FMO DATABASE

FMODB ID: LNYQ9

Calculation Name: 5HKC-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HKC

Chain ID: B

ChEMBL ID:

UniProt ID: P9WII3

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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-833563.238975
FMO2-HF: Nuclear repulsion	791465.785001
FMO2-HF: Total energy	-42097.453974
FMO2-MP2: Total energy	-42221.565541

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:2:VAL)

Summations of interaction energy for fragment #1(B:2:VAL)

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.
-4.644	-1.74	0.084	-1.281	-1.707	0.001

Interaction energy analysis for fragmet #1(B:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.010

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	B	4	SER	0	-0.016	-0.035	3.371	-0.977	1.810	0.087	-1.265	-1.610	0.001
4	B	5	ARG	1	0.755	0.823	4.721	0.658	0.676	-0.001	-0.004	-0.013	0.000
5	B	6	ALA	0	0.001	-0.007	8.397	-0.067	-0.067	0.000	0.000	0.000	0.000
6	B	7	GLU	-1	-0.740	-0.815	4.892	-4.216	-4.224	-0.001	-0.005	0.015	0.000
7	B	8	ILE	0	-0.022	-0.019	9.224	0.127	0.127	0.000	0.000	0.000	0.000
8	B	9	TYR	0	-0.019	-0.035	5.462	-0.303	-0.303	0.000	0.000	0.000	0.000
9	B	10	TRP	0	-0.032	-0.019	12.156	0.220	0.220	0.000	0.000	0.000	0.000
10	B	11	ALA	0	0.050	0.018	12.626	-0.133	-0.133	0.000	0.000	0.000	0.000
11	B	12	ASP	-1	-0.824	-0.902	14.306	-0.350	-0.350	0.000	0.000	0.000	0.000
12	B	13	LEU	0	-0.060	-0.033	16.068	-0.020	-0.020	0.000	0.000	0.000	0.000
13	B	14	GLY	0	-0.001	-0.005	17.237	0.047	0.047	0.000	0.000	0.000	0.000
14	B	15	PRO	0	-0.032	-0.001	18.209	0.007	0.007	0.000	0.000	0.000	0.000
15	B	16	PRO	0	0.011	-0.005	20.424	-0.006	-0.006	0.000	0.000	0.000	0.000
16	B	17	SER	0	-0.019	-0.019	23.244	0.019	0.019	0.000	0.000	0.000	0.000
17	B	18	GLY	0	0.019	0.000	26.992	0.003	0.003	0.000	0.000	0.000	0.000
18	B	19	SER	0	-0.013	-0.003	28.516	0.001	0.001	0.000	0.000	0.000	0.000
19	B	20	GLN	0	-0.030	-0.006	27.943	0.003	0.003	0.000	0.000	0.000	0.000
20	B	21	PRO	0	0.034	0.003	22.669	0.001	0.001	0.000	0.000	0.000	0.000
21	B	22	ALA	0	0.047	0.047	20.091	0.011	0.011	0.000	0.000	0.000	0.000
22	B	23	LYS	1	0.929	0.950	22.168	0.252	0.252	0.000	0.000	0.000	0.000
23	B	24	ARG	1	0.864	0.938	14.728	0.532	0.532	0.000	0.000	0.000	0.000
24	B	25	ARG	1	0.874	0.936	18.241	0.384	0.384	0.000	0.000	0.000	0.000
25	B	26	PRO	0	0.023	0.035	16.497	-0.059	-0.059	0.000	0.000	0.000	0.000
26	B	27	VAL	0	-0.010	-0.014	13.204	0.083	0.083	0.000	0.000	0.000	0.000
27	B	28	LEU	0	0.012	0.012	12.445	-0.117	-0.117	0.000	0.000	0.000	0.000
28	B	29	VAL	0	0.015	0.013	8.046	0.159	0.159	0.000	0.000	0.000	0.000
29	B	30	ILE	0	-0.003	-0.001	11.080	0.050	0.050	0.000	0.000	0.000	0.000
30	B	31	GLN	0	-0.012	0.003	9.461	0.164	0.164	0.000	0.000	0.000	0.000
31	B	32	SER	0	0.034	0.013	10.469	-0.107	-0.107	0.000	0.000	0.000	0.000
32	B	33	ASP	-1	-0.733	-0.880	6.459	-0.936	-0.936	0.000	0.000	0.000	0.000
33	B	34	PRO	0	-0.017	-0.003	6.936	0.143	0.143	0.000	0.000	0.000	0.000
34	B	35	TYR	0	0.008	0.013	9.197	0.164	0.164	0.000	0.000	0.000	0.000
35	B	36	ASN	0	-0.004	-0.001	5.473	0.225	0.225	0.000	0.000	0.000	0.000
36	B	37	ALA	0	0.025	0.018	4.673	0.005	0.112	-0.001	-0.007	-0.099	0.000
37	B	38	SER	0	-0.055	-0.018	5.520	0.360	0.360	0.000	0.000	0.000	0.000
38	B	39	ARG	1	0.967	0.958	8.253	-0.462	-0.462	0.000	0.000	0.000	0.000
39	B	40	LEU	0	-0.024	0.012	10.545	-0.044	-0.044	0.000	0.000	0.000	0.000
40	B	41	ALA	0	0.027	0.002	9.614	0.007	0.007	0.000	0.000	0.000	0.000
41	B	42	THR	0	-0.004	0.004	10.836	-0.089	-0.089	0.000	0.000	0.000	0.000
42	B	43	VAL	0	0.042	0.008	7.823	0.013	0.013	0.000	0.000	0.000	0.000
43	B	44	ILE	0	-0.008	0.008	11.027	0.016	0.016	0.000	0.000	0.000	0.000
44	B	45	ALA	0	0.006	-0.011	12.956	-0.114	-0.114	0.000	0.000	0.000	0.000
45	B	46	ALA	0	0.024	0.020	14.643	0.096	0.096	0.000	0.000	0.000	0.000
46	B	47	VAL	0	-0.017	-0.010	17.013	-0.065	-0.065	0.000	0.000	0.000	0.000
47	B	48	ILE	0	-0.018	0.001	16.166	0.030	0.030	0.000	0.000	0.000	0.000
48	B	49	THR	0	-0.070	-0.043	20.149	0.007	0.007	0.000	0.000	0.000	0.000
49	B	50	SER	0	-0.030	-0.060	23.709	-0.023	-0.023	0.000	0.000	0.000	0.000
50	B	51	ASN	0	-0.063	-0.033	26.135	0.016	0.016	0.000	0.000	0.000	0.000
51	B	52	ASP	-1	-0.811	-0.865	27.952	-0.219	-0.219	0.000	0.000	0.000	0.000
52	B	53	ALA	0	0.030	-0.004	30.918	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	54	LEU	0	-0.034	-0.026	31.446	0.004	0.004	0.000	0.000	0.000	0.000
54	B	55	ALA	0	-0.005	0.011	27.032	-0.004	-0.004	0.000	0.000	0.000	0.000
55	B	56	ALA	0	0.002	0.015	28.305	-0.010	-0.010	0.000	0.000	0.000	0.000
56	B	57	MET	0	0.047	0.014	28.271	0.015	0.015	0.000	0.000	0.000	0.000
57	B	58	PRO	0	-0.045	-0.035	28.855	-0.012	-0.012	0.000	0.000	0.000	0.000
58	B	59	GLY	0	-0.006	-0.006	26.870	0.009	0.009	0.000	0.000	0.000	0.000
59	B	60	ASN	0	-0.031	-0.010	24.192	-0.025	-0.025	0.000	0.000	0.000	0.000
60	B	61	VAL	0	-0.011	0.001	21.649	0.017	0.017	0.000	0.000	0.000	0.000
61	B	62	ASP	-1	-0.851	-0.907	22.594	-0.280	-0.280	0.000	0.000	0.000	0.000
62	B	63	LEU	0	-0.025	-0.024	17.692	-0.025	-0.025	0.000	0.000	0.000	0.000
63	B	64	PRO	0	0.050	0.027	21.585	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	65	ALA	0	0.030	0.017	21.325	-0.040	-0.040	0.000	0.000	0.000	0.000
65	B	66	THR	0	-0.020	-0.020	21.167	-0.025	-0.025	0.000	0.000	0.000	0.000
66	B	67	THR	0	-0.028	-0.001	18.113	0.005	0.005	0.000	0.000	0.000	0.000
67	B	68	THR	0	-0.006	-0.015	16.691	-0.052	-0.052	0.000	0.000	0.000	0.000
68	B	69	ARG	1	0.850	0.932	14.857	0.555	0.555	0.000	0.000	0.000	0.000
69	B	70	LEU	0	0.032	0.028	17.413	-0.011	-0.011	0.000	0.000	0.000	0.000
70	B	71	PRO	0	-0.022	-0.019	19.979	0.033	0.033	0.000	0.000	0.000	0.000
71	B	72	ARG	1	0.921	0.946	23.435	0.273	0.273	0.000	0.000	0.000	0.000
72	B	73	ASP	-1	-0.832	-0.898	23.806	-0.309	-0.309	0.000	0.000	0.000	0.000
73	B	74	SER	0	-0.050	-0.029	21.355	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	75	VAL	0	0.023	0.011	23.170	0.011	0.011	0.000	0.000	0.000	0.000
75	B	76	VAL	0	0.017	0.008	18.406	-0.025	-0.025	0.000	0.000	0.000	0.000
76	B	77	ASN	0	0.038	0.023	20.861	0.046	0.046	0.000	0.000	0.000	0.000
77	B	78	VAL	0	0.001	-0.003	20.609	-0.017	-0.017	0.000	0.000	0.000	0.000
78	B	79	THR	0	-0.007	-0.013	22.227	0.011	0.011	0.000	0.000	0.000	0.000
79	B	80	ALA	0	-0.049	-0.012	22.484	0.015	0.015	0.000	0.000	0.000	0.000
80	B	81	ILE	0	0.007	0.003	18.598	-0.050	-0.050	0.000	0.000	0.000	0.000
81	B	82	VAL	0	-0.028	-0.015	16.758	0.036	0.036	0.000	0.000	0.000	0.000
82	B	83	THR	0	-0.006	-0.012	14.961	-0.054	-0.054	0.000	0.000	0.000	0.000
83	B	84	LEU	0	0.002	0.018	12.947	0.056	0.056	0.000	0.000	0.000	0.000
84	B	85	ASN	0	-0.037	-0.042	12.028	0.053	0.053	0.000	0.000	0.000	0.000
85	B	86	LYS	1	0.805	0.898	5.931	-0.088	-0.088	0.000	0.000	0.000	0.000
86	B	87	THR	0	-0.041	-0.032	7.078	-0.340	-0.340	0.000	0.000	0.000	0.000
87	B	88	ASP	-1	-0.801	-0.876	9.254	-0.489	-0.489	0.000	0.000	0.000	0.000
88	B	89	LEU	0	-0.054	-0.027	7.874	0.107	0.107	0.000	0.000	0.000	0.000
89	B	90	THR	0	0.007	-0.013	8.158	-0.333	-0.333	0.000	0.000	0.000	0.000
90	B	91	ASP	-1	-0.837	-0.900	9.862	-0.840	-0.840	0.000	0.000	0.000	0.000
91	B	92	ARG	1	0.824	0.897	5.960	2.497	2.497	0.000	0.000	0.000	0.000
92	B	93	VAL	0	-0.010	-0.003	9.843	0.160	0.160	0.000	0.000	0.000	0.000
93	B	94	GLY	0	-0.036	-0.031	11.459	0.154	0.154	0.000	0.000	0.000	0.000
94	B	95	GLU	-1	-0.903	-0.927	8.826	-1.364	-1.364	0.000	0.000	0.000	0.000
95	B	96	VAL	0	-0.010	0.000	11.540	0.136	0.136	0.000	0.000	0.000	0.000
96	B	97	PRO	0	0.023	0.014	13.857	-0.008	-0.008	0.000	0.000	0.000	0.000
97	B	98	ALA	0	0.056	0.004	15.537	0.021	0.021	0.000	0.000	0.000	0.000
98	B	99	SER	0	0.020	0.015	16.456	0.004	0.004	0.000	0.000	0.000	0.000
99	B	100	LEU	0	0.061	0.022	18.552	0.013	0.013	0.000	0.000	0.000	0.000
100	B	101	MET	0	0.013	0.020	13.729	-0.020	-0.020	0.000	0.000	0.000	0.000
101	B	102	HIS	0	-0.001	0.003	17.155	0.029	0.029	0.000	0.000	0.000	0.000
102	B	103	GLU	-1	-0.845	-0.891	20.014	-0.213	-0.213	0.000	0.000	0.000	0.000
103	B	104	VAL	0	0.036	0.017	17.039	0.018	0.018	0.000	0.000	0.000	0.000
104	B	105	ASP	-1	-0.785	-0.864	17.018	-0.379	-0.379	0.000	0.000	0.000	0.000
105	B	106	ARG	1	0.749	0.867	19.772	0.246	0.246	0.000	0.000	0.000	0.000
106	B	107	GLY	0	0.022	0.014	22.938	0.021	0.021	0.000	0.000	0.000	0.000
107	B	108	LEU	0	-0.001	-0.019	17.501	0.014	0.014	0.000	0.000	0.000	0.000
108	B	109	ARG	1	0.899	0.933	21.646	0.233	0.233	0.000	0.000	0.000	0.000
109	B	110	ARG	1	0.943	0.983	24.132	0.174	0.174	0.000	0.000	0.000	0.000
110	B	111	VAL	0	-0.056	-0.033	24.278	0.013	0.013	0.000	0.000	0.000	0.000
111	B	112	LEU	0	-0.051	-0.024	21.635	0.000	0.000	0.000	0.000	0.000	0.000
112	B	113	ASP	-1	-0.934	-0.947	26.110	-0.102	-0.102	0.000	0.000	0.000	0.000
113	B	114	LEU	0	-0.071	-0.029	22.394	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:VAL)