FMO DATABASE

FMODB ID: QY2GY

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	OptH
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	-956932.242662
FMO2-HF: Nuclear repulsion	910470.722005
FMO2-HF: Total energy	-46461.520657
FMO2-MP2: Total energy	-46593.375353

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.
-2.467	1.147	-0.071	-1.756	-1.787	-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 : -0.031 / q_NPA : -0.050

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	0.012	0.036	3.735	-0.981	2.457	-0.070	-1.747	-1.621	-0.006
4	A	1	MET	0	0.016	0.016	7.264	0.001	0.001	0.000	0.000	0.000	0.000
5	A	2	SER	0	-0.074	-0.028	9.624	0.042	0.042	0.000	0.000	0.000	0.000
6	A	3	LEU	0	0.027	0.019	13.139	0.016	0.016	0.000	0.000	0.000	0.000
7	A	4	GLU	-1	-0.898	-0.945	15.210	-0.052	-0.052	0.000	0.000	0.000	0.000
8	A	5	LYS	1	0.824	0.887	15.747	-0.025	-0.025	0.000	0.000	0.000	0.000
9	A	6	LEU	0	-0.004	0.000	18.134	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	7	ASP	-1	-0.846	-0.915	21.097	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	8	THR	0	-0.041	-0.058	23.600	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	9	ASN	0	-0.036	-0.018	26.633	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	10	THR	0	0.085	0.053	25.122	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	11	PHE	0	-0.030	-0.011	23.693	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.935	-0.993	26.268	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	13	GLN	0	0.025	0.020	29.388	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	14	LEU	0	0.015	0.013	25.275	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	15	ILE	0	-0.044	-0.017	24.948	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	16	TYR	0	-0.077	-0.053	29.177	0.001	0.001	0.000	0.000	0.000	0.000
20	A	17	ASP	-1	-0.929	-0.953	32.726	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	18	GLU	-1	-1.021	-1.018	31.317	-0.037	-0.037	0.000	0.000	0.000	0.000
22	A	19	GLY	0	-0.003	0.015	32.505	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	20	LYS	1	0.941	0.970	26.958	0.046	0.046	0.000	0.000	0.000	0.000
24	A	21	ALA	0	0.003	0.013	28.693	0.002	0.002	0.000	0.000	0.000	0.000
25	A	22	CYS	0	-0.067	-0.019	23.649	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	23	LEU	0	0.026	0.031	18.341	0.005	0.005	0.000	0.000	0.000	0.000
27	A	24	VAL	0	0.006	0.005	19.820	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	25	MET	0	-0.016	0.000	11.531	0.001	0.001	0.000	0.000	0.000	0.000
29	A	26	PHE	0	-0.002	-0.002	16.745	0.018	0.018	0.000	0.000	0.000	0.000
30	A	27	SER	0	0.046	-0.047	12.355	0.017	0.017	0.000	0.000	0.000	0.000
31	A	28	ARG	1	0.942	0.971	12.280	-0.125	-0.125	0.000	0.000	0.000	0.000
32	A	29	LYS	1	0.941	0.973	9.866	-0.173	-0.173	0.000	0.000	0.000	0.000
33	A	30	ASN	0	0.015	-0.002	7.630	0.383	0.383	0.000	0.000	0.000	0.000
34	A	31	CYS	0	-0.118	-0.010	8.214	-0.136	-0.136	0.000	0.000	0.000	0.000
35	A	32	HIS	0	0.031	0.013	5.480	0.137	0.137	0.000	0.000	0.000	0.000
36	A	33	VAL	0	0.078	0.031	7.862	-0.097	-0.097	0.000	0.000	0.000	0.000
37	A	34	CYS	0	-0.044	0.010	9.774	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	35	GLN	0	-0.010	-0.003	4.433	-0.675	-0.499	-0.001	-0.009	-0.166	0.000
39	A	36	LYS	1	0.900	0.965	6.491	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	37	VAL	0	0.052	0.027	8.570	0.011	0.011	0.000	0.000	0.000	0.000
41	A	38	THR	0	-0.007	-0.017	7.944	0.049	0.049	0.000	0.000	0.000	0.000
42	A	39	PRO	0	-0.024	-0.017	7.482	0.002	0.002	0.000	0.000	0.000	0.000
43	A	40	VAL	0	0.053	0.046	10.167	0.021	0.021	0.000	0.000	0.000	0.000
44	A	41	LEU	0	0.009	0.000	13.198	0.030	0.030	0.000	0.000	0.000	0.000
45	A	42	GLU	-1	-0.883	-0.939	10.821	-0.348	-0.348	0.000	0.000	0.000	0.000
46	A	43	GLU	-1	-0.934	-0.971	13.959	-0.171	-0.171	0.000	0.000	0.000	0.000
47	A	44	LEU	0	0.016	0.006	15.834	0.020	0.020	0.000	0.000	0.000	0.000
48	A	45	ARG	1	0.856	0.907	15.218	0.193	0.193	0.000	0.000	0.000	0.000
49	A	46	LEU	0	-0.026	-0.014	17.134	0.008	0.008	0.000	0.000	0.000	0.000
50	A	47	ASN	0	-0.041	-0.011	20.501	0.008	0.008	0.000	0.000	0.000	0.000
51	A	48	TYR	0	-0.047	-0.022	22.192	0.009	0.009	0.000	0.000	0.000	0.000
52	A	49	GLU	-1	-0.941	-0.964	21.790	-0.112	-0.112	0.000	0.000	0.000	0.000
53	A	50	GLU	-1	-0.930	-0.979	24.355	-0.070	-0.070	0.000	0.000	0.000	0.000
54	A	51	SER	0	-0.158	-0.069	26.987	0.005	0.005	0.000	0.000	0.000	0.000
55	A	52	PHE	0	0.062	0.020	23.235	0.006	0.006	0.000	0.000	0.000	0.000
56	A	53	GLY	0	0.015	0.021	23.159	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	54	PHE	0	0.067	0.022	17.880	0.000	0.000	0.000	0.000	0.000	0.000
58	A	55	TYR	0	-0.004	-0.008	18.716	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	56	TYR	0	-0.011	-0.010	12.887	0.024	0.024	0.000	0.000	0.000	0.000
60	A	57	VAL	0	0.033	0.023	16.811	0.000	0.000	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.823	-0.904	15.461	0.139	0.139	0.000	0.000	0.000	0.000
62	A	59	VAL	0	0.002	-0.034	16.747	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	60	GLU	-1	-1.021	-1.019	15.259	0.125	0.125	0.000	0.000	0.000	0.000
64	A	61	GLU	-1	-0.879	-0.921	17.228	0.059	0.059	0.000	0.000	0.000	0.000
65	A	62	GLU	-1	-0.844	-0.916	20.380	0.003	0.003	0.000	0.000	0.000	0.000
66	A	63	LYS	1	0.891	0.935	22.490	-0.030	-0.030	0.000	0.000	0.000	0.000
67	A	64	THR	0	-0.004	-0.017	24.046	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	65	LEU	0	0.074	0.054	23.470	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	66	PHE	0	-0.016	-0.004	20.536	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	67	GLN	0	-0.030	-0.041	23.839	0.000	0.000	0.000	0.000	0.000	0.000
71	A	68	ARG	1	0.904	0.983	27.218	0.005	0.005	0.000	0.000	0.000	0.000
72	A	69	PHE	0	0.020	0.010	25.614	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	70	SER	0	-0.062	-0.030	27.677	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	71	LEU	0	-0.027	0.010	21.884	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	72	LYS	1	0.894	0.929	23.788	0.000	0.000	0.000	0.000	0.000	0.000
76	A	73	GLY	0	0.016	0.010	19.911	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	74	VAL	0	-0.052	-0.002	14.375	0.003	0.003	0.000	0.000	0.000	0.000
78	A	75	PRO	0	0.089	0.008	12.970	0.003	0.003	0.000	0.000	0.000	0.000
79	A	76	GLN	0	-0.053	-0.043	15.603	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	77	ILE	0	0.043	0.035	16.250	0.008	0.008	0.000	0.000	0.000	0.000
81	A	78	LEU	0	-0.090	-0.050	19.716	0.000	0.000	0.000	0.000	0.000	0.000
82	A	79	TYR	0	0.048	-0.017	21.320	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	80	PHE	0	0.000	-0.023	24.469	0.006	0.006	0.000	0.000	0.000	0.000
84	A	81	LYS	1	0.980	1.000	28.207	0.030	0.030	0.000	0.000	0.000	0.000
85	A	82	ASP	-1	-0.886	-0.923	30.999	-0.027	-0.027	0.000	0.000	0.000	0.000
86	A	83	GLY	0	-0.008	-0.002	32.373	0.002	0.002	0.000	0.000	0.000	0.000
87	A	84	GLU	-1	-0.969	-0.971	33.184	-0.020	-0.020	0.000	0.000	0.000	0.000
88	A	85	TYR	0	-0.095	-0.060	25.909	0.000	0.000	0.000	0.000	0.000	0.000
89	A	86	LYS	1	0.887	0.934	29.161	0.029	0.029	0.000	0.000	0.000	0.000
90	A	87	GLY	0	0.054	0.031	27.798	0.000	0.000	0.000	0.000	0.000	0.000
91	A	88	LYS	1	0.868	0.937	23.103	0.018	0.018	0.000	0.000	0.000	0.000
92	A	89	MET	0	0.056	0.115	20.149	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	90	ALA	0	-0.039	-0.030	19.512	0.004	0.004	0.000	0.000	0.000	0.000
94	A	91	GLY	0	-0.047	-0.027	16.356	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	92	ASP	-1	-0.905	-0.974	13.754	-0.191	-0.191	0.000	0.000	0.000	0.000
96	A	93	VAL	0	0.001	0.009	15.215	0.004	0.004	0.000	0.000	0.000	0.000
97	A	94	GLU	-1	-0.915	-0.958	15.807	-0.144	-0.144	0.000	0.000	0.000	0.000
98	A	95	ASP	-1	-0.898	-0.976	17.675	-0.121	-0.121	0.000	0.000	0.000	0.000
99	A	96	ASP	-1	-0.901	-0.938	19.027	-0.055	-0.055	0.000	0.000	0.000	0.000
100	A	97	GLU	-1	-0.922	-0.976	21.489	-0.052	-0.052	0.000	0.000	0.000	0.000
101	A	98	VAL	0	-0.054	-0.021	17.999	0.005	0.005	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.911	-0.968	21.493	-0.082	-0.082	0.000	0.000	0.000	0.000
103	A	100	GLN	0	-0.060	-0.033	23.697	0.005	0.005	0.000	0.000	0.000	0.000
104	A	101	MET	0	-0.040	-0.013	24.281	0.007	0.007	0.000	0.000	0.000	0.000
105	A	102	ILE	0	-0.024	-0.015	21.663	0.003	0.003	0.000	0.000	0.000	0.000
106	A	103	ALA	0	-0.015	-0.009	26.105	0.003	0.003	0.000	0.000	0.000	0.000
107	A	104	ASP	-1	-0.870	-0.926	29.281	-0.037	-0.037	0.000	0.000	0.000	0.000
108	A	105	VAL	0	-0.108	-0.062	27.419	0.003	0.003	0.000	0.000	0.000	0.000
109	A	106	LEU	0	-0.055	-0.037	28.471	0.002	0.002	0.000	0.000	0.000	0.000
110	A	107	GLU	-1	-0.974	-0.967	31.570	-0.036	-0.036	0.000	0.000	0.000	0.000
111	A	108	ASP	-1	-1.036	-1.008	34.124	-0.027	-0.027	0.000	0.000	0.000	0.000

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