FMO DATABASE

FMODB ID: 8N54Y

Calculation Name: 5GKM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GKM

Chain ID: A

ChEMBL ID:

UniProt ID: Q94C10

Base Structure: X-ray

Registration Date: 2023-09-26

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1538478.172565
FMO2-HF: Nuclear repulsion	1476954.551667
FMO2-HF: Total energy	-61523.620898
FMO2-MP2: Total energy	-61700.929288

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:75:LEU)

Summations of interaction energy for fragment #1(A:75:LEU)

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.
17.02	-69.536	141.92	-35.403	-19.961	-0.018

Interaction energy analysis for fragmet #1(A:75:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.053

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	77	SER	0	0.001	-0.024	3.714	-1.571	0.022	-0.008	-0.637	-0.948	0.000
4	A	78	MET	0	-0.052	0.051	2.086	26.206	-66.132	137.632	-31.781	-13.514	-0.002
5	A	79	VAL	0	0.024	0.000	3.876	-0.455	-0.174	0.002	-0.091	-0.192	0.000
6	A	80	PHE	0	-0.024	-0.030	3.392	-1.122	-0.196	0.036	-0.354	-0.608	0.002
7	A	81	GLU	-1	-0.896	-0.909	2.021	-4.707	-3.105	2.951	-2.094	-2.459	0.003
8	A	82	ARG	1	0.910	0.928	2.413	-1.469	-0.625	1.307	-0.402	-1.749	-0.021
9	A	83	PHE	0	0.002	0.013	4.649	0.751	0.876	-0.001	-0.008	-0.116	0.000
10	A	84	THR	0	0.008	0.000	4.869	-0.712	-0.583	-0.001	-0.003	-0.124	0.000
11	A	85	GLU	-1	-0.820	-0.931	6.695	-0.285	-0.285	0.000	0.000	0.000	0.000
12	A	86	ARG	1	0.791	0.886	7.441	0.282	0.282	0.000	0.000	0.000	0.000
13	A	87	ALA	0	-0.005	-0.003	8.580	0.077	0.077	0.000	0.000	0.000	0.000
14	A	88	ILE	0	0.025	0.015	3.773	-0.083	0.199	0.002	-0.033	-0.251	0.000
15	A	89	ARG	1	0.841	0.927	7.142	0.390	0.390	0.000	0.000	0.000	0.000
16	A	90	ALA	0	0.033	0.018	9.963	0.070	0.070	0.000	0.000	0.000	0.000
17	A	91	ILE	0	-0.011	0.009	7.914	0.051	0.051	0.000	0.000	0.000	0.000
18	A	92	ILE	0	0.028	0.037	6.599	0.059	0.059	0.000	0.000	0.000	0.000
19	A	93	PHE	0	-0.057	-0.047	10.388	0.022	0.022	0.000	0.000	0.000	0.000
20	A	94	SER	0	-0.019	-0.041	12.683	0.017	0.017	0.000	0.000	0.000	0.000
21	A	95	GLN	0	0.014	0.023	10.457	0.000	0.000	0.000	0.000	0.000	0.000
22	A	96	LYS	1	0.890	0.943	14.296	0.018	0.018	0.000	0.000	0.000	0.000
23	A	97	GLU	-1	-0.763	-0.864	16.541	-0.041	-0.041	0.000	0.000	0.000	0.000
24	A	98	ALA	0	0.027	0.036	17.866	0.002	0.002	0.000	0.000	0.000	0.000
25	A	99	LYS	1	0.942	0.978	18.330	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	100	SER	0	-0.111	-0.093	20.171	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	101	LEU	0	0.034	0.040	22.500	0.000	0.000	0.000	0.000	0.000	0.000
28	A	102	GLY	0	-0.009	-0.001	23.826	0.000	0.000	0.000	0.000	0.000	0.000
29	A	103	LYS	1	0.772	0.877	21.294	0.019	0.019	0.000	0.000	0.000	0.000
30	A	104	ASP	-1	-0.924	-0.967	20.199	0.011	0.011	0.000	0.000	0.000	0.000
31	A	105	MET	0	-0.018	-0.018	17.952	0.005	0.005	0.000	0.000	0.000	0.000
32	A	106	VAL	0	-0.002	0.014	14.325	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	107	TYR	0	0.041	0.027	17.413	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	108	THR	0	0.017	-0.022	18.897	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	109	GLN	0	0.036	0.009	20.078	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	110	HIS	0	0.052	0.028	18.376	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	111	LEU	0	-0.001	-0.002	13.879	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	112	LEU	0	-0.021	-0.006	16.924	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	113	LEU	0	-0.010	-0.003	19.660	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	114	GLY	0	0.017	0.010	15.489	0.000	0.000	0.000	0.000	0.000	0.000
41	A	115	LEU	0	-0.024	-0.021	14.753	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	116	ILE	0	-0.046	-0.016	16.957	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	117	ALA	0	-0.020	-0.011	17.506	0.004	0.004	0.000	0.000	0.000	0.000
44	A	118	GLU	-1	-0.853	-0.928	13.304	-0.201	-0.201	0.000	0.000	0.000	0.000
45	A	119	ASP	-1	-0.819	-0.896	16.533	-0.106	-0.106	0.000	0.000	0.000	0.000
46	A	120	ARG	1	0.944	0.969	15.510	0.093	0.093	0.000	0.000	0.000	0.000
47	A	121	ASP	-1	-0.830	-0.893	20.682	-0.053	-0.053	0.000	0.000	0.000	0.000
48	A	122	PRO	0	-0.032	-0.014	23.138	0.003	0.003	0.000	0.000	0.000	0.000
49	A	123	GLN	0	-0.026	-0.023	26.508	0.004	0.004	0.000	0.000	0.000	0.000
50	A	124	GLY	0	0.025	0.025	25.783	0.001	0.001	0.000	0.000	0.000	0.000
51	A	125	PHE	0	-0.006	-0.003	19.601	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	126	LEU	0	-0.022	-0.009	20.753	0.003	0.003	0.000	0.000	0.000	0.000
53	A	127	GLY	0	0.017	0.014	23.828	0.004	0.004	0.000	0.000	0.000	0.000
54	A	128	SER	0	-0.086	-0.060	26.550	0.007	0.007	0.000	0.000	0.000	0.000
55	A	129	GLY	0	0.016	0.011	28.578	0.003	0.003	0.000	0.000	0.000	0.000
56	A	130	ILE	0	-0.059	-0.022	25.501	0.003	0.003	0.000	0.000	0.000	0.000
57	A	131	THR	0	0.021	0.003	25.758	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	132	ILE	0	0.047	-0.004	21.166	0.001	0.001	0.000	0.000	0.000	0.000
59	A	133	ASP	-1	-0.889	-0.941	24.424	-0.029	-0.029	0.000	0.000	0.000	0.000
60	A	134	LYS	1	0.968	0.986	27.434	0.029	0.029	0.000	0.000	0.000	0.000
61	A	135	ALA	0	0.014	0.008	24.649	0.001	0.001	0.000	0.000	0.000	0.000
62	A	136	ARG	1	0.813	0.865	21.084	0.039	0.039	0.000	0.000	0.000	0.000
63	A	137	GLU	-1	-0.927	-0.951	26.149	-0.024	-0.024	0.000	0.000	0.000	0.000
64	A	138	ALA	0	-0.034	-0.012	28.537	0.001	0.001	0.000	0.000	0.000	0.000
65	A	139	VAL	0	-0.027	-0.025	24.193	0.001	0.001	0.000	0.000	0.000	0.000
66	A	140	TRP	0	0.033	0.027	27.398	0.001	0.001	0.000	0.000	0.000	0.000
67	A	141	SER	0	0.007	0.013	29.096	0.001	0.001	0.000	0.000	0.000	0.000
68	A	142	ILE	0	-0.138	-0.082	29.429	0.001	0.001	0.000	0.000	0.000	0.000
69	A	143	TRP	0	-0.068	-0.066	26.952	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	144	ASP	-1	-0.825	-0.900	28.454	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	145	GLU	-1	-0.915	-0.934	31.545	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	146	ALA	0	-0.051	-0.023	34.834	0.001	0.001	0.000	0.000	0.000	0.000
73	A	147	ASN	0	-0.069	-0.020	35.619	0.001	0.001	0.000	0.000	0.000	0.000
74	A	148	SER	0	0.076	0.042	31.042	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	149	ASP	-1	-0.831	-0.916	28.501	-0.036	-0.036	0.000	0.000	0.000	0.000
76	A	150	SER	0	0.014	-0.007	29.851	0.000	0.000	0.000	0.000	0.000	0.000
77	A	151	LYS	1	0.820	0.907	27.848	0.039	0.039	0.000	0.000	0.000	0.000
78	A	152	GLN	0	-0.067	-0.023	24.446	0.001	0.001	0.000	0.000	0.000	0.000
79	A	153	GLU	-1	-0.905	-0.947	26.362	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	154	GLU	-1	-0.871	-0.929	21.444	-0.032	-0.032	0.000	0.000	0.000	0.000
81	A	155	ALA	0	0.031	0.023	24.303	0.003	0.003	0.000	0.000	0.000	0.000
82	A	156	SER	0	-0.035	-0.021	19.848	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	157	SER	0	0.010	-0.007	19.639	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	158	THR	0	-0.069	-0.037	17.025	0.015	0.015	0.000	0.000	0.000	0.000
85	A	159	SER	0	0.029	0.005	18.580	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	160	TYR	0	0.028	0.015	15.806	0.007	0.007	0.000	0.000	0.000	0.000
87	A	161	SER	0	0.027	0.017	16.007	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	162	LYS	1	0.879	0.937	10.367	-0.112	-0.112	0.000	0.000	0.000	0.000
89	A	163	SER	0	0.030	0.003	14.749	0.006	0.006	0.000	0.000	0.000	0.000
90	A	164	THR	0	-0.007	-0.016	9.329	-0.027	-0.027	0.000	0.000	0.000	0.000
91	A	165	ASP	-1	-0.894	-0.929	10.147	0.221	0.221	0.000	0.000	0.000	0.000
92	A	166	MET	0	-0.095	-0.049	12.263	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	167	PRO	0	0.043	0.068	13.044	0.026	0.026	0.000	0.000	0.000	0.000
94	A	168	PHE	0	-0.011	-0.019	9.795	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	169	SER	0	0.066	0.024	15.145	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	170	ILE	0	-0.010	-0.010	17.572	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	171	SER	0	0.005	-0.021	19.195	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	172	THR	0	0.032	0.020	14.407	-0.018	-0.018	0.000	0.000	0.000	0.000
99	A	173	LYS	1	0.911	0.952	13.273	-0.031	-0.031	0.000	0.000	0.000	0.000
100	A	174	ARG	1	0.979	1.002	15.603	0.067	0.067	0.000	0.000	0.000	0.000
101	A	175	VAL	0	-0.006	0.001	15.949	-0.016	-0.016	0.000	0.000	0.000	0.000
102	A	176	PHE	0	-0.033	-0.024	11.504	-0.023	-0.023	0.000	0.000	0.000	0.000
103	A	177	GLU	-1	-0.907	-0.946	13.342	-0.330	-0.330	0.000	0.000	0.000	0.000
104	A	178	ALA	0	0.037	0.016	15.012	-0.017	-0.017	0.000	0.000	0.000	0.000
105	A	179	ALA	0	-0.040	-0.010	13.318	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	180	VAL	0	-0.019	-0.024	10.777	-0.039	-0.039	0.000	0.000	0.000	0.000
107	A	181	GLU	-1	-0.920	-0.962	13.268	-0.181	-0.181	0.000	0.000	0.000	0.000
108	A	182	TYR	0	-0.022	-0.032	16.668	0.020	0.020	0.000	0.000	0.000	0.000
109	A	183	SER	0	-0.045	-0.028	12.128	0.032	0.032	0.000	0.000	0.000	0.000
110	A	184	ARG	1	0.977	0.979	11.915	0.399	0.399	0.000	0.000	0.000	0.000
111	A	185	THR	0	-0.035	0.001	15.710	0.032	0.032	0.000	0.000	0.000	0.000
112	A	186	MET	0	-0.117	-0.067	17.618	0.016	0.016	0.000	0.000	0.000	0.000
113	A	187	ASP	-1	-0.934	-0.947	16.948	-0.094	-0.094	0.000	0.000	0.000	0.000
114	A	188	CYS	0	-0.059	-0.019	12.661	0.028	0.028	0.000	0.000	0.000	0.000
115	A	189	GLN	0	0.027	0.016	10.413	-0.034	-0.034	0.000	0.000	0.000	0.000
116	A	190	TYR	0	-0.006	-0.010	8.338	-0.072	-0.072	0.000	0.000	0.000	0.000
117	A	191	ILE	0	0.051	0.041	8.370	0.104	0.104	0.000	0.000	0.000	0.000
118	A	192	ALA	0	-0.033	-0.033	9.442	-0.141	-0.141	0.000	0.000	0.000	0.000
119	A	193	PRO	0	0.027	-0.001	11.816	0.011	0.011	0.000	0.000	0.000	0.000
120	A	194	GLU	-1	-0.773	-0.888	14.090	-0.180	-0.180	0.000	0.000	0.000	0.000
121	A	195	HIS	0	0.069	0.052	13.599	-0.026	-0.026	0.000	0.000	0.000	0.000
122	A	196	ILE	0	-0.006	-0.009	11.107	0.015	0.015	0.000	0.000	0.000	0.000
123	A	197	ALA	0	-0.019	-0.004	15.609	0.028	0.028	0.000	0.000	0.000	0.000
124	A	198	VAL	0	0.005	0.006	18.973	0.017	0.017	0.000	0.000	0.000	0.000
125	A	199	GLY	0	0.040	0.031	18.379	0.013	0.013	0.000	0.000	0.000	0.000
126	A	200	LEU	0	-0.026	-0.009	18.714	0.016	0.016	0.000	0.000	0.000	0.000
127	A	201	PHE	0	-0.024	-0.040	20.327	0.013	0.013	0.000	0.000	0.000	0.000
128	A	202	THR	0	-0.036	-0.024	22.429	0.005	0.005	0.000	0.000	0.000	0.000
129	A	203	VAL	0	-0.061	-0.020	20.305	0.007	0.007	0.000	0.000	0.000	0.000
130	A	204	ASP	-1	-0.779	-0.870	21.959	-0.073	-0.073	0.000	0.000	0.000	0.000
131	A	205	ASP	-1	-0.842	-0.877	23.271	-0.052	-0.052	0.000	0.000	0.000	0.000
132	A	206	GLY	0	-0.026	-0.018	25.898	0.006	0.006	0.000	0.000	0.000	0.000
133	A	207	SER	0	-0.088	-0.091	24.106	0.005	0.005	0.000	0.000	0.000	0.000
134	A	208	ALA	0	0.025	0.003	22.917	0.003	0.003	0.000	0.000	0.000	0.000
135	A	209	GLY	0	0.056	0.019	24.880	0.002	0.002	0.000	0.000	0.000	0.000
136	A	210	ARG	1	0.885	0.951	28.319	0.040	0.040	0.000	0.000	0.000	0.000
137	A	211	VAL	0	0.037	0.022	25.355	0.003	0.003	0.000	0.000	0.000	0.000
138	A	212	LEU	0	0.007	0.002	25.520	0.002	0.002	0.000	0.000	0.000	0.000
139	A	213	LYS	1	0.955	0.981	29.027	0.037	0.037	0.000	0.000	0.000	0.000
140	A	214	ARG	1	0.883	0.944	31.357	0.032	0.032	0.000	0.000	0.000	0.000
141	A	215	LEU	0	-0.030	-0.025	27.534	0.002	0.002	0.000	0.000	0.000	0.000
142	A	216	GLY	0	-0.006	0.023	31.907	0.001	0.001	0.000	0.000	0.000	0.000
143	A	217	ALA	0	-0.009	0.009	29.728	0.000	0.000	0.000	0.000	0.000	0.000
144	A	218	ASN	0	-0.014	-0.024	31.458	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	219	MET	0	0.069	0.041	26.405	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	220	ASN	0	0.021	0.002	27.613	-0.010	-0.010	0.000	0.000	0.000	0.000
147	A	221	LEU	0	0.007	0.002	28.696	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	222	LEU	0	0.015	0.019	25.096	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	223	THR	0	0.018	0.005	23.558	-0.010	-0.010	0.000	0.000	0.000	0.000
150	A	224	ALA	0	-0.009	-0.001	24.110	-0.006	-0.006	0.000	0.000	0.000	0.000
151	A	225	ALA	0	0.031	0.017	25.403	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	226	ALA	0	-0.009	-0.001	20.183	-0.003	-0.003	0.000	0.000	0.000	0.000
153	A	227	LEU	0	0.021	-0.002	20.799	-0.008	-0.008	0.000	0.000	0.000	0.000
154	A	228	THR	0	-0.051	-0.028	22.383	0.004	0.004	0.000	0.000	0.000	0.000
155	A	229	ARG	1	0.790	0.881	19.005	0.114	0.114	0.000	0.000	0.000	0.000
156	A	230	LEU	0	-0.059	-0.026	15.894	0.001	0.001	0.000	0.000	0.000	0.000
157	A	231	LYS	1	0.919	0.979	19.219	0.076	0.076	0.000	0.000	0.000	0.000
158	A	232	GLY	0	-0.013	0.015	21.049	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:75:LEU)