FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8N2NY

Calculation Name: 3AMI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AMI

Chain ID: A

ChEMBL ID:

UniProt ID: F2Z284

Base Structure: X-ray

Registration Date: 2023-09-26

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 422
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7314059.081066
FMO2-HF: Nuclear repulsion 7150548.628469
FMO2-HF: Total energy -163510.452597
FMO2-MP2: Total energy -163988.245747


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:29:PRO)


Summations of interaction energy for fragment #1(A:29:PRO)
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.
-8.683-3.9720.109-1.893-2.9240.009
Interaction energy analysis for fragmet #1(A:29:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.017
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].
3A31ALA0-0.051-0.0163.124-5.209-1.5750.104-1.658-2.0790.009
4A32SER00.0130.0173.908-1.272-0.6480.002-0.146-0.4790.000
5A33THR0-0.0090.0114.665-1.384-1.174-0.001-0.043-0.1650.000
6A34PHE0-0.045-0.0137.0080.2270.2270.0000.0000.0000.000
7A35GLU-1-0.880-0.95210.712-0.004-0.0040.0000.0000.0000.000
8A36THR0-0.0050.00213.7190.0410.0410.0000.0000.0000.000
9A37THR0-0.020-0.00417.465-0.029-0.0290.0000.0000.0000.000
10A38LEU00.0440.02020.4650.0110.0110.0000.0000.0000.000
11A39PRO00.0640.02723.540-0.005-0.0050.0000.0000.0000.000
12A40ASN0-0.038-0.02225.9280.0010.0010.0000.0000.0000.000
13A41GLY0-0.031-0.03624.991-0.007-0.0070.0000.0000.0000.000
14A42LEU0-0.0130.03020.745-0.004-0.0040.0000.0000.0000.000
15A43LYS10.8480.93115.326-0.007-0.0070.0000.0000.0000.000
16A44VAL0-0.005-0.00815.675-0.022-0.0220.0000.0000.0000.000
17A45VAL00.0110.00010.4830.0410.0410.0000.0000.0000.000
18A46VAL0-0.017-0.02210.899-0.044-0.0440.0000.0000.0000.000
19A47ARG10.8820.9413.6201.3741.6170.004-0.046-0.2010.000
20A48GLU-1-0.845-0.9297.4300.3910.3910.0000.0000.0000.000
21A49ASP-1-0.864-0.9496.863-0.845-0.8450.0000.0000.0000.000
22A50HIS10.8510.8988.794-0.039-0.0390.0000.0000.0000.000
23A51ARG10.9350.9859.5240.5500.5500.0000.0000.0000.000
24A52ALA00.009-0.00312.4890.0340.0340.0000.0000.0000.000
25A53PRO00.0320.04715.158-0.008-0.0080.0000.0000.0000.000
26A54THR0-0.099-0.05816.0640.0050.0050.0000.0000.0000.000
27A55LEU00.0120.01614.287-0.016-0.0160.0000.0000.0000.000
28A56VAL0-0.015-0.01213.7990.0170.0170.0000.0000.0000.000
29A57HIS0-0.003-0.00714.8730.0060.0060.0000.0000.0000.000
30A58MET00.0030.00515.834-0.010-0.0100.0000.0000.0000.000
31A59VAL00.0040.00918.1030.0090.0090.0000.0000.0000.000
32A60TRP00.010-0.00216.2460.0020.0020.0000.0000.0000.000
33A61TYR00.0650.02820.7250.0150.0150.0000.0000.0000.000
34A62ARG10.9650.99322.7580.0310.0310.0000.0000.0000.000
35A63VAL0-0.027-0.02624.7070.0100.0100.0000.0000.0000.000
36A64GLY00.0400.04727.234-0.008-0.0080.0000.0000.0000.000
37A65SER00.0840.02828.6360.0040.0040.0000.0000.0000.000
38A66MET0-0.100-0.02926.4590.0060.0060.0000.0000.0000.000
39A67ASP-1-0.795-0.87329.658-0.042-0.0420.0000.0000.0000.000
40A68GLU-1-0.825-0.89932.790-0.046-0.0460.0000.0000.0000.000
41A69THR0-0.021-0.00635.8320.0020.0020.0000.0000.0000.000
42A70THR0-0.018-0.02639.555-0.002-0.0020.0000.0000.0000.000
43A71GLY0-0.0010.01242.0730.0020.0020.0000.0000.0000.000
44A72THR0-0.022-0.00439.9600.0010.0010.0000.0000.0000.000
45A73THR0-0.087-0.04937.502-0.002-0.0020.0000.0000.0000.000
46A74GLY00.0420.01035.5490.0010.0010.0000.0000.0000.000
47A75VAL00.006-0.00635.539-0.001-0.0010.0000.0000.0000.000
48A76ALA0-0.051-0.02830.768-0.001-0.0010.0000.0000.0000.000
49A77HIS00.002-0.00531.0550.0000.0000.0000.0000.0000.000
50A78ALA00.0490.01732.600-0.002-0.0020.0000.0000.0000.000
51A79LEU0-0.035-0.02231.6010.0010.0010.0000.0000.0000.000
52A80GLU-1-0.851-0.90528.103-0.087-0.0870.0000.0000.0000.000
53A81HIS10.8730.92630.8950.0640.0640.0000.0000.0000.000
54A82MET0-0.028-0.00633.4970.0000.0000.0000.0000.0000.000
55A83MET00.0050.02728.4700.0060.0060.0000.0000.0000.000
56A84PHE0-0.035-0.00627.5420.0010.0010.0000.0000.0000.000
57A85LYS10.8380.90333.1030.0500.0500.0000.0000.0000.000
58A86GLY00.0050.01435.3480.0030.0030.0000.0000.0000.000
59A87THR00.0130.00233.1940.0000.0000.0000.0000.0000.000
60A88LYS10.9090.93836.4220.0160.0160.0000.0000.0000.000
61A89ASP-1-0.886-0.93036.218-0.015-0.0150.0000.0000.0000.000
62A90VAL0-0.086-0.03432.731-0.001-0.0010.0000.0000.0000.000
63A91GLY00.0520.03435.753-0.002-0.0020.0000.0000.0000.000
64A92PRO00.0410.00136.478-0.003-0.0030.0000.0000.0000.000
65A93GLY0-0.058-0.01835.3200.0010.0010.0000.0000.0000.000
66A94GLU-1-0.929-0.98134.526-0.042-0.0420.0000.0000.0000.000
67A95PHE00.0080.01025.6700.0000.0000.0000.0000.0000.000
68A96SER00.0430.00129.452-0.001-0.0010.0000.0000.0000.000
69A97LYS10.9240.97330.3800.0440.0440.0000.0000.0000.000
70A98ARG10.9530.97030.9350.0330.0330.0000.0000.0000.000
71A99VAL00.0320.03025.1530.0000.0000.0000.0000.0000.000
72A100ALA00.0150.01027.253-0.004-0.0040.0000.0000.0000.000
73A101ALA0-0.041-0.01829.302-0.001-0.0010.0000.0000.0000.000
74A102MET0-0.116-0.03826.0580.0020.0020.0000.0000.0000.000
75A103GLY0-0.009-0.00226.325-0.002-0.0020.0000.0000.0000.000
76A104GLY0-0.034-0.01223.848-0.011-0.0110.0000.0000.0000.000
77A105ARG10.8970.93920.5810.1740.1740.0000.0000.0000.000
78A106ASP-1-0.842-0.93623.140-0.097-0.0970.0000.0000.0000.000
79A107ASN0-0.0130.01323.8600.0080.0080.0000.0000.0000.000
80A108ALA00.004-0.00424.224-0.001-0.0010.0000.0000.0000.000
81A109PHE0-0.0230.00523.397-0.002-0.0020.0000.0000.0000.000
82A110THR00.024-0.00525.0620.0020.0020.0000.0000.0000.000
83A111THR0-0.042-0.01223.350-0.001-0.0010.0000.0000.0000.000
84A112ARG11.0020.98525.2760.0950.0950.0000.0000.0000.000
85A113ASP-1-0.739-0.84723.327-0.076-0.0760.0000.0000.0000.000
86A114TYR0-0.0100.00620.5280.0040.0040.0000.0000.0000.000
87A115THR00.007-0.00624.386-0.001-0.0010.0000.0000.0000.000
88A116ALA0-0.0190.00320.5010.0030.0030.0000.0000.0000.000
89A117TYR00.0030.00022.2050.0000.0000.0000.0000.0000.000
90A118TYR00.014-0.00119.033-0.006-0.0060.0000.0000.0000.000
91A119GLN00.022-0.00520.1510.0060.0060.0000.0000.0000.000
92A120GLN0-0.031-0.00216.988-0.018-0.0180.0000.0000.0000.000
93A121VAL0-0.001-0.01019.1020.0160.0160.0000.0000.0000.000
94A122PRO00.0440.02019.248-0.014-0.0140.0000.0000.0000.000
95A123SER00.0420.00716.9280.0090.0090.0000.0000.0000.000
96A124SER0-0.027-0.01018.8180.0090.0090.0000.0000.0000.000
97A125ARG10.8770.94121.9650.0560.0560.0000.0000.0000.000
98A126LEU00.0280.01317.324-0.003-0.0030.0000.0000.0000.000
99A127SER0-0.004-0.00521.0020.0010.0010.0000.0000.0000.000
100A128ASP-1-0.811-0.91424.055-0.036-0.0360.0000.0000.0000.000
101A129VAL00.006-0.00821.3420.0020.0020.0000.0000.0000.000
102A130MET0-0.035-0.00118.5470.0030.0030.0000.0000.0000.000
103A131GLY00.0250.01923.6180.0040.0040.0000.0000.0000.000
104A132LEU0-0.012-0.01127.0810.0020.0020.0000.0000.0000.000
105A133GLU-1-0.761-0.85423.298-0.076-0.0760.0000.0000.0000.000
106A134ALA0-0.0090.00526.1840.0020.0020.0000.0000.0000.000
107A135ASP-1-0.819-0.88527.465-0.023-0.0230.0000.0000.0000.000
108A136ARG10.7920.86526.0260.0700.0700.0000.0000.0000.000
109A137MET0-0.055-0.01524.2980.0020.0020.0000.0000.0000.000
110A138ALA0-0.051-0.01329.4380.0020.0020.0000.0000.0000.000
111A139ASN0-0.101-0.07432.7540.0040.0040.0000.0000.0000.000
112A140LEU0-0.037-0.01433.1040.0000.0000.0000.0000.0000.000
113A141VAL0-0.030-0.00935.5140.0030.0030.0000.0000.0000.000
114A142VAL0-0.0060.00438.784-0.002-0.0020.0000.0000.0000.000
115A143ASP-1-0.839-0.94040.205-0.024-0.0240.0000.0000.0000.000
116A144ASP-1-0.867-0.94743.323-0.025-0.0250.0000.0000.0000.000
117A145GLU-1-0.919-0.96946.010-0.026-0.0260.0000.0000.0000.000
118A146LEU0-0.095-0.04740.794-0.002-0.0020.0000.0000.0000.000
119A147PHE00.0400.00439.982-0.002-0.0020.0000.0000.0000.000
120A148LYS10.9350.96942.3660.0250.0250.0000.0000.0000.000
121A149LYS10.9210.97443.7360.0320.0320.0000.0000.0000.000
122A150GLU-1-0.832-0.91937.165-0.054-0.0540.0000.0000.0000.000
123A151ILE00.0330.01140.027-0.003-0.0030.0000.0000.0000.000
124A152GLN0-0.0110.00241.9020.0000.0000.0000.0000.0000.000
125A153VAL0-0.011-0.00538.243-0.001-0.0010.0000.0000.0000.000
126A154ILE00.0270.01036.316-0.003-0.0030.0000.0000.0000.000
127A155ALA0-0.020-0.01239.031-0.002-0.0020.0000.0000.0000.000
128A156GLU-1-0.959-0.99642.003-0.044-0.0440.0000.0000.0000.000
129A157GLU-1-0.916-0.96533.970-0.074-0.0740.0000.0000.0000.000
130A158ARG10.8600.92737.7860.0480.0480.0000.0000.0000.000
131A159ARG10.9270.97439.0160.0410.0410.0000.0000.0000.000
132A160TRP00.0480.03134.329-0.003-0.0030.0000.0000.0000.000
133A161ARG10.8930.95030.9240.0820.0820.0000.0000.0000.000
134A162THR0-0.015-0.02535.678-0.002-0.0020.0000.0000.0000.000
135A163ASP-1-0.949-0.97237.024-0.050-0.0500.0000.0000.0000.000
136A164ASP-1-0.853-0.90439.863-0.051-0.0510.0000.0000.0000.000
137A165LYS10.8590.93732.3010.0840.0840.0000.0000.0000.000
138A166PRO00.0420.01136.934-0.001-0.0010.0000.0000.0000.000
139A167ARG10.9790.97930.0480.0970.0970.0000.0000.0000.000
140A168SER0-0.026-0.00732.966-0.002-0.0020.0000.0000.0000.000
141A169LYS11.0161.01634.8010.0510.0510.0000.0000.0000.000
142A170ALA0-0.034-0.01236.7050.0030.0030.0000.0000.0000.000
143A171TYR0-0.001-0.01229.3500.0020.0020.0000.0000.0000.000
144A172GLU-1-0.865-0.93334.650-0.053-0.0530.0000.0000.0000.000
145A173ALA0-0.003-0.00136.5620.0030.0030.0000.0000.0000.000
146A174LEU0-0.002-0.00733.3970.0030.0030.0000.0000.0000.000
147A175MET0-0.026-0.01130.3590.0020.0020.0000.0000.0000.000
148A176ALA00.0020.00935.2870.0030.0030.0000.0000.0000.000
149A177ALA0-0.023-0.01538.6820.0030.0030.0000.0000.0000.000
150A178SER0-0.019-0.01334.8900.0030.0030.0000.0000.0000.000
151A179TYR0-0.021-0.01430.3000.0020.0020.0000.0000.0000.000
152A180VAL0-0.042-0.02936.9340.0000.0000.0000.0000.0000.000
153A181ALA0-0.058-0.03138.5700.0020.0020.0000.0000.0000.000
154A182HIS00.0400.02930.191-0.002-0.0020.0000.0000.0000.000
155A183PRO00.0530.02932.628-0.002-0.0020.0000.0000.0000.000
156A184TYR0-0.108-0.10625.935-0.003-0.0030.0000.0000.0000.000
157A185ARG10.8640.93232.0670.0360.0360.0000.0000.0000.000
158A186VAL0-0.066-0.01734.9240.0010.0010.0000.0000.0000.000
159A187PRO0-0.0190.00433.696-0.004-0.0040.0000.0000.0000.000
160A188VAL00.002-0.01129.0240.0030.0030.0000.0000.0000.000
161A189ILE0-0.030-0.00132.3140.0020.0020.0000.0000.0000.000
162A190GLY00.0680.03934.8830.0030.0030.0000.0000.0000.000
163A191TRP0-0.052-0.03837.548-0.002-0.0020.0000.0000.0000.000
164A192MET0-0.004-0.00240.9910.0000.0000.0000.0000.0000.000
165A193ASN00.013-0.01643.2710.0010.0010.0000.0000.0000.000
166A194ASP-1-0.788-0.87941.677-0.033-0.0330.0000.0000.0000.000
167A195ILE0-0.012-0.00939.0820.0010.0010.0000.0000.0000.000
168A196GLN0-0.066-0.04342.387-0.001-0.0010.0000.0000.0000.000
169A197ASN0-0.020-0.00145.5810.0020.0020.0000.0000.0000.000
170A198MET0-0.0460.03037.9540.0010.0010.0000.0000.0000.000
171A199THR0-0.020-0.01943.9410.0010.0010.0000.0000.0000.000
172A200ALA00.0550.00742.362-0.001-0.0010.0000.0000.0000.000
173A201GLN0-0.027-0.02641.782-0.001-0.0010.0000.0000.0000.000
174A202ASP-1-0.777-0.87141.048-0.027-0.0270.0000.0000.0000.000
175A203VAL0-0.009-0.01336.506-0.001-0.0010.0000.0000.0000.000
176A204ARG10.8300.91537.3550.0220.0220.0000.0000.0000.000
177A205ASP-1-0.854-0.92138.300-0.020-0.0200.0000.0000.0000.000
178A206TRP0-0.020-0.01931.9470.0030.0030.0000.0000.0000.000
179A207TYR00.004-0.00531.9190.0010.0010.0000.0000.0000.000
180A208LYS10.9530.97833.6740.0130.0130.0000.0000.0000.000
181A209ARG10.9180.97034.7000.0230.0230.0000.0000.0000.000
182A210TRP0-0.011-0.01830.3620.0030.0030.0000.0000.0000.000
183A211TYR00.0030.01428.921-0.006-0.0060.0000.0000.0000.000
184A212GLY00.0680.04429.6090.0020.0020.0000.0000.0000.000
185A213PRO00.0300.01026.093-0.004-0.0040.0000.0000.0000.000
186A214ASN0-0.047-0.02324.845-0.002-0.0020.0000.0000.0000.000
187A215ASN0-0.086-0.05225.7320.0030.0030.0000.0000.0000.000
188A216ALA00.0240.01522.876-0.010-0.0100.0000.0000.0000.000
189A217THR0-0.032-0.01516.4520.0110.0110.0000.0000.0000.000
190A218VAL0-0.0020.00717.226-0.016-0.0160.0000.0000.0000.000
191A219VAL0-0.011-0.00712.0540.0120.0120.0000.0000.0000.000
192A220VAL0-0.011-0.00813.207-0.002-0.0020.0000.0000.0000.000
193A221VAL00.0340.0128.714-0.001-0.0010.0000.0000.0000.000
194A222GLY00.0330.01510.3690.0080.0080.0000.0000.0000.000
195A223ASP-1-0.847-0.90011.412-0.022-0.0220.0000.0000.0000.000
196A224VAL0-0.031-0.02012.4220.0280.0280.0000.0000.0000.000
197A225GLU-1-0.868-0.93312.7300.2420.2420.0000.0000.0000.000
198A226HIS10.8510.91312.218-0.423-0.4230.0000.0000.0000.000
199A227GLU-1-0.827-0.90114.2490.1860.1860.0000.0000.0000.000
200A228ALA0-0.009-0.00417.701-0.022-0.0220.0000.0000.0000.000
201A229VAL00.0000.00315.009-0.021-0.0210.0000.0000.0000.000
202A230PHE0-0.005-0.01814.140-0.012-0.0120.0000.0000.0000.000
203A231ARG10.8300.87719.160-0.127-0.1270.0000.0000.0000.000
204A232LEU00.0020.00620.948-0.009-0.0090.0000.0000.0000.000
205A233ALA00.0300.03220.132-0.009-0.0090.0000.0000.0000.000
206A234GLU-1-0.865-0.91122.2210.0760.0760.0000.0000.0000.000
207A235GLN0-0.096-0.05724.981-0.010-0.0100.0000.0000.0000.000
208A236THR0-0.012-0.01324.346-0.006-0.0060.0000.0000.0000.000
209A237TYR00.0700.00321.5010.0000.0000.0000.0000.0000.000
210A238GLY0-0.014-0.01325.7180.0010.0010.0000.0000.0000.000
211A239LYS10.8540.94626.908-0.015-0.0150.0000.0000.0000.000
212A240LEU0-0.0020.01828.384-0.002-0.0020.0000.0000.0000.000
213A241ALA0-0.001-0.00930.6200.0040.0040.0000.0000.0000.000
214A242ARG10.9050.94927.358-0.025-0.0250.0000.0000.0000.000
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