FMO DATABASE

FMODB ID: 5J5VZ

Calculation Name: 3D7A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D7A

Chain ID: A

ChEMBL ID:

UniProt ID: O58738

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	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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1308690.89071
FMO2-HF: Nuclear repulsion	1252814.154145
FMO2-HF: Total energy	-55876.736565
FMO2-MP2: Total energy	-56039.043063

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:MET)

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

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.
-7.521	-5.239	0.011	-1.045	-1.249	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.031

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	MET	0	0.052	0.044	3.820	-1.718	0.076	-0.012	-0.895	-0.887	0.002
4	A	5	PHE	0	-0.031	-0.015	6.759	0.731	0.731	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.972	-0.987	7.729	-1.647	-1.647	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.970	-1.010	9.837	-0.347	-0.347	0.000	0.000	0.000	0.000
7	A	8	VAL	0	-0.033	-0.006	12.810	-0.045	-0.045	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.853	-0.923	15.328	-0.272	-0.272	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.022	-0.016	19.002	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.900	-0.949	21.702	-0.196	-0.196	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.014	-0.007	25.328	0.001	0.001	0.000	0.000	0.000	0.000
12	A	13	TYR	0	0.018	0.024	28.640	0.006	0.006	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.026	-0.013	31.510	0.002	0.002	0.000	0.000	0.000	0.000
14	A	15	TYR	0	0.051	0.005	34.040	0.001	0.001	0.000	0.000	0.000	0.000
15	A	16	PRO	0	0.063	0.030	37.756	0.003	0.003	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.009	-0.005	40.605	0.003	0.003	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.885	-0.908	34.855	-0.103	-0.103	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.873	-0.939	35.149	-0.055	-0.055	0.000	0.000	0.000	0.000
19	A	20	ILE	0	0.050	0.008	30.977	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.947	0.961	30.843	0.042	0.042	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.969	0.994	30.304	0.057	0.057	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.063	0.037	28.907	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.979	0.988	26.632	0.078	0.078	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.876	0.954	24.725	0.063	0.063	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.045	0.017	25.919	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	27	MET	0	0.000	0.013	23.300	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.061	-0.027	21.093	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.089	-0.043	21.287	0.008	0.008	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.042	-0.006	20.941	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	31	ILE	0	0.016	0.004	15.866	-0.039	-0.039	0.000	0.000	0.000	0.000
31	A	32	PRO	0	-0.007	-0.007	16.218	0.029	0.029	0.000	0.000	0.000	0.000
32	A	33	GLY	0	-0.002	-0.006	16.394	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.051	-0.007	17.394	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	35	GLN	0	-0.048	-0.024	18.133	0.052	0.052	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.018	-0.036	20.710	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.909	-0.935	24.072	-0.148	-0.148	0.000	0.000	0.000	0.000
37	A	38	ALA	0	-0.045	-0.037	26.421	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.023	-0.001	26.783	0.009	0.009	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.856	-0.934	32.132	-0.086	-0.086	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.901	0.949	33.351	0.121	0.121	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.011	0.023	37.396	0.001	0.001	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.961	-0.980	39.656	-0.091	-0.091	0.000	0.000	0.000	0.000
43	A	44	TYR	0	-0.037	-0.031	34.157	0.000	0.000	0.000	0.000	0.000	0.000
44	A	45	VAL	0	-0.010	0.007	32.260	0.000	0.000	0.000	0.000	0.000	0.000
45	A	46	ILE	0	-0.019	-0.002	28.599	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.056	-0.040	26.777	0.007	0.007	0.000	0.000	0.000	0.000
47	A	48	VAL	0	0.075	0.032	22.700	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.036	-0.021	21.707	0.019	0.019	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.920	0.962	17.787	0.281	0.281	0.000	0.000	0.000	0.000
50	A	51	THR	0	0.027	0.002	13.585	0.046	0.046	0.000	0.000	0.000	0.000
51	A	52	LYS	1	1.008	1.006	10.855	0.411	0.411	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.887	-0.920	9.297	-0.093	-0.093	0.000	0.000	0.000	0.000
53	A	54	LYS	1	1.028	0.995	3.098	-3.960	-3.472	0.023	-0.150	-0.362	0.001
54	A	55	ARG	1	0.903	0.938	7.106	-0.923	-0.923	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.006	0.014	9.774	0.051	0.051	0.000	0.000	0.000	0.000
56	A	57	LEU	0	0.033	0.017	11.088	0.063	0.063	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.049	-0.015	11.426	-0.080	-0.080	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.922	0.964	13.110	0.172	0.172	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.060	0.020	15.914	0.024	0.024	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.007	0.012	11.938	0.091	0.091	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.888	-0.945	15.315	-0.069	-0.069	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.058	-0.022	17.800	0.030	0.030	0.000	0.000	0.000	0.000
63	A	64	PHE	0	0.056	0.016	17.632	0.024	0.024	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.814	0.919	14.600	0.426	0.426	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.001	0.001	20.699	0.021	0.021	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.059	-0.045	23.238	0.013	0.013	0.000	0.000	0.000	0.000
67	A	68	GLN	0	-0.015	0.006	24.117	0.006	0.006	0.000	0.000	0.000	0.000
68	A	69	ILE	0	0.006	0.005	23.229	0.005	0.005	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.010	-0.001	18.538	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.875	-0.929	22.036	-0.233	-0.233	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.001	-0.009	24.615	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	73	ALA	0	-0.006	-0.006	20.433	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.702	0.838	18.586	0.398	0.398	0.000	0.000	0.000	0.000
74	A	75	MET	0	-0.007	0.001	21.340	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	76	MET	0	0.018	0.005	23.426	0.002	0.002	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.054	-0.035	16.904	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.858	-0.953	20.737	-0.426	-0.426	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.968	-0.973	22.368	-0.222	-0.222	0.000	0.000	0.000	0.000
79	A	80	GLY	0	-0.011	0.007	22.941	0.014	0.014	0.000	0.000	0.000	0.000
80	A	81	TYR	0	-0.076	-0.032	17.916	-0.031	-0.031	0.000	0.000	0.000	0.000
81	A	82	PHE	0	0.028	0.010	20.623	0.033	0.033	0.000	0.000	0.000	0.000
82	A	83	GLY	0	-0.014	-0.004	20.039	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.956	-0.987	14.367	-0.681	-0.681	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.943	-0.978	15.582	-0.511	-0.511	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.035	-0.009	15.247	0.009	0.009	0.000	0.000	0.000	0.000
86	A	87	ILE	0	-0.044	-0.010	18.799	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	88	ILE	0	0.009	0.008	19.948	0.018	0.018	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.930	0.974	23.113	0.207	0.207	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.018	0.001	23.781	0.004	0.004	0.000	0.000	0.000	0.000
90	A	91	HIS	0	0.090	0.030	26.853	0.007	0.007	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.811	0.888	29.016	0.120	0.120	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.022	-0.019	30.390	0.008	0.008	0.000	0.000	0.000	0.000
93	A	94	VAL	0	-0.024	-0.017	28.569	0.007	0.007	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.059	0.045	26.217	0.004	0.004	0.000	0.000	0.000	0.000
95	A	96	TYR	0	-0.033	-0.017	27.399	0.009	0.009	0.000	0.000	0.000	0.000
96	A	97	VAL	0	-0.043	-0.018	29.955	0.010	0.010	0.000	0.000	0.000	0.000
97	A	98	GLY	0	-0.042	-0.013	26.020	0.007	0.007	0.000	0.000	0.000	0.000
98	A	99	LYS	1	0.871	0.939	25.186	0.104	0.104	0.000	0.000	0.000	0.000
99	A	100	VAL	0	0.043	0.012	21.885	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	101	ASN	0	0.010	-0.003	25.275	0.007	0.007	0.000	0.000	0.000	0.000
101	A	102	PHE	0	0.064	0.023	22.136	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.044	-0.010	28.047	0.004	0.004	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.879	-0.955	29.983	-0.177	-0.177	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.853	-0.924	32.746	-0.114	-0.114	0.000	0.000	0.000	0.000
105	A	106	SER	0	-0.060	-0.034	32.420	0.007	0.007	0.000	0.000	0.000	0.000
106	A	107	PRO	0	-0.038	-0.039	34.546	0.002	0.002	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.007	-0.004	35.522	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.034	0.044	33.440	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	110	PRO	0	0.018	0.041	29.062	0.004	0.004	0.000	0.000	0.000	0.000
110	A	111	ILE	0	-0.059	-0.041	24.569	0.004	0.004	0.000	0.000	0.000	0.000
111	A	112	THR	0	-0.007	0.001	23.865	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	113	ILE	0	-0.051	-0.029	18.593	0.001	0.001	0.000	0.000	0.000	0.000
113	A	114	THR	0	0.092	0.036	18.462	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	115	ILE	0	-0.052	-0.026	13.373	-0.038	-0.038	0.000	0.000	0.000	0.000
115	A	116	ARG	1	1.037	1.028	12.845	0.666	0.666	0.000	0.000	0.000	0.000
116	A	117	THR	0	-0.039	-0.044	10.336	-0.149	-0.149	0.000	0.000	0.000	0.000
117	A	118	LYS	1	1.041	1.026	8.914	1.156	1.156	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.992	-0.996	7.103	-2.383	-2.383	0.000	0.000	0.000	0.000
119	A	120	PRO	0	0.076	0.044	11.226	-0.134	-0.134	0.000	0.000	0.000	0.000
120	A	121	GLN	0	0.019	0.002	14.126	0.037	0.037	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.958	0.970	8.839	1.158	1.158	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.032	0.033	10.356	-0.016	-0.016	0.000	0.000	0.000	0.000
123	A	124	MET	0	0.029	0.015	11.603	0.075	0.075	0.000	0.000	0.000	0.000
124	A	125	LYS	1	0.914	0.967	13.871	0.583	0.583	0.000	0.000	0.000	0.000
125	A	126	TRP	0	-0.020	0.006	8.846	-0.018	-0.018	0.000	0.000	0.000	0.000
126	A	127	LEU	0	-0.016	-0.019	12.114	0.112	0.112	0.000	0.000	0.000	0.000
127	A	128	ALA	0	-0.029	-0.019	13.889	0.095	0.095	0.000	0.000	0.000	0.000
128	A	129	PRO	0	0.019	0.038	15.865	0.017	0.017	0.000	0.000	0.000	0.000
129	A	130	ARG	1	0.948	0.966	17.862	0.293	0.293	0.000	0.000	0.000	0.000
130	A	131	THR	0	-0.038	-0.023	20.720	0.010	0.010	0.000	0.000	0.000	0.000
131	A	132	LYS	1	0.983	0.988	23.197	0.113	0.113	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.882	-0.939	26.611	-0.093	-0.093	0.000	0.000	0.000	0.000
133	A	134	GLY	0	-0.012	-0.007	23.192	0.010	0.010	0.000	0.000	0.000	0.000
134	A	135	VAL	0	-0.028	-0.013	22.175	-0.010	-0.010	0.000	0.000	0.000	0.000
135	A	136	PRO	0	-0.011	-0.007	19.270	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	137	ILE	0	-0.027	-0.011	21.448	0.021	0.021	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.784	-0.876	18.478	-0.411	-0.411	0.000	0.000	0.000	0.000

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