FMO DATABASE

FMODB ID: 1NMNZ

Calculation Name: 4YF2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YF2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9D9X8

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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1179083.567095
FMO2-HF: Nuclear repulsion	1125333.764157
FMO2-HF: Total energy	-53749.802938
FMO2-MP2: Total energy	-53900.538585

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:0:ALA)

Summations of interaction energy for fragment #1(A:0:ALA)

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.
-6.894	-2.585	6.801	-5.075	-6.034	-0.032

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.005

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	2	VAL	0	-0.014	-0.004	3.848	-0.043	2.088	-0.025	-1.200	-0.906	0.001
4	A	3	PHE	0	0.014	0.018	6.731	-0.427	-0.427	0.000	0.000	0.000	0.000
5	A	4	SER	0	0.008	0.008	10.158	0.018	0.018	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.905	0.924	13.454	-0.127	-0.127	0.000	0.000	0.000	0.000
7	A	6	CYS	0	-0.077	-0.018	16.225	0.003	0.003	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.881	-0.941	11.220	0.104	0.104	0.000	0.000	0.000	0.000
9	A	8	LEU	0	-0.018	-0.013	12.090	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.023	0.011	14.550	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.913	0.965	17.257	-0.068	-0.068	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.915	-0.968	12.485	0.095	0.095	0.000	0.000	0.000	0.000
13	A	12	MET	0	-0.044	-0.020	14.900	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	13	HIS	0	-0.038	-0.013	17.540	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.872	-0.935	17.859	0.053	0.053	0.000	0.000	0.000	0.000
16	A	15	PHE	0	-0.060	-0.029	13.703	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	16	GLY	0	-0.040	-0.012	19.264	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	17	LEU	0	-0.022	-0.031	17.847	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	18	ASP	-1	-0.864	-0.930	22.132	0.097	0.097	0.000	0.000	0.000	0.000
20	A	19	GLY	0	0.025	0.005	24.871	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.046	-0.018	23.906	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	21	ARG	1	0.807	0.877	26.221	-0.073	-0.073	0.000	0.000	0.000	0.000
23	A	22	GLY	0	0.000	0.012	28.448	0.000	0.000	0.000	0.000	0.000	0.000
24	A	23	TYR	0	-0.011	0.027	24.996	0.000	0.000	0.000	0.000	0.000	0.000
25	A	24	ASN	0	0.016	0.011	26.025	0.006	0.006	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.001	-0.018	20.242	0.013	0.013	0.000	0.000	0.000	0.000
27	A	26	ALA	0	0.033	0.019	21.437	0.021	0.021	0.000	0.000	0.000	0.000
28	A	27	ASP	-1	-0.841	-0.919	21.938	0.139	0.139	0.000	0.000	0.000	0.000
29	A	28	TRP	0	0.019	-0.007	18.549	0.022	0.022	0.000	0.000	0.000	0.000
30	A	29	VAL	0	-0.004	-0.001	17.176	0.044	0.044	0.000	0.000	0.000	0.000
31	A	30	CYS	0	-0.046	0.009	17.316	0.043	0.043	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.011	0.002	17.396	0.016	0.016	0.000	0.000	0.000	0.000
33	A	32	ALA	0	-0.015	-0.007	13.302	0.025	0.025	0.000	0.000	0.000	0.000
34	A	33	TYR	0	-0.050	-0.003	13.775	0.071	0.071	0.000	0.000	0.000	0.000
35	A	34	TYR	0	0.011	-0.020	14.985	0.021	0.021	0.000	0.000	0.000	0.000
36	A	35	THR	0	-0.088	-0.033	14.747	0.011	0.011	0.000	0.000	0.000	0.000
37	A	36	SER	0	0.014	-0.009	9.941	0.049	0.049	0.000	0.000	0.000	0.000
38	A	37	GLY	0	0.011	0.020	10.181	0.155	0.155	0.000	0.000	0.000	0.000
39	A	38	PHE	0	-0.059	-0.035	10.414	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	39	ASN	0	0.013	0.003	4.594	1.981	2.032	-0.001	-0.008	-0.041	0.000
41	A	40	THR	0	0.034	0.002	3.656	0.410	0.554	0.000	-0.037	-0.107	0.000
42	A	41	ASN	0	-0.033	-0.035	2.450	-9.553	-6.376	1.904	-2.289	-2.792	-0.019
43	A	42	ALA	0	-0.001	0.025	4.574	-0.954	-0.888	-0.001	-0.011	-0.054	0.000
44	A	43	VAL	0	-0.023	-0.020	7.769	-0.126	-0.126	0.000	0.000	0.000	0.000
45	A	44	ASP	-1	-0.903	-0.934	10.356	0.181	0.181	0.000	0.000	0.000	0.000
46	A	45	HIS	0	-0.012	-0.016	12.592	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.834	-0.908	16.752	0.125	0.125	0.000	0.000	0.000	0.000
48	A	47	ALA	0	-0.013	-0.013	20.102	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.859	-0.914	22.750	0.070	0.070	0.000	0.000	0.000	0.000
50	A	49	GLY	0	-0.028	-0.016	20.950	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	50	SER	0	-0.145	-0.084	19.839	0.000	0.000	0.000	0.000	0.000	0.000
52	A	51	THR	0	0.038	0.018	14.274	0.003	0.003	0.000	0.000	0.000	0.000
53	A	52	ASN	0	-0.084	-0.043	14.951	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	53	ASN	0	-0.018	-0.038	11.207	0.018	0.018	0.000	0.000	0.000	0.000
55	A	54	GLY	0	0.066	0.043	8.424	-0.052	-0.052	0.000	0.000	0.000	0.000
56	A	55	ILE	0	-0.007	0.001	9.403	-0.029	-0.029	0.000	0.000	0.000	0.000
57	A	56	PHE	0	0.030	0.015	10.624	-0.069	-0.069	0.000	0.000	0.000	0.000
58	A	57	GLN	0	-0.047	-0.024	11.067	-0.141	-0.141	0.000	0.000	0.000	0.000
59	A	58	ILE	0	0.021	0.010	14.074	-0.070	-0.070	0.000	0.000	0.000	0.000
60	A	59	SER	0	0.093	0.054	15.505	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	60	SER	0	0.047	-0.018	17.332	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	61	ARG	1	0.869	0.962	18.895	-0.103	-0.103	0.000	0.000	0.000	0.000
63	A	62	ARG	1	0.838	0.918	21.665	-0.083	-0.083	0.000	0.000	0.000	0.000
64	A	63	TRP	0	0.073	0.030	19.166	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	64	CYS	0	-0.006	0.018	14.011	0.004	0.004	0.000	0.000	0.000	0.000
66	A	65	ARG	1	0.932	0.968	18.216	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	66	THR	0	0.114	0.047	16.253	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.037	-0.032	18.833	0.001	0.001	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.005	0.002	21.314	0.001	0.001	0.000	0.000	0.000	0.000
70	A	69	SER	0	0.020	0.014	21.078	0.005	0.005	0.000	0.000	0.000	0.000
71	A	70	ASN	0	-0.066	-0.026	22.789	0.006	0.006	0.000	0.000	0.000	0.000
72	A	71	GLY	0	0.100	0.040	24.682	0.003	0.003	0.000	0.000	0.000	0.000
73	A	72	PRO	0	-0.079	-0.031	25.506	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	73	ASN	0	0.009	0.019	20.590	0.005	0.005	0.000	0.000	0.000	0.000
75	A	74	LEU	0	0.033	0.009	22.725	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	75	CYS	0	-0.186	-0.085	16.369	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	76	ARG	1	0.846	0.924	19.891	-0.042	-0.042	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.060	0.036	14.038	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	78	TYR	0	-0.012	0.005	14.887	0.008	0.008	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.050	0.026	10.014	0.036	0.036	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.904	-0.966	9.228	-0.061	-0.061	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.073	-0.023	10.185	0.007	0.007	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.054	-0.021	6.039	0.124	0.124	0.000	0.000	0.000	0.000
84	A	84	ASN	0	-0.023	0.002	4.562	-0.187	-0.089	-0.001	-0.005	-0.092	0.000
85	A	85	ASN	0	0.024	-0.007	2.189	1.203	-0.182	4.926	-1.516	-2.026	-0.014
86	A	86	ASP	-1	-0.896	-0.935	4.925	0.123	0.150	-0.001	-0.009	-0.016	0.000
87	A	87	LEU	0	0.048	0.011	8.637	0.050	0.050	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.979	0.996	10.615	-0.017	-0.017	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.891	-0.954	12.269	0.064	0.064	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.013	-0.011	10.727	0.007	0.007	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.007	0.016	13.324	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.003	-0.006	15.811	-0.020	-0.020	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.075	0.027	17.050	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	95	MET	0	0.010	0.006	18.805	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.923	0.966	20.919	-0.087	-0.087	0.000	0.000	0.000	0.000
96	A	97	ILE	0	-0.001	-0.001	19.252	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.007	0.014	22.178	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	99	GLN	0	-0.033	-0.022	24.725	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.886	-0.931	26.598	0.063	0.063	0.000	0.000	0.000	0.000
100	A	101	PRO	0	-0.043	-0.048	28.731	0.003	0.003	0.000	0.000	0.000	0.000
101	A	102	LEU	0	0.000	0.008	28.345	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	103	GLY	0	-0.014	0.019	26.843	0.003	0.003	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.044	-0.002	21.771	0.005	0.005	0.000	0.000	0.000	0.000
104	A	105	GLY	0	0.003	0.012	24.293	0.008	0.008	0.000	0.000	0.000	0.000
105	A	106	TYR	0	-0.068	-0.027	22.314	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	107	TRP	0	0.036	0.016	17.495	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.839	-0.917	20.106	0.183	0.183	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.002	-0.009	19.384	-0.010	-0.010	0.000	0.000	0.000	0.000
109	A	110	TRP	0	0.047	0.006	21.301	-0.011	-0.011	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.852	0.914	22.897	-0.128	-0.128	0.000	0.000	0.000	0.000
111	A	112	HIS	0	-0.025	-0.023	24.528	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	113	HIS	0	-0.031	-0.005	21.457	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	115	GLN	0	0.049	0.025	24.941	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	116	GLY	0	-0.060	-0.038	28.057	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.837	0.921	26.894	-0.118	-0.118	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.859	-0.917	29.569	0.083	0.083	0.000	0.000	0.000	0.000
117	A	119	LEU	0	-0.025	-0.017	24.164	0.007	0.007	0.000	0.000	0.000	0.000
118	A	120	SER	0	-0.007	-0.005	25.283	0.010	0.010	0.000	0.000	0.000	0.000
119	A	121	ASP	-1	-0.793	-0.894	25.275	0.099	0.099	0.000	0.000	0.000	0.000
120	A	122	TRP	0	-0.082	-0.055	18.028	0.017	0.017	0.000	0.000	0.000	0.000
121	A	123	VAL	0	-0.043	-0.040	21.226	0.015	0.015	0.000	0.000	0.000	0.000
122	A	124	ASP	-1	-0.834	-0.901	23.427	0.077	0.077	0.000	0.000	0.000	0.000
123	A	125	GLY	0	-0.047	-0.037	24.305	0.007	0.007	0.000	0.000	0.000	0.000
124	A	127	ASP	-1	-0.899	-0.955	22.393	0.035	0.035	0.000	0.000	0.000	0.000
125	A	128	PHE	0	-0.020	-0.019	21.070	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	129	LEU	0	-0.032	0.004	23.558	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)