FMO DATABASE

FMODB ID: R9158

Calculation Name: 5I27-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I27

Chain ID: A

ChEMBL ID:

UniProt ID: P10258

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-640643.282807
FMO2-HF: Nuclear repulsion	605766.151213
FMO2-HF: Total energy	-34877.131595
FMO2-MP2: Total energy	-34981.565573

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:7:SER)

Summations of interaction energy for fragment #1(A:7:SER)

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.
1.195	5.531	2.147	-2.343	-4.139	-0.011

Interaction energy analysis for fragmet #1(A:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.019

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	9	GLY	0	0.079	0.046	3.815	-0.328	1.116	-0.023	-0.650	-0.771	0.002
4	A	10	GLN	0	0.058	0.022	2.726	-3.097	-0.601	2.167	-1.575	-3.088	-0.013
5	A	11	LYS	1	0.981	0.988	4.594	2.243	2.363	-0.001	-0.012	-0.106	0.000
6	A	12	LEU	0	0.042	0.031	6.392	0.460	0.460	0.000	0.000	0.000	0.000
7	A	13	PHE	0	0.089	0.053	8.151	0.260	0.260	0.000	0.000	0.000	0.000
8	A	14	VAL	0	-0.001	-0.017	7.048	0.195	0.195	0.000	0.000	0.000	0.000
9	A	15	SER	0	-0.071	-0.037	9.516	0.236	0.236	0.000	0.000	0.000	0.000
10	A	16	VAL	0	0.015	0.001	11.970	0.136	0.136	0.000	0.000	0.000	0.000
11	A	17	LEU	0	0.008	0.008	12.385	0.092	0.092	0.000	0.000	0.000	0.000
12	A	18	GLN	0	-0.018	-0.014	12.714	0.024	0.024	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.967	0.998	15.372	0.415	0.415	0.000	0.000	0.000	0.000
14	A	20	LEU	0	0.029	0.008	17.168	0.046	0.046	0.000	0.000	0.000	0.000
15	A	21	LEU	0	0.020	-0.005	16.801	0.043	0.043	0.000	0.000	0.000	0.000
16	A	22	SER	0	0.014	0.021	19.002	0.036	0.036	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.981	-0.992	21.114	-0.241	-0.241	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.857	0.946	22.816	0.247	0.247	0.000	0.000	0.000	0.000
19	A	25	GLY	0	-0.023	-0.007	24.529	0.015	0.015	0.000	0.000	0.000	0.000
20	A	26	LEU	0	-0.055	-0.018	21.637	0.004	0.004	0.000	0.000	0.000	0.000
21	A	27	HIS	0	0.023	0.007	19.240	-0.049	-0.049	0.000	0.000	0.000	0.000
22	A	28	VAL	0	0.006	-0.004	14.327	0.018	0.018	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.981	0.986	14.514	0.241	0.241	0.000	0.000	0.000	0.000
24	A	30	GLU	-1	-0.848	-0.929	9.046	-0.986	-0.986	0.000	0.000	0.000	0.000
25	A	31	SER	0	0.018	0.003	9.591	-0.132	-0.132	0.000	0.000	0.000	0.000
26	A	32	SER	0	-0.005	-0.005	10.542	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	33	ALA	0	0.060	0.025	10.676	0.027	0.027	0.000	0.000	0.000	0.000
28	A	34	ILE	0	-0.036	-0.018	5.232	-0.110	-0.110	0.000	0.000	0.000	0.000
29	A	35	GLU	-1	-0.795	-0.901	7.234	-0.463	-0.463	0.000	0.000	0.000	0.000
30	A	36	PHE	0	-0.028	-0.007	9.674	0.107	0.107	0.000	0.000	0.000	0.000
31	A	37	TYR	0	0.040	0.017	3.976	-0.191	-0.108	0.000	-0.023	-0.060	0.000
32	A	38	GLN	0	-0.022	-0.025	3.423	0.462	0.655	0.004	-0.083	-0.114	0.000
33	A	39	PHE	0	-0.005	-0.004	6.755	0.258	0.258	0.000	0.000	0.000	0.000
34	A	40	LEU	0	-0.002	0.000	9.737	0.104	0.104	0.000	0.000	0.000	0.000
35	A	41	ILE	0	0.011	-0.001	4.811	0.156	0.156	0.000	0.000	0.000	0.000
36	A	42	LYS	1	0.873	0.966	9.033	0.139	0.139	0.000	0.000	0.000	0.000
37	A	43	VAL	0	-0.061	-0.037	10.818	0.027	0.027	0.000	0.000	0.000	0.000
38	A	44	SER	0	-0.023	-0.016	12.447	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	45	PRO	0	-0.014	-0.005	10.770	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	46	TRP	0	0.005	-0.014	11.683	0.065	0.065	0.000	0.000	0.000	0.000
41	A	47	PHE	0	-0.034	-0.017	11.271	-0.041	-0.041	0.000	0.000	0.000	0.000
42	A	48	PRO	0	-0.069	-0.051	8.247	-0.064	-0.064	0.000	0.000	0.000	0.000
43	A	49	GLU	-1	-0.972	-0.964	10.582	0.270	0.270	0.000	0.000	0.000	0.000
44	A	50	GLU	-1	-0.917	-0.978	13.434	0.128	0.128	0.000	0.000	0.000	0.000
45	A	51	GLY	0	-0.038	-0.019	14.765	-0.024	-0.024	0.000	0.000	0.000	0.000
46	A	52	GLY	0	-0.048	-0.028	15.402	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	53	LEU	0	-0.047	-0.031	15.236	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	54	ASN	0	0.037	0.025	17.791	0.011	0.011	0.000	0.000	0.000	0.000
49	A	55	LEU	0	0.067	0.022	20.795	0.006	0.006	0.000	0.000	0.000	0.000
50	A	56	GLN	0	0.008	-0.008	22.948	0.001	0.001	0.000	0.000	0.000	0.000
51	A	57	ASP	-1	-0.754	-0.858	18.016	-0.030	-0.030	0.000	0.000	0.000	0.000
52	A	58	TRP	0	-0.027	-0.015	14.106	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	59	LYS	1	0.932	0.947	19.304	0.063	0.063	0.000	0.000	0.000	0.000
54	A	60	ARG	1	0.881	0.961	19.247	-0.068	-0.068	0.000	0.000	0.000	0.000
55	A	61	VAL	0	0.072	0.037	14.979	0.012	0.012	0.000	0.000	0.000	0.000
56	A	62	GLY	0	0.011	0.012	17.677	0.002	0.002	0.000	0.000	0.000	0.000
57	A	63	ARG	1	0.888	0.936	20.018	0.023	0.023	0.000	0.000	0.000	0.000
58	A	64	GLU	-1	-0.800	-0.885	17.262	0.085	0.085	0.000	0.000	0.000	0.000
59	A	65	MET	0	-0.034	0.004	14.259	0.005	0.005	0.000	0.000	0.000	0.000
60	A	66	LYS	1	0.931	0.961	18.371	0.056	0.056	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.956	0.994	19.931	-0.076	-0.076	0.000	0.000	0.000	0.000
62	A	68	TYR	0	0.082	0.033	15.811	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	69	ALA	0	-0.019	-0.027	19.703	0.002	0.002	0.000	0.000	0.000	0.000
64	A	70	ALA	0	-0.068	-0.020	21.872	0.001	0.001	0.000	0.000	0.000	0.000
65	A	71	GLU	-1	-0.962	-0.979	20.735	0.080	0.080	0.000	0.000	0.000	0.000
66	A	72	HIS	0	-0.049	-0.037	19.092	0.018	0.018	0.000	0.000	0.000	0.000
67	A	73	GLY	0	0.046	0.046	22.034	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	74	THR	0	-0.040	-0.040	22.012	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.885	-0.931	21.514	-0.043	-0.043	0.000	0.000	0.000	0.000
70	A	76	SER	0	-0.028	-0.043	16.795	0.010	0.010	0.000	0.000	0.000	0.000
71	A	77	ILE	0	-0.025	0.028	16.628	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	78	PRO	0	-0.059	-0.017	13.426	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	79	LYS	1	0.918	0.952	15.401	0.284	0.284	0.000	0.000	0.000	0.000
74	A	80	GLN	0	-0.033	-0.033	13.277	0.074	0.074	0.000	0.000	0.000	0.000
75	A	81	ALA	0	-0.016	-0.001	15.293	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	82	TYR	0	0.056	0.022	16.471	0.000	0.000	0.000	0.000	0.000	0.000
77	A	83	PRO	0	0.021	-0.002	19.718	0.002	0.002	0.000	0.000	0.000	0.000
78	A	84	ILE	0	0.027	0.015	14.470	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	85	TRP	0	-0.014	-0.001	17.006	0.008	0.008	0.000	0.000	0.000	0.000
80	A	86	LEU	0	-0.012	-0.001	18.317	0.012	0.012	0.000	0.000	0.000	0.000
81	A	87	GLN	0	0.034	0.010	20.529	0.010	0.010	0.000	0.000	0.000	0.000
82	A	88	LEU	0	-0.010	-0.004	15.661	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	89	ARG	1	0.835	0.904	20.029	0.129	0.129	0.000	0.000	0.000	0.000
84	A	90	GLU	-1	-0.865	-0.920	22.381	-0.109	-0.109	0.000	0.000	0.000	0.000
85	A	91	ILE	0	-0.023	-0.010	20.766	0.005	0.005	0.000	0.000	0.000	0.000
86	A	92	LEU	0	-0.104	-0.035	19.323	0.005	0.005	0.000	0.000	0.000	0.000
87	A	93	THR	0	-0.028	-0.005	23.794	0.018	0.018	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:7:SER)