FMO DATABASE

FMODB ID: 2J6NR

Calculation Name: 1MK4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MK4

Chain ID: A

ChEMBL ID:

UniProt ID: P54562

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1586930.535495
FMO2-HF: Nuclear repulsion	1523663.132436
FMO2-HF: Total energy	-63267.403059
FMO2-MP2: Total energy	-63451.673329

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-17.409	-19.59	21.645	-5.335	-14.13	0.033

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.021

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	2	ASP	-1	-0.900	-0.935	3.795	-7.946	-4.056	-0.019	-1.981	-1.890	0.004
4	A	3	ILE	0	0.015	-0.013	6.290	0.227	0.227	0.000	0.000	0.000	0.000
5	A	4	ARG	1	0.832	0.917	9.224	1.394	1.394	0.000	0.000	0.000	0.000
6	A	5	THR	0	0.040	0.021	11.783	0.091	0.091	0.000	0.000	0.000	0.000
7	A	6	ILE	0	-0.053	-0.015	14.251	-0.124	-0.124	0.000	0.000	0.000	0.000
8	A	7	THR	0	0.019	0.008	15.380	0.025	0.025	0.000	0.000	0.000	0.000
9	A	8	SER	0	0.029	-0.015	17.808	0.028	0.028	0.000	0.000	0.000	0.000
10	A	9	SER	0	-0.021	-0.017	16.275	0.037	0.037	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.771	-0.860	13.923	-1.040	-1.040	0.000	0.000	0.000	0.000
12	A	11	TYR	0	-0.080	-0.041	16.534	0.072	0.072	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.844	-0.920	18.840	-0.433	-0.433	0.000	0.000	0.000	0.000
14	A	13	MET	0	0.020	0.025	11.236	0.034	0.034	0.000	0.000	0.000	0.000
15	A	14	VAL	0	0.012	0.004	15.669	0.062	0.062	0.000	0.000	0.000	0.000
16	A	15	THR	0	-0.083	-0.081	17.475	0.077	0.077	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.008	-0.007	18.437	0.048	0.048	0.000	0.000	0.000	0.000
18	A	17	VAL	0	0.087	0.043	15.715	0.043	0.043	0.000	0.000	0.000	0.000
19	A	18	LEU	0	-0.098	-0.045	19.148	0.048	0.048	0.000	0.000	0.000	0.000
20	A	19	ASN	0	-0.029	-0.018	22.327	0.035	0.035	0.000	0.000	0.000	0.000
21	A	20	GLU	-1	-0.971	-0.987	18.366	-0.099	-0.099	0.000	0.000	0.000	0.000
22	A	21	TRP	0	0.000	-0.001	13.964	0.045	0.045	0.000	0.000	0.000	0.000
23	A	22	TRP	0	-0.014	0.000	20.456	0.032	0.032	0.000	0.000	0.000	0.000
24	A	23	GLY	0	-0.007	-0.009	23.174	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.039	0.030	24.943	0.003	0.003	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.846	0.927	26.733	-0.048	-0.048	0.000	0.000	0.000	0.000
27	A	26	GLN	0	0.037	0.012	27.898	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	27	LEU	0	0.006	0.013	24.806	0.010	0.010	0.000	0.000	0.000	0.000
29	A	28	LYS	1	0.933	0.973	29.112	0.060	0.060	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.913	-0.957	28.751	-0.089	-0.089	0.000	0.000	0.000	0.000
31	A	30	LYS	1	0.924	0.982	24.213	0.195	0.195	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.020	-0.006	21.938	0.001	0.001	0.000	0.000	0.000	0.000
33	A	32	PRO	0	0.010	0.006	25.459	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	33	ARG	1	0.970	0.985	22.907	0.410	0.410	0.000	0.000	0.000	0.000
35	A	34	LEU	0	0.027	0.012	25.167	-0.025	-0.025	0.000	0.000	0.000	0.000
36	A	35	PHE	0	0.023	-0.001	23.820	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	36	PHE	0	-0.004	-0.014	18.238	0.000	0.000	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.866	-0.916	21.824	-0.478	-0.478	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.020	-0.006	24.526	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	39	PHE	0	-0.024	-0.006	24.247	0.018	0.018	0.000	0.000	0.000	0.000
41	A	40	GLN	0	-0.001	-0.015	19.685	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	41	ASP	-1	-0.887	-0.937	19.160	-0.531	-0.531	0.000	0.000	0.000	0.000
43	A	42	THR	0	-0.062	-0.039	20.407	0.014	0.014	0.000	0.000	0.000	0.000
44	A	43	SER	0	-0.027	-0.017	19.074	0.073	0.073	0.000	0.000	0.000	0.000
45	A	44	PHE	0	-0.010	-0.014	14.158	-0.055	-0.055	0.000	0.000	0.000	0.000
46	A	45	ILE	0	0.015	0.010	9.983	0.106	0.106	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.015	-0.013	9.551	-0.153	-0.153	0.000	0.000	0.000	0.000
48	A	47	SER	0	-0.080	-0.043	5.591	-0.322	-0.322	0.000	0.000	0.000	0.000
49	A	48	GLU	-1	-0.858	-0.943	3.798	0.332	1.563	0.020	-0.456	-0.795	0.001
50	A	49	HIS	0	-0.047	-0.035	1.914	-10.702	-13.702	21.549	-8.121	-10.429	0.033
51	A	50	ASN	0	0.003	0.005	2.637	1.642	-2.795	0.096	5.252	-0.911	-0.005
52	A	51	SER	0	0.010	0.022	4.432	0.357	0.492	-0.001	-0.029	-0.105	0.000
53	A	52	MET	0	-0.015	-0.012	7.294	0.324	0.324	0.000	0.000	0.000	0.000
54	A	53	THR	0	0.032	0.017	7.783	0.065	0.065	0.000	0.000	0.000	0.000
55	A	54	GLY	0	0.012	-0.008	10.907	0.089	0.089	0.000	0.000	0.000	0.000
56	A	55	PHE	0	-0.018	0.007	12.880	-0.117	-0.117	0.000	0.000	0.000	0.000
57	A	56	LEU	0	-0.015	-0.009	15.495	0.083	0.083	0.000	0.000	0.000	0.000
58	A	57	ILE	0	0.005	0.012	18.560	-0.056	-0.056	0.000	0.000	0.000	0.000
59	A	58	GLY	0	0.047	0.004	21.331	0.047	0.047	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.022	0.009	23.867	-0.030	-0.030	0.000	0.000	0.000	0.000
61	A	60	GLN	0	0.027	0.024	26.216	0.002	0.002	0.000	0.000	0.000	0.000
62	A	61	SER	0	-0.054	-0.023	28.908	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	62	GLN	0	0.020	-0.007	32.278	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	63	SER	0	-0.007	-0.008	34.644	0.001	0.001	0.000	0.000	0.000	0.000
65	A	64	ASP	-1	-0.855	-0.901	35.968	-0.069	-0.069	0.000	0.000	0.000	0.000
66	A	65	PRO	0	0.055	0.024	33.577	0.000	0.000	0.000	0.000	0.000	0.000
67	A	66	GLU	-1	-0.902	-0.928	32.208	-0.080	-0.080	0.000	0.000	0.000	0.000
68	A	67	THR	0	-0.071	-0.050	31.554	0.012	0.012	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.013	0.011	26.493	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	69	TYR	0	-0.034	-0.021	27.987	0.023	0.023	0.000	0.000	0.000	0.000
71	A	70	ILE	0	0.010	0.007	22.687	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	71	HIS	0	-0.024	-0.022	24.947	0.027	0.027	0.000	0.000	0.000	0.000
73	A	72	PHE	0	-0.009	-0.009	21.689	0.017	0.017	0.000	0.000	0.000	0.000
74	A	73	SER	0	-0.010	0.006	19.492	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	74	GLY	0	-0.011	-0.008	18.386	0.023	0.023	0.000	0.000	0.000	0.000
76	A	75	VAL	0	-0.073	-0.037	13.666	-0.028	-0.028	0.000	0.000	0.000	0.000
77	A	76	HIS	0	0.046	0.032	12.657	0.048	0.048	0.000	0.000	0.000	0.000
78	A	77	PRO	0	-0.010	-0.014	14.769	0.061	0.061	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.881	-0.924	12.836	0.476	0.476	0.000	0.000	0.000	0.000
80	A	79	PHE	0	-0.093	-0.046	7.289	0.116	0.116	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.905	0.971	8.657	-1.042	-1.042	0.000	0.000	0.000	0.000
82	A	81	LYS	1	1.002	0.989	14.523	-0.137	-0.137	0.000	0.000	0.000	0.000
83	A	82	MET	0	-0.023	-0.020	16.692	-0.033	-0.033	0.000	0.000	0.000	0.000
84	A	83	GLN	0	0.048	0.030	9.200	-0.078	-0.078	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.061	0.032	9.180	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	85	GLY	0	0.047	0.019	12.841	-0.084	-0.084	0.000	0.000	0.000	0.000
87	A	86	LYS	1	0.837	0.898	15.587	-0.287	-0.287	0.000	0.000	0.000	0.000
88	A	87	GLN	0	0.010	0.009	8.368	-0.028	-0.028	0.000	0.000	0.000	0.000
89	A	88	LEU	0	0.006	0.013	13.804	-0.068	-0.068	0.000	0.000	0.000	0.000
90	A	89	TYR	0	-0.022	-0.057	15.734	-0.047	-0.047	0.000	0.000	0.000	0.000
91	A	90	ASP	-1	-0.827	-0.904	15.963	0.114	0.114	0.000	0.000	0.000	0.000
92	A	91	VAL	0	0.011	0.012	13.043	-0.019	-0.019	0.000	0.000	0.000	0.000
93	A	92	PHE	0	-0.026	0.009	16.409	-0.036	-0.036	0.000	0.000	0.000	0.000
94	A	93	ILE	0	-0.003	-0.019	19.564	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	94	GLU	-1	-0.927	-0.972	18.387	-0.074	-0.074	0.000	0.000	0.000	0.000
96	A	95	THR	0	-0.030	-0.015	18.495	-0.031	-0.031	0.000	0.000	0.000	0.000
97	A	96	VAL	0	-0.009	-0.027	20.963	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	97	LYS	1	0.903	0.962	23.532	0.078	0.078	0.000	0.000	0.000	0.000
99	A	98	GLN	0	-0.047	-0.015	20.084	-0.020	-0.020	0.000	0.000	0.000	0.000
100	A	99	ARG	1	0.865	0.928	24.945	0.253	0.253	0.000	0.000	0.000	0.000
101	A	100	GLY	0	0.007	0.010	27.637	0.006	0.006	0.000	0.000	0.000	0.000
102	A	101	CYS	0	-0.089	-0.020	27.585	0.008	0.008	0.000	0.000	0.000	0.000
103	A	102	THR	0	0.017	-0.003	28.799	0.006	0.006	0.000	0.000	0.000	0.000
104	A	103	ARG	1	0.922	0.950	29.916	0.072	0.072	0.000	0.000	0.000	0.000
105	A	104	VAL	0	0.001	0.010	25.164	-0.017	-0.017	0.000	0.000	0.000	0.000
106	A	105	LYS	1	0.961	0.976	28.464	0.069	0.069	0.000	0.000	0.000	0.000
107	A	106	CYS	0	-0.003	0.013	26.593	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	107	VAL	0	0.041	0.024	29.609	0.011	0.011	0.000	0.000	0.000	0.000
109	A	108	THR	0	-0.003	0.002	29.573	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	109	SER	0	0.029	0.029	31.437	0.000	0.000	0.000	0.000	0.000	0.000
111	A	110	PRO	0	0.046	0.008	33.364	0.010	0.010	0.000	0.000	0.000	0.000
112	A	111	VAL	0	-0.009	-0.004	34.120	0.009	0.009	0.000	0.000	0.000	0.000
113	A	112	ASN	0	-0.008	0.010	27.829	0.023	0.023	0.000	0.000	0.000	0.000
114	A	113	LYS	1	1.024	0.988	30.378	-0.081	-0.081	0.000	0.000	0.000	0.000
115	A	114	VAL	0	0.031	0.029	24.423	0.008	0.008	0.000	0.000	0.000	0.000
116	A	115	SER	0	0.001	-0.004	25.927	0.012	0.012	0.000	0.000	0.000	0.000
117	A	116	ILE	0	0.054	0.031	26.992	0.002	0.002	0.000	0.000	0.000	0.000
118	A	117	ALA	0	-0.011	0.008	26.934	0.002	0.002	0.000	0.000	0.000	0.000
119	A	118	TYR	0	-0.038	-0.022	19.375	0.031	0.031	0.000	0.000	0.000	0.000
120	A	119	HIS	0	0.059	0.035	24.243	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	120	THR	0	0.027	0.015	26.224	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	121	LYS	1	0.888	0.953	22.111	-0.254	-0.254	0.000	0.000	0.000	0.000
123	A	122	LEU	0	-0.039	-0.019	19.979	0.015	0.015	0.000	0.000	0.000	0.000
124	A	123	GLY	0	-0.019	-0.018	23.844	-0.013	-0.013	0.000	0.000	0.000	0.000
125	A	124	PHE	0	-0.067	-0.026	24.304	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	125	ASP	-1	-0.882	-0.919	29.039	0.052	0.052	0.000	0.000	0.000	0.000
127	A	126	ILE	0	-0.058	-0.061	32.499	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	127	GLU	-1	-0.930	-0.968	34.977	-0.025	-0.025	0.000	0.000	0.000	0.000
129	A	128	LYS	1	0.927	0.952	37.762	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	129	GLY	0	0.043	0.023	41.319	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	130	THR	0	-0.036	-0.032	42.653	0.002	0.002	0.000	0.000	0.000	0.000
132	A	131	LYS	1	0.868	0.937	43.428	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	132	THR	0	-0.008	-0.001	42.421	0.001	0.001	0.000	0.000	0.000	0.000
134	A	133	VAL	0	-0.007	-0.002	39.830	0.000	0.000	0.000	0.000	0.000	0.000
135	A	134	ASN	0	-0.035	-0.025	38.203	0.004	0.004	0.000	0.000	0.000	0.000
136	A	135	GLY	0	0.032	0.007	39.439	0.006	0.006	0.000	0.000	0.000	0.000
137	A	136	ILE	0	-0.003	0.021	35.712	0.002	0.002	0.000	0.000	0.000	0.000
138	A	137	SER	0	-0.015	0.012	38.852	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	138	VAL	0	0.017	-0.016	38.289	0.000	0.000	0.000	0.000	0.000	0.000
140	A	139	PHE	0	0.039	0.026	39.292	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	140	ALA	0	-0.035	-0.039	40.977	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	141	ASN	0	-0.010	-0.015	42.404	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	142	TYR	0	0.012	0.019	35.913	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	143	ASP	-1	-0.816	-0.899	35.214	-0.063	-0.063	0.000	0.000	0.000	0.000
145	A	144	GLY	0	0.009	0.002	38.587	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	145	PRO	0	-0.032	-0.027	41.810	0.006	0.006	0.000	0.000	0.000	0.000
147	A	146	GLY	0	0.014	-0.002	43.026	0.000	0.000	0.000	0.000	0.000	0.000
148	A	147	GLN	0	-0.048	0.000	37.416	0.004	0.004	0.000	0.000	0.000	0.000
149	A	148	ASP	-1	-0.796	-0.884	39.469	-0.005	-0.005	0.000	0.000	0.000	0.000
150	A	149	ARG	1	0.799	0.880	34.279	0.032	0.032	0.000	0.000	0.000	0.000
151	A	150	VAL	0	0.000	0.008	33.698	0.002	0.002	0.000	0.000	0.000	0.000
152	A	151	LEU	0	0.029	0.009	33.761	-0.004	-0.004	0.000	0.000	0.000	0.000
153	A	152	PHE	0	-0.003	-0.004	29.711	0.012	0.012	0.000	0.000	0.000	0.000
154	A	153	VAL	0	0.027	0.001	31.228	-0.014	-0.014	0.000	0.000	0.000	0.000
155	A	154	LYS	1	0.924	0.983	24.329	-0.042	-0.042	0.000	0.000	0.000	0.000
156	A	155	ASN	0	0.015	0.016	29.583	-0.022	-0.022	0.000	0.000	0.000	0.000
157	A	156	ILE	0	-0.013	-0.003	25.465	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)