FMO DATABASE

FMODB ID: 89R7Y

Calculation Name: 5MDT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MDT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UTE3

Base Structure: X-ray

Registration Date: 2023-09-23

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1416949.392552
FMO2-HF: Nuclear repulsion	1359189.914155
FMO2-HF: Total energy	-57759.478397
FMO2-MP2: Total energy	-57928.947427

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-39.075	-50.097	41.159	-15.994	-14.142	-0.056

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.058 / q_NPA : -0.045

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	4	ILE	0	-0.009	0.004	3.874	-0.461	1.259	-0.016	-0.954	-0.749	0.003
4	A	5	ALA	0	0.032	0.016	6.629	-0.442	-0.442	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.813	-0.873	1.634	-22.700	-29.957	18.164	-6.882	-4.026	-0.048
6	A	7	PHE	0	-0.014	-0.008	4.784	-1.183	-1.048	-0.001	-0.010	-0.124	0.000
7	A	8	ASP	-1	-0.778	-0.880	6.991	0.595	0.595	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.049	0.033	8.485	-0.210	-0.210	0.000	0.000	0.000	0.000
9	A	10	ILE	0	-0.073	-0.032	5.814	-0.250	-0.250	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.001	-0.003	9.661	-0.063	-0.063	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.775	-0.870	12.473	0.154	0.154	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.079	-0.047	11.734	-0.062	-0.062	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.091	-0.035	14.004	-0.063	-0.063	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.798	-0.848	15.788	0.085	0.085	0.000	0.000	0.000	0.000
15	A	16	HIS	0	-0.018	-0.012	17.360	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	17	SER	0	-0.080	-0.045	18.182	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.974	0.955	20.081	0.146	0.146	0.000	0.000	0.000	0.000
18	A	19	THR	0	-0.011	-0.006	22.012	0.009	0.009	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.065	0.047	19.238	0.018	0.018	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.008	-0.013	18.945	0.008	0.008	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.019	-0.016	15.758	-0.046	-0.046	0.000	0.000	0.000	0.000
22	A	23	GLY	0	0.052	0.027	15.499	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	24	SER	0	0.026	0.010	13.091	0.008	0.008	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.940	0.978	10.957	0.295	0.295	0.000	0.000	0.000	0.000
25	A	26	ILE	0	0.046	0.026	10.975	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.001	0.020	11.552	0.071	0.071	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.893	0.936	5.122	3.336	3.336	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.007	0.000	6.618	-0.068	-0.068	0.000	0.000	0.000	0.000
29	A	30	THR	0	0.002	-0.004	7.622	0.356	0.356	0.000	0.000	0.000	0.000
30	A	31	ASN	0	-0.056	-0.030	5.701	0.739	0.739	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.008	0.012	1.976	0.923	-1.302	7.938	-2.286	-3.428	0.004
32	A	33	SER	0	-0.045	-0.030	3.827	1.940	2.059	-0.001	-0.001	-0.117	0.000
33	A	34	MET	0	-0.049	-0.019	6.906	0.173	0.173	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.864	-0.931	1.975	-13.978	-13.728	6.247	-3.263	-3.234	-0.036
35	A	36	ASN	0	-0.063	-0.041	2.047	-6.729	-10.592	8.830	-2.589	-2.378	0.021
36	A	37	VAL	0	0.046	0.033	5.795	-0.753	-0.749	-0.001	0.000	-0.002	0.000
37	A	38	SER	0	-0.006	-0.006	9.488	-0.158	-0.158	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.856	-0.914	8.220	1.188	1.188	0.000	0.000	0.000	0.000
39	A	40	ASN	0	-0.014	-0.013	10.330	-0.164	-0.164	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.032	0.013	11.469	-0.123	-0.123	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.017	-0.008	10.278	-0.220	-0.220	0.000	0.000	0.000	0.000
42	A	43	PHE	0	0.001	-0.001	4.374	-0.402	-0.307	-0.001	-0.009	-0.084	0.000
43	A	44	VAL	0	0.016	0.006	10.429	-0.186	-0.186	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.014	0.015	13.947	-0.118	-0.118	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.048	-0.064	11.672	-0.133	-0.133	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.013	0.001	12.581	-0.111	-0.111	0.000	0.000	0.000	0.000
47	A	48	TYR	0	0.014	0.004	14.811	-0.090	-0.090	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.933	0.957	16.208	-0.482	-0.482	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.022	0.008	15.624	-0.058	-0.058	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.019	-0.003	17.658	-0.046	-0.046	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.843	0.911	19.977	-0.188	-0.188	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.676	0.796	15.497	-0.202	-0.202	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.006	0.021	19.880	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	55	PRO	0	0.011	-0.004	21.816	0.002	0.002	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.058	0.024	24.724	0.001	0.001	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.032	-0.036	24.886	0.003	0.003	0.000	0.000	0.000	0.000
57	A	58	HIS	0	0.015	0.042	20.020	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.812	0.918	21.717	-0.094	-0.094	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.003	0.009	22.680	0.013	0.013	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.018	0.005	20.154	0.001	0.001	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.011	-0.002	17.755	0.003	0.003	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.034	0.015	17.939	0.033	0.033	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.009	-0.016	18.613	0.006	0.006	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.005	0.000	12.775	-0.014	-0.014	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.007	0.006	14.563	0.039	0.039	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.783	-0.861	16.547	0.073	0.073	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.025	-0.028	13.394	0.000	0.000	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.006	0.016	10.730	0.002	0.002	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.006	0.006	13.210	0.050	0.050	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.849	0.900	16.413	-0.021	-0.021	0.000	0.000	0.000	0.000
71	A	72	SER	0	0.003	-0.001	12.437	-0.036	-0.036	0.000	0.000	0.000	0.000
72	A	73	PHE	0	0.017	-0.006	10.520	0.012	0.012	0.000	0.000	0.000	0.000
73	A	74	GLN	0	0.016	0.024	14.733	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.875	-0.950	16.443	0.084	0.084	0.000	0.000	0.000	0.000
75	A	76	GLY	0	-0.031	-0.016	14.704	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	77	ALA	0	-0.003	0.003	15.573	0.003	0.003	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.857	0.923	18.571	-0.143	-0.143	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.906	0.952	14.549	-0.148	-0.148	0.000	0.000	0.000	0.000
79	A	80	ASN	0	-0.064	-0.026	15.642	-0.018	-0.018	0.000	0.000	0.000	0.000
80	A	81	ASN	0	-0.062	-0.023	19.822	-0.015	-0.015	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.736	-0.803	17.647	0.477	0.477	0.000	0.000	0.000	0.000
82	A	83	SER	0	0.012	-0.004	22.183	-0.013	-0.013	0.000	0.000	0.000	0.000
83	A	84	PHE	0	-0.007	-0.020	21.881	0.020	0.020	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.932	-0.965	23.747	0.170	0.170	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.085	-0.036	25.538	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	87	PRO	0	0.019	0.021	20.648	0.008	0.008	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.018	0.004	18.266	0.004	0.004	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.841	-0.924	18.064	0.560	0.560	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.019	-0.010	15.156	0.060	0.060	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.009	-0.035	14.047	0.144	0.144	0.000	0.000	0.000	0.000
91	A	92	PHE	0	-0.015	-0.016	10.786	0.013	0.013	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.009	-0.042	14.956	-0.031	-0.031	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.024	0.029	17.209	-0.040	-0.040	0.000	0.000	0.000	0.000
94	A	95	GLY	0	0.018	0.009	14.231	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	96	TRP	0	-0.057	-0.052	15.159	-0.043	-0.043	0.000	0.000	0.000	0.000
96	A	97	CYS	0	0.009	0.005	17.859	-0.041	-0.041	0.000	0.000	0.000	0.000
97	A	98	LYS	1	0.833	0.904	16.132	-0.649	-0.649	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.002	-0.005	16.267	-0.024	-0.024	0.000	0.000	0.000	0.000
99	A	100	ALA	0	0.021	0.016	18.209	-0.045	-0.045	0.000	0.000	0.000	0.000
100	A	101	GLU	-1	-0.921	-0.946	21.768	0.221	0.221	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.058	-0.027	17.444	-0.027	-0.027	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.008	-0.019	21.457	-0.029	-0.029	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.802	-0.899	23.062	0.123	0.123	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.008	-0.001	24.243	-0.016	-0.016	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.029	-0.014	19.461	-0.010	-0.010	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.011	0.007	23.965	-0.020	-0.020	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.007	0.012	26.449	-0.015	-0.015	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.771	-0.868	25.491	0.109	0.109	0.000	0.000	0.000	0.000
109	A	110	ALA	0	-0.009	-0.017	25.455	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	111	ILE	0	-0.037	-0.027	27.367	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	112	GLN	0	-0.063	-0.012	30.527	0.000	0.000	0.000	0.000	0.000	0.000
112	A	113	HIS	0	-0.022	-0.011	27.840	-0.015	-0.015	0.000	0.000	0.000	0.000
113	A	114	ALA	0	-0.028	-0.004	28.104	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	115	PRO	0	0.003	-0.002	29.222	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	116	SER	0	0.082	0.030	31.536	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	117	ALA	0	-0.026	-0.009	32.485	0.001	0.001	0.000	0.000	0.000	0.000
117	A	118	HIS	0	-0.026	-0.041	26.436	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	119	LEU	0	0.050	0.044	28.989	0.003	0.003	0.000	0.000	0.000	0.000
119	A	120	PRO	0	0.017	-0.009	30.806	0.004	0.004	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.859	0.943	26.850	0.035	0.035	0.000	0.000	0.000	0.000
121	A	122	ILE	0	0.071	0.030	25.673	0.001	0.001	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.015	0.018	27.249	0.008	0.008	0.000	0.000	0.000	0.000
123	A	124	LYS	1	0.964	0.984	27.904	0.011	0.011	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.025	0.007	22.070	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	126	CYS	0	-0.003	0.003	25.261	0.012	0.012	0.000	0.000	0.000	0.000
126	A	127	ASP	-1	-0.844	-0.917	27.693	0.028	0.028	0.000	0.000	0.000	0.000
127	A	128	ILE	0	-0.072	-0.033	22.764	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	129	TRP	0	-0.019	-0.040	21.122	0.009	0.009	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.803	-0.867	25.285	0.061	0.061	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.913	0.958	27.593	0.009	0.009	0.000	0.000	0.000	0.000
131	A	132	ALA	0	-0.031	-0.015	23.261	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.008	-0.003	24.892	0.013	0.013	0.000	0.000	0.000	0.000
133	A	134	THR	0	-0.051	-0.031	20.892	0.004	0.004	0.000	0.000	0.000	0.000
134	A	135	PHE	0	0.000	-0.001	21.216	0.025	0.025	0.000	0.000	0.000	0.000
135	A	136	PRO	0	0.079	0.036	25.986	-0.013	-0.013	0.000	0.000	0.000	0.000
136	A	137	PRO	0	0.056	0.017	29.623	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.848	-0.910	32.410	0.103	0.103	0.000	0.000	0.000	0.000
138	A	139	LYS	1	0.837	0.927	24.921	-0.185	-0.185	0.000	0.000	0.000	0.000
139	A	140	LEU	0	-0.009	-0.007	27.001	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	141	GLU	-1	-0.945	-0.968	30.435	0.060	0.060	0.000	0.000	0.000	0.000
141	A	142	SER	0	0.000	-0.016	32.011	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.064	-0.015	26.816	0.000	0.000	0.000	0.000	0.000	0.000
143	A	144	ARG	1	0.784	0.837	30.934	-0.056	-0.056	0.000	0.000	0.000	0.000
144	A	145	SER	0	-0.041	-0.013	33.305	-0.005	-0.005	0.000	0.000	0.000	0.000
145	A	146	LYS	1	0.898	0.937	31.035	-0.109	-0.109	0.000	0.000	0.000	0.000
146	A	147	LEU	0	0.008	-0.010	29.154	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	148	LYS	1	0.896	0.947	33.521	-0.031	-0.031	0.000	0.000	0.000	0.000
148	A	149	ASP	-1	-0.828	-0.905	37.075	0.046	0.046	0.000	0.000	0.000	0.000
149	A	150	ALA	0	-0.029	-0.011	34.651	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	151	MET	0	-0.113	-0.056	35.576	-0.007	-0.007	0.000	0.000	0.000	0.000
151	A	152	ALA	0	-0.009	0.002	38.087	-0.005	-0.005	0.000	0.000	0.000	0.000
152	A	153	LEU	0	-0.048	-0.011	41.573	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)