FMO DATABASE

FMODB ID: 145LZ

Calculation Name: 1DVK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DVK

Chain ID: A

ChEMBL ID:

UniProt ID: P33411

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	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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1508235.117318
FMO2-HF: Nuclear repulsion	1448375.661371
FMO2-HF: Total energy	-59859.455947
FMO2-MP2: Total energy	-60035.253885

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:79:MET)

Summations of interaction energy for fragment #1(A:79:MET)

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.
-5.245	-2.796	3.309	-0.869	-4.891	0.005

Interaction energy analysis for fragmet #1(A:79:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.006

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	81	ILE	0	0.130	0.044	3.084	-2.875	-0.282	3.246	-1.425	-4.415	0.005
4	A	82	GLN	0	-0.027	-0.007	3.971	-1.366	-1.721	0.058	0.600	-0.304	0.000
5	A	83	GLU	-1	-0.836	-0.880	6.289	2.147	2.147	0.000	0.000	0.000	0.000
6	A	84	ALA	0	0.017	0.009	3.512	-0.651	-0.440	0.005	-0.044	-0.172	0.000
7	A	85	ILE	0	0.010	-0.001	5.641	-0.269	-0.269	0.000	0.000	0.000	0.000
8	A	86	ALA	0	-0.004	-0.015	8.387	-0.144	-0.144	0.000	0.000	0.000	0.000
9	A	87	GLN	0	-0.071	-0.040	8.513	-0.191	-0.191	0.000	0.000	0.000	0.000
10	A	88	ASP	-1	-0.814	-0.880	9.214	-0.200	-0.200	0.000	0.000	0.000	0.000
11	A	89	LYS	1	0.797	0.901	11.006	-0.087	-0.087	0.000	0.000	0.000	0.000
12	A	90	THR	0	0.011	-0.008	12.785	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	91	ILE	0	-0.055	-0.010	11.230	0.001	0.001	0.000	0.000	0.000	0.000
14	A	92	SER	0	0.010	0.005	15.611	0.022	0.022	0.000	0.000	0.000	0.000
15	A	93	VAL	0	0.051	0.007	18.845	0.016	0.016	0.000	0.000	0.000	0.000
16	A	94	ILE	0	0.015	0.023	21.362	0.007	0.007	0.000	0.000	0.000	0.000
17	A	95	ILE	0	0.013	0.013	21.460	0.001	0.001	0.000	0.000	0.000	0.000
18	A	96	ASP	-1	-0.798	-0.866	21.802	-0.029	-0.029	0.000	0.000	0.000	0.000
19	A	97	PRO	0	0.041	-0.003	23.183	0.006	0.006	0.000	0.000	0.000	0.000
20	A	98	SER	0	-0.073	-0.048	24.277	0.000	0.000	0.000	0.000	0.000	0.000
21	A	99	GLN	0	-0.021	-0.020	19.306	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	100	ILE	0	-0.062	-0.020	20.774	0.013	0.013	0.000	0.000	0.000	0.000
23	A	101	GLY	0	0.008	-0.005	21.923	0.015	0.015	0.000	0.000	0.000	0.000
24	A	102	SER	0	-0.022	0.009	18.725	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	103	THR	0	0.023	-0.006	16.435	0.027	0.027	0.000	0.000	0.000	0.000
26	A	104	GLU	-1	-0.952	-0.970	13.598	-0.189	-0.189	0.000	0.000	0.000	0.000
27	A	105	GLY	0	0.035	0.018	13.550	0.026	0.026	0.000	0.000	0.000	0.000
28	A	106	LYS	1	0.858	0.932	14.222	-0.232	-0.232	0.000	0.000	0.000	0.000
29	A	107	PRO	0	0.006	-0.016	10.043	0.050	0.050	0.000	0.000	0.000	0.000
30	A	108	LEU	0	0.040	0.025	12.165	0.053	0.053	0.000	0.000	0.000	0.000
31	A	109	LEU	0	0.050	0.027	13.403	0.012	0.012	0.000	0.000	0.000	0.000
32	A	110	SER	0	-0.005	-0.014	14.326	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	111	MET	0	-0.003	0.014	12.506	0.042	0.042	0.000	0.000	0.000	0.000
34	A	112	LYS	1	0.862	0.912	14.902	-0.077	-0.077	0.000	0.000	0.000	0.000
35	A	113	CYS	0	-0.008	0.006	17.750	-0.021	-0.021	0.000	0.000	0.000	0.000
36	A	114	ASN	0	0.026	0.017	16.879	0.021	0.021	0.000	0.000	0.000	0.000
37	A	115	LEU	0	-0.033	-0.030	15.408	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	116	TYR	0	0.007	0.009	19.377	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	117	ILE	0	0.037	0.023	22.497	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	118	HIS	0	-0.018	-0.016	20.043	0.025	0.025	0.000	0.000	0.000	0.000
41	A	119	GLU	-1	-0.834	-0.891	23.538	0.080	0.080	0.000	0.000	0.000	0.000
42	A	120	ILE	0	0.051	0.040	25.210	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	121	LEU	0	-0.068	-0.044	25.679	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	122	SER	0	-0.049	-0.018	26.390	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	123	ARG	1	0.768	0.832	28.458	-0.083	-0.083	0.000	0.000	0.000	0.000
46	A	124	TRP	0	-0.016	-0.008	31.331	0.000	0.000	0.000	0.000	0.000	0.000
47	A	125	LYS	1	0.899	0.945	30.847	-0.112	-0.112	0.000	0.000	0.000	0.000
48	A	126	ALA	0	-0.033	-0.023	32.544	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	127	SER	0	0.016	0.011	34.266	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	128	LEU	0	-0.034	-0.015	35.479	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	129	GLU	-1	-0.974	-0.992	37.564	0.065	0.065	0.000	0.000	0.000	0.000
52	A	130	ALA	0	0.000	0.010	40.508	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	131	TYR	0	-0.005	0.001	37.349	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	132	HIS	1	0.846	0.903	38.892	-0.070	-0.070	0.000	0.000	0.000	0.000
55	A	133	PRO	0	0.093	0.033	38.568	0.007	0.007	0.000	0.000	0.000	0.000
56	A	134	GLU	-1	-0.827	-0.897	38.563	0.091	0.091	0.000	0.000	0.000	0.000
57	A	135	LEU	0	-0.011	0.007	37.570	0.005	0.005	0.000	0.000	0.000	0.000
58	A	136	PHE	0	0.018	0.031	30.705	0.012	0.012	0.000	0.000	0.000	0.000
59	A	137	LEU	0	0.001	-0.008	32.410	0.012	0.012	0.000	0.000	0.000	0.000
60	A	138	ASP	-1	-0.788	-0.903	32.471	0.151	0.151	0.000	0.000	0.000	0.000
61	A	139	THR	0	-0.025	-0.019	30.664	0.007	0.007	0.000	0.000	0.000	0.000
62	A	140	LYS	1	0.933	0.973	28.119	-0.162	-0.162	0.000	0.000	0.000	0.000
63	A	141	LYS	1	0.846	0.919	27.683	-0.138	-0.138	0.000	0.000	0.000	0.000
64	A	142	ALA	0	0.003	0.008	28.144	0.017	0.017	0.000	0.000	0.000	0.000
65	A	143	LEU	0	0.026	0.005	25.705	0.010	0.010	0.000	0.000	0.000	0.000
66	A	144	PHE	0	-0.023	0.007	21.946	0.024	0.024	0.000	0.000	0.000	0.000
67	A	145	PRO	0	-0.002	-0.010	21.938	0.037	0.037	0.000	0.000	0.000	0.000
68	A	146	LEU	0	0.034	0.030	20.798	0.036	0.036	0.000	0.000	0.000	0.000
69	A	147	LEU	0	0.021	0.005	19.988	0.030	0.030	0.000	0.000	0.000	0.000
70	A	148	LEU	0	-0.018	0.001	16.369	0.057	0.057	0.000	0.000	0.000	0.000
71	A	149	GLN	0	0.008	-0.005	15.965	0.065	0.065	0.000	0.000	0.000	0.000
72	A	150	LEU	0	-0.033	-0.002	15.662	0.048	0.048	0.000	0.000	0.000	0.000
73	A	151	ARG	1	0.856	0.919	13.114	-0.438	-0.438	0.000	0.000	0.000	0.000
74	A	152	ARG	1	0.909	0.956	11.418	-0.722	-0.722	0.000	0.000	0.000	0.000
75	A	153	ASN	0	0.030	0.024	10.549	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	154	GLN	0	-0.021	-0.028	13.087	-0.039	-0.039	0.000	0.000	0.000	0.000
77	A	155	LEU	0	-0.002	0.025	14.844	-0.039	-0.039	0.000	0.000	0.000	0.000
78	A	156	ALA	0	0.046	0.024	17.464	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	157	PRO	0	0.053	-0.002	17.920	0.006	0.006	0.000	0.000	0.000	0.000
80	A	158	ASP	-1	-0.829	-0.910	19.983	0.084	0.084	0.000	0.000	0.000	0.000
81	A	159	LEU	0	-0.013	-0.003	22.192	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	160	LEU	0	-0.024	-0.012	17.510	0.004	0.004	0.000	0.000	0.000	0.000
83	A	161	ILE	0	0.026	0.021	21.546	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	162	SER	0	0.017	0.003	23.784	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	163	LEU	0	-0.024	-0.009	22.328	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	164	ALA	0	0.036	0.008	22.237	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	165	THR	0	-0.004	-0.002	24.267	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	166	VAL	0	-0.056	-0.022	27.685	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	167	LEU	0	-0.030	-0.025	23.589	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	168	TYR	0	0.020	0.009	26.171	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	169	HIS	0	-0.003	-0.025	27.506	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	170	LEU	0	-0.025	-0.002	29.531	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	171	GLN	0	-0.039	-0.020	24.160	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	172	GLN	0	-0.021	0.004	29.276	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	173	PRO	0	0.058	0.026	33.100	0.001	0.001	0.000	0.000	0.000	0.000
96	A	174	LYS	1	0.907	0.949	36.171	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	175	GLU	-1	-0.853	-0.918	33.520	0.024	0.024	0.000	0.000	0.000	0.000
98	A	176	ILE	0	0.086	0.046	35.577	0.004	0.004	0.000	0.000	0.000	0.000
99	A	177	ASN	0	0.001	-0.018	36.961	0.005	0.005	0.000	0.000	0.000	0.000
100	A	178	LEU	0	0.015	0.023	35.395	0.002	0.002	0.000	0.000	0.000	0.000
101	A	179	ALA	0	0.036	0.028	32.844	0.004	0.004	0.000	0.000	0.000	0.000
102	A	180	VAL	0	0.025	0.008	33.974	0.007	0.007	0.000	0.000	0.000	0.000
103	A	181	GLN	0	0.020	0.006	36.594	0.002	0.002	0.000	0.000	0.000	0.000
104	A	182	SER	0	-0.041	-0.034	31.596	0.000	0.000	0.000	0.000	0.000	0.000
105	A	183	TYR	0	-0.069	-0.062	31.834	0.003	0.003	0.000	0.000	0.000	0.000
106	A	184	MET	0	0.018	0.004	33.469	0.004	0.004	0.000	0.000	0.000	0.000
107	A	185	LYS	1	0.954	1.001	33.224	-0.045	-0.045	0.000	0.000	0.000	0.000
108	A	186	LEU	0	0.045	0.031	28.008	0.004	0.004	0.000	0.000	0.000	0.000
109	A	187	SER	0	-0.104	-0.055	31.512	0.006	0.006	0.000	0.000	0.000	0.000
110	A	188	ILE	0	-0.032	-0.029	33.893	0.001	0.001	0.000	0.000	0.000	0.000
111	A	189	GLY	0	-0.015	0.009	31.322	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	190	ASN	0	0.003	-0.003	31.578	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	191	VAL	0	-0.014	0.002	27.285	0.006	0.006	0.000	0.000	0.000	0.000
114	A	192	ALA	0	-0.054	-0.020	29.077	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	193	TRP	0	0.043	0.019	24.742	0.006	0.006	0.000	0.000	0.000	0.000
116	A	194	PRO	0	-0.014	-0.020	27.982	0.000	0.000	0.000	0.000	0.000	0.000
117	A	195	ILE	0	-0.032	-0.022	30.848	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	196	GLY	0	0.002	0.014	34.025	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	197	VAL	0	-0.002	0.006	29.746	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	218	ALA	0	0.037	0.030	29.350	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	219	ASN	0	-0.075	-0.069	30.067	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	220	ILE	0	0.008	0.006	26.046	0.005	0.005	0.000	0.000	0.000	0.000
123	A	221	MET	0	-0.028	-0.006	26.141	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	222	ILE	0	-0.038	-0.020	27.254	0.012	0.012	0.000	0.000	0.000	0.000
125	A	223	ASP	-1	-0.773	-0.877	26.201	0.208	0.208	0.000	0.000	0.000	0.000
126	A	224	GLU	-1	-0.898	-0.942	28.453	0.145	0.145	0.000	0.000	0.000	0.000
127	A	225	ARG	1	0.969	0.972	24.004	-0.268	-0.268	0.000	0.000	0.000	0.000
128	A	226	THR	0	-0.069	-0.067	25.335	0.008	0.008	0.000	0.000	0.000	0.000
129	A	227	ARG	1	0.983	1.001	26.976	-0.124	-0.124	0.000	0.000	0.000	0.000
130	A	228	LEU	0	-0.010	0.002	29.292	-0.008	-0.008	0.000	0.000	0.000	0.000
131	A	229	TRP	0	0.040	0.018	24.109	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	230	ILE	0	0.039	0.014	28.216	-0.009	-0.009	0.000	0.000	0.000	0.000
133	A	231	THR	0	-0.016	0.012	30.207	-0.015	-0.015	0.000	0.000	0.000	0.000
134	A	232	SER	0	-0.017	-0.033	30.281	-0.012	-0.012	0.000	0.000	0.000	0.000
135	A	233	ILE	0	0.019	0.023	26.469	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	234	LYS	1	0.999	1.004	30.652	-0.098	-0.098	0.000	0.000	0.000	0.000
137	A	235	ARG	1	0.865	0.928	33.533	-0.130	-0.130	0.000	0.000	0.000	0.000
138	A	236	LEU	0	0.018	0.013	27.777	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	237	ILE	0	0.009	0.011	32.042	-0.006	-0.006	0.000	0.000	0.000	0.000
140	A	238	THR	0	-0.032	-0.016	34.046	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	239	PHE	0	-0.003	0.015	32.263	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	240	GLU	-1	-0.720	-0.841	31.103	0.070	0.070	0.000	0.000	0.000	0.000
143	A	241	GLU	-1	-0.941	-0.960	34.659	0.048	0.048	0.000	0.000	0.000	0.000
144	A	242	TRP	0	0.013	0.018	37.700	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	243	TYR	0	-0.018	-0.030	34.377	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	244	THR	0	-0.070	-0.054	35.330	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	245	SER	0	-0.037	-0.014	37.974	-0.006	-0.006	0.000	0.000	0.000	0.000
148	A	246	ASN	0	-0.093	-0.040	40.845	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	247	HIS	0	0.020	0.024	37.621	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:79:MET)