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: ZNNVN

Calculation Name: 3R1W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R1W

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-27

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 -1842120.608194
FMO2-HF: Nuclear repulsion 1773080.715662
FMO2-HF: Total energy -69039.892532
FMO2-MP2: Total energy -69239.264972


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:10:THR)


Summations of interaction energy for fragment #1(A:10: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.
-17.927-15.656.917-3.97-5.2260.027
Interaction energy analysis for fragmet #1(A:10:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.006
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].
3A12VAL00.0180.0223.300-1.1990.6380.005-0.836-1.0070.000
4A13ARG10.8280.9051.933-17.702-17.2806.913-3.117-4.2190.027
5A14THR00.0460.0175.4040.3850.3850.0000.0000.0000.000
6A15TYR0-0.049-0.0307.9550.0220.0220.0000.0000.0000.000
7A16GLN0-0.023-0.02010.5230.0000.0000.0000.0000.0000.000
8A17GLY00.0170.01912.7770.0100.0100.0000.0000.0000.000
9A18ILE00.0140.02513.707-0.013-0.0130.0000.0000.0000.000
10A19SER0-0.003-0.03410.072-0.029-0.0290.0000.0000.0000.000
11A20PRO0-0.027-0.0018.7630.0320.0320.0000.0000.0000.000
12A21LYS10.8630.93211.497-0.026-0.0260.0000.0000.0000.000
13A22LEU0-0.007-0.0129.5070.0270.0270.0000.0000.0000.000
14A23GLY00.0210.02313.953-0.015-0.0150.0000.0000.0000.000
15A24GLU-1-0.879-0.95716.4300.0590.0590.0000.0000.0000.000
16A25ARG10.7360.82517.771-0.054-0.0540.0000.0000.0000.000
17A26VAL00.0140.03313.1030.0110.0110.0000.0000.0000.000
18A27PHE0-0.018-0.00912.1930.0240.0240.0000.0000.0000.000
19A28VAL00.025-0.0057.946-0.041-0.0410.0000.0000.0000.000
20A29ASP-1-0.754-0.8578.5350.5070.5070.0000.0000.0000.000
21A30ARG10.8740.9535.111-0.117-0.1170.0000.0000.0000.000
22A31SER0-0.079-0.0584.410-0.510-0.492-0.001-0.0170.0000.000
23A32SER0-0.076-0.0376.9640.1240.1240.0000.0000.0000.000
24A33VAL0-0.021-0.0385.4280.1980.1980.0000.0000.0000.000
25A34ILE00.0210.0186.928-0.032-0.0320.0000.0000.0000.000
26A35ILE0-0.044-0.0386.756-0.216-0.2160.0000.0000.0000.000
27A36GLY00.0150.0118.7250.0530.0530.0000.0000.0000.000
28A37ASP-1-0.900-0.95211.367-0.002-0.0020.0000.0000.0000.000
29A38VAL0-0.002-0.01012.4580.0320.0320.0000.0000.0000.000
30A39GLU-1-0.838-0.90214.172-0.002-0.0020.0000.0000.0000.000
31A40LEU0-0.004-0.00612.7760.0200.0200.0000.0000.0000.000
32A41GLY00.0300.01716.629-0.011-0.0110.0000.0000.0000.000
33A42ASP-1-0.770-0.89318.6930.0620.0620.0000.0000.0000.000
34A43ASP-1-0.825-0.87919.5760.0770.0770.0000.0000.0000.000
35A44CYS0-0.0280.00817.1620.0120.0120.0000.0000.0000.000
36A45SER0-0.015-0.00815.4920.0130.0130.0000.0000.0000.000
37A46VAL00.002-0.00411.685-0.012-0.0120.0000.0000.0000.000
38A47TRP00.0000.00012.2720.0320.0320.0000.0000.0000.000
39A48PRO00.0320.01210.8480.0450.0450.0000.0000.0000.000
40A49LEU0-0.017-0.0159.829-0.032-0.0320.0000.0000.0000.000
41A50ALA0-0.0310.02011.3070.0200.0200.0000.0000.0000.000
42A51VAL0-0.031-0.02710.1910.1030.1030.0000.0000.0000.000
43A52ILE00.0040.00010.991-0.078-0.0780.0000.0000.0000.000
44A53ARG10.8500.91911.218-0.393-0.3930.0000.0000.0000.000
45A54GLY00.0780.04812.538-0.010-0.0100.0000.0000.0000.000
46A55ASP-1-0.758-0.87912.7790.2460.2460.0000.0000.0000.000
47A56MET0-0.051-0.02814.484-0.025-0.0250.0000.0000.0000.000
48A57HIS0-0.005-0.02017.820-0.012-0.0120.0000.0000.0000.000
49A58HIS00.0380.04017.6060.0140.0140.0000.0000.0000.000
50A59ILE00.001-0.01215.1370.0130.0130.0000.0000.0000.000
51A60ARG10.8680.92917.889-0.062-0.0620.0000.0000.0000.000
52A61ILE0-0.002-0.00116.5100.0080.0080.0000.0000.0000.000
53A62GLY00.0460.02919.765-0.006-0.0060.0000.0000.0000.000
54A63ALA0-0.003-0.01520.8250.0100.0100.0000.0000.0000.000
55A64ARG10.7010.79221.850-0.064-0.0640.0000.0000.0000.000
56A65THR0-0.0240.00220.1480.0000.0000.0000.0000.0000.000
57A66SER0-0.038-0.01118.9370.0080.0080.0000.0000.0000.000
58A67VAL00.0250.00315.682-0.006-0.0060.0000.0000.0000.000
59A68GLN00.018-0.00515.8440.0200.0200.0000.0000.0000.000
60A69ASP-1-0.770-0.87815.0720.2090.2090.0000.0000.0000.000
61A70GLY0-0.016-0.01314.456-0.027-0.0270.0000.0000.0000.000
62A71SER0-0.071-0.03715.702-0.009-0.0090.0000.0000.0000.000
63A72VAL0-0.035-0.01915.0590.0470.0470.0000.0000.0000.000
64A73LEU00.0050.00915.597-0.041-0.0410.0000.0000.0000.000
65A74HIS0-0.052-0.02915.2620.0260.0260.0000.0000.0000.000
66A75ILE00.0050.01217.360-0.023-0.0230.0000.0000.0000.000
67A76THR0-0.067-0.06019.9580.0190.0190.0000.0000.0000.000
68A77HIS00.0270.01421.491-0.019-0.0190.0000.0000.0000.000
69A78ALA00.0090.01222.839-0.002-0.0020.0000.0000.0000.000
70A79SER0-0.028-0.03326.159-0.001-0.0010.0000.0000.0000.000
71A80ASP-1-0.885-0.94728.7080.0510.0510.0000.0000.0000.000
72A81TYR0-0.049-0.02329.581-0.002-0.0020.0000.0000.0000.000
73A82ASN0-0.022-0.01127.6070.0010.0010.0000.0000.0000.000
74A83PRO00.0500.02728.7930.0010.0010.0000.0000.0000.000
75A84GLY00.0020.01128.7750.0000.0000.0000.0000.0000.000
76A85GLY00.0040.00225.3040.0010.0010.0000.0000.0000.000
77A86TYR0-0.067-0.02624.377-0.007-0.0070.0000.0000.0000.000
78A87PRO00.0310.02221.5190.0140.0140.0000.0000.0000.000
79A88LEU0-0.034-0.01518.5580.0040.0040.0000.0000.0000.000
80A89ILE0-0.048-0.01820.867-0.003-0.0030.0000.0000.0000.000
81A90ILE00.003-0.00820.0810.0020.0020.0000.0000.0000.000
82A91GLY00.0630.04023.159-0.003-0.0030.0000.0000.0000.000
83A92ASP-1-0.755-0.86724.0120.0690.0690.0000.0000.0000.000
84A93ASP-1-0.865-0.91525.3580.0610.0610.0000.0000.0000.000
85A94VAL0-0.029-0.00723.770-0.001-0.0010.0000.0000.0000.000
86A95THR0-0.022-0.01123.4330.0050.0050.0000.0000.0000.000
87A96ILE0-0.016-0.00120.357-0.006-0.0060.0000.0000.0000.000
88A97GLY00.0220.01020.8370.0100.0100.0000.0000.0000.000
89A98HIS0-0.040-0.04919.307-0.004-0.0040.0000.0000.0000.000
90A99GLN0-0.016-0.01018.936-0.023-0.0230.0000.0000.0000.000
91A100ALA00.0150.03720.154-0.005-0.0050.0000.0000.0000.000
92A101MET0-0.030-0.01019.1960.0310.0310.0000.0000.0000.000
93A102LEU0-0.002-0.00520.419-0.020-0.0200.0000.0000.0000.000
94A103HIS10.7860.85319.837-0.152-0.1520.0000.0000.0000.000
95A104GLY00.0380.03121.753-0.011-0.0110.0000.0000.0000.000
96A105CYS0-0.0150.01123.618-0.007-0.0070.0000.0000.0000.000
97A106THR00.001-0.00724.7740.0000.0000.0000.0000.0000.000
98A107ILE0-0.041-0.02824.1880.0000.0000.0000.0000.0000.000
99A108GLY00.0350.02626.935-0.001-0.0010.0000.0000.0000.000
100A109ASN0-0.030-0.04727.8300.0070.0070.0000.0000.0000.000
101A110ARG10.7600.85328.700-0.055-0.0550.0000.0000.0000.000
102A111VAL00.0060.01727.903-0.003-0.0030.0000.0000.0000.000
103A112LEU0-0.041-0.01327.5300.0050.0050.0000.0000.0000.000
104A113ILE00.0310.01124.679-0.004-0.0040.0000.0000.0000.000
105A114GLY00.0370.02525.1860.0080.0080.0000.0000.0000.000
106A115MET00.0190.01223.9810.0070.0070.0000.0000.0000.000
107A116LYS10.8840.92622.931-0.173-0.1730.0000.0000.0000.000
108A117SER0-0.053-0.01224.676-0.003-0.0030.0000.0000.0000.000
109A118MET0-0.012-0.01124.5920.0170.0170.0000.0000.0000.000
110A119ILE0-0.027-0.02225.083-0.014-0.0140.0000.0000.0000.000
111A120MET00.0030.00925.1090.0130.0130.0000.0000.0000.000
112A121ASP-1-0.701-0.81025.0500.1210.1210.0000.0000.0000.000
113A122GLY00.0440.01127.194-0.007-0.0070.0000.0000.0000.000
114A123ALA0-0.082-0.01628.870-0.006-0.0060.0000.0000.0000.000
115A124ILE00.012-0.00529.2140.0020.0020.0000.0000.0000.000
116A125VAL0-0.018-0.00629.062-0.004-0.0040.0000.0000.0000.000
117A126GLU-1-0.799-0.90030.7090.0500.0500.0000.0000.0000.000
118A127ASP-1-0.689-0.84032.0640.0570.0570.0000.0000.0000.000
119A128GLU-1-0.789-0.85332.6760.0430.0430.0000.0000.0000.000
120A129VAL0-0.0270.00732.322-0.002-0.0020.0000.0000.0000.000
121A130ILE0-0.007-0.01031.8030.0040.0040.0000.0000.0000.000
122A131VAL00.0040.00829.354-0.004-0.0040.0000.0000.0000.000
123A132ALA0-0.001-0.01130.1070.0040.0040.0000.0000.0000.000
124A133ALA00.0340.00228.5630.0050.0050.0000.0000.0000.000
125A134GLY0-0.037-0.00628.139-0.006-0.0060.0000.0000.0000.000
126A135ALA0-0.073-0.02329.370-0.002-0.0020.0000.0000.0000.000
127A136THR00.007-0.00529.3050.0090.0090.0000.0000.0000.000
128A137VAL0-0.017-0.01029.721-0.008-0.0080.0000.0000.0000.000
129A138SER00.036-0.00230.0910.0060.0060.0000.0000.0000.000
130A139PRO00.0680.02330.261-0.001-0.0010.0000.0000.0000.000
131A140GLY0-0.0170.00831.296-0.005-0.0050.0000.0000.0000.000
132A141LYS10.8170.91532.984-0.064-0.0640.0000.0000.0000.000
133A142VAL00.0690.04333.1190.0030.0030.0000.0000.0000.000
134A143LEU0-0.124-0.05732.283-0.001-0.0010.0000.0000.0000.000
135A144GLU-1-0.763-0.87035.4000.0440.0440.0000.0000.0000.000
136A145SER0-0.005-0.03336.3580.0010.0010.0000.0000.0000.000
137A146GLY00.0270.02236.838-0.003-0.0030.0000.0000.0000.000
138A147PHE0-0.038-0.02437.531-0.002-0.0020.0000.0000.0000.000
139A148VAL00.0140.00835.7050.0040.0040.0000.0000.0000.000
140A149TYR0-0.017-0.02334.440-0.003-0.0030.0000.0000.0000.000
141A150MET00.0250.01234.4740.0040.0040.0000.0000.0000.000
142A151GLY00.0090.00534.467-0.004-0.0040.0000.0000.0000.000
143A152THR00.0050.02432.1620.0040.0040.0000.0000.0000.000
144A153PRO00.0380.01234.575-0.002-0.0020.0000.0000.0000.000
145A154ALA0-0.021-0.01433.269-0.003-0.0030.0000.0000.0000.000
146A155LYS10.8750.94535.388-0.061-0.0610.0000.0000.0000.000
147A156LYS10.8370.90238.376-0.043-0.0430.0000.0000.0000.000
148A157VAL0-0.073-0.04039.582-0.001-0.0010.0000.0000.0000.000
149A158ARG10.8050.86638.143-0.053-0.0530.0000.0000.0000.000
150A159PRO00.0690.03840.6050.0030.0030.0000.0000.0000.000
151A160ILE0-0.070-0.02836.2160.0000.0000.0000.0000.0000.000
152A161THR0-0.005-0.03239.419-0.002-0.0020.0000.0000.0000.000
153A162GLU-1-0.864-0.94539.4850.0390.0390.0000.0000.0000.000
154A163LYS10.9640.98737.502-0.043-0.0430.0000.0000.0000.000
155A164GLU-1-0.745-0.80635.5500.0540.0540.0000.0000.0000.000
156A165ARG10.8990.93934.711-0.041-0.0410.0000.0000.0000.000
157A166SER0-0.068-0.04635.2230.0010.0010.0000.0000.0000.000
158A167PHE0-0.019-0.02129.4880.0010.0010.0000.0000.0000.000
159A168PHE00.0320.04430.1120.0040.0040.0000.0000.0000.000
160A169THR00.0730.03329.0560.0040.0040.0000.0000.0000.000
161A170TYR0-0.032-0.00629.6180.0010.0010.0000.0000.0000.000
162A171GLY0-0.002-0.00327.9100.0020.0020.0000.0000.0000.000
163A172ALA00.0550.03524.8670.0060.0060.0000.0000.0000.000
164A173GLY00.0540.02024.6730.0040.0040.0000.0000.0000.000
165A174ASN0-0.078-0.05025.485-0.006-0.0060.0000.0000.0000.000
166A175TYR00.0360.00919.190-0.001-0.0010.0000.0000.0000.000
167A176VAL00.0090.01520.8560.0100.0100.0000.0000.0000.000
168A177ARG10.9000.94121.732-0.060-0.0600.0000.0000.0000.000
169A178LEU0-0.068-0.01219.683-0.004-0.0040.0000.0000.0000.000
170A179LYS10.7450.84316.801-0.104-0.1040.0000.0000.0000.000
171A180ASP-1-0.797-0.88117.2170.1130.1130.0000.0000.0000.000
172A181LYS10.9150.95419.234-0.067-0.0670.0000.0000.0000.000
173A182HIS00.0400.01914.6650.0080.0080.0000.0000.0000.000
174A183LEU0-0.0160.01213.5000.0240.0240.0000.0000.0000.000
175A184ALA0-0.060-0.02815.5910.0000.0000.0000.0000.0000.000
176A185GLU-1-0.899-0.93615.9230.0540.0540.0000.0000.0000.000
177A186GLY0-0.019-0.00213.309-0.014-0.0140.0000.0000.0000.000
178A187TYR0-0.103-0.08910.9590.0430.0430.0000.0000.0000.000
179A188ASP-1-0.792-0.8798.6150.4110.4110.0000.0000.0000.000
180A189ARG10.7660.8947.4820.0500.0500.0000.0000.0000.000