FMO DATABASE

FMODB ID: Z63VN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1591045.317107
FMO2-HF: Nuclear repulsion	1527776.776236
FMO2-HF: Total energy	-63268.540871
FMO2-MP2: Total energy	-63452.780589

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.
-44.542	-39.939	21.223	-10.044	-15.781	-0.068

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 : -0.017 / q_NPA : -0.017

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	-0.822	-0.868	1.754	-40.229	-40.158	14.222	-7.082	-7.210	-0.070
4	A	3	ILE	0	0.015	-0.014	4.193	1.963	2.094	0.002	-0.036	-0.096	0.000
5	A	4	ARG	1	0.800	0.877	7.644	3.552	3.552	0.000	0.000	0.000	0.000
6	A	5	THR	0	0.046	0.026	9.555	0.136	0.136	0.000	0.000	0.000	0.000
7	A	6	ILE	0	-0.059	-0.013	12.104	-0.292	-0.292	0.000	0.000	0.000	0.000
8	A	7	THR	0	0.004	-0.019	13.738	0.151	0.151	0.000	0.000	0.000	0.000
9	A	8	SER	0	0.027	-0.026	16.299	0.022	0.022	0.000	0.000	0.000	0.000
10	A	9	SER	0	-0.016	-0.024	15.557	0.093	0.093	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.759	-0.819	12.475	-2.394	-2.394	0.000	0.000	0.000	0.000
12	A	11	TYR	0	-0.060	-0.030	15.461	0.062	0.062	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.774	-0.869	19.024	-0.836	-0.836	0.000	0.000	0.000	0.000
14	A	13	MET	0	0.002	0.024	11.621	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	14	VAL	0	0.011	-0.010	15.037	0.061	0.061	0.000	0.000	0.000	0.000
16	A	15	THR	0	-0.057	-0.065	17.152	0.123	0.123	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.034	-0.010	18.492	0.119	0.119	0.000	0.000	0.000	0.000
18	A	17	VAL	0	0.106	0.050	15.589	0.084	0.084	0.000	0.000	0.000	0.000
19	A	18	LEU	0	-0.088	-0.039	19.019	0.082	0.082	0.000	0.000	0.000	0.000
20	A	19	ASN	0	-0.102	-0.058	22.176	0.090	0.090	0.000	0.000	0.000	0.000
21	A	20	GLU	-1	-0.924	-0.955	18.885	-0.590	-0.590	0.000	0.000	0.000	0.000
22	A	21	TRP	0	0.023	0.003	13.685	0.061	0.061	0.000	0.000	0.000	0.000
23	A	22	TRP	0	-0.012	0.007	19.478	0.044	0.044	0.000	0.000	0.000	0.000
24	A	23	GLY	0	0.015	0.001	23.550	0.036	0.036	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.022	0.019	24.783	0.034	0.034	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.834	0.920	26.565	0.242	0.242	0.000	0.000	0.000	0.000
27	A	26	GLN	0	0.032	0.007	27.710	-0.037	-0.037	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.013	0.010	24.271	0.025	0.025	0.000	0.000	0.000	0.000
29	A	28	LYS	1	0.854	0.909	28.569	0.349	0.349	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.859	-0.907	27.954	-0.386	-0.386	0.000	0.000	0.000	0.000
31	A	30	LYS	1	0.930	0.966	25.439	0.502	0.502	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.049	0.026	20.785	0.004	0.004	0.000	0.000	0.000	0.000
33	A	32	PRO	0	0.031	0.017	24.766	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	33	ARG	1	0.827	0.889	21.749	0.796	0.796	0.000	0.000	0.000	0.000
35	A	34	LEU	0	0.023	0.015	23.693	-0.055	-0.055	0.000	0.000	0.000	0.000
36	A	35	PHE	0	0.039	0.004	21.977	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	36	PHE	0	0.007	-0.003	17.145	-0.035	-0.035	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.820	-0.862	20.240	-0.930	-0.930	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.031	-0.010	22.914	0.011	0.011	0.000	0.000	0.000	0.000
40	A	39	PHE	0	-0.001	0.001	22.149	0.045	0.045	0.000	0.000	0.000	0.000
41	A	40	GLN	0	-0.004	-0.008	17.578	-0.093	-0.093	0.000	0.000	0.000	0.000
42	A	41	ASP	-1	-0.811	-0.891	16.988	-1.065	-1.065	0.000	0.000	0.000	0.000
43	A	42	THR	0	-0.046	-0.041	18.604	0.030	0.030	0.000	0.000	0.000	0.000
44	A	43	SER	0	-0.028	-0.011	17.371	0.106	0.106	0.000	0.000	0.000	0.000
45	A	44	PHE	0	0.001	0.002	12.555	-0.104	-0.104	0.000	0.000	0.000	0.000
46	A	45	ILE	0	-0.006	-0.007	9.343	0.320	0.320	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.004	-0.018	7.705	-0.283	-0.283	0.000	0.000	0.000	0.000
48	A	47	SER	0	-0.065	-0.059	3.748	0.804	1.000	0.000	-0.039	-0.157	0.000
49	A	48	GLU	-1	-0.763	-0.905	4.610	-1.651	-1.097	-0.001	-0.094	-0.460	0.000
50	A	49	HIS	0	-0.006	-0.004	2.405	-4.736	-1.449	6.557	-3.785	-6.060	0.007
51	A	50	ASN	0	-0.019	-0.007	2.799	-3.989	-3.813	0.441	1.024	-1.641	-0.005
52	A	51	SER	0	-0.026	0.005	4.061	0.891	1.079	0.002	-0.032	-0.157	0.000
53	A	52	MET	0	0.012	-0.002	7.310	-0.216	-0.216	0.000	0.000	0.000	0.000
54	A	53	THR	0	0.035	0.020	8.437	0.366	0.366	0.000	0.000	0.000	0.000
55	A	54	GLY	0	0.016	-0.009	10.915	0.431	0.431	0.000	0.000	0.000	0.000
56	A	55	PHE	0	-0.022	-0.002	11.867	-0.334	-0.334	0.000	0.000	0.000	0.000
57	A	56	LEU	0	-0.027	-0.010	14.345	0.213	0.213	0.000	0.000	0.000	0.000
58	A	57	ILE	0	0.001	0.004	17.071	-0.097	-0.097	0.000	0.000	0.000	0.000
59	A	58	GLY	0	0.041	0.002	19.902	0.096	0.096	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.009	0.019	21.919	-0.044	-0.044	0.000	0.000	0.000	0.000
61	A	60	GLN	0	0.028	0.001	24.286	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	61	SER	0	-0.029	-0.012	26.933	0.007	0.007	0.000	0.000	0.000	0.000
63	A	62	GLN	0	0.016	-0.009	30.542	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	63	SER	0	-0.026	-0.008	32.553	0.011	0.011	0.000	0.000	0.000	0.000
65	A	64	ASP	-1	-0.791	-0.863	33.875	-0.317	-0.317	0.000	0.000	0.000	0.000
66	A	65	PRO	0	0.056	0.031	31.258	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	66	GLU	-1	-0.782	-0.854	30.111	-0.336	-0.336	0.000	0.000	0.000	0.000
68	A	67	THR	0	-0.099	-0.072	29.825	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.022	0.009	24.622	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	69	TYR	0	-0.030	-0.023	25.688	0.053	0.053	0.000	0.000	0.000	0.000
71	A	70	ILE	0	-0.004	0.005	21.379	-0.055	-0.055	0.000	0.000	0.000	0.000
72	A	71	HIS	0	-0.018	-0.014	23.610	0.060	0.060	0.000	0.000	0.000	0.000
73	A	72	PHE	0	-0.018	-0.016	20.537	0.048	0.048	0.000	0.000	0.000	0.000
74	A	73	SER	0	-0.024	-0.006	18.482	-0.072	-0.072	0.000	0.000	0.000	0.000
75	A	74	GLY	0	-0.013	-0.009	17.538	0.120	0.120	0.000	0.000	0.000	0.000
76	A	75	VAL	0	-0.065	-0.033	14.413	-0.147	-0.147	0.000	0.000	0.000	0.000
77	A	76	HIS	0	0.055	0.035	12.931	0.144	0.144	0.000	0.000	0.000	0.000
78	A	77	PRO	0	-0.008	-0.009	15.458	0.053	0.053	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.877	-0.920	13.356	-0.076	-0.076	0.000	0.000	0.000	0.000
80	A	79	PHE	0	-0.099	-0.058	8.019	0.067	0.067	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.809	0.896	8.989	0.128	0.128	0.000	0.000	0.000	0.000
82	A	81	LYS	1	0.950	0.980	15.682	0.535	0.535	0.000	0.000	0.000	0.000
83	A	82	MET	0	-0.013	-0.003	17.291	-0.096	-0.096	0.000	0.000	0.000	0.000
84	A	83	GLN	0	0.011	0.018	8.971	0.195	0.195	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.058	0.028	9.928	-0.049	-0.049	0.000	0.000	0.000	0.000
86	A	85	GLY	0	0.037	0.018	13.432	-0.140	-0.140	0.000	0.000	0.000	0.000
87	A	86	LYS	1	0.808	0.874	16.221	0.484	0.484	0.000	0.000	0.000	0.000
88	A	87	GLN	0	0.041	0.020	8.739	0.168	0.168	0.000	0.000	0.000	0.000
89	A	88	LEU	0	-0.009	0.007	12.739	-0.103	-0.103	0.000	0.000	0.000	0.000
90	A	89	TYR	0	0.000	-0.032	14.608	0.028	0.028	0.000	0.000	0.000	0.000
91	A	90	ASP	-1	-0.806	-0.881	15.140	-0.601	-0.601	0.000	0.000	0.000	0.000
92	A	91	VAL	0	0.018	0.012	11.605	0.053	0.053	0.000	0.000	0.000	0.000
93	A	92	PHE	0	-0.022	0.009	15.060	0.052	0.052	0.000	0.000	0.000	0.000
94	A	93	ILE	0	0.002	-0.009	18.108	0.072	0.072	0.000	0.000	0.000	0.000
95	A	94	GLU	-1	-0.830	-0.941	17.642	-0.516	-0.516	0.000	0.000	0.000	0.000
96	A	95	THR	0	-0.058	-0.012	16.732	0.010	0.010	0.000	0.000	0.000	0.000
97	A	96	VAL	0	-0.008	-0.026	19.267	0.058	0.058	0.000	0.000	0.000	0.000
98	A	97	LYS	1	0.872	0.945	22.528	0.519	0.519	0.000	0.000	0.000	0.000
99	A	98	GLN	0	-0.084	-0.046	18.303	0.056	0.056	0.000	0.000	0.000	0.000
100	A	99	ARG	1	0.788	0.890	22.030	0.770	0.770	0.000	0.000	0.000	0.000
101	A	100	GLY	0	0.007	0.012	26.122	0.031	0.031	0.000	0.000	0.000	0.000
102	A	101	CYS	0	-0.112	-0.044	25.832	0.017	0.017	0.000	0.000	0.000	0.000
103	A	102	THR	0	0.006	-0.020	27.052	-0.015	-0.015	0.000	0.000	0.000	0.000
104	A	103	ARG	1	0.783	0.884	28.547	0.343	0.343	0.000	0.000	0.000	0.000
105	A	104	VAL	0	0.001	0.014	24.028	-0.038	-0.038	0.000	0.000	0.000	0.000
106	A	105	LYS	1	0.839	0.898	27.255	0.355	0.355	0.000	0.000	0.000	0.000
107	A	106	CYS	0	0.006	0.016	25.763	-0.034	-0.034	0.000	0.000	0.000	0.000
108	A	107	VAL	0	0.045	0.026	28.225	0.042	0.042	0.000	0.000	0.000	0.000
109	A	108	THR	0	-0.020	-0.012	29.001	-0.030	-0.030	0.000	0.000	0.000	0.000
110	A	109	SER	0	0.051	0.033	31.098	0.027	0.027	0.000	0.000	0.000	0.000
111	A	110	PRO	0	0.045	0.007	33.640	0.000	0.000	0.000	0.000	0.000	0.000
112	A	111	VAL	0	-0.001	0.000	35.103	0.014	0.014	0.000	0.000	0.000	0.000
113	A	112	ASN	0	-0.011	0.012	27.915	0.020	0.020	0.000	0.000	0.000	0.000
114	A	113	LYS	1	0.999	0.969	30.893	0.138	0.138	0.000	0.000	0.000	0.000
115	A	114	VAL	0	0.032	0.031	25.301	0.002	0.002	0.000	0.000	0.000	0.000
116	A	115	SER	0	0.016	0.007	26.434	-0.021	-0.021	0.000	0.000	0.000	0.000
117	A	116	ILE	0	0.031	0.018	27.512	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	117	ALA	0	0.009	0.020	27.942	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	118	TYR	0	-0.021	-0.010	19.706	0.009	0.009	0.000	0.000	0.000	0.000
120	A	119	HIS	0	0.073	0.044	24.608	-0.057	-0.057	0.000	0.000	0.000	0.000
121	A	120	THR	0	0.017	-0.007	26.221	0.006	0.006	0.000	0.000	0.000	0.000
122	A	121	LYS	1	0.896	0.956	23.048	0.156	0.156	0.000	0.000	0.000	0.000
123	A	122	LEU	0	-0.010	0.003	20.152	0.012	0.012	0.000	0.000	0.000	0.000
124	A	123	GLY	0	0.008	0.016	24.051	-0.016	-0.016	0.000	0.000	0.000	0.000
125	A	124	PHE	0	-0.048	-0.032	23.630	-0.015	-0.015	0.000	0.000	0.000	0.000
126	A	125	ASP	-1	-0.885	-0.923	28.708	-0.218	-0.218	0.000	0.000	0.000	0.000
127	A	126	ILE	0	-0.045	-0.050	31.957	-0.022	-0.022	0.000	0.000	0.000	0.000
128	A	127	GLU	-1	-0.817	-0.884	34.591	-0.271	-0.271	0.000	0.000	0.000	0.000
129	A	128	LYS	1	0.899	0.940	37.071	0.162	0.162	0.000	0.000	0.000	0.000
130	A	129	GLY	0	0.066	0.038	40.694	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	130	THR	0	-0.031	-0.032	41.827	0.010	0.010	0.000	0.000	0.000	0.000
132	A	131	LYS	1	0.854	0.922	43.210	0.179	0.179	0.000	0.000	0.000	0.000
133	A	132	THR	0	0.016	0.003	42.569	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	133	VAL	0	-0.001	0.002	40.367	0.007	0.007	0.000	0.000	0.000	0.000
135	A	134	ASN	0	-0.046	-0.025	38.769	0.003	0.003	0.000	0.000	0.000	0.000
136	A	135	GLY	0	0.027	0.018	39.870	0.002	0.002	0.000	0.000	0.000	0.000
137	A	136	ILE	0	-0.004	0.012	35.790	0.000	0.000	0.000	0.000	0.000	0.000
138	A	137	SER	0	-0.010	0.002	39.048	0.002	0.002	0.000	0.000	0.000	0.000
139	A	138	VAL	0	0.010	-0.017	38.181	-0.013	-0.013	0.000	0.000	0.000	0.000
140	A	139	PHE	0	0.025	0.024	38.206	0.013	0.013	0.000	0.000	0.000	0.000
141	A	140	ALA	0	-0.017	-0.031	40.140	-0.007	-0.007	0.000	0.000	0.000	0.000
142	A	141	ASN	0	-0.014	-0.025	41.598	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	142	TYR	0	0.000	0.019	34.377	0.004	0.004	0.000	0.000	0.000	0.000
144	A	143	ASP	-1	-0.761	-0.868	33.695	-0.349	-0.349	0.000	0.000	0.000	0.000
145	A	144	GLY	0	-0.002	-0.002	37.249	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	145	PRO	0	-0.017	-0.011	40.638	0.005	0.005	0.000	0.000	0.000	0.000
147	A	146	GLY	0	0.008	-0.003	42.167	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	147	GLN	0	-0.047	-0.011	36.482	-0.015	-0.015	0.000	0.000	0.000	0.000
149	A	148	ASP	-1	-0.763	-0.858	38.359	-0.199	-0.199	0.000	0.000	0.000	0.000
150	A	149	ARG	1	0.732	0.847	33.294	0.292	0.292	0.000	0.000	0.000	0.000
151	A	150	VAL	0	-0.003	0.006	33.429	0.017	0.017	0.000	0.000	0.000	0.000
152	A	151	LEU	0	0.036	0.016	33.130	-0.022	-0.022	0.000	0.000	0.000	0.000
153	A	152	PHE	0	-0.015	-0.017	29.073	0.025	0.025	0.000	0.000	0.000	0.000
154	A	153	VAL	0	0.008	-0.003	30.384	-0.020	-0.020	0.000	0.000	0.000	0.000
155	A	154	LYS	1	0.858	0.919	24.135	0.375	0.375	0.000	0.000	0.000	0.000
156	A	155	ASN	0	0.032	0.024	28.326	-0.033	-0.033	0.000	0.000	0.000	0.000
157	A	156	ILE	0	-0.032	0.001	24.024	0.010	0.010	0.000	0.000	0.000	0.000

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