FMO DATABASE

FMODB ID: Z6Y3N

Calculation Name: 3UIY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UIY

Chain ID: A

ChEMBL ID:

UniProt ID: P12061

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	OptAll
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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1117155.787491
FMO2-HF: Nuclear repulsion	1066708.737321
FMO2-HF: Total energy	-50447.05017
FMO2-MP2: Total energy	-50596.66798

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:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

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.
-27.726	-9.953	14.877	-11.074	-21.575	-0.053

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : 0.007

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	5	LEU	0	0.028	0.024	2.874	-2.703	0.662	0.496	-1.623	-2.238	-0.001
4	A	6	MET	0	-0.025	-0.005	4.591	0.092	0.135	-0.001	-0.009	-0.032	0.000
5	A	7	ILE	0	0.026	0.003	8.315	0.048	0.048	0.000	0.000	0.000	0.000
6	A	8	LYS	1	0.897	0.946	11.162	0.322	0.322	0.000	0.000	0.000	0.000
7	A	9	ILE	0	0.038	0.020	14.628	0.029	0.029	0.000	0.000	0.000	0.000
8	A	10	ASN	0	-0.040	-0.017	17.575	-0.013	-0.013	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.788	-0.876	20.806	-0.151	-0.151	0.000	0.000	0.000	0.000
10	A	12	ALA	0	-0.030	-0.018	24.250	0.004	0.004	0.000	0.000	0.000	0.000
11	A	13	VAL	0	-0.010	-0.015	26.959	0.001	0.001	0.000	0.000	0.000	0.000
12	A	14	PHE	0	-0.008	-0.008	25.217	0.002	0.002	0.000	0.000	0.000	0.000
13	A	15	TYR	0	0.006	-0.004	31.078	0.002	0.002	0.000	0.000	0.000	0.000
14	A	16	ASP	-1	-0.842	-0.899	33.446	-0.067	-0.067	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.780	0.839	32.421	0.061	0.061	0.000	0.000	0.000	0.000
16	A	18	ILE	0	-0.029	-0.001	24.797	0.000	0.000	0.000	0.000	0.000	0.000
17	A	19	THR	0	0.070	0.031	27.466	0.003	0.003	0.000	0.000	0.000	0.000
18	A	20	SER	0	-0.009	-0.016	25.630	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	21	ASN	0	-0.012	-0.016	22.215	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.937	0.992	22.694	0.145	0.145	0.000	0.000	0.000	0.000
21	A	23	ILE	0	0.031	0.018	17.977	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	24	ILE	0	-0.044	-0.034	18.495	0.012	0.012	0.000	0.000	0.000	0.000
23	A	25	GLY	0	-0.008	-0.012	16.357	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	26	THR	0	-0.038	-0.019	12.915	0.032	0.032	0.000	0.000	0.000	0.000
25	A	27	GLY	0	0.000	-0.002	9.278	-0.021	-0.021	0.000	0.000	0.000	0.000
26	A	28	HIS	0	0.009	0.028	7.406	0.187	0.187	0.000	0.000	0.000	0.000
27	A	29	LEU	0	-0.020	-0.019	2.556	-1.059	-0.399	0.388	-0.170	-0.878	0.000
28	A	30	PHE	0	0.013	0.004	3.042	-0.046	0.488	0.024	-0.152	-0.406	0.000
29	A	31	ASN	0	0.019	-0.011	2.370	-6.067	-3.155	2.796	-2.756	-2.952	-0.029
30	A	32	ARG	1	0.801	0.863	2.204	1.096	3.456	3.991	-2.126	-4.226	-0.016
31	A	33	GLU	-1	-0.865	-0.914	3.908	-0.036	0.120	0.008	-0.076	-0.089	0.000
32	A	34	GLY	0	0.016	0.008	7.165	0.506	0.506	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.801	0.913	2.403	-13.952	-12.668	0.898	-0.751	-1.431	0.008
34	A	36	LYS	1	0.891	0.951	6.638	-0.648	-0.648	0.000	0.000	0.000	0.000
35	A	37	ILE	0	-0.018	-0.007	2.476	-0.792	-0.049	0.505	-0.206	-1.043	-0.001
36	A	38	LEU	0	0.026	0.019	5.700	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	39	ILE	0	-0.001	-0.004	5.139	-0.227	-0.227	0.000	0.000	0.000	0.000
38	A	40	SER	0	-0.007	-0.014	7.737	0.124	0.124	0.000	0.000	0.000	0.000
39	A	41	SER	0	-0.022	-0.039	9.748	-0.062	-0.062	0.000	0.000	0.000	0.000
40	A	42	SER	0	0.022	0.011	12.244	0.036	0.036	0.000	0.000	0.000	0.000
41	A	43	LEU	0	-0.026	0.002	14.607	0.020	0.020	0.000	0.000	0.000	0.000
42	A	44	GLU	-1	-0.767	-0.861	17.356	-0.058	-0.058	0.000	0.000	0.000	0.000
43	A	45	LYS	1	0.884	0.945	15.847	0.058	0.058	0.000	0.000	0.000	0.000
44	A	46	ILE	0	-0.039	-0.017	19.908	0.009	0.009	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.831	0.890	21.694	0.058	0.058	0.000	0.000	0.000	0.000
46	A	48	ASN	0	-0.002	0.005	23.966	0.001	0.001	0.000	0.000	0.000	0.000
47	A	49	THR	0	-0.006	-0.012	20.070	0.002	0.002	0.000	0.000	0.000	0.000
48	A	50	PRO	0	0.060	0.041	16.918	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	51	GLY	0	0.029	0.018	14.229	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	52	ALA	0	-0.009	0.005	15.190	-0.025	-0.025	0.000	0.000	0.000	0.000
51	A	53	TYR	0	-0.017	-0.018	13.441	0.001	0.001	0.000	0.000	0.000	0.000
52	A	54	ILE	0	-0.047	-0.023	18.820	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	55	ILE	0	0.007	0.021	18.356	0.001	0.001	0.000	0.000	0.000	0.000
54	A	56	ARG	1	0.813	0.875	21.481	0.097	0.097	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.014	0.013	24.301	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	58	GLN	0	-0.044	-0.035	22.850	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	59	ASN	0	-0.056	-0.034	26.696	0.008	0.008	0.000	0.000	0.000	0.000
58	A	60	ASN	0	0.029	0.006	30.032	0.009	0.009	0.000	0.000	0.000	0.000
59	A	61	SER	0	0.036	0.030	27.915	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	62	ALA	0	0.015	0.011	28.702	0.002	0.002	0.000	0.000	0.000	0.000
61	A	63	HIS	0	-0.057	-0.039	29.096	0.009	0.009	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.867	0.919	26.248	0.073	0.073	0.000	0.000	0.000	0.000
63	A	65	LEU	0	0.029	0.026	21.853	0.004	0.004	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.868	0.939	22.216	0.071	0.071	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.001	0.002	16.279	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.938	0.962	17.473	0.136	0.136	0.000	0.000	0.000	0.000
67	A	69	ILE	0	-0.024	0.003	10.990	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	70	GLY	0	0.020	0.011	12.753	0.033	0.033	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.003	-0.007	13.667	-0.034	-0.034	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.863	-0.935	15.436	-0.139	-0.139	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.832	-0.888	12.456	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	74	TRP	0	-0.096	-0.044	6.391	0.010	0.010	0.000	0.000	0.000	0.000
73	A	75	GLN	0	0.025	0.008	13.461	0.020	0.020	0.000	0.000	0.000	0.000
74	A	76	PRO	0	-0.005	-0.019	14.362	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.764	-0.847	14.190	0.111	0.111	0.000	0.000	0.000	0.000
76	A	78	ASN	0	-0.070	-0.051	16.153	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.014	-0.024	15.769	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	80	GLY	0	0.006	0.005	18.098	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	81	ILE	0	0.008	0.005	12.167	-0.030	-0.030	0.000	0.000	0.000	0.000
80	A	82	GLY	0	-0.013	-0.024	11.855	-0.034	-0.034	0.000	0.000	0.000	0.000
81	A	83	MET	0	-0.045	0.002	11.239	0.034	0.034	0.000	0.000	0.000	0.000
82	A	84	VAL	0	0.027	0.001	9.815	-0.037	-0.037	0.000	0.000	0.000	0.000
83	A	85	SER	0	-0.003	0.009	8.711	0.007	0.007	0.000	0.000	0.000	0.000
84	A	86	HIS	0	0.029	0.001	9.291	0.097	0.097	0.000	0.000	0.000	0.000
85	A	87	SER	0	0.030	0.008	11.400	0.110	0.110	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.904	-0.950	8.851	0.280	0.280	0.000	0.000	0.000	0.000
87	A	89	PHE	0	0.034	0.016	8.664	-0.022	-0.022	0.000	0.000	0.000	0.000
88	A	90	THR	0	-0.047	-0.021	8.337	-0.057	-0.057	0.000	0.000	0.000	0.000
89	A	91	ASN	0	0.014	0.003	7.437	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.838	-0.899	8.121	-0.618	-0.618	0.000	0.000	0.000	0.000
91	A	93	PHE	0	-0.023	-0.009	6.571	0.053	0.053	0.000	0.000	0.000	0.000
92	A	94	ASN	0	0.043	0.010	11.189	-0.042	-0.042	0.000	0.000	0.000	0.000
93	A	95	ILE	0	-0.013	-0.007	11.717	0.001	0.001	0.000	0.000	0.000	0.000
94	A	96	TYR	0	0.007	-0.010	15.416	0.017	0.017	0.000	0.000	0.000	0.000
95	A	97	PHE	0	0.046	0.026	18.951	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	98	PHE	0	-0.019	-0.019	21.236	0.007	0.007	0.000	0.000	0.000	0.000
97	A	99	GLY	0	0.012	0.007	23.318	0.009	0.009	0.000	0.000	0.000	0.000
98	A	100	ASN	0	-0.045	-0.033	26.834	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	101	GLY	0	0.051	0.035	29.748	0.006	0.006	0.000	0.000	0.000	0.000
100	A	102	ASP	-1	-0.798	-0.879	29.536	-0.083	-0.083	0.000	0.000	0.000	0.000
101	A	103	ILE	0	-0.034	0.003	25.466	0.000	0.000	0.000	0.000	0.000	0.000
102	A	104	PRO	0	-0.021	-0.006	28.981	0.001	0.001	0.000	0.000	0.000	0.000
103	A	105	VAL	0	0.024	0.021	29.347	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	106	ASP	-1	-0.704	-0.822	27.780	-0.114	-0.114	0.000	0.000	0.000	0.000
105	A	107	THR	0	-0.020	-0.021	23.579	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	108	TYR	0	-0.039	-0.033	21.940	0.012	0.012	0.000	0.000	0.000	0.000
107	A	109	LEU	0	0.033	0.016	17.515	-0.018	-0.018	0.000	0.000	0.000	0.000
108	A	110	ILE	0	0.000	-0.002	14.280	0.013	0.013	0.000	0.000	0.000	0.000
109	A	111	SER	0	-0.006	-0.011	13.416	-0.056	-0.056	0.000	0.000	0.000	0.000
110	A	112	ILE	0	-0.003	0.004	8.225	0.053	0.053	0.000	0.000	0.000	0.000
111	A	113	TYR	0	0.013	0.001	6.439	-0.098	-0.098	0.000	0.000	0.000	0.000
112	A	114	ALA	0	0.041	0.023	2.798	-0.811	-0.127	0.455	-0.291	-0.848	0.000
113	A	115	THR	0	-0.047	-0.040	2.982	-0.690	0.259	0.658	-0.452	-1.154	-0.003
114	A	116	GLU	-1	-0.715	-0.837	2.872	5.048	7.407	1.043	-1.064	-2.338	-0.014
115	A	117	ILE	0	-0.051	-0.026	4.440	-0.050	-0.013	0.000	-0.011	-0.026	0.000
116	A	118	GLU	-1	-0.942	-0.959	8.059	0.586	0.586	0.000	0.000	0.000	0.000
117	A	129	LYS	1	0.863	0.935	2.380	-7.107	-6.162	2.515	-0.900	-2.559	0.003
118	A	130	ALA	0	-0.030	-0.014	2.474	-1.279	-0.739	1.102	-0.467	-1.174	0.000
119	A	131	VAL	0	0.030	0.007	4.179	-0.126	0.076	-0.001	-0.020	-0.181	0.000
120	A	132	VAL	0	-0.045	-0.017	7.392	-0.216	-0.216	0.000	0.000	0.000	0.000
121	A	133	GLN	0	0.045	0.019	9.739	0.120	0.120	0.000	0.000	0.000	0.000
122	A	134	ALA	0	0.011	0.020	13.372	-0.030	-0.030	0.000	0.000	0.000	0.000
123	A	135	ALA	0	0.014	0.014	15.969	0.026	0.026	0.000	0.000	0.000	0.000
124	A	136	VAL	0	-0.008	-0.006	19.658	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	137	THR	0	0.030	0.008	21.348	0.010	0.010	0.000	0.000	0.000	0.000
126	A	138	ILE	0	-0.018	0.015	24.557	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	139	ALA	0	0.034	0.002	27.662	0.005	0.005	0.000	0.000	0.000	0.000
128	A	140	ALA	0	-0.001	0.003	30.946	0.001	0.001	0.000	0.000	0.000	0.000
129	A	141	LYS	1	0.853	0.911	29.173	0.133	0.133	0.000	0.000	0.000	0.000
130	A	142	LEU	0	-0.004	0.009	35.661	0.002	0.002	0.000	0.000	0.000	0.000
131	A	143	ASN	0	0.014	0.015	37.643	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)