FMO DATABASE

FMODB ID: JLNG9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-862645.771492
FMO2-HF: Nuclear repulsion	818811.683763
FMO2-HF: Total energy	-43834.087729
FMO2-MP2: Total energy	-43959.507977

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.
-6.46	-0.105	3.895	-3.964	-6.285	-0.007

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 : 0.061 / q_NPA : 0.034

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	-0.010	0.009	3.883	0.017	2.147	-0.007	-1.005	-1.117	0.004
4	A	8	GLN	0	-0.002	-0.007	5.125	-0.851	-0.694	-0.001	-0.015	-0.141	0.000
5	A	9	VAL	0	0.019	0.006	8.049	-0.032	-0.032	0.000	0.000	0.000	0.000
6	A	10	LEU	0	-0.036	-0.010	11.115	0.021	0.021	0.000	0.000	0.000	0.000
7	A	11	GLN	0	-0.006	-0.004	13.788	-0.030	-0.030	0.000	0.000	0.000	0.000
8	A	12	SER	0	-0.002	0.002	17.260	0.006	0.006	0.000	0.000	0.000	0.000
9	A	13	VAL	0	0.000	0.001	20.545	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	14	ALA	0	0.052	0.011	23.597	0.005	0.005	0.000	0.000	0.000	0.000
11	A	15	GLY	0	-0.007	0.003	25.431	0.001	0.001	0.000	0.000	0.000	0.000
12	A	16	GLN	0	-0.038	-0.003	23.598	0.006	0.006	0.000	0.000	0.000	0.000
13	A	17	THR	0	-0.005	-0.009	22.723	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.016	0.006	14.865	0.005	0.005	0.000	0.000	0.000	0.000
15	A	19	THR	0	0.002	-0.011	18.766	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	20	VAL	0	-0.013	-0.001	12.119	0.016	0.016	0.000	0.000	0.000	0.000
17	A	21	ARG	1	0.872	0.945	14.517	-0.131	-0.131	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.081	-0.002	7.779	0.017	0.017	0.000	0.000	0.000	0.000
19	A	23	GLN	0	0.054	0.028	13.472	-0.029	-0.029	0.000	0.000	0.000	0.000
20	A	24	TYR	0	-0.070	-0.069	13.788	0.016	0.016	0.000	0.000	0.000	0.000
21	A	25	PRO	0	0.020	0.024	15.522	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	26	PRO	0	0.038	0.002	18.485	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	27	THR	0	0.003	-0.007	19.448	0.001	0.001	0.000	0.000	0.000	0.000
24	A	28	GLY	0	0.010	0.011	22.386	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	29	SER	0	0.001	-0.008	25.742	0.001	0.001	0.000	0.000	0.000	0.000
26	A	30	LEU	0	-0.007	0.010	23.537	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	31	TYR	0	-0.026	-0.032	21.095	0.001	0.001	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.775	-0.867	16.700	0.039	0.039	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.900	0.972	18.790	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.793	0.890	15.505	-0.053	-0.053	0.000	0.000	0.000	0.000
31	A	35	GLY	0	-0.003	-0.015	14.279	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	36	TRP	0	-0.001	0.000	10.667	0.016	0.016	0.000	0.000	0.000	0.000
33	A	37	CYS	0	-0.066	-0.040	9.714	-0.067	-0.067	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.943	0.993	10.930	0.090	0.090	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.817	-0.879	5.609	-0.867	-0.867	0.000	0.000	0.000	0.000
36	A	40	ALA	0	0.001	-0.001	10.523	0.014	0.014	0.000	0.000	0.000	0.000
37	A	41	SER	0	0.021	-0.001	11.479	0.005	0.005	0.000	0.000	0.000	0.000
38	A	42	ALA	0	0.019	0.009	7.609	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	43	LEU	0	-0.011	0.002	8.035	0.116	0.116	0.000	0.000	0.000	0.000
40	A	44	VAL	0	-0.013	0.004	10.674	0.016	0.016	0.000	0.000	0.000	0.000
41	A	46	ILE	0	0.052	0.034	11.745	0.021	0.021	0.000	0.000	0.000	0.000
42	A	47	ARG	1	0.867	0.919	14.552	0.015	0.015	0.000	0.000	0.000	0.000
43	A	48	LEU	0	-0.018	0.002	15.282	0.001	0.001	0.000	0.000	0.000	0.000
44	A	49	VAL	0	0.053	0.034	17.144	0.003	0.003	0.000	0.000	0.000	0.000
45	A	50	THR	0	-0.017	-0.021	17.148	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	51	SER	0	0.007	0.025	18.690	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	52	SER	0	0.026	-0.013	20.283	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	53	LYS	1	0.977	0.976	22.916	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	54	PRO	0	0.017	0.037	23.868	0.001	0.001	0.000	0.000	0.000	0.000
50	A	55	ARG	1	0.772	0.847	24.789	-0.040	-0.040	0.000	0.000	0.000	0.000
51	A	56	THR	0	-0.056	-0.024	25.350	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	57	MET	0	0.041	0.018	25.421	0.004	0.004	0.000	0.000	0.000	0.000
53	A	58	ALA	0	-0.026	-0.005	22.274	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	59	TRP	0	0.086	0.035	23.019	0.002	0.002	0.000	0.000	0.000	0.000
55	A	60	THR	0	-0.053	-0.047	22.132	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	61	SER	0	0.021	0.015	23.440	0.000	0.000	0.000	0.000	0.000	0.000
57	A	62	ARG	1	0.796	0.878	21.279	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	63	PHE	0	-0.013	0.008	19.443	0.006	0.006	0.000	0.000	0.000	0.000
59	A	64	THR	0	-0.005	-0.007	20.622	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	65	ILE	0	-0.042	-0.028	16.681	0.009	0.009	0.000	0.000	0.000	0.000
61	A	66	TRP	0	0.022	0.029	20.463	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	67	ASP	-1	-0.715	-0.847	19.815	0.065	0.065	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.777	-0.875	21.248	0.037	0.037	0.000	0.000	0.000	0.000
64	A	69	PRO	0	0.014	0.003	21.956	0.004	0.004	0.000	0.000	0.000	0.000
65	A	70	ASP	-1	-0.817	-0.879	23.009	0.041	0.041	0.000	0.000	0.000	0.000
66	A	71	ALA	0	-0.017	0.000	23.399	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	72	GLY	0	0.008	0.015	20.743	0.006	0.006	0.000	0.000	0.000	0.000
68	A	73	PHE	0	0.011	-0.009	17.574	0.015	0.015	0.000	0.000	0.000	0.000
69	A	74	PHE	0	-0.017	-0.003	12.678	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	75	THR	0	-0.029	-0.030	16.745	0.023	0.023	0.000	0.000	0.000	0.000
71	A	76	VAL	0	0.034	0.021	14.196	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	77	THR	0	-0.019	-0.015	17.455	0.009	0.009	0.000	0.000	0.000	0.000
73	A	78	MET	0	-0.021	0.017	16.508	0.001	0.001	0.000	0.000	0.000	0.000
74	A	79	THR	0	0.021	0.006	20.292	0.000	0.000	0.000	0.000	0.000	0.000
75	A	80	ASP	-1	-0.826	-0.912	23.397	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	81	LEU	0	-0.024	-0.009	19.408	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	82	ARG	1	0.833	0.900	22.025	0.008	0.008	0.000	0.000	0.000	0.000
78	A	83	GLU	-1	-0.889	-0.928	21.209	-0.047	-0.047	0.000	0.000	0.000	0.000
79	A	84	GLU	-1	-0.802	-0.912	19.872	-0.034	-0.034	0.000	0.000	0.000	0.000
80	A	85	ASP	-1	-0.801	-0.869	17.851	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.010	0.008	15.921	0.011	0.011	0.000	0.000	0.000	0.000
82	A	87	GLY	0	0.010	0.005	12.610	-0.025	-0.025	0.000	0.000	0.000	0.000
83	A	88	HIS	0	0.000	0.001	7.113	0.142	0.142	0.000	0.000	0.000	0.000
84	A	89	TYR	0	-0.011	-0.029	8.359	-0.062	-0.062	0.000	0.000	0.000	0.000
85	A	90	TRP	0	-0.045	-0.054	2.311	-3.215	-1.293	1.376	-1.405	-1.893	-0.019
86	A	92	ARG	1	0.889	0.918	6.610	0.256	0.256	0.000	0.000	0.000	0.000
87	A	93	ILE	0	0.016	0.022	10.605	0.025	0.025	0.000	0.000	0.000	0.000
88	A	94	TYR	0	-0.037	-0.019	12.620	-0.030	-0.030	0.000	0.000	0.000	0.000
89	A	95	ARG	1	0.951	0.968	13.931	-0.036	-0.036	0.000	0.000	0.000	0.000
90	A	96	PRO	0	-0.025	-0.029	18.287	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	97	SER	0	-0.040	-0.032	20.788	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	98	ASP	-1	-0.773	-0.836	18.608	0.037	0.037	0.000	0.000	0.000	0.000
93	A	99	ASN	0	-0.059	-0.021	17.299	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	100	SER	0	0.001	-0.016	14.699	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	101	VAL	0	-0.023	-0.024	8.803	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	102	SER	0	-0.059	-0.045	12.175	0.008	0.008	0.000	0.000	0.000	0.000
97	A	103	LYS	1	0.913	0.960	8.755	-0.243	-0.243	0.000	0.000	0.000	0.000
98	A	104	SER	0	-0.016	-0.010	5.534	0.010	0.010	0.000	0.000	0.000	0.000
99	A	105	VAL	0	0.005	-0.008	5.376	0.009	0.009	0.000	0.000	0.000	0.000
100	A	106	ARG	1	0.792	0.886	2.522	-1.764	0.326	2.528	-1.525	-3.093	0.008
101	A	107	PHE	0	0.033	-0.010	4.521	0.326	0.382	-0.001	-0.014	-0.041	0.000
102	A	108	TYR	0	-0.004	-0.016	7.548	-0.185	-0.185	0.000	0.000	0.000	0.000
103	A	109	LEU	0	-0.009	0.016	9.787	0.002	0.002	0.000	0.000	0.000	0.000
104	A	110	VAL	0	0.009	0.000	13.358	-0.047	-0.047	0.000	0.000	0.000	0.000
105	A	111	VAL	0	0.012	0.007	16.508	0.019	0.019	0.000	0.000	0.000	0.000
106	A	112	SER	0	0.071	0.032	19.947	-0.006	-0.006	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)