FMO DATABASE

FMODB ID: 897KY

Calculation Name: 1MKH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MKH

Chain ID: A

ChEMBL ID:

UniProt ID: Q9V011

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	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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-800307.548183
FMO2-HF: Nuclear repulsion	758562.782262
FMO2-HF: Total energy	-41744.765921
FMO2-MP2: Total energy	-41867.565589

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:1:MET)

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

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.
-2.574	-0.393	0.278	-1.095	-1.364	-0.003

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.019

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	3	VAL	0	0.039	0.030	2.872	-3.884	-1.789	0.279	-1.088	-1.286	-0.003
4	A	4	LYS	1	0.861	0.915	5.364	1.346	1.432	-0.001	-0.007	-0.078	0.000
5	A	5	PHE	0	0.069	0.019	8.481	-0.073	-0.073	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.765	-0.877	11.816	-0.618	-0.618	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.861	-0.923	7.864	-1.429	-1.429	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.047	-0.018	10.221	-0.038	-0.038	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.042	-0.029	12.166	0.097	0.097	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.858	0.927	10.307	1.009	1.009	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.003	0.028	11.954	0.067	0.067	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.802	-0.881	15.683	-0.317	-0.317	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.011	0.003	15.298	0.015	0.015	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.807	0.870	19.829	0.329	0.329	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.035	0.022	23.424	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.025	0.016	25.584	0.008	0.008	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.887	0.953	28.080	0.140	0.140	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.003	0.016	27.747	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.014	-0.002	31.431	0.012	0.012	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.880	-0.940	33.828	-0.125	-0.125	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.015	0.020	32.016	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.949	0.984	33.910	0.146	0.146	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.781	-0.878	33.590	-0.140	-0.140	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.012	-0.003	29.168	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.027	0.013	33.113	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.021	-0.024	32.042	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.016	-0.011	29.006	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.819	-0.890	29.656	-0.159	-0.159	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.865	0.944	23.942	0.235	0.235	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.047	-0.031	25.128	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.022	-0.029	28.568	0.018	0.018	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.051	-0.039	28.951	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.000	-0.002	27.928	0.014	0.014	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.882	0.953	30.027	0.129	0.129	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.036	-0.036	26.903	0.006	0.006	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.849	-0.929	30.212	-0.165	-0.165	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.034	-0.054	26.013	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.025	-0.007	30.087	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.973	-0.982	30.481	-0.195	-0.195	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.840	-0.907	29.127	-0.229	-0.229	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.019	-0.020	31.789	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.815	0.912	23.610	0.290	0.290	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.014	0.018	28.769	0.008	0.008	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.041	-0.016	23.913	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.007	-0.023	25.663	0.020	0.020	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.037	0.027	24.345	-0.029	-0.029	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.018	-0.010	23.999	0.025	0.025	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.040	0.011	23.572	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.886	0.957	26.892	0.149	0.149	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.880	0.923	27.264	0.137	0.137	0.000	0.000	0.000	0.000
51	A	51	TYR	0	0.006	0.002	23.518	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.012	0.012	25.243	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.884	0.960	30.379	0.094	0.094	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.029	0.001	33.796	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.860	-0.928	34.880	-0.099	-0.099	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.858	-0.931	32.178	-0.123	-0.123	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.031	-0.027	28.255	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.001	0.007	31.599	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.019	-0.016	34.276	0.003	0.003	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.929	0.992	27.872	0.156	0.156	0.000	0.000	0.000	0.000
61	A	61	TYR	0	-0.034	-0.052	28.278	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.001	-0.001	24.662	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.030	0.011	19.662	0.001	0.001	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.004	-0.001	21.318	-0.014	-0.014	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.001	0.002	16.109	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.014	0.002	19.293	0.009	0.009	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.003	-0.009	17.390	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.025	0.035	15.618	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.839	-0.908	18.021	-0.352	-0.352	0.000	0.000	0.000	0.000
70	A	70	PRO	0	0.016	0.019	19.898	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.809	0.878	18.794	0.394	0.394	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.928	0.981	23.564	0.202	0.202	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.104	0.037	22.353	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.833	0.919	26.414	0.190	0.190	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.020	-0.019	27.975	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.017	0.007	29.601	0.011	0.011	0.000	0.000	0.000	0.000
77	A	77	GLY	0	-0.043	-0.014	28.201	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.032	0.023	23.807	0.012	0.012	0.000	0.000	0.000	0.000
79	A	79	GLN	0	0.016	-0.001	22.391	0.007	0.007	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.058	0.038	20.550	0.013	0.013	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.034	-0.032	16.892	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.024	0.011	20.505	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.015	-0.006	15.695	-0.024	-0.024	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.009	-0.021	18.033	0.050	0.050	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.011	0.013	16.635	-0.046	-0.046	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.902	-0.982	16.341	-0.331	-0.331	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.811	-0.884	16.621	-0.148	-0.148	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.030	-0.002	18.207	0.028	0.028	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.977	-0.989	19.522	-0.056	-0.056	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.822	0.906	22.665	0.103	0.103	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.025	0.009	21.005	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.020	-0.008	21.271	0.018	0.018	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.027	-0.011	21.089	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.011	0.008	16.880	0.015	0.015	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.014	-0.019	21.598	0.002	0.002	0.000	0.000	0.000	0.000
96	A	96	PRO	0	-0.051	-0.010	23.999	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.798	-0.891	25.675	-0.127	-0.127	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.835	0.905	27.583	0.137	0.137	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.828	-0.884	29.538	-0.133	-0.133	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.023	-0.024	27.628	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.917	0.968	31.107	0.176	0.176	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.039	0.020	30.224	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.075	0.029	27.932	0.006	0.006	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.054	-0.013	27.126	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.850	0.920	18.893	0.446	0.446	0.000	0.000	0.000	0.000
106	A	106	VAL	0	0.012	0.009	18.776	0.019	0.019	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.960	0.979	17.843	0.226	0.226	0.000	0.000	0.000	0.000

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