FMO DATABASE

FMODB ID: N9KQQ

Calculation Name: 1HKF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HKF

Chain ID: A

ChEMBL ID:

UniProt ID: O95944

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:

Apendix: None

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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-863246.437389
FMO2-HF: Nuclear repulsion	819413.029053
FMO2-HF: Total energy	-43833.408335
FMO2-MP2: Total energy	-43958.805458

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:5:SER)

Summations of interaction energy for fragment #1(A:5:SER)

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.
-3.99	2.531	1.58	-3.302	-4.798	-0.005

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.030

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	7	ALA	0	-0.015	0.011	3.797	-0.262	2.328	-0.022	-1.264	-1.304	0.005
4	A	8	GLN	0	0.005	0.006	5.463	-0.299	-0.162	-0.001	-0.012	-0.123	0.000
5	A	9	VAL	0	0.007	-0.002	8.352	-0.071	-0.071	0.000	0.000	0.000	0.000
6	A	10	LEU	0	-0.032	-0.008	11.513	0.062	0.062	0.000	0.000	0.000	0.000
7	A	11	GLN	0	0.015	0.003	14.064	-0.053	-0.053	0.000	0.000	0.000	0.000
8	A	12	SER	0	-0.009	-0.002	17.438	0.021	0.021	0.000	0.000	0.000	0.000
9	A	13	VAL	0	0.008	0.006	20.739	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	14	ALA	0	0.053	0.012	23.683	0.008	0.008	0.000	0.000	0.000	0.000
11	A	15	GLY	0	-0.004	0.007	25.133	0.004	0.004	0.000	0.000	0.000	0.000
12	A	16	GLN	0	-0.061	-0.026	23.644	0.014	0.014	0.000	0.000	0.000	0.000
13	A	17	THR	0	0.010	-0.002	23.185	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.023	-0.006	15.305	0.004	0.004	0.000	0.000	0.000	0.000
15	A	19	THR	0	0.015	0.004	19.057	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	20	VAL	0	-0.001	0.000	12.382	0.013	0.013	0.000	0.000	0.000	0.000
17	A	21	ARG	1	0.944	0.992	15.370	-0.164	-0.164	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.097	-0.001	8.197	0.060	0.060	0.000	0.000	0.000	0.000
19	A	23	GLN	0	0.050	0.020	13.645	-0.062	-0.062	0.000	0.000	0.000	0.000
20	A	24	TYR	0	-0.073	-0.078	13.865	0.066	0.066	0.000	0.000	0.000	0.000
21	A	25	PRO	0	0.014	0.021	15.553	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	26	PRO	0	0.047	0.004	18.583	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	27	THR	0	0.002	0.015	19.715	0.005	0.005	0.000	0.000	0.000	0.000
24	A	28	GLY	0	0.007	-0.001	22.654	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	29	SER	0	0.015	0.007	26.321	0.001	0.001	0.000	0.000	0.000	0.000
26	A	30	LEU	0	-0.022	0.002	24.052	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	31	TYR	0	-0.048	-0.059	21.559	0.004	0.004	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.793	-0.878	17.137	0.191	0.191	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.921	0.965	18.963	-0.062	-0.062	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.820	0.918	15.885	-0.140	-0.140	0.000	0.000	0.000	0.000
31	A	35	GLY	0	-0.018	-0.015	14.509	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	36	TRP	0	0.035	0.016	10.979	0.045	0.045	0.000	0.000	0.000	0.000
33	A	37	CYS	0	-0.087	-0.035	10.163	-0.091	-0.091	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.955	0.988	11.377	0.190	0.190	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.816	-0.871	5.589	-1.525	-1.525	0.000	0.000	0.000	0.000
36	A	40	ALA	0	-0.005	-0.005	10.500	0.002	0.002	0.000	0.000	0.000	0.000
37	A	41	SER	0	0.024	-0.003	11.607	0.004	0.004	0.000	0.000	0.000	0.000
38	A	42	ALA	0	-0.002	0.000	8.129	-0.055	-0.055	0.000	0.000	0.000	0.000
39	A	43	LEU	0	0.008	0.001	8.646	0.115	0.115	0.000	0.000	0.000	0.000
40	A	44	VAL	0	-0.012	0.009	11.118	0.032	0.032	0.000	0.000	0.000	0.000
41	A	46	ILE	0	0.052	0.031	12.169	0.045	0.045	0.000	0.000	0.000	0.000
42	A	47	ARG	1	0.847	0.915	15.157	-0.042	-0.042	0.000	0.000	0.000	0.000
43	A	48	LEU	0	-0.007	0.006	15.618	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	49	VAL	0	0.073	0.048	17.478	0.004	0.004	0.000	0.000	0.000	0.000
45	A	50	THR	0	-0.050	-0.037	17.500	0.010	0.010	0.000	0.000	0.000	0.000
46	A	51	SER	0	0.027	0.037	19.278	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	52	SER	0	0.004	-0.035	20.800	0.007	0.007	0.000	0.000	0.000	0.000
48	A	53	LYS	1	0.965	0.979	23.371	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	54	PRO	0	0.027	0.032	24.476	0.001	0.001	0.000	0.000	0.000	0.000
50	A	55	ARG	1	0.797	0.876	25.097	-0.085	-0.085	0.000	0.000	0.000	0.000
51	A	56	THR	0	-0.036	-0.016	25.487	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	57	MET	0	0.008	0.006	25.799	0.006	0.006	0.000	0.000	0.000	0.000
53	A	58	ALA	0	-0.042	-0.025	22.987	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	59	TRP	0	0.091	0.035	23.784	0.000	0.000	0.000	0.000	0.000	0.000
55	A	60	THR	0	-0.037	-0.023	22.898	0.000	0.000	0.000	0.000	0.000	0.000
56	A	61	SER	0	0.026	0.004	23.944	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	62	ARG	1	0.771	0.862	21.582	0.049	0.049	0.000	0.000	0.000	0.000
58	A	63	PHE	0	0.004	0.000	19.622	0.003	0.003	0.000	0.000	0.000	0.000
59	A	64	THR	0	0.000	0.010	21.133	0.003	0.003	0.000	0.000	0.000	0.000
60	A	65	ILE	0	-0.030	-0.025	17.025	0.010	0.010	0.000	0.000	0.000	0.000
61	A	66	TRP	0	0.063	0.052	20.771	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	67	ASP	-1	-0.740	-0.853	20.200	0.154	0.154	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.794	-0.888	21.763	0.078	0.078	0.000	0.000	0.000	0.000
64	A	69	PRO	0	-0.001	-0.003	22.254	0.007	0.007	0.000	0.000	0.000	0.000
65	A	70	ASP	-1	-0.844	-0.895	23.315	0.094	0.094	0.000	0.000	0.000	0.000
66	A	71	ALA	0	-0.033	-0.011	23.262	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	72	GLY	0	0.015	0.023	20.771	0.008	0.008	0.000	0.000	0.000	0.000
68	A	73	PHE	0	-0.049	-0.049	17.527	0.032	0.032	0.000	0.000	0.000	0.000
69	A	74	PHE	0	-0.012	0.007	13.141	-0.021	-0.021	0.000	0.000	0.000	0.000
70	A	75	THR	0	-0.032	-0.039	17.171	0.030	0.030	0.000	0.000	0.000	0.000
71	A	76	VAL	0	0.020	0.006	14.657	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	77	THR	0	-0.018	-0.005	17.872	0.006	0.006	0.000	0.000	0.000	0.000
73	A	78	MET	0	-0.009	0.018	16.730	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	79	THR	0	0.001	0.003	20.558	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	80	ASP	-1	-0.826	-0.912	23.885	-0.040	-0.040	0.000	0.000	0.000	0.000
76	A	81	LEU	0	-0.056	-0.020	19.451	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	82	ARG	1	0.938	0.956	22.020	0.053	0.053	0.000	0.000	0.000	0.000
78	A	83	GLU	-1	-0.880	-0.925	20.949	-0.130	-0.130	0.000	0.000	0.000	0.000
79	A	84	GLU	-1	-0.842	-0.925	19.602	-0.119	-0.119	0.000	0.000	0.000	0.000
80	A	85	ASP	-1	-0.836	-0.882	17.985	-0.083	-0.083	0.000	0.000	0.000	0.000
81	A	86	SER	0	0.007	0.010	15.735	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	87	GLY	0	0.017	0.005	12.438	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	88	HIS	0	-0.018	-0.001	6.939	-0.038	-0.038	0.000	0.000	0.000	0.000
84	A	89	TYR	0	-0.017	-0.033	8.736	0.045	0.045	0.000	0.000	0.000	0.000
85	A	90	TRP	0	-0.031	-0.052	2.424	-2.133	-0.508	0.525	-0.927	-1.224	-0.011
86	A	92	ARG	1	0.885	0.913	6.940	0.271	0.271	0.000	0.000	0.000	0.000
87	A	93	ILE	0	0.037	0.034	11.053	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	94	TYR	0	-0.042	-0.026	13.035	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	95	ARG	1	0.953	0.973	14.180	-0.207	-0.207	0.000	0.000	0.000	0.000
90	A	96	PRO	0	-0.044	-0.028	18.504	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	97	SER	0	0.017	0.001	21.066	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	98	ASP	-1	-0.769	-0.859	19.158	0.122	0.122	0.000	0.000	0.000	0.000
93	A	99	ASN	0	-0.071	-0.021	17.409	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	100	SER	0	-0.004	-0.008	15.229	0.007	0.007	0.000	0.000	0.000	0.000
95	A	101	VAL	0	-0.028	-0.031	9.381	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	102	SER	0	-0.053	-0.046	11.985	0.030	0.030	0.000	0.000	0.000	0.000
97	A	103	LYS	1	0.930	0.972	9.352	-0.659	-0.659	0.000	0.000	0.000	0.000
98	A	104	SER	0	-0.010	-0.008	5.653	-0.199	-0.199	0.000	0.000	0.000	0.000
99	A	105	VAL	0	-0.049	-0.017	5.365	0.373	0.373	0.000	0.000	0.000	0.000
100	A	106	ARG	1	0.823	0.897	2.465	0.256	2.395	1.079	-1.093	-2.124	0.001
101	A	107	PHE	0	0.023	-0.023	4.864	0.512	0.542	-0.001	-0.006	-0.023	0.000
102	A	108	TYR	0	0.024	0.001	7.940	-0.303	-0.303	0.000	0.000	0.000	0.000
103	A	109	LEU	0	-0.038	-0.001	9.792	0.084	0.084	0.000	0.000	0.000	0.000
104	A	110	VAL	0	0.024	0.004	13.504	-0.053	-0.053	0.000	0.000	0.000	0.000
105	A	111	VAL	0	0.019	0.001	16.073	0.034	0.034	0.000	0.000	0.000	0.000
106	A	112	SER	0	0.045	0.024	19.497	-0.009	-0.009	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)