FMO DATABASE

FMODB ID: R8V38

Calculation Name: 4EMK-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EMK

Chain ID: B

ChEMBL ID:

UniProt ID: O42978

Base Structure: X-ray

Registration Date: 2023-09-23

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-436596.956656
FMO2-HF: Nuclear repulsion	407987.388448
FMO2-HF: Total energy	-28609.568209
FMO2-MP2: Total energy	-28692.226623

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
1.174	3.749	-0.019	-1.435	-1.121	0.006

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.009

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	B	3	SER	0	0.025	0.002	3.869	-0.667	1.908	-0.019	-1.435	-1.121	0.006
4	B	4	SER	0	-0.013	-0.037	6.241	0.870	0.870	0.000	0.000	0.000	0.000
5	B	5	PRO	0	-0.009	-0.004	6.501	0.288	0.288	0.000	0.000	0.000	0.000
6	B	6	ASN	0	0.051	0.013	9.541	0.167	0.167	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.833	-0.870	10.586	-0.662	-0.662	0.000	0.000	0.000	0.000
8	B	8	PHE	0	-0.017	-0.016	11.764	0.120	0.120	0.000	0.000	0.000	0.000
9	B	9	LEU	0	0.003	-0.006	13.135	0.072	0.072	0.000	0.000	0.000	0.000
10	B	10	ASN	0	-0.002	-0.028	14.578	0.079	0.079	0.000	0.000	0.000	0.000
11	B	11	LYS	1	0.806	0.896	13.675	0.667	0.667	0.000	0.000	0.000	0.000
12	B	12	VAL	0	-0.042	-0.023	17.960	0.040	0.040	0.000	0.000	0.000	0.000
13	B	13	ILE	0	0.053	0.036	19.214	0.033	0.033	0.000	0.000	0.000	0.000
14	B	14	GLY	0	-0.022	-0.005	21.822	-0.006	-0.006	0.000	0.000	0.000	0.000
15	B	15	LYS	1	0.794	0.906	22.078	0.230	0.230	0.000	0.000	0.000	0.000
16	B	16	LYS	1	0.833	0.910	24.992	0.078	0.078	0.000	0.000	0.000	0.000
17	B	17	VAL	0	0.005	0.001	20.854	-0.014	-0.014	0.000	0.000	0.000	0.000
18	B	18	LEU	0	-0.052	-0.028	22.502	0.016	0.016	0.000	0.000	0.000	0.000
19	B	19	ILE	0	0.021	0.007	20.208	-0.011	-0.011	0.000	0.000	0.000	0.000
20	B	20	ARG	1	0.875	0.936	21.230	0.020	0.020	0.000	0.000	0.000	0.000
21	B	21	LEU	0	0.064	0.035	21.209	0.005	0.005	0.000	0.000	0.000	0.000
22	B	22	SER	0	0.027	-0.001	20.489	-0.005	-0.005	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.004	0.001	22.379	0.000	0.000	0.000	0.000	0.000	0.000
24	B	24	GLY	0	0.003	0.002	25.252	-0.002	-0.002	0.000	0.000	0.000	0.000
25	B	25	VAL	0	-0.040	-0.008	26.992	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	26	ASP	-1	-0.805	-0.880	26.038	-0.030	-0.030	0.000	0.000	0.000	0.000
27	B	27	TYR	0	-0.018	-0.040	25.116	0.002	0.002	0.000	0.000	0.000	0.000
28	B	28	LYS	1	0.858	0.922	25.838	0.033	0.033	0.000	0.000	0.000	0.000
29	B	29	GLY	0	0.044	0.034	26.237	0.006	0.006	0.000	0.000	0.000	0.000
30	B	30	ILE	0	-0.021	-0.001	26.190	-0.009	-0.009	0.000	0.000	0.000	0.000
31	B	31	LEU	0	0.007	0.020	18.759	0.011	0.011	0.000	0.000	0.000	0.000
32	B	32	SER	0	0.013	-0.029	23.413	-0.015	-0.015	0.000	0.000	0.000	0.000
33	B	33	CYS	0	-0.045	-0.027	21.365	-0.006	-0.006	0.000	0.000	0.000	0.000
34	B	34	LEU	0	0.015	0.007	14.811	0.010	0.010	0.000	0.000	0.000	0.000
35	B	35	ASP	-1	-0.760	-0.855	16.343	-0.005	-0.005	0.000	0.000	0.000	0.000
36	B	36	GLY	0	0.001	-0.010	12.813	-0.035	-0.035	0.000	0.000	0.000	0.000
37	B	37	TYR	0	-0.058	-0.024	11.532	0.034	0.034	0.000	0.000	0.000	0.000
38	B	38	MET	0	0.003	0.001	10.560	-0.009	-0.009	0.000	0.000	0.000	0.000
39	B	39	ASN	0	-0.045	-0.027	14.442	0.021	0.021	0.000	0.000	0.000	0.000
40	B	40	LEU	0	-0.017	-0.008	16.557	-0.027	-0.027	0.000	0.000	0.000	0.000
41	B	41	ALA	0	0.018	0.011	20.100	0.018	0.018	0.000	0.000	0.000	0.000
42	B	42	LEU	0	-0.047	-0.032	22.394	-0.016	-0.016	0.000	0.000	0.000	0.000
43	B	43	GLU	-1	-0.745	-0.834	25.778	-0.076	-0.076	0.000	0.000	0.000	0.000
44	B	44	ARG	1	0.796	0.879	29.030	0.054	0.054	0.000	0.000	0.000	0.000
45	B	45	THR	0	-0.008	-0.010	27.601	-0.006	-0.006	0.000	0.000	0.000	0.000
46	B	46	GLU	-1	-0.803	-0.869	30.093	-0.044	-0.044	0.000	0.000	0.000	0.000
47	B	47	GLU	-1	-0.759	-0.841	29.863	-0.008	-0.008	0.000	0.000	0.000	0.000
48	B	48	TYR	0	-0.038	-0.036	30.364	0.000	0.000	0.000	0.000	0.000	0.000
49	B	49	VAL	0	0.078	0.046	30.856	0.003	0.003	0.000	0.000	0.000	0.000
50	B	50	ASN	0	0.010	-0.001	32.967	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	51	GLY	0	0.012	0.012	33.542	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	52	LYS	1	0.918	0.961	34.840	0.006	0.006	0.000	0.000	0.000	0.000
53	B	53	LYS	1	0.886	0.928	34.643	0.035	0.035	0.000	0.000	0.000	0.000
54	B	54	THR	0	-0.062	-0.037	34.321	0.002	0.002	0.000	0.000	0.000	0.000
55	B	55	ASN	0	0.051	0.031	33.789	0.000	0.000	0.000	0.000	0.000	0.000
56	B	56	VAL	0	-0.062	-0.044	33.777	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	57	TYR	0	-0.025	-0.025	31.044	0.004	0.004	0.000	0.000	0.000	0.000
58	B	58	GLY	0	-0.018	0.001	32.448	-0.005	-0.005	0.000	0.000	0.000	0.000
59	B	59	ASP	-1	-0.848	-0.925	30.422	-0.047	-0.047	0.000	0.000	0.000	0.000
60	B	60	ALA	0	-0.041	-0.034	27.644	0.007	0.007	0.000	0.000	0.000	0.000
61	B	61	PHE	0	0.007	0.007	21.482	-0.007	-0.007	0.000	0.000	0.000	0.000
62	B	62	ILE	0	0.004	0.001	20.804	0.009	0.009	0.000	0.000	0.000	0.000
63	B	63	ARG	1	0.900	0.947	14.620	-0.127	-0.127	0.000	0.000	0.000	0.000
64	B	64	GLY	0	0.071	0.030	16.275	0.012	0.012	0.000	0.000	0.000	0.000
65	B	65	ASN	0	-0.074	-0.042	12.437	0.024	0.024	0.000	0.000	0.000	0.000
66	B	66	ASN	0	-0.038	-0.021	14.745	0.031	0.031	0.000	0.000	0.000	0.000
67	B	67	VAL	0	-0.030	0.000	17.055	-0.006	-0.006	0.000	0.000	0.000	0.000
68	B	68	LEU	0	-0.049	-0.021	16.840	0.010	0.010	0.000	0.000	0.000	0.000
69	B	69	TYR	0	0.010	-0.009	16.487	0.005	0.005	0.000	0.000	0.000	0.000
70	B	70	VAL	0	0.022	0.005	16.454	0.008	0.008	0.000	0.000	0.000	0.000
71	B	71	SER	0	-0.021	-0.008	16.862	-0.022	-0.022	0.000	0.000	0.000	0.000
72	B	72	ALA	0	0.037	0.020	19.259	0.007	0.007	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.019	-0.001	20.979	0.016	0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)