FMO DATABASE

FMODB ID: 94972

Calculation Name: 5D4L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D4L

Chain ID: A

ChEMBL ID:

UniProt ID: D5X329

Base Structure: X-ray

Registration Date: 2023-09-19

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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-702877.800978
FMO2-HF: Nuclear repulsion	664119.362607
FMO2-HF: Total energy	-38758.438371
FMO2-MP2: Total energy	-38872.261706

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:ALA)

Summations of interaction energy for fragment #1(A:3:ALA)

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.
0.173	2.834	0.22	-1.025	-1.856	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.001

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	5	LYS	1	0.898	0.948	3.866	-0.138	1.135	-0.018	-0.617	-0.638	0.001
4	A	6	LEU	0	0.045	0.025	6.745	-0.028	-0.028	0.000	0.000	0.000	0.000
5	A	7	TYR	0	-0.029	-0.023	9.384	-0.131	-0.131	0.000	0.000	0.000	0.000
6	A	8	PRO	0	0.016	0.012	13.324	0.026	0.026	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.028	-0.011	16.821	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.883	0.934	19.655	-0.029	-0.029	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.762	0.868	22.182	-0.091	-0.091	0.000	0.000	0.000	0.000
10	A	12	LEU	0	0.031	0.019	24.018	0.007	0.007	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.790	-0.892	27.427	0.070	0.070	0.000	0.000	0.000	0.000
12	A	14	ILE	0	0.017	0.009	29.833	0.001	0.001	0.000	0.000	0.000	0.000
13	A	15	ILE	0	-0.029	-0.004	32.967	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	16	LEU	0	0.036	0.016	35.415	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.741	-0.878	38.580	0.011	0.011	0.000	0.000	0.000	0.000
16	A	18	GLY	0	-0.013	-0.016	38.812	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	19	ALA	0	-0.041	-0.019	39.865	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	20	HIS	0	-0.032	-0.028	40.791	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.952	0.979	35.012	0.001	0.001	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.948	-0.970	36.359	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	23	PHE	0	0.048	0.025	37.498	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.026	0.009	35.114	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.028	-0.024	32.376	0.001	0.001	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.795	-0.872	33.415	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.051	-0.012	34.962	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.018	-0.014	29.092	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.826	-0.908	30.373	-0.037	-0.037	0.000	0.000	0.000	0.000
28	A	30	ARG	1	0.791	0.863	31.692	0.014	0.014	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.038	0.000	31.016	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	32	GLY	0	-0.002	0.009	28.817	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.033	-0.023	25.573	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.836	0.907	21.315	0.078	0.078	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.041	0.028	23.687	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	36	TYR	0	-0.089	-0.047	24.885	0.007	0.007	0.000	0.000	0.000	0.000
35	A	37	THR	0	-0.057	-0.020	23.522	0.000	0.000	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.019	-0.004	26.614	0.002	0.002	0.000	0.000	0.000	0.000
37	A	39	VAL	0	-0.003	0.018	28.583	0.001	0.001	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.047	0.004	31.088	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	41	ASN	0	-0.048	-0.031	34.799	0.002	0.002	0.000	0.000	0.000	0.000
40	A	42	LEU	0	-0.003	0.017	33.195	0.003	0.003	0.000	0.000	0.000	0.000
41	A	43	SER	0	0.008	0.005	37.396	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.011	-0.004	39.608	0.003	0.003	0.000	0.000	0.000	0.000
43	A	45	LYS	1	0.785	0.865	41.792	-0.028	-0.028	0.000	0.000	0.000	0.000
44	A	46	GLY	0	0.021	0.012	43.817	0.002	0.002	0.000	0.000	0.000	0.000
45	A	47	SER	0	-0.002	-0.001	43.612	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	48	HIS	0	0.039	0.014	35.641	0.002	0.002	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.001	-0.015	38.257	0.002	0.002	0.000	0.000	0.000	0.000
48	A	50	MET	0	-0.046	0.002	39.547	0.001	0.001	0.000	0.000	0.000	0.000
49	A	51	TYR	0	0.004	-0.001	41.265	0.001	0.001	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.925	-0.974	44.223	0.022	0.022	0.000	0.000	0.000	0.000
51	A	53	GLY	0	-0.016	-0.014	47.765	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	54	HIS	0	-0.036	-0.007	42.119	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.034	-0.010	46.138	0.001	0.001	0.000	0.000	0.000	0.000
54	A	56	MET	0	-0.053	-0.026	45.008	0.002	0.002	0.000	0.000	0.000	0.000
55	A	57	PHE	0	-0.010	0.015	38.820	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	58	ASN	0	-0.093	-0.088	44.768	0.001	0.001	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.771	-0.873	45.815	0.026	0.026	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.923	-0.927	46.933	0.016	0.016	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.778	-0.877	43.150	0.017	0.017	0.000	0.000	0.000	0.000
60	A	62	ALA	0	-0.014	-0.011	42.281	0.002	0.002	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.042	-0.003	38.188	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	64	ILE	0	-0.051	-0.031	34.645	0.000	0.000	0.000	0.000	0.000	0.000
63	A	65	MET	0	0.006	0.001	30.001	0.002	0.002	0.000	0.000	0.000	0.000
64	A	66	ILE	0	0.002	0.010	29.688	0.000	0.000	0.000	0.000	0.000	0.000
65	A	67	ILE	0	-0.027	-0.011	24.689	0.004	0.004	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.033	0.007	24.979	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	69	ALA	0	-0.035	-0.007	20.003	0.008	0.008	0.000	0.000	0.000	0.000
68	A	70	VAL	0	-0.010	-0.010	22.155	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	71	PRO	0	0.026	0.003	21.223	0.011	0.011	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.941	-0.984	22.772	0.010	0.010	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.889	-0.943	24.098	-0.046	-0.046	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.010	-0.003	25.898	0.000	0.000	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.027	-0.017	26.894	0.003	0.003	0.000	0.000	0.000	0.000
74	A	76	GLY	0	0.017	0.021	29.654	0.002	0.002	0.000	0.000	0.000	0.000
75	A	77	PRO	0	0.074	0.022	31.627	0.001	0.001	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.020	-0.002	29.057	0.000	0.000	0.000	0.000	0.000	0.000
77	A	79	LEU	0	-0.022	-0.012	32.530	0.002	0.002	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.957	-0.982	35.190	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	81	GLY	0	-0.012	-0.004	36.727	0.000	0.000	0.000	0.000	0.000	0.000
80	A	82	PHE	0	-0.022	-0.028	33.258	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	GLN	0	-0.056	-0.022	38.285	0.003	0.003	0.000	0.000	0.000	0.000
82	A	84	PRO	0	0.026	0.007	40.899	0.001	0.001	0.000	0.000	0.000	0.000
83	A	85	PHE	0	-0.050	-0.011	40.318	0.000	0.000	0.000	0.000	0.000	0.000
84	A	86	PHE	0	0.019	-0.001	36.947	0.001	0.001	0.000	0.000	0.000	0.000
85	A	87	GLU	-1	-0.873	-0.923	42.868	0.008	0.008	0.000	0.000	0.000	0.000
86	A	88	ALA	0	-0.051	-0.020	45.875	0.000	0.000	0.000	0.000	0.000	0.000
87	A	89	HIS	1	0.781	0.890	43.479	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	90	SER	0	0.031	0.028	43.710	0.001	0.001	0.000	0.000	0.000	0.000
89	A	91	GLY	0	-0.007	-0.030	39.658	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.034	-0.008	35.619	0.000	0.000	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.018	-0.002	31.561	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	94	PHE	0	-0.029	0.013	30.743	0.002	0.002	0.000	0.000	0.000	0.000
93	A	95	VAL	0	0.018	-0.009	27.531	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	96	HIS	0	-0.020	-0.011	24.428	0.015	0.015	0.000	0.000	0.000	0.000
95	A	97	ASP	-1	-0.797	-0.880	21.724	0.060	0.060	0.000	0.000	0.000	0.000
96	A	98	ILE	0	-0.025	-0.015	18.380	0.019	0.019	0.000	0.000	0.000	0.000
97	A	99	GLN	0	-0.011	-0.020	13.914	0.023	0.023	0.000	0.000	0.000	0.000
98	A	100	VAL	0	0.019	0.025	13.557	0.035	0.035	0.000	0.000	0.000	0.000
99	A	101	GLY	0	0.014	0.004	9.539	0.012	0.012	0.000	0.000	0.000	0.000
100	A	102	ARG	1	0.908	0.950	7.824	0.739	0.739	0.000	0.000	0.000	0.000
101	A	103	PRO	0	0.030	0.020	4.593	-0.338	-0.243	-0.001	-0.047	-0.047	0.000
102	A	104	ILE	0	0.002	0.001	2.787	-0.083	1.210	0.239	-0.361	-1.171	0.000

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