FMO DATABASE

FMODB ID: Z6Y7N

Calculation Name: 3B48-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B48

Chain ID: A

ChEMBL ID:

UniProt ID: Q835L8

Base Structure: X-ray

Registration Date: 2023-06-21

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1081013.206344
FMO2-HF: Nuclear repulsion	1030304.293181
FMO2-HF: Total energy	-50708.913163
FMO2-MP2: Total energy	-50853.947213

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-14.871	-6.841	9.384	-4.614	-12.8	-0.033

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.016

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	3	ALA	0	0.047	0.035	3.598	-0.123	1.925	0.117	-0.707	-1.458	0.000
4	A	4	ASP	-1	-0.765	-0.860	5.121	0.002	0.058	0.001	-0.025	-0.033	0.000
5	A	5	ILE	0	-0.016	-0.012	8.510	0.108	0.108	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.001	0.002	10.932	-0.059	-0.059	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.026	-0.012	13.913	-0.027	-0.027	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.044	0.023	17.072	-0.012	-0.012	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.004	-0.051	19.832	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.027	-0.006	23.365	0.007	0.007	0.000	0.000	0.000	0.000
11	A	11	SER	0	0.014	-0.006	25.928	0.000	0.000	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.960	0.959	24.567	-0.115	-0.115	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.017	-0.012	25.010	0.002	0.002	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.005	0.006	22.676	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.020	0.000	20.287	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.813	-0.851	20.519	0.123	0.123	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.016	0.012	22.150	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.022	-0.021	17.398	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.799	0.876	16.941	-0.210	-0.210	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.910	-0.953	18.157	0.049	0.049	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.065	-0.028	18.879	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.025	-0.028	13.499	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.806	-0.885	15.515	0.135	0.135	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.070	-0.030	16.779	0.003	0.003	0.000	0.000	0.000	0.000
25	A	25	MET	0	-0.128	-0.053	17.627	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.011	-0.004	12.759	-0.029	-0.029	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.064	0.059	13.385	0.035	0.035	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.078	-0.073	8.893	-0.139	-0.139	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.936	-0.941	10.261	0.148	0.148	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.995	-1.011	7.348	1.232	1.232	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.035	-0.004	5.573	0.068	0.068	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.003	0.012	8.903	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.003	0.002	11.410	0.045	0.045	0.000	0.000	0.000	0.000
34	A	34	HIS	0	-0.008	-0.025	12.663	-0.083	-0.083	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.011	-0.030	16.233	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.054	-0.043	16.830	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.006	0.013	20.624	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.057	-0.025	23.303	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.062	-0.018	26.115	0.009	0.009	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.082	0.030	27.859	0.001	0.001	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.929	-0.944	28.878	0.079	0.079	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.003	-0.004	29.048	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.102	-0.076	30.136	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.045	-0.028	30.094	0.005	0.005	0.000	0.000	0.000	0.000
45	A	45	GLY	0	-0.025	-0.018	29.029	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.036	0.011	25.622	0.005	0.005	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.842	-0.938	24.689	0.124	0.124	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.001	0.003	22.363	0.012	0.012	0.000	0.000	0.000	0.000
49	A	49	MET	0	0.000	0.014	21.794	0.015	0.015	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.978	1.001	21.305	-0.154	-0.154	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.033	0.004	16.699	0.025	0.025	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.035	0.015	17.594	0.036	0.036	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.888	-0.938	18.747	0.203	0.203	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.026	-0.027	14.786	0.018	0.018	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.076	-0.039	12.501	0.044	0.044	0.000	0.000	0.000	0.000
56	A	56	ASN	0	-0.083	-0.055	15.180	0.018	0.018	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.989	-0.983	17.911	0.244	0.244	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.057	0.000	12.534	0.025	0.025	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.855	-0.930	10.654	0.659	0.659	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.034	-0.032	11.437	0.017	0.017	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.934	-0.970	7.766	1.010	1.010	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.829	0.899	6.163	-0.655	-0.655	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.875	-0.924	2.166	-0.624	-0.352	2.063	-0.479	-1.856	-0.002
64	A	64	PHE	0	0.021	0.003	5.509	0.054	0.054	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.011	0.000	5.546	-0.227	-0.136	-0.001	-0.004	-0.086	0.000
66	A	66	ILE	0	0.008	-0.008	9.357	-0.111	-0.111	0.000	0.000	0.000	0.000
67	A	67	PHE	0	0.021	0.016	10.662	-0.054	-0.054	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.047	0.012	15.444	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.794	-0.857	19.190	0.056	0.056	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.054	-0.034	22.338	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.019	-0.005	24.390	0.008	0.008	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.016	-0.008	25.690	0.002	0.002	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.019	0.012	22.038	0.006	0.006	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.030	0.020	20.706	0.017	0.017	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.041	0.024	21.291	0.007	0.007	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.035	-0.015	22.571	0.002	0.002	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.005	-0.018	17.535	0.018	0.018	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.908	-0.937	17.974	0.100	0.100	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.010	-0.005	19.829	0.001	0.001	0.000	0.000	0.000	0.000
80	A	80	ALA	0	-0.008	-0.019	18.525	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.014	0.001	13.486	0.011	0.011	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.896	-0.954	17.233	0.089	0.089	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.146	-0.051	20.375	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.054	-0.012	14.543	0.019	0.019	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.899	-0.948	17.349	0.117	0.117	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.928	-0.973	16.128	0.077	0.077	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.940	-0.975	13.925	0.142	0.142	0.000	0.000	0.000	0.000
88	A	88	GLN	0	-0.024	-0.034	12.132	0.015	0.015	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.005	-0.011	11.754	0.052	0.052	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.914	0.973	7.692	0.147	0.147	0.000	0.000	0.000	0.000
91	A	91	HIS	1	0.831	0.914	6.521	-0.602	-0.602	0.000	0.000	0.000	0.000
92	A	92	TYR	0	0.006	0.011	7.866	0.283	0.283	0.000	0.000	0.000	0.000
93	A	93	HIS	1	0.772	0.863	5.294	-0.769	-0.769	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.041	0.035	9.880	0.047	0.047	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.024	-0.010	10.505	-0.025	-0.025	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.964	-0.964	13.092	-0.021	-0.021	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.032	-0.001	14.830	-0.037	-0.037	0.000	0.000	0.000	0.000
98	A	98	PRO	0	-0.039	-0.008	16.806	0.017	0.017	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.009	0.005	17.640	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.012	-0.006	17.531	0.008	0.008	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.836	-0.939	17.479	-0.045	-0.045	0.000	0.000	0.000	0.000
102	A	102	GLY	0	0.039	0.023	15.304	-0.038	-0.038	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.023	0.013	13.168	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	104	PHE	0	-0.019	-0.010	12.495	-0.030	-0.030	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.007	0.005	12.821	-0.060	-0.060	0.000	0.000	0.000	0.000
106	A	106	SER	0	-0.010	-0.012	8.812	-0.092	-0.092	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.036	0.014	7.929	-0.246	-0.246	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.033	-0.009	8.933	-0.158	-0.158	0.000	0.000	0.000	0.000
109	A	109	THR	0	-0.052	-0.015	7.398	-0.257	-0.257	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.044	0.009	4.462	-0.416	-0.299	-0.001	-0.012	-0.104	0.000
111	A	111	GLY	0	0.035	0.051	3.978	-1.534	-1.390	-0.001	-0.053	-0.091	0.000
112	A	112	VAL	0	-0.144	-0.079	6.242	0.348	0.348	0.000	0.000	0.000	0.000
113	A	113	SER	0	-0.040	-0.022	5.347	0.278	0.278	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.904	-0.947	2.411	-8.500	-6.572	2.463	-1.620	-2.771	-0.004
115	A	115	ASP	-1	-0.848	-0.924	2.544	-5.177	-3.734	1.575	-0.773	-2.244	-0.027
116	A	116	LEU	0	0.025	0.000	2.348	-0.892	0.161	2.815	-0.777	-3.091	0.000
117	A	117	THR	0	-0.061	-0.059	4.020	0.388	0.555	0.010	-0.001	-0.175	0.000
118	A	118	GLN	0	-0.021	-0.023	7.081	0.316	0.316	0.000	0.000	0.000	0.000
119	A	119	ILE	0	0.002	0.017	3.049	-0.313	0.398	0.343	-0.163	-0.891	0.000
120	A	120	LEU	0	-0.015	-0.005	6.907	0.124	0.124	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.016	0.022	9.597	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.920	-0.959	10.939	-0.389	-0.389	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.022	-0.011	11.338	0.047	0.047	0.000	0.000	0.000	0.000
124	A	124	GLN	0	-0.040	-0.039	12.585	0.024	0.024	0.000	0.000	0.000	0.000
125	A	125	ASN	0	-0.123	-0.051	15.418	0.029	0.029	0.000	0.000	0.000	0.000
126	A	126	ALA	0	0.019	0.031	15.800	-0.008	-0.008	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.021	-0.001	17.816	0.020	0.020	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.866	0.941	21.221	0.113	0.113	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.891	0.929	23.088	0.052	0.052	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.005	0.006	25.696	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	131	TRP	0	-0.016	-0.014	27.594	0.006	0.006	0.000	0.000	0.000	0.000
132	A	132	ASN	0	0.031	0.025	29.907	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:1:MET)