FMO DATABASE

FMODB ID: R8YV8

Calculation Name: 4OB4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OB4

Chain ID: A

ChEMBL ID:

UniProt ID: Q7AKQ8

Base Structure: X-ray

Registration Date: 2023-09-22

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	69
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-410350.399966
FMO2-HF: Nuclear repulsion	384147.330053
FMO2-HF: Total energy	-26203.069913
FMO2-MP2: Total energy	-26281.901456

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:SER)

Summations of interaction energy for fragment #1(A:3: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.
-2.981	1.113	1.206	-1.93	-3.37	0.007

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.003

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

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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	TYR	0	0.038	0.019	3.380	-2.745	-0.814	0.053	-0.825	-1.159	0.003
4	A	6	ALA	0	0.008	-0.005	2.798	-1.217	-0.394	0.261	-0.304	-0.780	0.000
5	A	7	LYS	1	0.915	0.956	2.241	0.172	1.430	0.893	-0.800	-1.351	0.004
6	A	8	GLN	0	-0.011	-0.021	5.753	0.438	0.438	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.031	0.002	7.600	0.111	0.111	0.000	0.000	0.000	0.000
8	A	10	GLY	0	-0.007	0.001	8.377	0.072	0.072	0.000	0.000	0.000	0.000
9	A	11	ALA	0	-0.002	-0.016	10.116	0.045	0.045	0.000	0.000	0.000	0.000
10	A	12	LYS	1	0.893	0.934	12.144	0.002	0.002	0.000	0.000	0.000	0.000
11	A	13	LEU	0	-0.005	0.006	11.338	0.019	0.019	0.000	0.000	0.000	0.000
12	A	14	ARG	1	0.944	0.988	12.395	0.183	0.183	0.000	0.000	0.000	0.000
13	A	15	ALA	0	-0.009	-0.005	16.039	0.010	0.010	0.000	0.000	0.000	0.000
14	A	16	ILE	0	0.051	0.025	17.563	0.006	0.006	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.777	0.900	17.509	0.043	0.043	0.000	0.000	0.000	0.000
16	A	18	THR	0	-0.096	-0.065	19.701	0.002	0.002	0.000	0.000	0.000	0.000
17	A	19	GLN	0	0.030	0.031	21.780	0.008	0.008	0.000	0.000	0.000	0.000
18	A	20	GLN	0	-0.066	-0.018	23.654	0.006	0.006	0.000	0.000	0.000	0.000
19	A	21	GLY	0	-0.011	-0.010	25.540	0.003	0.003	0.000	0.000	0.000	0.000
20	A	22	LEU	0	0.004	0.025	24.112	0.001	0.001	0.000	0.000	0.000	0.000
21	A	23	SER	0	0.025	-0.002	22.654	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	24	LEU	0	0.013	-0.012	16.959	0.005	0.005	0.000	0.000	0.000	0.000
23	A	25	HIS	0	0.011	0.014	21.207	0.008	0.008	0.000	0.000	0.000	0.000
24	A	26	GLY	0	0.056	0.024	24.482	0.004	0.004	0.000	0.000	0.000	0.000
25	A	27	VAL	0	-0.022	-0.007	20.744	0.003	0.003	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.871	-0.932	23.509	0.036	0.036	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.895	-0.963	24.674	0.008	0.008	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.947	0.990	27.106	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	31	SER	0	-0.085	-0.041	24.880	0.004	0.004	0.000	0.000	0.000	0.000
30	A	32	GLN	0	0.013	0.003	27.024	0.003	0.003	0.000	0.000	0.000	0.000
31	A	33	GLY	0	0.044	0.038	26.120	0.002	0.002	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.846	0.926	22.864	-0.056	-0.056	0.000	0.000	0.000	0.000
33	A	35	TRP	0	-0.031	-0.022	17.939	0.012	0.012	0.000	0.000	0.000	0.000
34	A	36	LYS	1	0.922	0.954	20.049	-0.059	-0.059	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.083	0.047	19.006	0.005	0.005	0.000	0.000	0.000	0.000
36	A	38	VAL	0	0.016	0.005	17.204	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	39	VAL	0	-0.051	-0.028	15.324	0.012	0.012	0.000	0.000	0.000	0.000
38	A	40	VAL	0	0.057	0.025	14.209	0.012	0.012	0.000	0.000	0.000	0.000
39	A	41	GLY	0	0.032	0.010	14.009	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	42	SER	0	-0.089	-0.060	11.353	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	43	TYR	0	0.012	-0.004	9.508	0.031	0.031	0.000	0.000	0.000	0.000
42	A	44	GLU	-1	-0.798	-0.887	9.288	-0.120	-0.120	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.830	0.913	9.285	-0.064	-0.064	0.000	0.000	0.000	0.000
44	A	46	GLY	0	0.008	0.009	5.343	-0.123	-0.123	0.000	0.000	0.000	0.000
45	A	47	ASP	-1	-0.882	-0.927	5.026	0.432	0.514	-0.001	-0.001	-0.080	0.000
46	A	48	ARG	1	0.931	0.963	7.595	-0.053	-0.053	0.000	0.000	0.000	0.000
47	A	49	ALA	0	-0.005	0.000	7.157	-0.108	-0.108	0.000	0.000	0.000	0.000
48	A	50	VAL	0	0.020	0.017	8.543	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	51	THR	0	0.001	-0.004	10.519	0.012	0.012	0.000	0.000	0.000	0.000
50	A	52	VAL	0	0.077	0.017	12.575	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	53	GLN	0	0.035	0.009	14.341	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	54	ARG	1	0.911	0.980	15.228	-0.128	-0.128	0.000	0.000	0.000	0.000
53	A	55	LEU	0	0.010	-0.004	12.341	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.011	0.007	15.588	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.841	-0.929	18.776	0.079	0.079	0.000	0.000	0.000	0.000
56	A	58	LEU	0	-0.041	-0.019	15.947	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	59	ALA	0	-0.003	0.010	18.534	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.892	-0.934	20.129	0.050	0.050	0.000	0.000	0.000	0.000
59	A	61	PHE	0	-0.098	-0.057	22.086	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.038	-0.040	18.191	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.017	0.027	23.520	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	64	VAL	0	-0.016	-0.010	20.293	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	65	PRO	0	0.052	0.015	21.843	0.007	0.007	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.076	0.026	16.793	0.000	0.000	0.000	0.000	0.000	0.000
65	A	67	GLN	0	-0.033	-0.023	16.749	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	68	GLU	-1	-0.927	-0.953	16.489	0.025	0.025	0.000	0.000	0.000	0.000
67	A	69	LEU	0	-0.062	-0.033	14.630	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.007	-0.007	11.423	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	71	PRO	0	-0.019	0.021	8.246	0.001	0.001	0.000	0.000	0.000	0.000

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