FMO DATABASE

FMODB ID: 85RMY

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	OptH
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	-863583.552801
FMO2-HF: Nuclear repulsion	819750.757142
FMO2-HF: Total energy	-43832.79566
FMO2-MP2: Total energy	-43958.306163

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.
-2.905	3.02	1.194	-2.885	-4.233	-0.003

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 : 0.040 / q_NPA : 0.025

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	7	ALA	0	-0.002	0.014	3.797	0.035	2.561	-0.022	-1.219	-1.284	0.004
4	A	8	GLN	0	0.002	0.005	5.455	-0.040	0.079	-0.001	-0.011	-0.107	0.000
5	A	9	VAL	0	0.008	0.000	8.342	-0.078	-0.078	0.000	0.000	0.000	0.000
6	A	10	LEU	0	-0.029	-0.005	11.505	0.089	0.089	0.000	0.000	0.000	0.000
7	A	11	GLN	0	0.019	0.008	14.061	-0.071	-0.071	0.000	0.000	0.000	0.000
8	A	12	SER	0	-0.005	-0.001	17.389	0.029	0.029	0.000	0.000	0.000	0.000
9	A	13	VAL	0	0.001	0.001	20.715	-0.024	-0.024	0.000	0.000	0.000	0.000
10	A	14	ALA	0	0.050	0.007	23.532	0.012	0.012	0.000	0.000	0.000	0.000
11	A	15	GLY	0	-0.007	0.010	25.003	0.004	0.004	0.000	0.000	0.000	0.000
12	A	16	GLN	0	-0.067	-0.030	23.565	0.020	0.020	0.000	0.000	0.000	0.000
13	A	17	THR	0	0.019	0.004	22.963	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.026	-0.002	15.490	0.003	0.003	0.000	0.000	0.000	0.000
15	A	19	THR	0	-0.001	-0.002	19.061	0.007	0.007	0.000	0.000	0.000	0.000
16	A	20	VAL	0	-0.003	-0.003	12.404	0.011	0.011	0.000	0.000	0.000	0.000
17	A	21	ARG	1	0.965	0.998	15.349	-0.250	-0.250	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.116	-0.019	8.226	0.030	0.030	0.000	0.000	0.000	0.000
19	A	23	GLN	0	0.052	0.023	13.648	-0.093	-0.093	0.000	0.000	0.000	0.000
20	A	24	TYR	0	-0.075	-0.082	13.866	0.118	0.118	0.000	0.000	0.000	0.000
21	A	25	PRO	0	0.004	0.018	15.519	-0.039	-0.039	0.000	0.000	0.000	0.000
22	A	26	PRO	0	0.064	0.014	18.584	0.003	0.003	0.000	0.000	0.000	0.000
23	A	27	THR	0	0.010	0.016	20.138	0.009	0.009	0.000	0.000	0.000	0.000
24	A	28	GLY	0	0.000	-0.004	22.864	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	29	SER	0	0.013	0.006	26.547	0.002	0.002	0.000	0.000	0.000	0.000
26	A	30	LEU	0	-0.016	0.003	24.158	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	31	TYR	0	-0.048	-0.048	21.749	0.010	0.010	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.811	-0.897	17.405	0.387	0.387	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.961	0.993	19.116	-0.158	-0.158	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.835	0.926	16.055	-0.275	-0.275	0.000	0.000	0.000	0.000
31	A	35	GLY	0	-0.012	-0.012	14.654	-0.055	-0.055	0.000	0.000	0.000	0.000
32	A	36	TRP	0	0.042	0.029	11.060	0.099	0.099	0.000	0.000	0.000	0.000
33	A	37	CYS	0	-0.088	-0.038	10.211	-0.101	-0.101	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.968	0.995	11.353	0.244	0.244	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.827	-0.861	5.627	-1.701	-1.701	0.000	0.000	0.000	0.000
36	A	40	ALA	0	-0.012	-0.007	10.528	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	41	SER	0	0.025	0.000	11.620	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	42	ALA	0	0.002	0.001	8.028	-0.036	-0.036	0.000	0.000	0.000	0.000
39	A	43	LEU	0	0.005	-0.002	8.755	0.155	0.155	0.000	0.000	0.000	0.000
40	A	44	VAL	0	-0.015	0.008	11.241	0.063	0.063	0.000	0.000	0.000	0.000
41	A	46	ILE	0	0.056	0.029	12.162	0.060	0.060	0.000	0.000	0.000	0.000
42	A	47	ARG	1	0.836	0.897	15.149	-0.170	-0.170	0.000	0.000	0.000	0.000
43	A	48	LEU	0	-0.011	0.004	15.478	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	49	VAL	0	0.072	0.047	17.518	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	50	THR	0	-0.044	-0.025	17.576	0.033	0.033	0.000	0.000	0.000	0.000
46	A	51	SER	0	0.030	0.040	19.412	-0.027	-0.027	0.000	0.000	0.000	0.000
47	A	52	SER	0	-0.028	-0.048	20.957	0.018	0.018	0.000	0.000	0.000	0.000
48	A	53	LYS	1	0.963	0.975	23.528	-0.109	-0.109	0.000	0.000	0.000	0.000
49	A	54	PRO	0	0.019	0.034	24.649	0.002	0.002	0.000	0.000	0.000	0.000
50	A	55	ARG	1	0.910	0.952	25.254	-0.160	-0.160	0.000	0.000	0.000	0.000
51	A	56	THR	0	-0.016	-0.011	25.594	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	57	MET	0	0.000	-0.002	25.913	0.010	0.010	0.000	0.000	0.000	0.000
53	A	58	ALA	0	-0.044	-0.024	23.034	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	59	TRP	0	0.086	0.059	23.852	0.004	0.004	0.000	0.000	0.000	0.000
55	A	60	THR	0	-0.026	-0.024	22.786	0.005	0.005	0.000	0.000	0.000	0.000
56	A	61	SER	0	0.045	-0.001	23.947	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	62	ARG	1	0.806	0.889	21.466	0.031	0.031	0.000	0.000	0.000	0.000
58	A	63	PHE	0	-0.011	-0.007	19.225	0.004	0.004	0.000	0.000	0.000	0.000
59	A	64	THR	0	0.003	0.011	21.223	0.004	0.004	0.000	0.000	0.000	0.000
60	A	65	ILE	0	-0.031	-0.019	17.064	0.019	0.019	0.000	0.000	0.000	0.000
61	A	66	TRP	0	0.052	0.048	20.852	-0.016	-0.016	0.000	0.000	0.000	0.000
62	A	67	ASP	-1	-0.737	-0.871	20.295	0.293	0.293	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.801	-0.897	21.909	0.148	0.148	0.000	0.000	0.000	0.000
64	A	69	PRO	0	-0.034	-0.019	22.359	0.008	0.008	0.000	0.000	0.000	0.000
65	A	70	ASP	-1	-0.914	-0.940	23.422	0.168	0.168	0.000	0.000	0.000	0.000
66	A	71	ALA	0	-0.047	-0.020	23.248	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	72	GLY	0	0.008	0.018	20.773	0.010	0.010	0.000	0.000	0.000	0.000
68	A	73	PHE	0	-0.052	-0.046	17.432	0.050	0.050	0.000	0.000	0.000	0.000
69	A	74	PHE	0	-0.009	0.011	13.421	-0.031	-0.031	0.000	0.000	0.000	0.000
70	A	75	THR	0	-0.027	-0.033	17.176	0.041	0.041	0.000	0.000	0.000	0.000
71	A	76	VAL	0	0.005	-0.001	14.774	-0.019	-0.019	0.000	0.000	0.000	0.000
72	A	77	THR	0	-0.016	-0.007	17.920	0.000	0.000	0.000	0.000	0.000	0.000
73	A	78	MET	0	-0.007	0.018	17.035	0.002	0.002	0.000	0.000	0.000	0.000
74	A	79	THR	0	0.017	0.006	20.521	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	80	ASP	-1	-0.848	-0.931	23.812	-0.029	-0.029	0.000	0.000	0.000	0.000
76	A	81	LEU	0	-0.039	-0.018	19.349	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	82	ARG	1	0.944	0.969	21.937	0.045	0.045	0.000	0.000	0.000	0.000
78	A	83	GLU	-1	-0.897	-0.941	20.831	-0.162	-0.162	0.000	0.000	0.000	0.000
79	A	84	GLU	-1	-0.849	-0.939	19.440	-0.148	-0.148	0.000	0.000	0.000	0.000
80	A	85	ASP	-1	-0.868	-0.903	17.981	-0.076	-0.076	0.000	0.000	0.000	0.000
81	A	86	SER	0	0.038	0.044	15.588	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	87	GLY	0	0.015	0.000	12.265	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	88	HIS	0	-0.010	0.008	6.681	-0.059	-0.059	0.000	0.000	0.000	0.000
84	A	89	TYR	0	-0.034	-0.045	8.719	0.083	0.083	0.000	0.000	0.000	0.000
85	A	90	TRP	0	-0.011	-0.040	2.522	-1.378	-0.109	0.282	-0.643	-0.908	-0.006
86	A	92	ARG	1	0.907	0.926	7.254	-0.138	-0.138	0.000	0.000	0.000	0.000
87	A	93	ILE	0	0.027	0.029	11.220	-0.085	-0.085	0.000	0.000	0.000	0.000
88	A	94	TYR	0	-0.038	-0.024	13.522	0.039	0.039	0.000	0.000	0.000	0.000
89	A	95	ARG	1	0.971	0.967	14.233	-0.444	-0.444	0.000	0.000	0.000	0.000
90	A	96	PRO	0	-0.043	-0.027	18.742	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	97	SER	0	0.040	-0.001	22.108	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	98	ASP	-1	-0.791	-0.868	19.269	0.250	0.250	0.000	0.000	0.000	0.000
93	A	99	ASN	0	-0.057	-0.014	18.057	0.000	0.000	0.000	0.000	0.000	0.000
94	A	100	SER	0	-0.041	-0.002	15.531	0.037	0.037	0.000	0.000	0.000	0.000
95	A	101	VAL	0	-0.022	-0.030	9.626	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	102	SER	0	-0.068	-0.043	12.238	0.067	0.067	0.000	0.000	0.000	0.000
97	A	103	LYS	1	0.924	0.965	9.678	-1.002	-1.002	0.000	0.000	0.000	0.000
98	A	104	SER	0	-0.030	-0.025	5.940	-0.330	-0.330	0.000	0.000	0.000	0.000
99	A	105	VAL	0	-0.027	-0.001	5.380	0.634	0.634	0.000	0.000	0.000	0.000
100	A	106	ARG	1	0.842	0.885	2.282	1.021	3.006	0.936	-1.006	-1.916	-0.001
101	A	107	PHE	0	0.019	-0.018	4.833	0.428	0.454	-0.001	-0.006	-0.018	0.000
102	A	108	TYR	0	0.024	-0.001	7.944	-0.358	-0.358	0.000	0.000	0.000	0.000
103	A	109	LEU	0	-0.042	-0.004	9.638	0.112	0.112	0.000	0.000	0.000	0.000
104	A	110	VAL	0	0.017	-0.003	13.375	-0.068	-0.068	0.000	0.000	0.000	0.000
105	A	111	VAL	0	0.004	-0.007	15.882	0.045	0.045	0.000	0.000	0.000	0.000
106	A	112	SER	0	0.039	0.020	19.329	-0.013	-0.013	0.000	0.000	0.000	0.000

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