FMO DATABASE

FMODB ID: VRN21

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1365241.574891
FMO2-HF: Nuclear repulsion	1307905.301044
FMO2-HF: Total energy	-57336.273848
FMO2-MP2: Total energy	-57502.433781

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.
-33.606	-23.278	19.679	-8.365	-21.642	0.03

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 : 0.011 / q_NPA : 0.014

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	0.057	0.037	1.904	-11.813	-14.950	12.383	-3.831	-5.415	0.062
4	A	122	GLU	-1	-0.895	-0.969	3.330	-2.724	-2.934	0.131	0.916	-0.837	-0.001
5	A	123	VAL	0	-0.028	-0.025	3.943	-0.432	-0.348	0.003	-0.004	-0.082	0.000
6	A	124	LYS	1	0.919	0.979	6.522	-0.162	-0.162	0.000	0.000	0.000	0.000
7	A	125	HIS	0	0.030	0.007	10.317	-0.278	-0.278	0.000	0.000	0.000	0.000
8	A	126	GLU	-1	-0.894	-0.936	13.215	-0.396	-0.396	0.000	0.000	0.000	0.000
9	A	127	GLY	0	0.011	0.019	15.263	0.065	0.065	0.000	0.000	0.000	0.000
10	A	128	LYS	1	0.886	0.927	14.732	0.276	0.276	0.000	0.000	0.000	0.000
11	A	129	VAL	0	-0.012	0.001	9.004	-0.247	-0.247	0.000	0.000	0.000	0.000
12	A	130	THR	0	-0.033	-0.036	9.860	0.070	0.070	0.000	0.000	0.000	0.000
13	A	131	GLY	0	-0.005	-0.003	7.112	-0.045	-0.045	0.000	0.000	0.000	0.000
14	A	132	TYR	0	-0.054	-0.011	3.843	-0.250	2.014	-0.019	-1.074	-1.170	-0.002
17	A	136	VAL	0	-0.003	-0.022	2.708	-2.841	0.766	3.256	-2.299	-4.563	-0.011
18	A	137	GLY	0	0.003	0.004	4.768	-0.779	-0.640	0.009	-0.016	-0.132	0.000
19	A	138	ASP	-1	-0.883	-0.936	7.644	-0.856	-0.856	0.000	0.000	0.000	0.000
20	A	139	LYS	1	0.929	0.958	8.298	1.236	1.236	0.000	0.000	0.000	0.000
21	A	140	VAL	0	0.042	0.027	4.427	-0.586	-0.290	-0.001	-0.065	-0.230	0.000
22	A	141	MET	0	-0.062	-0.040	3.457	0.753	1.819	0.007	-0.288	-0.785	0.000
23	A	142	LYS	1	0.959	0.979	2.685	-2.276	-2.638	0.625	0.852	-1.116	-0.009
24	A	143	PRO	0	-0.005	0.004	4.416	2.438	2.629	-0.001	-0.015	-0.175	0.000
25	A	144	ALA	0	-0.018	-0.006	7.507	0.163	0.163	0.000	0.000	0.000	0.000
26	A	145	HIS	1	0.809	0.889	10.184	2.190	2.190	0.000	0.000	0.000	0.000
27	A	146	VAL	0	-0.057	-0.023	7.385	0.331	0.331	0.000	0.000	0.000	0.000
28	A	147	LYS	1	0.990	0.993	9.694	1.091	1.091	0.000	0.000	0.000	0.000
29	A	148	GLY	0	0.059	0.036	10.162	-0.127	-0.127	0.000	0.000	0.000	0.000
30	A	149	VAL	0	-0.022	-0.012	9.321	-0.314	-0.314	0.000	0.000	0.000	0.000
31	A	150	ILE	0	0.008	-0.016	4.620	-0.256	-0.149	-0.002	-0.006	-0.099	0.000
32	A	151	ASP	-1	-0.905	-0.936	7.226	0.516	0.516	0.000	0.000	0.000	0.000
33	A	152	ASN	0	0.024	0.001	7.460	0.247	0.247	0.000	0.000	0.000	0.000
34	A	153	ALA	0	0.011	-0.002	9.255	-0.266	-0.266	0.000	0.000	0.000	0.000
35	A	154	ASP	-1	-0.833	-0.927	11.122	-0.263	-0.263	0.000	0.000	0.000	0.000
36	A	155	LEU	0	0.010	-0.014	5.098	-0.293	-0.195	-0.002	-0.003	-0.093	0.000
37	A	156	ALA	0	-0.050	-0.007	9.144	-0.460	-0.460	0.000	0.000	0.000	0.000
38	A	157	LYS	1	0.873	0.929	10.830	0.487	0.487	0.000	0.000	0.000	0.000
39	A	158	LEU	0	0.004	0.033	9.532	0.054	0.054	0.000	0.000	0.000	0.000
40	A	159	ALA	0	0.009	0.007	13.093	-0.070	-0.070	0.000	0.000	0.000	0.000
41	A	160	PHE	0	-0.010	-0.004	6.833	-0.128	-0.128	0.000	0.000	0.000	0.000
42	A	161	LYS	1	0.935	0.981	12.165	1.335	1.335	0.000	0.000	0.000	0.000
43	A	162	LYS	1	0.952	0.964	12.002	1.439	1.439	0.000	0.000	0.000	0.000
44	A	163	SER	0	-0.049	-0.014	12.739	0.331	0.331	0.000	0.000	0.000	0.000
45	A	164	SER	0	0.054	0.014	13.579	-0.199	-0.199	0.000	0.000	0.000	0.000
46	A	165	LYS	1	0.936	0.986	16.076	0.721	0.721	0.000	0.000	0.000	0.000
47	A	166	TYR	0	0.015	-0.025	12.267	0.127	0.127	0.000	0.000	0.000	0.000
48	A	167	ASP	-1	-0.799	-0.863	11.601	-2.451	-2.451	0.000	0.000	0.000	0.000
49	A	168	LEU	0	0.027	0.012	6.930	-0.520	-0.520	0.000	0.000	0.000	0.000
50	A	169	GLU	-1	-0.855	-0.963	8.031	-2.292	-2.292	0.000	0.000	0.000	0.000
51	A	170	CYS	0	-0.036	-0.011	7.493	-0.569	-0.569	0.000	0.000	0.000	0.000
52	A	171	ALA	0	0.054	0.025	8.213	0.566	0.566	0.000	0.000	0.000	0.000
53	A	172	GLN	0	-0.024	-0.016	9.351	-0.109	-0.109	0.000	0.000	0.000	0.000
54	A	173	ILE	0	0.029	0.030	6.071	0.066	0.066	0.000	0.000	0.000	0.000
55	A	174	PRO	0	0.011	0.021	9.468	0.110	0.110	0.000	0.000	0.000	0.000
56	A	175	VAL	0	0.023	-0.022	11.050	0.001	0.001	0.000	0.000	0.000	0.000
57	A	176	HIS	0	-0.017	-0.018	12.095	-0.044	-0.044	0.000	0.000	0.000	0.000
58	A	177	MET	0	0.041	0.032	7.019	0.043	0.043	0.000	0.000	0.000	0.000
59	A	178	ARG	1	0.849	0.932	7.004	0.328	0.328	0.000	0.000	0.000	0.000
60	A	179	SER	0	0.004	0.015	8.330	0.092	0.092	0.000	0.000	0.000	0.000
61	A	180	ASP	-1	-0.931	-0.964	4.407	-0.585	-0.522	-0.002	-0.007	-0.054	0.000
62	A	181	ALA	0	-0.053	-0.006	3.248	-3.308	-2.129	0.028	-0.496	-0.711	-0.004
63	A	182	SER	0	0.011	0.001	2.147	-0.768	-0.162	1.684	-0.822	-1.468	-0.003
64	A	183	LYS	1	0.964	0.972	4.171	-1.347	-1.239	0.000	-0.029	-0.079	0.000
65	A	184	TYR	0	0.023	0.022	7.025	0.876	0.876	0.000	0.000	0.000	0.000
66	A	185	THR	0	-0.016	-0.016	8.264	-0.353	-0.353	0.000	0.000	0.000	0.000
67	A	186	HIS	0	0.033	0.007	11.584	0.052	0.052	0.000	0.000	0.000	0.000
68	A	187	GLU	-1	-0.910	-0.951	14.295	0.511	0.511	0.000	0.000	0.000	0.000
69	A	188	LYS	1	0.807	0.926	13.217	-0.238	-0.238	0.000	0.000	0.000	0.000
70	A	189	PRO	0	0.012	0.019	16.117	-0.100	-0.100	0.000	0.000	0.000	0.000
71	A	190	GLU	-1	-0.830	-0.917	18.635	0.341	0.341	0.000	0.000	0.000	0.000
72	A	191	GLY	0	0.007	0.002	20.273	0.019	0.019	0.000	0.000	0.000	0.000
73	A	192	HIS	0	-0.070	-0.037	18.062	-0.028	-0.028	0.000	0.000	0.000	0.000
74	A	193	TYR	0	-0.024	-0.030	12.675	0.114	0.114	0.000	0.000	0.000	0.000
75	A	194	ASN	0	-0.029	-0.023	11.117	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	195	TRP	0	0.048	0.008	9.028	0.377	0.377	0.000	0.000	0.000	0.000
77	A	196	HIS	0	-0.004	0.006	9.392	-0.251	-0.251	0.000	0.000	0.000	0.000
78	A	197	HIS	1	0.834	0.916	10.949	-1.116	-1.116	0.000	0.000	0.000	0.000
79	A	198	GLY	0	0.043	0.032	14.201	-0.207	-0.207	0.000	0.000	0.000	0.000
80	A	199	ALA	0	0.012	0.008	14.287	0.174	0.174	0.000	0.000	0.000	0.000
81	A	200	VAL	0	-0.004	-0.009	12.580	-0.065	-0.065	0.000	0.000	0.000	0.000
82	A	201	GLN	0	-0.027	-0.005	16.050	0.070	0.070	0.000	0.000	0.000	0.000
83	A	202	TYR	0	-0.048	-0.024	16.542	-0.044	-0.044	0.000	0.000	0.000	0.000
84	A	203	SER	0	0.078	0.032	18.645	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	204	GLY	0	0.024	0.022	21.878	-0.031	-0.031	0.000	0.000	0.000	0.000
86	A	205	GLY	0	-0.031	-0.014	19.485	-0.041	-0.041	0.000	0.000	0.000	0.000
87	A	206	ARG	1	0.859	0.906	18.443	-0.061	-0.061	0.000	0.000	0.000	0.000
88	A	207	PHE	0	0.045	0.020	13.109	0.087	0.087	0.000	0.000	0.000	0.000
89	A	208	THR	0	0.006	-0.006	16.747	-0.089	-0.089	0.000	0.000	0.000	0.000
90	A	209	ILE	0	-0.054	-0.004	14.466	0.120	0.120	0.000	0.000	0.000	0.000
91	A	210	PRO	0	-0.011	0.000	17.865	-0.081	-0.081	0.000	0.000	0.000	0.000
92	A	211	THR	0	0.043	-0.005	19.910	0.027	0.027	0.000	0.000	0.000	0.000
93	A	212	GLY	0	0.036	0.026	19.872	0.010	0.010	0.000	0.000	0.000	0.000
94	A	213	ALA	0	-0.053	-0.013	16.501	0.035	0.035	0.000	0.000	0.000	0.000
95	A	214	GLY	0	-0.049	-0.028	14.518	0.101	0.101	0.000	0.000	0.000	0.000
96	A	215	LYS	1	0.961	1.003	15.040	-0.360	-0.360	0.000	0.000	0.000	0.000
97	A	216	PRO	0	0.063	-0.003	14.250	-0.076	-0.076	0.000	0.000	0.000	0.000
98	A	217	GLY	0	0.007	0.004	11.054	0.132	0.132	0.000	0.000	0.000	0.000
99	A	218	ASP	-1	-0.822	-0.903	9.874	0.465	0.465	0.000	0.000	0.000	0.000
100	A	219	SER	0	-0.013	-0.013	7.847	0.272	0.272	0.000	0.000	0.000	0.000
101	A	220	GLY	0	0.006	-0.008	4.329	-0.595	-0.552	-0.002	-0.017	-0.024	0.000
102	A	221	ARG	1	0.825	0.916	3.234	-2.247	-1.240	0.060	-0.335	-0.732	-0.002
103	A	222	PRO	0	0.005	0.003	3.027	-3.241	-1.703	1.257	-0.524	-2.272	0.000
104	A	223	ILE	0	0.014	0.016	5.099	-0.211	-0.156	-0.002	-0.020	-0.033	0.000
105	A	224	PHE	0	-0.015	-0.027	5.418	0.010	0.181	-0.002	-0.007	-0.163	0.000
106	A	225	ASP	-1	-0.724	-0.846	9.048	1.203	1.203	0.000	0.000	0.000	0.000
107	A	226	ASN	0	0.058	0.003	11.601	0.271	0.271	0.000	0.000	0.000	0.000
108	A	227	LYS	1	0.832	0.926	12.767	-1.183	-1.183	0.000	0.000	0.000	0.000
109	A	228	GLY	0	0.023	0.020	8.706	-0.142	-0.142	0.000	0.000	0.000	0.000
110	A	229	ARG	1	0.769	0.888	7.405	-0.404	-0.404	0.000	0.000	0.000	0.000
111	A	230	VAL	0	-0.006	-0.013	3.450	-0.807	0.006	0.248	-0.188	-0.873	0.000
112	A	231	VAL	0	0.003	0.000	6.751	-0.780	-0.780	0.000	0.000	0.000	0.000
113	A	232	ALA	0	-0.005	-0.024	8.046	-0.576	-0.576	0.000	0.000	0.000	0.000
114	A	233	ILE	0	-0.043	-0.009	3.282	0.276	0.878	0.021	-0.087	-0.536	0.000
115	A	234	VAL	0	0.025	0.017	6.426	-0.399	-0.399	0.000	0.000	0.000	0.000
116	A	235	LEU	0	-0.052	-0.020	8.198	-0.971	-0.971	0.000	0.000	0.000	0.000
117	A	236	GLY	0	0.038	0.002	10.560	-0.073	-0.073	0.000	0.000	0.000	0.000
118	A	237	GLY	0	-0.011	0.002	13.932	0.119	0.119	0.000	0.000	0.000	0.000
119	A	238	ALA	0	0.063	0.063	16.830	-0.021	-0.021	0.000	0.000	0.000	0.000
120	A	239	ASN	0	-0.008	-0.014	20.578	0.096	0.096	0.000	0.000	0.000	0.000
121	A	240	GLU	-1	-0.786	-0.872	22.472	-0.040	-0.040	0.000	0.000	0.000	0.000
122	A	241	GLY	0	0.028	0.019	25.241	0.024	0.024	0.000	0.000	0.000	0.000
123	A	242	SER	0	-0.002	-0.010	25.925	0.005	0.005	0.000	0.000	0.000	0.000
124	A	243	ARG	1	0.903	0.957	19.900	-0.328	-0.328	0.000	0.000	0.000	0.000
125	A	244	THR	0	0.030	0.014	18.112	-0.051	-0.051	0.000	0.000	0.000	0.000
126	A	245	ALA	0	0.004	0.006	19.000	0.084	0.084	0.000	0.000	0.000	0.000
127	A	246	LEU	0	-0.045	-0.033	12.387	-0.065	-0.065	0.000	0.000	0.000	0.000
128	A	247	SER	0	0.013	0.009	14.378	0.020	0.020	0.000	0.000	0.000	0.000
129	A	248	VAL	0	-0.027	-0.029	10.564	-0.109	-0.109	0.000	0.000	0.000	0.000
130	A	249	VAL	0	0.036	0.043	7.737	0.012	0.012	0.000	0.000	0.000	0.000
131	A	250	THR	0	0.023	-0.009	9.036	0.344	0.344	0.000	0.000	0.000	0.000
132	A	251	TRP	0	0.024	0.014	5.528	-0.084	-0.084	0.000	0.000	0.000	0.000
133	A	252	ASN	0	-0.058	-0.038	12.462	0.137	0.137	0.000	0.000	0.000	0.000
134	A	253	LYS	1	0.976	0.969	16.234	-0.111	-0.111	0.000	0.000	0.000	0.000
135	A	254	ASP	-1	-0.890	-0.922	15.618	-0.254	-0.254	0.000	0.000	0.000	0.000
136	A	255	MET	0	0.009	0.022	15.017	-0.068	-0.068	0.000	0.000	0.000	0.000
137	A	256	VAL	0	-0.035	-0.029	10.146	0.051	0.051	0.000	0.000	0.000	0.000
138	A	257	THR	0	-0.004	-0.009	12.738	-0.052	-0.052	0.000	0.000	0.000	0.000
139	A	258	ARG	1	0.917	0.949	12.519	0.986	0.986	0.000	0.000	0.000	0.000
140	A	259	VAL	0	-0.030	0.002	14.052	0.060	0.060	0.000	0.000	0.000	0.000
141	A	260	THR	0	-0.012	-0.021	15.204	-0.078	-0.078	0.000	0.000	0.000	0.000
142	A	261	PRO	0	-0.017	0.003	17.324	0.018	0.018	0.000	0.000	0.000	0.000
143	A	262	GLU	-1	-0.876	-0.914	20.567	-0.286	-0.286	0.000	0.000	0.000	0.000
144	A	263	GLY	0	0.040	0.006	23.447	0.034	0.034	0.000	0.000	0.000	0.000
145	A	264	SER	0	-0.100	-0.074	18.015	0.025	0.025	0.000	0.000	0.000	0.000
146	A	265	GLU	-1	-0.872	-0.912	17.882	-0.458	-0.458	0.000	0.000	0.000	0.000
147	A	266	GLU	-1	-1.002	-1.015	13.956	-1.363	-1.363	0.000	0.000	0.000	0.000
148	A	267	TRP	0	0.023	0.021	10.407	-0.034	-0.034	0.000	0.000	0.000	0.000

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