FMO DATABASE

FMODB ID: K94L3

Calculation Name: 3GNJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GNJ

Chain ID: A

ChEMBL ID:

UniProt ID: B8G0E7

Base Structure: X-ray

Registration Date: 2023-09-20

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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-957471.258203
FMO2-HF: Nuclear repulsion	911008.795664
FMO2-HF: Total energy	-46462.462538
FMO2-MP2: Total energy	-46594.349518

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:-2:SER)

Summations of interaction energy for fragment #1(A:-2: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.
-2.874	0.489	-0.07	-1.63	-1.663	-0.006

Interaction energy analysis for fragmet #1(A:-2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.033

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	0	ALA	0	0.009	0.033	3.735	-0.565	2.636	-0.069	-1.622	-1.510	-0.006
4	A	1	MET	0	0.008	0.016	7.151	-0.077	-0.077	0.000	0.000	0.000	0.000
5	A	2	SER	0	-0.091	-0.071	9.528	0.068	0.068	0.000	0.000	0.000	0.000
6	A	3	LEU	0	-0.005	0.012	13.037	0.029	0.029	0.000	0.000	0.000	0.000
7	A	4	GLU	-1	-0.895	-0.950	15.108	-0.091	-0.091	0.000	0.000	0.000	0.000
8	A	5	LYS	1	0.841	0.905	15.916	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	6	LEU	0	-0.016	-0.004	18.030	0.002	0.002	0.000	0.000	0.000	0.000
10	A	7	ASP	-1	-0.831	-0.901	21.002	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	8	THR	0	-0.044	-0.075	23.528	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	9	ASN	0	-0.055	-0.011	26.543	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	10	THR	0	0.061	0.012	24.967	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	11	PHE	0	-0.018	-0.011	23.462	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.868	-0.935	26.175	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	13	GLN	0	0.025	0.019	29.439	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	14	LEU	0	-0.012	0.007	24.919	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	15	ILE	0	-0.037	-0.017	24.886	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	16	TYR	0	-0.060	-0.050	29.091	0.003	0.003	0.000	0.000	0.000	0.000
20	A	17	ASP	-1	-0.923	-0.953	32.640	-0.031	-0.031	0.000	0.000	0.000	0.000
21	A	18	GLU	-1	-0.897	-0.947	30.639	-0.066	-0.066	0.000	0.000	0.000	0.000
22	A	19	GLY	0	-0.009	0.014	32.421	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	20	LYS	1	0.819	0.897	27.102	0.073	0.073	0.000	0.000	0.000	0.000
24	A	21	ALA	0	0.019	0.023	28.616	0.003	0.003	0.000	0.000	0.000	0.000
25	A	22	CYS	0	-0.071	-0.029	23.647	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	23	LEU	0	0.017	0.027	18.377	0.010	0.010	0.000	0.000	0.000	0.000
27	A	24	VAL	0	0.013	0.008	19.730	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	25	MET	0	-0.002	0.006	11.412	0.007	0.007	0.000	0.000	0.000	0.000
29	A	26	PHE	0	-0.013	-0.008	16.691	0.024	0.024	0.000	0.000	0.000	0.000
30	A	27	SER	0	0.017	-0.059	11.904	0.010	0.010	0.000	0.000	0.000	0.000
31	A	28	ARG	1	0.829	0.902	12.748	-0.236	-0.236	0.000	0.000	0.000	0.000
32	A	29	LYS	1	0.904	0.920	9.861	-0.240	-0.240	0.000	0.000	0.000	0.000
33	A	30	ASN	0	0.000	-0.016	7.715	0.389	0.389	0.000	0.000	0.000	0.000
34	A	31	CYS	0	-0.073	-0.005	8.269	-0.088	-0.088	0.000	0.000	0.000	0.000
35	A	32	HIS	0	0.005	0.003	5.133	0.130	0.130	0.000	0.000	0.000	0.000
36	A	33	VAL	0	0.078	0.027	7.883	-0.133	-0.133	0.000	0.000	0.000	0.000
37	A	34	CYS	0	-0.003	0.037	9.643	-0.047	-0.047	0.000	0.000	0.000	0.000
38	A	35	GLN	0	-0.017	-0.004	4.421	-0.693	-0.531	-0.001	-0.008	-0.153	0.000
39	A	36	LYS	1	0.860	0.940	6.468	-0.062	-0.062	0.000	0.000	0.000	0.000
40	A	37	VAL	0	0.046	0.025	8.575	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	38	THR	0	-0.012	-0.029	7.874	0.058	0.058	0.000	0.000	0.000	0.000
42	A	39	PRO	0	-0.027	-0.017	7.356	0.001	0.001	0.000	0.000	0.000	0.000
43	A	40	VAL	0	0.040	0.040	10.118	0.026	0.026	0.000	0.000	0.000	0.000
44	A	41	LEU	0	0.014	0.004	13.152	0.044	0.044	0.000	0.000	0.000	0.000
45	A	42	GLU	-1	-0.821	-0.893	11.005	-0.527	-0.527	0.000	0.000	0.000	0.000
46	A	43	GLU	-1	-0.937	-0.967	13.911	-0.351	-0.351	0.000	0.000	0.000	0.000
47	A	44	LEU	0	-0.002	-0.007	15.780	0.033	0.033	0.000	0.000	0.000	0.000
48	A	45	ARG	1	0.864	0.922	15.053	0.334	0.334	0.000	0.000	0.000	0.000
49	A	46	LEU	0	-0.033	-0.014	17.438	0.013	0.013	0.000	0.000	0.000	0.000
50	A	47	ASN	0	-0.067	-0.024	20.431	0.013	0.013	0.000	0.000	0.000	0.000
51	A	48	TYR	0	-0.107	-0.080	22.293	0.022	0.022	0.000	0.000	0.000	0.000
52	A	49	GLU	-1	-0.918	-0.950	21.618	-0.203	-0.203	0.000	0.000	0.000	0.000
53	A	50	GLU	-1	-0.925	-0.974	24.273	-0.126	-0.126	0.000	0.000	0.000	0.000
54	A	51	SER	0	-0.157	-0.076	26.754	0.008	0.008	0.000	0.000	0.000	0.000
55	A	52	PHE	0	0.058	0.017	23.104	0.011	0.011	0.000	0.000	0.000	0.000
56	A	53	GLY	0	0.021	0.025	23.071	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	54	PHE	0	0.059	0.016	17.779	0.001	0.001	0.000	0.000	0.000	0.000
58	A	55	TYR	0	0.007	-0.003	18.631	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	56	TYR	0	-0.038	-0.034	13.092	0.028	0.028	0.000	0.000	0.000	0.000
60	A	57	VAL	0	0.033	0.027	16.722	0.004	0.004	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.764	-0.869	14.416	0.230	0.230	0.000	0.000	0.000	0.000
62	A	59	VAL	0	0.001	-0.023	16.716	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	60	GLU	-1	-0.934	-0.958	15.177	0.244	0.244	0.000	0.000	0.000	0.000
64	A	61	GLU	-1	-0.834	-0.887	16.841	0.095	0.095	0.000	0.000	0.000	0.000
65	A	62	GLU	-1	-0.819	-0.883	20.380	0.008	0.008	0.000	0.000	0.000	0.000
66	A	63	LYS	1	0.888	0.928	22.490	-0.072	-0.072	0.000	0.000	0.000	0.000
67	A	64	THR	0	0.001	-0.011	24.072	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	65	LEU	0	0.080	0.059	23.501	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	66	PHE	0	-0.011	-0.005	20.443	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	67	GLN	0	-0.028	-0.028	23.780	0.003	0.003	0.000	0.000	0.000	0.000
71	A	68	ARG	1	0.815	0.917	27.186	0.005	0.005	0.000	0.000	0.000	0.000
72	A	69	PHE	0	0.027	0.014	25.479	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	70	SER	0	-0.048	-0.022	27.625	0.001	0.001	0.000	0.000	0.000	0.000
74	A	71	LEU	0	-0.018	0.013	21.695	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	72	LYS	1	0.851	0.907	23.828	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	73	GLY	0	0.029	0.018	19.940	0.002	0.002	0.000	0.000	0.000	0.000
77	A	74	VAL	0	-0.053	0.009	14.405	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	75	PRO	0	0.058	0.014	13.118	0.017	0.017	0.000	0.000	0.000	0.000
79	A	76	GLN	0	-0.045	-0.049	15.574	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	77	ILE	0	0.037	0.041	16.219	0.009	0.009	0.000	0.000	0.000	0.000
81	A	78	LEU	0	-0.074	-0.033	19.668	0.004	0.004	0.000	0.000	0.000	0.000
82	A	79	TYR	0	0.058	-0.016	21.138	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	80	PHE	0	-0.005	-0.027	24.293	0.012	0.012	0.000	0.000	0.000	0.000
84	A	81	LYS	1	0.868	0.917	28.138	0.046	0.046	0.000	0.000	0.000	0.000
85	A	82	ASP	-1	-0.833	-0.887	30.927	-0.045	-0.045	0.000	0.000	0.000	0.000
86	A	83	GLY	0	-0.003	0.004	32.294	0.004	0.004	0.000	0.000	0.000	0.000
87	A	84	GLU	-1	-0.971	-0.972	33.112	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	85	TYR	0	-0.093	-0.064	25.837	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	86	LYS	1	0.819	0.898	29.177	0.048	0.048	0.000	0.000	0.000	0.000
90	A	87	GLY	0	0.048	0.029	27.757	0.000	0.000	0.000	0.000	0.000	0.000
91	A	88	LYS	1	0.830	0.919	23.110	0.014	0.014	0.000	0.000	0.000	0.000
92	A	89	MET	0	0.058	0.107	20.051	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	90	ALA	0	-0.053	-0.045	19.475	0.007	0.007	0.000	0.000	0.000	0.000
94	A	91	GLY	0	-0.036	-0.015	16.357	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	92	ASP	-1	-0.861	-0.951	13.181	-0.242	-0.242	0.000	0.000	0.000	0.000
96	A	93	VAL	0	0.000	0.009	15.225	0.004	0.004	0.000	0.000	0.000	0.000
97	A	94	GLU	-1	-0.916	-0.955	15.805	-0.223	-0.223	0.000	0.000	0.000	0.000
98	A	95	ASP	-1	-0.871	-0.964	17.745	-0.206	-0.206	0.000	0.000	0.000	0.000
99	A	96	ASP	-1	-0.943	-0.959	19.011	-0.093	-0.093	0.000	0.000	0.000	0.000
100	A	97	GLU	-1	-0.925	-0.971	21.269	-0.076	-0.076	0.000	0.000	0.000	0.000
101	A	98	VAL	0	-0.042	-0.023	18.086	0.008	0.008	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.844	-0.912	21.461	-0.151	-0.151	0.000	0.000	0.000	0.000
103	A	100	GLN	0	-0.064	-0.030	23.662	0.006	0.006	0.000	0.000	0.000	0.000
104	A	101	MET	0	-0.038	-0.012	24.273	0.011	0.011	0.000	0.000	0.000	0.000
105	A	102	ILE	0	-0.008	-0.010	21.642	0.006	0.006	0.000	0.000	0.000	0.000
106	A	103	ALA	0	-0.006	0.000	26.055	0.006	0.006	0.000	0.000	0.000	0.000
107	A	104	ASP	-1	-0.879	-0.934	29.224	-0.060	-0.060	0.000	0.000	0.000	0.000
108	A	105	VAL	0	-0.093	-0.057	27.423	0.006	0.006	0.000	0.000	0.000	0.000
109	A	106	LEU	0	-0.049	-0.032	28.180	0.004	0.004	0.000	0.000	0.000	0.000
110	A	107	GLU	-1	-0.936	-0.947	31.510	-0.062	-0.062	0.000	0.000	0.000	0.000
111	A	108	ASP	-1	-0.951	-0.946	34.078	-0.042	-0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:SER)