0130.00123.9930.0030.0030.0000.0000.0000.000
131A144MLY10.9320.98527.636-0.009-0.0090.0000.0000.0000.000
132A145PRO0-0.038-0.03330.2520.0060.0060.0000.0000.0000.000
133A146HIS0-0.013-0.00330.0910.0040.0040.0000.0000.0000.000
134A147HIS00.0540.06527.2440.0030.0030.0000.0000.0000.000
135A148SER00.0390.00732.821-0.003-0.0030.0000.0000.0000.000
136A149PHE00.020-0.02734.8630.0020.0020.0000.0000.0000.000
137A150LEU00.0410.02736.0060.0020.0020.0000.0000.0000.000
138A151VAL00.0380.02430.0970.0070.0070.0000.0000.0000.000
139A152MLY10.8390.94430.556-0.013-0.0130.0000.0000.0000.000
140A153PRO00.006-0.00230.2800.0020.0020.0000.0000.0000.000
141A154ILE00.0160.02527.3260.0070.0070.0000.0000.0000.000
142A155PHE00.0610.02023.8650.0120.0120.0000.0000.0000.000
143A156SER0-0.037-0.02025.5630.0040.0040.0000.0000.0000.000
144A157ALA00.000-0.00226.7080.0020.0020.0000.0000.0000.000
145A158ALA00.0100.01622.6510.0110.0110.0000.0000.0000.000
146A159MET0-0.022-0.00621.7260.0050.0050.0000.0000.0000.000
147A160SER0-0.043-0.02422.268-0.005-0.0050.0000.0000.0000.000
148A161ALA0-0.0250.00622.633-0.001-0.0010.0000.0000.0000.000
149A162CYS0-0.089-0.02618.2960.0260.0260.0000.0000.0000.000
150A163PRO0-0.0060.02014.668-0.008-0.0080.0000.0000.0000.000
151A164TYR00.0210.00917.449-0.041-0.0410.0000.0000.0000.000
152A165ARG10.8330.87914.5790.1750.1750.0000.0000.0000.000
153A166MLY10.8280.92112.1790.0850.0850.0000.0000.0000.000
154A167ASP-1-0.827-0.91812.2280.3750.3750.0000.0000.0000.000
155A168PHE0-0.065-0.04310.3050.1430.1430.0000.0000.0000.000
156A169TYR0-0.023-0.0598.2220.1070.1070.0000.0000.0000.000
157A170ALA00.0450.0347.0380.0570.0570.0000.0000.0000.000
158A171MLY10.8650.9337.212-0.408-0.4080.0000.0000.0000.000
159A172LEU0-0.056-0.0314.2510.2100.404-0.001-0.045-0.1480.000
160A173GLY00.0430.0122.456-0.7110.8921.906-1.487-2.022-0.018
161A174ASP-1-0.941-0.9563.6721.3751.4480.013-0.023-0.0620.000
162A175ASP-1-0.900-0.9534.823-1.583-1.5830.0000.0000.0000.000
163A176GLU-1-0.870-0.9545.740-0.764-0.7640.0000.0000.0000.000
164A177GLN0-0.079-0.0477.852-0.031-0.0310.0000.0000.0000.000
165A178MLY10.9510.9872.6365.2476.0530.313-0.216-0.9040.001
166A179VAL0-0.0010.0092.766-1.970-1.2370.156-0.196-0.6920.000
167A180GLN00.000-0.0014.3610.1580.175-0.001-0.008-0.0080.000
168A181GLU-1-0.905-0.9467.457-1.330-1.3300.0000.0000.0000.000
169A182GLU-1-0.769-0.8551.588-29.931-39.11123.432-9.481-4.771-0.082
170A183LEU00.011-0.0035.9960.8170.8170.0000.0000.0000.000
171A184ARG10.8420.8987.3191.2241.2240.0000.0000.0000.000
172A185GLU-1-0.924-0.9468.526-1.677-1.6770.0000.0000.0000.000
173A186TYR0-0.006-0.0057.6770.3640.3640.0000.0000.0000.000
174A187LEU0-0.006-0.0189.7620.2250.2250.0000.0000.0000.000
175A188VAL0-0.0030.00312.5870.1250.1250.0000.0000.0000.000
176A189ALA00.0000.00912.8790.0920.0920.0000.0000.0000.000
177A190LEU0-0.034-0.02113.6950.0870.0870.0000.0000.0000.000
178A191ASP-1-0.843-0.93015.410-0.211-0.2110.0000.0000.0000.000
179A192MLY10.9390.97617.8180.3960.3960.0000.0000.0000.000
180A193ILE00.007-0.00516.6500.0400.0400.0000.0000.0000.000
181A194VAL00.0090.00319.0160.0340.0340.0000.0000.0000.000
182A195ASN0-0.047-0.03221.3570.0490.0490.0000.0000.0000.000
183A196ILE0-0.075-0.03122.1840.0180.0180.0000.0000.0000.000
184A197LEU00.0150.00822.2200.0180.0180.0000.0000.0000.000
185A198MLY10.8530.94424.5990.1230.1230.0000.0000.0000.000
186A199ARG10.9891.00025.4440.1750.1750.0000.0000.0000.000
187A200PHE0-0.0040.00428.6770.0080.0080.0000.0000.0000.000
188A201LEU0-0.016-0.00827.3440.0100.0100.0000.0000.0000.000
189A202GLU-1-0.975-0.97830.219-0.079-0.0790.0000.0000.0000.000
190A203SER0-0.063-0.04433.3990.0050.0050.0000.0000.0000.000
191A204MLY10.9430.93535.4520.0560.0560.0000.0000.0000.000
192A205GLU-1-0.806-0.87734.670-0.065-0.0650.0000.0000.0000.000
193A206ALA00.0250.03933.0280.0040.0040.0000.0000.0000.000
194A207MLY10.8570.93935.0720.0470.0470.0000.0000.0000.000
195A208TRP00.0420.02233.6610.0020.0020.0000.0000.0000.000