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: 6GGYZ

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1840041.962135
FMO2-HF: Nuclear repulsion 1771002.159119
FMO2-HF: Total energy -69039.803017
FMO2-MP2: Total energy -69239.166281


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.
-9.779-4.5650.903-2.422-3.6970.005
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 : -0.005 / q_NPA : -0.020
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].
3A12VAL00.0130.0203.266-2.300-0.1310.002-0.974-1.198-0.001
4A13ARG10.8510.9162.508-8.627-5.5750.903-1.438-2.5180.006
5A14THR00.0480.0225.2830.2280.255-0.001-0.003-0.0230.000
6A15TYR0-0.027-0.0118.191-0.040-0.0400.0000.0000.0000.000
7A16GLN0-0.011-0.01410.6150.0210.0210.0000.0000.0000.000
8A17GLY00.0100.00512.7380.0090.0090.0000.0000.0000.000
9A18ILE00.0260.03113.4720.0010.0010.0000.0000.0000.000
10A19SER0-0.026-0.0359.849-0.024-0.0240.0000.0000.0000.000
11A20PRO0-0.0100.0068.3490.0140.0140.0000.0000.0000.000
12A21LYS10.8290.91711.250-0.093-0.0930.0000.0000.0000.000
13A22LEU0-0.018-0.0209.6590.0150.0150.0000.0000.0000.000
14A23GLY00.0220.02414.182-0.018-0.0180.0000.0000.0000.000
15A24GLU-1-0.931-0.98016.6630.1490.1490.0000.0000.0000.000
16A25ARG10.7720.85017.634-0.119-0.1190.0000.0000.0000.000
17A26VAL00.0140.02613.322-0.002-0.0020.0000.0000.0000.000
18A27PHE0-0.021-0.00112.0560.0390.0390.0000.0000.0000.000
19A28VAL00.0160.0008.100-0.038-0.0380.0000.0000.0000.000
20A29ASP-1-0.754-0.8599.0480.3660.3660.0000.0000.0000.000
21A30ARG10.9100.9615.4130.1170.1170.0000.0000.0000.000
22A31SER0-0.095-0.0774.895-0.311-0.345-0.001-0.0070.0420.000
23A32SER0-0.084-0.0337.4370.1210.1210.0000.0000.0000.000
24A33VAL0-0.019-0.0305.3600.1580.1580.0000.0000.0000.000
25A34ILE00.0080.0106.638-0.049-0.0490.0000.0000.0000.000
26A35ILE0-0.038-0.0296.678-0.147-0.1470.0000.0000.0000.000
27A36GLY00.0230.0028.7450.0280.0280.0000.0000.0000.000
28A37ASP-1-0.889-0.93411.3400.0950.0950.0000.0000.0000.000
29A38VAL0-0.020-0.01912.2150.0110.0110.0000.0000.0000.000
30A39GLU-1-0.847-0.91013.7170.1050.1050.0000.0000.0000.000
31A40LEU0-0.013-0.01312.8190.0040.0040.0000.0000.0000.000
32A41GLY00.0520.02116.4170.0000.0000.0000.0000.0000.000
33A42ASP-1-0.789-0.89918.5800.1380.1380.0000.0000.0000.000
34A43ASP-1-0.817-0.89019.6050.1210.1210.0000.0000.0000.000
35A44CYS0-0.0100.01816.713-0.006-0.0060.0000.0000.0000.000
36A45SER0-0.028-0.01515.6100.0120.0120.0000.0000.0000.000
37A46VAL0-0.010-0.00311.760-0.021-0.0210.0000.0000.0000.000
38A47TRP0-0.024-0.01512.4800.0310.0310.0000.0000.0000.000
39A48PRO00.0240.00511.4360.0420.0420.0000.0000.0000.000
40A49LEU0-0.020-0.01410.164-0.020-0.0200.0000.0000.0000.000
41A50ALA0-0.0140.02711.936-0.011-0.0110.0000.0000.0000.000
42A51VAL0-0.027-0.02910.3330.0890.0890.0000.0000.0000.000
43A52ILE00.0140.00811.017-0.066-0.0660.0000.0000.0000.000
44A53ARG10.8570.90611.280-0.303-0.3030.0000.0000.0000.000
45A54GLY00.0630.03612.335-0.018-0.0180.0000.0000.0000.000
46A55ASP-1-0.759-0.86212.7020.2200.2200.0000.0000.0000.000
47A56MET0-0.090-0.06214.339-0.026-0.0260.0000.0000.0000.000
48A57HIS0-0.002-0.01317.517-0.010-0.0100.0000.0000.0000.000
49A58HIS00.0220.03317.3970.0170.0170.0000.0000.0000.000
50A59ILE0-0.016-0.02115.1020.0030.0030.0000.0000.0000.000
51A60ARG10.9380.97317.360-0.096-0.0960.0000.0000.0000.000
52A61ILE0-0.003-0.00316.579-0.002-0.0020.0000.0000.0000.000
53A62GLY00.0300.02619.7510.0020.0020.0000.0000.0000.000
54A63ALA0-0.015-0.02420.9140.0140.0140.0000.0000.0000.000
55A64ARG10.7190.81921.992-0.101-0.1010.0000.0000.0000.000
56A65THR00.0100.00720.159-0.010-0.0100.0000.0000.0000.000
57A66SER0-0.030-0.00118.9880.0150.0150.0000.0000.0000.000
58A67VAL00.0310.00515.749-0.011-0.0110.0000.0000.0000.000
59A68GLN00.004-0.01516.2620.0190.0190.0000.0000.0000.000
60A69ASP-1-0.770-0.88015.6630.1900.1900.0000.0000.0000.000
61A70GLY0-0.0040.00115.150-0.025-0.0250.0000.0000.0000.000
62A71SER0-0.065-0.03416.318-0.014-0.0140.0000.0000.0000.000
63A72VAL0-0.025-0.01114.9870.0440.0440.0000.0000.0000.000
64A73LEU0-0.017-0.00515.543-0.036-0.0360.0000.0000.0000.000
65A74HIS0-0.042-0.02015.2450.0200.0200.0000.0000.0000.000
66A75ILE00.0290.02217.308-0.016-0.0160.0000.0000.0000.000
67A76THR0-0.059-0.06420.0560.0110.0110.0000.0000.0000.000
68A77HIS0-0.0070.00121.188-0.013-0.0130.0000.0000.0000.000
69A78ALA00.0200.01422.714-0.003-0.0030.0000.0000.0000.000
70A79SER0-0.026-0.02925.992-0.003-0.0030.0000.0000.0000.000
71A80ASP-1-0.872-0.94328.4580.0470.0470.0000.0000.0000.000
72A81TYR0-0.070-0.03329.286-0.001-0.0010.0000.0000.0000.000
73A82ASN0-0.012-0.00627.5680.0000.0000.0000.0000.0000.000
74A83PRO00.0670.04428.5770.0030.0030.0000.0000.0000.000
75A84GLY00.0010.00528.5190.0000.0000.0000.0000.0000.000
76A85GLY0-0.004-0.00825.1690.0030.0030.0000.0000.0000.000
77A86TYR0-0.071-0.02924.295-0.005-0.0050.0000.0000.0000.000
78A87PRO00.0360.02921.7560.0100.0100.0000.0000.0000.000
79A88LEU0-0.030-0.01418.6660.0000.0000.0000.0000.0000.000
80A89ILE0-0.048-0.01920.9590.0030.0030.0000.0000.0000.000
81A90ILE00.002-0.00920.008-0.003-0.0030.0000.0000.0000.000
82A91GLY00.0550.04423.0210.0030.0030.0000.0000.0000.000
83A92ASP-1-0.754-0.87323.9210.1080.1080.0000.0000.0000.000
84A93ASP-1-0.869-0.91025.2540.0820.0820.0000.0000.0000.000
85A94VAL0-0.027-0.01123.827-0.006-0.0060.0000.0000.0000.000
86A95THR0-0.029-0.00923.5190.0070.0070.0000.0000.0000.000
87A96ILE0-0.008-0.00320.257-0.009-0.0090.0000.0000.0000.000
88A97GLY00.0200.00921.2300.0100.0100.0000.0000.0000.000
89A98HIS0-0.040-0.04919.9520.0000.0000.0000.0000.0000.000
90A99GLN0-0.031-0.01619.523-0.023-0.0230.0000.0000.0000.000
91A100ALA00.0060.03420.525-0.009-0.0090.0000.0000.0000.000
92A101MET0-0.0070.00019.1400.0240.0240.0000.0000.0000.000
93A102LEU0-0.006-0.00720.423-0.018-0.0180.0000.0000.0000.000
94A103HIS10.7730.85419.863-0.139-0.1390.0000.0000.0000.000
95A104GLY00.0610.04221.671-0.010-0.0100.0000.0000.0000.000
96A105CYS0-0.0280.00923.533-0.007-0.0070.0000.0000.0000.000
97A106THR00.010-0.00124.9410.0030.0030.0000.0000.0000.000
98A107ILE0-0.048-0.03424.187-0.003-0.0030.0000.0000.0000.000
99A108GLY00.0420.03226.8470.0020.0020.0000.0000.0000.000
100A109ASN0-0.036-0.04427.7380.0110.0110.0000.0000.0000.000
101A110ARG10.7870.87428.798-0.072-0.0720.0000.0000.0000.000
102A111VAL00.0060.02128.046-0.005-0.0050.0000.0000.0000.000
103A112LEU0-0.029-0.00527.6820.0060.0060.0000.0000.0000.000
104A113ILE00.0240.00224.884-0.005-0.0050.0000.0000.0000.000
105A114GLY00.0290.02325.8400.0060.0060.0000.0000.0000.000
106A115MET00.0200.01224.5810.0070.0070.0000.0000.0000.000
107A116LYS10.8970.92923.550-0.142-0.1420.0000.0000.0000.000
108A117SER0-0.068-0.02125.190-0.005-0.0050.0000.0000.0000.000
109A118MET00.004-0.00624.8720.0140.0140.0000.0000.0000.000
110A119ILE0-0.022-0.01825.214-0.012-0.0120.0000.0000.0000.000
111A120MET0-0.014-0.00525.2680.0110.0110.0000.0000.0000.000
112A121ASP-1-0.674-0.79524.7570.1140.1140.0000.0000.0000.000
113A122GLY00.019-0.00927.159-0.007-0.0070.0000.0000.0000.000
114A123ALA0-0.090-0.02128.975-0.005-0.0050.0000.0000.0000.000
115A124ILE00.012-0.00829.3220.0040.0040.0000.0000.0000.000
116A125VAL0-0.043-0.02129.259-0.004-0.0040.0000.0000.0000.000
117A126GLU-1-0.818-0.90730.8600.0600.0600.0000.0000.0000.000
118A127ASP-1-0.715-0.86132.2710.0740.0740.0000.0000.0000.000
119A128GLU-1-0.783-0.86232.7150.0530.0530.0000.0000.0000.000
120A129VAL0-0.0250.00832.650-0.004-0.0040.0000.0000.0000.000
121A130ILE0-0.013-0.01032.0460.0040.0040.0000.0000.0000.000
122A131VAL0-0.0030.00529.558-0.005-0.0050.0000.0000.0000.000
123A132ALA0-0.002-0.01430.5280.0040.0040.0000.0000.0000.000
124A133ALA00.020-0.00529.1910.0040.0040.0000.0000.0000.000
125A134GLY0-0.0270.00028.615-0.006-0.0060.0000.0000.0000.000
126A135ALA0-0.071-0.02029.904-0.002-0.0020.0000.0000.0000.000
127A136THR00.0150.00229.5070.0080.0080.0000.0000.0000.000
128A137VAL0-0.016-0.01129.958-0.008-0.0080.0000.0000.0000.000
129A138SER00.015-0.01030.3240.0050.0050.0000.0000.0000.000
130A139PRO00.0670.02330.1620.0000.0000.0000.0000.0000.000
131A140GLY0-0.0010.01731.345-0.005-0.0050.0000.0000.0000.000
132A141LYS10.8800.95733.350-0.063-0.0630.0000.0000.0000.000
133A142VAL00.0490.02633.4270.0040.0040.0000.0000.0000.000
134A143LEU0-0.120-0.05832.356-0.003-0.0030.0000.0000.0000.000
135A144GLU-1-0.784-0.88635.6820.0480.0480.0000.0000.0000.000
136A145SER00.000-0.03936.6450.0000.0000.0000.0000.0000.000
137A146GLY00.0190.01637.150-0.003-0.0030.0000.0000.0000.000
138A147PHE0-0.042-0.02437.928-0.003-0.0030.0000.0000.0000.000
139A148VAL00.0130.00835.9530.0040.0040.0000.0000.0000.000
140A149TYR00.0090.00434.588-0.004-0.0040.0000.0000.0000.000
141A150MET00.0420.02034.6720.0040.0040.0000.0000.0000.000
142A151GLY00.0060.00334.917-0.004-0.0040.0000.0000.0000.000
143A152THR0-0.0040.03132.3960.0040.0040.0000.0000.0000.000
144A153PRO00.0390.00634.887-0.002-0.0020.0000.0000.0000.000
145A154ALA0-0.030-0.01433.729-0.003-0.0030.0000.0000.0000.000
146A155LYS10.8650.92235.834-0.057-0.0570.0000.0000.0000.000
147A156LYS10.8360.90438.876-0.046-0.0460.0000.0000.0000.000
148A157VAL0-0.073-0.04239.964-0.002-0.0020.0000.0000.0000.000
149A158ARG10.8140.87038.392-0.055-0.0550.0000.0000.0000.000
150A159PRO00.0520.03540.9040.0030.0030.0000.0000.0000.000
151A160ILE0-0.071-0.03536.5660.0000.0000.0000.0000.0000.000
152A161THR00.012-0.02039.788-0.002-0.0020.0000.0000.0000.000
153A162GLU-1-0.876-0.94839.8830.0440.0440.0000.0000.0000.000
154A163LYS10.9760.98438.131-0.044-0.0440.0000.0000.0000.000
155A164GLU-1-0.740-0.80536.1630.0580.0580.0000.0000.0000.000
156A165ARG10.8980.94335.199-0.048-0.0480.0000.0000.0000.000
157A166SER0-0.072-0.04335.3720.0020.0020.0000.0000.0000.000
158A167PHE0-0.001-0.01529.5490.0020.0020.0000.0000.0000.000
159A168PHE00.0410.05130.6530.0040.0040.0000.0000.0000.000
160A169THR00.0540.02629.5040.0040.0040.0000.0000.0000.000
161A170TYR0-0.033-0.01329.9680.0030.0030.0000.0000.0000.000
162A171GLY0-0.013-0.01028.5930.0020.0020.0000.0000.0000.000
163A172ALA00.0530.03525.3830.0060.0060.0000.0000.0000.000
164A173GLY00.0500.02025.0330.0060.0060.0000.0000.0000.000
165A174ASN0-0.073-0.05526.091-0.003-0.0030.0000.0000.0000.000
166A175TYR00.0340.00719.826-0.004-0.0040.0000.0000.0000.000
167A176VAL00.0160.02921.3030.0110.0110.0000.0000.0000.000
168A177ARG10.9310.96021.911-0.071-0.0710.0000.0000.0000.000
169A178LEU0-0.063-0.02020.372-0.003-0.0030.0000.0000.0000.000
170A179LYS10.7570.84917.057-0.160-0.1600.0000.0000.0000.000
171A180ASP-1-0.815-0.88717.5430.1540.1540.0000.0000.0000.000
172A181LYS10.9050.94919.487-0.074-0.0740.0000.0000.0000.000
173A182HIS00.0400.01515.1600.0000.0000.0000.0000.0000.000
174A183LEU0-0.017-0.00213.6090.0080.0080.0000.0000.0000.000
175A184ALA0-0.057-0.02715.6690.0000.0000.0000.0000.0000.000
176A185GLU-1-0.899-0.91716.1880.0260.0260.0000.0000.0000.000
177A186GLY0-0.046-0.02013.498-0.026-0.0260.0000.0000.0000.000
178A187TYR0-0.123-0.09711.3290.0050.0050.0000.0000.0000.000
179A188ASP-1-0.788-0.8798.7460.4200.4200.0000.0000.0000.000
180A189ARG10.8000.9157.4150.0190.0190.0000.0000.0000.000