FMO DATABASE

FMODB ID: NNL4Q

Calculation Name: 3GAX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GAX

Chain ID: A

ChEMBL ID:

UniProt ID: P01034

Base Structure: X-ray

Registration Date: 2023-09-23

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-833671.596144
FMO2-HF: Nuclear repulsion	788784.13412
FMO2-HF: Total energy	-44887.462024
FMO2-MP2: Total energy	-45012.550659

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:12:GLY)

Summations of interaction energy for fragment #1(A:12: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.
-2.614	-1.284	3.323	-2.165	-2.488	-0.015

Interaction energy analysis for fragmet #1(A:12: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 : 0.023

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	14	MET	0	-0.003	0.004	3.844	-0.166	1.316	-0.007	-0.802	-0.673	0.004
4	A	15	ASP	-1	-0.889	-0.956	6.552	-0.729	-0.729	0.000	0.000	0.000	0.000
5	A	16	ALA	0	-0.042	-0.019	9.865	-0.103	-0.103	0.000	0.000	0.000	0.000
6	A	17	SER	0	0.022	0.010	12.485	0.144	0.144	0.000	0.000	0.000	0.000
7	A	18	VAL	0	0.045	0.009	16.126	-0.030	-0.030	0.000	0.000	0.000	0.000
8	A	19	GLU	-1	-0.878	-0.949	18.971	-0.388	-0.388	0.000	0.000	0.000	0.000
9	A	20	GLU	-1	-0.841	-0.886	14.246	-1.051	-1.051	0.000	0.000	0.000	0.000
10	A	21	GLU	-1	-0.854	-0.919	18.454	-0.420	-0.420	0.000	0.000	0.000	0.000
11	A	22	GLY	0	0.052	0.028	16.881	0.023	0.023	0.000	0.000	0.000	0.000
12	A	23	VAL	0	0.012	0.005	14.160	0.002	0.002	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.877	0.940	16.764	0.451	0.451	0.000	0.000	0.000	0.000
14	A	25	ARG	1	0.877	0.920	20.004	0.397	0.397	0.000	0.000	0.000	0.000
15	A	26	ALA	0	-0.009	-0.006	16.125	0.041	0.041	0.000	0.000	0.000	0.000
16	A	27	LEU	0	-0.002	-0.013	18.158	0.036	0.036	0.000	0.000	0.000	0.000
17	A	28	ASP	-1	-0.903	-0.941	19.709	-0.282	-0.282	0.000	0.000	0.000	0.000
18	A	29	PHE	0	-0.028	-0.024	19.019	0.030	0.030	0.000	0.000	0.000	0.000
19	A	30	ALA	0	0.009	0.009	18.675	0.032	0.032	0.000	0.000	0.000	0.000
20	A	31	VAL	0	-0.002	-0.006	20.795	0.035	0.035	0.000	0.000	0.000	0.000
21	A	32	GLY	0	0.013	0.010	23.742	0.027	0.027	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.837	-0.916	22.706	-0.167	-0.167	0.000	0.000	0.000	0.000
23	A	34	TYR	0	0.000	-0.002	23.585	0.023	0.023	0.000	0.000	0.000	0.000
24	A	35	ASN	0	-0.015	-0.021	25.263	0.031	0.031	0.000	0.000	0.000	0.000
25	A	36	LYS	1	0.785	0.881	26.702	0.183	0.183	0.000	0.000	0.000	0.000
26	A	37	ALA	0	-0.013	-0.006	26.793	0.012	0.012	0.000	0.000	0.000	0.000
27	A	38	SER	0	-0.002	0.031	28.777	0.014	0.014	0.000	0.000	0.000	0.000
28	A	39	ASN	0	-0.010	-0.023	30.620	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	40	ASP	-1	-0.783	-0.853	32.968	-0.084	-0.084	0.000	0.000	0.000	0.000
30	A	41	MET	0	0.022	0.010	34.833	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	42	TYR	0	-0.055	-0.032	35.827	0.000	0.000	0.000	0.000	0.000	0.000
32	A	43	HIS	0	0.070	0.050	32.222	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	44	SER	0	-0.038	-0.018	28.628	0.008	0.008	0.000	0.000	0.000	0.000
34	A	45	ARG	1	0.882	0.961	27.413	0.155	0.155	0.000	0.000	0.000	0.000
35	A	46	ALA	0	0.049	0.019	23.285	0.011	0.011	0.000	0.000	0.000	0.000
36	A	47	CYS	0	-0.066	-0.021	25.192	0.003	0.003	0.000	0.000	0.000	0.000
37	A	48	GLN	0	-0.033	-0.031	22.132	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	49	VAL	0	-0.004	0.008	17.978	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	50	VAL	0	-0.048	-0.013	17.681	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	51	ARG	1	0.871	0.895	11.282	0.353	0.353	0.000	0.000	0.000	0.000
41	A	52	ALA	0	0.009	0.016	13.255	0.014	0.014	0.000	0.000	0.000	0.000
42	A	53	ARG	1	0.960	0.988	7.319	0.873	0.873	0.000	0.000	0.000	0.000
43	A	54	LYS	1	0.863	0.911	8.063	1.689	1.689	0.000	0.000	0.000	0.000
44	A	55	GLN	0	0.031	0.027	2.315	-4.377	-4.529	3.330	-1.363	-1.815	-0.019
45	A	56	ILE	0	-0.006	0.012	5.903	0.934	0.934	0.000	0.000	0.000	0.000
46	A	57	VAL	0	0.017	-0.004	6.103	-0.362	-0.362	0.000	0.000	0.000	0.000
47	A	58	ALA	0	0.034	0.029	8.429	0.090	0.090	0.000	0.000	0.000	0.000
48	A	59	GLY	0	0.022	0.019	11.858	0.119	0.119	0.000	0.000	0.000	0.000
49	A	60	VAL	0	-0.051	-0.037	10.074	-0.214	-0.214	0.000	0.000	0.000	0.000
50	A	61	ASN	0	0.009	0.023	8.030	0.454	0.454	0.000	0.000	0.000	0.000
51	A	62	TYR	0	0.025	-0.001	9.183	-0.427	-0.427	0.000	0.000	0.000	0.000
52	A	63	PHE	0	-0.016	-0.015	6.341	0.198	0.198	0.000	0.000	0.000	0.000
53	A	64	LEU	0	-0.013	-0.003	10.907	-0.066	-0.066	0.000	0.000	0.000	0.000
54	A	65	ASP	-1	-0.789	-0.846	13.574	-0.330	-0.330	0.000	0.000	0.000	0.000
55	A	66	VAL	0	0.025	0.007	16.329	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	67	GLU	-1	-0.792	-0.877	19.891	-0.121	-0.121	0.000	0.000	0.000	0.000
57	A	68	LEU	0	-0.002	-0.006	22.996	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	69	CYS	0	-0.050	-0.024	25.776	0.022	0.022	0.000	0.000	0.000	0.000
59	A	70	ARG	1	0.812	0.874	29.523	0.081	0.081	0.000	0.000	0.000	0.000
60	A	71	THR	0	-0.010	-0.023	32.296	0.003	0.003	0.000	0.000	0.000	0.000
61	A	72	THR	0	-0.013	-0.014	34.822	0.004	0.004	0.000	0.000	0.000	0.000
62	A	73	CYS	0	-0.029	0.016	35.103	0.013	0.013	0.000	0.000	0.000	0.000
63	A	74	THR	0	0.022	0.011	36.827	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	75	LYS	1	0.853	0.920	32.150	0.106	0.106	0.000	0.000	0.000	0.000
65	A	76	THR	0	-0.031	-0.001	36.273	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	77	GLN	0	0.022	-0.020	39.163	0.002	0.002	0.000	0.000	0.000	0.000
67	A	78	PRO	0	-0.062	0.023	36.590	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	79	ASN	0	0.040	-0.019	38.286	0.001	0.001	0.000	0.000	0.000	0.000
69	A	80	LEU	0	-0.045	-0.030	34.909	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	81	ASP	-1	-0.798	-0.910	29.791	-0.176	-0.176	0.000	0.000	0.000	0.000
71	A	82	ASN	0	-0.034	-0.023	32.565	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	84	PRO	0	0.041	0.023	34.719	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	85	PHE	0	-0.007	-0.020	28.862	0.004	0.004	0.000	0.000	0.000	0.000
74	A	86	HIS	0	0.038	0.016	34.486	0.002	0.002	0.000	0.000	0.000	0.000
75	A	87	ASP	-1	-0.830	-0.905	35.804	-0.077	-0.077	0.000	0.000	0.000	0.000
76	A	88	GLN	0	0.025	0.004	38.158	0.003	0.003	0.000	0.000	0.000	0.000
77	A	89	PRO	0	0.016	0.016	35.489	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	90	HIS	0	0.022	0.000	35.257	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	91	LEU	0	-0.007	0.002	37.299	0.001	0.001	0.000	0.000	0.000	0.000
80	A	92	LYS	1	0.828	0.914	31.854	0.088	0.088	0.000	0.000	0.000	0.000
81	A	93	ARG	1	0.839	0.900	31.423	0.057	0.057	0.000	0.000	0.000	0.000
82	A	94	LYS	1	0.870	0.926	26.426	0.125	0.125	0.000	0.000	0.000	0.000
83	A	95	ALA	0	0.015	0.020	25.448	0.012	0.012	0.000	0.000	0.000	0.000
84	A	96	PHE	0	-0.005	-0.002	17.093	-0.020	-0.020	0.000	0.000	0.000	0.000
85	A	97	CYS	0	-0.004	-0.005	19.560	0.001	0.001	0.000	0.000	0.000	0.000
86	A	98	SER	0	0.008	-0.008	14.453	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	99	PHE	0	-0.025	-0.018	15.565	0.042	0.042	0.000	0.000	0.000	0.000
88	A	100	GLN	0	-0.024	-0.027	10.365	0.023	0.023	0.000	0.000	0.000	0.000
89	A	101	ILE	0	-0.038	-0.017	13.008	0.093	0.093	0.000	0.000	0.000	0.000
90	A	102	TYR	0	-0.032	-0.017	12.268	-0.135	-0.135	0.000	0.000	0.000	0.000
91	A	103	ALA	0	0.033	0.001	13.780	0.108	0.108	0.000	0.000	0.000	0.000
92	A	104	VAL	0	0.033	0.021	14.330	-0.114	-0.114	0.000	0.000	0.000	0.000
93	A	105	PRO	0	0.005	-0.003	15.777	0.067	0.067	0.000	0.000	0.000	0.000
94	A	106	TRP	0	0.052	0.026	13.289	0.026	0.026	0.000	0.000	0.000	0.000
95	A	107	GLN	0	-0.066	-0.039	20.006	0.058	0.058	0.000	0.000	0.000	0.000
96	A	108	GLY	0	0.006	0.023	21.503	0.028	0.028	0.000	0.000	0.000	0.000
97	A	109	THR	0	-0.024	-0.008	19.542	0.006	0.006	0.000	0.000	0.000	0.000
98	A	110	MET	0	-0.008	-0.020	18.107	-0.079	-0.079	0.000	0.000	0.000	0.000
99	A	111	THR	0	-0.018	0.006	17.405	0.054	0.054	0.000	0.000	0.000	0.000
100	A	112	LEU	0	0.024	0.007	16.991	-0.059	-0.059	0.000	0.000	0.000	0.000
101	A	113	SER	0	-0.023	-0.001	13.833	0.014	0.014	0.000	0.000	0.000	0.000
102	A	114	LYS	1	0.975	0.980	13.224	0.096	0.096	0.000	0.000	0.000	0.000
103	A	115	SER	0	0.011	0.004	16.445	-0.054	-0.054	0.000	0.000	0.000	0.000
104	A	116	THR	0	-0.022	0.001	17.444	0.034	0.034	0.000	0.000	0.000	0.000
105	A	118	GLN	0	0.016	0.016	22.384	0.024	0.024	0.000	0.000	0.000	0.000
106	A	119	ASP	-1	-0.810	-0.892	24.887	-0.076	-0.076	0.000	0.000	0.000	0.000
107	A	120	ALA	0	-0.059	-0.024	25.466	0.014	0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:GLY)