FMO DATABASE

FMODB ID: ZYZ7N

Calculation Name: 3DB5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DB5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UKN5

Base Structure: X-ray

Registration Date: 2023-03-14

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1102137.106974
FMO2-HF: Nuclear repulsion	1050192.460437
FMO2-HF: Total energy	-51944.646537
FMO2-MP2: Total energy	-52094.949552

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:4:PRO)

Summations of interaction energy for fragment #1(A:4:PRO)

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.
-1.583	0.61	-0.006	-1.072	-1.115	0.004

Interaction energy analysis for fragmet #1(A:4:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.006

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

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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	6	THR	0	-0.001	-0.002	3.568	-1.573	0.620	-0.006	-1.072	-1.115	0.004
4	A	7	PHE	0	0.006	-0.012	5.860	0.354	0.354	0.000	0.000	0.000	0.000
5	A	8	VAL	0	0.001	-0.006	9.007	0.022	0.022	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.039	-0.011	12.534	0.058	0.058	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.881	-0.929	15.221	-0.300	-0.300	0.000	0.000	0.000	0.000
8	A	11	THR	0	-0.044	-0.037	18.815	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	12	PRO	0	-0.027	-0.014	20.538	0.022	0.022	0.000	0.000	0.000	0.000
10	A	13	ILE	0	-0.011	0.001	23.033	0.006	0.006	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.928	-0.963	26.528	-0.148	-0.148	0.000	0.000	0.000	0.000
12	A	15	SER	0	0.000	-0.012	29.391	0.005	0.005	0.000	0.000	0.000	0.000
13	A	16	ARG	1	0.988	0.986	32.510	0.070	0.070	0.000	0.000	0.000	0.000
14	A	17	ALA	0	-0.016	0.004	35.398	0.000	0.000	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.850	0.885	32.402	0.116	0.116	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.004	0.014	30.503	0.000	0.000	0.000	0.000	0.000	0.000
17	A	20	SER	0	-0.082	-0.040	34.642	0.004	0.004	0.000	0.000	0.000	0.000
18	A	21	LEU	0	-0.004	0.001	37.555	0.006	0.006	0.000	0.000	0.000	0.000
19	A	22	PRO	0	-0.005	-0.003	38.768	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.882	0.941	38.830	0.091	0.091	0.000	0.000	0.000	0.000
21	A	24	GLN	0	-0.013	-0.011	39.783	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	25	LEU	0	-0.015	-0.002	41.450	0.004	0.004	0.000	0.000	0.000	0.000
23	A	26	VAL	0	0.037	0.008	38.059	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.029	0.001	35.755	0.006	0.006	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.958	0.973	37.080	0.085	0.085	0.000	0.000	0.000	0.000
26	A	29	GLN	0	-0.036	0.000	38.915	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	30	SER	0	-0.067	-0.069	40.533	0.002	0.002	0.000	0.000	0.000	0.000
28	A	31	ILE	0	0.004	0.022	44.142	0.000	0.000	0.000	0.000	0.000	0.000
29	A	32	VAL	0	-0.107	-0.072	47.192	0.001	0.001	0.000	0.000	0.000	0.000
30	A	33	GLY	0	0.043	0.014	46.545	0.003	0.003	0.000	0.000	0.000	0.000
31	A	34	ALA	0	-0.034	-0.016	44.137	0.002	0.002	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.844	-0.928	40.624	-0.066	-0.066	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.038	0.018	36.690	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	37	GLY	0	0.062	0.033	39.935	0.005	0.005	0.000	0.000	0.000	0.000
35	A	38	VAL	0	-0.014	-0.004	41.110	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	39	TRP	0	-0.034	-0.020	42.175	0.004	0.004	0.000	0.000	0.000	0.000
37	A	40	THR	0	-0.020	-0.021	43.078	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	41	GLY	0	0.035	0.024	42.208	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.862	-0.923	43.070	-0.089	-0.089	0.000	0.000	0.000	0.000
40	A	43	THR	0	0.002	-0.015	46.230	0.001	0.001	0.000	0.000	0.000	0.000
41	A	44	ILE	0	-0.026	-0.003	46.735	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	45	PRO	0	0.032	0.026	50.798	0.002	0.002	0.000	0.000	0.000	0.000
43	A	46	VAL	0	0.021	0.030	54.326	0.000	0.000	0.000	0.000	0.000	0.000
44	A	47	ARG	1	0.880	0.933	56.703	0.046	0.046	0.000	0.000	0.000	0.000
45	A	48	THR	0	0.027	0.033	50.446	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	49	CYS	0	-0.052	-0.034	52.901	0.000	0.000	0.000	0.000	0.000	0.000
47	A	50	PHE	0	0.034	0.017	46.991	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.012	0.016	48.321	0.003	0.003	0.000	0.000	0.000	0.000
49	A	52	PRO	0	0.004	-0.010	48.330	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	53	LEU	0	-0.031	-0.041	46.223	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	54	ILE	0	-0.064	-0.024	42.805	0.002	0.002	0.000	0.000	0.000	0.000
52	A	55	GLY	0	0.042	-0.015	44.048	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	56	GLN	0	0.030	0.024	41.699	0.001	0.001	0.000	0.000	0.000	0.000
54	A	57	GLN	0	0.007	0.000	45.420	0.000	0.000	0.000	0.000	0.000	0.000
55	A	58	SER	0	0.012	0.001	48.743	0.001	0.001	0.000	0.000	0.000	0.000
56	A	59	HIS	0	0.028	0.032	50.965	0.000	0.000	0.000	0.000	0.000	0.000
57	A	71	VAL	0	0.025	-0.009	48.267	0.000	0.000	0.000	0.000	0.000	0.000
58	A	72	ASN	0	-0.022	-0.013	48.723	0.000	0.000	0.000	0.000	0.000	0.000
59	A	73	HIS	0	0.025	0.028	45.637	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	74	ILE	0	0.006	-0.006	48.190	0.000	0.000	0.000	0.000	0.000	0.000
61	A	75	TRP	0	-0.022	-0.001	48.731	0.002	0.002	0.000	0.000	0.000	0.000
62	A	76	LYS	1	0.953	0.975	52.944	0.033	0.033	0.000	0.000	0.000	0.000
63	A	77	ILE	0	0.013	0.017	53.898	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	78	TYR	0	-0.007	-0.018	57.085	0.001	0.001	0.000	0.000	0.000	0.000
65	A	79	HIS	0	0.011	0.010	60.540	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	80	ASN	0	-0.002	-0.011	62.481	0.001	0.001	0.000	0.000	0.000	0.000
67	A	81	GLY	0	-0.002	0.008	65.446	0.001	0.001	0.000	0.000	0.000	0.000
68	A	82	VAL	0	0.028	0.030	62.358	0.001	0.001	0.000	0.000	0.000	0.000
69	A	83	LEU	0	-0.070	-0.042	57.515	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	84	GLU	-1	-0.909	-0.961	58.165	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	85	PHE	0	-0.024	-0.019	52.157	0.000	0.000	0.000	0.000	0.000	0.000
72	A	86	CYS	0	-0.039	-0.019	52.455	0.000	0.000	0.000	0.000	0.000	0.000
73	A	87	ILE	0	-0.002	0.016	47.745	0.000	0.000	0.000	0.000	0.000	0.000
74	A	88	ILE	0	0.017	0.007	45.004	0.000	0.000	0.000	0.000	0.000	0.000
75	A	89	THR	0	-0.045	-0.058	44.307	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	90	THR	0	0.066	0.027	41.503	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	91	ASP	-1	-0.810	-0.890	37.150	-0.074	-0.074	0.000	0.000	0.000	0.000
78	A	92	GLU	-1	-0.739	-0.865	34.488	-0.102	-0.102	0.000	0.000	0.000	0.000
79	A	93	ASN	0	-0.070	-0.039	33.174	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	94	GLU	-1	-0.942	-0.978	36.242	-0.057	-0.057	0.000	0.000	0.000	0.000
81	A	95	CYS	0	-0.090	-0.014	39.512	0.005	0.005	0.000	0.000	0.000	0.000
82	A	96	ASN	0	0.035	0.014	39.542	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	97	TRP	0	0.096	0.027	39.953	0.003	0.003	0.000	0.000	0.000	0.000
84	A	98	MET	0	-0.073	-0.007	41.060	0.001	0.001	0.000	0.000	0.000	0.000
85	A	99	MET	0	-0.024	0.001	39.577	0.002	0.002	0.000	0.000	0.000	0.000
86	A	100	PHE	0	-0.024	-0.014	36.850	0.001	0.001	0.000	0.000	0.000	0.000
87	A	101	VAL	0	-0.067	-0.016	42.646	0.000	0.000	0.000	0.000	0.000	0.000
88	A	102	ARG	1	0.905	0.939	41.439	0.073	0.073	0.000	0.000	0.000	0.000
89	A	103	LYS	1	0.916	0.965	47.851	0.044	0.044	0.000	0.000	0.000	0.000
90	A	104	ALA	0	0.006	0.012	51.569	0.000	0.000	0.000	0.000	0.000	0.000
91	A	105	ARG	1	0.840	0.894	51.759	0.054	0.054	0.000	0.000	0.000	0.000
92	A	106	ASN	0	-0.038	-0.014	55.394	0.002	0.002	0.000	0.000	0.000	0.000
93	A	107	ARG	1	0.961	0.961	57.749	0.034	0.034	0.000	0.000	0.000	0.000
94	A	108	GLU	-1	-0.897	-0.944	58.768	-0.040	-0.040	0.000	0.000	0.000	0.000
95	A	109	GLU	-1	-0.819	-0.888	53.163	-0.053	-0.053	0.000	0.000	0.000	0.000
96	A	110	GLN	0	-0.031	-0.020	54.237	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	111	ASN	0	0.037	0.016	51.176	0.001	0.001	0.000	0.000	0.000	0.000
98	A	112	LEU	0	0.018	0.018	49.457	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	113	VAL	0	-0.028	-0.008	54.239	0.001	0.001	0.000	0.000	0.000	0.000
100	A	114	ALA	0	0.016	-0.001	53.553	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	115	TYR	0	-0.032	-0.034	55.255	0.002	0.002	0.000	0.000	0.000	0.000
102	A	116	PRO	0	0.023	0.005	56.104	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	117	HIS	0	-0.010	-0.012	56.666	0.002	0.002	0.000	0.000	0.000	0.000
104	A	118	ASP	-1	-0.876	-0.934	56.745	-0.039	-0.039	0.000	0.000	0.000	0.000
105	A	119	GLY	0	-0.008	-0.007	56.638	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	120	LYS	1	0.863	0.938	49.987	0.045	0.045	0.000	0.000	0.000	0.000
107	A	121	ILE	0	-0.008	0.009	51.438	0.001	0.001	0.000	0.000	0.000	0.000
108	A	122	PHE	0	0.048	0.025	51.450	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	123	PHE	0	-0.007	-0.006	47.849	0.002	0.002	0.000	0.000	0.000	0.000
110	A	124	CYS	0	-0.006	0.000	52.457	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	125	THR	0	-0.014	-0.018	52.198	0.002	0.002	0.000	0.000	0.000	0.000
112	A	126	SER	0	-0.032	-0.026	54.855	0.002	0.002	0.000	0.000	0.000	0.000
113	A	127	GLN	0	-0.048	-0.021	56.421	0.003	0.003	0.000	0.000	0.000	0.000
114	A	128	ASP	-1	-0.812	-0.917	55.144	-0.055	-0.055	0.000	0.000	0.000	0.000
115	A	129	ILE	0	-0.061	-0.022	50.239	0.001	0.001	0.000	0.000	0.000	0.000
116	A	130	PRO	0	0.002	0.003	51.039	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	131	PRO	0	0.046	0.034	46.126	0.000	0.000	0.000	0.000	0.000	0.000
118	A	132	GLU	-1	-0.926	-0.973	43.505	-0.087	-0.087	0.000	0.000	0.000	0.000
119	A	133	ASN	0	-0.092	-0.041	45.942	0.005	0.005	0.000	0.000	0.000	0.000
120	A	134	GLU	-1	-0.759	-0.855	45.695	-0.071	-0.071	0.000	0.000	0.000	0.000
121	A	135	LEU	0	-0.044	-0.028	46.443	0.004	0.004	0.000	0.000	0.000	0.000
122	A	136	LEU	0	0.005	0.002	48.311	0.000	0.000	0.000	0.000	0.000	0.000
123	A	137	PHE	0	0.008	0.016	49.889	0.003	0.003	0.000	0.000	0.000	0.000
124	A	138	TYR	0	-0.021	-0.025	53.050	0.002	0.002	0.000	0.000	0.000	0.000
125	A	139	TYR	0	0.021	0.035	54.129	0.000	0.000	0.000	0.000	0.000	0.000
126	A	140	SER	0	0.065	0.024	58.156	0.001	0.001	0.000	0.000	0.000	0.000
127	A	141	ARG	1	0.854	0.927	60.950	0.037	0.037	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:PRO)