FMO DATABASE

FMODB ID: LZQ49

Calculation Name: 1GAK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GAK

Chain ID: A

ChEMBL ID:

UniProt ID: Q25063

Base Structure: X-ray

Registration Date: 2023-06-22

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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1355277.12155
FMO2-HF: Nuclear repulsion	1296324.941288
FMO2-HF: Total energy	-58952.180262
FMO2-MP2: Total energy	-59119.044502

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:1:PHE)

Summations of interaction energy for fragment #1(A:1:PHE)

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.
-3.129	2.872	2.573	-3.408	-5.165	-0.015

Interaction energy analysis for fragmet #1(A:1:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.008

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	3	ASP	-1	-0.839	-0.915	3.226	-2.182	1.318	-0.020	-1.781	-1.699	-0.004
4	A	4	VAL	0	-0.022	-0.001	5.096	-0.281	-0.155	-0.001	-0.005	-0.119	0.000
5	A	5	VAL	0	0.043	0.021	7.148	-0.217	-0.217	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.045	-0.015	10.639	0.045	0.045	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.048	0.032	13.051	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.965	0.976	16.465	0.148	0.148	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.040	0.016	18.636	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.836	-0.929	15.325	-0.100	-0.100	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.054	0.006	13.147	0.035	0.035	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.057	-0.031	16.388	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.028	-0.012	18.634	0.010	0.010	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.032	0.030	13.876	0.012	0.012	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.038	-0.018	17.158	0.018	0.018	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.827	0.890	18.958	0.106	0.106	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.003	0.011	20.425	0.010	0.010	0.000	0.000	0.000	0.000
18	A	18	MET	0	-0.026	0.008	15.920	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.010	-0.007	19.611	0.007	0.007	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.019	-0.009	22.500	0.009	0.009	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.002	0.016	21.547	0.007	0.007	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.007	0.003	19.664	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.717	-0.842	23.931	-0.096	-0.096	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.844	-0.891	27.040	-0.067	-0.067	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.832	-0.903	24.761	-0.068	-0.068	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.029	0.002	27.578	0.003	0.003	0.000	0.000	0.000	0.000
27	A	27	HIS	0	-0.045	-0.046	29.039	0.007	0.007	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.835	0.910	28.667	0.069	0.069	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.037	-0.014	28.081	0.004	0.004	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.001	-0.004	32.542	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.955	0.962	34.921	0.045	0.045	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.990	1.026	31.729	0.060	0.060	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.053	0.023	35.655	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.919	0.960	38.358	0.048	0.048	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.918	-0.964	40.284	-0.038	-0.038	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.057	-0.020	39.985	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.862	0.938	43.903	0.034	0.034	0.000	0.000	0.000	0.000
38	A	38	TRP	0	0.038	0.029	42.573	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.008	-0.030	41.787	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.024	0.040	35.174	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.041	0.023	39.274	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.016	-0.014	37.554	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.056	0.013	36.090	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.038	0.017	33.317	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.028	0.001	32.961	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.041	-0.025	31.304	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.024	0.003	30.242	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.018	0.027	28.372	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.900	0.940	26.825	0.072	0.072	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.900	0.963	25.895	0.095	0.095	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.068	0.060	23.193	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.001	0.012	22.204	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.724	0.827	21.033	0.095	0.095	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.871	-0.939	20.543	-0.157	-0.157	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.889	0.958	13.610	0.254	0.254	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.052	-0.031	16.361	-0.044	-0.044	0.000	0.000	0.000	0.000
57	A	57	MET	0	0.007	-0.034	15.880	-0.033	-0.033	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.979	1.027	14.418	0.239	0.239	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.020	0.002	10.148	0.008	0.008	0.000	0.000	0.000	0.000
60	A	60	CYS	0	-0.035	-0.011	11.204	-0.074	-0.074	0.000	0.000	0.000	0.000
61	A	61	MET	0	-0.006	-0.012	9.687	0.059	0.059	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.802	-0.893	6.629	-1.725	-1.725	0.000	0.000	0.000	0.000
63	A	63	TYR	0	-0.051	-0.033	8.245	0.076	0.076	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.023	-0.015	10.792	0.087	0.087	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.927	0.982	5.126	1.610	1.610	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.009	-0.043	2.344	-1.461	0.663	2.592	-1.578	-3.138	-0.011
67	A	67	SER	0	-0.054	-0.025	7.379	0.202	0.202	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.814	0.870	10.610	0.162	0.162	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.929	0.984	3.563	-0.568	-0.317	0.002	-0.044	-0.209	0.000
70	A	70	ILE	0	-0.003	-0.006	8.383	0.109	0.109	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.047	-0.019	10.539	0.022	0.022	0.000	0.000	0.000	0.000
72	A	72	GLN	0	0.032	0.019	9.237	0.011	0.011	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.003	-0.001	7.052	0.029	0.029	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.878	0.943	11.006	-0.101	-0.101	0.000	0.000	0.000	0.000
75	A	75	HIS	0	0.033	0.028	14.087	-0.036	-0.036	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.038	-0.018	15.624	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	77	PRO	0	0.008	0.010	16.487	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.061	0.040	13.995	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	79	ASN	0	0.059	0.024	17.229	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	80	LYS	1	1.045	1.020	19.655	0.047	0.047	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.970	0.998	21.548	0.007	0.007	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.025	-0.044	18.298	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.066	0.037	14.621	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.037	-0.029	17.506	-0.020	-0.020	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.945	0.965	19.976	0.029	0.029	0.000	0.000	0.000	0.000
86	A	86	MET	0	0.013	0.029	12.874	0.007	0.007	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.043	0.021	16.021	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.775	0.864	17.324	0.074	0.074	0.000	0.000	0.000	0.000
89	A	89	PHE	0	-0.002	0.007	12.751	0.000	0.000	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.023	0.011	12.663	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.025	0.002	15.240	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	92	TYR	0	-0.015	-0.015	17.605	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.909	0.955	12.437	0.165	0.165	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.017	0.001	13.373	-0.016	-0.016	0.000	0.000	0.000	0.000
95	A	95	TYR	0	0.077	0.051	16.873	0.007	0.007	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.022	0.008	19.362	0.007	0.007	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.032	0.013	16.000	0.004	0.004	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.007	-0.004	19.359	0.005	0.005	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.880	0.932	21.853	0.093	0.093	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.882	-0.937	22.156	-0.094	-0.094	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.014	0.006	20.355	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	TYR	0	-0.087	-0.099	24.564	0.010	0.010	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.003	0.009	27.187	0.007	0.007	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.802	-0.918	25.877	-0.096	-0.096	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.028	0.006	28.490	0.004	0.004	0.000	0.000	0.000	0.000
106	A	106	PHE	0	-0.054	-0.040	30.817	0.005	0.005	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.917	0.961	28.920	0.083	0.083	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.896	-0.927	30.378	-0.081	-0.081	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.134	-0.064	33.763	0.003	0.003	0.000	0.000	0.000	0.000
110	A	110	GLN	0	-0.043	-0.025	36.639	0.006	0.006	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.029	0.015	37.619	0.004	0.004	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.010	0.001	37.354	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.951	0.992	38.930	0.048	0.048	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.026	0.005	37.049	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	115	PRO	0	-0.023	-0.011	35.462	0.003	0.003	0.000	0.000	0.000	0.000
116	A	116	LYN	0	0.101	0.057	38.644	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.009	-0.014	35.637	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	118	THR	0	0.071	0.019	37.630	0.002	0.002	0.000	0.000	0.000	0.000
119	A	119	ALA	0	0.031	-0.002	38.319	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.029	0.014	35.201	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	121	MET	0	-0.002	0.022	33.760	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	122	ARG	1	0.987	0.992	33.760	0.046	0.046	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.977	0.995	33.469	0.066	0.066	0.000	0.000	0.000	0.000
124	A	124	TYR	0	0.024	-0.001	25.308	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.021	-0.010	29.797	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.010	-0.007	30.981	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.848	0.932	26.111	0.111	0.111	0.000	0.000	0.000	0.000
128	A	128	ASP	-1	-0.704	-0.827	26.020	-0.104	-0.104	0.000	0.000	0.000	0.000
129	A	129	PRO	0	0.062	0.028	23.389	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	130	GLY	0	0.015	0.003	21.801	-0.016	-0.016	0.000	0.000	0.000	0.000
131	A	131	THR	0	-0.032	0.000	22.581	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.055	-0.016	21.713	0.005	0.005	0.000	0.000	0.000	0.000
133	A	133	PRO	0	-0.006	0.002	19.738	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.975	0.970	13.643	0.208	0.208	0.000	0.000	0.000	0.000
135	A	136	ASN	0	0.003	0.010	8.485	0.125	0.125	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.912	-0.936	12.558	-0.217	-0.217	0.000	0.000	0.000	0.000

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