FMO DATABASE

FMODB ID: 6YGYZ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1256767.58963
FMO2-HF: Nuclear repulsion	1203474.309738
FMO2-HF: Total energy	-53293.279892
FMO2-MP2: Total energy	-53450.733013

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.
-3.039	2.356	0.994	-2.471	-3.918	-0.008

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 : 0.016 / q_NPA : 0.006

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

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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	-0.027	-0.026	3.806	0.942	2.850	-0.028	-0.949	-0.932	0.003
4	A	10	SER	0	0.047	0.032	7.101	-0.348	-0.348	0.000	0.000	0.000	0.000
5	A	11	GLU	-1	-0.855	-0.960	9.170	0.252	0.252	0.000	0.000	0.000	0.000
6	A	12	ASP	-1	-0.921	-0.943	12.523	0.456	0.456	0.000	0.000	0.000	0.000
7	A	13	VAL	0	-0.054	-0.026	9.627	-0.096	-0.096	0.000	0.000	0.000	0.000
8	A	14	LYS	1	0.859	0.924	9.613	-0.460	-0.460	0.000	0.000	0.000	0.000
9	A	15	GLU	-1	-0.820	-0.886	13.797	0.177	0.177	0.000	0.000	0.000	0.000
10	A	16	ILE	0	0.031	0.007	15.267	-0.057	-0.057	0.000	0.000	0.000	0.000
11	A	17	PHE	0	-0.018	-0.018	10.410	-0.045	-0.045	0.000	0.000	0.000	0.000
12	A	18	ALA	0	-0.011	0.004	16.134	-0.046	-0.046	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.813	0.890	19.242	-0.270	-0.270	0.000	0.000	0.000	0.000
14	A	20	ALA	0	0.014	0.008	18.485	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	21	ARG	1	0.954	0.984	15.723	-0.219	-0.219	0.000	0.000	0.000	0.000
16	A	22	ASN	0	-0.080	-0.030	21.234	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	23	GLY	0	0.054	0.010	23.655	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	24	LYS	1	0.849	0.934	23.677	-0.147	-0.147	0.000	0.000	0.000	0.000
19	A	25	TYR	0	-0.004	0.000	20.585	0.009	0.009	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.728	0.868	22.961	-0.100	-0.100	0.000	0.000	0.000	0.000
21	A	27	LEU	0	0.008	0.006	19.040	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.011	-0.002	15.196	0.014	0.014	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.907	0.955	14.821	-0.245	-0.245	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.042	-0.027	8.866	0.041	0.041	0.000	0.000	0.000	0.000
25	A	31	SER	0	0.002	-0.012	10.200	-0.137	-0.137	0.000	0.000	0.000	0.000
26	A	32	ILE	0	-0.029	-0.015	4.842	0.230	0.230	0.000	0.000	0.000	0.000
27	A	33	GLU	-1	-0.941	-0.970	7.400	0.146	0.146	0.000	0.000	0.000	0.000
28	A	34	ASN	0	-0.042	-0.028	7.501	0.144	0.144	0.000	0.000	0.000	0.000
29	A	35	GLU	-1	-0.967	-0.983	3.255	-2.162	-1.607	0.012	-0.114	-0.453	0.000
30	A	36	GLN	0	0.015	0.010	2.707	0.627	2.161	0.939	-1.101	-1.372	-0.010
31	A	37	LEU	0	-0.043	-0.014	3.936	-1.946	-1.695	0.001	-0.029	-0.222	0.000
32	A	38	VAL	0	0.051	0.020	6.276	-0.177	-0.177	0.000	0.000	0.000	0.000
33	A	39	VAL	0	0.010	-0.011	10.044	-0.124	-0.124	0.000	0.000	0.000	0.000
34	A	40	GLY	0	-0.004	0.011	13.268	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	41	SER	0	-0.008	-0.010	15.440	-0.048	-0.048	0.000	0.000	0.000	0.000
36	A	42	CYS	0	0.001	-0.002	17.667	0.020	0.020	0.000	0.000	0.000	0.000
37	A	43	SER	0	0.002	0.013	20.039	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	44	PRO	0	0.018	0.012	23.524	0.004	0.004	0.000	0.000	0.000	0.000
39	A	45	PRO	0	-0.041	-0.027	25.909	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	46	SER	0	-0.071	-0.016	27.981	0.001	0.001	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.901	-0.950	31.258	0.065	0.065	0.000	0.000	0.000	0.000
42	A	48	SER	0	-0.037	-0.021	31.463	0.003	0.003	0.000	0.000	0.000	0.000
43	A	49	TRP	0	0.023	-0.016	27.104	0.003	0.003	0.000	0.000	0.000	0.000
44	A	50	GLU	-1	-0.874	-0.932	28.507	0.050	0.050	0.000	0.000	0.000	0.000
45	A	51	GLN	0	-0.017	-0.006	30.811	0.001	0.001	0.000	0.000	0.000	0.000
46	A	52	ASP	-1	-0.669	-0.816	27.478	0.093	0.093	0.000	0.000	0.000	0.000
47	A	53	TYR	0	-0.053	-0.058	23.371	0.007	0.007	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.788	-0.933	25.913	0.072	0.072	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.030	-0.026	27.243	0.002	0.002	0.000	0.000	0.000	0.000
50	A	56	PHE	0	-0.019	-0.015	24.094	0.007	0.007	0.000	0.000	0.000	0.000
51	A	57	VAL	0	-0.002	-0.008	20.946	0.014	0.014	0.000	0.000	0.000	0.000
52	A	58	LEU	0	-0.046	0.022	22.156	0.007	0.007	0.000	0.000	0.000	0.000
53	A	59	PRO	0	-0.038	-0.020	23.841	0.000	0.000	0.000	0.000	0.000	0.000
54	A	60	LEU	0	-0.006	0.017	19.532	0.008	0.008	0.000	0.000	0.000	0.000
55	A	61	LEU	0	-0.034	-0.012	18.472	0.021	0.021	0.000	0.000	0.000	0.000
56	A	62	GLU	-1	-0.914	-0.954	17.855	0.151	0.151	0.000	0.000	0.000	0.000
57	A	63	ASP	-1	-0.867	-0.946	19.999	0.059	0.059	0.000	0.000	0.000	0.000
58	A	64	LYS	1	0.861	0.922	19.899	-0.045	-0.045	0.000	0.000	0.000	0.000
59	A	65	GLN	0	-0.013	-0.016	12.904	-0.032	-0.032	0.000	0.000	0.000	0.000
60	A	66	PRO	0	-0.043	-0.025	12.319	0.005	0.005	0.000	0.000	0.000	0.000
61	A	67	CYS	0	-0.069	-0.013	12.014	0.037	0.037	0.000	0.000	0.000	0.000
62	A	68	TYR	0	0.001	-0.036	7.163	-0.052	-0.052	0.000	0.000	0.000	0.000
63	A	69	VAL	0	0.019	0.008	12.806	0.040	0.040	0.000	0.000	0.000	0.000
64	A	70	LEU	0	-0.018	0.007	13.010	-0.026	-0.026	0.000	0.000	0.000	0.000
65	A	71	PHE	0	0.042	0.003	16.684	0.010	0.010	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.863	0.948	20.488	-0.128	-0.128	0.000	0.000	0.000	0.000
67	A	73	LEU	0	0.031	0.025	22.694	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	74	ASP	-1	-0.780	-0.909	25.866	0.081	0.081	0.000	0.000	0.000	0.000
69	A	75	SER	0	-0.072	-0.046	27.886	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	76	GLN	0	-0.011	-0.025	27.107	0.005	0.005	0.000	0.000	0.000	0.000
71	A	77	ASN	0	0.057	0.041	23.299	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	78	ALA	0	-0.012	-0.029	27.500	0.003	0.003	0.000	0.000	0.000	0.000
73	A	79	GLN	0	-0.072	-0.034	20.407	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	80	GLY	0	0.046	0.037	24.145	0.010	0.010	0.000	0.000	0.000	0.000
75	A	81	TYR	0	-0.046	-0.024	23.844	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.861	-0.897	22.966	0.053	0.053	0.000	0.000	0.000	0.000
77	A	83	TRP	0	-0.027	-0.027	19.022	0.016	0.016	0.000	0.000	0.000	0.000
78	A	84	ILE	0	0.008	0.022	20.016	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	85	PHE	0	-0.051	-0.042	10.574	0.021	0.021	0.000	0.000	0.000	0.000
80	A	86	ILE	0	0.018	0.013	16.526	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	87	ALA	0	-0.029	-0.022	13.671	0.033	0.033	0.000	0.000	0.000	0.000
82	A	88	TRP	0	0.009	0.003	14.612	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	89	SER	0	-0.036	-0.046	14.067	0.009	0.009	0.000	0.000	0.000	0.000
84	A	90	PRO	0	0.036	0.048	16.153	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	91	ASP	-1	-0.842	-0.930	18.383	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	92	HIS	0	-0.026	-0.009	20.759	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	93	SER	0	0.017	0.019	15.716	0.011	0.011	0.000	0.000	0.000	0.000
88	A	94	HIS	0	0.050	0.012	14.856	-0.022	-0.022	0.000	0.000	0.000	0.000
89	A	95	VAL	0	0.060	0.014	14.416	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	96	ARG	1	0.986	0.994	10.120	0.299	0.299	0.000	0.000	0.000	0.000
91	A	97	GLN	0	0.055	0.047	9.892	0.023	0.023	0.000	0.000	0.000	0.000
92	A	98	LYS	1	0.878	0.941	10.324	0.031	0.031	0.000	0.000	0.000	0.000
93	A	99	MET	0	-0.052	-0.025	9.902	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	100	LEU	0	0.027	0.021	4.368	-0.123	-0.010	-0.001	-0.009	-0.103	0.000
95	A	101	TYR	0	0.073	0.049	6.034	0.026	0.026	0.000	0.000	0.000	0.000
96	A	102	ALA	0	0.001	0.027	8.432	0.008	0.008	0.000	0.000	0.000	0.000
97	A	103	ALA	0	-0.045	-0.023	6.014	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	104	THR	0	-0.007	-0.002	3.153	-0.870	-0.200	0.068	-0.187	-0.551	-0.001
99	A	105	ARG	1	0.879	0.938	5.541	0.047	0.047	0.000	0.000	0.000	0.000
100	A	106	ALA	0	0.001	-0.011	8.303	0.044	0.044	0.000	0.000	0.000	0.000
101	A	107	THR	0	0.010	0.010	3.476	-0.085	0.279	0.003	-0.082	-0.285	0.000
102	A	108	LEU	0	0.057	0.039	6.411	0.113	0.113	0.000	0.000	0.000	0.000
103	A	109	LYS	1	0.915	0.961	8.007	0.057	0.057	0.000	0.000	0.000	0.000
104	A	110	LYS	1	0.913	0.958	8.750	0.255	0.255	0.000	0.000	0.000	0.000
105	A	111	GLU	-1	-0.812	-0.897	6.983	0.422	0.422	0.000	0.000	0.000	0.000
106	A	112	PHE	0	-0.027	-0.004	10.340	0.044	0.044	0.000	0.000	0.000	0.000
107	A	113	GLY	0	0.021	0.008	13.112	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	114	GLY	0	-0.007	-0.027	14.969	0.002	0.002	0.000	0.000	0.000	0.000
109	A	115	GLY	0	0.003	0.011	16.186	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	116	HIS	0	-0.031	-0.014	17.668	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	117	ILE	0	-0.064	-0.030	15.576	0.010	0.010	0.000	0.000	0.000	0.000
112	A	118	LYS	1	0.909	0.969	19.027	-0.054	-0.054	0.000	0.000	0.000	0.000
113	A	119	ASP	-1	-0.805	-0.880	21.234	0.030	0.030	0.000	0.000	0.000	0.000
114	A	120	GLU	-1	-0.836	-0.916	15.568	0.006	0.006	0.000	0.000	0.000	0.000
115	A	121	VAL	0	0.018	0.017	18.349	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	122	PHE	0	-0.022	-0.014	15.236	0.010	0.010	0.000	0.000	0.000	0.000
117	A	123	GLY	0	0.033	0.010	18.243	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	124	THR	0	-0.070	-0.018	18.820	0.007	0.007	0.000	0.000	0.000	0.000
119	A	125	VAL	0	0.043	0.017	20.866	0.004	0.004	0.000	0.000	0.000	0.000
120	A	126	LYS	1	0.966	0.964	23.756	-0.076	-0.076	0.000	0.000	0.000	0.000
121	A	127	GLU	-1	-0.984	-0.980	24.886	0.027	0.027	0.000	0.000	0.000	0.000
122	A	128	ASP	-1	-0.797	-0.903	22.989	0.023	0.023	0.000	0.000	0.000	0.000
123	A	129	VAL	0	-0.060	-0.039	20.021	0.001	0.001	0.000	0.000	0.000	0.000
124	A	130	SER	0	0.038	0.050	23.334	0.009	0.009	0.000	0.000	0.000	0.000
125	A	131	LEU	0	0.010	0.000	26.328	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	132	HIS	0	-0.037	-0.023	28.137	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	133	GLY	0	0.083	0.038	26.975	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	134	TYR	0	-0.065	-0.057	23.921	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	135	LYS	1	0.858	0.904	26.266	-0.046	-0.046	0.000	0.000	0.000	0.000
130	A	136	LYS	1	0.950	0.974	28.848	-0.021	-0.021	0.000	0.000	0.000	0.000
131	A	137	TYR	0	-0.063	-0.025	22.410	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	138	LEU	0	-0.053	-0.024	26.475	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	139	LEU	0	-0.079	-0.010	28.630	-0.004	-0.004	0.000	0.000	0.000	0.000

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