FMO DATABASE

FMODB ID: 72Z1K

Calculation Name: 5FVL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FVL

Chain ID: A

ChEMBL ID:

UniProt ID: Q04272

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	OptHSide
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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-544663.311574
FMO2-HF: Nuclear repulsion	511230.139786
FMO2-HF: Total energy	-33433.171788
FMO2-MP2: Total energy	-33531.292501

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-1.402	0.102	-0.022	-0.698	-0.783	0.002

Interaction energy analysis for fragmet #1(A:0:HIS)

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 : 0.002

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	2	SER	0	0.046	0.033	3.823	1.770	3.274	-0.022	-0.698	-0.783	0.002
4	A	3	THR	0	0.019	0.020	6.826	-0.977	-0.977	0.000	0.000	0.000	0.000
5	A	4	GLY	0	-0.008	-0.001	10.488	0.079	0.079	0.000	0.000	0.000	0.000
6	A	5	ASP	-1	-0.849	-0.932	9.732	-0.076	-0.076	0.000	0.000	0.000	0.000
7	A	6	PHE	0	-0.029	-0.026	11.298	-0.209	-0.209	0.000	0.000	0.000	0.000
8	A	7	LEU	0	0.039	0.017	12.927	-0.148	-0.148	0.000	0.000	0.000	0.000
9	A	8	THR	0	0.040	0.016	9.331	-0.033	-0.033	0.000	0.000	0.000	0.000
10	A	9	LYS	1	0.847	0.921	7.324	0.596	0.596	0.000	0.000	0.000	0.000
11	A	10	GLY	0	0.018	0.005	9.328	-0.237	-0.237	0.000	0.000	0.000	0.000
12	A	11	ILE	0	-0.018	-0.017	12.454	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.849	-0.920	6.042	-3.752	-3.752	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.073	-0.026	8.225	-0.121	-0.121	0.000	0.000	0.000	0.000
15	A	14	VAL	0	0.038	0.018	10.622	0.108	0.108	0.000	0.000	0.000	0.000
16	A	15	GLN	0	-0.041	-0.022	12.165	0.003	0.003	0.000	0.000	0.000	0.000
17	A	16	LYS	1	0.904	0.945	5.775	4.090	4.090	0.000	0.000	0.000	0.000
18	A	17	ALA	0	0.016	0.007	12.400	0.091	0.091	0.000	0.000	0.000	0.000
19	A	18	ILE	0	0.009	0.012	15.281	0.115	0.115	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.902	-0.927	14.763	-0.867	-0.867	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.038	-0.021	12.783	0.067	0.067	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.778	-0.840	17.061	-0.552	-0.552	0.000	0.000	0.000	0.000
23	A	22	THR	0	-0.040	-0.036	20.191	0.090	0.090	0.000	0.000	0.000	0.000
24	A	23	ALA	0	-0.042	-0.007	19.269	0.062	0.062	0.000	0.000	0.000	0.000
25	A	24	THR	0	-0.098	-0.043	21.347	0.041	0.041	0.000	0.000	0.000	0.000
26	A	25	GLN	0	-0.022	-0.005	18.180	0.012	0.012	0.000	0.000	0.000	0.000
27	A	26	TYR	0	0.043	-0.009	18.673	-0.078	-0.078	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.873	-0.921	18.649	-0.794	-0.794	0.000	0.000	0.000	0.000
29	A	28	GLU	-1	-0.856	-0.943	14.316	-1.058	-1.058	0.000	0.000	0.000	0.000
30	A	29	ALA	0	-0.028	-0.016	14.917	-0.147	-0.147	0.000	0.000	0.000	0.000
31	A	30	TYR	0	0.001	-0.003	16.576	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	31	THR	0	-0.013	-0.004	13.006	0.005	0.005	0.000	0.000	0.000	0.000
33	A	32	ALA	0	-0.039	-0.011	12.470	-0.106	-0.106	0.000	0.000	0.000	0.000
34	A	33	TYR	0	-0.030	-0.052	13.384	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	34	TYR	0	0.020	0.001	16.548	0.072	0.072	0.000	0.000	0.000	0.000
36	A	35	ASN	0	0.010	0.019	11.238	0.162	0.162	0.000	0.000	0.000	0.000
37	A	36	GLY	0	-0.010	-0.013	12.800	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	37	LEU	0	-0.022	-0.024	13.710	0.117	0.117	0.000	0.000	0.000	0.000
39	A	38	ASP	-1	-0.863	-0.922	15.364	-0.708	-0.708	0.000	0.000	0.000	0.000
40	A	39	TYR	0	-0.044	-0.030	10.090	0.233	0.233	0.000	0.000	0.000	0.000
41	A	40	LEU	0	0.012	-0.002	14.519	0.151	0.151	0.000	0.000	0.000	0.000
42	A	41	MET	0	0.011	0.023	17.009	0.122	0.122	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.037	-0.015	15.343	0.100	0.100	0.000	0.000	0.000	0.000
44	A	43	ALA	0	-0.043	-0.034	16.414	0.087	0.087	0.000	0.000	0.000	0.000
45	A	44	LEU	0	-0.014	-0.014	18.260	0.078	0.078	0.000	0.000	0.000	0.000
46	A	45	LYS	1	0.866	0.949	21.445	0.220	0.220	0.000	0.000	0.000	0.000
47	A	46	TYR	0	-0.023	-0.015	19.583	0.058	0.058	0.000	0.000	0.000	0.000
48	A	47	GLU	-1	-0.797	-0.874	21.664	-0.137	-0.137	0.000	0.000	0.000	0.000
49	A	48	LYS	1	0.918	0.948	22.872	0.018	0.018	0.000	0.000	0.000	0.000
50	A	49	ASN	0	-0.006	0.006	25.241	0.006	0.006	0.000	0.000	0.000	0.000
51	A	50	PRO	0	0.053	0.016	26.655	-0.025	-0.025	0.000	0.000	0.000	0.000
52	A	51	LYS	1	1.005	1.007	28.145	0.144	0.144	0.000	0.000	0.000	0.000
53	A	52	SER	0	0.011	0.000	22.997	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.905	0.947	24.017	0.133	0.133	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.821	-0.898	25.349	-0.220	-0.220	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.043	-0.017	24.475	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	56	ILE	0	0.022	0.005	19.726	-0.029	-0.029	0.000	0.000	0.000	0.000
58	A	57	ARG	1	0.867	0.927	22.300	0.203	0.203	0.000	0.000	0.000	0.000
59	A	58	ALA	0	-0.007	0.000	24.764	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	59	LYS	1	0.824	0.893	21.040	0.429	0.429	0.000	0.000	0.000	0.000
61	A	60	PHE	0	-0.009	0.003	20.117	-0.030	-0.030	0.000	0.000	0.000	0.000
62	A	61	THR	0	-0.026	-0.023	22.104	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.822	-0.884	23.499	-0.450	-0.450	0.000	0.000	0.000	0.000
64	A	63	TYR	0	0.031	-0.005	18.503	-0.019	-0.019	0.000	0.000	0.000	0.000
65	A	64	LEU	0	0.017	0.021	21.763	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	65	ASN	0	-0.022	-0.020	23.582	0.009	0.009	0.000	0.000	0.000	0.000
67	A	66	ARG	1	0.794	0.870	22.529	0.552	0.552	0.000	0.000	0.000	0.000
68	A	67	ALA	0	0.038	0.004	21.050	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.824	-0.893	22.707	-0.366	-0.366	0.000	0.000	0.000	0.000
70	A	69	GLN	0	0.012	0.002	26.176	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	70	LEU	0	-0.003	0.004	20.728	0.012	0.012	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.837	0.916	22.614	0.558	0.558	0.000	0.000	0.000	0.000
73	A	72	LYS	1	0.773	0.865	25.160	0.375	0.375	0.000	0.000	0.000	0.000
74	A	73	HIS	0	-0.005	0.003	25.815	0.034	0.034	0.000	0.000	0.000	0.000
75	A	74	LEU	0	0.003	-0.010	21.601	0.013	0.013	0.000	0.000	0.000	0.000
76	A	75	GLU	-1	-0.832	-0.891	25.672	-0.474	-0.474	0.000	0.000	0.000	0.000
77	A	76	SER	0	-0.041	-0.018	28.348	0.031	0.031	0.000	0.000	0.000	0.000
78	A	77	GLU	-1	-0.929	-0.966	28.260	-0.336	-0.336	0.000	0.000	0.000	0.000
79	A	78	GLU	-1	-0.928	-0.953	27.371	-0.419	-0.419	0.000	0.000	0.000	0.000
80	A	79	ALA	0	-0.067	-0.036	29.655	0.022	0.022	0.000	0.000	0.000	0.000
81	A	80	ASN	0	-0.084	-0.051	33.086	0.034	0.034	0.000	0.000	0.000	0.000
82	A	81	ALA	0	-0.035	0.002	31.113	0.016	0.016	0.000	0.000	0.000	0.000
83	A	82	ALA	0	-0.089	-0.033	33.149	0.016	0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)