FMO DATABASE

FMODB ID: GNRQ1

Calculation Name: 1VCQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VCQ

Chain ID: A

ChEMBL ID:

UniProt ID: P03315

Base Structure: X-ray

Registration Date: 2023-03-13

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	148
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1365188.63954
FMO2-HF: Nuclear repulsion	1307850.306056
FMO2-HF: Total energy	-57338.333483
FMO2-MP2: Total energy	-57504.39356

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:119:CYS)

Summations of interaction energy for fragment #1(A:119:CYS)

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.
-36.726	-30.272	27.004	-9.42	-24.041	-0.033

Interaction energy analysis for fragmet #1(A:119:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.004

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	121	PHE	0	0.047	0.036	1.845	-14.839	-17.543	9.073	-2.750	-3.620	0.038
4	A	122	GLU	-1	-0.818	-0.928	3.118	3.150	4.061	0.534	-0.330	-1.116	0.000
5	A	123	VAL	0	-0.044	-0.022	4.256	-1.240	-1.205	-0.001	-0.013	-0.021	0.000
6	A	124	LYS	1	0.816	0.889	6.889	-0.397	-0.397	0.000	0.000	0.000	0.000
7	A	125	HIS	0	-0.008	-0.031	10.701	-0.419	-0.419	0.000	0.000	0.000	0.000
8	A	126	GLU	-1	-0.875	-0.921	13.643	-0.357	-0.357	0.000	0.000	0.000	0.000
9	A	127	GLY	0	0.045	0.037	15.734	0.076	0.076	0.000	0.000	0.000	0.000
10	A	128	LYS	1	0.854	0.914	14.860	0.112	0.112	0.000	0.000	0.000	0.000
11	A	129	VAL	0	0.008	0.018	8.949	-0.239	-0.239	0.000	0.000	0.000	0.000
12	A	130	THR	0	-0.030	-0.031	9.803	0.055	0.055	0.000	0.000	0.000	0.000
13	A	131	GLY	0	-0.008	-0.017	7.118	-0.071	-0.071	0.000	0.000	0.000	0.000
14	A	132	TYR	0	-0.046	-0.012	3.780	-0.956	1.557	-0.015	-1.218	-1.280	-0.003
17	A	136	VAL	0	0.021	-0.019	2.386	0.360	1.614	6.523	-2.033	-5.743	-0.020
18	A	137	GLY	0	-0.003	-0.002	4.826	-0.962	-0.846	0.006	-0.019	-0.104	0.000
19	A	138	ASP	-1	-0.809	-0.894	7.991	-1.521	-1.521	0.000	0.000	0.000	0.000
20	A	139	LYS	1	0.833	0.901	7.881	1.654	1.654	0.000	0.000	0.000	0.000
21	A	140	VAL	0	0.046	0.032	4.269	-0.873	-0.608	-0.001	-0.069	-0.194	0.000
22	A	141	MET	0	-0.057	-0.024	2.842	1.926	3.321	0.035	-0.411	-1.019	0.000
23	A	142	LYS	1	0.878	0.921	1.933	-8.079	-13.218	6.898	0.775	-2.534	-0.036
24	A	143	PRO	0	0.041	0.017	4.385	2.768	2.952	-0.001	-0.015	-0.169	0.000
25	A	144	ALA	0	-0.051	-0.018	7.330	0.106	0.106	0.000	0.000	0.000	0.000
26	A	145	HIS	1	0.833	0.882	10.210	2.178	2.178	0.000	0.000	0.000	0.000
27	A	146	VAL	0	-0.028	-0.006	7.380	0.428	0.428	0.000	0.000	0.000	0.000
28	A	147	LYS	1	0.942	0.983	10.051	1.113	1.113	0.000	0.000	0.000	0.000
29	A	148	GLY	0	0.071	0.049	10.648	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	149	VAL	0	-0.032	-0.017	9.253	-0.460	-0.460	0.000	0.000	0.000	0.000
31	A	150	ILE	0	0.005	-0.007	4.578	-0.162	-0.033	-0.002	-0.011	-0.116	0.000
32	A	151	ASP	-1	-0.838	-0.895	7.138	0.680	0.680	0.000	0.000	0.000	0.000
33	A	152	ASN	0	-0.005	-0.031	8.301	0.164	0.164	0.000	0.000	0.000	0.000
34	A	153	ALA	0	0.016	0.015	10.205	-0.369	-0.369	0.000	0.000	0.000	0.000
35	A	154	ASP	-1	-0.770	-0.877	11.009	-0.736	-0.736	0.000	0.000	0.000	0.000
36	A	155	LEU	0	0.031	-0.006	5.577	-0.305	-0.305	0.000	0.000	0.000	0.000
37	A	156	ALA	0	-0.031	0.003	9.681	-0.421	-0.421	0.000	0.000	0.000	0.000
38	A	157	LYS	1	0.854	0.918	11.183	1.205	1.205	0.000	0.000	0.000	0.000
39	A	158	LEU	0	-0.025	0.013	9.206	0.082	0.082	0.000	0.000	0.000	0.000
40	A	159	ALA	0	0.012	0.004	12.898	-0.091	-0.091	0.000	0.000	0.000	0.000
41	A	160	PHE	0	-0.041	-0.014	6.556	-0.232	-0.232	0.000	0.000	0.000	0.000
42	A	161	LYS	1	0.961	0.986	11.369	1.920	1.920	0.000	0.000	0.000	0.000
43	A	162	LYS	1	0.834	0.924	11.346	2.268	2.268	0.000	0.000	0.000	0.000
44	A	163	SER	0	-0.026	-0.015	12.603	0.407	0.407	0.000	0.000	0.000	0.000
45	A	164	SER	0	0.056	0.022	13.512	-0.179	-0.179	0.000	0.000	0.000	0.000
46	A	165	LYS	1	0.956	0.982	15.940	0.820	0.820	0.000	0.000	0.000	0.000
47	A	166	TYR	0	-0.023	-0.038	12.195	0.194	0.194	0.000	0.000	0.000	0.000
48	A	167	ASP	-1	-0.747	-0.846	11.436	-2.658	-2.658	0.000	0.000	0.000	0.000
49	A	168	LEU	0	0.003	0.018	6.618	-0.561	-0.561	0.000	0.000	0.000	0.000
50	A	169	GLU	-1	-0.796	-0.902	7.732	-2.620	-2.620	0.000	0.000	0.000	0.000
51	A	170	CYS	0	-0.027	-0.019	6.677	-1.507	-1.507	0.000	0.000	0.000	0.000
52	A	171	ALA	0	0.073	0.042	7.662	0.924	0.924	0.000	0.000	0.000	0.000
53	A	172	GLN	0	-0.021	-0.009	8.639	-0.391	-0.391	0.000	0.000	0.000	0.000
54	A	173	ILE	0	-0.002	0.016	5.911	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	174	PRO	0	0.036	0.027	9.488	0.287	0.287	0.000	0.000	0.000	0.000
56	A	175	VAL	0	0.034	-0.014	10.737	-0.036	-0.036	0.000	0.000	0.000	0.000
57	A	176	HIS	0	-0.032	-0.028	11.858	-0.041	-0.041	0.000	0.000	0.000	0.000
58	A	177	MET	0	0.017	0.024	6.764	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	178	ARG	1	0.832	0.910	6.533	0.718	0.718	0.000	0.000	0.000	0.000
60	A	179	SER	0	-0.035	-0.030	8.406	0.141	0.141	0.000	0.000	0.000	0.000
61	A	180	ASP	-1	-0.870	-0.911	4.052	-1.172	-1.056	-0.001	-0.023	-0.092	0.000
62	A	181	ALA	0	-0.061	-0.024	2.848	-4.499	-2.365	0.345	-1.091	-1.388	-0.010
63	A	182	SER	0	0.012	0.011	2.135	-1.612	-0.471	2.226	-1.203	-2.164	-0.002
64	A	183	LYS	1	0.970	0.973	3.582	-1.050	-0.924	0.008	0.030	-0.164	0.000
65	A	184	TYR	0	-0.021	0.000	7.067	0.898	0.898	0.000	0.000	0.000	0.000
66	A	185	THR	0	-0.014	-0.035	8.184	-0.368	-0.368	0.000	0.000	0.000	0.000
67	A	186	HIS	0	0.009	0.009	11.666	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	187	GLU	-1	-0.856	-0.878	14.435	0.810	0.810	0.000	0.000	0.000	0.000
69	A	188	LYS	1	0.863	0.917	13.393	-0.295	-0.295	0.000	0.000	0.000	0.000
70	A	189	PRO	0	0.008	0.023	16.632	-0.109	-0.109	0.000	0.000	0.000	0.000
71	A	190	GLU	-1	-0.797	-0.889	19.147	0.463	0.463	0.000	0.000	0.000	0.000
72	A	191	GLY	0	-0.006	-0.004	20.629	0.010	0.010	0.000	0.000	0.000	0.000
73	A	192	HIS	0	-0.053	-0.028	18.308	-0.044	-0.044	0.000	0.000	0.000	0.000
74	A	193	TYR	0	-0.001	-0.010	12.882	0.089	0.089	0.000	0.000	0.000	0.000
75	A	194	ASN	0	-0.057	-0.031	11.585	-0.154	-0.154	0.000	0.000	0.000	0.000
76	A	195	TRP	0	0.079	0.027	9.182	0.562	0.562	0.000	0.000	0.000	0.000
77	A	196	HIS	0	0.008	0.003	9.193	-0.303	-0.303	0.000	0.000	0.000	0.000
78	A	197	HIS	1	0.782	0.883	11.073	-2.142	-2.142	0.000	0.000	0.000	0.000
79	A	198	GLY	0	0.057	0.044	14.106	-0.298	-0.298	0.000	0.000	0.000	0.000
80	A	199	ALA	0	0.006	-0.002	14.465	0.250	0.250	0.000	0.000	0.000	0.000
81	A	200	VAL	0	-0.031	-0.015	12.606	-0.080	-0.080	0.000	0.000	0.000	0.000
82	A	201	GLN	0	-0.020	0.000	15.995	0.034	0.034	0.000	0.000	0.000	0.000
83	A	202	TYR	0	-0.014	-0.016	16.721	-0.029	-0.029	0.000	0.000	0.000	0.000
84	A	203	SER	0	0.037	0.015	18.932	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	204	GLY	0	0.033	0.013	22.037	-0.032	-0.032	0.000	0.000	0.000	0.000
86	A	205	GLY	0	-0.031	-0.006	19.863	-0.053	-0.053	0.000	0.000	0.000	0.000
87	A	206	ARG	1	0.778	0.842	18.625	-0.155	-0.155	0.000	0.000	0.000	0.000
88	A	207	PHE	0	0.039	0.010	13.560	0.082	0.082	0.000	0.000	0.000	0.000
89	A	208	THR	0	0.043	0.026	16.855	-0.101	-0.101	0.000	0.000	0.000	0.000
90	A	209	ILE	0	-0.020	0.000	14.983	0.154	0.154	0.000	0.000	0.000	0.000
91	A	210	PRO	0	0.029	0.010	18.258	-0.105	-0.105	0.000	0.000	0.000	0.000
92	A	211	THR	0	0.025	0.005	20.006	0.060	0.060	0.000	0.000	0.000	0.000
93	A	212	GLY	0	0.021	0.020	20.520	0.004	0.004	0.000	0.000	0.000	0.000
94	A	213	ALA	0	-0.032	-0.007	17.343	0.046	0.046	0.000	0.000	0.000	0.000
95	A	214	GLY	0	-0.023	-0.032	15.077	0.236	0.236	0.000	0.000	0.000	0.000
96	A	215	LYS	1	0.871	0.954	13.648	-0.931	-0.931	0.000	0.000	0.000	0.000
97	A	216	PRO	0	0.067	0.007	13.982	-0.032	-0.032	0.000	0.000	0.000	0.000
98	A	217	GLY	0	0.036	0.019	11.263	0.152	0.152	0.000	0.000	0.000	0.000
99	A	218	ASP	-1	-0.816	-0.879	9.789	1.604	1.604	0.000	0.000	0.000	0.000
100	A	219	SER	0	-0.008	-0.021	8.181	0.449	0.449	0.000	0.000	0.000	0.000
101	A	220	GLY	0	-0.009	-0.020	4.243	-0.660	-0.650	-0.002	-0.014	0.006	0.000
102	A	221	ARG	1	0.834	0.927	3.443	-2.065	-1.322	0.020	-0.192	-0.572	-0.001
103	A	222	PRO	0	0.004	0.004	2.901	-4.009	-2.343	1.075	-0.522	-2.219	0.001
104	A	223	ILE	0	-0.001	-0.002	5.039	-0.362	-0.304	-0.002	-0.017	-0.039	0.000
105	A	224	PHE	0	0.012	0.001	6.242	0.149	0.149	0.000	0.000	0.000	0.000
106	A	225	ASP	-1	-0.751	-0.844	9.301	1.178	1.178	0.000	0.000	0.000	0.000
107	A	226	ASN	0	0.034	0.006	11.656	0.264	0.264	0.000	0.000	0.000	0.000
108	A	227	LYS	1	0.835	0.896	13.155	-1.263	-1.263	0.000	0.000	0.000	0.000
109	A	228	GLY	0	0.010	0.003	9.144	-0.192	-0.192	0.000	0.000	0.000	0.000
110	A	229	ARG	1	0.765	0.873	7.445	-0.421	-0.421	0.000	0.000	0.000	0.000
111	A	230	VAL	0	-0.022	-0.018	3.557	-0.587	0.163	0.180	-0.166	-0.764	0.000
112	A	231	VAL	0	-0.013	-0.011	6.940	-0.952	-0.952	0.000	0.000	0.000	0.000
113	A	232	ALA	0	-0.012	-0.020	8.440	-0.672	-0.672	0.000	0.000	0.000	0.000
114	A	233	ILE	0	-0.018	-0.003	2.842	0.424	1.175	0.106	-0.128	-0.729	0.000
115	A	234	VAL	0	0.020	0.023	6.436	-0.625	-0.625	0.000	0.000	0.000	0.000
116	A	235	LEU	0	-0.026	-0.001	8.496	-0.953	-0.953	0.000	0.000	0.000	0.000
117	A	236	GLY	0	0.033	0.010	10.896	-0.126	-0.126	0.000	0.000	0.000	0.000
118	A	237	GLY	0	0.006	0.010	13.877	0.168	0.168	0.000	0.000	0.000	0.000
119	A	238	ALA	0	0.039	0.052	17.108	-0.045	-0.045	0.000	0.000	0.000	0.000
120	A	239	ASN	0	-0.013	-0.018	20.908	0.105	0.105	0.000	0.000	0.000	0.000
121	A	240	GLU	-1	-0.771	-0.840	22.948	0.110	0.110	0.000	0.000	0.000	0.000
122	A	241	GLY	0	0.027	0.017	25.741	0.004	0.004	0.000	0.000	0.000	0.000
123	A	242	SER	0	-0.013	-0.014	25.940	0.007	0.007	0.000	0.000	0.000	0.000
124	A	243	ARG	1	0.854	0.927	20.160	-0.521	-0.521	0.000	0.000	0.000	0.000
125	A	244	THR	0	0.033	0.010	18.062	-0.074	-0.074	0.000	0.000	0.000	0.000
126	A	245	ALA	0	0.011	0.017	18.835	0.106	0.106	0.000	0.000	0.000	0.000
127	A	246	LEU	0	-0.034	-0.023	12.460	-0.067	-0.067	0.000	0.000	0.000	0.000
128	A	247	SER	0	0.019	0.022	14.699	-0.064	-0.064	0.000	0.000	0.000	0.000
129	A	248	VAL	0	0.004	-0.014	10.653	-0.053	-0.053	0.000	0.000	0.000	0.000
130	A	249	VAL	0	0.029	0.022	7.874	-0.066	-0.066	0.000	0.000	0.000	0.000
131	A	250	THR	0	-0.005	-0.018	9.181	0.474	0.474	0.000	0.000	0.000	0.000
132	A	251	TRP	0	0.060	0.030	5.486	-0.124	-0.124	0.000	0.000	0.000	0.000
133	A	252	ASN	0	-0.017	-0.019	12.325	0.252	0.252	0.000	0.000	0.000	0.000
134	A	253	LYS	1	0.960	0.961	16.147	-0.078	-0.078	0.000	0.000	0.000	0.000
135	A	254	ASP	-1	-0.850	-0.901	15.097	-0.381	-0.381	0.000	0.000	0.000	0.000
136	A	255	MET	0	-0.002	0.017	15.087	-0.138	-0.138	0.000	0.000	0.000	0.000
137	A	256	VAL	0	-0.008	-0.011	10.302	0.086	0.086	0.000	0.000	0.000	0.000
138	A	257	THR	0	-0.034	-0.017	12.515	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	258	ARG	1	0.861	0.933	12.395	1.055	1.055	0.000	0.000	0.000	0.000
140	A	259	VAL	0	0.005	0.009	14.115	0.087	0.087	0.000	0.000	0.000	0.000
141	A	260	THR	0	0.005	-0.014	15.281	-0.062	-0.062	0.000	0.000	0.000	0.000
142	A	261	PRO	0	-0.015	0.005	17.496	0.002	0.002	0.000	0.000	0.000	0.000
143	A	262	GLU	-1	-0.866	-0.915	20.593	-0.234	-0.234	0.000	0.000	0.000	0.000
144	A	263	GLY	0	0.028	0.009	23.313	0.043	0.043	0.000	0.000	0.000	0.000
145	A	264	SER	0	-0.110	-0.080	17.926	0.049	0.049	0.000	0.000	0.000	0.000
146	A	265	GLU	-1	-0.892	-0.929	17.737	-0.361	-0.361	0.000	0.000	0.000	0.000
147	A	266	GLU	-1	-0.926	-0.987	13.747	-1.397	-1.397	0.000	0.000	0.000	0.000
148	A	267	TRP	0	-0.017	0.006	10.644	-0.014	-0.014	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:119:CYS)