FMO DATABASE

FMODB ID: NN2KQ

Calculation Name: 5GKK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GKK

Chain ID: A

ChEMBL ID:

UniProt ID: Q70PR2

Base Structure: X-ray

Registration Date: 2023-09-22

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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1528212.520503
FMO2-HF: Nuclear repulsion	1465782.674608
FMO2-HF: Total energy	-62429.845895
FMO2-MP2: Total energy	-62609.286786

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:MET)

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

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.
-13.088	-11.178	14.936	-4.148	-12.699	-0.011

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : 0.005

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	LEU	0	-0.030	-0.021	3.291	-1.547	0.861	0.391	-0.903	-1.896	0.001
4	A	4	LYS	1	0.987	0.988	5.608	-0.096	-0.096	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.073	0.021	9.285	0.006	0.006	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.840	-0.927	11.845	-0.029	-0.029	0.000	0.000	0.000	0.000
7	A	7	TRP	0	-0.037	-0.011	4.503	-0.101	0.110	-0.001	-0.017	-0.193	0.000
8	A	8	VAL	0	-0.003	-0.005	8.153	-0.058	-0.058	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.018	-0.001	9.807	-0.038	-0.038	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.019	0.022	12.244	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.020	0.007	7.063	-0.063	-0.063	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.023	-0.005	9.937	-0.035	-0.035	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.708	-0.831	12.339	-0.104	-0.104	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.023	0.002	13.284	0.014	0.014	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.918	-0.979	10.308	-0.353	-0.353	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.084	-0.033	12.893	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	17	CYS	0	-0.027	-0.027	14.285	0.041	0.041	0.000	0.000	0.000	0.000
18	A	18	PHE	0	-0.008	0.003	17.403	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	19	TYR	0	0.069	0.016	20.199	0.010	0.010	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.073	0.025	22.586	0.002	0.002	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.017	0.009	25.979	0.002	0.002	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.058	0.023	27.601	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.081	-0.045	30.119	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.947	0.976	32.510	0.051	0.051	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.045	-0.028	33.053	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	ARG	1	1.016	0.998	36.290	0.035	0.035	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.053	-0.017	36.605	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.001	0.017	35.363	0.002	0.002	0.000	0.000	0.000	0.000
29	A	29	LYS	1	1.021	1.003	38.847	0.023	0.023	0.000	0.000	0.000	0.000
30	A	30	THR	0	0.002	0.001	37.621	0.001	0.001	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.046	0.038	39.872	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.072	-0.092	35.085	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.007	-0.005	29.455	0.003	0.003	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.064	0.030	28.667	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.083	-0.054	25.116	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.022	0.023	23.831	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.845	-0.919	19.600	-0.164	-0.164	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.030	0.042	13.069	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.816	0.890	15.018	0.177	0.177	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.062	0.042	9.151	0.010	0.010	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.003	-0.002	11.897	-0.045	-0.045	0.000	0.000	0.000	0.000
42	A	42	GLN	0	0.034	0.018	7.349	-0.116	-0.116	0.000	0.000	0.000	0.000
43	A	43	HIS	0	0.076	0.034	10.666	0.004	0.004	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.983	0.984	9.869	0.219	0.219	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.933	0.968	9.084	0.343	0.343	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.885	-0.934	5.795	-1.187	-1.187	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.025	-0.018	5.900	-0.253	-0.253	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.024	0.002	2.367	-6.313	-3.194	2.032	-1.751	-3.400	-0.013
49	A	49	VAL	0	0.062	0.020	1.995	-1.455	-3.198	8.749	-3.176	-3.831	-0.003
50	A	50	LEU	0	-0.022	-0.001	2.948	3.579	0.259	0.033	3.574	-0.288	-0.002
51	A	51	TYR	0	0.002	-0.016	5.517	0.368	0.368	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.024	0.022	2.316	0.375	-0.027	3.491	-1.082	-2.007	-0.001
53	A	53	LEU	0	0.020	0.011	4.034	0.636	0.923	0.002	-0.064	-0.224	0.000
54	A	54	ARG	1	0.878	0.948	6.986	0.349	0.349	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.868	0.932	2.983	-8.546	-7.196	0.239	-0.729	-0.860	0.007
56	A	56	PHE	0	-0.013	0.011	6.786	0.168	0.168	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.022	0.005	8.398	0.112	0.112	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.035	0.022	10.726	0.063	0.063	0.000	0.000	0.000	0.000
59	A	59	CYS	0	-0.178	-0.090	12.226	0.035	0.035	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.058	0.032	12.919	-0.057	-0.057	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.075	-0.036	14.019	0.031	0.031	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.070	0.044	9.210	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.888	0.951	12.447	0.261	0.261	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.977	0.989	14.545	0.190	0.190	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.118	-0.080	16.124	0.020	0.020	0.000	0.000	0.000	0.000
66	A	66	HIS	0	0.028	0.005	17.791	0.030	0.030	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.894	-0.923	18.775	-0.215	-0.215	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.887	-0.940	16.134	-0.279	-0.279	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.941	0.965	14.247	0.188	0.188	0.000	0.000	0.000	0.000
70	A	70	TYR	0	-0.008	-0.020	11.504	0.053	0.053	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.845	-0.914	12.583	-0.287	-0.287	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.008	0.017	9.236	0.020	0.020	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.957	0.962	11.816	0.220	0.220	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.005	-0.001	13.162	0.027	0.027	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.877	0.908	16.720	0.136	0.136	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.922	0.968	20.034	0.075	0.075	0.000	0.000	0.000	0.000
77	A	77	ARG	1	1.097	1.035	21.320	0.036	0.036	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.012	0.009	21.380	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.034	0.003	18.209	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.938	0.990	20.229	0.033	0.033	0.000	0.000	0.000	0.000
81	A	82	LYS	1	1.006	1.005	15.925	0.002	0.002	0.000	0.000	0.000	0.000
82	A	83	VAL	0	-0.026	-0.009	15.086	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.006	-0.007	17.266	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.904	-0.960	19.664	-0.026	-0.026	0.000	0.000	0.000	0.000
85	A	86	PHE	0	-0.068	-0.021	13.054	0.003	0.003	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.039	-0.015	13.534	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.895	-0.909	18.880	-0.038	-0.038	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.911	0.963	18.952	0.032	0.032	0.000	0.000	0.000	0.000
89	A	90	HIS	0	-0.041	-0.006	16.648	0.016	0.016	0.000	0.000	0.000	0.000
90	A	91	PRO	0	0.012	0.004	18.144	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.042	-0.016	15.859	0.000	0.000	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.937	0.946	18.428	0.056	0.056	0.000	0.000	0.000	0.000
93	A	94	THR	0	-0.019	-0.026	18.313	0.005	0.005	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.951	0.959	20.902	0.068	0.068	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.928	0.978	16.228	0.197	0.197	0.000	0.000	0.000	0.000
96	A	97	ASN	0	0.043	0.018	20.605	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.044	-0.026	22.329	0.006	0.006	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.789	-0.895	22.299	-0.107	-0.107	0.000	0.000	0.000	0.000
99	A	100	PHE	0	-0.020	-0.001	20.482	0.003	0.003	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.940	0.959	22.404	0.064	0.064	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.908	0.970	25.792	0.073	0.073	0.000	0.000	0.000	0.000
102	A	103	PHE	0	0.009	0.005	20.954	0.002	0.002	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.867	0.909	24.412	0.055	0.055	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.949	0.982	25.758	0.053	0.053	0.000	0.000	0.000	0.000
105	A	106	ILE	0	0.064	0.028	27.903	0.004	0.004	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.001	-0.008	22.913	0.003	0.003	0.000	0.000	0.000	0.000
107	A	108	ILE	0	0.016	0.014	27.633	0.005	0.005	0.000	0.000	0.000	0.000
108	A	109	MET	0	-0.033	-0.017	30.026	0.003	0.003	0.000	0.000	0.000	0.000
109	A	110	MET	0	-0.063	-0.032	29.119	0.000	0.000	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.982	-0.997	26.948	-0.039	-0.039	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.911	0.967	31.270	0.030	0.030	0.000	0.000	0.000	0.000
112	A	113	GLY	0	-0.004	0.009	34.205	0.002	0.002	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.821	-0.926	35.670	-0.032	-0.032	0.000	0.000	0.000	0.000
114	A	115	HIS	0	-0.008	0.003	33.236	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.065	-0.037	35.802	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	117	THR	0	-0.047	-0.014	38.624	0.002	0.002	0.000	0.000	0.000	0.000
117	A	118	LYN	0	0.071	0.035	39.944	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.851	-0.947	40.886	-0.033	-0.033	0.000	0.000	0.000	0.000
119	A	120	GLY	0	-0.001	0.013	38.645	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	121	LEU	0	-0.056	-0.041	34.954	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	122	ILE	0	0.040	0.017	36.280	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	123	LYS	1	0.990	1.008	36.065	0.035	0.035	0.000	0.000	0.000	0.000
123	A	124	ILE	0	-0.040	-0.031	31.368	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.032	-0.018	32.484	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	126	GLU	-1	-0.877	-0.945	33.631	-0.045	-0.045	0.000	0.000	0.000	0.000
126	A	127	ILE	0	-0.033	-0.016	30.083	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	128	ALA	0	-0.025	-0.029	29.184	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	129	MET	0	-0.010	-0.001	29.514	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.951	-0.956	31.550	-0.054	-0.054	0.000	0.000	0.000	0.000
130	A	131	MET	0	-0.121	-0.057	24.308	0.000	0.000	0.000	0.000	0.000	0.000
131	A	132	ASN	0	-0.034	-0.002	24.357	0.007	0.007	0.000	0.000	0.000	0.000
132	A	133	THR	0	-0.037	-0.017	23.087	-0.013	-0.013	0.000	0.000	0.000	0.000
133	A	134	GLY	0	0.044	0.018	24.519	0.008	0.008	0.000	0.000	0.000	0.000
134	A	135	ASN	0	-0.075	-0.062	26.467	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	136	HIS	0	0.074	0.023	28.870	0.002	0.002	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.875	-0.926	32.003	-0.057	-0.057	0.000	0.000	0.000	0.000
137	A	138	ARG	1	0.890	0.952	29.328	0.085	0.085	0.000	0.000	0.000	0.000
138	A	139	LEU	0	-0.015	-0.005	30.024	0.004	0.004	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.989	0.992	34.100	0.059	0.059	0.000	0.000	0.000	0.000
140	A	141	ARG	1	0.948	0.975	35.302	0.061	0.061	0.000	0.000	0.000	0.000
141	A	142	THR	0	-0.034	-0.029	35.583	0.002	0.002	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.015	-0.012	37.383	0.003	0.003	0.000	0.000	0.000	0.000
143	A	144	GLU	-1	-0.942	-0.955	39.942	-0.042	-0.042	0.000	0.000	0.000	0.000
144	A	145	GLU	-1	-0.799	-0.850	39.758	-0.047	-0.047	0.000	0.000	0.000	0.000
145	A	146	ILE	0	-0.071	-0.030	38.568	0.002	0.002	0.000	0.000	0.000	0.000
146	A	147	ARG	1	0.911	0.978	41.902	0.041	0.041	0.000	0.000	0.000	0.000

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