FMO DATABASE

FMODB ID: J2L79

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1540910.118206
FMO2-HF: Nuclear repulsion	1479384.740637
FMO2-HF: Total energy	-61525.377569
FMO2-MP2: Total energy	-61703.740498

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.
-11.911	-8.525	14.292	-6.041	-11.636	-0.044

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 : -0.022 / q_NPA : -0.033

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	-0.028	-0.015	3.884	-1.919	-0.433	-0.010	-0.635	-0.841	0.000
4	A	78	MET	0	-0.023	0.018	2.439	-0.721	-0.915	5.164	-1.059	-3.911	0.001
5	A	79	VAL	0	0.004	-0.008	4.270	-0.381	-0.267	-0.001	-0.030	-0.083	0.000
6	A	80	PHE	0	0.002	-0.008	2.806	-0.358	0.400	0.126	-0.147	-0.737	0.000
7	A	81	GLU	-1	-0.894	-0.925	2.387	-3.316	-1.372	1.408	-1.080	-2.272	-0.002
8	A	82	ARG	1	0.919	0.953	1.963	-5.189	-6.755	7.292	-2.927	-2.798	-0.043
9	A	83	PHE	0	-0.007	-0.003	4.810	0.996	0.996	0.000	0.000	0.000	0.000
10	A	84	THR	0	0.001	-0.014	4.766	-0.672	-0.510	-0.001	-0.004	-0.157	0.000
11	A	85	GLU	-1	-0.786	-0.865	6.399	-0.312	-0.312	0.000	0.000	0.000	0.000
12	A	86	ARG	1	0.818	0.881	7.386	0.343	0.343	0.000	0.000	0.000	0.000
13	A	87	ALA	0	0.009	0.010	8.026	0.073	0.073	0.000	0.000	0.000	0.000
14	A	88	ILE	0	0.011	0.004	2.802	-0.596	0.086	0.314	-0.159	-0.837	0.000
15	A	89	ARG	1	0.751	0.851	5.964	0.387	0.387	0.000	0.000	0.000	0.000
16	A	90	ALA	0	0.034	0.011	9.067	0.058	0.058	0.000	0.000	0.000	0.000
17	A	91	ILE	0	-0.034	0.001	7.444	0.067	0.067	0.000	0.000	0.000	0.000
18	A	92	ILE	0	0.039	0.032	5.973	0.075	0.075	0.000	0.000	0.000	0.000
19	A	93	PHE	0	-0.043	-0.033	10.120	0.055	0.055	0.000	0.000	0.000	0.000
20	A	94	SER	0	-0.017	-0.019	12.616	0.030	0.030	0.000	0.000	0.000	0.000
21	A	95	GLN	0	-0.010	-0.023	10.536	0.026	0.026	0.000	0.000	0.000	0.000
22	A	96	LYS	1	0.862	0.938	14.009	0.162	0.162	0.000	0.000	0.000	0.000
23	A	97	GLU	-1	-0.754	-0.844	16.427	-0.131	-0.131	0.000	0.000	0.000	0.000
24	A	98	ALA	0	0.033	0.024	17.861	0.017	0.017	0.000	0.000	0.000	0.000
25	A	99	LYS	1	0.781	0.881	18.275	0.144	0.144	0.000	0.000	0.000	0.000
26	A	100	SER	0	-0.072	-0.045	20.155	0.016	0.016	0.000	0.000	0.000	0.000
27	A	101	LEU	0	-0.008	-0.005	22.414	0.009	0.009	0.000	0.000	0.000	0.000
28	A	102	GLY	0	0.030	0.010	24.062	0.001	0.001	0.000	0.000	0.000	0.000
29	A	103	LYS	1	0.793	0.896	21.585	0.124	0.124	0.000	0.000	0.000	0.000
30	A	104	ASP	-1	-0.812	-0.910	20.251	-0.136	-0.136	0.000	0.000	0.000	0.000
31	A	105	MET	0	-0.025	0.005	18.149	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	106	VAL	0	-0.010	0.006	14.400	0.014	0.014	0.000	0.000	0.000	0.000
33	A	107	TYR	0	0.027	0.008	17.361	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	108	THR	0	0.027	-0.013	18.778	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	109	GLN	0	0.023	-0.003	19.820	-0.021	-0.021	0.000	0.000	0.000	0.000
36	A	110	HIS	0	0.043	0.018	18.458	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	111	LEU	0	-0.001	-0.002	13.499	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	112	LEU	0	-0.019	-0.004	16.587	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	113	LEU	0	-0.022	0.000	19.152	0.003	0.003	0.000	0.000	0.000	0.000
40	A	114	GLY	0	0.023	0.000	14.973	0.010	0.010	0.000	0.000	0.000	0.000
41	A	115	LEU	0	-0.030	-0.023	14.052	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	116	ILE	0	-0.043	-0.019	16.066	0.014	0.014	0.000	0.000	0.000	0.000
43	A	117	ALA	0	-0.006	0.003	16.655	0.018	0.018	0.000	0.000	0.000	0.000
44	A	118	GLU	-1	-0.783	-0.876	12.120	-0.255	-0.255	0.000	0.000	0.000	0.000
45	A	119	ASP	-1	-0.783	-0.844	15.409	-0.182	-0.182	0.000	0.000	0.000	0.000
46	A	120	ARG	1	0.866	0.929	13.160	0.166	0.166	0.000	0.000	0.000	0.000
47	A	121	ASP	-1	-0.823	-0.884	19.830	-0.092	-0.092	0.000	0.000	0.000	0.000
48	A	122	PRO	0	-0.018	-0.014	22.556	0.002	0.002	0.000	0.000	0.000	0.000
49	A	123	GLN	0	-0.033	-0.012	25.943	0.007	0.007	0.000	0.000	0.000	0.000
50	A	124	GLY	0	0.023	0.019	24.652	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	125	PHE	0	0.024	-0.004	18.601	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	126	LEU	0	-0.078	-0.039	19.898	0.005	0.005	0.000	0.000	0.000	0.000
53	A	127	GLY	0	0.021	0.025	22.932	0.007	0.007	0.000	0.000	0.000	0.000
54	A	128	SER	0	-0.072	-0.054	25.609	0.010	0.010	0.000	0.000	0.000	0.000
55	A	129	GLY	0	0.022	0.011	27.832	0.004	0.004	0.000	0.000	0.000	0.000
56	A	130	ILE	0	-0.044	-0.022	24.361	0.002	0.002	0.000	0.000	0.000	0.000
57	A	131	THR	0	0.020	0.000	24.642	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	132	ILE	0	0.003	-0.004	20.377	0.000	0.000	0.000	0.000	0.000	0.000
59	A	133	ASP	-1	-0.829	-0.905	23.528	-0.095	-0.095	0.000	0.000	0.000	0.000
60	A	134	LYS	1	0.866	0.909	26.515	0.074	0.074	0.000	0.000	0.000	0.000
61	A	135	ALA	0	0.018	0.016	24.041	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	136	ARG	1	0.763	0.828	20.499	0.117	0.117	0.000	0.000	0.000	0.000
63	A	137	GLU	-1	-0.804	-0.879	25.712	-0.077	-0.077	0.000	0.000	0.000	0.000
64	A	138	ALA	0	-0.025	-0.009	28.041	0.002	0.002	0.000	0.000	0.000	0.000
65	A	139	VAL	0	-0.015	-0.021	23.766	0.000	0.000	0.000	0.000	0.000	0.000
66	A	140	TRP	0	0.034	0.008	27.109	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	141	SER	0	0.025	0.015	29.144	0.004	0.004	0.000	0.000	0.000	0.000
68	A	142	ILE	0	-0.113	-0.052	29.203	0.004	0.004	0.000	0.000	0.000	0.000
69	A	143	TRP	0	-0.051	-0.053	26.905	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	144	ASP	-1	-0.810	-0.875	28.468	-0.114	-0.114	0.000	0.000	0.000	0.000
71	A	145	GLU	-1	-0.897	-0.928	31.655	-0.067	-0.067	0.000	0.000	0.000	0.000
72	A	146	ALA	0	-0.040	-0.022	34.549	0.005	0.005	0.000	0.000	0.000	0.000
73	A	147	ASN	0	-0.045	-0.015	35.092	0.001	0.001	0.000	0.000	0.000	0.000
74	A	148	SER	0	0.041	0.034	31.007	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	149	ASP	-1	-0.774	-0.879	28.430	-0.136	-0.136	0.000	0.000	0.000	0.000
76	A	150	SER	0	0.054	0.020	29.207	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	151	LYS	1	0.738	0.873	26.858	0.152	0.152	0.000	0.000	0.000	0.000
78	A	152	GLN	0	-0.089	-0.045	24.402	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	153	GLU	-1	-0.884	-0.940	25.867	-0.109	-0.109	0.000	0.000	0.000	0.000
80	A	154	GLU	-1	-0.806	-0.872	21.165	-0.227	-0.227	0.000	0.000	0.000	0.000
81	A	155	ALA	0	0.017	0.015	23.876	0.000	0.000	0.000	0.000	0.000	0.000
82	A	156	SER	0	-0.029	-0.022	19.889	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	157	SER	0	0.013	-0.005	20.024	0.016	0.016	0.000	0.000	0.000	0.000
84	A	158	THR	0	-0.063	-0.032	17.918	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	159	SER	0	0.053	0.014	19.595	0.007	0.007	0.000	0.000	0.000	0.000
86	A	160	TYR	0	-0.016	-0.011	15.714	0.006	0.006	0.000	0.000	0.000	0.000
87	A	161	SER	0	0.010	0.009	16.260	0.008	0.008	0.000	0.000	0.000	0.000
88	A	162	LYS	1	0.836	0.892	11.145	0.143	0.143	0.000	0.000	0.000	0.000
89	A	163	SER	0	0.023	-0.007	14.215	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	164	THR	0	0.004	-0.006	9.034	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	165	ASP	-1	-0.825	-0.862	10.069	-0.225	-0.225	0.000	0.000	0.000	0.000
92	A	166	MET	0	-0.050	0.016	12.455	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	167	PRO	0	0.010	0.020	13.342	-0.047	-0.047	0.000	0.000	0.000	0.000
94	A	168	PHE	0	0.041	0.009	9.595	0.007	0.007	0.000	0.000	0.000	0.000
95	A	169	SER	0	0.059	0.020	14.786	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	170	ILE	0	-0.002	-0.019	17.345	-0.039	-0.039	0.000	0.000	0.000	0.000
97	A	171	SER	0	-0.024	-0.006	19.001	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	172	THR	0	0.002	-0.025	14.159	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	173	LYS	1	0.860	0.930	14.094	0.350	0.350	0.000	0.000	0.000	0.000
100	A	174	ARG	1	0.936	0.976	15.249	0.196	0.196	0.000	0.000	0.000	0.000
101	A	175	VAL	0	-0.010	-0.001	15.658	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	176	PHE	0	-0.032	-0.027	10.485	-0.035	-0.035	0.000	0.000	0.000	0.000
103	A	177	GLU	-1	-0.763	-0.856	13.090	-0.649	-0.649	0.000	0.000	0.000	0.000
104	A	178	ALA	0	0.041	0.028	14.572	0.000	0.000	0.000	0.000	0.000	0.000
105	A	179	ALA	0	-0.039	-0.009	13.224	0.024	0.024	0.000	0.000	0.000	0.000
106	A	180	VAL	0	-0.019	-0.013	10.808	-0.017	-0.017	0.000	0.000	0.000	0.000
107	A	181	GLU	-1	-0.932	-0.966	13.361	-0.275	-0.275	0.000	0.000	0.000	0.000
108	A	182	TYR	0	-0.025	-0.026	16.957	0.051	0.051	0.000	0.000	0.000	0.000
109	A	183	SER	0	-0.031	-0.030	11.916	0.056	0.056	0.000	0.000	0.000	0.000
110	A	184	ARG	1	0.852	0.886	12.925	0.560	0.560	0.000	0.000	0.000	0.000
111	A	185	THR	0	-0.053	-0.036	15.776	0.053	0.053	0.000	0.000	0.000	0.000
112	A	186	MET	0	-0.109	-0.049	17.165	0.022	0.022	0.000	0.000	0.000	0.000
113	A	187	ASP	-1	-0.909	-0.943	16.620	-0.092	-0.092	0.000	0.000	0.000	0.000
114	A	188	CYS	0	-0.071	-0.020	12.368	0.039	0.039	0.000	0.000	0.000	0.000
115	A	189	GLN	0	0.011	0.011	10.346	-0.035	-0.035	0.000	0.000	0.000	0.000
116	A	190	TYR	0	0.008	0.004	8.090	-0.081	-0.081	0.000	0.000	0.000	0.000
117	A	191	ILE	0	0.048	0.042	8.002	0.149	0.149	0.000	0.000	0.000	0.000
118	A	192	ALA	0	0.011	0.009	9.463	-0.157	-0.157	0.000	0.000	0.000	0.000
119	A	193	PRO	0	0.016	-0.009	11.531	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	194	GLU	-1	-0.776	-0.872	13.664	-0.281	-0.281	0.000	0.000	0.000	0.000
121	A	195	HIS	0	0.073	0.033	13.854	-0.030	-0.030	0.000	0.000	0.000	0.000
122	A	196	ILE	0	-0.004	-0.006	10.403	0.017	0.017	0.000	0.000	0.000	0.000
123	A	197	ALA	0	-0.016	0.002	15.075	0.032	0.032	0.000	0.000	0.000	0.000
124	A	198	VAL	0	0.013	0.001	18.398	0.024	0.024	0.000	0.000	0.000	0.000
125	A	199	GLY	0	0.045	0.042	18.152	0.021	0.021	0.000	0.000	0.000	0.000
126	A	200	LEU	0	-0.036	-0.025	18.146	0.025	0.025	0.000	0.000	0.000	0.000
127	A	201	PHE	0	-0.010	-0.031	20.023	0.022	0.022	0.000	0.000	0.000	0.000
128	A	202	THR	0	-0.045	-0.031	22.364	0.015	0.015	0.000	0.000	0.000	0.000
129	A	203	VAL	0	-0.057	-0.019	19.758	0.012	0.012	0.000	0.000	0.000	0.000
130	A	204	ASP	-1	-0.756	-0.861	22.009	-0.212	-0.212	0.000	0.000	0.000	0.000
131	A	205	ASP	-1	-0.781	-0.852	22.896	-0.174	-0.174	0.000	0.000	0.000	0.000
132	A	206	GLY	0	-0.006	0.004	25.476	0.015	0.015	0.000	0.000	0.000	0.000
133	A	207	SER	0	-0.078	-0.073	24.006	0.017	0.017	0.000	0.000	0.000	0.000
134	A	208	ALA	0	0.024	0.004	22.593	0.007	0.007	0.000	0.000	0.000	0.000
135	A	209	GLY	0	0.043	0.013	24.456	0.010	0.010	0.000	0.000	0.000	0.000
136	A	210	ARG	1	0.784	0.892	28.047	0.135	0.135	0.000	0.000	0.000	0.000
137	A	211	VAL	0	0.026	0.020	24.813	0.009	0.009	0.000	0.000	0.000	0.000
138	A	212	LEU	0	0.012	0.002	24.694	0.009	0.009	0.000	0.000	0.000	0.000
139	A	213	LYS	1	0.956	0.981	28.309	0.100	0.100	0.000	0.000	0.000	0.000
140	A	214	ARG	1	0.834	0.906	30.804	0.097	0.097	0.000	0.000	0.000	0.000
141	A	215	LEU	0	-0.018	-0.011	26.774	0.006	0.006	0.000	0.000	0.000	0.000
142	A	216	GLY	0	-0.016	0.010	31.164	0.003	0.003	0.000	0.000	0.000	0.000
143	A	217	ALA	0	-0.002	0.007	28.879	0.003	0.003	0.000	0.000	0.000	0.000
144	A	218	ASN	0	0.008	-0.014	30.621	-0.010	-0.010	0.000	0.000	0.000	0.000
145	A	219	MET	0	0.062	0.039	25.619	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	220	ASN	0	0.017	0.022	26.637	-0.015	-0.015	0.000	0.000	0.000	0.000
147	A	221	LEU	0	0.013	0.004	28.244	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	222	LEU	0	0.020	0.023	24.157	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	223	THR	0	-0.007	-0.020	23.514	-0.016	-0.016	0.000	0.000	0.000	0.000
150	A	224	ALA	0	0.001	-0.001	24.102	-0.008	-0.008	0.000	0.000	0.000	0.000
151	A	225	ALA	0	0.031	0.032	24.763	0.002	0.002	0.000	0.000	0.000	0.000
152	A	226	ALA	0	0.005	0.007	19.994	0.000	0.000	0.000	0.000	0.000	0.000
153	A	227	LEU	0	0.006	-0.009	20.827	-0.007	-0.007	0.000	0.000	0.000	0.000
154	A	228	THR	0	-0.071	-0.047	22.596	0.016	0.016	0.000	0.000	0.000	0.000
155	A	229	ARG	1	0.761	0.817	18.849	0.188	0.188	0.000	0.000	0.000	0.000
156	A	230	LEU	0	-0.059	-0.029	15.879	0.005	0.005	0.000	0.000	0.000	0.000
157	A	231	LYS	1	0.889	0.964	19.209	0.128	0.128	0.000	0.000	0.000	0.000
158	A	232	GLY	0	-0.024	0.005	20.908	0.020	0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:75:LEU)