FMO DATABASE

FMODB ID: KRN13

Calculation Name: 3MJZ-J-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJZ

Chain ID: J

ChEMBL ID:

UniProt ID: F2Z288

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	132
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1040889.281179
FMO2-HF: Nuclear repulsion	992287.369104
FMO2-HF: Total energy	-48601.912075
FMO2-MP2: Total energy	-48747.916295

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(J:1:PRO )

Summations of interaction energy for fragment #1(J:1:PRO )

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.
-160.971	-152.707	18.212	-11.163	-15.314	-0.091

Interaction energy analysis for fragmet #1(J:1:PRO )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.842 / q_NPA : 0.904

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	J	3	ILE	0	-0.031	-0.018	2.222	2.650	4.072	1.861	-0.943	-2.340	-0.002
4	J	4	ARG	1	0.960	0.985	5.012	29.882	29.917	0.000	-0.006	-0.030	0.000
5	J	5	ILE	0	-0.002	-0.008	8.327	0.174	0.174	0.000	0.000	0.000	0.000
6	J	6	ASP	-1	-0.841	-0.916	10.868	-19.392	-19.392	0.000	0.000	0.000	0.000
7	J	7	LEU	0	-0.001	0.000	14.332	0.375	0.375	0.000	0.000	0.000	0.000
8	J	8	THR	0	0.052	0.016	17.120	0.041	0.041	0.000	0.000	0.000	0.000
9	J	9	SER	0	-0.094	-0.058	20.913	-0.181	-0.181	0.000	0.000	0.000	0.000
10	J	10	ASP	-1	-0.827	-0.883	23.083	-12.272	-12.272	0.000	0.000	0.000	0.000
11	J	11	ARG	1	0.897	0.973	19.094	14.631	14.631	0.000	0.000	0.000	0.000
12	J	12	SER	0	0.030	0.003	22.360	-0.334	-0.334	0.000	0.000	0.000	0.000
13	J	13	ARG	1	0.957	0.950	20.235	13.602	13.602	0.000	0.000	0.000	0.000
14	J	14	GLU	-1	-0.929	-0.967	19.083	-14.396	-14.396	0.000	0.000	0.000	0.000
15	J	15	GLN	0	0.015	-0.002	18.677	-0.704	-0.704	0.000	0.000	0.000	0.000
16	J	16	ARG	1	0.942	0.977	16.015	14.503	14.503	0.000	0.000	0.000	0.000
17	J	17	ARG	1	0.941	0.983	14.369	15.534	15.534	0.000	0.000	0.000	0.000
18	J	18	ALA	0	0.019	0.019	13.774	-1.143	-1.143	0.000	0.000	0.000	0.000
19	J	19	ILE	0	0.011	0.009	12.463	-0.706	-0.706	0.000	0.000	0.000	0.000
20	J	20	ALA	0	-0.014	-0.011	10.098	-1.414	-1.414	0.000	0.000	0.000	0.000
21	J	21	ASP	-1	-0.804	-0.902	9.149	-24.454	-24.454	0.000	0.000	0.000	0.000
22	J	22	ALA	0	0.060	0.047	10.645	-1.034	-1.034	0.000	0.000	0.000	0.000
23	J	23	VAL	0	-0.006	-0.001	6.233	-1.127	-1.127	0.000	0.000	0.000	0.000
24	J	24	HIS	0	-0.075	-0.053	4.934	-5.592	-5.592	0.000	0.000	0.000	0.000
25	J	25	ASP	-1	-0.894	-0.950	6.896	-25.101	-25.101	0.000	0.000	0.000	0.000
26	J	26	ALA	0	-0.005	0.002	9.300	0.108	0.108	0.000	0.000	0.000	0.000
27	J	27	LEU	0	-0.062	-0.042	2.837	-2.055	-1.311	0.134	-0.160	-0.718	-0.001
28	J	28	VAL	0	-0.037	-0.024	5.776	-1.904	-1.904	0.000	0.000	0.000	0.000
29	J	29	GLU	-1	-0.955	-0.952	7.383	-18.695	-18.695	0.000	0.000	0.000	0.000
30	J	30	VAL	0	-0.077	-0.038	8.507	0.906	0.906	0.000	0.000	0.000	0.000
31	J	31	LEU	0	-0.081	-0.061	3.320	0.027	0.370	0.019	-0.073	-0.289	0.000
32	J	32	ALA	0	-0.006	0.018	7.257	0.093	0.093	0.000	0.000	0.000	0.000
33	J	33	ILE	0	-0.055	-0.020	1.777	0.383	-3.692	8.141	-1.613	-2.454	-0.011
34	J	34	PRO	0	0.043	0.014	5.481	3.395	3.395	0.000	0.000	0.000	0.000
35	J	35	ALA	0	0.076	0.034	6.085	-3.740	-3.740	0.000	0.000	0.000	0.000
36	J	36	ARG	1	0.921	0.950	7.929	22.384	22.384	0.000	0.000	0.000	0.000
37	J	37	ASP	-1	-0.881	-0.931	2.941	-81.739	-78.767	0.336	-1.823	-1.485	-0.019
38	J	38	ARG	1	0.815	0.893	2.946	14.702	16.189	0.115	-0.798	-0.805	-0.009
39	J	39	PHE	0	-0.011	-0.007	3.217	7.802	8.423	0.004	-0.151	-0.474	-0.001
40	J	40	GLN	0	0.004	-0.008	5.290	-1.815	-1.815	0.000	0.000	0.000	0.000
41	J	41	ILE	0	-0.019	0.000	7.748	3.051	3.051	0.000	0.000	0.000	0.000
42	J	42	LEU	0	-0.016	-0.004	10.836	0.122	0.122	0.000	0.000	0.000	0.000
43	J	43	THR	0	-0.017	-0.007	13.242	1.075	1.075	0.000	0.000	0.000	0.000
44	J	44	ALA	0	-0.083	-0.043	15.982	0.027	0.027	0.000	0.000	0.000	0.000
45	J	45	HIS	0	-0.011	-0.006	16.836	1.043	1.043	0.000	0.000	0.000	0.000
46	J	46	ASP	-1	-0.845	-0.923	21.349	-11.321	-11.321	0.000	0.000	0.000	0.000
47	J	47	PRO	0	-0.005	-0.025	23.615	-0.277	-0.277	0.000	0.000	0.000	0.000
48	J	48	SER	0	-0.050	-0.017	24.653	0.047	0.047	0.000	0.000	0.000	0.000
49	J	49	ASP	-1	-0.920	-0.960	22.843	-11.837	-11.837	0.000	0.000	0.000	0.000
50	J	50	ILE	0	-0.084	-0.032	18.521	-0.578	-0.578	0.000	0.000	0.000	0.000
51	J	51	ILE	0	0.019	0.013	21.548	0.457	0.457	0.000	0.000	0.000	0.000
52	J	52	ALA	0	-0.025	-0.012	19.510	-0.457	-0.457	0.000	0.000	0.000	0.000
53	J	53	GLU	-1	-0.926	-0.963	21.404	-10.595	-10.595	0.000	0.000	0.000	0.000
54	J	54	ASP	-1	-0.781	-0.893	22.538	-11.409	-11.409	0.000	0.000	0.000	0.000
55	J	55	ALA	0	-0.044	-0.021	22.316	-0.207	-0.207	0.000	0.000	0.000	0.000
56	J	56	GLY	0	-0.011	0.000	24.443	0.170	0.170	0.000	0.000	0.000	0.000
57	J	57	LEU	0	-0.085	-0.036	22.665	0.238	0.238	0.000	0.000	0.000	0.000
58	J	58	GLY	0	-0.023	0.007	26.830	0.287	0.287	0.000	0.000	0.000	0.000
59	J	59	PHE	0	-0.102	-0.064	21.686	0.062	0.062	0.000	0.000	0.000	0.000
60	J	60	GLN	0	0.001	0.000	27.288	0.014	0.014	0.000	0.000	0.000	0.000
61	J	61	ARG	1	0.826	0.896	18.887	13.768	13.768	0.000	0.000	0.000	0.000
62	J	62	SER	0	-0.016	-0.014	24.136	0.685	0.685	0.000	0.000	0.000	0.000
63	J	63	PRO	0	-0.005	-0.020	24.047	-0.369	-0.369	0.000	0.000	0.000	0.000
64	J	64	SER	0	-0.026	-0.014	22.248	-0.200	-0.200	0.000	0.000	0.000	0.000
65	J	65	VAL	0	0.011	0.017	17.807	-0.463	-0.463	0.000	0.000	0.000	0.000
66	J	66	VAL	0	-0.022	-0.021	13.455	-0.384	-0.384	0.000	0.000	0.000	0.000
67	J	67	ILE	0	-0.006	0.002	12.187	-0.248	-0.248	0.000	0.000	0.000	0.000
68	J	68	ILE	0	-0.017	-0.002	7.341	-1.446	-1.446	0.000	0.000	0.000	0.000
69	J	69	HIS	0	0.004	-0.022	8.036	1.077	1.077	0.000	0.000	0.000	0.000
70	J	70	VAL	0	-0.006	-0.006	2.526	-4.715	-4.257	0.432	-0.230	-0.659	0.000
71	J	71	PHE	0	0.018	0.012	3.707	4.312	4.695	0.003	-0.131	-0.256	0.000
72	J	72	THR	0	-0.033	-0.028	2.194	-29.707	-27.491	6.780	-4.476	-4.520	-0.039
73	J	73	GLN	0	0.041	0.020	3.551	13.243	13.390	0.031	0.026	-0.204	-0.001
74	J	74	ALA	0	0.033	0.013	6.453	-0.260	-0.260	0.000	0.000	0.000	0.000
75	J	75	GLY	0	0.011	0.004	9.337	-0.076	-0.076	0.000	0.000	0.000	0.000
76	J	76	ARG	1	0.895	0.958	4.715	41.748	41.813	0.000	-0.001	-0.063	0.000
77	J	77	THR	0	0.030	0.018	10.057	0.934	0.934	0.000	0.000	0.000	0.000
78	J	78	ILE	0	0.052	0.017	12.412	-1.359	-1.359	0.000	0.000	0.000	0.000
79	J	79	GLU	-1	-0.835	-0.933	14.282	-16.740	-16.740	0.000	0.000	0.000	0.000
80	J	80	THR	0	-0.062	-0.044	9.214	-0.234	-0.234	0.000	0.000	0.000	0.000
81	J	81	LYS	1	0.888	0.946	8.884	23.721	23.721	0.000	0.000	0.000	0.000
82	J	82	GLN	0	0.023	0.015	10.879	-0.074	-0.074	0.000	0.000	0.000	0.000
83	J	83	ARG	1	0.978	0.989	11.997	20.504	20.504	0.000	0.000	0.000	0.000
84	J	84	VAL	0	0.010	0.025	6.894	-0.270	-0.270	0.000	0.000	0.000	0.000
85	J	85	PHE	0	0.025	0.001	9.655	0.063	0.063	0.000	0.000	0.000	0.000
86	J	86	ALA	0	-0.009	0.013	12.195	0.706	0.706	0.000	0.000	0.000	0.000
87	J	87	ALA	0	0.086	0.039	10.864	0.531	0.531	0.000	0.000	0.000	0.000
88	J	88	ILE	0	-0.060	-0.032	7.383	-0.033	-0.033	0.000	0.000	0.000	0.000
89	J	89	THR	0	-0.028	-0.041	11.493	0.949	0.949	0.000	0.000	0.000	0.000
90	J	90	GLU	-1	-0.950	-0.970	15.089	-15.747	-15.747	0.000	0.000	0.000	0.000
91	J	91	SER	0	0.023	0.011	13.373	0.871	0.871	0.000	0.000	0.000	0.000
92	J	92	LEU	0	-0.053	-0.024	12.691	0.430	0.430	0.000	0.000	0.000	0.000
93	J	93	ALA	0	0.032	0.029	16.311	0.781	0.781	0.000	0.000	0.000	0.000
94	J	94	PRO	0	-0.054	-0.026	18.549	0.699	0.699	0.000	0.000	0.000	0.000
95	J	95	ILE	0	-0.039	-0.006	15.902	0.462	0.462	0.000	0.000	0.000	0.000
96	J	96	GLY	0	-0.003	-0.004	19.906	0.389	0.389	0.000	0.000	0.000	0.000
97	J	97	VAL	0	-0.070	-0.034	17.023	0.266	0.266	0.000	0.000	0.000	0.000
98	J	98	ALA	0	0.060	0.039	19.880	-0.137	-0.137	0.000	0.000	0.000	0.000
99	J	99	GLY	0	0.037	-0.005	19.260	-0.499	-0.499	0.000	0.000	0.000	0.000
100	J	100	SER	0	0.010	0.004	19.704	-0.247	-0.247	0.000	0.000	0.000	0.000
101	J	101	ASP	-1	-0.814	-0.891	20.177	-12.832	-12.832	0.000	0.000	0.000	0.000
102	J	102	VAL	0	-0.013	-0.001	14.120	-0.666	-0.666	0.000	0.000	0.000	0.000
103	J	103	PHE	0	-0.016	-0.006	14.199	0.534	0.534	0.000	0.000	0.000	0.000
104	J	104	ILE	0	0.004	0.001	9.016	-1.295	-1.295	0.000	0.000	0.000	0.000
105	J	105	ALA	0	0.007	0.020	9.985	1.355	1.355	0.000	0.000	0.000	0.000
106	J	106	ILE	0	-0.019	-0.020	6.137	-2.755	-2.755	0.000	0.000	0.000	0.000
107	J	107	THR	0	-0.025	-0.001	7.473	3.388	3.388	0.000	0.000	0.000	0.000
108	J	108	GLU	-1	-0.854	-0.929	7.070	-30.527	-30.527	0.000	0.000	0.000	0.000
109	J	109	ASN	0	-0.005	-0.004	6.098	-0.528	-0.528	0.000	0.000	0.000	0.000
110	J	110	ALA	0	0.011	0.009	8.792	-0.741	-0.741	0.000	0.000	0.000	0.000
111	J	111	PRO	0	0.036	0.005	8.009	-2.180	-2.180	0.000	0.000	0.000	0.000
112	J	112	HIS	0	-0.010	-0.014	9.095	-0.748	-0.748	0.000	0.000	0.000	0.000
113	J	113	ASP	-1	-0.857	-0.916	8.902	-23.219	-23.219	0.000	0.000	0.000	0.000
114	J	114	TRP	0	-0.090	-0.039	2.835	-9.473	-8.161	0.356	-0.779	-0.889	-0.008
115	J	115	SER	0	-0.043	-0.037	8.652	3.010	3.010	0.000	0.000	0.000	0.000
116	J	116	PHE	0	-0.043	-0.016	4.429	-0.246	-0.177	0.000	-0.004	-0.064	0.000
117	J	117	GLY	0	0.025	0.015	9.313	1.200	1.200	0.000	0.000	0.000	0.000
118	J	118	PHE	0	-0.039	-0.041	12.992	0.353	0.353	0.000	0.000	0.000	0.000
119	J	119	GLY	0	0.007	0.023	15.562	0.967	0.967	0.000	0.000	0.000	0.000
120	J	120	SER	0	-0.022	-0.004	14.972	0.554	0.554	0.000	0.000	0.000	0.000
121	J	121	ALA	0	0.086	0.048	12.145	-1.686	-1.686	0.000	0.000	0.000	0.000
122	J	122	GLN	0	0.089	0.027	10.412	-1.257	-1.257	0.000	0.000	0.000	0.000
123	J	123	TYR	0	0.004	0.006	5.036	-3.459	-3.394	0.000	-0.001	-0.064	0.000
124	J	124	VAL	0	-0.038	-0.006	11.123	1.371	1.371	0.000	0.000	0.000	0.000
125	J	125	THR	0	-0.030	-0.021	14.456	0.927	0.927	0.000	0.000	0.000	0.000
126	J	126	GLY	0	0.013	0.019	14.582	1.098	1.098	0.000	0.000	0.000	0.000
127	J	127	GLU	-1	-0.999	-0.991	14.303	-19.588	-19.588	0.000	0.000	0.000	0.000
128	J	128	LEU	0	-0.043	-0.026	7.279	-0.253	-0.253	0.000	0.000	0.000	0.000
129	J	129	ALA	0	0.001	-0.001	11.327	0.110	0.110	0.000	0.000	0.000	0.000
130	J	130	ILE	0	0.011	0.001	9.202	-3.432	-3.432	0.000	0.000	0.000	0.000
131	J	131	PRO	0	-0.074	-0.036	6.004	1.729	1.729	0.000	0.000	0.000	0.000
132	J	132	NME	0	0.028	0.029	9.246	1.081	1.081	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(J:1:PRO )