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: LJGJ9

Calculation Name: 1X1P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1X1P

Chain ID: A

ChEMBL ID:

UniProt ID: O74035

Base Structure: X-ray

Registration Date: 2023-03-13

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2355171.135859
FMO2-HF: Nuclear repulsion 2275016.439093
FMO2-HF: Total energy -80154.696766
FMO2-MP2: Total energy -80393.782172


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.
-12.146-2.08611.133-7.536-13.659-0.062
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 : -0.035 / q_NPA : -0.016
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].
3A3ILE00.0640.0343.177-1.0630.1902.177-0.927-2.5040.002
4A4ALA00.008-0.0085.486-0.532-0.518-0.001-0.008-0.0050.000
5A5GLY0-0.0210.0019.117-0.159-0.1590.0000.0000.0000.000
6A6ILE0-0.052-0.02412.5360.0430.0430.0000.0000.0000.000
7A7ASP-1-0.796-0.89215.7620.0810.0810.0000.0000.0000.000
8A8GLH0-0.052-0.07919.2810.0170.0170.0000.0000.0000.000
9A9ALA0-0.0150.00823.035-0.019-0.0190.0000.0000.0000.000
10A10GLY0-0.102-0.06026.092-0.014-0.0140.0000.0000.0000.000
11A11ARG10.9950.99226.801-0.054-0.0540.0000.0000.0000.000
12A12GLY00.0710.03828.7820.0020.0020.0000.0000.0000.000
13A13PRO0-0.074-0.02230.923-0.008-0.0080.0000.0000.0000.000
14A14VAL0-0.007-0.01533.9580.0010.0010.0000.0000.0000.000
15A15ILE0-0.0020.00337.0680.0000.0000.0000.0000.0000.000
16A16GLY00.0490.02435.1580.0000.0000.0000.0000.0000.000
17A17PRO00.0000.00930.343-0.004-0.0040.0000.0000.0000.000
18A18MET0-0.0040.00026.212-0.001-0.0010.0000.0000.0000.000
19A19VAL0-0.013-0.00524.5050.0120.0120.0000.0000.0000.000
20A20ILE00.0190.00920.270-0.015-0.0150.0000.0000.0000.000
21A21ALA0-0.033-0.01519.6690.0110.0110.0000.0000.0000.000
22A22ALA00.0240.01215.076-0.018-0.0180.0000.0000.0000.000
23A23VAL0-0.030-0.01512.561-0.008-0.0080.0000.0000.0000.000
24A24VAL00.0210.0137.6370.0510.0510.0000.0000.0000.000
25A25VAL0-0.024-0.0187.349-0.150-0.1500.0000.0000.0000.000
26A26ASP-1-0.749-0.8502.554-4.145-2.2740.772-1.131-1.512-0.014
27A27GLU-1-0.894-0.9542.301-10.332-6.3463.693-2.891-4.788-0.030
28A28ASN0-0.117-0.0744.1600.9651.2230.000-0.026-0.2320.000
29A29SER0-0.027-0.0106.6060.2750.2750.0000.0000.0000.000
30A30LEU0-0.0060.0097.2680.1700.1700.0000.0000.0000.000
31A31PRO00.0180.0048.4940.1370.1370.0000.0000.0000.000
32A32LYS10.8690.91711.6530.3030.3030.0000.0000.0000.000
33A33LEU00.0190.01411.8130.0470.0470.0000.0000.0000.000
34A34GLU-1-0.767-0.85314.133-0.142-0.1420.0000.0000.0000.000
35A35GLU-1-0.870-0.91314.641-0.227-0.2270.0000.0000.0000.000
36A36LEU0-0.006-0.00216.9520.0130.0130.0000.0000.0000.000
37A37LYS10.7930.89719.0040.1450.1450.0000.0000.0000.000
38A38VAL00.0380.03016.2600.0120.0120.0000.0000.0000.000
39A39ARG10.8180.89716.4580.1460.1460.0000.0000.0000.000
40A40ASP-1-0.880-0.94220.876-0.064-0.0640.0000.0000.0000.000
41A41SER0-0.008-0.02222.3150.0080.0080.0000.0000.0000.000
42A42LYS10.7870.86823.069-0.009-0.0090.0000.0000.0000.000
43A43LYS10.8250.91025.8240.0380.0380.0000.0000.0000.000
44A44LEU0-0.0400.00825.6550.0000.0000.0000.0000.0000.000
45A45THR00.0300.00629.5770.0060.0060.0000.0000.0000.000
46A46PRO00.0870.03830.3750.0010.0010.0000.0000.0000.000
47A47LYS11.0040.99429.833-0.043-0.0430.0000.0000.0000.000
48A48ARG10.8880.95029.064-0.010-0.0100.0000.0000.0000.000
49A49ARG10.9460.97024.893-0.057-0.0570.0000.0000.0000.000
50A50GLU-1-0.819-0.89925.2220.1020.1020.0000.0000.0000.000
51A51LYS10.8440.94525.749-0.048-0.0480.0000.0000.0000.000
52A52LEU00.1180.05321.1180.0120.0120.0000.0000.0000.000
53A53PHE00.0140.01120.7990.0130.0130.0000.0000.0000.000
54A54ASN0-0.050-0.03920.7720.0340.0340.0000.0000.0000.000
55A55GLU-1-0.903-0.96719.9470.0530.0530.0000.0000.0000.000
56A56ILE0-0.003-0.00715.887-0.001-0.0010.0000.0000.0000.000
57A57LEU0-0.019-0.00915.6580.0300.0300.0000.0000.0000.000
58A58GLY0-0.0340.00416.7560.0350.0350.0000.0000.0000.000
59A59VAL0-0.081-0.05012.693-0.019-0.0190.0000.0000.0000.000
60A60LEU0-0.047-0.01311.192-0.036-0.0360.0000.0000.0000.000
61A61ASP-1-0.786-0.8846.5151.2651.2650.0000.0000.0000.000
62A62ASP-1-0.799-0.9029.7971.0111.0110.0000.0000.0000.000
63A63TYR0-0.041-0.03012.471-0.073-0.0730.0000.0000.0000.000
64A64VAL0-0.0120.00315.525-0.012-0.0120.0000.0000.0000.000
65A65ILE0-0.021-0.00718.669-0.019-0.0190.0000.0000.0000.000
66A66LEU0-0.003-0.00821.8640.0010.0010.0000.0000.0000.000
67A67GLU-1-0.912-0.95924.0990.1510.1510.0000.0000.0000.000
68A68LEU0-0.006-0.00126.3100.0040.0040.0000.0000.0000.000
69A69PRO0-0.018-0.01529.883-0.009-0.0090.0000.0000.0000.000
70A70PRO00.0020.01632.3760.0020.0020.0000.0000.0000.000
71A71ASP-1-0.768-0.87232.7770.0920.0920.0000.0000.0000.000
72A72VAL0-0.057-0.02935.258-0.002-0.0020.0000.0000.0000.000
73A73ILE0-0.043-0.03438.730-0.003-0.0030.0000.0000.0000.000
74A74GLY00.0040.02839.950-0.002-0.0020.0000.0000.0000.000
75A75SER0-0.104-0.06835.701-0.004-0.0040.0000.0000.0000.000
76A76ARG10.7990.88330.784-0.069-0.0690.0000.0000.0000.000
77A77GLU-1-0.851-0.93934.7820.0460.0460.0000.0000.0000.000
78A78GLY0-0.050-0.02034.536-0.002-0.0020.0000.0000.0000.000
79A79THR00.0540.02430.0330.0000.0000.0000.0000.0000.000
80A80LEU00.0190.02730.8280.0050.0050.0000.0000.0000.000
81A81ASN00.010-0.00326.0690.0110.0110.0000.0000.0000.000
82A82GLU-1-0.847-0.92125.9180.0700.0700.0000.0000.0000.000
83A83PHE0-0.020-0.01526.1450.0070.0070.0000.0000.0000.000
84A84GLU-1-0.858-0.88222.2580.1330.1330.0000.0000.0000.000
85A85VAL00.0590.03519.6740.0260.0260.0000.0000.0000.000
86A86GLU-1-0.775-0.86220.2030.1890.1890.0000.0000.0000.000
87A87ASN0-0.016-0.02422.0860.0320.0320.0000.0000.0000.000
88A88PHE00.0210.00317.0570.0320.0320.0000.0000.0000.000
89A89ALA00.0430.03117.3840.0520.0520.0000.0000.0000.000
90A90LYS10.8110.89118.446-0.151-0.1510.0000.0000.0000.000
91A91ALA00.0050.01718.6590.0300.0300.0000.0000.0000.000
92A92LEU00.0630.02512.4430.0600.0600.0000.0000.0000.000
93A93ASN00.006-0.00315.3260.1410.1410.0000.0000.0000.000
94A94SER0-0.061-0.03017.5610.0130.0130.0000.0000.0000.000
95A95LEU0-0.0360.00012.298-0.022-0.0220.0000.0000.0000.000
96A96LYS10.8340.91714.007-0.680-0.6800.0000.0000.0000.000
97A97VAL0-0.018-0.0137.8530.0770.0770.0000.0000.0000.000
98A98LYS10.7680.8829.838-0.855-0.8550.0000.0000.0000.000
99A99PRO0-0.030-0.0046.5130.4450.4450.0000.0000.0000.000
100A100ASP-1-0.805-0.8992.7582.9305.3463.017-2.183-3.250-0.017
101A101VAL0-0.006-0.0032.170-2.051-1.8301.476-0.368-1.330-0.003
102A102ILE0-0.035-0.0174.9980.4660.507-0.001-0.002-0.0380.000
103A103TYR00.0160.0146.482-0.240-0.2400.0000.0000.0000.000
104A104ALA00.020-0.01410.8880.0620.0620.0000.0000.0000.000
105A105ASP-1-0.786-0.90014.579-0.004-0.0040.0000.0000.0000.000
106A106ALA0-0.008-0.00818.0680.0160.0160.0000.0000.0000.000
107A107ALA00.0080.00420.408-0.012-0.0120.0000.0000.0000.000
108A108ASP-1-0.912-0.95624.1450.0260.0260.0000.0000.0000.000
109A109VAL0-0.061-0.03922.440-0.011-0.0110.0000.0000.0000.000
110A110ASP-1-0.877-0.95722.450-0.037-0.0370.0000.0000.0000.000
111A111GLU-1-0.779-0.87818.209-0.077-0.0770.0000.0000.0000.000
112A112GLU-1-0.911-0.95016.609-0.118-0.1180.0000.0000.0000.000
113A113ARG10.7810.86717.458-0.003-0.0030.0000.0000.0000.000
114A114PHE00.0050.00317.6860.0190.0190.0000.0000.0000.000
115A115ALA0-0.009-0.00413.7590.0310.0310.0000.0000.0000.000
116A116ARG10.8100.88914.9610.0080.0080.0000.0000.0000.000
117A117GLU-1-0.801-0.88116.5870.0610.0610.0000.0000.0000.000
118A118LEU0-0.037-0.02614.6690.0260.0260.0000.0000.0000.000
119A119GLY00.0460.01813.9620.0440.0440.0000.0000.0000.000
120A120GLU-1-0.860-0.91714.7100.0900.0900.0000.0000.0000.000
121A121ARG10.7750.88317.898-0.162-0.1620.0000.0000.0000.000
122A122LEU00.0060.01712.3210.0270.0270.0000.0000.0000.000
123A123ASN0-0.062-0.04516.3680.0130.0130.0000.0000.0000.000
124A124PHE0-0.041-0.0409.9930.0270.0270.0000.0000.0000.000
125A125GLU-1-0.916-0.95710.3920.0390.0390.0000.0000.0000.000
126A126ALA00.0240.0097.3660.2460.2460.0000.0000.0000.000
127A127GLU-1-0.943-0.9525.459-1.122-1.1220.0000.0000.0000.000
128A128VAL0-0.022-0.0187.3430.2240.2240.0000.0000.0000.000
129A129VAL0-0.0040.0048.931-0.080-0.0800.0000.0000.0000.000
130A130ALA00.008-0.00611.5890.0720.0720.0000.0000.0000.000
131A131LYS10.7950.87714.8810.0600.0600.0000.0000.0000.000
132A132HIS00.0460.03418.0510.0290.0290.0000.0000.0000.000
133A133LYS10.8190.90920.727-0.002-0.0020.0000.0000.0000.000
134A134ALA00.0540.03715.593-0.021-0.0210.0000.0000.0000.000
135A135ASP-1-0.782-0.89016.9670.0280.0280.0000.0000.0000.000
136A136ASP-1-0.856-0.90019.119-0.022-0.0220.0000.0000.0000.000
137A137ILE0-0.063-0.01715.588-0.027-0.0270.0000.0000.0000.000
138A138PHE00.0700.01912.025-0.038-0.0380.0000.0000.0000.000
139A139PRO0-0.004-0.00512.9410.0580.0580.0000.0000.0000.000
140A140VAL00.0680.0319.644-0.012-0.0120.0000.0000.0000.000
141A141VAL00.0130.01212.5810.0490.0490.0000.0000.0000.000
142A142SER0-0.017-0.02615.1260.0030.0030.0000.0000.0000.000
143A143ALA0-0.033-0.01815.006-0.002-0.0020.0000.0000.0000.000
144A144ALA00.0220.01715.7100.0080.0080.0000.0000.0000.000
145A145SER00.005-0.00217.534-0.013-0.0130.0000.0000.0000.000
146A146ILE0-0.090-0.04319.703-0.009-0.0090.0000.0000.0000.000
147A147LEU00.0120.00717.778-0.010-0.0100.0000.0000.0000.000
148A148ALA00.0530.03621.645-0.005-0.0050.0000.0000.0000.000
149A149LYS10.7960.87223.418-0.086-0.0860.0000.0000.0000.000
150A150VAL0-0.034-0.02325.406-0.011-0.0110.0000.0000.0000.000
151A151THR0-0.009-0.00324.839-0.005-0.0050.0000.0000.0000.000
152A152ARG10.8410.91927.648-0.101-0.1010.0000.0000.0000.000
153A153ASP-1-0.848-0.90629.6380.0690.0690.0000.0000.0000.000
154A154ARG10.8040.88526.099-0.137-0.1370.0000.0000.0000.000
155A155ALA00.0250.02431.934-0.005-0.0050.0000.0000.0000.000
156A156VAL0-0.028-0.01733.692-0.005-0.0050.0000.0000.0000.000
157A157GLU-1-0.910-0.97435.4090.0550.0550.0000.0000.0000.000
158A158LYS10.8200.87035.780-0.088-0.0880.0000.0000.0000.000
159A159LEU00.0040.01237.630-0.002-0.0020.0000.0000.0000.000
160A160LYS10.8250.91438.515-0.059-0.0590.0000.0000.0000.000
161A161GLU-1-0.894-0.91839.5640.0720.0720.0000.0000.0000.000
162A162GLU-1-0.911-0.92043.2820.0720.0720.0000.0000.0000.000
163A163TYR0-0.074-0.06443.233-0.004-0.0040.0000.0000.0000.000
164A164GLY00.0120.02045.603-0.004-0.0040.0000.0000.0000.000
165A165GLU-1-0.841-0.91842.1250.0480.0480.0000.0000.0000.000
166A166ILE00.0430.02039.250-0.003-0.0030.0000.0000.0000.000
167A167GLY0-0.0080.00940.9180.0010.0010.0000.0000.0000.000
168A168SER0-0.053-0.06235.3780.0040.0040.0000.0000.0000.000
169A169GLY00.0560.03335.5610.0060.0060.0000.0000.0000.000
170A170TYR00.0170.01230.6760.0060.0060.0000.0000.0000.000
171A171PRO00.0770.04136.375-0.004-0.0040.0000.0000.0000.000
172A172SER00.0310.01337.596-0.003-0.0030.0000.0000.0000.000
173A173ASP-1-0.771-0.82138.7770.0360.0360.0000.0000.0000.000
174A174PRO00.027-0.01540.6110.0020.0020.0000.0000.0000.000
175A175ARG10.8160.87240.114-0.037-0.0370.0000.0000.0000.000
176A176THR0-0.019-0.01239.9610.0010.0010.0000.0000.0000.000
177A177ARG10.8070.89742.832-0.034-0.0340.0000.0000.0000.000
178A178ALA00.0180.01545.1830.0000.0000.0000.0000.0000.000
179A179PHE00.0180.01444.0780.0000.0000.0000.0000.0000.000
180A180LEU00.0100.00642.5340.0000.0000.0000.0000.0000.000
181A181GLU-1-0.853-0.90947.0440.0300.0300.0000.0000.0000.000
182A182ASN0-0.041-0.02750.304-0.002-0.0020.0000.0000.0000.000
183A183TYR0-0.010-0.01849.009-0.001-0.0010.0000.0000.0000.000
184A184TYR0-0.002-0.00850.164-0.001-0.0010.0000.0000.0000.000
185A185ARG10.7270.83752.342-0.031-0.0310.0000.0000.0000.000
186A186GLU-1-0.883-0.91454.0400.0400.0400.0000.0000.0000.000
187A187HIS10.7830.88352.139-0.044-0.0440.0000.0000.0000.000
188A188GLY00.0130.01855.1140.0010.0010.0000.0000.0000.000
189A189GLU-1-0.902-0.92450.8810.0560.0560.0000.0000.0000.000
190A190PHE0-0.002-0.02946.183-0.002-0.0020.0000.0000.0000.000
191A191PRO00.0280.03344.7050.0010.0010.0000.0000.0000.000
192A192PRO00.0510.01044.3370.0020.0020.0000.0000.0000.000
193A193ILE0-0.0330.00040.4030.0050.0050.0000.0000.0000.000
194A194VAL0-0.040-0.02139.8640.0020.0020.0000.0000.0000.000
195A195ARG10.9100.95435.296-0.098-0.0980.0000.0000.0000.000
196A196LYS10.8670.93841.649-0.050-0.0500.0000.0000.0000.000
197A197GLY00.0320.00043.1320.0030.0030.0000.0000.0000.000
198A198ALA0-0.033-0.00841.959-0.003-0.0030.0000.0000.0000.000
199A199GLY00.0680.04441.8230.0030.0030.0000.0000.0000.000
200A200ALA0-0.058-0.03842.978-0.002-0.0020.0000.0000.0000.000
201A201ILE00.0030.01141.822-0.003-0.0030.0000.0000.0000.000
202A202ILE00.0490.01244.3750.0010.0010.0000.0000.0000.000
203A203GLY00.0390.00946.6270.0020.0020.0000.0000.0000.000
204A204LEU0-0.031-0.01249.2450.0000.0000.0000.0000.0000.000
205A205ALA00.0450.02152.9660.0000.0000.0000.0000.0000.000
206A206VAL0-0.047-0.03454.8370.0000.0000.0000.0000.0000.000
207A207GLY00.0520.03157.633-0.001-0.0010.0000.0000.0000.000
208A208GLY00.0040.01756.570-0.001-0.0010.0000.0000.0000.000
209A209VAL0-0.023-0.02150.6430.0000.0000.0000.0000.0000.000
210A210VAL00.0310.02850.3430.0010.0010.0000.0000.0000.000
211A211ILE0-0.031-0.01345.3030.0030.0030.0000.0000.0000.000
212A212ALA00.0160.00743.864-0.002-0.0020.0000.0000.0000.000