FMO DATABASE

FMODB ID: JQV19

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

Total energy (hartree)

FMO2-HF: Electronic energy	-832340.034677
FMO2-HF: Nuclear repulsion	787452.004307
FMO2-HF: Total energy	-44888.03037
FMO2-MP2: Total energy	-45013.0243

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.
-2.064	-4.531	7.706	-2.791	-2.448	-0.018

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 : 0.040 / q_NPA : 0.017

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	0.015	0.032	3.877	0.646	1.882	-0.005	-0.594	-0.637	0.003
4	A	15	ASP	-1	-0.878	-0.963	6.359	-0.838	-0.838	0.000	0.000	0.000	0.000
5	A	16	ALA	0	-0.063	-0.033	9.854	-0.092	-0.092	0.000	0.000	0.000	0.000
6	A	17	SER	0	0.013	-0.021	12.703	0.111	0.111	0.000	0.000	0.000	0.000
7	A	18	VAL	0	0.028	0.010	16.523	-0.025	-0.025	0.000	0.000	0.000	0.000
8	A	19	GLU	-1	-0.827	-0.883	19.354	-0.391	-0.391	0.000	0.000	0.000	0.000
9	A	20	GLU	-1	-0.823	-0.893	14.384	-0.993	-0.993	0.000	0.000	0.000	0.000
10	A	21	GLU	-1	-0.851	-0.902	18.792	-0.389	-0.389	0.000	0.000	0.000	0.000
11	A	22	GLY	0	0.045	0.015	17.356	0.023	0.023	0.000	0.000	0.000	0.000
12	A	23	VAL	0	-0.003	0.003	14.424	-0.017	-0.017	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.859	0.927	17.067	0.430	0.430	0.000	0.000	0.000	0.000
14	A	25	ARG	1	0.883	0.921	20.142	0.370	0.370	0.000	0.000	0.000	0.000
15	A	26	ALA	0	0.013	-0.002	16.330	0.033	0.033	0.000	0.000	0.000	0.000
16	A	27	LEU	0	0.005	0.003	18.361	0.027	0.027	0.000	0.000	0.000	0.000
17	A	28	ASP	-1	-0.889	-0.952	20.195	-0.299	-0.299	0.000	0.000	0.000	0.000
18	A	29	PHE	0	-0.028	-0.016	19.116	0.033	0.033	0.000	0.000	0.000	0.000
19	A	30	ALA	0	0.010	0.007	19.248	0.030	0.030	0.000	0.000	0.000	0.000
20	A	31	VAL	0	-0.001	-0.004	21.395	0.033	0.033	0.000	0.000	0.000	0.000
21	A	32	GLY	0	0.023	0.018	24.514	0.028	0.028	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.819	-0.906	22.768	-0.182	-0.182	0.000	0.000	0.000	0.000
23	A	34	TYR	0	0.012	0.008	24.377	0.022	0.022	0.000	0.000	0.000	0.000
24	A	35	ASN	0	-0.030	-0.017	26.090	0.033	0.033	0.000	0.000	0.000	0.000
25	A	36	LYS	1	0.781	0.884	26.417	0.195	0.195	0.000	0.000	0.000	0.000
26	A	37	ALA	0	-0.011	0.004	27.197	0.012	0.012	0.000	0.000	0.000	0.000
27	A	38	SER	0	-0.010	-0.015	29.210	0.012	0.012	0.000	0.000	0.000	0.000
28	A	39	ASN	0	-0.012	-0.027	31.156	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	40	ASP	-1	-0.794	-0.853	33.517	-0.091	-0.091	0.000	0.000	0.000	0.000
30	A	41	MET	0	0.034	0.017	35.341	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	42	TYR	0	-0.039	-0.022	36.157	0.001	0.001	0.000	0.000	0.000	0.000
32	A	43	HIS	0	0.044	0.038	32.884	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	44	SER	0	-0.040	-0.016	29.402	0.009	0.009	0.000	0.000	0.000	0.000
34	A	45	ARG	1	0.835	0.912	27.672	0.161	0.161	0.000	0.000	0.000	0.000
35	A	46	ALA	0	0.037	0.010	23.408	0.009	0.009	0.000	0.000	0.000	0.000
36	A	47	CYS	0	-0.044	-0.013	25.339	0.003	0.003	0.000	0.000	0.000	0.000
37	A	48	GLN	0	-0.050	-0.035	21.916	0.002	0.002	0.000	0.000	0.000	0.000
38	A	49	VAL	0	-0.007	-0.004	17.861	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	50	VAL	0	-0.011	0.001	17.540	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	51	ARG	1	0.882	0.920	11.154	0.471	0.471	0.000	0.000	0.000	0.000
41	A	52	ALA	0	0.005	0.010	13.388	0.022	0.022	0.000	0.000	0.000	0.000
42	A	53	ARG	1	0.920	0.955	7.387	1.029	1.029	0.000	0.000	0.000	0.000
43	A	54	LYS	1	0.821	0.894	8.172	1.643	1.643	0.000	0.000	0.000	0.000
44	A	55	GLN	0	0.034	0.014	1.935	-4.687	-8.390	7.711	-2.197	-1.811	-0.021
45	A	56	ILE	0	0.012	0.017	6.005	0.820	0.820	0.000	0.000	0.000	0.000
46	A	57	VAL	0	0.002	-0.006	6.510	-0.264	-0.264	0.000	0.000	0.000	0.000
47	A	58	ALA	0	0.045	0.036	8.882	0.097	0.097	0.000	0.000	0.000	0.000
48	A	59	GLY	0	0.007	0.003	12.207	0.096	0.096	0.000	0.000	0.000	0.000
49	A	60	VAL	0	-0.036	-0.021	10.040	-0.179	-0.179	0.000	0.000	0.000	0.000
50	A	61	ASN	0	-0.005	0.009	7.776	0.388	0.388	0.000	0.000	0.000	0.000
51	A	62	TYR	0	0.048	0.015	8.873	-0.462	-0.462	0.000	0.000	0.000	0.000
52	A	63	PHE	0	-0.033	-0.032	6.529	0.174	0.174	0.000	0.000	0.000	0.000
53	A	64	LEU	0	-0.008	0.004	11.149	-0.061	-0.061	0.000	0.000	0.000	0.000
54	A	65	ASP	-1	-0.763	-0.833	12.994	-0.467	-0.467	0.000	0.000	0.000	0.000
55	A	66	VAL	0	0.001	-0.006	16.045	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	67	GLU	-1	-0.794	-0.876	19.793	-0.142	-0.142	0.000	0.000	0.000	0.000
57	A	68	LEU	0	0.023	0.013	23.345	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	69	CYS	0	-0.039	-0.014	25.980	0.020	0.020	0.000	0.000	0.000	0.000
59	A	70	ARG	1	0.793	0.867	29.750	0.088	0.088	0.000	0.000	0.000	0.000
60	A	71	THR	0	-0.011	-0.030	32.792	0.001	0.001	0.000	0.000	0.000	0.000
61	A	72	THR	0	-0.004	-0.011	35.374	0.004	0.004	0.000	0.000	0.000	0.000
62	A	73	CYS	0	-0.039	0.005	34.852	0.012	0.012	0.000	0.000	0.000	0.000
63	A	74	THR	0	0.038	0.017	37.451	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	75	LYS	1	0.821	0.898	32.335	0.116	0.116	0.000	0.000	0.000	0.000
65	A	76	THR	0	-0.038	-0.006	36.850	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	77	GLN	0	0.017	-0.007	39.336	0.004	0.004	0.000	0.000	0.000	0.000
67	A	78	PRO	0	-0.042	0.001	36.861	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	79	ASN	0	-0.004	-0.016	38.683	0.003	0.003	0.000	0.000	0.000	0.000
69	A	80	LEU	0	-0.005	-0.007	35.181	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	81	ASP	-1	-0.780	-0.888	30.195	-0.185	-0.185	0.000	0.000	0.000	0.000
71	A	82	ASN	0	-0.025	-0.015	33.137	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	84	PRO	0	0.045	0.035	34.652	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	85	PHE	0	0.014	-0.009	29.087	0.005	0.005	0.000	0.000	0.000	0.000
74	A	86	HIS	0	0.028	0.017	34.658	0.003	0.003	0.000	0.000	0.000	0.000
75	A	87	ASP	-1	-0.788	-0.878	36.203	-0.080	-0.080	0.000	0.000	0.000	0.000
76	A	88	GLN	0	-0.025	-0.025	37.722	0.002	0.002	0.000	0.000	0.000	0.000
77	A	89	PRO	0	0.008	0.002	35.235	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	90	HIS	0	0.046	0.005	35.072	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	91	LEU	0	-0.011	0.012	37.353	0.001	0.001	0.000	0.000	0.000	0.000
80	A	92	LYS	1	0.833	0.915	32.253	0.097	0.097	0.000	0.000	0.000	0.000
81	A	93	ARG	1	0.812	0.870	31.300	0.071	0.071	0.000	0.000	0.000	0.000
82	A	94	LYS	1	0.883	0.936	26.209	0.142	0.142	0.000	0.000	0.000	0.000
83	A	95	ALA	0	0.016	0.019	25.955	0.012	0.012	0.000	0.000	0.000	0.000
84	A	96	PHE	0	-0.003	0.015	16.828	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	97	CYS	0	-0.021	-0.018	19.634	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	98	SER	0	0.007	-0.002	14.576	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	99	PHE	0	-0.021	-0.025	15.519	0.048	0.048	0.000	0.000	0.000	0.000
88	A	100	GLN	0	-0.019	-0.021	10.403	0.028	0.028	0.000	0.000	0.000	0.000
89	A	101	ILE	0	-0.020	-0.012	13.072	0.097	0.097	0.000	0.000	0.000	0.000
90	A	102	TYR	0	-0.044	-0.010	11.946	-0.132	-0.132	0.000	0.000	0.000	0.000
91	A	103	ALA	0	0.032	0.008	13.516	0.111	0.111	0.000	0.000	0.000	0.000
92	A	104	VAL	0	0.030	0.012	14.372	-0.096	-0.096	0.000	0.000	0.000	0.000
93	A	105	PRO	0	0.028	0.015	15.972	0.061	0.061	0.000	0.000	0.000	0.000
94	A	106	TRP	0	0.038	0.023	13.648	0.029	0.029	0.000	0.000	0.000	0.000
95	A	107	GLN	0	-0.072	-0.047	20.296	0.055	0.055	0.000	0.000	0.000	0.000
96	A	108	GLY	0	0.009	0.021	21.760	0.022	0.022	0.000	0.000	0.000	0.000
97	A	109	THR	0	-0.020	-0.004	19.137	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	110	MET	0	-0.021	-0.020	18.020	-0.076	-0.076	0.000	0.000	0.000	0.000
99	A	111	THR	0	-0.010	-0.006	16.676	0.059	0.059	0.000	0.000	0.000	0.000
100	A	112	LEU	0	0.025	0.016	16.751	-0.061	-0.061	0.000	0.000	0.000	0.000
101	A	113	SER	0	-0.015	-0.013	13.878	0.012	0.012	0.000	0.000	0.000	0.000
102	A	114	LYS	1	0.919	0.959	12.926	0.266	0.266	0.000	0.000	0.000	0.000
103	A	115	SER	0	0.019	0.014	16.705	-0.056	-0.056	0.000	0.000	0.000	0.000
104	A	116	THR	0	-0.020	-0.002	17.436	0.038	0.038	0.000	0.000	0.000	0.000
105	A	118	GLN	0	0.008	0.009	22.438	0.025	0.025	0.000	0.000	0.000	0.000
106	A	119	ASP	-1	-0.776	-0.847	25.134	-0.091	-0.091	0.000	0.000	0.000	0.000
107	A	120	ALA	0	-0.087	-0.051	25.404	0.012	0.012	0.000	0.000	0.000	0.000

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