FMO DATABASE

FMODB ID: 2J23R

Calculation Name: 3N3E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N3E

Chain ID: A

ChEMBL ID:

UniProt ID: Q8UUZ6

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-779108.519387
FMO2-HF: Nuclear repulsion	737260.129326
FMO2-HF: Total energy	-41848.390061
FMO2-MP2: Total energy	-41971.157449

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:61:GLY)

Summations of interaction energy for fragment #1(A:61:GLY)

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.
-0.371	2.168	0.007	-1.393	-1.153	0.002

Interaction energy analysis for fragmet #1(A:61:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.027

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	63	SER	0	-0.053	-0.033	3.192	0.897	2.976	0.000	-1.154	-0.925	0.003
4	A	64	GLU	-1	-0.793	-0.844	3.556	-3.182	-2.722	0.007	-0.239	-0.228	-0.001
5	A	65	VAL	0	-0.001	-0.007	5.835	0.398	0.398	0.000	0.000	0.000	0.000
6	A	66	ARG	1	0.820	0.881	8.085	1.280	1.280	0.000	0.000	0.000	0.000
7	A	67	SER	0	0.013	-0.005	12.213	0.018	0.018	0.000	0.000	0.000	0.000
8	A	68	ASP	-1	-0.804	-0.870	15.766	-0.276	-0.276	0.000	0.000	0.000	0.000
9	A	69	ARG	1	0.875	0.902	18.948	0.153	0.153	0.000	0.000	0.000	0.000
10	A	70	GLU	-1	-0.808	-0.872	21.712	-0.200	-0.200	0.000	0.000	0.000	0.000
11	A	71	LYS	1	0.851	0.903	18.100	0.317	0.317	0.000	0.000	0.000	0.000
12	A	72	PHE	0	0.025	0.022	14.054	0.005	0.005	0.000	0.000	0.000	0.000
13	A	73	THR	0	-0.011	-0.018	12.839	0.029	0.029	0.000	0.000	0.000	0.000
14	A	74	VAL	0	-0.008	0.008	9.884	-0.036	-0.036	0.000	0.000	0.000	0.000
15	A	75	TYR	0	0.029	0.021	7.754	0.179	0.179	0.000	0.000	0.000	0.000
16	A	76	LEU	0	-0.050	-0.030	7.816	-0.462	-0.462	0.000	0.000	0.000	0.000
17	A	77	ASP	-1	-0.799	-0.872	6.725	-1.384	-1.384	0.000	0.000	0.000	0.000
18	A	78	VAL	0	-0.021	-0.016	8.678	0.077	0.077	0.000	0.000	0.000	0.000
19	A	79	LYS	1	0.884	0.924	8.271	1.422	1.422	0.000	0.000	0.000	0.000
20	A	80	HIS	0	-0.064	-0.060	13.166	0.030	0.030	0.000	0.000	0.000	0.000
21	A	81	PHE	0	-0.084	-0.027	14.056	0.064	0.064	0.000	0.000	0.000	0.000
22	A	82	SER	0	0.012	-0.015	17.593	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	83	PRO	0	0.007	-0.025	20.127	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	84	ASP	-1	-0.902	-0.938	21.506	-0.285	-0.285	0.000	0.000	0.000	0.000
25	A	85	GLU	-1	-0.819	-0.856	20.254	-0.319	-0.319	0.000	0.000	0.000	0.000
26	A	86	LEU	0	-0.033	-0.033	15.786	-0.047	-0.047	0.000	0.000	0.000	0.000
27	A	87	SER	0	0.028	0.028	19.673	0.029	0.029	0.000	0.000	0.000	0.000
28	A	88	VAL	0	-0.011	-0.018	17.791	-0.034	-0.034	0.000	0.000	0.000	0.000
29	A	89	LYS	1	0.919	0.956	20.175	0.304	0.304	0.000	0.000	0.000	0.000
30	A	90	VAL	0	-0.023	-0.001	20.534	-0.042	-0.042	0.000	0.000	0.000	0.000
31	A	91	THR	0	-0.027	-0.040	22.235	0.022	0.022	0.000	0.000	0.000	0.000
32	A	92	ASP	-1	-0.858	-0.924	22.796	-0.156	-0.156	0.000	0.000	0.000	0.000
33	A	93	ASP	-1	-0.807	-0.867	22.782	-0.171	-0.171	0.000	0.000	0.000	0.000
34	A	94	TYR	0	-0.038	-0.019	17.358	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	95	VAL	0	0.022	0.016	16.460	0.012	0.012	0.000	0.000	0.000	0.000
36	A	96	GLU	-1	-0.857	-0.914	16.701	-0.315	-0.315	0.000	0.000	0.000	0.000
37	A	97	ILE	0	0.003	-0.007	12.989	-0.018	-0.018	0.000	0.000	0.000	0.000
38	A	98	GLN	0	-0.025	-0.007	16.230	0.000	0.000	0.000	0.000	0.000	0.000
39	A	99	GLY	0	0.041	0.025	16.647	0.004	0.004	0.000	0.000	0.000	0.000
40	A	100	LYS	1	0.880	0.938	17.479	0.230	0.230	0.000	0.000	0.000	0.000
41	A	101	HIS	1	0.850	0.907	17.692	0.359	0.359	0.000	0.000	0.000	0.000
42	A	102	GLY	0	-0.015	-0.005	19.561	0.013	0.013	0.000	0.000	0.000	0.000
43	A	103	GLU	-1	-0.814	-0.852	18.512	-0.315	-0.315	0.000	0.000	0.000	0.000
44	A	104	ARG	1	0.990	0.981	22.843	0.127	0.127	0.000	0.000	0.000	0.000
45	A	105	GLN	0	-0.084	-0.047	20.188	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	106	ASP	-1	-0.836	-0.917	24.331	-0.051	-0.051	0.000	0.000	0.000	0.000
47	A	107	ASP	-1	-0.925	-0.966	26.672	-0.033	-0.033	0.000	0.000	0.000	0.000
48	A	108	HIS	0	-0.059	-0.026	30.148	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	109	GLY	0	0.009	0.022	26.267	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	110	TYR	0	-0.051	-0.043	24.405	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	111	ILE	0	-0.015	0.006	18.331	0.012	0.012	0.000	0.000	0.000	0.000
52	A	112	SER	0	0.026	0.002	20.421	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	113	ARG	1	0.803	0.891	14.032	0.326	0.326	0.000	0.000	0.000	0.000
54	A	114	GLU	-1	-0.830	-0.917	16.399	-0.256	-0.256	0.000	0.000	0.000	0.000
55	A	115	PHE	0	-0.047	-0.022	13.152	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	116	HIS	0	0.042	0.006	15.152	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	117	ARG	1	0.883	0.945	6.961	1.374	1.374	0.000	0.000	0.000	0.000
58	A	118	ARG	1	0.915	0.945	14.245	0.259	0.259	0.000	0.000	0.000	0.000
59	A	119	TYR	0	0.007	0.011	9.364	-0.066	-0.066	0.000	0.000	0.000	0.000
60	A	120	ARG	1	0.923	0.963	14.565	0.199	0.199	0.000	0.000	0.000	0.000
61	A	121	LEU	0	0.010	0.006	16.428	-0.035	-0.035	0.000	0.000	0.000	0.000
62	A	122	PRO	0	-0.021	-0.007	17.200	0.040	0.040	0.000	0.000	0.000	0.000
63	A	123	SER	0	0.003	-0.007	20.217	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	124	ASN	0	0.008	0.009	22.883	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	125	VAL	0	-0.034	-0.011	19.423	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	126	ASP	-1	-0.772	-0.857	22.866	-0.200	-0.200	0.000	0.000	0.000	0.000
67	A	127	GLN	0	0.009	-0.027	23.147	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	128	SER	0	-0.062	-0.032	24.720	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	129	ALA	0	0.018	0.010	25.597	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	130	ILE	0	-0.073	-0.017	19.589	-0.026	-0.026	0.000	0.000	0.000	0.000
71	A	131	THR	0	-0.012	-0.005	20.764	0.010	0.010	0.000	0.000	0.000	0.000
72	A	132	CYS	0	-0.043	-0.020	16.843	-0.052	-0.052	0.000	0.000	0.000	0.000
73	A	133	THR	0	0.011	0.010	17.610	0.036	0.036	0.000	0.000	0.000	0.000
74	A	134	LEU	0	0.010	0.002	15.313	-0.096	-0.096	0.000	0.000	0.000	0.000
75	A	135	SER	0	-0.004	-0.020	15.338	0.046	0.046	0.000	0.000	0.000	0.000
76	A	136	ALA	0	-0.003	-0.016	16.959	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	137	ASP	-1	-0.837	-0.888	14.192	-0.555	-0.555	0.000	0.000	0.000	0.000
78	A	138	GLY	0	-0.005	-0.001	13.417	-0.065	-0.065	0.000	0.000	0.000	0.000
79	A	139	LEU	0	-0.041	-0.015	9.052	-0.206	-0.206	0.000	0.000	0.000	0.000
80	A	140	LEU	0	0.014	0.010	11.947	0.184	0.184	0.000	0.000	0.000	0.000
81	A	141	THR	0	-0.005	-0.017	11.804	-0.279	-0.279	0.000	0.000	0.000	0.000
82	A	142	LEU	0	-0.003	0.003	13.664	0.129	0.129	0.000	0.000	0.000	0.000
83	A	143	CYS	0	-0.030	-0.025	15.138	-0.040	-0.040	0.000	0.000	0.000	0.000
84	A	144	GLY	0	0.089	0.030	17.910	0.035	0.035	0.000	0.000	0.000	0.000
85	A	145	PRO	0	0.022	0.007	19.836	0.005	0.005	0.000	0.000	0.000	0.000
86	A	146	LYS	1	0.791	0.899	18.529	0.281	0.281	0.000	0.000	0.000	0.000
87	A	147	THR	0	-0.018	-0.001	24.070	0.007	0.007	0.000	0.000	0.000	0.000
88	A	148	SER	0	-0.044	-0.034	27.584	0.007	0.007	0.000	0.000	0.000	0.000
89	A	149	GLY	0	0.019	0.015	30.428	0.000	0.000	0.000	0.000	0.000	0.000
90	A	150	ILE	0	-0.003	-0.009	33.396	0.001	0.001	0.000	0.000	0.000	0.000
91	A	151	ASP	-1	-0.900	-0.947	33.111	-0.118	-0.118	0.000	0.000	0.000	0.000
92	A	152	ALA	0	0.010	-0.005	28.917	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	153	GLY	0	0.005	0.002	28.009	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	154	ARG	1	0.746	0.848	26.796	0.144	0.144	0.000	0.000	0.000	0.000
95	A	155	GLY	0	0.020	-0.005	27.204	0.015	0.015	0.000	0.000	0.000	0.000
96	A	156	ASP	-1	-0.857	-0.914	26.359	-0.203	-0.203	0.000	0.000	0.000	0.000
97	A	157	ARG	1	0.779	0.882	24.454	0.293	0.293	0.000	0.000	0.000	0.000
98	A	158	THR	0	0.010	0.005	24.889	-0.019	-0.019	0.000	0.000	0.000	0.000
99	A	159	ILE	0	-0.049	-0.030	20.165	0.013	0.013	0.000	0.000	0.000	0.000
100	A	160	PRO	0	0.003	-0.005	22.582	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	161	VAL	0	0.030	0.019	18.772	-0.024	-0.024	0.000	0.000	0.000	0.000
102	A	162	THR	0	-0.009	-0.001	21.396	0.035	0.035	0.000	0.000	0.000	0.000
103	A	163	ARG	1	0.855	0.909	19.935	0.341	0.341	0.000	0.000	0.000	0.000
104	A	164	GLU	-1	-0.801	-0.860	18.146	-0.502	-0.502	0.000	0.000	0.000	0.000
105	A	165	ASP	-1	-0.925	-0.959	21.668	-0.299	-0.299	0.000	0.000	0.000	0.000
106	A	166	LYS	1	0.797	0.879	18.356	0.503	0.503	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:61:GLY)