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: 14Q4Z

Calculation Name: 1G62-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1G62

Chain ID: A

ChEMBL ID:

UniProt ID: Q12522

Base Structure: X-ray

Registration Date: 2023-06-21

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2674210.372057
FMO2-HF: Nuclear repulsion 2589082.915319
FMO2-HF: Total energy -85127.456738
FMO2-MP2: Total energy -85375.140272


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-27.645-18.04412.671-9.217-13.057-0.096
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : 0.010
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].
3A3THR0-0.025-0.0282.553-3.805-0.7691.232-1.681-2.587-0.007
4A4ARG10.8030.9045.0741.8971.964-0.001-0.004-0.0620.000
5A5THR00.002-0.0018.402-0.011-0.0110.0000.0000.0000.000
6A6GLN0-0.021-0.02911.9240.1070.1070.0000.0000.0000.000
7A7PHE0-0.0140.01215.576-0.001-0.0010.0000.0000.0000.000
8A8GLU-1-0.846-0.90618.294-0.322-0.3220.0000.0000.0000.000
9A9ASN0-0.011-0.01219.527-0.006-0.0060.0000.0000.0000.000
10A10SER0-0.0150.00819.618-0.001-0.0010.0000.0000.0000.000
11A11ASN0-0.001-0.01315.650-0.127-0.1270.0000.0000.0000.000
12A12GLU-1-0.823-0.90015.087-0.527-0.5270.0000.0000.0000.000
13A13ILE00.0410.02612.0600.0880.0880.0000.0000.0000.000
14A14GLY00.0590.05415.4340.0070.0070.0000.0000.0000.000
15A15VAL0-0.050-0.02116.4140.0870.0870.0000.0000.0000.000
16A16PHE0-0.038-0.03118.2090.0590.0590.0000.0000.0000.000
17A17SER0-0.011-0.02014.323-0.045-0.0450.0000.0000.0000.000
18A18LYS10.8340.91115.2030.4720.4720.0000.0000.0000.000
19A19LEU00.0240.0197.673-0.008-0.0080.0000.0000.0000.000
20A20THR00.0380.03212.4140.0740.0740.0000.0000.0000.000
21A21ASN0-0.038-0.04610.422-0.176-0.1760.0000.0000.0000.000
22A22THR0-0.061-0.03011.9800.0550.0550.0000.0000.0000.000
23A23TYR00.0180.00413.9510.0180.0180.0000.0000.0000.000
24A24CYS0-0.0090.01111.920-0.103-0.1030.0000.0000.0000.000
25A25LEU0-0.0250.00213.9700.0860.0860.0000.0000.0000.000
26A26VAL00.0500.01414.514-0.071-0.0710.0000.0000.0000.000
27A27ALA00.0430.02717.4960.0690.0690.0000.0000.0000.000
28A28VAL0-0.036-0.00820.348-0.025-0.0250.0000.0000.0000.000
29A29GLY00.0030.01122.9480.0100.0100.0000.0000.0000.000
30A30GLY00.0370.02119.7460.0070.0070.0000.0000.0000.000
31A31SER0-0.023-0.01618.3870.0100.0100.0000.0000.0000.000
32A32GLU-1-0.815-0.89416.258-0.651-0.6510.0000.0000.0000.000
33A33ASN0-0.038-0.02613.278-0.079-0.0790.0000.0000.0000.000
34A34PHE00.0210.00913.306-0.138-0.1380.0000.0000.0000.000
35A35TYR0-0.009-0.02513.058-0.099-0.0990.0000.0000.0000.000
36A36SER00.024-0.02212.245-0.105-0.1050.0000.0000.0000.000
37A37ALA0-0.053-0.0099.138-0.123-0.1230.0000.0000.0000.000
38A38PHE00.0150.0117.572-0.509-0.5090.0000.0000.0000.000
39A39GLU-1-0.885-0.9728.325-0.801-0.8010.0000.0000.0000.000
40A40ALA0-0.040-0.0188.2900.1820.1820.0000.0000.0000.000
41A41GLU-1-0.847-0.9151.911-16.736-17.4238.287-3.936-3.665-0.052
42A42LEU0-0.067-0.0325.5250.4890.4890.0000.0000.0000.000
43A43GLY00.0270.0118.0530.3260.3260.0000.0000.0000.000
44A44ASP-1-0.965-0.99210.830-0.260-0.2600.0000.0000.0000.000
45A45ALA0-0.068-0.01310.5140.0660.0660.0000.0000.0000.000
46A46ILE0-0.029-0.01310.3620.0590.0590.0000.0000.0000.000
47A47PRO00.0020.00713.608-0.071-0.0710.0000.0000.0000.000
48A48ILE00.0510.03011.662-0.046-0.0460.0000.0000.0000.000
49A49VAL00.0080.00715.4200.0270.0270.0000.0000.0000.000
50A50HIS10.8400.92416.5850.5150.5150.0000.0000.0000.000
51A51THR00.000-0.01020.2220.0570.0570.0000.0000.0000.000
52A52THR0-0.061-0.05322.919-0.025-0.0250.0000.0000.0000.000
53A53ILE00.0310.01023.8140.0040.0040.0000.0000.0000.000
54A54ALA00.0200.02326.731-0.001-0.0010.0000.0000.0000.000
55A55GLY0-0.030-0.01529.6960.0070.0070.0000.0000.0000.000
56A56THR0-0.101-0.05727.003-0.017-0.0170.0000.0000.0000.000
57A57ARG10.8760.87523.5640.3540.3540.0000.0000.0000.000
58A58ILE0-0.0080.01722.526-0.036-0.0360.0000.0000.0000.000
59A59ILE00.0200.00418.4620.0130.0130.0000.0000.0000.000
60A60GLY00.0210.04118.8960.0110.0110.0000.0000.0000.000
61A61ARG10.7950.86918.6870.4080.4080.0000.0000.0000.000
62A62MET0-0.065-0.02822.6380.0340.0340.0000.0000.0000.000
63A63THR00.0170.00220.6980.0140.0140.0000.0000.0000.000
64A64ALA00.0240.01720.192-0.028-0.0280.0000.0000.0000.000
65A65GLY00.0330.00819.3510.0180.0180.0000.0000.0000.000
66A66ASN0-0.0010.00216.722-0.031-0.0310.0000.0000.0000.000
67A67ARG10.9040.93614.083-0.012-0.0120.0000.0000.0000.000
68A68ARG10.7630.85617.4040.0350.0350.0000.0000.0000.000
69A69GLY00.0440.02720.9080.0110.0110.0000.0000.0000.000
70A70LEU0-0.037-0.01920.128-0.027-0.0270.0000.0000.0000.000
71A71LEU00.0070.01322.5660.0210.0210.0000.0000.0000.000
72A72VAL00.0180.00024.234-0.028-0.0280.0000.0000.0000.000
73A73PRO00.0540.03626.7120.0180.0180.0000.0000.0000.000
74A74THR00.010-0.02529.959-0.003-0.0030.0000.0000.0000.000
75A75GLN0-0.002-0.01532.5110.0040.0040.0000.0000.0000.000
76A76THR0-0.045-0.02327.998-0.012-0.0120.0000.0000.0000.000
77A77THR0-0.009-0.02330.8750.0140.0140.0000.0000.0000.000
78A78ASP-1-0.765-0.87031.369-0.129-0.1290.0000.0000.0000.000
79A79GLN00.0140.00532.1530.0020.0020.0000.0000.0000.000
80A80GLU-1-0.712-0.79827.490-0.222-0.2220.0000.0000.0000.000
81A81LEU00.0150.01227.247-0.011-0.0110.0000.0000.0000.000
82A82GLN0-0.045-0.02828.1510.0050.0050.0000.0000.0000.000
83A83HIS0-0.017-0.01723.4590.0210.0210.0000.0000.0000.000
84A84LEU00.0110.00622.266-0.010-0.0100.0000.0000.0000.000
85A85ARG10.8190.89123.9820.1380.1380.0000.0000.0000.000
86A86ASN0-0.047-0.01326.5180.0150.0150.0000.0000.0000.000
87A87SER0-0.023-0.00821.5750.0000.0000.0000.0000.0000.000
88A88LEU0-0.0210.00119.457-0.024-0.0240.0000.0000.0000.000
89A89PRO00.0440.02818.7010.0230.0230.0000.0000.0000.000
90A90ASP-1-0.892-0.95621.816-0.098-0.0980.0000.0000.0000.000
91A91SER0-0.082-0.03820.8030.0040.0040.0000.0000.0000.000
92A92VAL0-0.0430.00420.3070.0050.0050.0000.0000.0000.000
93A93LYS10.7920.88822.8330.0620.0620.0000.0000.0000.000
94A94ILE00.011-0.00123.945-0.014-0.0140.0000.0000.0000.000
95A95GLN0-0.037-0.02326.2830.0150.0150.0000.0000.0000.000
96A96ARG10.7500.84228.2380.1190.1190.0000.0000.0000.000
97A97VAL00.0230.01228.4010.0130.0130.0000.0000.0000.000
98A98GLU-1-0.832-0.85731.273-0.122-0.1220.0000.0000.0000.000
99A99GLU-1-0.779-0.90529.437-0.141-0.1410.0000.0000.0000.000
100A100ARG10.7890.84833.0980.1120.1120.0000.0000.0000.000
101A101LEU00.0070.02331.5680.0010.0010.0000.0000.0000.000
102A102SER0-0.045-0.03828.556-0.011-0.0110.0000.0000.0000.000
103A103ALA00.0100.02526.3480.0050.0050.0000.0000.0000.000
104A104LEU00.0860.03125.170-0.006-0.0060.0000.0000.0000.000
105A105GLY0-0.0070.00621.9110.0060.0060.0000.0000.0000.000
106A106ASN0-0.051-0.03321.792-0.040-0.0400.0000.0000.0000.000
107A107VAL0-0.047-0.01024.5040.0130.0130.0000.0000.0000.000
108A108ILE00.0160.00622.5170.0210.0210.0000.0000.0000.000
109A109CYS0-0.0300.00418.716-0.029-0.0290.0000.0000.0000.000
110A110CYS0-0.035-0.01218.4240.0290.0290.0000.0000.0000.000
111A111ASN00.0870.05715.621-0.045-0.0450.0000.0000.0000.000
112A112ASP-1-0.786-0.88715.240-0.096-0.0960.0000.0000.0000.000
113A113TYR0-0.023-0.00116.9550.0240.0240.0000.0000.0000.000
114A114VAL00.0250.01720.378-0.002-0.0020.0000.0000.0000.000
115A115ALA00.000-0.01320.752-0.025-0.0250.0000.0000.0000.000
116A116LEU00.0000.01122.7800.0170.0170.0000.0000.0000.000
117A117VAL0-0.019-0.02424.401-0.024-0.0240.0000.0000.0000.000
118A118HIS00.0530.02027.1590.0140.0140.0000.0000.0000.000
119A119PRO0-0.004-0.00429.6190.0060.0060.0000.0000.0000.000
120A120ASP-1-0.917-0.96832.669-0.072-0.0720.0000.0000.0000.000
121A121ILE0-0.063-0.02130.256-0.001-0.0010.0000.0000.0000.000
122A122ASP-1-0.820-0.88733.978-0.069-0.0690.0000.0000.0000.000
123A123ARG10.7300.80134.7680.0370.0370.0000.0000.0000.000
124A124GLU-1-0.790-0.87835.203-0.046-0.0460.0000.0000.0000.000
125A125THR0-0.033-0.04831.162-0.004-0.0040.0000.0000.0000.000
126A126GLU-1-0.817-0.87830.711-0.056-0.0560.0000.0000.0000.000
127A127GLU-1-0.804-0.87830.463-0.035-0.0350.0000.0000.0000.000
128A128LEU0-0.028-0.00830.6630.0010.0010.0000.0000.0000.000
129A129ILE0-0.019-0.01625.619-0.007-0.0070.0000.0000.0000.000
130A130SER0-0.038-0.02326.571-0.001-0.0010.0000.0000.0000.000
131A131ASP-1-0.823-0.91127.583-0.054-0.0540.0000.0000.0000.000
132A132VAL0-0.048-0.02725.1920.0020.0020.0000.0000.0000.000
133A133LEU0-0.0040.01121.546-0.007-0.0070.0000.0000.0000.000
134A134GLY00.0150.01623.1040.0080.0080.0000.0000.0000.000
135A135VAL0-0.067-0.01421.7080.0130.0130.0000.0000.0000.000
136A136GLU-1-0.865-0.91224.8840.0320.0320.0000.0000.0000.000
137A137VAL0-0.018-0.01525.317-0.011-0.0110.0000.0000.0000.000
138A138PHE00.0190.00526.2370.0080.0080.0000.0000.0000.000
139A139ARG10.7790.87427.8710.0410.0410.0000.0000.0000.000
140A140GLN00.0230.01027.1130.0030.0030.0000.0000.0000.000
141A141THR0-0.021-0.01028.510-0.011-0.0110.0000.0000.0000.000
142A142ILE00.0420.04122.4950.0100.0100.0000.0000.0000.000
143A143SER00.003-0.00125.357-0.014-0.0140.0000.0000.0000.000
144A144GLY0-0.0040.00727.223-0.003-0.0030.0000.0000.0000.000
145A145ASN0-0.105-0.06026.165-0.009-0.0090.0000.0000.0000.000
146A146ILE00.0630.01728.181-0.001-0.0010.0000.0000.0000.000
147A147LEU0-0.055-0.01226.427-0.003-0.0030.0000.0000.0000.000
148A148VAL00.0650.02524.128-0.022-0.0220.0000.0000.0000.000
149A149GLY00.0190.02121.031-0.008-0.0080.0000.0000.0000.000
150A150SER0-0.031-0.02520.432-0.047-0.0470.0000.0000.0000.000
151A151TYR0-0.075-0.04121.089-0.028-0.0280.0000.0000.0000.000
152A152CYS00.015-0.00218.7870.0380.0380.0000.0000.0000.000
153A153SER0-0.0120.00114.010-0.047-0.0470.0000.0000.0000.000
154A154LEU0-0.006-0.00614.3740.0620.0620.0000.0000.0000.000
155A155SER00.0520.0379.895-0.050-0.0500.0000.0000.0000.000
156A156ASN0-0.048-0.05812.4080.0000.0000.0000.0000.0000.000
157A157GLN0-0.0120.0039.1690.1970.1970.0000.0000.0000.000
158A158GLY00.0480.02612.2450.1040.1040.0000.0000.0000.000
159A159GLY00.006-0.01213.687-0.097-0.0970.0000.0000.0000.000
160A160LEU0-0.058-0.01012.3160.0440.0440.0000.0000.0000.000
161A161VAL00.017-0.00415.671-0.044-0.0440.0000.0000.0000.000
162A162HIS00.0900.04118.7430.0010.0010.0000.0000.0000.000
163A163PRO0-0.0120.01019.6780.0270.0270.0000.0000.0000.000
164A164GLN0-0.065-0.03821.0700.0060.0060.0000.0000.0000.000
165A165THR0-0.027-0.02222.6020.0070.0070.0000.0000.0000.000
166A166SER0-0.016-0.03524.1290.0150.0150.0000.0000.0000.000
167A167VAL0-0.002-0.01424.7620.0020.0020.0000.0000.0000.000
168A168GLN00.0260.02425.8250.0080.0080.0000.0000.0000.000
169A169ASP-1-0.804-0.87226.029-0.017-0.0170.0000.0000.0000.000
170A170GLN0-0.027-0.02120.6990.0110.0110.0000.0000.0000.000
171A171GLU-1-0.903-0.93523.1670.0990.0990.0000.0000.0000.000
172A172GLU-1-0.916-0.95225.3060.0280.0280.0000.0000.0000.000
173A173LEU00.008-0.01123.412-0.001-0.0010.0000.0000.0000.000
174A174SER0-0.011-0.02721.1440.0050.0050.0000.0000.0000.000
175A175SER0-0.088-0.05122.1600.0190.0190.0000.0000.0000.000
176A176LEU0-0.064-0.01925.1000.0030.0030.0000.0000.0000.000
177A177LEU0-0.011-0.02419.682-0.009-0.0090.0000.0000.0000.000
178A178GLN0-0.066-0.02320.0590.0210.0210.0000.0000.0000.000
179A179VAL0-0.0200.00816.0120.0400.0400.0000.0000.0000.000
180A180PRO0-0.019-0.01615.769-0.032-0.0320.0000.0000.0000.000
181A181LEU0-0.0170.00916.272-0.018-0.0180.0000.0000.0000.000
182A182VAL0-0.006-0.00315.3930.0250.0250.0000.0000.0000.000
183A183ALA0-0.0130.00117.209-0.045-0.0450.0000.0000.0000.000
184A184GLY0-0.026-0.02215.7770.0240.0240.0000.0000.0000.000
185A185THR0-0.083-0.05515.2870.0120.0120.0000.0000.0000.000
186A186VAL00.0210.01811.550-0.026-0.0260.0000.0000.0000.000
187A187ASN0-0.084-0.04212.877-0.018-0.0180.0000.0000.0000.000
188A188ARG10.8040.88314.4250.4780.4780.0000.0000.0000.000
189A189GLY00.0060.00116.2440.0430.0430.0000.0000.0000.000
190A190SER0-0.065-0.02717.2750.0550.0550.0000.0000.0000.000
191A191SER00.0630.01017.707-0.018-0.0180.0000.0000.0000.000
192A192VAL0-0.0090.01720.0500.0220.0220.0000.0000.0000.000
193A193VAL00.0530.00815.656-0.056-0.0560.0000.0000.0000.000
194A194GLY0-0.0030.02616.017-0.055-0.0550.0000.0000.0000.000
195A195ALA0-0.048-0.02917.700-0.025-0.0250.0000.0000.0000.000
196A196GLY0-0.002-0.01915.969-0.053-0.0530.0000.0000.0000.000
197A197MET0-0.046-0.01810.254-0.065-0.0650.0000.0000.0000.000
198A198VAL0-0.021-0.00210.0570.1670.1670.0000.0000.0000.000
199A199VAL0-0.008-0.0107.410-0.325-0.3250.0000.0000.0000.000
200A200ASN00.0040.0046.6660.0080.0080.0000.0000.0000.000
201A201ASP-1-0.775-0.8877.7550.1350.1350.0000.0000.0000.000
202A202TYR0-0.073-0.0364.2670.3240.511-0.001-0.033-0.1530.000
203A203LEU00.0230.0282.415-4.684-2.1741.418-1.711-2.217-0.016
204A204ALA00.0010.0003.5632.0442.3510.003-0.058-0.2520.000
205A205VAL00.0140.0245.925-0.859-0.8590.0000.0000.0000.000
206A206THR00.003-0.0187.7400.5580.5580.0000.0000.0000.000
207A207GLY00.0880.03810.350-0.083-0.0830.0000.0000.0000.000
208A208LEU0-0.044-0.02811.340-0.061-0.0610.0000.0000.0000.000
209A209ASP-1-0.788-0.87512.221-0.508-0.5080.0000.0000.0000.000
210A210THR0-0.0480.0009.1230.1050.1050.0000.0000.0000.000
211A211THR0-0.013-0.02510.285-0.094-0.0940.0000.0000.0000.000
212A212ALA00.006-0.0058.606-0.101-0.1010.0000.0000.0000.000
213A213PRO00.0290.0048.683-0.017-0.0170.0000.0000.0000.000
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