FMO DATABASE

FMODB ID: R8Y88

Calculation Name: 1M4J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1M4J

Chain ID: A

ChEMBL ID:

UniProt ID: Q91YR1

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1261066.657206
FMO2-HF: Nuclear repulsion	1207772.478706
FMO2-HF: Total energy	-53294.178501
FMO2-MP2: Total energy	-53451.6304

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:7:ILE)

Summations of interaction energy for fragment #1(A:7:ILE)

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.
-11.741	-10.54	9.565	-5.446	-5.322	-0.041

Interaction energy analysis for fragmet #1(A:7:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.010

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	9	ALA	0	-0.006	0.002	3.880	-2.274	-0.642	-0.019	-0.880	-0.734	0.003
4	A	10	SER	0	0.023	-0.014	6.986	0.388	0.388	0.000	0.000	0.000	0.000
5	A	11	GLU	-1	-0.822	-0.935	9.100	0.374	0.374	0.000	0.000	0.000	0.000
6	A	12	ASP	-1	-0.845	-0.889	12.422	0.085	0.085	0.000	0.000	0.000	0.000
7	A	13	VAL	0	-0.034	-0.012	9.825	-0.047	-0.047	0.000	0.000	0.000	0.000
8	A	14	LYS	1	0.804	0.909	8.799	-0.586	-0.586	0.000	0.000	0.000	0.000
9	A	15	GLU	-1	-0.815	-0.853	14.047	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	16	ILE	0	0.050	0.017	15.085	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	17	PHE	0	0.013	-0.008	10.838	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	18	ALA	0	-0.049	-0.008	16.844	0.002	0.002	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.770	0.843	19.915	0.018	0.018	0.000	0.000	0.000	0.000
14	A	20	ALA	0	0.008	0.004	18.943	0.000	0.000	0.000	0.000	0.000	0.000
15	A	21	ARG	1	0.908	0.944	15.674	0.004	0.004	0.000	0.000	0.000	0.000
16	A	22	ASN	0	-0.039	-0.009	21.834	0.003	0.003	0.000	0.000	0.000	0.000
17	A	23	GLY	0	0.057	0.018	24.300	0.004	0.004	0.000	0.000	0.000	0.000
18	A	24	LYS	1	0.851	0.926	24.505	0.011	0.011	0.000	0.000	0.000	0.000
19	A	25	TYR	0	-0.021	-0.010	20.764	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.728	0.835	23.713	0.079	0.079	0.000	0.000	0.000	0.000
21	A	27	LEU	0	0.005	0.008	19.485	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.014	-0.018	15.710	0.011	0.011	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.847	0.916	15.065	0.307	0.307	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.066	-0.032	9.318	0.001	0.001	0.000	0.000	0.000	0.000
25	A	31	SER	0	0.038	0.001	10.231	0.054	0.054	0.000	0.000	0.000	0.000
26	A	32	ILE	0	-0.047	-0.023	4.595	-0.182	-0.091	-0.001	-0.007	-0.083	0.000
27	A	33	GLU	-1	-0.939	-0.968	7.027	-0.325	-0.325	0.000	0.000	0.000	0.000
28	A	34	ASN	0	-0.039	-0.026	6.915	-0.083	-0.083	0.000	0.000	0.000	0.000
29	A	35	GLU	-1	-0.929	-0.961	3.250	-2.403	-1.633	0.026	-0.282	-0.515	0.000
30	A	36	GLN	0	0.000	0.010	1.867	-7.280	-10.008	9.510	-4.001	-2.781	-0.043
31	A	37	LEU	0	-0.035	-0.022	3.970	0.189	0.441	-0.001	-0.039	-0.212	0.000
32	A	38	VAL	0	0.031	0.005	6.297	0.382	0.382	0.000	0.000	0.000	0.000
33	A	39	VAL	0	0.002	-0.009	9.720	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	40	GLY	0	0.012	0.018	13.402	0.018	0.018	0.000	0.000	0.000	0.000
35	A	41	SER	0	-0.017	-0.015	15.197	0.042	0.042	0.000	0.000	0.000	0.000
36	A	42	CYS	0	-0.031	-0.004	17.724	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	43	SER	0	0.033	0.013	20.286	0.003	0.003	0.000	0.000	0.000	0.000
38	A	44	PRO	0	-0.001	0.000	23.833	0.000	0.000	0.000	0.000	0.000	0.000
39	A	45	PRO	0	-0.033	-0.014	26.481	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	46	SER	0	-0.085	-0.036	28.608	0.003	0.003	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.899	-0.921	31.727	-0.050	-0.050	0.000	0.000	0.000	0.000
42	A	48	SER	0	-0.027	-0.035	31.674	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	49	TRP	0	0.018	-0.014	27.640	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	50	GLU	-1	-0.824	-0.904	28.757	-0.070	-0.070	0.000	0.000	0.000	0.000
45	A	51	GLN	0	-0.008	0.006	31.187	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	52	ASP	-1	-0.671	-0.823	27.818	-0.080	-0.080	0.000	0.000	0.000	0.000
47	A	53	TYR	0	-0.028	-0.025	23.975	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.811	-0.920	26.491	-0.115	-0.115	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.043	-0.028	27.913	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	56	PHE	0	-0.031	-0.018	24.448	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	57	VAL	0	-0.001	-0.003	21.399	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	58	LEU	0	-0.015	-0.002	22.449	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	59	PRO	0	-0.011	-0.008	24.028	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	60	LEU	0	0.009	0.019	19.746	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	61	LEU	0	-0.040	-0.006	18.750	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	62	GLU	-1	-0.821	-0.909	17.433	-0.308	-0.308	0.000	0.000	0.000	0.000
57	A	63	ASP	-1	-0.829	-0.911	19.705	-0.194	-0.194	0.000	0.000	0.000	0.000
58	A	64	LYS	1	0.868	0.918	20.021	0.196	0.196	0.000	0.000	0.000	0.000
59	A	65	GLN	0	-0.011	-0.006	12.310	0.010	0.010	0.000	0.000	0.000	0.000
60	A	66	PRO	0	-0.034	-0.016	12.337	0.021	0.021	0.000	0.000	0.000	0.000
61	A	67	CYS	0	-0.073	-0.006	12.225	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	68	TYR	0	0.023	-0.027	7.869	-0.054	-0.054	0.000	0.000	0.000	0.000
63	A	69	VAL	0	0.005	-0.001	13.471	0.004	0.004	0.000	0.000	0.000	0.000
64	A	70	LEU	0	-0.011	0.015	13.530	0.015	0.015	0.000	0.000	0.000	0.000
65	A	71	PHE	0	0.026	-0.003	17.216	0.009	0.009	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.820	0.928	21.063	0.070	0.070	0.000	0.000	0.000	0.000
67	A	73	LEU	0	0.048	0.028	23.439	0.002	0.002	0.000	0.000	0.000	0.000
68	A	74	ASP	-1	-0.788	-0.890	26.611	-0.056	-0.056	0.000	0.000	0.000	0.000
69	A	75	SER	0	-0.054	-0.034	28.395	0.004	0.004	0.000	0.000	0.000	0.000
70	A	76	GLN	0	-0.016	-0.031	27.994	0.000	0.000	0.000	0.000	0.000	0.000
71	A	77	ASN	0	-0.006	-0.001	24.141	0.009	0.009	0.000	0.000	0.000	0.000
72	A	78	ALA	0	-0.005	-0.010	27.027	0.002	0.002	0.000	0.000	0.000	0.000
73	A	79	GLN	0	-0.054	-0.027	19.927	0.010	0.010	0.000	0.000	0.000	0.000
74	A	80	GLY	0	0.032	0.030	24.396	0.000	0.000	0.000	0.000	0.000	0.000
75	A	81	TYR	0	-0.034	-0.026	24.706	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.811	-0.866	23.665	-0.044	-0.044	0.000	0.000	0.000	0.000
77	A	83	TRP	0	-0.043	-0.031	19.461	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	84	ILE	0	0.007	0.020	20.411	0.003	0.003	0.000	0.000	0.000	0.000
79	A	85	PHE	0	-0.042	-0.033	11.042	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	86	ILE	0	0.013	0.015	17.136	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	87	ALA	0	-0.021	-0.015	13.828	-0.046	-0.046	0.000	0.000	0.000	0.000
82	A	88	TRP	0	0.022	-0.003	14.690	0.047	0.047	0.000	0.000	0.000	0.000
83	A	89	SER	0	-0.013	-0.035	14.447	-0.073	-0.073	0.000	0.000	0.000	0.000
84	A	90	PRO	0	0.042	0.060	16.568	0.028	0.028	0.000	0.000	0.000	0.000
85	A	91	ASP	-1	-0.783	-0.881	18.916	-0.209	-0.209	0.000	0.000	0.000	0.000
86	A	92	HIS	0	-0.043	-0.017	20.949	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	93	SER	0	-0.013	-0.004	15.897	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	94	HIS	0	0.046	0.018	14.899	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	95	VAL	0	0.071	0.022	14.495	-0.041	-0.041	0.000	0.000	0.000	0.000
90	A	96	ARG	1	0.964	0.978	8.463	0.518	0.518	0.000	0.000	0.000	0.000
91	A	97	GLN	0	0.057	0.037	9.887	-0.104	-0.104	0.000	0.000	0.000	0.000
92	A	98	LYS	1	0.847	0.923	10.439	0.180	0.180	0.000	0.000	0.000	0.000
93	A	99	MET	0	-0.041	-0.020	9.945	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	100	LEU	0	0.018	0.022	3.950	-0.086	0.070	0.000	-0.021	-0.135	0.000
95	A	101	TYR	0	0.074	0.050	6.248	-0.219	-0.219	0.000	0.000	0.000	0.000
96	A	102	ALA	0	0.013	0.019	8.789	0.011	0.011	0.000	0.000	0.000	0.000
97	A	103	ALA	0	-0.035	-0.017	6.081	0.049	0.049	0.000	0.000	0.000	0.000
98	A	104	THR	0	-0.017	-0.016	3.381	-0.680	-0.071	0.046	-0.125	-0.529	-0.001
99	A	105	ARG	1	0.841	0.916	5.171	0.289	0.281	-0.001	-0.001	0.009	0.000
100	A	106	ALA	0	0.009	0.001	7.858	0.076	0.076	0.000	0.000	0.000	0.000
101	A	107	THR	0	0.004	-0.001	3.373	0.018	0.445	0.005	-0.090	-0.342	0.000
102	A	108	LEU	0	0.044	0.029	6.494	0.162	0.162	0.000	0.000	0.000	0.000
103	A	109	LYS	1	0.861	0.928	8.746	0.240	0.240	0.000	0.000	0.000	0.000
104	A	110	LYS	1	0.926	0.961	7.943	-0.367	-0.367	0.000	0.000	0.000	0.000
105	A	111	GLU	-1	-0.813	-0.917	7.275	0.563	0.563	0.000	0.000	0.000	0.000
106	A	112	PHE	0	0.011	0.009	10.354	0.046	0.046	0.000	0.000	0.000	0.000
107	A	113	GLY	0	0.007	0.018	13.335	0.029	0.029	0.000	0.000	0.000	0.000
108	A	114	GLY	0	-0.002	-0.022	14.907	-0.017	-0.017	0.000	0.000	0.000	0.000
109	A	115	GLY	0	0.020	0.015	16.262	-0.011	-0.011	0.000	0.000	0.000	0.000
110	A	116	HIS	0	-0.023	-0.010	17.705	0.011	0.011	0.000	0.000	0.000	0.000
111	A	117	ILE	0	-0.074	-0.036	15.764	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	118	LYS	1	0.875	0.947	19.238	0.071	0.071	0.000	0.000	0.000	0.000
113	A	119	ASP	-1	-0.771	-0.844	21.406	-0.077	-0.077	0.000	0.000	0.000	0.000
114	A	120	GLU	-1	-0.758	-0.852	15.284	-0.178	-0.178	0.000	0.000	0.000	0.000
115	A	121	VAL	0	0.004	0.016	18.399	0.015	0.015	0.000	0.000	0.000	0.000
116	A	122	PHE	0	-0.008	-0.011	15.311	-0.031	-0.031	0.000	0.000	0.000	0.000
117	A	123	GLY	0	0.037	0.018	18.671	0.025	0.025	0.000	0.000	0.000	0.000
118	A	124	THR	0	-0.094	-0.047	19.158	-0.026	-0.026	0.000	0.000	0.000	0.000
119	A	125	VAL	0	0.012	-0.009	21.271	0.000	0.000	0.000	0.000	0.000	0.000
120	A	126	LYS	1	0.865	0.906	23.378	0.176	0.176	0.000	0.000	0.000	0.000
121	A	127	GLU	-1	-0.876	-0.925	25.284	-0.094	-0.094	0.000	0.000	0.000	0.000
122	A	128	ASP	-1	-0.803	-0.905	23.316	-0.146	-0.146	0.000	0.000	0.000	0.000
123	A	129	VAL	0	-0.021	-0.016	20.230	0.002	0.002	0.000	0.000	0.000	0.000
124	A	130	SER	0	0.008	0.028	23.512	0.001	0.001	0.000	0.000	0.000	0.000
125	A	131	LEU	0	-0.007	0.002	26.627	0.000	0.000	0.000	0.000	0.000	0.000
126	A	132	HIS	0	-0.017	-0.012	28.639	0.001	0.001	0.000	0.000	0.000	0.000
127	A	133	GLY	0	0.040	0.017	26.899	0.005	0.005	0.000	0.000	0.000	0.000
128	A	134	TYR	0	-0.045	-0.056	24.714	0.005	0.005	0.000	0.000	0.000	0.000
129	A	135	LYS	1	0.830	0.889	26.759	0.070	0.070	0.000	0.000	0.000	0.000
130	A	136	LYS	1	0.858	0.928	28.942	0.104	0.104	0.000	0.000	0.000	0.000
131	A	137	TYR	0	-0.065	-0.040	21.241	0.006	0.006	0.000	0.000	0.000	0.000
132	A	138	LEU	0	-0.030	-0.014	27.129	0.006	0.006	0.000	0.000	0.000	0.000
133	A	139	LEU	0	-0.115	-0.033	28.943	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ILE)