FMO DATABASE

FMODB ID: 491VN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-959182.106794
FMO2-HF: Nuclear repulsion	912719.200192
FMO2-HF: Total energy	-46462.906602
FMO2-MP2: Total energy	-46594.75574

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.
-1.648	0.628	-0.025	-1.167	-1.084	0

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 : -0.015 / 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].
3	A	0	ALA	0	-0.008	0.005	3.865	1.381	3.463	-0.024	-1.153	-0.904
4	A	1	MET	0	-0.023	0.003	7.143	-0.133	-0.133	0.000	0.000	0.000
5	A	2	SER	0	-0.099	-0.077	9.705	0.085	0.085	0.000	0.000	0.000
6	A	3	LEU	0	0.011	0.020	13.031	0.029	0.029	0.000	0.000	0.000
7	A	4	GLU	-1	-0.904	-0.951	15.127	-0.075	-0.075	0.000	0.000	0.000
8	A	5	LYS	1	0.811	0.905	15.655	-0.064	-0.064	0.000	0.000	0.000
9	A	6	LEU	0	-0.010	0.008	17.824	0.003	0.003	0.000	0.000	0.000
10	A	7	ASP	-1	-0.829	-0.903	20.562	0.021	0.021	0.000	0.000	0.000
11	A	8	THR	0	-0.053	-0.080	23.399	-0.011	-0.011	0.000	0.000	0.000
12	A	9	ASN	0	-0.076	-0.032	26.379	-0.008	-0.008	0.000	0.000	0.000
13	A	10	THR	0	0.036	-0.011	24.777	-0.006	-0.006	0.000	0.000	0.000
14	A	11	PHE	0	-0.015	-0.008	23.516	-0.008	-0.008	0.000	0.000	0.000
15	A	12	GLU	-1	-0.823	-0.900	26.031	-0.011	-0.011	0.000	0.000	0.000
16	A	13	GLN	0	-0.007	0.001	29.440	-0.003	-0.003	0.000	0.000	0.000
17	A	14	LEU	0	-0.013	0.003	24.581	-0.003	-0.003	0.000	0.000	0.000
18	A	15	ILE	0	-0.023	-0.015	24.844	-0.005	-0.005	0.000	0.000	0.000
19	A	16	TYR	0	-0.063	-0.043	29.038	0.002	0.002	0.000	0.000	0.000
20	A	17	ASP	-1	-0.927	-0.956	32.723	-0.031	-0.031	0.000	0.000	0.000
21	A	18	GLU	-1	-0.861	-0.930	30.377	-0.070	-0.070	0.000	0.000	0.000
22	A	19	GLY	0	-0.027	-0.005	32.641	-0.003	-0.003	0.000	0.000	0.000
23	A	20	LYS	1	0.806	0.900	27.420	0.079	0.079	0.000	0.000	0.000
24	A	21	ALA	0	0.020	0.015	28.634	0.001	0.001	0.000	0.000	0.000
25	A	22	CYS	0	-0.080	-0.028	23.899	-0.005	-0.005	0.000	0.000	0.000
26	A	23	LEU	0	0.019	0.033	18.638	0.010	0.010	0.000	0.000	0.000
27	A	24	VAL	0	-0.005	-0.011	19.948	-0.001	-0.001	0.000	0.000	0.000
28	A	25	MET	0	0.000	0.015	11.778	0.006	0.006	0.000	0.000	0.000
29	A	26	PHE	0	-0.004	-0.013	16.622	0.033	0.033	0.000	0.000	0.000
30	A	27	SER	0	0.068	0.007	11.624	0.002	0.002	0.000	0.000	0.000
31	A	28	ARG	1	0.817	0.871	12.407	-0.215	-0.215	0.000	0.000	0.000
32	A	29	LYS	1	0.874	0.925	9.489	-0.333	-0.333	0.000	0.000	0.000
33	A	30	ASN	0	0.007	-0.006	7.464	0.380	0.380	0.000	0.000	0.000
34	A	31	CYS	0	-0.078	-0.017	8.400	-0.144	-0.144	0.000	0.000	0.000
35	A	32	HIS	0	-0.012	-0.021	5.211	0.228	0.228	0.000	0.000	0.000
36	A	33	VAL	0	0.052	0.023	7.968	-0.161	-0.161	0.000	0.000	0.000
37	A	34	CYS	0	-0.007	0.002	9.401	-0.058	-0.058	0.000	0.000	0.000
38	A	35	GLN	0	-0.023	0.013	4.404	-0.933	-0.739	-0.001	-0.014	-0.180
39	A	36	LYS	1	0.839	0.948	6.467	-0.007	-0.007	0.000	0.000	0.000
40	A	37	VAL	0	0.033	0.007	8.928	0.007	0.007	0.000	0.000	0.000
41	A	38	THR	0	-0.011	-0.032	8.353	0.079	0.079	0.000	0.000	0.000
42	A	39	PRO	0	-0.022	-0.021	7.719	0.024	0.024	0.000	0.000	0.000
43	A	40	VAL	0	0.036	0.041	10.408	0.052	0.052	0.000	0.000	0.000
44	A	41	LEU	0	0.012	-0.002	13.487	0.057	0.057	0.000	0.000	0.000
45	A	42	GLU	-1	-0.783	-0.876	11.414	-0.514	-0.514	0.000	0.000	0.000
46	A	43	GLU	-1	-0.939	-0.960	14.306	-0.479	-0.479	0.000	0.000	0.000
47	A	44	LEU	0	-0.004	-0.008	16.067	0.046	0.046	0.000	0.000	0.000
48	A	45	ARG	1	0.836	0.918	15.110	0.385	0.385	0.000	0.000	0.000
49	A	46	LEU	0	-0.006	-0.007	18.128	0.028	0.028	0.000	0.000	0.000
50	A	47	ASN	0	-0.094	-0.036	21.218	0.009	0.009	0.000	0.000	0.000
51	A	48	TYR	0	-0.104	-0.075	22.826	0.028	0.028	0.000	0.000	0.000
52	A	49	GLU	-1	-0.881	-0.939	21.741	-0.226	-0.226	0.000	0.000	0.000
53	A	50	GLU	-1	-0.952	-0.976	24.352	-0.141	-0.141	0.000	0.000	0.000
54	A	51	SER	0	-0.158	-0.087	27.463	0.013	0.013	0.000	0.000	0.000
55	A	52	PHE	0	0.029	-0.001	23.508	0.011	0.011	0.000	0.000	0.000
56	A	53	GLY	0	0.027	0.027	23.423	-0.014	-0.014	0.000	0.000	0.000
57	A	54	PHE	0	0.048	0.008	17.903	-0.003	-0.003	0.000	0.000	0.000
58	A	55	TYR	0	0.022	0.007	18.602	-0.008	-0.008	0.000	0.000	0.000
59	A	56	TYR	0	-0.050	-0.053	13.143	0.018	0.018	0.000	0.000	0.000
60	A	57	VAL	0	0.028	0.019	16.806	0.017	0.017	0.000	0.000	0.000
61	A	58	ASP	-1	-0.773	-0.875	14.003	0.255	0.255	0.000	0.000	0.000
62	A	59	VAL	0	-0.007	-0.020	16.594	-0.004	-0.004	0.000	0.000	0.000
63	A	60	GLU	-1	-0.876	-0.913	14.867	0.262	0.262	0.000	0.000	0.000
64	A	61	GLU	-1	-0.832	-0.887	16.559	0.158	0.158	0.000	0.000	0.000
65	A	62	GLU	-1	-0.782	-0.870	20.243	0.022	0.022	0.000	0.000	0.000
66	A	63	LYS	1	0.884	0.932	22.222	-0.082	-0.082	0.000	0.000	0.000
67	A	64	THR	0	0.000	0.002	23.745	-0.005	-0.005	0.000	0.000	0.000
68	A	65	LEU	0	0.048	0.041	23.035	-0.006	-0.006	0.000	0.000	0.000
69	A	66	PHE	0	-0.017	-0.007	20.101	-0.004	-0.004	0.000	0.000	0.000
70	A	67	GLN	0	-0.021	-0.022	23.637	0.002	0.002	0.000	0.000	0.000
71	A	68	ARG	1	0.813	0.912	27.140	0.005	0.005	0.000	0.000	0.000
72	A	69	PHE	0	0.041	0.031	25.421	-0.004	-0.004	0.000	0.000	0.000
73	A	70	SER	0	-0.059	-0.037	27.328	-0.001	-0.001	0.000	0.000	0.000
74	A	71	LEU	0	-0.017	0.009	21.630	-0.001	-0.001	0.000	0.000	0.000
75	A	72	LYS	1	0.862	0.916	23.811	0.001	0.001	0.000	0.000	0.000
76	A	73	GLY	0	-0.005	0.003	19.828	0.005	0.005	0.000	0.000	0.000
77	A	74	VAL	0	-0.027	0.015	13.898	0.000	0.000	0.000	0.000	0.000
78	A	75	PRO	0	0.070	0.016	13.207	0.017	0.017	0.000	0.000	0.000
79	A	76	GLN	0	-0.062	-0.045	15.479	-0.004	-0.004	0.000	0.000	0.000
80	A	77	ILE	0	0.022	0.026	16.494	0.008	0.008	0.000	0.000	0.000
81	A	78	LEU	0	-0.055	-0.017	19.850	0.005	0.005	0.000	0.000	0.000
82	A	79	TYR	0	0.068	-0.007	21.219	-0.012	-0.012	0.000	0.000	0.000
83	A	80	PHE	0	-0.024	-0.035	24.496	0.013	0.013	0.000	0.000	0.000
84	A	81	LYS	1	0.897	0.932	28.300	0.061	0.061	0.000	0.000	0.000
85	A	82	ASP	-1	-0.833	-0.886	31.244	-0.057	-0.057	0.000	0.000	0.000
86	A	83	GLY	0	-0.001	0.011	32.760	0.005	0.005	0.000	0.000	0.000
87	A	84	GLU	-1	-0.952	-0.965	33.080	-0.043	-0.043	0.000	0.000	0.000
88	A	85	TYR	0	-0.055	-0.056	26.365	-0.004	-0.004	0.000	0.000	0.000
89	A	86	LYS	1	0.791	0.889	29.524	0.063	0.063	0.000	0.000	0.000
90	A	87	GLY	0	0.051	0.032	28.130	-0.001	-0.001	0.000	0.000	0.000
91	A	88	LYS	1	0.809	0.899	23.255	0.045	0.045	0.000	0.000	0.000
92	A	89	MET	0	0.059	0.102	20.213	-0.005	-0.005	0.000	0.000	0.000
93	A	90	ALA	0	-0.060	-0.055	19.524	0.010	0.010	0.000	0.000	0.000
94	A	91	GLY	0	-0.008	0.004	16.652	-0.004	-0.004	0.000	0.000	0.000
95	A	92	ASP	-1	-0.884	-0.970	13.115	-0.386	-0.386	0.000	0.000	0.000
96	A	93	VAL	0	-0.003	0.005	15.328	-0.006	-0.006	0.000	0.000	0.000
97	A	94	GLU	-1	-0.876	-0.940	15.837	-0.382	-0.382	0.000	0.000	0.000
98	A	95	ASP	-1	-0.873	-0.956	18.018	-0.291	-0.291	0.000	0.000	0.000
99	A	96	ASP	-1	-0.946	-0.968	19.181	-0.143	-0.143	0.000	0.000	0.000
100	A	97	GLU	-1	-0.923	-0.965	21.336	-0.134	-0.134	0.000	0.000	0.000
101	A	98	VAL	0	-0.037	-0.024	18.303	0.013	0.013	0.000	0.000	0.000
102	A	99	GLU	-1	-0.799	-0.882	21.719	-0.209	-0.209	0.000	0.000	0.000
103	A	100	GLN	0	-0.072	-0.034	23.902	0.010	0.010	0.000	0.000	0.000
104	A	101	MET	0	-0.035	-0.015	24.333	0.015	0.015	0.000	0.000	0.000
105	A	102	ILE	0	-0.021	-0.014	21.853	0.009	0.009	0.000	0.000	0.000
106	A	103	ALA	0	0.010	0.010	26.204	0.009	0.009	0.000	0.000	0.000
107	A	104	ASP	-1	-0.889	-0.945	29.382	-0.093	-0.093	0.000	0.000	0.000
108	A	105	VAL	0	-0.088	-0.046	27.512	0.009	0.009	0.000	0.000	0.000
109	A	106	LEU	0	-0.025	-0.022	28.580	0.007	0.007	0.000	0.000	0.000
110	A	107	GLU	-1	-0.934	-0.950	31.786	-0.082	-0.082	0.000	0.000	0.000
111	A	108	ASP	-1	-0.956	-0.952	34.216	-0.055	-0.055	0.000	0.000	0.000

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Highlights

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