FMO DATABASE

FMODB ID: G5JR1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1406776.674871
FMO2-HF: Nuclear repulsion	1349017.407072
FMO2-HF: Total energy	-57759.2678
FMO2-MP2: Total energy	-57928.736548

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.
-34.856	-30.136	16.312	-10.179	-10.852	-0.054

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 : -0.050 / q_NPA : -0.037

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	0.013	0.009	3.846	-4.115	-0.690	-0.035	-2.024	-1.366	0.004
4	A	5	ALA	0	0.027	0.021	6.353	-0.341	-0.341	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.823	-0.907	1.877	-19.158	-19.388	6.362	-3.139	-2.994	-0.035
6	A	7	PHE	0	-0.010	-0.009	4.944	-0.723	-0.638	-0.001	-0.007	-0.077	0.000
7	A	8	ASP	-1	-0.787	-0.889	7.242	0.162	0.162	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.045	0.035	8.568	-0.065	-0.065	0.000	0.000	0.000	0.000
9	A	10	ILE	0	-0.077	-0.047	6.311	-0.075	-0.075	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.018	-0.011	10.054	0.046	0.046	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.814	-0.889	12.647	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.078	-0.034	12.329	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.091	-0.043	14.374	0.009	0.009	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.799	-0.853	16.237	-0.061	-0.061	0.000	0.000	0.000	0.000
15	A	16	HIS	0	-0.022	-0.019	17.713	0.039	0.039	0.000	0.000	0.000	0.000
16	A	17	SER	0	-0.106	-0.049	18.578	0.000	0.000	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.984	0.965	20.501	0.188	0.188	0.000	0.000	0.000	0.000
18	A	19	THR	0	-0.001	-0.009	22.755	0.010	0.010	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.077	0.062	19.705	0.014	0.014	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.011	-0.014	19.575	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.022	-0.018	16.110	-0.034	-0.034	0.000	0.000	0.000	0.000
22	A	23	GLY	0	0.056	0.031	16.078	-0.038	-0.038	0.000	0.000	0.000	0.000
23	A	24	SER	0	0.016	0.004	13.589	-0.038	-0.038	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.974	0.986	11.562	0.485	0.485	0.000	0.000	0.000	0.000
25	A	26	ILE	0	0.049	0.035	11.260	-0.116	-0.116	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.006	0.014	11.525	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.881	0.938	5.773	2.870	2.870	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.008	0.000	6.718	-0.486	-0.486	0.000	0.000	0.000	0.000
29	A	30	THR	0	0.013	0.004	7.462	0.113	0.113	0.000	0.000	0.000	0.000
30	A	31	ASN	0	-0.009	0.004	5.821	0.656	0.656	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.001	0.010	2.115	-0.293	-0.692	4.448	-1.540	-2.508	0.001
32	A	33	SER	0	-0.041	-0.021	3.780	1.445	1.548	-0.001	-0.022	-0.079	0.000
33	A	34	MET	0	-0.052	-0.029	6.749	0.421	0.421	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.919	-0.958	2.068	-13.121	-12.527	5.112	-2.697	-3.009	-0.030
35	A	36	ASN	0	-0.059	-0.032	2.858	-2.651	-1.509	0.427	-0.750	-0.819	0.006
36	A	37	VAL	0	0.069	0.048	6.045	-0.345	-0.345	0.000	0.000	0.000	0.000
37	A	38	SER	0	0.024	0.021	9.599	-0.079	-0.079	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.916	-0.962	8.588	0.720	0.720	0.000	0.000	0.000	0.000
39	A	40	ASN	0	-0.024	-0.032	10.625	-0.139	-0.139	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.019	0.008	11.698	-0.084	-0.084	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.030	-0.010	10.588	-0.139	-0.139	0.000	0.000	0.000	0.000
42	A	43	PHE	0	0.009	0.002	4.958	-0.107	-0.107	0.000	0.000	0.000	0.000
43	A	44	VAL	0	-0.002	-0.001	10.821	-0.103	-0.103	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.012	0.005	14.282	-0.049	-0.049	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.031	-0.054	12.159	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.012	-0.001	12.877	-0.058	-0.058	0.000	0.000	0.000	0.000
47	A	48	TYR	0	-0.001	0.004	15.278	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.934	0.956	17.058	-0.150	-0.150	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.016	0.007	16.055	-0.019	-0.019	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.035	0.005	18.171	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.836	0.908	20.620	0.011	0.011	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.729	0.829	15.739	0.051	0.051	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.001	0.019	20.557	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	55	PRO	0	0.043	0.017	22.339	0.012	0.012	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.051	0.019	25.092	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.043	-0.040	25.554	0.002	0.002	0.000	0.000	0.000	0.000
57	A	58	HIS	0	-0.001	0.009	20.536	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.815	0.921	22.064	0.052	0.052	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.009	0.001	22.714	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.033	0.014	20.539	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.001	0.000	18.073	-0.036	-0.036	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.024	0.013	18.225	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.012	-0.017	18.974	0.003	0.003	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.003	0.005	13.015	-0.037	-0.037	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.002	0.004	14.810	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.797	-0.862	16.749	-0.221	-0.221	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.034	-0.029	13.209	0.022	0.022	0.000	0.000	0.000	0.000
68	A	69	ILE	0	0.002	0.012	10.891	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.001	0.010	13.332	0.044	0.044	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.844	0.888	16.497	0.282	0.282	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.006	-0.001	12.300	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	73	PHE	0	0.006	-0.016	10.309	0.027	0.027	0.000	0.000	0.000	0.000
73	A	74	GLN	0	0.020	0.026	14.548	0.018	0.018	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.887	-0.953	16.267	-0.151	-0.151	0.000	0.000	0.000	0.000
75	A	76	GLY	0	-0.027	-0.013	14.793	0.011	0.011	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.016	0.010	15.728	0.030	0.030	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.879	0.943	18.562	0.104	0.104	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.909	0.957	14.709	0.106	0.106	0.000	0.000	0.000	0.000
79	A	80	ASN	0	-0.071	-0.032	15.768	0.015	0.015	0.000	0.000	0.000	0.000
80	A	81	ASN	0	-0.065	-0.023	19.940	0.007	0.007	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.740	-0.809	17.746	0.176	0.176	0.000	0.000	0.000	0.000
82	A	83	SER	0	0.002	-0.004	22.182	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	84	PHE	0	-0.004	-0.016	21.856	0.012	0.012	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.932	-0.967	23.791	0.033	0.033	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.069	-0.032	26.022	0.009	0.009	0.000	0.000	0.000	0.000
86	A	87	PRO	0	0.022	0.013	20.777	0.005	0.005	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.010	0.009	18.469	0.013	0.013	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.809	-0.909	18.172	0.221	0.221	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.036	-0.014	15.163	0.014	0.014	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.003	-0.035	14.021	0.094	0.094	0.000	0.000	0.000	0.000
91	A	92	PHE	0	-0.022	-0.026	11.019	-0.018	-0.018	0.000	0.000	0.000	0.000
92	A	93	SER	0	0.010	-0.028	15.060	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.019	0.032	17.417	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	95	GLY	0	0.010	0.003	14.281	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	96	TRP	0	-0.042	-0.032	15.225	-0.034	-0.034	0.000	0.000	0.000	0.000
96	A	97	CYS	0	0.008	0.006	17.838	-0.021	-0.021	0.000	0.000	0.000	0.000
97	A	98	LYS	1	0.853	0.921	16.355	-0.239	-0.239	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.001	-0.007	16.203	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	100	ALA	0	0.008	-0.001	18.168	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	101	GLU	-1	-0.930	-0.957	21.685	0.045	0.045	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.058	-0.017	17.697	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.023	-0.027	21.531	-0.020	-0.020	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.845	-0.912	23.192	-0.027	-0.027	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.014	-0.005	24.563	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.009	-0.007	19.682	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.009	0.007	24.189	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	108	ALA	0	-0.007	0.001	26.783	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.781	-0.872	26.066	-0.044	-0.044	0.000	0.000	0.000	0.000
109	A	110	ALA	0	-0.004	-0.010	25.934	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	111	ILE	0	-0.036	-0.024	27.896	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	112	GLN	0	-0.059	-0.013	31.212	0.002	0.002	0.000	0.000	0.000	0.000
112	A	113	HIS	0	-0.018	-0.010	28.783	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	114	ALA	0	-0.031	-0.006	28.368	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	115	PRO	0	0.011	0.001	29.687	0.006	0.006	0.000	0.000	0.000	0.000
115	A	116	SER	0	0.104	0.038	32.084	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	117	ALA	0	-0.031	-0.014	33.017	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	118	HIS	0	-0.038	-0.033	26.987	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	119	LEU	0	0.053	0.044	29.284	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	120	PRO	0	0.016	-0.006	30.999	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.880	0.942	27.063	0.149	0.149	0.000	0.000	0.000	0.000
121	A	122	ILE	0	0.062	0.035	26.181	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.014	0.011	27.722	0.002	0.002	0.000	0.000	0.000	0.000
123	A	124	LYS	1	0.943	0.968	27.989	0.120	0.120	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.013	0.011	22.389	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	126	CYS	0	-0.014	-0.001	25.652	0.005	0.005	0.000	0.000	0.000	0.000
126	A	127	ASP	-1	-0.836	-0.905	28.050	-0.091	-0.091	0.000	0.000	0.000	0.000
127	A	128	ILE	0	-0.069	-0.031	22.747	0.001	0.001	0.000	0.000	0.000	0.000
128	A	129	TRP	0	-0.021	-0.041	21.319	0.011	0.011	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.808	-0.867	25.290	-0.055	-0.055	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.910	0.958	27.425	0.136	0.136	0.000	0.000	0.000	0.000
131	A	132	ALA	0	-0.037	-0.017	23.081	0.001	0.001	0.000	0.000	0.000	0.000
132	A	133	SER	0	0.005	0.009	24.741	0.009	0.009	0.000	0.000	0.000	0.000
133	A	134	THR	0	-0.058	-0.039	20.959	0.005	0.005	0.000	0.000	0.000	0.000
134	A	135	PHE	0	0.006	-0.004	21.370	0.013	0.013	0.000	0.000	0.000	0.000
135	A	136	PRO	0	0.069	0.033	26.027	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	137	PRO	0	0.056	0.009	29.583	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.864	-0.917	32.454	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	139	LYS	1	0.824	0.909	24.886	0.009	0.009	0.000	0.000	0.000	0.000
139	A	140	LEU	0	-0.004	-0.013	27.224	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	141	GLU	-1	-0.937	-0.953	30.751	-0.031	-0.031	0.000	0.000	0.000	0.000
141	A	142	SER	0	-0.013	-0.009	32.344	0.000	0.000	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.056	-0.030	27.197	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	144	ARG	1	0.799	0.845	31.403	0.065	0.065	0.000	0.000	0.000	0.000
144	A	145	SER	0	-0.015	0.002	33.665	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	146	LYS	1	0.999	1.000	32.535	0.023	0.023	0.000	0.000	0.000	0.000
146	A	147	LEU	0	-0.009	-0.013	29.702	-0.002	-0.002	0.000	0.000	0.000	0.000
147	A	148	LYS	1	0.890	0.935	34.089	0.061	0.061	0.000	0.000	0.000	0.000
148	A	149	ASP	-1	-0.876	-0.925	37.552	-0.034	-0.034	0.000	0.000	0.000	0.000
149	A	150	ALA	0	-0.017	-0.008	35.280	0.001	0.001	0.000	0.000	0.000	0.000
150	A	151	MET	0	-0.131	-0.062	35.676	-0.005	-0.005	0.000	0.000	0.000	0.000
151	A	152	ALA	0	0.011	0.010	38.283	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	153	LEU	0	-0.040	-0.005	41.841	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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