FMO DATABASE

FMODB ID: 72GVK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-778095.883982
FMO2-HF: Nuclear repulsion	736247.745731
FMO2-HF: Total energy	-41848.138251
FMO2-MP2: Total energy	-41970.849402

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.
-1.068	1.615	-0.008	-1.472	-1.204	0.004

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 : 0.047 / q_NPA : 0.022

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	-0.028	-0.013	3.382	-0.139	2.339	-0.007	-1.414	-1.057	0.004
4	A	64	GLU	-1	-0.790	-0.846	4.094	-1.980	-1.775	-0.001	-0.058	-0.147	0.000
5	A	65	VAL	0	-0.008	-0.005	5.923	0.284	0.284	0.000	0.000	0.000	0.000
6	A	66	ARG	1	0.824	0.879	8.304	1.265	1.265	0.000	0.000	0.000	0.000
7	A	67	SER	0	0.008	-0.002	12.053	0.025	0.025	0.000	0.000	0.000	0.000
8	A	68	ASP	-1	-0.776	-0.867	15.682	-0.280	-0.280	0.000	0.000	0.000	0.000
9	A	69	ARG	1	0.865	0.906	18.800	0.145	0.145	0.000	0.000	0.000	0.000
10	A	70	GLU	-1	-0.830	-0.894	21.662	-0.185	-0.185	0.000	0.000	0.000	0.000
11	A	71	LYS	1	0.863	0.923	17.933	0.332	0.332	0.000	0.000	0.000	0.000
12	A	72	PHE	0	-0.014	-0.005	14.307	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	73	THR	0	-0.008	-0.011	12.775	0.027	0.027	0.000	0.000	0.000	0.000
14	A	74	VAL	0	-0.003	0.006	9.945	-0.040	-0.040	0.000	0.000	0.000	0.000
15	A	75	TYR	0	0.024	0.012	7.941	0.187	0.187	0.000	0.000	0.000	0.000
16	A	76	LEU	0	-0.047	-0.030	7.354	-0.549	-0.549	0.000	0.000	0.000	0.000
17	A	77	ASP	-1	-0.805	-0.881	6.444	-1.725	-1.725	0.000	0.000	0.000	0.000
18	A	78	VAL	0	-0.043	-0.033	8.491	0.091	0.091	0.000	0.000	0.000	0.000
19	A	79	LYS	1	0.903	0.929	7.910	1.609	1.609	0.000	0.000	0.000	0.000
20	A	80	HIS	0	-0.067	-0.053	12.777	0.039	0.039	0.000	0.000	0.000	0.000
21	A	81	PHE	0	-0.057	-0.010	13.691	0.079	0.079	0.000	0.000	0.000	0.000
22	A	82	SER	0	-0.011	-0.027	17.160	-0.025	-0.025	0.000	0.000	0.000	0.000
23	A	83	PRO	0	0.019	-0.019	19.972	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	84	ASP	-1	-0.899	-0.939	21.315	-0.264	-0.264	0.000	0.000	0.000	0.000
25	A	85	GLU	-1	-0.848	-0.871	19.997	-0.318	-0.318	0.000	0.000	0.000	0.000
26	A	86	LEU	0	-0.034	-0.025	15.584	-0.032	-0.032	0.000	0.000	0.000	0.000
27	A	87	SER	0	0.005	0.010	19.431	0.042	0.042	0.000	0.000	0.000	0.000
28	A	88	VAL	0	0.000	-0.015	17.706	-0.031	-0.031	0.000	0.000	0.000	0.000
29	A	89	LYS	1	0.960	0.986	20.236	0.248	0.248	0.000	0.000	0.000	0.000
30	A	90	VAL	0	-0.027	-0.001	20.837	-0.029	-0.029	0.000	0.000	0.000	0.000
31	A	91	THR	0	-0.015	-0.027	22.281	0.017	0.017	0.000	0.000	0.000	0.000
32	A	92	ASP	-1	-0.903	-0.956	22.986	-0.110	-0.110	0.000	0.000	0.000	0.000
33	A	93	ASP	-1	-0.828	-0.864	23.008	-0.130	-0.130	0.000	0.000	0.000	0.000
34	A	94	TYR	0	-0.006	-0.004	17.474	0.004	0.004	0.000	0.000	0.000	0.000
35	A	95	VAL	0	0.001	0.004	16.552	0.003	0.003	0.000	0.000	0.000	0.000
36	A	96	GLU	-1	-0.865	-0.929	16.778	-0.240	-0.240	0.000	0.000	0.000	0.000
37	A	97	ILE	0	-0.006	-0.014	13.185	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	98	GLN	0	-0.038	-0.013	15.895	0.011	0.011	0.000	0.000	0.000	0.000
39	A	99	GLY	0	0.058	0.032	16.480	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	100	LYS	1	0.891	0.950	17.415	0.211	0.211	0.000	0.000	0.000	0.000
41	A	101	HIS	1	0.834	0.897	17.486	0.344	0.344	0.000	0.000	0.000	0.000
42	A	102	GLY	0	-0.010	-0.002	19.344	0.015	0.015	0.000	0.000	0.000	0.000
43	A	103	GLU	-1	-0.824	-0.875	18.023	-0.329	-0.329	0.000	0.000	0.000	0.000
44	A	104	ARG	1	0.990	0.973	22.579	0.131	0.131	0.000	0.000	0.000	0.000
45	A	105	GLN	0	-0.075	-0.040	19.954	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	106	ASP	-1	-0.871	-0.940	24.074	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	107	ASP	-1	-0.919	-0.953	26.355	-0.033	-0.033	0.000	0.000	0.000	0.000
48	A	108	HIS	0	-0.064	-0.031	29.641	0.000	0.000	0.000	0.000	0.000	0.000
49	A	109	GLY	0	0.035	0.039	25.827	0.003	0.003	0.000	0.000	0.000	0.000
50	A	110	TYR	0	-0.048	-0.046	23.909	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	111	ILE	0	-0.015	0.011	17.808	0.014	0.014	0.000	0.000	0.000	0.000
52	A	112	SER	0	0.024	0.000	20.279	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	113	ARG	1	0.822	0.904	13.789	0.310	0.310	0.000	0.000	0.000	0.000
54	A	114	GLU	-1	-0.834	-0.922	16.504	-0.208	-0.208	0.000	0.000	0.000	0.000
55	A	115	PHE	0	-0.062	-0.022	12.894	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	116	HIS	0	0.042	0.002	14.905	-0.027	-0.027	0.000	0.000	0.000	0.000
57	A	117	ARG	1	0.883	0.946	6.852	0.928	0.928	0.000	0.000	0.000	0.000
58	A	118	ARG	1	0.929	0.965	13.906	0.173	0.173	0.000	0.000	0.000	0.000
59	A	119	TYR	0	-0.009	-0.002	9.366	-0.054	-0.054	0.000	0.000	0.000	0.000
60	A	120	ARG	1	0.936	0.960	14.623	0.104	0.104	0.000	0.000	0.000	0.000
61	A	121	LEU	0	0.005	0.007	16.295	-0.039	-0.039	0.000	0.000	0.000	0.000
62	A	122	PRO	0	-0.038	-0.013	17.396	0.036	0.036	0.000	0.000	0.000	0.000
63	A	123	SER	0	0.020	0.001	20.435	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	124	ASN	0	0.005	-0.002	22.547	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	125	VAL	0	-0.026	0.000	19.231	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	126	ASP	-1	-0.758	-0.851	22.670	-0.178	-0.178	0.000	0.000	0.000	0.000
67	A	127	GLN	0	0.015	-0.031	23.089	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	128	SER	0	-0.075	-0.043	24.532	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	129	ALA	0	0.009	0.005	25.327	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	130	ILE	0	-0.080	-0.027	19.275	-0.025	-0.025	0.000	0.000	0.000	0.000
71	A	131	THR	0	-0.010	0.001	20.619	0.006	0.006	0.000	0.000	0.000	0.000
72	A	132	CYS	0	-0.030	-0.009	16.753	-0.050	-0.050	0.000	0.000	0.000	0.000
73	A	133	THR	0	0.014	0.010	17.545	0.030	0.030	0.000	0.000	0.000	0.000
74	A	134	LEU	0	0.005	0.005	15.113	-0.091	-0.091	0.000	0.000	0.000	0.000
75	A	135	SER	0	-0.007	-0.013	15.156	0.055	0.055	0.000	0.000	0.000	0.000
76	A	136	ALA	0	-0.033	-0.030	17.087	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	137	ASP	-1	-0.886	-0.936	13.771	-0.647	-0.647	0.000	0.000	0.000	0.000
78	A	138	GLY	0	-0.003	0.002	13.133	-0.103	-0.103	0.000	0.000	0.000	0.000
79	A	139	LEU	0	-0.033	-0.004	9.030	-0.212	-0.212	0.000	0.000	0.000	0.000
80	A	140	LEU	0	0.005	0.005	11.691	0.215	0.215	0.000	0.000	0.000	0.000
81	A	141	THR	0	0.005	-0.010	11.887	-0.240	-0.240	0.000	0.000	0.000	0.000
82	A	142	LEU	0	-0.011	0.002	13.646	0.122	0.122	0.000	0.000	0.000	0.000
83	A	143	CYS	0	-0.042	-0.031	15.106	-0.034	-0.034	0.000	0.000	0.000	0.000
84	A	144	GLY	0	0.098	0.034	17.820	0.038	0.038	0.000	0.000	0.000	0.000
85	A	145	PRO	0	0.017	0.011	19.753	0.004	0.004	0.000	0.000	0.000	0.000
86	A	146	LYS	1	0.819	0.917	18.293	0.251	0.251	0.000	0.000	0.000	0.000
87	A	147	THR	0	0.000	0.007	23.788	0.004	0.004	0.000	0.000	0.000	0.000
88	A	148	SER	0	-0.053	-0.029	27.495	0.009	0.009	0.000	0.000	0.000	0.000
89	A	149	GLY	0	0.010	0.004	30.197	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	150	ILE	0	-0.007	-0.013	32.941	0.000	0.000	0.000	0.000	0.000	0.000
91	A	151	ASP	-1	-0.922	-0.952	33.374	-0.103	-0.103	0.000	0.000	0.000	0.000
92	A	152	ALA	0	0.014	-0.001	29.187	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	153	GLY	0	0.020	0.014	28.256	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	154	ARG	1	0.791	0.864	27.097	0.106	0.106	0.000	0.000	0.000	0.000
95	A	155	GLY	0	0.009	-0.012	27.360	0.013	0.013	0.000	0.000	0.000	0.000
96	A	156	ASP	-1	-0.845	-0.912	26.488	-0.170	-0.170	0.000	0.000	0.000	0.000
97	A	157	ARG	1	0.806	0.899	24.083	0.265	0.265	0.000	0.000	0.000	0.000
98	A	158	THR	0	-0.008	-0.006	25.024	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	159	ILE	0	-0.053	-0.033	20.298	0.011	0.011	0.000	0.000	0.000	0.000
100	A	160	PRO	0	0.001	-0.001	22.862	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	161	VAL	0	0.031	0.014	19.061	-0.029	-0.029	0.000	0.000	0.000	0.000
102	A	162	THR	0	-0.005	0.003	21.525	0.035	0.035	0.000	0.000	0.000	0.000
103	A	163	ARG	1	0.882	0.927	19.816	0.366	0.366	0.000	0.000	0.000	0.000
104	A	164	GLU	-1	-0.815	-0.881	18.244	-0.519	-0.519	0.000	0.000	0.000	0.000
105	A	165	ASP	-1	-0.956	-0.961	22.017	-0.297	-0.297	0.000	0.000	0.000	0.000
106	A	166	LYS	1	0.886	0.921	18.707	0.510	0.510	0.000	0.000	0.000	0.000

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