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: K9NQ3

Calculation Name: 1X9G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1X9G

Chain ID: A

ChEMBL ID:

UniProt ID: D0VWV0

Base Structure: X-ray

Registration Date: 2023-09-20

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2220215.495601
FMO2-HF: Nuclear repulsion 2143353.081348
FMO2-HF: Total energy -76862.414253
FMO2-MP2: Total energy -77082.729849


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.
-10.743-12.5238.688-2.986-3.9220.022
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 : 0.081 / q_NPA : 0.034
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].
3A3ARG10.9250.9542.549-9.740-11.6858.688-2.965-3.7780.022
4A4LEU0-0.0060.0506.326-0.075-0.0750.0000.0000.0000.000
5A5MET00.0410.0319.3210.1410.1410.0000.0000.0000.000
6A6PRO0-0.0270.00210.3510.0060.0060.0000.0000.0000.000
7A7HIS00.0240.00212.028-0.036-0.0360.0000.0000.0000.000
8A8TYR0-0.024-0.04815.3430.0090.0090.0000.0000.0000.000
9A9SER0-0.026-0.00817.880-0.014-0.0140.0000.0000.0000.000
10A10LYS10.8660.9429.644-0.788-0.7880.0000.0000.0000.000
11A11GLY0-0.062-0.03514.2000.0800.0800.0000.0000.0000.000
12A12LYS10.9450.98915.412-0.278-0.2780.0000.0000.0000.000
13A13THR0-0.028-0.02015.8030.0920.0920.0000.0000.0000.000
14A14ALA00.0150.02117.596-0.045-0.0450.0000.0000.0000.000
15A15PHE0-0.006-0.01519.4660.0340.0340.0000.0000.0000.000
16A16LEU00.0150.00421.268-0.022-0.0220.0000.0000.0000.000
17A17CYS0-0.015-0.01623.2530.0030.0030.0000.0000.0000.000
18A18VAL0-0.012-0.02723.849-0.013-0.0130.0000.0000.0000.000
19A19ASP-1-0.737-0.85127.0270.1190.1190.0000.0000.0000.000
20A20LEU00.0060.01928.790-0.006-0.0060.0000.0000.0000.000
21A21GLN0-0.040-0.03532.0980.0010.0010.0000.0000.0000.000
22A22GLU-1-0.832-0.91335.6650.0840.0840.0000.0000.0000.000
23A23ALA0-0.028-0.01338.093-0.001-0.0010.0000.0000.0000.000
24A24PHE0-0.014-0.02134.010-0.003-0.0030.0000.0000.0000.000
25A25SER0-0.009-0.01336.5450.0000.0000.0000.0000.0000.000
26A26LYS10.8930.94937.500-0.078-0.0780.0000.0000.0000.000
27A27ARG10.8110.90436.930-0.074-0.0740.0000.0000.0000.000
28A28ILE00.0090.00631.408-0.001-0.0010.0000.0000.0000.000
29A29GLU-1-0.819-0.88433.9410.1080.1080.0000.0000.0000.000
30A30ASN00.009-0.02428.228-0.009-0.0090.0000.0000.0000.000
31A31PHE00.0390.02631.4630.0100.0100.0000.0000.0000.000
32A32ALA00.0480.02332.6700.0040.0040.0000.0000.0000.000
33A33ASN00.0380.00329.361-0.004-0.0040.0000.0000.0000.000
34A34CYS0-0.035-0.01528.1710.0140.0140.0000.0000.0000.000
35A35VAL00.0050.01228.9530.0080.0080.0000.0000.0000.000
36A36PHE00.0040.01128.9170.0050.0050.0000.0000.0000.000
37A37VAL0-0.0050.00524.3490.0090.0090.0000.0000.0000.000
38A38ALA00.0220.01126.6370.0130.0130.0000.0000.0000.000
39A39ASN00.032-0.00228.2630.0040.0040.0000.0000.0000.000
40A40ARG10.9000.95825.531-0.215-0.2150.0000.0000.0000.000
41A41LEU0-0.012-0.02621.5650.0110.0110.0000.0000.0000.000
42A42ALA0-0.0280.00825.4540.0050.0050.0000.0000.0000.000
43A43ARG10.7770.83428.487-0.151-0.1510.0000.0000.0000.000
44A44LEU00.000-0.00721.700-0.001-0.0010.0000.0000.0000.000
45A45HIS0-0.0140.00924.747-0.010-0.0100.0000.0000.0000.000
46A46GLU-1-0.814-0.88225.7220.1480.1480.0000.0000.0000.000
47A47VAL0-0.112-0.05626.595-0.009-0.0090.0000.0000.0000.000
48A48VAL0-0.036-0.00922.031-0.003-0.0030.0000.0000.0000.000
49A49PRO00.0610.04223.8730.0160.0160.0000.0000.0000.000
50A50GLU-1-0.875-0.93724.6660.2110.2110.0000.0000.0000.000
51A51ASN0-0.084-0.05519.8950.0140.0140.0000.0000.0000.000
52A52THR0-0.013-0.00919.9050.0320.0320.0000.0000.0000.000
53A53LYS10.8420.91221.874-0.229-0.2290.0000.0000.0000.000
54A54TYR0-0.016-0.02323.2900.0170.0170.0000.0000.0000.000
55A55ILE00.0170.01323.090-0.015-0.0150.0000.0000.0000.000
56A56VAL00.0020.02026.6700.0090.0090.0000.0000.0000.000
57A57THR00.0320.00726.938-0.003-0.0030.0000.0000.0000.000
58A58GLU-1-0.816-0.90629.8780.0940.0940.0000.0000.0000.000
59A59HIS00.0200.00631.8430.0000.0000.0000.0000.0000.000
60A60TYR0-0.048-0.02533.687-0.003-0.0030.0000.0000.0000.000
61A61PRO00.0800.04536.228-0.003-0.0030.0000.0000.0000.000
62A62LYS10.9420.97638.548-0.055-0.0550.0000.0000.0000.000
63A63GLY0-0.062-0.03641.532-0.002-0.0020.0000.0000.0000.000
64A64LEU0-0.031-0.03240.8330.0010.0010.0000.0000.0000.000
65A65GLY00.0430.02638.6390.0030.0030.0000.0000.0000.000
66A66ARG10.8680.93938.183-0.080-0.0800.0000.0000.0000.000
67A67ILE0-0.030-0.03032.5040.0010.0010.0000.0000.0000.000
68A68VAL00.002-0.00135.7620.0000.0000.0000.0000.0000.000
69A69PRO00.0270.01336.5900.0050.0050.0000.0000.0000.000
70A70GLU-1-0.963-0.97536.4060.1160.1160.0000.0000.0000.000
71A71ILE0-0.0160.00831.4310.0080.0080.0000.0000.0000.000
72A72THR00.0000.00734.741-0.003-0.0030.0000.0000.0000.000
73A73LEU00.0170.00131.6080.0080.0080.0000.0000.0000.000
74A74PRO00.0150.02829.172-0.007-0.0070.0000.0000.0000.000
75A75LYS10.9180.94532.453-0.106-0.1060.0000.0000.0000.000
76A76THR0-0.009-0.02729.394-0.009-0.0090.0000.0000.0000.000
77A77ALA0-0.070-0.01529.5640.0050.0050.0000.0000.0000.000
78A78HIS00.0150.00627.999-0.013-0.0130.0000.0000.0000.000
79A79LEU0-0.027-0.01629.5150.0070.0070.0000.0000.0000.000
80A80ILE0-0.0060.00328.655-0.006-0.0060.0000.0000.0000.000
81A81GLU-1-0.859-0.92632.1370.0810.0810.0000.0000.0000.000
82A82LYS10.7980.89328.715-0.115-0.1150.0000.0000.0000.000
83A83THR00.018-0.00933.2090.0000.0000.0000.0000.0000.000
84A84ARG10.8420.91724.471-0.088-0.0880.0000.0000.0000.000
85A85PHE00.017-0.00328.5480.0050.0050.0000.0000.0000.000
86A86SER0-0.039-0.04723.3590.0150.0150.0000.0000.0000.000
87A87CYS0-0.035-0.03523.658-0.010-0.0100.0000.0000.0000.000
88A88VAL00.0160.02120.6970.0030.0030.0000.0000.0000.000
89A89VAL0-0.027-0.00424.056-0.018-0.0180.0000.0000.0000.000
90A90PRO00.0890.02626.3230.0100.0100.0000.0000.0000.000
91A91GLN00.0140.00927.2290.0040.0040.0000.0000.0000.000
92A92VAL0-0.032-0.02523.1540.0060.0060.0000.0000.0000.000
93A93GLU-1-0.910-0.96722.3780.1090.1090.0000.0000.0000.000
94A94GLU-1-0.817-0.90322.2850.1010.1010.0000.0000.0000.000
95A95LEU0-0.081-0.02023.9740.0100.0100.0000.0000.0000.000
96A96LEU0-0.053-0.04418.8650.0320.0320.0000.0000.0000.000
97A97GLU-1-0.887-0.93918.7770.1300.1300.0000.0000.0000.000
98A98ASP-1-0.879-0.91418.4500.2130.2130.0000.0000.0000.000
99A99VAL0-0.051-0.02216.6010.0270.0270.0000.0000.0000.000
100A100ASP-1-0.810-0.88711.6330.6090.6090.0000.0000.0000.000
101A101ASN0-0.059-0.04211.3940.2730.2730.0000.0000.0000.000
102A102ALA00.0540.03313.837-0.085-0.0850.0000.0000.0000.000
103A103VAL0-0.001-0.00715.6610.0400.0400.0000.0000.0000.000
104A104VAL0-0.003-0.00517.966-0.040-0.0400.0000.0000.0000.000
105A105PHE0-0.003-0.01520.1000.0070.0070.0000.0000.0000.000
106A106GLY00.0530.02123.126-0.010-0.0100.0000.0000.0000.000
107A107ILE0-0.055-0.01026.3010.0030.0030.0000.0000.0000.000
108A108GLU-1-0.711-0.85228.1670.0970.0970.0000.0000.0000.000
109A109GLY00.015-0.01624.2670.0020.0020.0000.0000.0000.000
110A110HIS00.0370.01123.6930.0160.0160.0000.0000.0000.000
111A111ALA0-0.010-0.00325.906-0.010-0.0100.0000.0000.0000.000
112A112CYS00.0050.00025.6230.0000.0000.0000.0000.0000.000
113A113ILE0-0.0270.03121.4560.0100.0100.0000.0000.0000.000
114A114LEU00.0240.01620.2380.0160.0160.0000.0000.0000.000
115A115GLN0-0.028-0.02720.6840.0040.0040.0000.0000.0000.000
116A116THR00.0470.01320.541-0.003-0.0030.0000.0000.0000.000
117A117VAL0-0.039-0.02916.4360.0160.0160.0000.0000.0000.000
118A118ALA00.0000.00516.5260.0240.0240.0000.0000.0000.000
119A119ASP-1-0.728-0.81917.2550.1030.1030.0000.0000.0000.000
120A120LEU00.010-0.01615.6800.0070.0070.0000.0000.0000.000
121A121LEU0-0.090-0.03611.2370.0500.0500.0000.0000.0000.000
122A122ASP-1-0.893-0.94313.1610.0680.0680.0000.0000.0000.000
123A123MET0-0.088-0.02615.642-0.018-0.0180.0000.0000.0000.000
124A124ASN0-0.082-0.04110.531-0.006-0.0060.0000.0000.0000.000
125A125LYS10.8660.94110.908-0.192-0.1920.0000.0000.0000.000
126A126ARG10.8160.9216.487-1.648-1.6480.0000.0000.0000.000
127A127VAL00.0280.00010.600-0.115-0.1150.0000.0000.0000.000
128A128PHE0-0.041-0.0279.9630.0530.0530.0000.0000.0000.000
129A129LEU00.0240.01514.458-0.051-0.0510.0000.0000.0000.000
130A130PRO00.0140.01817.6150.0100.0100.0000.0000.0000.000
131A131LYS10.9720.96420.254-0.248-0.2480.0000.0000.0000.000
132A132ASP-1-0.768-0.89221.9430.2280.2280.0000.0000.0000.000
133A133GLY00.0020.02423.796-0.016-0.0160.0000.0000.0000.000
134A134LEU0-0.0230.00920.674-0.002-0.0020.0000.0000.0000.000
135A135GLY00.0620.02525.314-0.005-0.0050.0000.0000.0000.000
136A136SER0-0.033-0.04028.3080.0050.0050.0000.0000.0000.000
137A137GLN0-0.037-0.02430.192-0.007-0.0070.0000.0000.0000.000
138A138LYS10.9400.97732.864-0.074-0.0740.0000.0000.0000.000
139A139LYS10.8830.91230.687-0.101-0.1010.0000.0000.0000.000
140A140THR0-0.007-0.00429.4030.0100.0100.0000.0000.0000.000
141A141ASP-1-0.829-0.91528.9030.0830.0830.0000.0000.0000.000
142A142PHE00.0030.01324.9170.0060.0060.0000.0000.0000.000
143A143LYS10.9220.93824.927-0.106-0.1060.0000.0000.0000.000
144A144ALA00.0020.00924.1000.0090.0090.0000.0000.0000.000
145A145ALA00.0660.04922.8680.0020.0020.0000.0000.0000.000
146A146ILE0-0.019-0.01320.2340.0140.0140.0000.0000.0000.000
147A147LYS10.9180.96719.023-0.130-0.1300.0000.0000.0000.000
148A148LEU00.0410.02918.4400.0040.0040.0000.0000.0000.000
149A149MET00.0420.04616.5100.0070.0070.0000.0000.0000.000
150A150SER0-0.059-0.04414.6030.0400.0400.0000.0000.0000.000
151A151SER0-0.134-0.06913.6940.0160.0160.0000.0000.0000.000
152A152TRP00.0430.01412.545-0.035-0.0350.0000.0000.0000.000
153A153GLY00.0030.0248.9600.0750.0750.0000.0000.0000.000
154A154PRO0-0.022-0.0253.978-0.306-0.1410.000-0.021-0.1440.000
155A155ASN00.018-0.0086.0710.8790.8790.0000.0000.0000.000
156A156CYS00.0180.0367.844-0.040-0.0400.0000.0000.0000.000
157A157GLH0-0.052-0.0658.0690.0180.0180.0000.0000.0000.000
158A158ILE00.0180.01412.171-0.022-0.0220.0000.0000.0000.000
159A159THR0-0.026-0.01814.5340.0080.0080.0000.0000.0000.000
160A160THR0-0.023-0.01417.339-0.030-0.0300.0000.0000.0000.000
161A161SER00.014-0.03119.6640.0280.0280.0000.0000.0000.000
162A162GLU-1-0.918-0.94821.9290.2760.2760.0000.0000.0000.000
163A163SER0-0.004-0.00517.2190.0330.0330.0000.0000.0000.000
164A164ILE00.018-0.00816.2550.0330.0330.0000.0000.0000.000
165A165LEU0-0.013-0.00718.1450.0200.0200.0000.0000.0000.000
166A166LEU00.0390.01519.5470.0050.0050.0000.0000.0000.000
167A167GLN0-0.039-0.00213.5340.0940.0940.0000.0000.0000.000
168A168MET00.0340.02415.1940.0370.0370.0000.0000.0000.000
169A169THR0-0.034-0.00417.260-0.021-0.0210.0000.0000.0000.000
170A170LYS10.7880.88311.592-0.741-0.7410.0000.0000.0000.000
171A171ASP-1-0.819-0.90617.4240.3040.3040.0000.0000.0000.000
172A172ALA00.0070.00220.736-0.012-0.0120.0000.0000.0000.000
173A173MET0-0.089-0.05023.981-0.029-0.0290.0000.0000.0000.000
174A174ASP-1-0.742-0.83321.4900.2790.2790.0000.0000.0000.000
175A175PRO00.0130.00424.126-0.011-0.0110.0000.0000.0000.000
176A176ASN00.006-0.02424.669-0.027-0.0270.0000.0000.0000.000
177A177PHE00.0410.03624.029-0.005-0.0050.0000.0000.0000.000
178A178LYS10.9660.97726.289-0.145-0.1450.0000.0000.0000.000
179A179ARG10.9030.96028.939-0.181-0.1810.0000.0000.0000.000
180A180ILE00.0700.03223.472-0.006-0.0060.0000.0000.0000.000
181A181SER0-0.008-0.01127.148-0.005-0.0050.0000.0000.0000.000
182A182LYS10.8290.91728.274-0.165-0.1650.0000.0000.0000.000
183A183LEU0-0.0010.00726.940-0.008-0.0080.0000.0000.0000.000
184A184LEU0-0.011-0.01024.215-0.003-0.0030.0000.0000.0000.000
185A185LYS10.8550.95028.622-0.183-0.1830.0000.0000.0000.000
186A186GLU-1-0.896-0.93931.6970.1550.1550.0000.0000.0000.000
187A187GLU-1-0.882-0.94931.4230.1700.1700.0000.0000.0000.000
188A188PRO0-0.063-0.03529.896-0.006-0.0060.0000.0000.0000.000
189A189PRO0-0.023-0.00632.695-0.006-0.0060.0000.0000.0000.000
190A190ILE0-0.0220.00033.194-0.007-0.0070.0000.0000.0000.000
191A191PRO00.0170.01332.3430.0100.0100.0000.0000.0000.000
192A192LEU0-0.0150.00526.4030.0020.0020.0000.0000.0000.000