FMO DATABASE

FMODB ID: 6N44Z

Calculation Name: 5D5X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D5X

Chain ID: B

ChEMBL ID:

UniProt ID: G0SB31

Base Structure: X-ray

Registration Date: 2023-06-22

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-891047.445404
FMO2-HF: Nuclear repulsion	847874.281779
FMO2-HF: Total energy	-43173.163625
FMO2-MP2: Total energy	-43302.076522

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(B:41:SER)

Summations of interaction energy for fragment #1(B:41: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.
-23.973	-18.595	1.845	-3.232	-3.993	0.019

Interaction energy analysis for fragmet #1(B:41:SER)

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 : -0.002

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	B	43	PHE	0	-0.030	-0.011	3.788	-6.209	-3.208	0.011	-1.514	-1.498	0.003
4	B	44	VAL	0	0.104	0.045	4.067	-1.348	-1.127	-0.001	-0.021	-0.200	0.000
5	B	45	ARG	1	0.976	1.003	3.659	2.359	2.731	0.002	-0.076	-0.299	0.000
6	B	46	LYS	1	0.888	0.959	7.379	-1.853	-1.853	0.000	0.000	0.000	0.000
7	B	47	LEU	0	-0.005	0.006	8.625	-0.160	-0.160	0.000	0.000	0.000	0.000
8	B	48	TYR	0	-0.036	-0.043	9.762	-0.138	-0.138	0.000	0.000	0.000	0.000
9	B	49	LYS	1	0.874	0.948	11.364	-0.160	-0.160	0.000	0.000	0.000	0.000
10	B	50	MET	0	-0.048	-0.022	13.051	0.007	0.007	0.000	0.000	0.000	0.000
11	B	51	LEU	0	0.003	-0.005	13.875	-0.040	-0.040	0.000	0.000	0.000	0.000
12	B	52	GLU	-1	-0.844	-0.916	15.703	-0.064	-0.064	0.000	0.000	0.000	0.000
13	B	53	ASP	-1	-0.885	-0.912	18.030	0.194	0.194	0.000	0.000	0.000	0.000
14	B	54	PRO	0	0.025	0.006	20.478	0.021	0.021	0.000	0.000	0.000	0.000
15	B	55	SER	0	-0.050	-0.047	23.600	0.007	0.007	0.000	0.000	0.000	0.000
16	B	56	TYR	0	-0.062	-0.062	18.372	0.003	0.003	0.000	0.000	0.000	0.000
17	B	57	HIS	0	0.049	0.034	23.317	0.026	0.026	0.000	0.000	0.000	0.000
18	B	58	SER	0	0.012	0.005	24.891	0.000	0.000	0.000	0.000	0.000	0.000
19	B	59	VAL	0	-0.040	0.003	21.985	0.009	0.009	0.000	0.000	0.000	0.000
20	B	60	VAL	0	-0.032	-0.036	17.775	0.036	0.036	0.000	0.000	0.000	0.000
21	B	61	ARG	1	0.900	0.962	20.041	-0.201	-0.201	0.000	0.000	0.000	0.000
22	B	62	TRP	0	0.011	-0.006	14.095	0.038	0.038	0.000	0.000	0.000	0.000
23	B	63	SER	0	0.014	-0.003	20.020	-0.005	-0.005	0.000	0.000	0.000	0.000
24	B	64	ASP	-1	-0.872	-0.930	22.410	0.108	0.108	0.000	0.000	0.000	0.000
25	B	65	ASP	-1	-0.894	-0.939	23.421	0.066	0.066	0.000	0.000	0.000	0.000
26	B	66	GLY	0	-0.083	-0.043	20.484	-0.019	-0.019	0.000	0.000	0.000	0.000
27	B	67	ASP	-1	-0.901	-0.953	18.408	0.088	0.088	0.000	0.000	0.000	0.000
28	B	68	SER	0	-0.101	-0.081	16.996	0.015	0.015	0.000	0.000	0.000	0.000
29	B	69	PHE	0	-0.003	0.002	13.391	0.029	0.029	0.000	0.000	0.000	0.000
30	B	70	VAL	0	0.063	0.032	18.062	0.039	0.039	0.000	0.000	0.000	0.000
31	B	71	VAL	0	-0.080	-0.045	18.593	0.017	0.017	0.000	0.000	0.000	0.000
32	B	72	LEU	0	0.009	-0.007	21.220	-0.012	-0.012	0.000	0.000	0.000	0.000
33	B	73	GLU	-1	-0.814	-0.899	24.563	0.228	0.228	0.000	0.000	0.000	0.000
34	B	74	ASN	0	0.045	0.001	22.338	-0.003	-0.003	0.000	0.000	0.000	0.000
35	B	75	GLU	-1	-0.798	-0.856	23.310	0.381	0.381	0.000	0.000	0.000	0.000
36	B	76	LYS	1	1.002	0.991	25.083	-0.223	-0.223	0.000	0.000	0.000	0.000
37	B	77	PHE	0	0.037	0.055	16.106	0.017	0.017	0.000	0.000	0.000	0.000
38	B	78	THR	0	-0.077	-0.077	20.505	0.069	0.069	0.000	0.000	0.000	0.000
39	B	79	LYS	1	0.824	0.893	21.118	-0.305	-0.305	0.000	0.000	0.000	0.000
40	B	80	THR	0	-0.072	-0.054	22.996	-0.017	-0.017	0.000	0.000	0.000	0.000
41	B	81	ILE	0	0.024	0.023	17.738	0.023	0.023	0.000	0.000	0.000	0.000
42	B	82	LEU	0	-0.052	-0.025	15.325	0.072	0.072	0.000	0.000	0.000	0.000
43	B	83	PRO	0	-0.028	-0.007	15.725	0.136	0.136	0.000	0.000	0.000	0.000
44	B	84	LYS	1	0.956	0.980	16.293	-0.333	-0.333	0.000	0.000	0.000	0.000
45	B	85	HIS	0	0.011	0.039	13.321	-0.066	-0.066	0.000	0.000	0.000	0.000
46	B	86	PHE	0	-0.044	-0.038	8.944	0.277	0.277	0.000	0.000	0.000	0.000
47	B	87	LYS	1	0.917	0.979	12.169	-0.569	-0.569	0.000	0.000	0.000	0.000
48	B	88	HIS	0	0.000	-0.004	12.947	-0.203	-0.203	0.000	0.000	0.000	0.000
49	B	89	SER	0	0.064	0.021	16.415	0.008	0.008	0.000	0.000	0.000	0.000
50	B	90	ASN	0	0.039	0.020	18.230	-0.087	-0.087	0.000	0.000	0.000	0.000
51	B	91	PHE	0	0.095	0.033	17.784	0.132	0.132	0.000	0.000	0.000	0.000
52	B	92	ALA	0	0.068	0.034	17.663	0.067	0.067	0.000	0.000	0.000	0.000
53	B	93	SER	0	-0.023	-0.013	14.798	0.006	0.006	0.000	0.000	0.000	0.000
54	B	94	PHE	0	0.001	0.010	11.945	0.249	0.249	0.000	0.000	0.000	0.000
55	B	95	VAL	0	0.037	0.026	13.132	0.126	0.126	0.000	0.000	0.000	0.000
56	B	96	ARG	1	0.901	0.954	13.635	-0.927	-0.927	0.000	0.000	0.000	0.000
57	B	97	GLN	0	0.023	-0.017	6.495	-0.462	-0.462	0.000	0.000	0.000	0.000
58	B	98	LEU	0	0.023	0.027	9.609	0.178	0.178	0.000	0.000	0.000	0.000
59	B	99	ASN	0	0.062	0.028	10.907	-0.082	-0.082	0.000	0.000	0.000	0.000
60	B	100	LYS	1	0.820	0.915	9.039	-1.685	-1.685	0.000	0.000	0.000	0.000
61	B	101	TYR	0	-0.030	-0.032	2.372	-4.190	-2.694	1.835	-1.582	-1.749	0.016
62	B	102	ASP	-1	-0.864	-0.937	8.293	0.046	0.046	0.000	0.000	0.000	0.000
63	B	103	PHE	0	-0.039	0.001	8.553	-0.082	-0.082	0.000	0.000	0.000	0.000
64	B	104	HIS	0	-0.009	-0.005	12.981	0.050	0.050	0.000	0.000	0.000	0.000
65	B	105	LYS	1	0.897	0.955	16.693	-0.371	-0.371	0.000	0.000	0.000	0.000
66	B	106	VAL	0	0.043	0.008	19.310	-0.025	-0.025	0.000	0.000	0.000	0.000
67	B	107	ARG	1	0.786	0.884	21.831	-0.216	-0.216	0.000	0.000	0.000	0.000
68	B	108	HIS	0	0.074	0.054	25.235	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	109	ASN	0	0.005	-0.011	27.790	0.011	0.011	0.000	0.000	0.000	0.000
70	B	110	ASP	-1	-1.014	-1.018	31.388	0.106	0.106	0.000	0.000	0.000	0.000
71	B	111	GLU	-1	-0.757	-0.864	33.383	0.082	0.082	0.000	0.000	0.000	0.000
72	B	112	ASN	0	-0.136	-0.075	34.185	-0.007	-0.007	0.000	0.000	0.000	0.000
73	B	113	GLY	0	0.048	0.037	33.681	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	114	GLU	-1	-0.860	-0.924	28.631	0.111	0.111	0.000	0.000	0.000	0.000
75	B	115	SER	0	-0.101	-0.040	30.435	0.004	0.004	0.000	0.000	0.000	0.000
76	B	116	PRO	0	-0.061	-0.032	28.077	0.000	0.000	0.000	0.000	0.000	0.000
77	B	117	TYR	0	0.002	-0.022	25.186	0.002	0.002	0.000	0.000	0.000	0.000
78	B	118	GLY	0	0.062	0.031	28.441	0.005	0.005	0.000	0.000	0.000	0.000
79	B	119	ARG	1	0.905	0.933	28.738	-0.152	-0.152	0.000	0.000	0.000	0.000
80	B	120	ASP	-1	-0.946	-0.965	28.026	0.255	0.255	0.000	0.000	0.000	0.000
81	B	121	ALA	0	0.031	0.032	24.870	0.029	0.029	0.000	0.000	0.000	0.000
82	B	122	TRP	0	-0.111	-0.064	20.137	0.033	0.033	0.000	0.000	0.000	0.000
83	B	123	GLU	-1	-0.799	-0.861	20.185	0.249	0.249	0.000	0.000	0.000	0.000
84	B	124	PHE	0	-0.053	-0.036	15.130	0.038	0.038	0.000	0.000	0.000	0.000
85	B	125	LYS	1	1.021	1.008	16.083	-0.152	-0.152	0.000	0.000	0.000	0.000
86	B	126	HIS	0	0.030	0.011	10.363	-0.008	-0.008	0.000	0.000	0.000	0.000
87	B	127	PRO	0	0.046	0.028	13.848	-0.034	-0.034	0.000	0.000	0.000	0.000
88	B	128	GLU	-1	-0.881	-0.922	11.450	-0.298	-0.298	0.000	0.000	0.000	0.000
89	B	129	PHE	0	-0.070	-0.036	9.799	-0.048	-0.048	0.000	0.000	0.000	0.000
90	B	130	ARG	1	0.970	0.968	12.565	0.174	0.174	0.000	0.000	0.000	0.000
91	B	131	ALA	0	0.043	0.028	15.227	-0.048	-0.048	0.000	0.000	0.000	0.000
92	B	132	ASP	-1	-0.892	-0.927	17.408	-0.127	-0.127	0.000	0.000	0.000	0.000
93	B	133	ARG	1	0.845	0.922	14.610	0.286	0.286	0.000	0.000	0.000	0.000
94	B	134	LYS	1	0.873	0.935	12.794	0.164	0.164	0.000	0.000	0.000	0.000
95	B	135	ASP	-1	-0.889	-0.960	11.829	-0.555	-0.555	0.000	0.000	0.000	0.000
96	B	136	ASN	0	-0.030	-0.025	11.840	-0.187	-0.187	0.000	0.000	0.000	0.000
97	B	137	LEU	0	-0.032	-0.026	7.238	-0.025	-0.025	0.000	0.000	0.000	0.000
98	B	138	ASP	-1	-0.894	-0.939	5.790	-2.654	-2.654	0.000	0.000	0.000	0.000
99	B	139	ASN	0	-0.118	-0.057	6.772	-0.198	-0.198	0.000	0.000	0.000	0.000
100	B	140	ILE	0	-0.019	0.016	6.441	0.370	0.370	0.000	0.000	0.000	0.000
101	B	141	ARG	1	0.948	0.964	4.831	0.418	0.483	-0.001	-0.005	-0.059	0.000
102	B	142	ARG	1	0.887	0.938	4.088	-6.098	-5.875	-0.001	-0.034	-0.188	0.000
103	B	143	LYS	1	0.914	0.988	6.626	-0.787	-0.787	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:41:SER)