FMO DATABASE

FMODB ID: 3Q2JL

Calculation Name: 1IIB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1IIB

Chain ID: A

ChEMBL ID:

UniProt ID: P69795

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	OptH
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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-734167.372379
FMO2-HF: Nuclear repulsion	695858.71084
FMO2-HF: Total energy	-38308.661539
FMO2-MP2: Total energy	-38421.144001

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
-72.566	-68.696	12.351	-6.515	-9.705	-0.046

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.950 / q_NPA : 0.955

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 ES EX CT+mix DI(MP2)

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].
3	A	5	HIS	0	0.023	0.011	3.781	-3.959	-2.243	-0.017	-0.674	-1.024	0.002
4	A	6	ILE	0	0.017	0.011	5.892	3.765	3.765	0.000	0.000	0.000	0.000
5	A	7	TYR	0	-0.035	-0.022	8.207	0.020	0.020	0.000	0.000	0.000	0.000
6	A	8	LEU	0	-0.008	-0.004	11.569	1.257	1.257	0.000	0.000	0.000	0.000
7	A	9	PHE	0	0.008	0.015	14.659	-0.096	-0.096	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.007	-0.022	18.096	0.657	0.657	0.000	0.000	0.000	0.000
9	A	11	SER	0	0.097	0.065	21.340	-0.266	-0.266	0.000	0.000	0.000	0.000
10	A	12	ALA	0	-0.036	-0.009	23.812	0.315	0.315	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.030	0.011	21.500	-0.611	-0.611	0.000	0.000	0.000	0.000
12	A	14	MET	0	0.039	0.007	20.685	-0.941	-0.941	0.000	0.000	0.000	0.000
13	A	15	SER	0	0.036	0.016	20.787	-0.439	-0.439	0.000	0.000	0.000	0.000
14	A	16	THR	0	0.025	0.019	17.157	-0.541	-0.541	0.000	0.000	0.000	0.000
15	A	17	SER	0	0.029	0.012	16.355	-1.397	-1.397	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.032	-0.003	15.953	-1.111	-1.111	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.025	0.012	16.214	-0.674	-0.674	0.000	0.000	0.000	0.000
18	A	20	VAL	0	0.035	0.011	11.245	-1.071	-1.071	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.066	-0.030	11.755	-1.804	-1.804	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.969	0.977	12.385	15.634	15.634	0.000	0.000	0.000	0.000
21	A	23	MET	0	-0.019	-0.004	11.401	-0.124	-0.124	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.892	0.942	7.706	29.530	29.530	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.002	0.016	8.287	-2.271	-2.271	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.014	-0.022	10.791	-0.465	-0.465	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.006	-0.012	6.689	0.812	0.812	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.919	-0.942	5.518	-51.368	-51.368	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.894	0.956	7.896	21.102	21.102	0.000	0.000	0.000	0.000
28	A	30	TYR	0	-0.103	-0.063	10.681	2.337	2.337	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.909	-0.936	6.951	-27.848	-27.848	0.000	0.000	0.000	0.000
30	A	32	VAL	0	-0.024	-0.006	6.338	0.086	0.086	0.000	0.000	0.000	0.000
31	A	33	PRO	0	-0.002	-0.004	2.491	-9.469	-8.424	1.328	-0.538	-1.834	0.000
32	A	34	VAL	0	-0.040	-0.030	2.095	1.849	0.795	9.934	-4.380	-4.501	-0.041
33	A	35	ILE	0	-0.003	0.008	2.403	-13.802	-11.719	1.107	-0.903	-2.286	-0.007
34	A	36	ILE	0	-0.008	-0.002	4.476	5.727	5.807	-0.001	-0.020	-0.060	0.000
35	A	37	GLU	-1	-0.896	-0.947	8.213	-30.964	-30.964	0.000	0.000	0.000	0.000
36	A	38	ALA	0	-0.010	0.000	11.102	1.044	1.044	0.000	0.000	0.000	0.000
37	A	39	PHE	0	0.001	-0.004	12.097	0.013	0.013	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.039	0.022	17.159	0.223	0.223	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.817	-0.949	20.103	-12.753	-12.753	0.000	0.000	0.000	0.000
40	A	42	THR	0	-0.001	-0.001	21.926	0.003	0.003	0.000	0.000	0.000	0.000
41	A	43	LEU	0	-0.023	-0.001	18.138	0.077	0.077	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.003	0.003	18.087	-0.663	-0.663	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.031	0.003	18.143	-0.418	-0.418	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.943	-0.966	18.366	-14.531	-14.531	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.916	0.946	13.598	17.555	17.555	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.037	0.021	13.573	-1.293	-1.293	0.000	0.000	0.000	0.000
47	A	49	GLN	0	-0.005	-0.007	14.042	-0.878	-0.878	0.000	0.000	0.000	0.000
48	A	50	ASN	0	-0.056	-0.028	10.574	0.085	0.085	0.000	0.000	0.000	0.000
49	A	51	ALA	0	-0.022	0.012	9.352	-2.157	-2.157	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.851	-0.923	6.259	-28.249	-28.249	0.000	0.000	0.000	0.000
51	A	53	VAL	0	-0.033	-0.026	9.403	1.472	1.472	0.000	0.000	0.000	0.000
52	A	54	VAL	0	-0.020	0.004	11.699	-1.158	-1.158	0.000	0.000	0.000	0.000
53	A	55	LEU	0	0.015	0.003	13.660	0.750	0.750	0.000	0.000	0.000	0.000
54	A	56	LEU	0	0.013	-0.003	16.170	-0.187	-0.187	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.017	0.007	19.581	0.022	0.022	0.000	0.000	0.000	0.000
56	A	58	PRO	0	0.029	-0.002	21.374	0.452	0.452	0.000	0.000	0.000	0.000
57	A	59	GLN	0	-0.008	-0.004	24.269	0.148	0.148	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.000	0.001	21.326	0.365	0.365	0.000	0.000	0.000	0.000
59	A	61	ALA	0	0.035	0.024	24.911	-0.050	-0.050	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.010	-0.010	25.907	0.038	0.038	0.000	0.000	0.000	0.000
61	A	63	MET	0	0.035	0.018	25.265	0.117	0.117	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.025	-0.002	22.386	-0.179	-0.179	0.000	0.000	0.000	0.000
63	A	65	PRO	0	-0.012	-0.016	24.408	-0.206	-0.206	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.952	-0.976	26.499	-10.258	-10.258	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.024	0.006	19.949	-0.198	-0.198	0.000	0.000	0.000	0.000
66	A	68	GLN	0	-0.029	-0.015	21.781	0.051	0.051	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.941	0.962	22.940	9.918	9.918	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.034	0.006	21.959	0.066	0.066	0.000	0.000	0.000	0.000
69	A	71	LEU	0	-0.061	-0.025	16.940	-0.370	-0.370	0.000	0.000	0.000	0.000
70	A	72	PRO	0	0.030	0.022	19.675	-0.243	-0.243	0.000	0.000	0.000	0.000
71	A	73	ASN	0	-0.025	-0.016	16.462	0.137	0.137	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.850	0.928	11.854	18.377	18.377	0.000	0.000	0.000	0.000
73	A	75	PRO	0	-0.004	0.025	13.518	0.810	0.810	0.000	0.000	0.000	0.000
74	A	76	VAL	0	0.019	-0.006	15.560	-0.832	-0.832	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.960	-0.989	17.192	-14.305	-14.305	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.003	0.007	18.868	-0.480	-0.480	0.000	0.000	0.000	0.000
77	A	79	ILE	0	-0.031	-0.009	16.940	-0.134	-0.134	0.000	0.000	0.000	0.000
78	A	80	ASP	-1	-0.808	-0.917	20.290	-11.785	-11.785	0.000	0.000	0.000	0.000
79	A	81	SER	0	0.036	-0.005	23.083	-0.334	-0.334	0.000	0.000	0.000	0.000
80	A	82	LEU	0	0.028	0.023	25.521	-0.025	-0.025	0.000	0.000	0.000	0.000
81	A	83	LEU	0	-0.055	-0.020	19.843	-0.172	-0.172	0.000	0.000	0.000	0.000
82	A	84	TYR	0	-0.012	-0.025	20.150	-0.273	-0.273	0.000	0.000	0.000	0.000
83	A	85	GLY	0	-0.022	-0.009	22.298	-0.155	-0.155	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.927	0.969	23.761	12.335	12.335	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.039	-0.018	18.800	-0.291	-0.291	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.863	-0.939	19.387	-16.336	-16.336	0.000	0.000	0.000	0.000
87	A	89	GLY	0	0.022	-0.002	15.311	-0.455	-0.455	0.000	0.000	0.000	0.000
88	A	90	LEU	0	0.001	0.000	14.677	-1.073	-1.073	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.020	0.013	15.733	-0.468	-0.468	0.000	0.000	0.000	0.000
90	A	92	VAL	0	0.041	0.004	14.941	0.159	0.159	0.000	0.000	0.000	0.000
91	A	93	LEU	0	-0.011	0.010	9.132	-0.347	-0.347	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.915	0.947	12.259	16.084	16.084	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.024	0.018	14.364	0.211	0.211	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.044	0.030	11.359	0.372	0.372	0.000	0.000	0.000	0.000
95	A	97	VAL	0	0.004	0.001	8.591	-0.169	-0.169	0.000	0.000	0.000	0.000
96	A	98	ALA	0	-0.038	-0.020	10.810	0.613	0.613	0.000	0.000	0.000	0.000
97	A	99	ALA	0	0.034	0.020	13.857	0.571	0.571	0.000	0.000	0.000	0.000
98	A	100	ILE	0	0.000	0.001	7.551	0.241	0.241	0.000	0.000	0.000	0.000
99	A	101	LYS	1	0.917	0.950	11.540	17.733	17.733	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.931	0.964	13.194	13.256	13.256	0.000	0.000	0.000	0.000
101	A	103	ALA	0	0.001	0.007	13.744	0.738	0.738	0.000	0.000	0.000	0.000
102	A	104	ALA	0	-0.042	-0.007	12.366	0.352	0.352	0.000	0.000	0.000	0.000
103	A	105	ALA	0	-0.031	-0.005	14.514	0.601	0.601	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)