FMO DATABASE

FMODB ID: KGML3

Calculation Name: 3N3W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N3W

Chain ID: A

ChEMBL ID:

UniProt ID: Q9PM40

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	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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1323710.815855
FMO2-HF: Nuclear repulsion	1268108.597164
FMO2-HF: Total energy	-55602.218691
FMO2-MP2: Total energy	-55767.644805

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.
-15.781	-6.459	11.027	-5.577	-14.771	-0.019

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 : 0.027 / q_NPA : 0.025

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	ASN	0	0.017	0.012	3.053	-2.626	0.560	0.126	-1.640	-1.672	0.001
4	A	4	ILE	0	0.063	0.050	2.382	-0.672	-0.320	4.887	-1.296	-3.944	-0.005
5	A	5	GLU	-1	-0.777	-0.909	3.916	-1.933	-1.666	0.006	-0.072	-0.201	0.000
6	A	6	LYS	1	0.883	0.932	7.057	1.099	1.099	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.016	0.026	5.637	-0.033	0.082	-0.001	-0.007	-0.107	0.000
8	A	8	GLU	-1	-0.799	-0.913	7.645	0.057	0.057	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.028	-0.017	10.139	0.018	0.018	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.058	-0.029	11.339	0.003	0.003	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.005	0.008	9.838	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.114	-0.056	13.662	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.044	-0.047	12.453	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.956	-0.964	10.682	-0.074	-0.074	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.035	-0.033	8.969	0.042	0.042	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.812	0.909	10.817	-0.273	-0.273	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.835	-0.918	10.594	0.944	0.944	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.977	0.980	5.277	-1.774	-1.774	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.089	-0.073	6.304	1.138	1.138	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.025	0.030	8.019	-0.114	-0.114	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.023	0.023	5.077	-0.268	-0.131	-0.001	-0.020	-0.116	0.000
22	A	22	ILE	0	0.008	-0.011	2.859	-1.745	-0.033	0.546	-0.378	-1.880	0.001
23	A	23	HIS	0	-0.066	-0.013	4.438	-1.165	-1.085	-0.001	-0.008	-0.071	0.000
24	A	24	ALA	0	0.011	-0.006	7.245	-0.302	-0.302	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.021	0.014	2.746	-1.184	-0.219	1.214	-0.444	-1.734	-0.005
26	A	26	THR	0	-0.066	-0.030	4.647	-0.631	-0.538	-0.001	-0.003	-0.088	0.000
27	A	27	HIS	0	0.164	0.094	6.157	0.320	0.320	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.812	0.870	9.137	0.133	0.133	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.071	-0.041	11.916	0.049	0.049	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.053	-0.004	6.526	0.028	0.028	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.953	0.978	7.580	-0.755	-0.755	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.973	0.984	11.896	-0.123	-0.123	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.046	-0.038	14.837	0.033	0.033	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.025	0.013	7.306	0.124	0.124	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.012	-0.004	9.705	-0.032	-0.032	0.000	0.000	0.000	0.000
36	A	36	ASN	0	0.062	0.024	8.539	0.107	0.107	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.769	-0.861	10.576	-0.046	-0.046	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.942	0.965	14.252	-0.081	-0.081	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.001	0.006	10.301	0.004	0.004	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.894	-0.947	13.299	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	PHE	0	0.029	0.030	14.655	0.008	0.008	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.063	-0.030	16.899	0.002	0.002	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.042	-0.003	15.987	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.871	-0.906	16.936	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.016	0.009	19.373	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.036	-0.014	19.073	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.004	-0.008	16.920	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.800	-0.890	21.308	0.006	0.006	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.016	0.001	24.324	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.042	-0.017	21.623	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.001	-0.008	23.591	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.012	0.007	26.278	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.807	-0.882	28.578	0.027	0.027	0.000	0.000	0.000	0.000
54	A	54	TYR	0	0.012	0.003	27.942	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.032	-0.021	29.789	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.013	0.001	32.153	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	57	HIS	0	-0.039	-0.031	31.958	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.863	0.936	31.488	0.011	0.011	0.000	0.000	0.000	0.000
59	A	59	PHE	0	-0.015	-0.018	33.515	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.044	0.045	37.671	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.828	0.902	39.703	0.002	0.002	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.886	-0.953	40.897	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.038	-0.009	41.766	0.001	0.001	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.947	-0.948	43.280	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.034	0.010	39.257	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.882	-0.935	35.917	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.045	-0.008	33.557	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	68	SER	0	0.026	0.018	32.042	0.000	0.000	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.910	0.957	31.187	0.016	0.016	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.016	-0.011	31.201	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.835	0.915	26.857	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.006	0.017	26.705	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.030	-0.018	26.549	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.037	-0.033	25.030	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.020	0.001	21.991	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.051	0.000	21.818	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.814	-0.935	18.795	-0.097	-0.097	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.953	0.974	19.376	0.062	0.062	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.039	-0.024	20.855	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	80	PHE	0	0.069	0.039	16.764	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.041	0.032	15.828	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.821	0.922	16.392	0.054	0.054	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.022	0.008	15.650	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.022	0.031	12.349	0.006	0.006	0.000	0.000	0.000	0.000
85	A	85	ASN	0	0.016	-0.012	12.873	-0.021	-0.021	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.100	-0.049	14.938	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.026	-0.019	11.029	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.013	-0.007	10.393	0.031	0.031	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.019	0.007	7.895	0.003	0.003	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.084	0.044	7.518	-0.137	-0.137	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.942	-0.961	7.725	-0.639	-0.639	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.049	-0.032	3.381	-1.211	-0.123	0.375	-0.277	-1.187	0.001
93	A	93	ILE	0	-0.041	-0.008	2.836	-4.597	-3.140	0.803	-0.948	-1.311	-0.011
94	A	94	LEU	0	-0.021	0.005	2.307	-0.223	-0.392	3.075	-0.480	-2.426	-0.001
95	A	95	MET	0	-0.002	-0.003	4.899	0.532	0.571	-0.001	-0.004	-0.034	0.000
96	A	96	SER	0	-0.024	-0.005	8.651	0.044	0.044	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.092	0.030	11.563	-0.034	-0.034	0.000	0.000	0.000	0.000
98	A	98	ALA	0	-0.013	-0.003	13.313	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.800	-0.888	12.550	-0.205	-0.205	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.895	-0.962	9.351	-0.593	-0.593	0.000	0.000	0.000	0.000
101	A	101	ASN	0	-0.039	-0.022	13.050	0.007	0.007	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.110	-0.041	16.411	0.032	0.032	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.045	0.014	16.087	0.016	0.016	0.000	0.000	0.000	0.000
104	A	104	GLY	0	-0.026	-0.034	13.106	0.009	0.009	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.819	0.893	9.177	0.583	0.583	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.900	-0.948	11.853	-0.262	-0.262	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.779	0.890	14.781	0.232	0.232	0.000	0.000	0.000	0.000
108	A	108	PRO	0	0.010	0.000	14.957	-0.017	-0.017	0.000	0.000	0.000	0.000
109	A	109	SER	0	0.061	0.025	16.198	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	110	ILE	0	-0.032	0.004	10.731	0.000	0.000	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.027	-0.009	11.041	-0.025	-0.025	0.000	0.000	0.000	0.000
112	A	112	SER	0	0.002	-0.009	12.269	0.027	0.027	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.867	-0.932	12.591	-0.104	-0.104	0.000	0.000	0.000	0.000
114	A	114	ALA	0	-0.039	-0.025	8.089	0.027	0.027	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.013	-0.008	9.961	0.083	0.083	0.000	0.000	0.000	0.000
116	A	116	GLH	0	-0.030	-0.039	12.092	0.043	0.043	0.000	0.000	0.000	0.000
117	A	117	ALA	0	0.002	0.007	9.969	0.040	0.040	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.027	-0.019	7.630	0.085	0.085	0.000	0.000	0.000	0.000
119	A	119	ILE	0	0.011	0.006	10.809	0.040	0.040	0.000	0.000	0.000	0.000
120	A	120	GLY	0	0.043	0.018	14.338	0.007	0.007	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.035	-0.017	11.257	0.014	0.014	0.000	0.000	0.000	0.000
122	A	122	ILE	0	0.006	0.007	12.826	0.016	0.016	0.000	0.000	0.000	0.000
123	A	123	HIS	0	0.015	0.011	15.092	-0.019	-0.019	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.057	-0.030	15.006	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.773	-0.855	13.078	0.371	0.371	0.000	0.000	0.000	0.000
126	A	126	ALA	0	-0.052	-0.031	17.214	-0.016	-0.016	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.028	0.031	19.278	-0.021	-0.021	0.000	0.000	0.000	0.000
128	A	128	PHE	0	0.014	-0.003	20.998	0.000	0.000	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.882	-0.948	22.542	0.064	0.064	0.000	0.000	0.000	0.000
130	A	130	PHE	0	0.008	0.001	18.767	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	131	ALA	0	0.042	0.012	18.283	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.845	0.903	19.268	-0.042	-0.042	0.000	0.000	0.000	0.000
133	A	133	THR	0	-0.023	-0.009	21.692	-0.013	-0.013	0.000	0.000	0.000	0.000
134	A	134	ILE	0	-0.026	-0.004	15.197	-0.011	-0.011	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.023	0.002	18.498	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.005	-0.012	19.369	-0.014	-0.014	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.917	0.979	16.198	-0.004	-0.004	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.052	-0.028	15.023	-0.013	-0.013	0.000	0.000	0.000	0.000
139	A	139	ILE	0	0.036	0.010	19.173	-0.013	-0.013	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.935	-0.971	22.179	-0.021	-0.021	0.000	0.000	0.000	0.000
141	A	141	LYS	1	0.877	0.932	18.815	0.051	0.051	0.000	0.000	0.000	0.000
142	A	142	ASN	0	-0.068	-0.027	18.480	-0.019	-0.019	0.000	0.000	0.000	0.000
143	A	143	PHE	0	-0.054	-0.014	21.886	-0.008	-0.008	0.000	0.000	0.000	0.000
144	A	144	PRO	0	0.020	0.031	26.067	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:1:MET)