FMO DATABASE

FMODB ID: 82M8Y

Calculation Name: 1VMO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VMO

Chain ID: A

ChEMBL ID:

UniProt ID: P41366

Base Structure: X-ray

Registration Date: 2023-06-20

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	159
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1620522.650078
FMO2-HF: Nuclear repulsion	1556560.883191
FMO2-HF: Total energy	-63961.766887
FMO2-MP2: Total energy	-64145.53075

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:1:ARG)

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

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.
33.384	40.545	9.69	-6.559	-10.292	-0.069

Interaction energy analysis for fragmet #1(A:1:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.896 / q_NPA : 0.941

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	3	ARG	1	0.802	0.871	1.986	0.295	2.539	6.359	-4.147	-4.456	-0.047
4	A	4	GLU	-1	-0.809	-0.877	2.485	-45.763	-43.323	1.934	-1.546	-2.827	-0.018
5	A	5	TYR	0	-0.014	-0.027	2.308	4.416	5.702	1.309	-0.520	-2.075	-0.002
6	A	6	THR	0	0.005	-0.002	5.339	-1.438	-1.438	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.012	-0.010	8.145	1.074	1.074	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.013	-0.012	7.772	-1.645	-1.645	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.016	-0.005	10.161	1.269	1.269	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.008	-0.014	13.486	-0.440	-0.440	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.023	0.009	16.025	0.296	0.296	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.032	-0.009	19.841	-0.224	-0.224	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.033	-0.038	22.352	0.295	0.295	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.052	0.039	21.763	-0.539	-0.539	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.008	0.014	22.452	0.141	0.141	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.054	-0.041	20.310	-1.117	-1.117	0.000	0.000	0.000	0.000
17	A	17	TRP	0	0.009	0.009	20.451	-0.769	-0.769	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.084	0.044	20.463	-0.393	-0.393	0.000	0.000	0.000	0.000
19	A	19	LYN	0	-0.021	0.010	14.293	-0.447	-0.447	0.000	0.000	0.000	0.000
20	A	20	TRP	0	-0.035	-0.042	11.710	-0.322	-0.322	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.044	0.023	12.295	-0.159	-0.159	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.019	0.012	8.374	-1.686	-1.686	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.840	0.945	4.202	32.782	33.015	-0.001	-0.031	-0.202	0.000
24	A	24	GLN	0	0.028	0.026	6.059	-1.107	-1.107	0.000	0.000	0.000	0.000
25	A	25	PHE	0	0.021	-0.024	3.130	-2.459	-1.501	0.089	-0.315	-0.732	-0.002
26	A	26	CYS	0	0.000	0.031	8.194	0.398	0.398	0.000	0.000	0.000	0.000
27	A	27	HIS	0	0.034	0.034	9.463	-3.655	-3.655	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.052	-0.045	10.579	-1.210	-1.210	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.023	0.007	12.579	0.334	0.334	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.030	-0.036	12.316	-1.447	-1.447	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.079	0.026	14.090	0.562	0.562	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.018	-0.022	15.619	0.005	0.005	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.068	0.041	19.062	0.799	0.799	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.044	-0.020	19.046	-0.984	-0.984	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.025	0.028	20.442	0.598	0.598	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.003	-0.001	20.919	-0.726	-0.726	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.811	0.916	22.464	11.782	11.782	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.031	0.010	24.118	-0.180	-0.180	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.716	-0.834	27.283	-8.838	-8.838	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.027	-0.001	30.683	0.079	0.079	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.080	0.049	33.382	0.074	0.074	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.051	-0.032	35.500	0.058	0.058	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.050	0.012	38.267	-0.117	-0.117	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.006	-0.001	40.940	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.766	0.870	34.880	8.166	8.166	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.886	-0.931	36.472	-7.633	-7.633	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.923	-0.969	33.246	-8.620	-8.620	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.002	-0.003	29.700	-0.085	-0.085	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.004	-0.001	25.522	-0.152	-0.152	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.054	-0.011	22.487	0.013	0.013	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.007	-0.019	22.861	-0.130	-0.130	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.004	-0.006	19.363	-0.483	-0.483	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.014	0.004	16.896	0.432	0.432	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.827	0.894	16.498	13.144	13.144	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.023	-0.014	13.326	0.544	0.544	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.958	0.985	16.605	12.524	12.524	0.000	0.000	0.000	0.000
57	A	58	LEU	0	0.001	-0.004	16.614	0.595	0.595	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.747	-0.827	14.579	-18.744	-18.744	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.006	0.004	18.145	0.163	0.163	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.072	-0.059	14.500	-0.168	-0.168	0.000	0.000	0.000	0.000
61	A	62	VAL	0	0.004	-0.020	15.973	0.472	0.472	0.000	0.000	0.000	0.000
62	A	63	ILE	0	-0.047	-0.012	10.626	-0.739	-0.739	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.747	-0.860	13.169	-14.042	-14.042	0.000	0.000	0.000	0.000
64	A	65	SER	0	-0.033	-0.040	10.568	-1.161	-1.161	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.004	0.025	12.537	0.395	0.395	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.027	0.002	15.212	0.095	0.095	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.040	0.028	18.641	0.019	0.019	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.812	0.917	22.187	10.135	10.135	0.000	0.000	0.000	0.000
69	A	70	TRP	0	0.015	0.016	24.927	0.344	0.344	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.032	0.019	25.964	-0.353	-0.353	0.000	0.000	0.000	0.000
71	A	72	THR	0	-0.018	-0.018	27.744	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	73	TRP	0	-0.043	-0.034	19.118	-0.148	-0.148	0.000	0.000	0.000	0.000
73	A	74	THR	0	0.026	0.020	25.703	0.189	0.189	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.032	0.015	26.014	-0.189	-0.189	0.000	0.000	0.000	0.000
75	A	76	PHE	0	-0.064	-0.043	19.792	-0.151	-0.151	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.040	0.049	24.526	0.311	0.311	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.043	-0.052	23.204	-0.684	-0.684	0.000	0.000	0.000	0.000
78	A	79	CYS	0	-0.028	0.004	20.856	-0.551	-0.551	0.000	0.000	0.000	0.000
79	A	80	PRO	0	0.015	0.008	24.631	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.042	-0.020	26.326	0.274	0.274	0.000	0.000	0.000	0.000
81	A	82	GLY	0	-0.053	-0.010	23.026	-0.307	-0.307	0.000	0.000	0.000	0.000
82	A	83	TYR	0	0.008	-0.015	17.294	-0.421	-0.421	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.004	-0.011	16.651	0.437	0.437	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.042	-0.032	16.609	-0.922	-0.922	0.000	0.000	0.000	0.000
85	A	86	SER	0	-0.058	-0.038	17.524	-0.130	-0.130	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.052	0.016	16.076	0.125	0.125	0.000	0.000	0.000	0.000
87	A	88	SER	0	0.022	0.007	20.127	0.116	0.116	0.000	0.000	0.000	0.000
88	A	89	LEU	0	0.055	0.018	20.610	-0.062	-0.062	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.844	0.944	23.555	9.427	9.427	0.000	0.000	0.000	0.000
90	A	91	SER	0	0.074	0.054	26.028	-0.299	-0.299	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.818	-0.896	28.064	-9.071	-9.071	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.834	0.912	28.778	9.452	9.452	0.000	0.000	0.000	0.000
93	A	94	SER	0	0.067	0.056	29.232	0.195	0.195	0.000	0.000	0.000	0.000
94	A	95	GLN	0	0.009	0.005	31.740	0.081	0.081	0.000	0.000	0.000	0.000
95	A	96	GLY	0	-0.017	-0.011	32.023	-0.262	-0.262	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.003	-0.013	31.472	0.057	0.057	0.000	0.000	0.000	0.000
97	A	98	GLY	0	0.040	0.046	31.687	-0.092	-0.092	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.828	-0.911	27.325	-10.133	-10.133	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.858	-0.942	28.074	-9.292	-9.292	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.076	-0.060	25.789	0.136	0.136	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.021	0.019	24.494	-0.507	-0.507	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.029	-0.022	21.876	0.135	0.135	0.000	0.000	0.000	0.000
103	A	104	ASN	0	0.006	-0.022	24.004	-0.106	-0.106	0.000	0.000	0.000	0.000
104	A	105	ASN	0	-0.052	-0.042	25.639	-0.237	-0.237	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.047	-0.019	19.101	-0.313	-0.313	0.000	0.000	0.000	0.000
106	A	107	GLN	0	-0.020	0.003	23.448	0.522	0.522	0.000	0.000	0.000	0.000
107	A	108	PHE	0	0.009	-0.007	16.916	-0.619	-0.619	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.880	0.941	21.270	11.588	11.588	0.000	0.000	0.000	0.000
109	A	111	SER	0	-0.022	-0.025	20.254	0.231	0.231	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.749	-0.879	22.695	-11.215	-11.215	0.000	0.000	0.000	0.000
111	A	113	GLU	-1	-0.788	-0.858	25.582	-10.804	-10.804	0.000	0.000	0.000	0.000
112	A	114	ALA	0	0.002	0.029	26.382	0.272	0.272	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.032	-0.029	25.576	-0.498	-0.498	0.000	0.000	0.000	0.000
114	A	116	LEU	0	-0.022	-0.008	23.390	0.267	0.267	0.000	0.000	0.000	0.000
115	A	117	VAL	0	0.015	-0.011	25.117	-0.457	-0.457	0.000	0.000	0.000	0.000
116	A	118	GLY	0	0.016	0.011	25.932	0.088	0.088	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.884	-0.931	26.784	-9.292	-9.292	0.000	0.000	0.000	0.000
118	A	120	GLY	0	0.000	-0.017	28.104	-0.229	-0.229	0.000	0.000	0.000	0.000
119	A	121	LEU	0	0.008	0.025	28.877	0.276	0.276	0.000	0.000	0.000	0.000
120	A	122	SER	0	-0.056	-0.050	30.513	-0.173	-0.173	0.000	0.000	0.000	0.000
121	A	123	TRP	0	0.077	0.057	33.028	0.062	0.062	0.000	0.000	0.000	0.000
122	A	124	GLY	0	0.071	0.038	31.329	-0.294	-0.294	0.000	0.000	0.000	0.000
123	A	125	ARG	1	0.869	0.924	30.982	8.555	8.555	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.014	0.007	25.723	-0.188	-0.188	0.000	0.000	0.000	0.000
125	A	127	GLY	0	0.027	0.032	26.121	0.290	0.290	0.000	0.000	0.000	0.000
126	A	128	PRO	0	-0.026	-0.011	24.500	0.000	0.000	0.000	0.000	0.000	0.000
127	A	129	TRP	0	-0.008	-0.008	22.310	-0.406	-0.406	0.000	0.000	0.000	0.000
128	A	130	SER	0	-0.007	0.006	17.586	0.049	0.049	0.000	0.000	0.000	0.000
129	A	131	LYS	1	0.947	0.968	16.663	14.731	14.731	0.000	0.000	0.000	0.000
130	A	132	ARG	1	0.874	0.918	17.703	11.967	11.967	0.000	0.000	0.000	0.000
131	A	133	CYS	0	-0.042	-0.011	8.292	0.992	0.992	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.924	0.974	13.650	18.029	18.029	0.000	0.000	0.000	0.000
133	A	135	ILE	0	0.026	0.020	12.059	-1.824	-1.824	0.000	0.000	0.000	0.000
134	A	136	CYS	0	-0.020	0.000	8.318	-3.462	-3.462	0.000	0.000	0.000	0.000
135	A	137	GLY	0	0.055	0.025	8.090	-1.439	-1.439	0.000	0.000	0.000	0.000
136	A	138	LEU	0	-0.036	0.002	8.892	1.176	1.176	0.000	0.000	0.000	0.000
137	A	139	GLN	0	0.028	0.000	8.594	-2.494	-2.494	0.000	0.000	0.000	0.000
138	A	140	THR	0	0.029	-0.004	10.426	0.372	0.372	0.000	0.000	0.000	0.000
139	A	141	LYS	1	0.791	0.878	13.656	13.840	13.840	0.000	0.000	0.000	0.000
140	A	142	VAL	0	-0.017	-0.013	16.350	0.560	0.560	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.765	-0.873	19.191	-12.151	-12.151	0.000	0.000	0.000	0.000
142	A	144	SER	0	-0.004	-0.013	22.296	0.130	0.130	0.000	0.000	0.000	0.000
143	A	145	PRO	0	-0.029	0.010	19.116	0.378	0.378	0.000	0.000	0.000	0.000
144	A	146	GLN	0	0.049	0.000	22.121	0.046	0.046	0.000	0.000	0.000	0.000
145	A	147	GLY	0	0.012	0.015	24.477	0.377	0.377	0.000	0.000	0.000	0.000
146	A	148	LEU	0	0.028	-0.003	27.438	0.130	0.130	0.000	0.000	0.000	0.000
147	A	149	ARG	1	0.820	0.888	29.264	8.614	8.614	0.000	0.000	0.000	0.000
148	A	150	ASP	-1	-0.862	-0.935	30.080	-8.702	-8.702	0.000	0.000	0.000	0.000
149	A	151	ASP	-1	-0.848	-0.921	28.169	-9.528	-9.528	0.000	0.000	0.000	0.000
150	A	152	THR	0	-0.148	-0.065	23.941	-0.321	-0.321	0.000	0.000	0.000	0.000
151	A	153	ALA	0	0.076	0.040	24.315	0.100	0.100	0.000	0.000	0.000	0.000
152	A	154	LEU	0	-0.055	-0.026	18.090	-0.561	-0.561	0.000	0.000	0.000	0.000
153	A	155	ASN	0	0.013	0.002	20.315	0.499	0.499	0.000	0.000	0.000	0.000
154	A	156	ASN	0	0.001	0.003	17.324	-0.225	-0.225	0.000	0.000	0.000	0.000
155	A	157	VAL	0	-0.011	-0.012	14.904	-0.463	-0.463	0.000	0.000	0.000	0.000
156	A	158	ARG	1	0.833	0.945	10.234	21.393	21.393	0.000	0.000	0.000	0.000
157	A	159	PHE	0	0.038	0.016	10.813	-0.927	-0.927	0.000	0.000	0.000	0.000
158	A	160	PHE	0	-0.034	-0.012	6.193	-1.038	-1.038	0.000	0.000	0.000	0.000
159	A	163	LYS	1	0.908	0.960	8.786	33.802	33.802	0.000	0.000	0.000	0.000

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