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: 2K18R

Calculation Name: 1X1P-A-Xray310

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 212
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2353860.94749
FMO2-HF: Nuclear repulsion 2273710.06248
FMO2-HF: Total energy -80150.88501
FMO2-MP2: Total energy -80390.310228


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.
-12.147-11.05525.71-10.353-16.445-0.07
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 : -0.041 / q_NPA : -0.022
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].
3A3ILE 00.0550.0352.850-0.428-0.0214.166-1.373-3.1990.003
4A4ALA 00.0290.0015.633-0.729-0.7240.000-0.0120.0070.000
5A5GLY 0-0.035-0.0089.243-0.011-0.0110.0000.0000.0000.000
6A6ILE 0-0.058-0.02212.365-0.017-0.0170.0000.0000.0000.000
7A7ASP -1-0.792-0.90415.6570.1570.1570.0000.0000.0000.000
8A8GLH 0-0.078-0.06619.1750.0020.0020.0000.0000.0000.000
9A9ALA 0-0.0330.02322.767-0.014-0.0140.0000.0000.0000.000
10A10GLY 0-0.063-0.06025.572-0.006-0.0060.0000.0000.0000.000
11A11ARG 10.9760.98127.157-0.075-0.0750.0000.0000.0000.000
12A12GLY 00.1090.05529.0300.0040.0040.0000.0000.0000.000
13A13PRO 0-0.096-0.04030.921-0.008-0.0080.0000.0000.0000.000
14A14VAL 00.0370.01033.9570.0010.0010.0000.0000.0000.000
15A15ILE 00.001-0.00236.9570.0000.0000.0000.0000.0000.000
16A16GLY 0-0.009-0.01634.6520.0010.0010.0000.0000.0000.000
17A17PRO 00.0020.00230.1870.0000.0000.0000.0000.0000.000
18A18MET 00.0030.00725.660-0.002-0.0020.0000.0000.0000.000
19A19VAL 0-0.0180.00223.8830.0060.0060.0000.0000.0000.000
20A20ILE 00.0160.00520.022-0.003-0.0030.0000.0000.0000.000
21A21ALA 0-0.046-0.01919.3310.0020.0020.0000.0000.0000.000
22A22ALA 00.0380.02214.9070.0080.0080.0000.0000.0000.000
23A23VAL 0-0.041-0.02312.382-0.025-0.0250.0000.0000.0000.000
24A24VAL 00.0310.0087.9510.0830.0830.0000.0000.0000.000
25A25VAL 0-0.0010.0046.919-0.109-0.1090.0000.0000.0000.000
26A26ASP -1-0.846-0.9173.172-4.273-2.8620.058-0.686-0.783-0.006
27A27GLU -1-0.861-0.9461.990-8.740-11.72115.948-5.373-7.593-0.040
28A28ASN 0-0.059-0.0263.5410.4280.7060.0160.045-0.3380.000
29A29SER 0-0.034-0.0376.5430.3560.3560.0000.0000.0000.000
30A30LEU 00.0030.0246.2430.2700.2700.0000.0000.0000.000
31A31PRO 00.0310.0078.0170.1950.1950.0000.0000.0000.000
32A32LYS 11.0051.00511.2300.4090.4090.0000.0000.0000.000
33A33LEU 00.0290.01910.7890.0620.0620.0000.0000.0000.000
34A34GLU -1-0.793-0.88013.482-0.013-0.0130.0000.0000.0000.000
35A35GLU -1-0.976-0.98214.935-0.262-0.2620.0000.0000.0000.000
36A36LEU 0-0.046-0.01616.4610.0220.0220.0000.0000.0000.000
37A37LYS 10.7780.88718.4620.1310.1310.0000.0000.0000.000
38A38VAL 00.0310.01715.6180.0150.0150.0000.0000.0000.000
39A39ARG 10.8440.91415.5580.0120.0120.0000.0000.0000.000
40A40ASP -1-0.925-0.94219.867-0.023-0.0230.0000.0000.0000.000
41A41SER 00.029-0.00821.519-0.001-0.0010.0000.0000.0000.000
42A42LYS 10.8400.91023.325-0.068-0.0680.0000.0000.0000.000
43A43LYS 10.8270.90025.4010.0010.0010.0000.0000.0000.000
44A44LEU 00.0140.02624.5070.0000.0000.0000.0000.0000.000
45A45THR 00.0330.03128.5430.0050.0050.0000.0000.0000.000
46A46PRO 00.0750.03829.6860.0000.0000.0000.0000.0000.000
47A47LYS 11.0270.98929.427-0.019-0.0190.0000.0000.0000.000
48A48ARG 10.9050.94628.4670.0010.0010.0000.0000.0000.000
49A49ARG 10.8910.94724.465-0.050-0.0500.0000.0000.0000.000
50A50GLU -1-0.862-0.92924.6490.0600.0600.0000.0000.0000.000
51A51LYS 10.8800.94025.248-0.008-0.0080.0000.0000.0000.000
52A52LEU 00.1120.05519.6970.0010.0010.0000.0000.0000.000
53A53PHE 0-0.0100.01020.6390.0010.0010.0000.0000.0000.000
54A54ASN 0-0.014-0.01420.5740.0190.0190.0000.0000.0000.000
55A55GLU -1-0.935-0.96919.804-0.024-0.0240.0000.0000.0000.000
56A56ILE 0-0.017-0.02015.493-0.017-0.0170.0000.0000.0000.000
57A57LEU 0-0.042-0.02115.7130.0040.0040.0000.0000.0000.000
58A58GLY 0-0.0320.00316.4550.0140.0140.0000.0000.0000.000
59A59VAL 0-0.056-0.03812.599-0.019-0.0190.0000.0000.0000.000
60A60LEU 0-0.093-0.03011.276-0.046-0.0460.0000.0000.0000.000
61A61ASP -1-0.784-0.8867.1810.1380.1380.0000.0000.0000.000
62A62ASP -1-0.818-0.92510.3480.6070.6070.0000.0000.0000.000
63A63TYR 0-0.050-0.03812.827-0.033-0.0330.0000.0000.0000.000
64A64VAL 00.0000.01015.680-0.013-0.0130.0000.0000.0000.000
65A65ILE 0-0.022-0.01018.657-0.005-0.0050.0000.0000.0000.000
66A66LEU 00.003-0.00721.881-0.009-0.0090.0000.0000.0000.000
67A67GLU -1-0.927-0.96724.0160.1140.1140.0000.0000.0000.000
68A68LEU 0-0.036-0.01725.529-0.002-0.0020.0000.0000.0000.000
69A69PRO 0-0.040-0.02429.332-0.007-0.0070.0000.0000.0000.000
70A70PRO 0-0.021-0.00332.0290.0030.0030.0000.0000.0000.000
71A71ASP -1-0.842-0.91832.3520.0940.0940.0000.0000.0000.000
72A72VAL 0-0.092-0.05035.083-0.004-0.0040.0000.0000.0000.000
73A73ILE 0-0.016-0.03938.4570.0000.0000.0000.0000.0000.000
74A74GLY 00.0590.05039.961-0.001-0.0010.0000.0000.0000.000
75A75SER 0-0.049-0.01035.655-0.002-0.0020.0000.0000.0000.000
76A76ARG 10.8350.93930.971-0.080-0.0800.0000.0000.0000.000
77A77GLU -1-0.885-0.95634.8940.0570.0570.0000.0000.0000.000
78A78GLY 0-0.060-0.01834.9220.0000.0000.0000.0000.0000.000
79A79THR 00.0510.01929.9370.0010.0010.0000.0000.0000.000
80A80LEU 00.0130.00031.1410.0040.0040.0000.0000.0000.000
81A81ASN 00.004-0.00425.9930.0040.0040.0000.0000.0000.000
82A82GLU -1-0.882-0.95925.9790.0900.0900.0000.0000.0000.000
83A83PHE 0-0.041-0.01526.4490.0030.0030.0000.0000.0000.000
84A84GLU -1-0.893-0.91122.4950.1580.1580.0000.0000.0000.000
85A85VAL 00.0750.04319.6070.0200.0200.0000.0000.0000.000
86A86GLU -1-0.900-0.94420.3840.1600.1600.0000.0000.0000.000
87A87ASN 0-0.032-0.04621.9930.0150.0150.0000.0000.0000.000
88A88PHE 00.0310.00917.2480.0200.0200.0000.0000.0000.000
89A89ALA 00.0330.03117.1330.0330.0330.0000.0000.0000.000
90A90LYS 10.8300.91717.925-0.140-0.1400.0000.0000.0000.000
91A91ALA 00.0330.01918.4700.0160.0160.0000.0000.0000.000
92A92LEU 00.0810.04012.2030.0330.0330.0000.0000.0000.000
93A93ASN 0-0.067-0.02914.9830.0760.0760.0000.0000.0000.000
94A94SER 0-0.104-0.06116.922-0.016-0.0160.0000.0000.0000.000
95A95LEU 0-0.063-0.01112.263-0.016-0.0160.0000.0000.0000.000
96A96LYS 10.8770.94314.231-0.396-0.3960.0000.0000.0000.000
97A97VAL 0-0.029-0.0288.3360.0550.0550.0000.0000.0000.000
98A98LYS 10.8820.9589.661-0.635-0.6350.0000.0000.0000.000
99A99PRO 0-0.031-0.0116.5930.3760.3760.0000.0000.0000.000
100A100ASP -1-0.817-0.9182.2280.5641.7055.142-2.769-3.513-0.025
101A101VAL 00.0090.0032.546-1.331-0.5370.380-0.183-0.991-0.002
102A102ILE 0-0.025-0.0225.1520.3040.3410.000-0.002-0.0350.000
103A103TYR 0-0.009-0.0116.558-0.034-0.0340.0000.0000.0000.000
104A104ALA 0-0.001-0.03811.319-0.030-0.0300.0000.0000.0000.000
105A105ASP -1-0.861-0.94614.8550.1320.1320.0000.0000.0000.000
106A106ALA 0-0.038-0.00918.358-0.003-0.0030.0000.0000.0000.000
107A107ALA 00.0330.00120.451-0.012-0.0120.0000.0000.0000.000
108A108ASP -1-0.978-1.00224.1810.0700.0700.0000.0000.0000.000
109A109VAL 0-0.0210.01122.443-0.007-0.0070.0000.0000.0000.000
110A110ASP -1-0.913-0.98522.7980.0720.0720.0000.0000.0000.000
111A111GLU -1-0.869-0.94418.6860.0990.0990.0000.0000.0000.000
112A112GLU -1-0.907-0.95517.5420.0710.0710.0000.0000.0000.000
113A113ARG 10.9100.96118.183-0.080-0.0800.0000.0000.0000.000
114A114PHE 0-0.008-0.00617.4990.0070.0070.0000.0000.0000.000
115A115ALA 00.019-0.00214.0020.0160.0160.0000.0000.0000.000
116A116ARG 10.9360.99715.078-0.082-0.0820.0000.0000.0000.000
117A117GLU -1-0.921-0.98916.9350.1180.1180.0000.0000.0000.000
118A118LEU 0-0.053-0.02914.4840.0070.0070.0000.0000.0000.000
119A119GLY 00.0270.01013.6560.0220.0220.0000.0000.0000.000
120A120GLU -1-0.962-0.98214.4320.1280.1280.0000.0000.0000.000
121A121ARG 10.8770.93917.493-0.166-0.1660.0000.0000.0000.000
122A122LEU 0-0.044-0.00511.9550.0080.0080.0000.0000.0000.000
123A123ASN 0-0.037-0.02115.9260.0090.0090.0000.0000.0000.000
124A124PHE 0-0.035-0.0449.6190.0230.0230.0000.0000.0000.000
125A125GLU -1-0.982-0.9808.8090.0880.0880.0000.0000.0000.000
126A126ALA 00.0790.0277.3170.0820.0820.0000.0000.0000.000
127A127GLU -1-0.959-0.9555.9570.0940.0940.0000.0000.0000.000
128A128VAL 0-0.015-0.0067.7140.1810.1810.0000.0000.0000.000
129A129VAL 0-0.0040.0049.797-0.084-0.0840.0000.0000.0000.000
130A130ALA 00.000-0.00612.0140.0540.0540.0000.0000.0000.000
131A131LYS 10.9150.95215.223-0.128-0.1280.0000.0000.0000.000
132A132HIS 00.0280.03218.3650.0160.0160.0000.0000.0000.000
133A133LYS 10.9080.96920.804-0.061-0.0610.0000.0000.0000.000
134A134ALA 00.0750.05115.887-0.010-0.0100.0000.0000.0000.000
135A135ASP -1-0.830-0.91016.7330.1120.1120.0000.0000.0000.000
136A136ASP -1-0.888-0.94718.5860.0420.0420.0000.0000.0000.000
137A137ILE 0-0.086-0.02915.085-0.028-0.0280.0000.0000.0000.000
138A138PHE 00.047-0.00211.125-0.027-0.0270.0000.0000.0000.000
139A139PRO 00.0480.02111.9170.0110.0110.0000.0000.0000.000
140A140VAL 00.0580.0499.664-0.051-0.0510.0000.0000.0000.000
141A141VAL 00.0400.01912.1840.0080.0080.0000.0000.0000.000
142A142SER 0-0.028-0.00314.705-0.037-0.0370.0000.0000.0000.000
143A143ALA 0-0.017-0.03314.518-0.012-0.0120.0000.0000.0000.000
144A144ALA 00.0140.01515.203-0.012-0.0120.0000.0000.0000.000
145A145SER 00.0260.01717.132-0.020-0.0200.0000.0000.0000.000
146A146ILE 0-0.067-0.03619.350-0.022-0.0220.0000.0000.0000.000
147A147LEU 00.000-0.00517.625-0.014-0.0140.0000.0000.0000.000
148A148ALA 00.0380.01921.415-0.008-0.0080.0000.0000.0000.000
149A149LYS 10.8980.94323.424-0.079-0.0790.0000.0000.0000.000
150A150VAL 0-0.052-0.01924.312-0.009-0.0090.0000.0000.0000.000
151A151THR 00.0460.03024.618-0.008-0.0080.0000.0000.0000.000
152A152ARG 10.9070.96327.296-0.088-0.0880.0000.0000.0000.000
153A153ASP -1-0.905-0.97929.3120.0610.0610.0000.0000.0000.000
154A154ARG 10.8540.92726.856-0.081-0.0810.0000.0000.0000.000
155A155ALA 00.0410.02931.673-0.005-0.0050.0000.0000.0000.000
156A156VAL 0-0.007-0.00733.536-0.004-0.0040.0000.0000.0000.000
157A157GLU -1-0.976-0.98634.8950.0390.0390.0000.0000.0000.000
158A158LYS 10.9580.96535.806-0.061-0.0610.0000.0000.0000.000
159A159LEU 00.0050.00937.061-0.002-0.0020.0000.0000.0000.000
160A160LYS 10.8940.96938.314-0.047-0.0470.0000.0000.0000.000
161A161GLU -1-0.988-0.99139.3680.0440.0440.0000.0000.0000.000
162A162GLU -1-0.981-0.97842.6900.0490.0490.0000.0000.0000.000
163A163TYR 0-0.062-0.03943.051-0.002-0.0020.0000.0000.0000.000
164A164GLY 00.0040.00945.172-0.002-0.0020.0000.0000.0000.000
165A165GLU -1-0.907-0.96242.0640.0400.0400.0000.0000.0000.000
166A166ILE 00.0630.03439.3250.0000.0000.0000.0000.0000.000
167A167GLY 0-0.044-0.03540.7970.0020.0020.0000.0000.0000.000
168A168SER 0-0.095-0.07535.2870.0030.0030.0000.0000.0000.000
169A169GLY 00.0470.02935.6020.0050.0050.0000.0000.0000.000
170A170TYR 0-0.0020.01930.7550.0060.0060.0000.0000.0000.000
171A171PRO 00.0900.05136.562-0.005-0.0050.0000.0000.0000.000
172A172SER 00.006-0.00737.503-0.002-0.0020.0000.0000.0000.000
173A173ASP -1-0.825-0.88538.5340.0380.0380.0000.0000.0000.000
174A174PRO 00.0370.01040.4270.0000.0000.0000.0000.0000.000
175A175ARG 10.9030.93739.347-0.037-0.0370.0000.0000.0000.000
176A176THR 00.0020.01240.0470.0000.0000.0000.0000.0000.000
177A177ARG 10.8210.90842.838-0.040-0.0400.0000.0000.0000.000
178A178ALA 00.0340.02145.130-0.001-0.0010.0000.0000.0000.000
179A179PHE 0-0.026-0.00843.5770.0000.0000.0000.0000.0000.000
180A180LEU 00.009-0.00742.6060.0000.0000.0000.0000.0000.000
181A181GLU -1-0.907-0.95346.8520.0320.0320.0000.0000.0000.000
182A182ASN 0-0.066-0.04649.877-0.002-0.0020.0000.0000.0000.000
183A183TYR 00.0440.03648.558-0.001-0.0010.0000.0000.0000.000
184A184TYR 00.0470.02550.2250.0000.0000.0000.0000.0000.000
185A185ARG 10.8570.92452.187-0.029-0.0290.0000.0000.0000.000
186A186GLU -1-1.009-0.99854.3650.0290.0290.0000.0000.0000.000
187A187HIS 10.8740.94151.784-0.035-0.0350.0000.0000.0000.000
188A188GLY 0-0.0250.00354.8240.0000.0000.0000.0000.0000.000
189A189GLU -1-0.959-0.98150.6400.0440.0440.0000.0000.0000.000
190A190PHE 0-0.029-0.02846.208-0.001-0.0010.0000.0000.0000.000
191A191PRO 00.0150.02044.5390.0000.0000.0000.0000.0000.000
192A192PRO 00.0700.02244.3160.0020.0020.0000.0000.0000.000
193A193ILE 0-0.046-0.01340.3290.0040.0040.0000.0000.0000.000
194A194VAL 0-0.022-0.00739.7820.0030.0030.0000.0000.0000.000
195A195ARG 10.9740.99235.885-0.084-0.0840.0000.0000.0000.000
196A196LYS 10.9030.94641.266-0.048-0.0480.0000.0000.0000.000
197A197GLY 00.004-0.02642.4450.0010.0010.0000.0000.0000.000
198A198ALA 0-0.066-0.02341.501-0.003-0.0030.0000.0000.0000.000
199A199GLY 00.0790.04142.1540.0020.0020.0000.0000.0000.000
200A200ALA 0-0.036-0.05142.913-0.002-0.0020.0000.0000.0000.000
201A201ILE 0-0.057-0.00942.487-0.001-0.0010.0000.0000.0000.000
202A202ILE 00.0350.00744.936-0.001-0.0010.0000.0000.0000.000
203A203GLY 00.099-0.01346.6890.0020.0020.0000.0000.0000.000
204A204LEU 0-0.0110.00149.0090.0000.0000.0000.0000.0000.000
205A205ALA 00.0340.01952.7500.0000.0000.0000.0000.0000.000
206A206VAL 0-0.062-0.03654.7850.0000.0000.0000.0000.0000.000
207A207GLY 00.0660.03358.4140.0000.0000.0000.0000.0000.000
208A208GLY 0-0.0010.01056.8180.0000.0000.0000.0000.0000.000
209A209VAL 0-0.029-0.02650.5810.0000.0000.0000.0000.0000.000
210A210VAL 0-0.0380.00849.7860.0010.0010.0000.0000.0000.000
211A211ILE 0-0.0660.00845.0400.0020.0020.0000.0000.0000.000
212A212ALA -1-0.776-0.84944.0220.0470.0470.0000.0000.0000.000