FMO DATABASE

FMODB ID: LL279

Calculation Name: 1DVK-A-Xray309

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	152
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1518222.569281
FMO2-HF: Nuclear repulsion	1458173.731374
FMO2-HF: Total energy	-60048.837907
FMO2-MP2: Total energy	-60225.384395

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.
-4.575	-5.262	8.101	-1.807	-5.606	0.01

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 : 0.036 / q_NPA : 0.017

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	0.114	0.036	2.550	-1.858	-2.378	8.025	-2.401	-5.103	0.010
4	A	82	GLN	0	-0.022	-0.014	3.956	-1.416	-1.791	0.070	0.636	-0.331	0.000
5	A	83	GLU	-1	-0.932	-0.965	5.874	1.325	1.325	0.000	0.000	0.000	0.000
6	A	84	ALA	0	0.010	0.006	3.475	-0.604	-0.396	0.006	-0.042	-0.172	0.000
7	A	85	ILE	0	0.003	0.003	5.627	-0.191	-0.191	0.000	0.000	0.000	0.000
8	A	86	ALA	0	-0.005	-0.017	8.538	-0.143	-0.143	0.000	0.000	0.000	0.000
9	A	87	GLN	0	-0.085	-0.040	8.844	-0.207	-0.207	0.000	0.000	0.000	0.000
10	A	88	ASP	-1	-0.802	-0.898	9.509	-0.027	-0.027	0.000	0.000	0.000	0.000
11	A	89	LYS	1	0.845	0.929	11.197	-0.084	-0.084	0.000	0.000	0.000	0.000
12	A	90	THR	0	0.010	0.011	13.392	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	91	ILE	0	-0.050	-0.008	11.679	0.006	0.006	0.000	0.000	0.000	0.000
14	A	92	SER	0	-0.005	-0.004	15.918	0.007	0.007	0.000	0.000	0.000	0.000
15	A	93	VAL	0	0.055	0.004	19.107	0.020	0.020	0.000	0.000	0.000	0.000
16	A	94	ILE	0	0.012	0.018	21.592	0.005	0.005	0.000	0.000	0.000	0.000
17	A	95	ILE	0	-0.012	0.001	21.781	0.010	0.010	0.000	0.000	0.000	0.000
18	A	96	ASP	-1	-0.809	-0.860	22.239	0.030	0.030	0.000	0.000	0.000	0.000
19	A	97	PRO	0	0.039	0.000	23.337	0.009	0.009	0.000	0.000	0.000	0.000
20	A	98	SER	0	-0.073	-0.057	24.580	0.000	0.000	0.000	0.000	0.000	0.000
21	A	99	GLN	0	-0.020	-0.026	18.318	0.016	0.016	0.000	0.000	0.000	0.000
22	A	100	ILE	0	-0.045	-0.010	20.537	0.014	0.014	0.000	0.000	0.000	0.000
23	A	101	GLY	0	0.008	-0.004	21.763	0.011	0.011	0.000	0.000	0.000	0.000
24	A	102	SER	0	-0.038	0.003	18.322	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	103	THR	0	0.030	-0.006	15.977	0.021	0.021	0.000	0.000	0.000	0.000
26	A	104	GLU	-1	-0.949	-0.968	13.416	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	105	GLY	0	0.030	0.020	13.306	0.058	0.058	0.000	0.000	0.000	0.000
28	A	106	LYS	1	0.858	0.940	14.026	-0.235	-0.235	0.000	0.000	0.000	0.000
29	A	107	PRO	0	-0.011	-0.026	9.843	0.026	0.026	0.000	0.000	0.000	0.000
30	A	108	LEU	0	0.059	0.036	11.992	0.036	0.036	0.000	0.000	0.000	0.000
31	A	109	LEU	0	0.043	0.022	13.558	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	110	SER	0	-0.014	-0.023	14.233	-0.026	-0.026	0.000	0.000	0.000	0.000
33	A	111	MET	0	-0.006	0.016	12.647	0.018	0.018	0.000	0.000	0.000	0.000
34	A	112	LYS	1	0.893	0.932	15.020	-0.157	-0.157	0.000	0.000	0.000	0.000
35	A	113	CYS	0	-0.010	0.010	17.944	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	114	ASN	0	0.047	0.018	16.918	0.014	0.014	0.000	0.000	0.000	0.000
37	A	115	LEU	0	-0.046	-0.039	15.633	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	116	TYR	0	0.038	0.023	19.464	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	117	ILE	0	0.035	0.026	22.572	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	118	HIS	0	-0.054	-0.043	19.714	0.016	0.016	0.000	0.000	0.000	0.000
41	A	119	GLU	-1	-0.830	-0.895	23.539	0.084	0.084	0.000	0.000	0.000	0.000
42	A	120	ILE	0	0.052	0.037	25.282	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	121	LEU	0	-0.071	-0.046	25.450	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	122	SER	0	-0.052	-0.018	26.420	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	123	ARG	1	0.841	0.904	28.460	-0.089	-0.089	0.000	0.000	0.000	0.000
46	A	124	TRP	0	-0.006	-0.002	31.356	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	125	LYS	1	0.884	0.934	30.712	-0.100	-0.100	0.000	0.000	0.000	0.000
48	A	126	ALA	0	-0.022	-0.014	32.535	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	127	SER	0	0.022	0.017	34.264	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	128	LEU	0	-0.042	-0.017	35.214	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	129	GLU	-1	-0.963	-0.989	37.520	0.057	0.057	0.000	0.000	0.000	0.000
52	A	130	ALA	0	0.002	0.012	40.492	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	131	TYR	0	-0.021	-0.009	37.216	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	132	HIS	1	0.869	0.934	38.858	-0.063	-0.063	0.000	0.000	0.000	0.000
55	A	133	PRO	0	0.070	0.022	38.487	0.006	0.006	0.000	0.000	0.000	0.000
56	A	134	GLU	-1	-0.857	-0.944	38.445	0.080	0.080	0.000	0.000	0.000	0.000
57	A	135	LEU	0	0.022	0.028	37.373	0.005	0.005	0.000	0.000	0.000	0.000
58	A	136	PHE	0	0.004	0.025	30.446	0.011	0.011	0.000	0.000	0.000	0.000
59	A	137	LEU	0	-0.011	-0.018	32.063	0.011	0.011	0.000	0.000	0.000	0.000
60	A	138	ASP	-1	-0.828	-0.926	32.290	0.124	0.124	0.000	0.000	0.000	0.000
61	A	139	THR	0	-0.042	-0.030	30.507	0.006	0.006	0.000	0.000	0.000	0.000
62	A	140	LYS	1	0.900	0.964	28.340	-0.131	-0.131	0.000	0.000	0.000	0.000
63	A	141	LYS	1	0.932	0.964	27.514	-0.123	-0.123	0.000	0.000	0.000	0.000
64	A	142	ALA	0	0.009	0.015	28.140	0.014	0.014	0.000	0.000	0.000	0.000
65	A	143	LEU	0	0.018	-0.001	25.571	0.009	0.009	0.000	0.000	0.000	0.000
66	A	144	PHE	0	-0.022	0.008	21.912	0.022	0.022	0.000	0.000	0.000	0.000
67	A	145	PRO	0	-0.012	-0.016	21.878	0.032	0.032	0.000	0.000	0.000	0.000
68	A	146	LEU	0	0.041	0.036	20.736	0.030	0.030	0.000	0.000	0.000	0.000
69	A	147	LEU	0	0.021	0.004	20.018	0.028	0.028	0.000	0.000	0.000	0.000
70	A	148	LEU	0	-0.020	0.002	16.291	0.052	0.052	0.000	0.000	0.000	0.000
71	A	149	GLN	0	0.005	-0.008	16.045	0.055	0.055	0.000	0.000	0.000	0.000
72	A	150	LEU	0	-0.033	0.000	15.669	0.045	0.045	0.000	0.000	0.000	0.000
73	A	151	ARG	1	0.878	0.956	12.959	-0.359	-0.359	0.000	0.000	0.000	0.000
74	A	152	ARG	1	0.907	0.948	11.470	-0.597	-0.597	0.000	0.000	0.000	0.000
75	A	153	ASN	0	0.046	0.030	10.463	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	154	GLN	0	-0.023	-0.029	12.754	-0.073	-0.073	0.000	0.000	0.000	0.000
77	A	155	LEU	0	0.009	0.022	14.794	-0.040	-0.040	0.000	0.000	0.000	0.000
78	A	156	ALA	0	0.035	0.019	17.292	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	157	PRO	0	0.042	-0.008	17.727	0.007	0.007	0.000	0.000	0.000	0.000
80	A	158	ASP	-1	-0.813	-0.899	19.815	0.084	0.084	0.000	0.000	0.000	0.000
81	A	159	LEU	0	-0.020	-0.009	22.059	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	160	LEU	0	-0.035	-0.014	17.329	0.003	0.003	0.000	0.000	0.000	0.000
83	A	161	ILE	0	0.031	0.021	21.392	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	162	SER	0	0.012	0.001	23.640	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	163	LEU	0	-0.025	-0.007	22.165	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	164	ALA	0	0.045	0.009	22.107	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	165	THR	0	-0.005	-0.015	24.132	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	166	VAL	0	-0.046	-0.016	27.530	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	167	LEU	0	-0.044	-0.038	23.806	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	168	TYR	0	0.038	0.020	26.367	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	169	HIS	0	0.001	-0.017	27.727	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	170	LEU	0	-0.036	-0.006	29.634	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	171	GLN	0	-0.042	-0.020	24.415	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	172	GLN	0	-0.011	0.013	29.653	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	173	PRO	0	0.060	0.028	33.371	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	174	LYS	1	0.910	0.949	36.415	-0.027	-0.027	0.000	0.000	0.000	0.000
97	A	175	GLU	-1	-0.872	-0.934	34.040	0.042	0.042	0.000	0.000	0.000	0.000
98	A	176	ILE	0	0.098	0.052	35.751	0.004	0.004	0.000	0.000	0.000	0.000
99	A	177	ASN	0	0.004	-0.019	37.155	0.004	0.004	0.000	0.000	0.000	0.000
100	A	178	LEU	0	0.011	0.020	35.444	0.001	0.001	0.000	0.000	0.000	0.000
101	A	179	ALA	0	0.038	0.041	32.952	0.004	0.004	0.000	0.000	0.000	0.000
102	A	180	VAL	0	0.021	0.009	33.863	0.006	0.006	0.000	0.000	0.000	0.000
103	A	181	GLN	0	0.016	0.005	36.487	0.001	0.001	0.000	0.000	0.000	0.000
104	A	182	SER	0	-0.048	-0.044	31.444	0.000	0.000	0.000	0.000	0.000	0.000
105	A	183	TYR	0	-0.057	-0.042	31.894	0.002	0.002	0.000	0.000	0.000	0.000
106	A	184	MET	0	0.028	0.005	33.369	0.003	0.003	0.000	0.000	0.000	0.000
107	A	185	LYS	1	0.953	1.001	33.096	-0.053	-0.053	0.000	0.000	0.000	0.000
108	A	186	LEU	0	0.046	0.034	27.872	0.003	0.003	0.000	0.000	0.000	0.000
109	A	187	SER	0	-0.109	-0.063	31.346	0.004	0.004	0.000	0.000	0.000	0.000
110	A	188	ILE	0	-0.025	-0.019	33.780	0.000	0.000	0.000	0.000	0.000	0.000
111	A	189	GLY	0	-0.030	0.001	31.284	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	190	ASN	0	-0.004	-0.007	31.470	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	191	VAL	0	-0.002	0.000	27.107	0.006	0.006	0.000	0.000	0.000	0.000
114	A	192	ALA	0	-0.060	-0.019	28.931	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	193	TRP	0	0.044	0.026	24.869	0.008	0.008	0.000	0.000	0.000	0.000
116	A	194	PRO	0	-0.015	-0.022	27.724	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	195	ILE	0	-0.015	-0.011	30.647	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	196	GLY	0	-0.006	0.002	34.077	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	197	VAL	0	-0.029	-0.013	29.708	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	198	NME	0	0.031	0.028	32.955	0.000	0.000	0.000	0.000	0.000	0.000
121	A	217	ACE	0	0.030	0.000	27.439	0.001	0.001	0.000	0.000	0.000	0.000
122	A	218	ALA	0	-0.038	-0.014	28.012	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	219	ASN	0	-0.009	-0.016	29.925	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	220	ILE	0	-0.001	0.014	26.166	0.005	0.005	0.000	0.000	0.000	0.000
125	A	221	MET	0	-0.008	-0.002	26.091	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	222	ILE	0	-0.049	-0.025	27.211	0.011	0.011	0.000	0.000	0.000	0.000
127	A	223	ASP	-1	-0.851	-0.927	26.396	0.164	0.164	0.000	0.000	0.000	0.000
128	A	224	GLU	-1	-0.890	-0.948	28.401	0.123	0.123	0.000	0.000	0.000	0.000
129	A	225	ARG	1	0.983	0.982	23.997	-0.216	-0.216	0.000	0.000	0.000	0.000
130	A	226	THR	0	-0.022	-0.030	25.259	0.010	0.010	0.000	0.000	0.000	0.000
131	A	227	ARG	1	0.990	1.000	26.920	-0.108	-0.108	0.000	0.000	0.000	0.000
132	A	228	LEU	0	0.000	0.001	29.065	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	229	TRP	0	0.034	0.020	24.219	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	230	ILE	0	0.040	0.014	28.397	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	231	THR	0	-0.008	0.006	30.184	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	232	SER	0	-0.015	-0.033	30.213	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	233	ILE	0	0.016	0.021	26.657	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	234	LYS	1	1.009	1.008	30.634	-0.091	-0.091	0.000	0.000	0.000	0.000
139	A	235	ARG	1	0.850	0.913	33.435	-0.115	-0.115	0.000	0.000	0.000	0.000
140	A	236	LEU	0	0.013	0.013	27.717	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	237	ILE	0	0.012	0.015	32.076	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	238	THR	0	-0.042	-0.012	34.130	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	239	PHE	0	0.009	0.020	32.564	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	240	GLU	-1	-0.783	-0.898	32.354	0.072	0.072	0.000	0.000	0.000	0.000
145	A	241	GLU	-1	-0.952	-0.971	34.772	0.050	0.050	0.000	0.000	0.000	0.000
146	A	242	TRP	0	0.005	0.011	38.065	-0.003	-0.003	0.000	0.000	0.000	0.000
147	A	243	TYR	0	0.003	-0.016	34.631	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	244	THR	0	-0.072	-0.048	35.561	-0.005	-0.005	0.000	0.000	0.000	0.000
149	A	245	SER	0	-0.038	-0.016	38.144	-0.005	-0.005	0.000	0.000	0.000	0.000
150	A	246	ASN	0	-0.081	-0.032	41.003	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	247	HIS	0	-0.024	-0.028	38.052	0.003	0.003	0.000	0.000	0.000	0.000
152	A	1	NME	0	0.004	0.025	41.796	-0.002	-0.002	0.000	0.000	0.000	0.000

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