FMO DATABASE

FMODB ID: 894KY

Calculation Name: 3GUV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GUV

Chain ID: A

ChEMBL ID:

UniProt ID:

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	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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1377990.215835
FMO2-HF: Nuclear repulsion	1317488.006589
FMO2-HF: Total energy	-60502.209246
FMO2-MP2: Total energy	-60675.262271

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:5:LYS)

Summations of interaction energy for fragment #1(A:5:LYS)

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.
-202.114	-200.105	29.34	-17.064	-14.284	-0.183

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.857 / q_NPA : 0.907

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	7	LYS	1	0.882	0.947	3.370	35.136	37.222	-0.005	-0.901	-1.180	0.004
4	A	8	VAL	0	-0.027	-0.012	5.769	3.569	3.569	0.000	0.000	0.000	0.000
5	A	9	TYR	0	0.003	-0.024	8.765	0.035	0.035	0.000	0.000	0.000	0.000
6	A	10	LEU	0	-0.013	-0.004	11.277	-0.140	-0.140	0.000	0.000	0.000	0.000
7	A	11	TYR	0	-0.049	-0.062	14.360	1.003	1.003	0.000	0.000	0.000	0.000
8	A	12	THR	0	0.016	0.003	18.123	-0.135	-0.135	0.000	0.000	0.000	0.000
9	A	13	ARG	1	0.726	0.850	21.070	11.514	11.514	0.000	0.000	0.000	0.000
10	A	14	VAL	0	0.015	0.038	24.872	-0.054	-0.054	0.000	0.000	0.000	0.000
11	A	15	SER	0	-0.033	-0.035	28.385	-0.053	-0.053	0.000	0.000	0.000	0.000
12	A	16	THR	0	-0.032	-0.026	30.897	0.279	0.279	0.000	0.000	0.000	0.000
13	A	17	SER	0	0.066	0.012	32.852	-0.067	-0.067	0.000	0.000	0.000	0.000
14	A	18	ILE	0	0.012	-0.004	29.077	-0.093	-0.093	0.000	0.000	0.000	0.000
15	A	19	GLN	0	-0.020	-0.016	31.875	-0.073	-0.073	0.000	0.000	0.000	0.000
16	A	20	ILE	0	-0.014	0.011	34.191	0.121	0.121	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.698	-0.834	29.459	-10.475	-10.475	0.000	0.000	0.000	0.000
18	A	22	GLY	0	0.034	0.023	28.754	-0.417	-0.417	0.000	0.000	0.000	0.000
19	A	23	TYR	0	-0.008	-0.002	27.733	-0.523	-0.523	0.000	0.000	0.000	0.000
20	A	24	SER	0	-0.032	-0.016	26.926	-0.420	-0.420	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.021	-0.003	24.088	-0.583	-0.583	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.776	-0.890	22.139	-14.404	-14.404	0.000	0.000	0.000	0.000
23	A	27	ALA	0	0.017	0.025	20.954	-0.824	-0.824	0.000	0.000	0.000	0.000
24	A	28	GLN	0	-0.040	-0.021	20.647	-0.928	-0.928	0.000	0.000	0.000	0.000
25	A	29	LYS	1	0.833	0.891	17.932	13.421	13.421	0.000	0.000	0.000	0.000
26	A	30	SER	0	-0.021	-0.018	16.505	-1.414	-1.414	0.000	0.000	0.000	0.000
27	A	31	ARG	1	0.830	0.901	15.849	13.993	13.993	0.000	0.000	0.000	0.000
28	A	32	MET	0	-0.035	-0.009	14.651	-0.667	-0.667	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.849	0.912	11.949	19.239	19.239	0.000	0.000	0.000	0.000
30	A	34	ALA	0	-0.004	0.007	10.935	-2.582	-2.582	0.000	0.000	0.000	0.000
31	A	35	PHE	0	0.032	0.005	11.182	-1.864	-1.864	0.000	0.000	0.000	0.000
32	A	36	ALA	0	0.015	0.007	8.368	-1.371	-1.371	0.000	0.000	0.000	0.000
33	A	37	ILE	0	0.008	0.007	6.714	-4.328	-4.328	0.000	0.000	0.000	0.000
34	A	38	TYR	0	-0.057	-0.037	6.634	-3.166	-3.166	0.000	0.000	0.000	0.000
35	A	39	ASN	0	-0.072	-0.033	7.835	2.140	2.140	0.000	0.000	0.000	0.000
36	A	40	ASP	-1	-0.852	-0.893	1.742	-151.431	-157.324	26.905	-12.751	-8.261	-0.150
37	A	41	TYR	0	-0.026	-0.017	2.553	-12.445	-9.273	1.052	-1.825	-2.398	-0.024
38	A	42	GLU	-1	-0.831	-0.902	2.233	-50.764	-48.187	1.387	-1.559	-2.405	-0.013
39	A	43	ILE	0	-0.021	-0.020	4.287	5.025	5.092	0.001	-0.028	-0.040	0.000
40	A	44	VAL	0	-0.006	0.004	6.599	-0.092	-0.092	0.000	0.000	0.000	0.000
41	A	45	GLY	0	0.010	0.002	9.281	2.047	2.047	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.847	-0.908	12.878	-21.560	-21.560	0.000	0.000	0.000	0.000
43	A	47	TYR	0	-0.096	-0.065	15.061	0.762	0.762	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.779	-0.900	19.051	-13.480	-13.480	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.767	-0.844	22.288	-11.434	-11.434	0.000	0.000	0.000	0.000
46	A	50	ALA	0	-0.004	-0.028	25.706	0.254	0.254	0.000	0.000	0.000	0.000
47	A	51	GLY	0	0.064	0.019	26.888	0.127	0.127	0.000	0.000	0.000	0.000
48	A	52	LYS	1	0.863	0.932	25.528	12.405	12.405	0.000	0.000	0.000	0.000
49	A	53	SER	0	-0.011	-0.003	31.478	0.305	0.305	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.039	0.025	34.134	0.007	0.007	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.803	0.880	32.826	9.486	9.486	0.000	0.000	0.000	0.000
52	A	56	SER	0	0.009	-0.003	36.592	-0.118	-0.118	0.000	0.000	0.000	0.000
53	A	57	ILE	0	0.004	0.008	33.949	-0.088	-0.088	0.000	0.000	0.000	0.000
54	A	58	GLU	-1	-0.785	-0.844	29.233	-9.850	-9.850	0.000	0.000	0.000	0.000
55	A	59	GLY	0	-0.009	-0.006	31.025	0.000	0.000	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.851	0.904	25.208	11.067	11.067	0.000	0.000	0.000	0.000
57	A	61	ILE	0	0.036	0.035	26.698	-0.107	-0.107	0.000	0.000	0.000	0.000
58	A	62	GLN	0	0.030	0.004	21.961	-0.612	-0.612	0.000	0.000	0.000	0.000
59	A	63	PHE	0	0.014	0.006	21.741	-0.582	-0.582	0.000	0.000	0.000	0.000
60	A	64	ASN	0	0.022	-0.001	22.287	-0.382	-0.382	0.000	0.000	0.000	0.000
61	A	65	ARG	1	0.874	0.949	18.674	14.242	14.242	0.000	0.000	0.000	0.000
62	A	66	MET	0	0.008	0.019	16.942	-0.542	-0.542	0.000	0.000	0.000	0.000
63	A	67	MET	0	0.019	0.005	18.733	-0.638	-0.638	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.859	-0.895	21.194	-11.451	-11.451	0.000	0.000	0.000	0.000
65	A	69	ASP	-1	-0.812	-0.884	16.625	-14.998	-14.998	0.000	0.000	0.000	0.000
66	A	70	ILE	0	-0.027	-0.015	15.815	-0.574	-0.574	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.797	0.883	17.157	11.845	11.845	0.000	0.000	0.000	0.000
68	A	72	SER	0	-0.068	-0.043	18.694	0.086	0.086	0.000	0.000	0.000	0.000
69	A	73	GLY	0	0.020	0.008	14.925	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.775	0.888	13.402	16.270	16.270	0.000	0.000	0.000	0.000
71	A	75	ASP	-1	-0.775	-0.847	10.423	-19.280	-19.280	0.000	0.000	0.000	0.000
72	A	76	GLY	0	-0.003	-0.006	8.913	-2.185	-2.185	0.000	0.000	0.000	0.000
73	A	77	VAL	0	-0.057	-0.021	8.286	-1.986	-1.986	0.000	0.000	0.000	0.000
74	A	78	SER	0	0.029	0.010	8.191	0.560	0.560	0.000	0.000	0.000	0.000
75	A	79	PHE	0	-0.043	-0.028	8.683	1.402	1.402	0.000	0.000	0.000	0.000
76	A	80	VAL	0	0.027	0.020	11.522	-0.618	-0.618	0.000	0.000	0.000	0.000
77	A	81	LEU	0	-0.003	0.002	10.316	0.561	0.561	0.000	0.000	0.000	0.000
78	A	82	VAL	0	0.011	-0.014	13.924	0.633	0.633	0.000	0.000	0.000	0.000
79	A	83	PHE	0	0.042	0.020	17.622	-0.274	-0.274	0.000	0.000	0.000	0.000
80	A	84	LYS	1	0.866	0.909	19.792	12.163	12.163	0.000	0.000	0.000	0.000
81	A	85	LEU	0	0.070	0.036	21.986	0.160	0.160	0.000	0.000	0.000	0.000
82	A	86	SER	0	-0.002	0.000	23.959	0.174	0.174	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.734	0.851	23.506	11.551	11.551	0.000	0.000	0.000	0.000
84	A	88	PHE	0	0.057	0.032	20.281	-0.416	-0.416	0.000	0.000	0.000	0.000
85	A	89	ALA	0	0.023	0.025	23.344	0.140	0.140	0.000	0.000	0.000	0.000
86	A	90	ARG	1	0.777	0.860	26.609	10.515	10.515	0.000	0.000	0.000	0.000
87	A	91	ASN	0	0.016	0.019	30.010	0.215	0.215	0.000	0.000	0.000	0.000
88	A	92	ALA	0	0.039	0.009	29.478	-0.378	-0.378	0.000	0.000	0.000	0.000
89	A	93	ALA	0	0.043	0.015	29.284	-0.283	-0.283	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.773	-0.854	28.451	-10.870	-10.870	0.000	0.000	0.000	0.000
91	A	95	VAL	0	-0.042	-0.012	24.044	-0.441	-0.441	0.000	0.000	0.000	0.000
92	A	96	LEU	0	-0.024	-0.004	24.795	-0.429	-0.429	0.000	0.000	0.000	0.000
93	A	97	SER	0	0.000	-0.012	25.787	-0.314	-0.314	0.000	0.000	0.000	0.000
94	A	98	THR	0	-0.010	-0.016	21.889	-0.199	-0.199	0.000	0.000	0.000	0.000
95	A	99	LEU	0	0.003	-0.010	19.444	-0.416	-0.416	0.000	0.000	0.000	0.000
96	A	100	GLN	0	-0.011	-0.015	21.309	-0.231	-0.231	0.000	0.000	0.000	0.000
97	A	101	ILE	0	0.020	0.013	22.458	-0.154	-0.154	0.000	0.000	0.000	0.000
98	A	102	MET	0	-0.066	-0.030	16.696	-0.091	-0.091	0.000	0.000	0.000	0.000
99	A	103	GLN	0	-0.016	-0.023	17.993	0.115	0.115	0.000	0.000	0.000	0.000
100	A	104	ASP	-1	-0.985	-0.971	18.959	-11.819	-11.819	0.000	0.000	0.000	0.000
101	A	105	TYR	0	-0.001	-0.002	17.658	0.159	0.159	0.000	0.000	0.000	0.000
102	A	106	GLY	0	-0.012	0.000	15.027	-0.765	-0.765	0.000	0.000	0.000	0.000
103	A	107	VAL	0	-0.066	-0.020	13.399	-1.146	-1.146	0.000	0.000	0.000	0.000
104	A	108	ASN	0	0.029	0.010	13.516	1.886	1.886	0.000	0.000	0.000	0.000
105	A	109	LEU	0	-0.003	-0.007	14.597	-0.545	-0.545	0.000	0.000	0.000	0.000
106	A	110	ILE	0	0.002	0.003	11.314	0.102	0.102	0.000	0.000	0.000	0.000
107	A	111	CYS	0	-0.086	-0.028	15.419	-0.022	-0.022	0.000	0.000	0.000	0.000
108	A	112	VAL	0	-0.008	-0.011	14.588	0.182	0.182	0.000	0.000	0.000	0.000
109	A	113	GLU	-1	-0.826	-0.878	17.233	-13.143	-13.143	0.000	0.000	0.000	0.000
110	A	114	ASP	-1	-0.781	-0.910	20.996	-12.661	-12.661	0.000	0.000	0.000	0.000
111	A	115	GLY	0	-0.001	0.007	18.827	0.405	0.405	0.000	0.000	0.000	0.000
112	A	116	ILE	0	-0.027	-0.012	18.932	-0.237	-0.237	0.000	0.000	0.000	0.000
113	A	117	ASP	-1	-0.704	-0.823	13.726	-20.546	-20.546	0.000	0.000	0.000	0.000
114	A	118	SER	0	0.000	-0.010	16.868	0.288	0.288	0.000	0.000	0.000	0.000
115	A	119	SER	0	-0.073	-0.054	13.770	0.156	0.156	0.000	0.000	0.000	0.000
116	A	120	LYS	1	0.825	0.891	11.995	20.685	20.685	0.000	0.000	0.000	0.000
117	A	121	ASP	-1	-0.752	-0.858	17.640	-11.542	-11.542	0.000	0.000	0.000	0.000
118	A	122	ALA	0	0.005	-0.001	21.009	-0.021	-0.021	0.000	0.000	0.000	0.000
119	A	123	GLY	0	0.001	-0.002	22.728	0.419	0.419	0.000	0.000	0.000	0.000
120	A	124	LYS	1	0.866	0.950	24.109	10.291	10.291	0.000	0.000	0.000	0.000
121	A	125	LEU	0	0.015	0.011	25.025	0.462	0.462	0.000	0.000	0.000	0.000
122	A	126	MET	0	0.003	0.002	21.365	0.213	0.213	0.000	0.000	0.000	0.000
123	A	127	ILE	0	0.035	0.010	23.316	0.365	0.365	0.000	0.000	0.000	0.000
124	A	128	SER	0	-0.043	-0.037	26.617	0.482	0.482	0.000	0.000	0.000	0.000
125	A	129	VAL	0	0.014	0.004	28.790	0.352	0.352	0.000	0.000	0.000	0.000
126	A	130	LEU	0	-0.002	0.002	25.037	0.276	0.276	0.000	0.000	0.000	0.000
127	A	131	SER	0	0.004	0.001	29.555	0.309	0.309	0.000	0.000	0.000	0.000
128	A	132	ALA	0	0.017	0.009	31.965	0.279	0.279	0.000	0.000	0.000	0.000
129	A	133	VAL	0	-0.002	-0.010	32.283	0.246	0.246	0.000	0.000	0.000	0.000
130	A	134	ALA	0	0.023	0.007	32.336	0.211	0.211	0.000	0.000	0.000	0.000
131	A	135	GLU	-1	-0.783	-0.855	34.373	-7.571	-7.571	0.000	0.000	0.000	0.000
132	A	136	ILE	0	0.008	0.013	37.234	0.237	0.237	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.808	-0.893	33.854	-8.928	-8.928	0.000	0.000	0.000	0.000
134	A	138	ARG	1	0.837	0.898	34.255	8.525	8.525	0.000	0.000	0.000	0.000
135	A	139	GLU	-1	-0.794	-0.872	39.857	-6.682	-6.682	0.000	0.000	0.000	0.000
136	A	140	ASN	0	-0.069	-0.040	41.290	0.280	0.280	0.000	0.000	0.000	0.000
137	A	141	ILE	0	0.013	0.015	40.391	0.148	0.148	0.000	0.000	0.000	0.000
138	A	142	ARG	1	0.747	0.847	41.555	7.293	7.293	0.000	0.000	0.000	0.000
139	A	143	ILE	0	0.028	0.012	45.985	0.167	0.167	0.000	0.000	0.000	0.000
140	A	144	GLN	0	-0.006	-0.007	43.298	0.111	0.111	0.000	0.000	0.000	0.000
141	A	145	THR	0	-0.036	-0.026	46.411	0.108	0.108	0.000	0.000	0.000	0.000
142	A	146	MET	0	-0.013	0.001	48.987	0.162	0.162	0.000	0.000	0.000	0.000
143	A	147	GLU	-1	-0.875	-0.947	51.422	-5.650	-5.650	0.000	0.000	0.000	0.000
144	A	148	GLY	0	-0.027	-0.006	51.650	0.111	0.111	0.000	0.000	0.000	0.000
145	A	149	CYS	0	-0.084	-0.051	52.430	0.102	0.102	0.000	0.000	0.000	0.000
146	A	150	ILE	0	0.004	0.005	55.136	0.130	0.130	0.000	0.000	0.000	0.000
147	A	151	GLN	0	-0.008	-0.002	56.176	0.216	0.216	0.000	0.000	0.000	0.000
148	A	152	LYS	1	0.829	0.887	55.859	5.636	5.636	0.000	0.000	0.000	0.000
149	A	153	ALA	0	-0.015	0.000	58.495	0.084	0.084	0.000	0.000	0.000	0.000
150	A	154	ARG	1	0.844	0.922	61.119	5.175	5.175	0.000	0.000	0.000	0.000
151	A	155	GLU	-1	-0.853	-0.892	58.712	-5.336	-5.336	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)