FMO DATABASE

FMODB ID: G5Z71

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	OptHSide
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	-1372985.701819
FMO2-HF: Nuclear repulsion	1312483.807456
FMO2-HF: Total energy	-60501.894363
FMO2-MP2: Total energy	-60674.952025

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.
-204.772	-199.229	27.344	-17.959	-14.928	-0.188

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 : 0.841 / q_NPA : 0.898

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	0.901	0.955	3.475	31.997	34.606	0.019	-1.175	-1.452	0.005
4	A	8	VAL	0	-0.013	-0.007	5.853	3.569	3.569	0.000	0.000	0.000	0.000
5	A	9	TYR	0	0.000	-0.027	8.588	-0.251	-0.251	0.000	0.000	0.000	0.000
6	A	10	LEU	0	-0.027	-0.022	11.109	0.025	0.025	0.000	0.000	0.000	0.000
7	A	11	TYR	0	-0.026	-0.044	14.028	1.033	1.033	0.000	0.000	0.000	0.000
8	A	12	THR	0	0.016	-0.003	17.698	-0.158	-0.158	0.000	0.000	0.000	0.000
9	A	13	ARG	1	0.754	0.873	20.569	11.687	11.687	0.000	0.000	0.000	0.000
10	A	14	VAL	0	0.023	0.031	24.392	-0.119	-0.119	0.000	0.000	0.000	0.000
11	A	15	SER	0	-0.029	-0.029	27.815	0.007	0.007	0.000	0.000	0.000	0.000
12	A	16	THR	0	-0.052	-0.032	30.393	0.280	0.280	0.000	0.000	0.000	0.000
13	A	17	SER	0	0.092	0.025	32.665	-0.079	-0.079	0.000	0.000	0.000	0.000
14	A	18	ILE	0	0.017	-0.003	28.652	-0.105	-0.105	0.000	0.000	0.000	0.000
15	A	19	GLN	0	-0.022	-0.014	31.401	-0.078	-0.078	0.000	0.000	0.000	0.000
16	A	20	ILE	0	-0.008	0.015	34.260	0.064	0.064	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.721	-0.858	29.388	-10.574	-10.574	0.000	0.000	0.000	0.000
18	A	22	GLY	0	0.025	0.003	28.349	-0.401	-0.401	0.000	0.000	0.000	0.000
19	A	23	TYR	0	-0.001	0.010	27.355	-0.579	-0.579	0.000	0.000	0.000	0.000
20	A	24	SER	0	-0.018	0.005	26.570	-0.351	-0.351	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.032	-0.007	23.702	-0.528	-0.528	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.787	-0.905	21.621	-14.210	-14.210	0.000	0.000	0.000	0.000
23	A	27	ALA	0	-0.012	0.009	20.602	-0.789	-0.789	0.000	0.000	0.000	0.000
24	A	28	GLN	0	-0.042	-0.028	20.450	-0.845	-0.845	0.000	0.000	0.000	0.000
25	A	29	LYS	1	0.844	0.904	17.645	13.687	13.687	0.000	0.000	0.000	0.000
26	A	30	SER	0	-0.012	-0.012	16.076	-1.401	-1.401	0.000	0.000	0.000	0.000
27	A	31	ARG	1	0.870	0.935	15.362	14.123	14.123	0.000	0.000	0.000	0.000
28	A	32	MET	0	-0.043	-0.014	14.377	-0.713	-0.713	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.844	0.907	11.634	19.537	19.537	0.000	0.000	0.000	0.000
30	A	34	ALA	0	-0.011	0.003	10.563	-2.797	-2.797	0.000	0.000	0.000	0.000
31	A	35	PHE	0	0.017	0.005	10.560	-2.129	-2.129	0.000	0.000	0.000	0.000
32	A	36	ALA	0	0.033	0.012	7.961	-1.506	-1.506	0.000	0.000	0.000	0.000
33	A	37	ILE	0	-0.003	0.001	6.343	-4.818	-4.818	0.000	0.000	0.000	0.000
34	A	38	TYR	0	-0.034	-0.024	6.066	-4.091	-4.091	0.000	0.000	0.000	0.000
35	A	39	ASN	0	-0.086	-0.044	7.747	1.336	1.336	0.000	0.000	0.000	0.000
36	A	40	ASP	-1	-0.838	-0.882	1.656	-149.694	-152.597	25.495	-13.609	-8.983	-0.159
37	A	41	TYR	0	-0.034	-0.023	2.668	-9.378	-5.993	0.861	-1.939	-2.307	-0.025
38	A	42	GLU	-1	-0.848	-0.911	2.431	-51.805	-49.402	0.969	-1.219	-2.154	-0.009
39	A	43	ILE	0	-0.036	-0.021	4.387	4.969	5.018	0.000	-0.017	-0.032	0.000
40	A	44	VAL	0	0.013	0.003	6.738	-0.149	-0.149	0.000	0.000	0.000	0.000
41	A	45	GLY	0	0.003	-0.001	9.455	2.014	2.014	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.853	-0.905	13.016	-21.780	-21.780	0.000	0.000	0.000	0.000
43	A	47	TYR	0	-0.109	-0.073	15.153	0.753	0.753	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.796	-0.917	18.907	-13.792	-13.792	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.777	-0.856	21.893	-11.637	-11.637	0.000	0.000	0.000	0.000
46	A	50	ALA	0	-0.009	-0.028	25.416	0.161	0.161	0.000	0.000	0.000	0.000
47	A	51	GLY	0	0.056	0.014	26.854	0.200	0.200	0.000	0.000	0.000	0.000
48	A	52	LYS	1	0.879	0.946	25.496	12.343	12.343	0.000	0.000	0.000	0.000
49	A	53	SER	0	-0.012	0.017	31.779	0.297	0.297	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.060	0.020	34.424	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.810	0.911	32.533	9.551	9.551	0.000	0.000	0.000	0.000
52	A	56	SER	0	0.014	0.005	36.511	-0.105	-0.105	0.000	0.000	0.000	0.000
53	A	57	ILE	0	-0.018	-0.007	33.537	-0.137	-0.137	0.000	0.000	0.000	0.000
54	A	58	GLU	-1	-0.751	-0.847	28.799	-10.120	-10.120	0.000	0.000	0.000	0.000
55	A	59	GLY	0	-0.070	-0.039	30.786	0.062	0.062	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.873	0.913	24.879	11.093	11.093	0.000	0.000	0.000	0.000
57	A	61	ILE	0	0.040	0.032	26.421	-0.179	-0.179	0.000	0.000	0.000	0.000
58	A	62	GLN	0	0.038	0.020	22.187	-0.536	-0.536	0.000	0.000	0.000	0.000
59	A	63	PHE	0	0.028	0.018	21.828	-0.543	-0.543	0.000	0.000	0.000	0.000
60	A	64	ASN	0	-0.007	-0.011	22.367	-0.351	-0.351	0.000	0.000	0.000	0.000
61	A	65	ARG	1	0.893	0.947	19.175	13.990	13.990	0.000	0.000	0.000	0.000
62	A	66	MET	0	-0.002	0.008	17.089	-0.517	-0.517	0.000	0.000	0.000	0.000
63	A	67	MET	0	0.019	0.000	18.840	-0.613	-0.613	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.850	-0.905	20.996	-11.553	-11.553	0.000	0.000	0.000	0.000
65	A	69	ASP	-1	-0.830	-0.896	16.888	-14.851	-14.851	0.000	0.000	0.000	0.000
66	A	70	ILE	0	-0.046	-0.015	15.822	-0.538	-0.538	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.802	0.892	17.519	11.648	11.648	0.000	0.000	0.000	0.000
68	A	72	SER	0	-0.050	-0.027	19.142	-0.077	-0.077	0.000	0.000	0.000	0.000
69	A	73	GLY	0	0.004	0.013	15.271	0.072	0.072	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.790	0.883	13.944	16.255	16.255	0.000	0.000	0.000	0.000
71	A	75	ASP	-1	-0.772	-0.844	10.832	-19.309	-19.309	0.000	0.000	0.000	0.000
72	A	76	GLY	0	-0.008	0.002	9.559	-1.938	-1.938	0.000	0.000	0.000	0.000
73	A	77	VAL	0	-0.048	-0.020	8.711	-2.167	-2.167	0.000	0.000	0.000	0.000
74	A	78	SER	0	0.029	0.009	8.053	0.394	0.394	0.000	0.000	0.000	0.000
75	A	79	PHE	0	-0.039	-0.028	8.683	1.429	1.429	0.000	0.000	0.000	0.000
76	A	80	VAL	0	0.029	0.019	11.320	-0.651	-0.651	0.000	0.000	0.000	0.000
77	A	81	LEU	0	-0.010	-0.002	10.339	0.470	0.470	0.000	0.000	0.000	0.000
78	A	82	VAL	0	0.024	0.002	13.962	0.562	0.562	0.000	0.000	0.000	0.000
79	A	83	PHE	0	0.017	0.003	17.370	-0.464	-0.464	0.000	0.000	0.000	0.000
80	A	84	LYS	1	0.891	0.944	19.553	12.192	12.192	0.000	0.000	0.000	0.000
81	A	85	LEU	0	0.106	0.051	21.948	0.105	0.105	0.000	0.000	0.000	0.000
82	A	86	SER	0	-0.028	-0.009	23.706	0.108	0.108	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.754	0.861	23.060	11.740	11.740	0.000	0.000	0.000	0.000
84	A	88	PHE	0	0.068	0.023	20.249	-0.532	-0.532	0.000	0.000	0.000	0.000
85	A	89	ALA	0	0.034	0.044	23.369	0.166	0.166	0.000	0.000	0.000	0.000
86	A	90	ARG	1	0.783	0.862	26.493	10.612	10.612	0.000	0.000	0.000	0.000
87	A	91	ASN	0	0.006	0.017	29.865	0.196	0.196	0.000	0.000	0.000	0.000
88	A	92	ALA	0	0.055	0.015	29.461	-0.394	-0.394	0.000	0.000	0.000	0.000
89	A	93	ALA	0	0.010	0.001	29.393	-0.274	-0.274	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.810	-0.895	28.141	-10.788	-10.788	0.000	0.000	0.000	0.000
91	A	95	VAL	0	-0.032	-0.002	24.006	-0.421	-0.421	0.000	0.000	0.000	0.000
92	A	96	LEU	0	-0.030	-0.008	24.793	-0.430	-0.430	0.000	0.000	0.000	0.000
93	A	97	SER	0	0.014	0.007	25.956	-0.271	-0.271	0.000	0.000	0.000	0.000
94	A	98	THR	0	-0.030	-0.027	21.861	-0.218	-0.218	0.000	0.000	0.000	0.000
95	A	99	LEU	0	-0.004	-0.015	19.719	-0.435	-0.435	0.000	0.000	0.000	0.000
96	A	100	GLN	0	-0.001	-0.005	21.500	-0.181	-0.181	0.000	0.000	0.000	0.000
97	A	101	ILE	0	0.021	0.016	22.520	-0.129	-0.129	0.000	0.000	0.000	0.000
98	A	102	MET	0	-0.028	-0.015	16.582	-0.076	-0.076	0.000	0.000	0.000	0.000
99	A	103	GLN	0	-0.028	-0.016	18.089	0.055	0.055	0.000	0.000	0.000	0.000
100	A	104	ASP	-1	-0.967	-0.966	19.084	-11.745	-11.745	0.000	0.000	0.000	0.000
101	A	105	TYR	0	-0.038	-0.020	18.333	0.206	0.206	0.000	0.000	0.000	0.000
102	A	106	GLY	0	-0.004	0.005	15.148	-0.713	-0.713	0.000	0.000	0.000	0.000
103	A	107	VAL	0	-0.060	-0.021	13.347	-1.193	-1.193	0.000	0.000	0.000	0.000
104	A	108	ASN	0	0.026	0.009	13.665	1.952	1.952	0.000	0.000	0.000	0.000
105	A	109	LEU	0	-0.008	-0.009	14.374	-0.705	-0.705	0.000	0.000	0.000	0.000
106	A	110	ILE	0	0.002	0.009	11.102	0.128	0.128	0.000	0.000	0.000	0.000
107	A	111	CYS	0	-0.093	-0.023	15.181	0.148	0.148	0.000	0.000	0.000	0.000
108	A	112	VAL	0	0.026	-0.005	14.448	0.130	0.130	0.000	0.000	0.000	0.000
109	A	113	GLU	-1	-0.857	-0.916	17.076	-13.168	-13.168	0.000	0.000	0.000	0.000
110	A	114	ASP	-1	-0.812	-0.935	20.718	-12.963	-12.963	0.000	0.000	0.000	0.000
111	A	115	GLY	0	0.006	0.015	18.454	0.372	0.372	0.000	0.000	0.000	0.000
112	A	116	ILE	0	-0.036	-0.007	19.271	0.075	0.075	0.000	0.000	0.000	0.000
113	A	117	ASP	-1	-0.708	-0.829	13.719	-20.705	-20.705	0.000	0.000	0.000	0.000
114	A	118	SER	0	0.003	-0.019	16.730	0.315	0.315	0.000	0.000	0.000	0.000
115	A	119	SER	0	-0.084	-0.059	13.648	0.231	0.231	0.000	0.000	0.000	0.000
116	A	120	LYS	1	0.817	0.895	11.855	20.900	20.900	0.000	0.000	0.000	0.000
117	A	121	ASP	-1	-0.765	-0.868	17.278	-11.710	-11.710	0.000	0.000	0.000	0.000
118	A	122	ALA	0	0.012	0.014	20.631	0.112	0.112	0.000	0.000	0.000	0.000
119	A	123	GLY	0	-0.021	-0.023	22.568	0.510	0.510	0.000	0.000	0.000	0.000
120	A	124	LYS	1	0.877	0.951	23.626	10.347	10.347	0.000	0.000	0.000	0.000
121	A	125	LEU	0	0.020	-0.004	24.643	0.425	0.425	0.000	0.000	0.000	0.000
122	A	126	MET	0	0.002	-0.003	21.168	0.213	0.213	0.000	0.000	0.000	0.000
123	A	127	ILE	0	0.046	0.019	23.591	0.352	0.352	0.000	0.000	0.000	0.000
124	A	128	SER	0	-0.042	-0.029	26.517	0.456	0.456	0.000	0.000	0.000	0.000
125	A	129	VAL	0	0.036	0.029	28.698	0.354	0.354	0.000	0.000	0.000	0.000
126	A	130	LEU	0	0.024	0.014	24.937	0.294	0.294	0.000	0.000	0.000	0.000
127	A	131	SER	0	0.000	-0.001	29.484	0.333	0.333	0.000	0.000	0.000	0.000
128	A	132	ALA	0	-0.003	0.000	31.787	0.278	0.278	0.000	0.000	0.000	0.000
129	A	133	VAL	0	-0.021	-0.018	32.207	0.260	0.260	0.000	0.000	0.000	0.000
130	A	134	ALA	0	-0.001	-0.001	32.218	0.184	0.184	0.000	0.000	0.000	0.000
131	A	135	GLU	-1	-0.769	-0.861	34.219	-7.569	-7.569	0.000	0.000	0.000	0.000
132	A	136	ILE	0	-0.002	0.010	36.893	0.238	0.238	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.784	-0.887	33.909	-8.881	-8.881	0.000	0.000	0.000	0.000
134	A	138	ARG	1	0.852	0.898	34.112	8.542	8.542	0.000	0.000	0.000	0.000
135	A	139	GLU	-1	-0.812	-0.879	39.758	-6.715	-6.715	0.000	0.000	0.000	0.000
136	A	140	ASN	0	-0.059	-0.049	41.209	0.274	0.274	0.000	0.000	0.000	0.000
137	A	141	ILE	0	0.000	0.014	40.311	0.144	0.144	0.000	0.000	0.000	0.000
138	A	142	ARG	1	0.769	0.857	41.527	7.304	7.304	0.000	0.000	0.000	0.000
139	A	143	ILE	0	0.029	0.025	46.004	0.173	0.173	0.000	0.000	0.000	0.000
140	A	144	GLN	0	-0.002	0.000	43.185	0.126	0.126	0.000	0.000	0.000	0.000
141	A	145	THR	0	-0.041	-0.026	46.492	0.109	0.109	0.000	0.000	0.000	0.000
142	A	146	MET	0	-0.002	0.003	49.067	0.162	0.162	0.000	0.000	0.000	0.000
143	A	147	GLU	-1	-0.899	-0.957	51.369	-5.658	-5.658	0.000	0.000	0.000	0.000
144	A	148	GLY	0	-0.016	-0.008	51.709	0.115	0.115	0.000	0.000	0.000	0.000
145	A	149	CYS	0	-0.098	-0.061	52.500	0.090	0.090	0.000	0.000	0.000	0.000
146	A	150	ILE	0	0.018	0.014	55.182	0.131	0.131	0.000	0.000	0.000	0.000
147	A	151	GLN	0	-0.015	0.001	56.216	0.218	0.218	0.000	0.000	0.000	0.000
148	A	152	LYS	1	0.826	0.883	56.023	5.610	5.610	0.000	0.000	0.000	0.000
149	A	153	ALA	0	-0.020	0.001	58.415	0.081	0.081	0.000	0.000	0.000	0.000
150	A	154	ARG	1	0.856	0.929	61.054	5.182	5.182	0.000	0.000	0.000	0.000
151	A	155	GLU	-1	-0.848	-0.888	58.786	-5.314	-5.314	0.000	0.000	0.000	0.000

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