FMO DATABASE

FMODB ID: 6N9YZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1587951.524974
FMO2-HF: Nuclear repulsion	1524683.267839
FMO2-HF: Total energy	-63268.257136
FMO2-MP2: Total energy	-63452.490628

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.
-41.161	-36.333	18.876	-8.725	-14.98	-0.04

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 : -0.015

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	-0.841	-0.886	1.832	-38.629	-36.080	9.902	-6.176	-6.275	-0.053
4	A	3	ILE	0	0.012	-0.011	4.709	1.557	1.606	-0.001	-0.011	-0.037	0.000
5	A	4	ARG	1	0.818	0.891	8.035	3.254	3.254	0.000	0.000	0.000	0.000
6	A	5	THR	0	0.041	0.024	9.758	0.160	0.160	0.000	0.000	0.000	0.000
7	A	6	ILE	0	-0.062	-0.021	12.659	-0.212	-0.212	0.000	0.000	0.000	0.000
8	A	7	THR	0	0.002	-0.017	14.120	0.139	0.139	0.000	0.000	0.000	0.000
9	A	8	SER	0	0.021	-0.034	16.681	0.018	0.018	0.000	0.000	0.000	0.000
10	A	9	SER	0	-0.021	-0.023	16.130	0.086	0.086	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.771	-0.829	13.191	-2.137	-2.137	0.000	0.000	0.000	0.000
12	A	11	TYR	0	-0.084	-0.046	16.209	0.066	0.066	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.776	-0.887	19.177	-0.785	-0.785	0.000	0.000	0.000	0.000
14	A	13	MET	0	0.021	0.027	11.522	-0.019	-0.019	0.000	0.000	0.000	0.000
15	A	14	VAL	0	0.016	0.005	15.472	0.052	0.052	0.000	0.000	0.000	0.000
16	A	15	THR	0	-0.060	-0.056	17.567	0.123	0.123	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.018	-0.014	18.607	0.103	0.103	0.000	0.000	0.000	0.000
18	A	17	VAL	0	0.082	0.043	15.887	0.075	0.075	0.000	0.000	0.000	0.000
19	A	18	LEU	0	-0.112	-0.042	19.317	0.070	0.070	0.000	0.000	0.000	0.000
20	A	19	ASN	0	-0.060	-0.035	22.487	0.057	0.057	0.000	0.000	0.000	0.000
21	A	20	GLU	-1	-0.941	-0.972	18.699	-0.450	-0.450	0.000	0.000	0.000	0.000
22	A	21	TRP	0	0.002	-0.002	14.023	0.031	0.031	0.000	0.000	0.000	0.000
23	A	22	TRP	0	-0.007	0.002	20.337	0.030	0.030	0.000	0.000	0.000	0.000
24	A	23	GLY	0	0.001	-0.005	23.182	0.024	0.024	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.038	0.030	24.953	0.027	0.027	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.844	0.926	26.742	0.165	0.165	0.000	0.000	0.000	0.000
27	A	26	GLN	0	0.032	0.012	28.077	-0.034	-0.034	0.000	0.000	0.000	0.000
28	A	27	LEU	0	0.007	0.015	24.992	0.020	0.020	0.000	0.000	0.000	0.000
29	A	28	LYS	1	0.864	0.928	29.265	0.303	0.303	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.875	-0.931	28.704	-0.350	-0.350	0.000	0.000	0.000	0.000
31	A	30	LYS	1	0.974	0.989	24.973	0.484	0.484	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.019	0.004	21.589	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	32	PRO	0	0.016	0.016	25.092	-0.025	-0.025	0.000	0.000	0.000	0.000
34	A	33	ARG	1	0.870	0.919	22.261	0.744	0.744	0.000	0.000	0.000	0.000
35	A	34	LEU	0	0.015	0.009	24.337	-0.047	-0.047	0.000	0.000	0.000	0.000
36	A	35	PHE	0	0.027	0.000	22.728	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	36	PHE	0	0.001	-0.009	17.755	-0.028	-0.028	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.825	-0.863	20.691	-0.870	-0.870	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.022	-0.010	23.349	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	39	PHE	0	-0.013	0.001	22.673	0.037	0.037	0.000	0.000	0.000	0.000
41	A	40	GLN	0	-0.003	-0.011	18.119	-0.084	-0.084	0.000	0.000	0.000	0.000
42	A	41	ASP	-1	-0.841	-0.914	17.374	-1.066	-1.066	0.000	0.000	0.000	0.000
43	A	42	THR	0	-0.041	-0.022	18.283	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	43	SER	0	-0.037	-0.024	17.501	0.112	0.112	0.000	0.000	0.000	0.000
45	A	44	PHE	0	-0.011	-0.012	12.507	-0.109	-0.109	0.000	0.000	0.000	0.000
46	A	45	ILE	0	0.002	0.003	9.697	0.318	0.318	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.004	-0.010	8.340	-0.385	-0.385	0.000	0.000	0.000	0.000
48	A	47	SER	0	-0.095	-0.068	4.525	0.931	1.045	-0.001	-0.009	-0.104	0.000
49	A	48	GLU	-1	-0.823	-0.934	3.653	-2.337	-1.536	0.004	-0.191	-0.614	0.000
50	A	49	HIS	0	-0.022	-0.017	2.097	-4.318	-2.073	8.901	-4.078	-7.068	0.014
51	A	50	ASN	0	-0.023	-0.005	2.835	-0.806	-1.876	0.072	1.758	-0.761	-0.001
52	A	51	SER	0	0.025	0.031	4.586	0.831	0.971	-0.001	-0.018	-0.121	0.000
53	A	52	MET	0	-0.009	-0.008	7.498	-0.166	-0.166	0.000	0.000	0.000	0.000
54	A	53	THR	0	0.031	0.014	7.787	0.322	0.322	0.000	0.000	0.000	0.000
55	A	54	GLY	0	0.019	-0.006	10.924	0.374	0.374	0.000	0.000	0.000	0.000
56	A	55	PHE	0	-0.024	0.003	12.378	-0.300	-0.300	0.000	0.000	0.000	0.000
57	A	56	LEU	0	-0.020	-0.012	14.800	0.200	0.200	0.000	0.000	0.000	0.000
58	A	57	ILE	0	0.006	0.010	17.406	-0.098	-0.098	0.000	0.000	0.000	0.000
59	A	58	GLY	0	0.050	0.007	20.152	0.093	0.093	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.025	0.006	22.276	-0.044	-0.044	0.000	0.000	0.000	0.000
61	A	60	GLN	0	0.028	0.022	24.489	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	61	SER	0	-0.042	-0.020	26.979	0.007	0.007	0.000	0.000	0.000	0.000
63	A	62	GLN	0	0.021	-0.006	30.556	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	63	SER	0	-0.005	-0.004	32.746	0.007	0.007	0.000	0.000	0.000	0.000
65	A	64	ASP	-1	-0.823	-0.886	34.277	-0.299	-0.299	0.000	0.000	0.000	0.000
66	A	65	PRO	0	0.059	0.026	31.838	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	66	GLU	-1	-0.799	-0.871	30.744	-0.318	-0.318	0.000	0.000	0.000	0.000
68	A	67	THR	0	-0.088	-0.067	30.437	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.016	0.010	25.066	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	69	TYR	0	-0.025	-0.016	26.279	0.049	0.049	0.000	0.000	0.000	0.000
71	A	70	ILE	0	0.003	0.006	21.707	-0.051	-0.051	0.000	0.000	0.000	0.000
72	A	71	HIS	0	-0.019	-0.020	23.701	0.061	0.061	0.000	0.000	0.000	0.000
73	A	72	PHE	0	-0.020	-0.017	21.198	0.049	0.049	0.000	0.000	0.000	0.000
74	A	73	SER	0	-0.001	0.011	18.665	-0.076	-0.076	0.000	0.000	0.000	0.000
75	A	74	GLY	0	-0.015	-0.010	17.896	0.114	0.114	0.000	0.000	0.000	0.000
76	A	75	VAL	0	-0.077	-0.037	13.709	-0.139	-0.139	0.000	0.000	0.000	0.000
77	A	76	HIS	0	0.049	0.029	12.641	0.126	0.126	0.000	0.000	0.000	0.000
78	A	77	PRO	0	-0.006	-0.008	14.780	0.062	0.062	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.891	-0.928	12.857	0.131	0.131	0.000	0.000	0.000	0.000
80	A	79	PHE	0	-0.100	-0.045	7.332	0.093	0.093	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.899	0.944	8.597	-0.228	-0.228	0.000	0.000	0.000	0.000
82	A	81	LYS	1	0.976	0.986	14.531	0.322	0.322	0.000	0.000	0.000	0.000
83	A	82	MET	0	-0.034	-0.023	16.703	-0.092	-0.092	0.000	0.000	0.000	0.000
84	A	83	GLN	0	0.036	0.026	8.667	0.200	0.200	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.070	0.039	9.280	-0.047	-0.047	0.000	0.000	0.000	0.000
86	A	85	GLY	0	0.051	0.021	12.855	-0.161	-0.161	0.000	0.000	0.000	0.000
87	A	86	LYS	1	0.789	0.864	15.740	0.378	0.378	0.000	0.000	0.000	0.000
88	A	87	GLN	0	0.042	0.032	8.340	0.128	0.128	0.000	0.000	0.000	0.000
89	A	88	LEU	0	0.002	0.013	13.047	-0.086	-0.086	0.000	0.000	0.000	0.000
90	A	89	TYR	0	-0.015	-0.046	15.018	0.018	0.018	0.000	0.000	0.000	0.000
91	A	90	ASP	-1	-0.807	-0.882	15.526	-0.520	-0.520	0.000	0.000	0.000	0.000
92	A	91	VAL	0	0.020	0.014	12.003	0.042	0.042	0.000	0.000	0.000	0.000
93	A	92	PHE	0	-0.020	0.010	15.445	0.039	0.039	0.000	0.000	0.000	0.000
94	A	93	ILE	0	-0.007	-0.017	18.442	0.068	0.068	0.000	0.000	0.000	0.000
95	A	94	GLU	-1	-0.868	-0.954	17.536	-0.526	-0.526	0.000	0.000	0.000	0.000
96	A	95	THR	0	-0.038	-0.012	17.205	0.005	0.005	0.000	0.000	0.000	0.000
97	A	96	VAL	0	-0.004	-0.024	19.631	0.056	0.056	0.000	0.000	0.000	0.000
98	A	97	LYS	1	0.885	0.965	22.503	0.518	0.518	0.000	0.000	0.000	0.000
99	A	98	GLN	0	-0.071	-0.033	18.524	0.040	0.040	0.000	0.000	0.000	0.000
100	A	99	ARG	1	0.815	0.899	22.509	0.735	0.735	0.000	0.000	0.000	0.000
101	A	100	GLY	0	0.010	0.015	26.178	0.031	0.031	0.000	0.000	0.000	0.000
102	A	101	CYS	0	-0.104	-0.034	26.442	0.020	0.020	0.000	0.000	0.000	0.000
103	A	102	THR	0	-0.004	-0.017	27.766	-0.009	-0.009	0.000	0.000	0.000	0.000
104	A	103	ARG	1	0.827	0.904	29.146	0.329	0.329	0.000	0.000	0.000	0.000
105	A	104	VAL	0	-0.005	0.006	24.309	-0.033	-0.033	0.000	0.000	0.000	0.000
106	A	105	LYS	1	0.850	0.900	27.591	0.325	0.325	0.000	0.000	0.000	0.000
107	A	106	CYS	0	-0.012	0.007	26.149	-0.032	-0.032	0.000	0.000	0.000	0.000
108	A	107	VAL	0	0.048	0.027	28.588	0.039	0.039	0.000	0.000	0.000	0.000
109	A	108	THR	0	-0.006	0.000	29.281	-0.026	-0.026	0.000	0.000	0.000	0.000
110	A	109	SER	0	0.031	0.028	31.279	0.021	0.021	0.000	0.000	0.000	0.000
111	A	110	PRO	0	0.058	0.012	33.378	0.002	0.002	0.000	0.000	0.000	0.000
112	A	111	VAL	0	-0.024	-0.012	34.397	0.012	0.012	0.000	0.000	0.000	0.000
113	A	112	ASN	0	-0.009	0.012	27.692	0.023	0.023	0.000	0.000	0.000	0.000
114	A	113	LYS	1	1.023	0.989	30.390	0.095	0.095	0.000	0.000	0.000	0.000
115	A	114	VAL	0	0.034	0.029	24.428	0.001	0.001	0.000	0.000	0.000	0.000
116	A	115	SER	0	0.005	-0.003	25.941	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	116	ILE	0	0.041	0.022	27.005	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	117	ALA	0	-0.008	0.016	26.997	0.002	0.002	0.000	0.000	0.000	0.000
119	A	118	TYR	0	-0.034	-0.023	19.312	0.019	0.019	0.000	0.000	0.000	0.000
120	A	119	HIS	0	0.066	0.036	24.241	-0.053	-0.053	0.000	0.000	0.000	0.000
121	A	120	THR	0	0.022	0.007	26.224	0.000	0.000	0.000	0.000	0.000	0.000
122	A	121	LYS	1	0.896	0.957	22.470	0.076	0.076	0.000	0.000	0.000	0.000
123	A	122	LEU	0	-0.028	-0.013	19.883	0.013	0.013	0.000	0.000	0.000	0.000
124	A	123	GLY	0	-0.004	-0.007	23.847	-0.027	-0.027	0.000	0.000	0.000	0.000
125	A	124	PHE	0	-0.059	-0.023	24.169	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	125	ASP	-1	-0.880	-0.916	29.046	-0.176	-0.176	0.000	0.000	0.000	0.000
127	A	126	ILE	0	-0.050	-0.055	32.506	-0.020	-0.020	0.000	0.000	0.000	0.000
128	A	127	GLU	-1	-0.817	-0.895	34.982	-0.247	-0.247	0.000	0.000	0.000	0.000
129	A	128	LYS	1	0.933	0.958	37.583	0.138	0.138	0.000	0.000	0.000	0.000
130	A	129	GLY	0	0.043	0.031	41.253	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	130	THR	0	-0.053	-0.045	42.329	0.007	0.007	0.000	0.000	0.000	0.000
132	A	131	LYS	1	0.851	0.918	43.494	0.149	0.149	0.000	0.000	0.000	0.000
133	A	132	THR	0	-0.006	-0.002	42.470	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	133	VAL	0	0.003	0.005	39.961	0.007	0.007	0.000	0.000	0.000	0.000
135	A	134	ASN	0	-0.036	-0.026	38.438	0.004	0.004	0.000	0.000	0.000	0.000
136	A	135	GLY	0	0.035	0.009	39.449	0.002	0.002	0.000	0.000	0.000	0.000
137	A	136	ILE	0	-0.009	0.016	35.687	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	137	SER	0	-0.014	0.003	38.864	0.000	0.000	0.000	0.000	0.000	0.000
139	A	138	VAL	0	0.016	-0.014	38.313	-0.012	-0.012	0.000	0.000	0.000	0.000
140	A	139	PHE	0	0.047	0.026	38.535	0.010	0.010	0.000	0.000	0.000	0.000
141	A	140	ALA	0	-0.027	-0.034	40.404	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	141	ASN	0	-0.019	-0.019	41.754	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	142	TYR	0	0.016	0.023	34.847	0.004	0.004	0.000	0.000	0.000	0.000
144	A	143	ASP	-1	-0.811	-0.887	34.329	-0.306	-0.306	0.000	0.000	0.000	0.000
145	A	144	GLY	0	0.015	0.004	37.848	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	145	PRO	0	-0.018	-0.020	41.182	0.005	0.005	0.000	0.000	0.000	0.000
147	A	146	GLY	0	0.006	-0.003	42.645	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	147	GLN	0	-0.036	-0.003	37.009	-0.012	-0.012	0.000	0.000	0.000	0.000
149	A	148	ASP	-1	-0.782	-0.864	38.829	-0.168	-0.168	0.000	0.000	0.000	0.000
150	A	149	ARG	1	0.785	0.871	33.626	0.253	0.253	0.000	0.000	0.000	0.000
151	A	150	VAL	0	-0.018	-0.002	33.696	0.015	0.015	0.000	0.000	0.000	0.000
152	A	151	LEU	0	0.036	0.014	33.387	-0.019	-0.019	0.000	0.000	0.000	0.000
153	A	152	PHE	0	-0.013	-0.012	29.290	0.025	0.025	0.000	0.000	0.000	0.000
154	A	153	VAL	0	0.021	-0.003	30.681	-0.023	-0.023	0.000	0.000	0.000	0.000
155	A	154	LYS	1	0.885	0.959	24.439	0.336	0.336	0.000	0.000	0.000	0.000
156	A	155	ASN	0	0.021	0.018	28.934	-0.034	-0.034	0.000	0.000	0.000	0.000
157	A	156	ILE	0	-0.022	-0.003	24.705	0.017	0.017	0.000	0.000	0.000	0.000

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