FMO DATABASE

FMODB ID: MVRYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1353731.47882
FMO2-HF: Nuclear repulsion	1294778.242225
FMO2-HF: Total energy	-58953.236595
FMO2-MP2: Total energy	-59119.883212

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.
-3.201	2.851	0.832	-2.736	-4.147	-0.008

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 : 0.029 / 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	-0.805	-0.871	3.148	-3.146	0.035	0.011	-1.621	-1.571	-0.002
4	A	4	VAL	0	-0.013	-0.004	4.994	-0.394	-0.270	-0.001	-0.006	-0.117	0.000
5	A	5	VAL	0	0.053	0.038	7.428	-0.219	-0.219	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.033	-0.018	10.874	0.037	0.037	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.033	-0.007	13.096	0.000	0.000	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.892	0.927	16.801	0.138	0.138	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.063	0.030	19.035	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.796	-0.867	15.705	-0.124	-0.124	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.045	0.001	13.619	0.028	0.028	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.033	-0.023	16.581	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.027	-0.014	18.778	0.013	0.013	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.034	0.030	14.140	0.012	0.012	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.044	0.004	17.414	0.013	0.013	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.822	0.884	19.453	0.110	0.110	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.005	-0.002	20.575	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	MET	0	-0.050	-0.001	16.479	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.012	-0.010	19.879	0.009	0.009	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.021	0.000	22.787	0.007	0.007	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.031	0.026	21.932	0.006	0.006	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.006	0.003	19.972	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.720	-0.849	24.304	-0.096	-0.096	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.820	-0.862	27.424	-0.079	-0.079	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.817	-0.902	25.606	-0.077	-0.077	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.033	0.009	28.055	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	HIS	0	-0.036	-0.039	29.592	0.009	0.009	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.818	0.900	29.354	0.080	0.080	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.037	-0.019	28.652	0.004	0.004	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.022	0.000	33.077	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.767	0.867	35.392	0.048	0.048	0.000	0.000	0.000	0.000
32	A	32	ARG	1	1.000	1.007	33.291	0.064	0.064	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.045	0.022	35.676	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.948	0.979	37.578	0.053	0.053	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.821	-0.884	40.778	-0.042	-0.042	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.032	-0.016	40.282	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.894	0.944	44.494	0.036	0.036	0.000	0.000	0.000	0.000
38	A	38	TRP	0	0.036	0.035	43.481	0.000	0.000	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.029	-0.034	42.072	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.014	0.027	35.378	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.032	0.024	39.485	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.006	-0.020	37.969	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.031	0.002	36.437	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.044	0.026	33.367	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.023	0.005	33.110	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.006	-0.015	31.143	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.045	0.011	30.451	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.001	0.018	28.551	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.875	0.926	27.100	0.072	0.072	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.852	0.948	26.496	0.091	0.091	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.039	0.032	23.469	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.001	-0.001	22.513	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.793	0.878	21.528	0.094	0.094	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.779	-0.890	20.938	-0.138	-0.138	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.912	0.958	13.684	0.266	0.266	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.033	-0.006	16.780	-0.039	-0.039	0.000	0.000	0.000	0.000
57	A	57	MET	0	0.028	-0.012	16.176	-0.032	-0.032	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.934	0.987	14.833	0.223	0.223	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.020	0.014	10.264	0.034	0.034	0.000	0.000	0.000	0.000
60	A	60	CYS	0	-0.057	-0.004	11.595	-0.082	-0.082	0.000	0.000	0.000	0.000
61	A	61	MET	0	-0.010	-0.003	8.918	0.058	0.058	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.786	-0.878	7.059	-1.345	-1.345	0.000	0.000	0.000	0.000
63	A	63	TYR	0	-0.048	-0.032	8.607	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.011	0.000	11.102	0.062	0.062	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.852	0.925	4.813	1.509	1.652	-0.001	-0.034	-0.108	0.000
66	A	66	TYR	0	0.006	-0.022	2.592	-1.521	0.897	0.823	-1.054	-2.186	-0.006
67	A	67	SER	0	-0.064	-0.039	7.633	0.197	0.197	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.799	0.875	10.386	0.200	0.200	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.853	0.914	3.780	0.060	0.246	0.000	-0.021	-0.165	0.000
70	A	70	ILE	0	-0.008	-0.012	8.243	0.130	0.130	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.034	-0.022	10.337	0.038	0.038	0.000	0.000	0.000	0.000
72	A	72	GLN	0	0.028	0.005	9.934	-0.020	-0.020	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.019	0.007	7.224	0.031	0.031	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.877	0.951	11.126	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	HIS	0	0.040	0.028	14.260	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.016	0.003	15.791	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	77	PRO	0	0.027	0.018	16.593	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.045	0.035	13.944	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	79	ASN	0	0.016	-0.003	17.197	0.006	0.006	0.000	0.000	0.000	0.000
80	A	80	LYS	1	1.024	1.018	19.740	0.051	0.051	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.965	0.993	21.667	0.026	0.026	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.014	-0.022	18.032	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.061	0.029	14.311	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.034	-0.025	17.553	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.950	0.972	20.314	0.058	0.058	0.000	0.000	0.000	0.000
86	A	86	MET	0	0.008	0.017	13.034	0.009	0.009	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.041	0.022	16.253	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.778	0.851	17.740	0.089	0.089	0.000	0.000	0.000	0.000
89	A	89	PHE	0	0.001	0.006	13.561	0.002	0.002	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.032	0.010	12.816	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.022	0.013	15.474	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	92	TYR	0	0.001	-0.013	18.298	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.905	0.952	13.790	0.187	0.187	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.006	0.004	14.017	-0.016	-0.016	0.000	0.000	0.000	0.000
95	A	95	TYR	0	0.040	0.031	17.382	0.011	0.011	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.018	0.006	19.872	0.009	0.009	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.039	0.014	16.392	0.005	0.005	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.022	-0.011	19.819	0.006	0.006	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.900	0.949	22.412	0.102	0.102	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.879	-0.931	22.791	-0.095	-0.095	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.004	0.002	20.632	0.004	0.004	0.000	0.000	0.000	0.000
102	A	102	TYR	0	-0.087	-0.088	24.991	0.010	0.010	0.000	0.000	0.000	0.000
103	A	103	ALA	0	-0.001	0.001	27.720	0.007	0.007	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.791	-0.874	25.894	-0.098	-0.098	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.034	-0.014	28.732	0.006	0.006	0.000	0.000	0.000	0.000
106	A	106	PHE	0	-0.055	-0.037	31.208	0.006	0.006	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.855	0.924	28.619	0.086	0.086	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.846	-0.915	30.586	-0.075	-0.075	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.077	-0.030	34.010	0.002	0.002	0.000	0.000	0.000	0.000
110	A	110	GLN	0	-0.054	-0.035	36.794	0.006	0.006	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.055	0.032	38.063	0.003	0.003	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.007	-0.014	38.008	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.929	0.978	39.254	0.046	0.046	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.017	0.004	37.035	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	115	PRO	0	-0.017	-0.002	35.585	0.003	0.003	0.000	0.000	0.000	0.000
116	A	116	LYN	0	0.093	0.042	38.769	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.011	-0.006	35.630	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	118	THR	0	0.091	0.024	37.750	0.002	0.002	0.000	0.000	0.000	0.000
119	A	119	ALA	0	0.019	0.000	38.832	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.033	0.019	35.190	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	121	MET	0	-0.007	0.035	33.999	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	122	ARG	1	0.963	0.970	34.111	0.043	0.043	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.974	1.001	33.466	0.055	0.055	0.000	0.000	0.000	0.000
124	A	124	TYR	0	-0.041	-0.045	25.853	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	125	SER	0	0.000	-0.001	29.938	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.030	-0.030	31.338	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.801	0.927	25.878	0.107	0.107	0.000	0.000	0.000	0.000
128	A	128	ASP	-1	-0.700	-0.829	26.330	-0.107	-0.107	0.000	0.000	0.000	0.000
129	A	129	PRO	0	0.047	0.016	23.185	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.010	-0.004	22.168	-0.014	-0.014	0.000	0.000	0.000	0.000
131	A	131	THR	0	0.017	0.025	23.016	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.056	-0.026	22.106	0.007	0.007	0.000	0.000	0.000	0.000
133	A	133	PRO	0	0.014	0.011	19.782	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.919	0.937	13.797	0.196	0.196	0.000	0.000	0.000	0.000
135	A	136	ASN	0	0.021	-0.002	8.397	0.065	0.065	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.849	-0.906	12.756	-0.161	-0.161	0.000	0.000	0.000	0.000

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