FMO DATABASE

FMODB ID: V56N1

Calculation Name: 4W4K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4W4K

Chain ID: A

ChEMBL ID:

UniProt ID: I6X486

Base Structure: X-ray

Registration Date: 2023-06-26

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-426657.645301
FMO2-HF: Nuclear repulsion	396131.913865
FMO2-HF: Total energy	-30525.731436
FMO2-MP2: Total energy	-30616.158553

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:8:PRO)

Summations of interaction energy for fragment #1(A:8:PRO)

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.
-2.95	2.689	0.365	-2.199	-3.807	0.005

Interaction energy analysis for fragmet #1(A:8:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.029

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	10	ALA	0	0.000	-0.013	2.837	-2.472	0.614	0.050	-1.469	-1.666	0.006
4	A	11	LEU	0	-0.013	0.007	2.704	-0.310	0.950	0.244	-0.393	-1.112	0.000
5	A	12	THR	0	0.080	0.037	4.682	0.319	0.503	-0.001	-0.032	-0.152	0.000
6	A	13	VAL	0	-0.004	0.002	6.654	0.393	0.393	0.000	0.000	0.000	0.000
7	A	14	ALA	0	0.016	0.008	7.622	0.194	0.194	0.000	0.000	0.000	0.000
8	A	15	ALA	0	0.006	-0.003	8.769	0.121	0.121	0.000	0.000	0.000	0.000
9	A	16	THR	0	-0.040	-0.019	10.585	0.099	0.099	0.000	0.000	0.000	0.000
10	A	17	GLU	-1	-0.963	-0.981	12.114	-0.151	-0.151	0.000	0.000	0.000	0.000
11	A	18	VAL	0	0.001	0.004	13.102	0.045	0.045	0.000	0.000	0.000	0.000
12	A	19	ARG	1	0.947	0.968	11.766	0.342	0.342	0.000	0.000	0.000	0.000
13	A	20	ARG	1	0.981	1.007	16.727	0.166	0.166	0.000	0.000	0.000	0.000
14	A	21	ILE	0	-0.047	-0.027	16.995	0.020	0.020	0.000	0.000	0.000	0.000
15	A	22	ARG	1	0.854	0.931	19.225	0.100	0.100	0.000	0.000	0.000	0.000
16	A	23	ASP	-1	-0.871	-0.944	20.892	-0.120	-0.120	0.000	0.000	0.000	0.000
17	A	24	ARG	1	0.931	0.968	22.704	0.065	0.065	0.000	0.000	0.000	0.000
18	A	25	ALA	0	-0.003	-0.001	24.005	0.008	0.008	0.000	0.000	0.000	0.000
19	A	26	ILE	0	0.048	0.019	24.813	0.007	0.007	0.000	0.000	0.000	0.000
20	A	27	GLN	0	-0.025	-0.008	26.844	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	28	SER	0	-0.083	-0.043	28.584	0.006	0.006	0.000	0.000	0.000	0.000
22	A	29	ASP	-1	-0.776	-0.882	29.898	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	30	ALA	0	-0.012	-0.019	31.198	0.003	0.003	0.000	0.000	0.000	0.000
24	A	31	GLN	0	-0.042	-0.009	32.790	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	32	VAL	0	0.005	-0.006	34.656	0.002	0.002	0.000	0.000	0.000	0.000
26	A	33	ALA	0	0.029	0.032	35.808	0.003	0.003	0.000	0.000	0.000	0.000
27	A	34	PRO	0	-0.021	-0.002	37.613	0.003	0.003	0.000	0.000	0.000	0.000
28	A	35	MET	0	-0.010	0.000	40.314	0.001	0.001	0.000	0.000	0.000	0.000
29	A	36	THR	0	-0.001	-0.005	38.017	0.001	0.001	0.000	0.000	0.000	0.000
30	A	37	THR	0	-0.071	-0.054	39.308	0.002	0.002	0.000	0.000	0.000	0.000
31	A	38	ALA	0	0.014	0.011	42.186	0.001	0.001	0.000	0.000	0.000	0.000
32	A	39	VAL	0	0.004	0.008	44.765	0.000	0.000	0.000	0.000	0.000	0.000
33	A	40	ARG	1	0.880	0.939	47.275	0.012	0.012	0.000	0.000	0.000	0.000
34	A	41	PRO	0	0.013	0.004	50.996	0.000	0.000	0.000	0.000	0.000	0.000
35	A	42	PRO	0	-0.017	0.009	53.048	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	43	ALA	0	0.010	0.004	55.500	0.000	0.000	0.000	0.000	0.000	0.000
37	A	44	ALA	0	0.010	-0.006	57.968	0.000	0.000	0.000	0.000	0.000	0.000
38	A	45	ASP	-1	-0.783	-0.842	59.340	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	46	LEU	0	0.075	0.006	58.474	0.000	0.000	0.000	0.000	0.000	0.000
40	A	47	VAL	0	-0.047	-0.015	56.064	0.000	0.000	0.000	0.000	0.000	0.000
41	A	48	SER	0	-0.030	-0.055	54.802	0.000	0.000	0.000	0.000	0.000	0.000
42	A	49	GLU	-1	-0.900	-0.953	53.416	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	50	LYS	1	0.936	0.970	52.284	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	51	ALA	0	0.014	0.014	50.382	0.000	0.000	0.000	0.000	0.000	0.000
45	A	52	ALA	0	0.002	-0.001	48.703	0.000	0.000	0.000	0.000	0.000	0.000
46	A	53	THR	0	-0.014	-0.019	47.644	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	54	PHE	0	-0.011	-0.001	43.952	0.000	0.000	0.000	0.000	0.000	0.000
48	A	55	LEU	0	0.009	-0.005	44.163	0.000	0.000	0.000	0.000	0.000	0.000
49	A	56	VAL	0	-0.014	0.010	42.780	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	57	GLU	-1	-0.921	-0.975	41.921	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	58	TYR	0	-0.050	-0.016	39.035	0.000	0.000	0.000	0.000	0.000	0.000
52	A	59	ALA	0	0.030	0.019	38.336	0.000	0.000	0.000	0.000	0.000	0.000
53	A	60	ARG	1	0.931	0.958	37.043	0.012	0.012	0.000	0.000	0.000	0.000
54	A	61	LYS	1	0.969	0.982	36.365	0.000	0.000	0.000	0.000	0.000	0.000
55	A	62	TYR	0	0.016	0.018	30.920	0.002	0.002	0.000	0.000	0.000	0.000
56	A	63	ARG	1	0.861	0.910	32.430	0.029	0.029	0.000	0.000	0.000	0.000
57	A	64	GLN	0	-0.052	-0.024	31.385	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	65	THR	0	-0.009	0.004	29.764	0.002	0.002	0.000	0.000	0.000	0.000
59	A	66	ILE	0	-0.007	0.003	27.085	0.002	0.002	0.000	0.000	0.000	0.000
60	A	67	ALA	0	-0.002	0.001	26.478	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	68	ALA	0	0.017	0.009	25.971	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	69	ALA	0	0.012	0.003	24.027	0.003	0.003	0.000	0.000	0.000	0.000
63	A	70	ALA	0	-0.033	-0.027	22.184	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	71	VAL	0	0.031	0.017	21.107	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	72	VAL	0	0.030	0.025	19.751	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	73	LEU	0	-0.039	-0.023	17.781	0.006	0.006	0.000	0.000	0.000	0.000
67	A	74	GLU	-1	-0.875	-0.932	16.266	-0.100	-0.100	0.000	0.000	0.000	0.000
68	A	75	GLU	-1	-0.921	-0.962	15.803	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	76	PHE	0	-0.016	-0.006	12.227	0.006	0.006	0.000	0.000	0.000	0.000
70	A	77	ALA	0	0.030	0.005	11.869	0.009	0.009	0.000	0.000	0.000	0.000
71	A	78	HIS	0	0.001	0.007	10.928	-0.099	-0.099	0.000	0.000	0.000	0.000
72	A	79	ALA	0	0.010	0.006	11.198	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	80	LEU	0	-0.046	-0.016	7.836	0.108	0.108	0.000	0.000	0.000	0.000
74	A	81	THR	0	-0.011	-0.017	6.353	-0.133	-0.133	0.000	0.000	0.000	0.000
75	A	82	THR	0	-0.003	-0.001	7.493	-0.082	-0.082	0.000	0.000	0.000	0.000
76	A	83	GLY	0	-0.041	-0.020	6.936	0.020	0.020	0.000	0.000	0.000	0.000
77	A	84	ALA	0	-0.022	-0.017	3.102	0.037	0.517	0.062	-0.165	-0.378	-0.001
78	A	85	ASP	-1	-0.885	-0.934	3.939	-1.203	-0.890	0.001	-0.072	-0.241	0.000
79	A	86	LYS	1	0.904	0.947	6.751	-0.144	-0.144	0.000	0.000	0.000	0.000
80	A	87	TYR	0	-0.108	-0.061	5.300	-0.174	-0.174	0.000	0.000	0.000	0.000
81	A	88	ALA	0	0.040	0.028	3.333	0.042	0.350	0.010	-0.066	-0.253	0.000
82	A	89	THR	0	-0.073	-0.016	5.105	-0.061	-0.053	-0.001	-0.002	-0.005	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:PRO)