FMO DATABASE

FMODB ID: 2NQ2R

Calculation Name: 3F8X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F8X

Chain ID: A

ChEMBL ID:

UniProt ID: Q6D504

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1116257.033575
FMO2-HF: Nuclear repulsion	1065759.002748
FMO2-HF: Total energy	-50498.030827
FMO2-MP2: Total energy	-50645.798691

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:16:SER)

Summations of interaction energy for fragment #1(A:16: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.
-44.389	-47.37	15.238	-6.112	-6.144	0.048

Interaction energy analysis for fragmet #1(A:16:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : 0.009

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	18	ASN	0	0.005	0.016	3.636	-2.362	-0.938	-0.006	-0.630	-0.788	0.001
4	A	19	ALA	0	0.083	0.029	6.115	-0.487	-0.487	0.000	0.000	0.000	0.000
5	A	20	ALA	0	0.017	0.026	8.489	-0.094	-0.094	0.000	0.000	0.000	0.000
6	A	21	VAL	0	0.032	0.014	7.484	-0.042	-0.042	0.000	0.000	0.000	0.000
7	A	22	GLN	0	-0.049	-0.019	5.786	0.143	0.143	0.000	0.000	0.000	0.000
8	A	23	SER	0	-0.026	-0.029	8.504	0.157	0.157	0.000	0.000	0.000	0.000
9	A	24	GLY	0	0.036	0.027	11.879	0.104	0.104	0.000	0.000	0.000	0.000
10	A	25	LEU	0	-0.039	-0.018	9.108	0.074	0.074	0.000	0.000	0.000	0.000
11	A	26	GLN	0	-0.045	-0.019	12.024	0.099	0.099	0.000	0.000	0.000	0.000
12	A	27	GLU	-1	-0.786	-0.875	14.174	-0.333	-0.333	0.000	0.000	0.000	0.000
13	A	28	TRP	0	0.003	-0.011	14.745	0.080	0.080	0.000	0.000	0.000	0.000
14	A	29	HIS	0	-0.022	-0.026	12.715	0.128	0.128	0.000	0.000	0.000	0.000
15	A	30	ARG	1	0.651	0.792	17.159	0.394	0.394	0.000	0.000	0.000	0.000
16	A	31	ILE	0	0.012	0.005	19.901	0.042	0.042	0.000	0.000	0.000	0.000
17	A	32	ILE	0	-0.043	-0.012	19.270	0.039	0.039	0.000	0.000	0.000	0.000
18	A	33	ALA	0	-0.069	-0.033	21.176	0.029	0.029	0.000	0.000	0.000	0.000
19	A	34	GLU	-1	-0.910	-0.953	22.886	-0.297	-0.297	0.000	0.000	0.000	0.000
20	A	35	ALA	0	-0.034	-0.006	24.862	0.027	0.027	0.000	0.000	0.000	0.000
21	A	36	ASP	-1	-0.820	-0.893	24.687	-0.235	-0.235	0.000	0.000	0.000	0.000
22	A	37	TRP	0	0.049	-0.003	23.289	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	38	GLU	-1	-0.905	-0.962	26.470	-0.163	-0.163	0.000	0.000	0.000	0.000
24	A	39	ARG	1	0.873	0.940	23.476	0.223	0.223	0.000	0.000	0.000	0.000
25	A	40	LEU	0	-0.012	0.004	20.290	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	41	PRO	0	0.033	-0.003	22.048	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	42	ASP	-1	-0.878	-0.925	22.698	-0.164	-0.164	0.000	0.000	0.000	0.000
28	A	43	LEU	0	-0.050	-0.013	15.724	0.003	0.003	0.000	0.000	0.000	0.000
29	A	44	LEU	0	-0.019	0.010	18.016	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	45	ALA	0	0.005	0.000	18.534	0.022	0.022	0.000	0.000	0.000	0.000
31	A	46	GLU	-1	-0.895	-0.957	20.417	-0.063	-0.063	0.000	0.000	0.000	0.000
32	A	47	ASP	-1	-0.952	-0.981	21.441	0.047	0.047	0.000	0.000	0.000	0.000
33	A	48	VAL	0	-0.024	0.007	19.196	0.008	0.008	0.000	0.000	0.000	0.000
34	A	49	VAL	0	0.024	0.018	19.984	0.005	0.005	0.000	0.000	0.000	0.000
35	A	50	PHE	0	0.004	-0.014	20.294	-0.031	-0.031	0.000	0.000	0.000	0.000
36	A	51	SER	0	0.013	0.008	21.386	0.030	0.030	0.000	0.000	0.000	0.000
37	A	52	ASN	0	0.024	0.014	22.435	-0.022	-0.022	0.000	0.000	0.000	0.000
38	A	53	PRO	0	0.036	-0.002	24.389	0.011	0.011	0.000	0.000	0.000	0.000
39	A	54	SER	0	-0.028	-0.012	26.196	0.007	0.007	0.000	0.000	0.000	0.000
40	A	55	THR	0	-0.044	-0.020	28.891	0.013	0.013	0.000	0.000	0.000	0.000
41	A	56	PHE	0	-0.044	-0.013	25.730	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	57	ASP	-1	-0.932	-0.965	26.614	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	58	PRO	0	-0.030	-0.010	23.696	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	59	TYR	0	-0.045	-0.021	25.696	0.012	0.012	0.000	0.000	0.000	0.000
45	A	60	HIS	0	0.019	-0.002	24.607	0.000	0.000	0.000	0.000	0.000	0.000
46	A	61	GLY	0	0.016	0.023	24.861	0.003	0.003	0.000	0.000	0.000	0.000
47	A	62	LYS	1	0.859	0.910	23.269	0.079	0.079	0.000	0.000	0.000	0.000
48	A	63	GLY	0	-0.012	0.003	25.998	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	64	PRO	0	0.027	-0.002	27.956	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	65	LEU	0	0.028	0.032	21.137	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	66	MET	0	-0.007	-0.009	25.752	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	67	VAL	0	-0.031	0.001	27.643	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	68	ILE	0	-0.028	-0.024	27.531	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	69	LEU	0	0.002	0.012	21.709	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	70	PRO	0	0.062	0.025	26.108	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	71	ALA	0	0.006	0.015	28.209	0.000	0.000	0.000	0.000	0.000	0.000
57	A	72	VAL	0	-0.006	-0.003	26.135	0.002	0.002	0.000	0.000	0.000	0.000
58	A	73	PHE	0	0.025	-0.009	21.469	0.001	0.001	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.089	-0.031	27.539	0.003	0.003	0.000	0.000	0.000	0.000
60	A	75	VAL	0	-0.057	-0.040	30.790	0.009	0.009	0.000	0.000	0.000	0.000
61	A	76	LEU	0	-0.049	-0.008	25.486	0.002	0.002	0.000	0.000	0.000	0.000
62	A	77	GLU	-1	-0.831	-0.903	29.356	-0.171	-0.171	0.000	0.000	0.000	0.000
63	A	78	ASN	0	-0.092	-0.077	28.313	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	79	PHE	0	0.034	0.031	20.098	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	80	GLN	0	-0.044	-0.026	22.160	-0.033	-0.033	0.000	0.000	0.000	0.000
66	A	81	TYR	0	0.008	-0.021	16.652	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	82	ALA	0	-0.038	-0.028	17.741	0.012	0.012	0.000	0.000	0.000	0.000
68	A	83	ARG	1	0.745	0.843	14.926	0.324	0.324	0.000	0.000	0.000	0.000
69	A	84	HIS	0	0.004	0.003	10.332	-0.097	-0.097	0.000	0.000	0.000	0.000
70	A	85	PHE	0	-0.028	-0.009	8.799	-0.032	-0.032	0.000	0.000	0.000	0.000
71	A	86	SER	0	0.011	0.009	4.217	-0.574	-0.415	-0.001	-0.041	-0.118	0.000
72	A	87	SER	0	0.002	0.005	4.487	0.143	0.250	-0.001	-0.014	-0.091	0.000
73	A	88	LYS	1	0.830	0.877	1.891	-40.549	-45.212	15.241	-5.470	-5.107	0.047
74	A	89	SER	0	-0.010	-0.038	3.580	-0.223	-0.231	0.005	0.043	-0.040	0.000
75	A	90	GLY	0	0.089	0.064	6.509	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	91	TYR	0	-0.044	-0.031	5.913	-0.555	-0.555	0.000	0.000	0.000	0.000
77	A	92	VAL	0	-0.004	0.009	8.977	0.250	0.250	0.000	0.000	0.000	0.000
78	A	93	LEU	0	0.002	-0.001	11.285	-0.143	-0.143	0.000	0.000	0.000	0.000
79	A	94	GLU	-1	-0.753	-0.845	14.044	-0.324	-0.324	0.000	0.000	0.000	0.000
80	A	95	PHE	0	0.008	0.015	17.102	-0.035	-0.035	0.000	0.000	0.000	0.000
81	A	96	ASN	0	-0.052	-0.037	20.169	0.053	0.053	0.000	0.000	0.000	0.000
82	A	97	ALA	0	0.042	0.021	23.767	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	98	ASN	0	-0.045	-0.020	26.747	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	99	MET	0	0.042	0.033	30.411	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	100	GLY	0	0.022	0.008	33.152	0.010	0.010	0.000	0.000	0.000	0.000
86	A	101	ASP	-1	-0.971	-0.982	34.958	-0.129	-0.129	0.000	0.000	0.000	0.000
87	A	102	GLH	0	-0.086	-0.057	34.114	0.002	0.002	0.000	0.000	0.000	0.000
88	A	103	LEU	0	-0.014	-0.016	30.005	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	104	LEU	0	-0.029	-0.015	25.777	0.012	0.012	0.000	0.000	0.000	0.000
90	A	105	THR	0	-0.012	-0.003	22.918	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	106	GLY	0	0.033	0.005	21.783	0.033	0.033	0.000	0.000	0.000	0.000
92	A	107	VAL	0	-0.061	-0.023	16.567	-0.041	-0.041	0.000	0.000	0.000	0.000
93	A	108	ASP	-1	-0.746	-0.858	16.126	-0.359	-0.359	0.000	0.000	0.000	0.000
94	A	109	LEU	0	-0.063	-0.031	12.969	-0.096	-0.096	0.000	0.000	0.000	0.000
95	A	110	ILE	0	0.012	-0.004	12.216	0.070	0.070	0.000	0.000	0.000	0.000
96	A	111	GLU	-1	-0.824	-0.890	9.852	-0.360	-0.360	0.000	0.000	0.000	0.000
97	A	112	PHE	0	0.012	-0.007	10.093	-0.034	-0.034	0.000	0.000	0.000	0.000
98	A	113	ASN	0	0.057	0.031	11.268	0.102	0.102	0.000	0.000	0.000	0.000
99	A	114	ASP	-1	-0.898	-0.973	10.813	0.723	0.723	0.000	0.000	0.000	0.000
100	A	115	ALA	0	-0.081	-0.036	12.507	-0.059	-0.059	0.000	0.000	0.000	0.000
101	A	116	GLY	0	-0.017	-0.010	12.404	-0.067	-0.067	0.000	0.000	0.000	0.000
102	A	117	LYS	1	0.806	0.898	13.411	0.173	0.173	0.000	0.000	0.000	0.000
103	A	118	ILE	0	0.007	0.011	14.623	0.029	0.029	0.000	0.000	0.000	0.000
104	A	119	THR	0	-0.018	-0.045	14.957	0.039	0.039	0.000	0.000	0.000	0.000
105	A	120	ASP	-1	-0.871	-0.906	15.442	0.032	0.032	0.000	0.000	0.000	0.000
106	A	121	LEU	0	0.003	0.011	15.722	-0.070	-0.070	0.000	0.000	0.000	0.000
107	A	122	VAL	0	-0.022	-0.012	17.307	0.047	0.047	0.000	0.000	0.000	0.000
108	A	123	VAL	0	0.020	0.016	18.323	-0.046	-0.046	0.000	0.000	0.000	0.000
109	A	124	MET	0	-0.040	-0.019	20.849	0.033	0.033	0.000	0.000	0.000	0.000
110	A	125	MET	0	0.018	0.009	22.057	-0.024	-0.024	0.000	0.000	0.000	0.000
111	A	126	ARG	1	0.859	0.957	24.271	0.218	0.218	0.000	0.000	0.000	0.000
112	A	127	PRO	0	0.061	0.005	27.090	-0.013	-0.013	0.000	0.000	0.000	0.000
113	A	128	ALA	0	0.089	0.016	29.866	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	129	SER	0	-0.014	-0.008	31.008	0.000	0.000	0.000	0.000	0.000	0.000
115	A	130	VAL	0	0.071	0.046	31.257	0.004	0.004	0.000	0.000	0.000	0.000
116	A	131	VAL	0	0.020	0.015	28.024	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	132	ILE	0	-0.033	-0.007	30.931	0.004	0.004	0.000	0.000	0.000	0.000
118	A	133	ASP	-1	-0.836	-0.893	34.254	-0.099	-0.099	0.000	0.000	0.000	0.000
119	A	134	LEU	0	0.003	-0.011	28.474	0.002	0.002	0.000	0.000	0.000	0.000
120	A	135	SER	0	-0.009	-0.020	31.948	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	136	VAL	0	-0.036	-0.005	33.358	0.005	0.005	0.000	0.000	0.000	0.000
122	A	137	GLU	-1	-0.812	-0.885	35.207	-0.104	-0.104	0.000	0.000	0.000	0.000
123	A	138	VAL	0	0.018	0.002	30.725	0.001	0.001	0.000	0.000	0.000	0.000
124	A	139	GLY	0	0.026	0.015	33.945	0.003	0.003	0.000	0.000	0.000	0.000
125	A	140	LYS	1	0.838	0.909	36.368	0.097	0.097	0.000	0.000	0.000	0.000
126	A	141	ARG	1	0.838	0.909	34.432	0.138	0.138	0.000	0.000	0.000	0.000
127	A	142	ILE	0	0.023	0.029	31.999	0.000	0.000	0.000	0.000	0.000	0.000
128	A	143	ALA	0	-0.038	-0.018	36.118	0.004	0.004	0.000	0.000	0.000	0.000
129	A	144	ALA	0	-0.058	-0.032	39.733	0.003	0.003	0.000	0.000	0.000	0.000
130	A	145	ALA	0	-0.025	-0.001	36.799	0.002	0.002	0.000	0.000	0.000	0.000
131	A	146	GLN	0	-0.090	-0.039	35.948	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:SER)