FMO DATABASE

FMODB ID: YV7V2

Calculation Name: 4G3K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4G3K

Chain ID: A

ChEMBL ID:

UniProt ID: O66591

Base Structure: X-ray

Registration Date: 2023-09-23

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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1475357.616911
FMO2-HF: Nuclear repulsion	1415898.311385
FMO2-HF: Total energy	-59459.305526
FMO2-MP2: Total energy	-59636.232462

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:2:ASP)

Summations of interaction energy for fragment #1(A:2:ASP)

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.
-147.317	-138.53	3.112	-5.278	-6.621	0.056

Interaction energy analysis for fragmet #1(A:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.879 / q_NPA : -0.956

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	4	LYS	1	0.944	0.968	2.577	-62.219	-56.599	0.975	-3.201	-3.394	0.032
4	A	5	VAL	0	0.109	0.071	2.484	-17.364	-14.513	2.137	-2.023	-2.965	0.024
5	A	6	GLH	0	-0.040	-0.033	4.552	-10.385	-10.069	0.000	-0.054	-0.262	0.000
6	A	7	ILE	0	-0.015	-0.003	6.944	-5.723	-5.723	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.910	-0.945	7.618	36.656	36.656	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.003	-0.008	8.111	-4.363	-4.363	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.015	-0.012	10.527	-2.912	-2.912	0.000	0.000	0.000	0.000
10	A	11	TYR	0	-0.001	-0.007	12.201	-2.588	-2.588	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.856	-0.941	13.102	18.867	18.867	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.044	-0.028	14.459	-1.642	-1.642	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.052	-0.028	16.302	-1.511	-1.511	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.887	0.966	16.954	-19.579	-19.579	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.007	0.007	18.397	-0.739	-0.739	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.026	-0.001	20.428	-0.775	-0.775	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.067	-0.024	21.966	-0.713	-0.713	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.066	-0.047	24.238	-0.465	-0.465	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.037	-0.026	26.007	-0.616	-0.616	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.037	0.011	27.296	0.210	0.210	0.000	0.000	0.000	0.000
21	A	22	ASN	0	0.016	0.019	29.425	0.257	0.257	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.094	0.040	25.042	0.473	0.473	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.874	-0.939	26.566	10.953	10.953	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.077	-0.030	27.809	0.238	0.238	0.000	0.000	0.000	0.000
25	A	26	THR	0	0.020	0.006	22.827	0.520	0.520	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.018	-0.022	21.932	0.733	0.733	0.000	0.000	0.000	0.000
27	A	28	PRO	0	0.006	0.005	21.269	0.821	0.821	0.000	0.000	0.000	0.000
28	A	29	TYR	0	-0.012	-0.006	20.304	0.762	0.762	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.046	0.027	16.928	1.069	1.069	0.000	0.000	0.000	0.000
30	A	31	PHE	0	-0.010	-0.027	16.507	1.268	1.268	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.923	0.961	16.801	-15.271	-15.271	0.000	0.000	0.000	0.000
32	A	33	LEU	0	0.002	0.009	13.602	0.699	0.699	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.028	0.011	12.005	1.822	1.822	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.900	0.959	11.953	-15.364	-15.364	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.902	0.942	12.927	-17.571	-17.571	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.017	0.028	8.574	0.267	0.267	0.000	0.000	0.000	0.000
37	A	38	MET	0	-0.012	0.009	7.050	4.952	4.952	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.028	0.027	8.327	0.759	0.759	0.000	0.000	0.000	0.000
39	A	40	PHE	0	-0.049	-0.029	10.555	-1.489	-1.489	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.915	-0.980	13.205	17.158	17.158	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.842	0.936	16.857	-14.978	-14.978	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.013	0.004	15.280	-0.331	-0.331	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.033	-0.033	19.656	-0.411	-0.411	0.000	0.000	0.000	0.000
44	A	45	LEU	0	0.010	0.022	22.418	0.397	0.397	0.000	0.000	0.000	0.000
45	A	46	THR	0	-0.007	-0.005	24.286	-0.344	-0.344	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.000	0.011	26.778	0.159	0.159	0.000	0.000	0.000	0.000
47	A	48	TYR	0	-0.010	-0.020	29.766	-0.081	-0.081	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.825	-0.921	33.302	8.229	8.229	0.000	0.000	0.000	0.000
49	A	50	PRO	0	-0.087	-0.043	35.733	-0.094	-0.094	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.002	0.008	37.569	-0.090	-0.090	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.020	-0.016	40.448	-0.073	-0.073	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.916	-0.945	37.359	8.170	8.170	0.000	0.000	0.000	0.000
53	A	54	GLN	0	-0.036	-0.013	37.456	0.153	0.153	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.039	-0.034	32.017	0.197	0.197	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.035	-0.009	33.159	-0.172	-0.172	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.011	0.009	28.213	0.056	0.056	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.866	0.924	26.843	-11.028	-11.028	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.013	0.030	25.065	-0.127	-0.127	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.028	0.004	24.062	0.170	0.170	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.023	0.006	19.249	-0.051	-0.051	0.000	0.000	0.000	0.000
61	A	62	SER	0	0.002	-0.009	21.203	-0.390	-0.390	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.012	-0.020	21.593	0.573	0.573	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.949	0.970	23.210	-11.654	-11.654	0.000	0.000	0.000	0.000
64	A	65	PHE	0	0.042	0.025	22.984	0.447	0.447	0.000	0.000	0.000	0.000
65	A	66	PRO	0	-0.039	-0.019	26.856	-0.302	-0.302	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.986	0.981	30.009	-8.605	-8.605	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.902	-0.941	33.029	8.692	8.692	0.000	0.000	0.000	0.000
68	A	69	GLY	0	-0.025	0.004	30.509	-0.107	-0.107	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.013	-0.005	28.967	0.435	0.435	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.875	0.964	20.352	-14.149	-14.149	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.974	0.967	26.014	-11.034	-11.034	0.000	0.000	0.000	0.000
72	A	73	GLY	0	0.068	0.029	24.204	-0.264	-0.264	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.812	-0.916	24.933	11.667	11.667	0.000	0.000	0.000	0.000
74	A	75	GLY	0	-0.020	-0.003	26.906	-0.261	-0.261	0.000	0.000	0.000	0.000
75	A	76	ILE	0	-0.014	0.004	26.824	-0.254	-0.254	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.012	-0.010	25.090	-0.105	-0.105	0.000	0.000	0.000	0.000
77	A	78	GLY	0	0.038	0.026	28.400	0.154	0.154	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.911	0.938	30.615	-8.786	-8.786	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.066	0.037	28.180	-0.147	-0.147	0.000	0.000	0.000	0.000
80	A	81	TRP	0	0.082	0.034	26.217	0.008	0.008	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.893	0.943	27.644	-8.798	-8.798	0.000	0.000	0.000	0.000
82	A	83	HIS	0	0.021	0.020	29.414	-0.184	-0.184	0.000	0.000	0.000	0.000
83	A	84	GLY	0	-0.032	-0.011	27.135	0.011	0.011	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.022	-0.026	24.314	0.358	0.358	0.000	0.000	0.000	0.000
85	A	86	PRO	0	-0.023	-0.018	19.708	-0.140	-0.140	0.000	0.000	0.000	0.000
86	A	87	ILE	0	0.004	0.017	21.849	-0.289	-0.289	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.017	-0.007	17.392	0.566	0.566	0.000	0.000	0.000	0.000
88	A	89	ILE	0	-0.023	0.002	20.338	-0.555	-0.555	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.012	-0.016	17.966	0.360	0.360	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.881	-0.958	18.522	13.736	13.736	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.045	-0.003	21.225	-0.518	-0.518	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.043	-0.019	23.497	-0.498	-0.498	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.008	0.009	25.589	-0.537	-0.537	0.000	0.000	0.000	0.000
94	A	110	LYS	1	0.956	0.983	14.064	-19.149	-19.149	0.000	0.000	0.000	0.000
95	A	111	LYS	1	0.944	0.978	16.637	-15.227	-15.227	0.000	0.000	0.000	0.000
96	A	112	ILE	0	0.014	-0.002	16.576	0.821	0.821	0.000	0.000	0.000	0.000
97	A	113	ALA	0	0.002	0.014	15.551	-0.748	-0.748	0.000	0.000	0.000	0.000
98	A	114	PHE	0	0.009	-0.002	17.612	0.269	0.269	0.000	0.000	0.000	0.000
99	A	115	ILE	0	-0.003	-0.006	13.928	-0.159	-0.159	0.000	0.000	0.000	0.000
100	A	116	ALA	0	0.023	0.008	18.413	-0.169	-0.169	0.000	0.000	0.000	0.000
101	A	117	VAL	0	-0.007	0.000	17.653	-0.293	-0.293	0.000	0.000	0.000	0.000
102	A	118	PRO	0	-0.013	0.001	20.917	-0.301	-0.301	0.000	0.000	0.000	0.000
103	A	119	ILE	0	0.015	0.001	23.255	0.361	0.361	0.000	0.000	0.000	0.000
104	A	120	LYS	1	0.924	0.965	23.850	-13.004	-13.004	0.000	0.000	0.000	0.000
105	A	121	SER	0	0.040	0.021	26.996	0.329	0.329	0.000	0.000	0.000	0.000
106	A	122	GLY	0	0.010	0.003	29.561	-0.256	-0.256	0.000	0.000	0.000	0.000
107	A	123	GLY	0	-0.015	0.004	31.374	-0.304	-0.304	0.000	0.000	0.000	0.000
108	A	124	LYS	1	0.964	0.977	31.426	-8.145	-8.145	0.000	0.000	0.000	0.000
109	A	125	VAL	0	0.010	0.010	28.098	0.263	0.263	0.000	0.000	0.000	0.000
110	A	126	ILE	0	-0.011	-0.009	29.162	-0.332	-0.332	0.000	0.000	0.000	0.000
111	A	127	GLY	0	0.051	0.016	27.920	-0.182	-0.182	0.000	0.000	0.000	0.000
112	A	128	VAL	0	-0.068	-0.005	23.784	0.162	0.162	0.000	0.000	0.000	0.000
113	A	129	LEU	0	0.019	0.012	18.113	-0.126	-0.126	0.000	0.000	0.000	0.000
114	A	130	SER	0	0.007	-0.001	20.167	0.180	0.180	0.000	0.000	0.000	0.000
115	A	131	ALA	0	-0.052	-0.039	15.944	0.113	0.113	0.000	0.000	0.000	0.000
116	A	132	ASP	-1	-0.807	-0.902	17.377	14.272	14.272	0.000	0.000	0.000	0.000
117	A	133	LYS	1	0.899	0.950	8.913	-27.102	-27.102	0.000	0.000	0.000	0.000
118	A	134	GLU	-1	-0.892	-0.942	13.915	17.586	17.586	0.000	0.000	0.000	0.000
119	A	135	ILE	0	-0.046	-0.012	11.388	1.651	1.651	0.000	0.000	0.000	0.000
120	A	136	ASN	0	-0.002	-0.030	9.230	-0.921	-0.921	0.000	0.000	0.000	0.000
121	A	137	GLU	-1	-0.877	-0.953	11.419	18.600	18.600	0.000	0.000	0.000	0.000
122	A	138	LYS	1	0.873	0.946	7.392	-25.138	-25.138	0.000	0.000	0.000	0.000
123	A	139	ASP	-1	-0.856	-0.906	5.279	42.339	42.339	0.000	0.000	0.000	0.000
124	A	140	SER	0	-0.006	-0.003	7.488	-3.156	-3.156	0.000	0.000	0.000	0.000
125	A	141	LEU	0	0.028	-0.007	9.243	1.158	1.158	0.000	0.000	0.000	0.000
126	A	142	ASP	-1	-0.897	-0.962	11.914	19.109	19.109	0.000	0.000	0.000	0.000
127	A	143	GLU	-1	-0.884	-0.926	6.223	29.407	29.407	0.000	0.000	0.000	0.000
128	A	144	TYR	0	-0.002	-0.008	6.513	-0.383	-0.383	0.000	0.000	0.000	0.000
129	A	145	THR	0	0.010	0.003	10.267	-1.452	-1.452	0.000	0.000	0.000	0.000
130	A	146	ARG	1	0.975	0.988	10.594	-23.942	-23.942	0.000	0.000	0.000	0.000
131	A	147	PHE	0	0.020	0.015	9.764	-1.069	-1.069	0.000	0.000	0.000	0.000
132	A	148	LEU	0	0.027	-0.003	11.934	-1.010	-1.010	0.000	0.000	0.000	0.000
133	A	149	SER	0	-0.012	-0.011	14.613	-1.660	-1.660	0.000	0.000	0.000	0.000
134	A	150	MET	0	-0.015	0.001	12.450	-0.736	-0.736	0.000	0.000	0.000	0.000
135	A	151	ILE	0	0.012	0.010	13.684	-0.927	-0.927	0.000	0.000	0.000	0.000
136	A	152	ALA	0	0.019	0.009	16.991	-0.956	-0.956	0.000	0.000	0.000	0.000
137	A	153	THR	0	-0.040	-0.021	19.596	-1.017	-1.017	0.000	0.000	0.000	0.000
138	A	154	LEU	0	-0.020	-0.006	17.392	-0.717	-0.717	0.000	0.000	0.000	0.000
139	A	155	ILE	0	0.029	0.008	20.030	-0.652	-0.652	0.000	0.000	0.000	0.000
140	A	156	ALA	0	0.009	0.010	22.842	-0.669	-0.669	0.000	0.000	0.000	0.000
141	A	157	ASN	0	-0.001	0.000	24.637	-0.713	-0.713	0.000	0.000	0.000	0.000
142	A	158	SER	0	0.044	0.023	24.550	-0.484	-0.484	0.000	0.000	0.000	0.000
143	A	159	PHE	0	0.039	0.027	26.900	-0.484	-0.484	0.000	0.000	0.000	0.000
144	A	160	SER	0	-0.066	-0.050	28.935	-0.548	-0.548	0.000	0.000	0.000	0.000
145	A	161	LEU	0	-0.033	-0.024	29.345	-0.432	-0.432	0.000	0.000	0.000	0.000
146	A	162	GLU	-1	-0.844	-0.928	30.864	9.878	9.878	0.000	0.000	0.000	0.000
147	A	163	ARG	1	0.927	0.964	32.602	-9.541	-9.541	0.000	0.000	0.000	0.000
148	A	164	LYS	1	0.924	0.960	32.716	-9.792	-9.792	0.000	0.000	0.000	0.000
149	A	165	VAL	0	0.064	0.042	34.323	-0.241	-0.241	0.000	0.000	0.000	0.000
150	A	166	GLN	0	-0.033	-0.018	36.822	-0.069	-0.069	0.000	0.000	0.000	0.000
151	A	167	ALA	0	-0.069	-0.038	38.702	-0.252	-0.252	0.000	0.000	0.000	0.000
152	A	168	GLU	-1	-0.926	-0.972	39.930	8.003	8.003	0.000	0.000	0.000	0.000
153	A	169	ARG	1	0.916	0.974	39.551	-8.090	-8.090	0.000	0.000	0.000	0.000
154	A	170	LYS	1	0.901	0.950	42.723	-7.459	-7.459	0.000	0.000	0.000	0.000
155	A	171	SER	0	0.015	0.031	45.233	-0.187	-0.187	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASP)