FMO DATABASE

FMODB ID: 3N57L

Calculation Name: 1DVO-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DVO

Chain ID: A

ChEMBL ID:

UniProt ID: P29367

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	-1292274.332727
FMO2-HF: Nuclear repulsion	1231616.462995
FMO2-HF: Total energy	-60657.869732
FMO2-MP2: Total energy	-60835.192321

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:33:PRO )

Summations of interaction energy for fragment #1(A:33:PRO )

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.
-5.651	-3.464	4.446	-2.66	-3.974	0.014

Interaction energy analysis for fragmet #1(A:33:PRO )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / 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	35	LYS	1	1.068	1.023	3.634	-1.733	0.290	-0.004	-1.212	-0.807	0.005
4	A	36	TRP	0	0.036	0.021	6.435	0.059	0.059	0.000	0.000	0.000	0.000
5	A	37	LYS	1	0.932	0.971	1.876	-1.712	-2.490	4.394	-1.241	-2.376	0.009
6	A	38	VAL	0	0.054	0.031	3.202	-0.830	-0.199	0.054	-0.138	-0.547	0.000
7	A	39	LYS	1	0.959	0.979	5.427	-0.447	-0.447	0.000	0.000	0.000	0.000
8	A	40	LYS	1	0.974	0.985	8.165	-0.347	-0.347	0.000	0.000	0.000	0.000
9	A	41	GLN	0	0.034	0.008	3.942	-0.003	0.308	0.002	-0.069	-0.244	0.000
10	A	42	LYS	1	1.016	0.997	8.252	-0.416	-0.416	0.000	0.000	0.000	0.000
11	A	43	LEU	0	-0.027	-0.005	10.244	-0.035	-0.035	0.000	0.000	0.000	0.000
12	A	44	ALA	0	0.011	0.010	11.648	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	45	GLU	-1	-0.924	-0.965	9.709	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	46	LYS	1	0.851	0.927	13.605	-0.109	-0.109	0.000	0.000	0.000	0.000
15	A	47	ALA	0	0.032	0.014	16.095	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	48	ALA	0	0.007	0.008	16.358	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	49	ARG	1	0.992	0.996	13.866	-0.060	-0.060	0.000	0.000	0.000	0.000
18	A	50	GLU	-1	-0.874	-0.937	19.768	0.069	0.069	0.000	0.000	0.000	0.000
19	A	51	ALA	0	-0.010	0.012	21.313	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	52	GLU	-1	-0.941	-0.975	21.553	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	53	LEU	0	-0.007	-0.004	23.637	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	54	THR	0	-0.022	-0.035	25.714	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	55	ALA	0	-0.006	0.004	26.334	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	56	LYS	1	0.992	0.993	27.400	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	57	LYS	1	0.925	0.978	29.795	-0.022	-0.022	0.000	0.000	0.000	0.000
26	A	58	ALA	0	0.005	0.005	31.420	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	59	GLN	0	-0.028	-0.014	31.675	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	60	ALA	0	0.030	0.006	33.826	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	61	ARG	1	0.967	0.978	34.817	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	62	GLN	0	-0.041	-0.014	35.267	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	63	ALA	0	-0.017	-0.004	38.193	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	64	LEU	0	0.031	0.013	39.881	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	65	SER	0	0.007	0.015	41.764	0.000	0.000	0.000	0.000	0.000	0.000
34	A	66	ILE	0	0.011	0.004	43.813	0.000	0.000	0.000	0.000	0.000	0.000
35	A	67	TYR	0	-0.043	-0.025	43.362	0.000	0.000	0.000	0.000	0.000	0.000
36	A	68	LEU	0	-0.031	-0.020	43.732	0.000	0.000	0.000	0.000	0.000	0.000
37	A	69	ASN	0	0.043	0.025	47.763	0.001	0.001	0.000	0.000	0.000	0.000
38	A	70	LEU	0	-0.078	-0.030	50.688	0.000	0.000	0.000	0.000	0.000	0.000
39	A	71	PRO	0	-0.007	0.018	51.751	0.000	0.000	0.000	0.000	0.000	0.000
40	A	72	THR	0	0.050	0.023	49.920	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	73	LEU	0	0.021	-0.003	52.588	0.000	0.000	0.000	0.000	0.000	0.000
42	A	74	ASP	-1	-0.846	-0.924	53.762	0.007	0.007	0.000	0.000	0.000	0.000
43	A	75	GLU	-1	-0.857	-0.935	51.690	0.008	0.008	0.000	0.000	0.000	0.000
44	A	76	ALA	0	-0.064	-0.030	55.981	0.000	0.000	0.000	0.000	0.000	0.000
45	A	77	VAL	0	0.044	0.010	58.580	0.000	0.000	0.000	0.000	0.000	0.000
46	A	78	ASN	0	-0.009	-0.002	57.164	0.000	0.000	0.000	0.000	0.000	0.000
47	A	79	THR	0	-0.135	-0.063	59.320	0.000	0.000	0.000	0.000	0.000	0.000
48	A	80	LEU	0	-0.056	-0.047	61.845	0.000	0.000	0.000	0.000	0.000	0.000
49	A	81	LYS	1	0.932	0.978	63.905	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	82	PRO	0	-0.011	-0.009	64.140	0.000	0.000	0.000	0.000	0.000	0.000
51	A	83	TRP	0	-0.006	-0.001	65.723	0.000	0.000	0.000	0.000	0.000	0.000
52	A	84	TRP	0	-0.004	-0.010	67.116	0.000	0.000	0.000	0.000	0.000	0.000
53	A	85	PRO	0	0.043	0.020	68.782	0.000	0.000	0.000	0.000	0.000	0.000
54	A	86	GLY	0	0.057	0.041	69.834	0.000	0.000	0.000	0.000	0.000	0.000
55	A	87	LEU	0	-0.043	-0.027	68.153	0.000	0.000	0.000	0.000	0.000	0.000
56	A	88	PHE	0	-0.068	-0.045	62.994	0.000	0.000	0.000	0.000	0.000	0.000
57	A	89	ASP	-1	-0.912	-0.932	66.311	0.003	0.003	0.000	0.000	0.000	0.000
58	A	90	GLY	0	0.038	0.012	64.941	0.000	0.000	0.000	0.000	0.000	0.000
59	A	91	ASP	-1	-0.926	-0.980	59.575	0.006	0.006	0.000	0.000	0.000	0.000
60	A	92	THR	0	-0.044	-0.016	61.223	0.000	0.000	0.000	0.000	0.000	0.000
61	A	93	PRO	0	-0.047	-0.026	60.982	0.000	0.000	0.000	0.000	0.000	0.000
62	A	94	ARG	1	0.948	0.999	64.067	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	95	LEU	0	-0.032	-0.019	65.635	0.000	0.000	0.000	0.000	0.000	0.000
64	A	96	LEU	0	-0.007	-0.028	65.407	0.000	0.000	0.000	0.000	0.000	0.000
65	A	97	ALA	0	0.064	0.053	69.282	0.000	0.000	0.000	0.000	0.000	0.000
66	A	98	CYS	0	-0.044	-0.025	71.632	0.000	0.000	0.000	0.000	0.000	0.000
67	A	99	GLY	0	-0.009	-0.012	71.819	0.000	0.000	0.000	0.000	0.000	0.000
68	A	100	ILE	0	0.050	0.029	69.739	0.000	0.000	0.000	0.000	0.000	0.000
69	A	101	ARG	1	0.913	0.944	65.212	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	102	ASP	-1	-0.910	-0.952	70.256	0.003	0.003	0.000	0.000	0.000	0.000
71	A	103	VAL	0	0.070	0.047	73.471	0.000	0.000	0.000	0.000	0.000	0.000
72	A	104	LEU	0	-0.045	-0.031	68.568	0.000	0.000	0.000	0.000	0.000	0.000
73	A	105	LEU	0	-0.052	-0.053	69.030	0.000	0.000	0.000	0.000	0.000	0.000
74	A	106	GLU	-1	-0.924	-0.943	72.153	0.003	0.003	0.000	0.000	0.000	0.000
75	A	107	ASP	-1	-0.766	-0.883	73.697	0.004	0.004	0.000	0.000	0.000	0.000
76	A	108	VAL	0	-0.067	-0.038	69.260	0.000	0.000	0.000	0.000	0.000	0.000
77	A	109	ALA	0	-0.010	0.002	72.381	0.000	0.000	0.000	0.000	0.000	0.000
78	A	110	GLN	0	-0.017	-0.001	74.812	0.000	0.000	0.000	0.000	0.000	0.000
79	A	111	ARG	1	0.807	0.897	72.713	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	112	ASN	0	-0.032	-0.005	73.028	0.000	0.000	0.000	0.000	0.000	0.000
81	A	113	ILE	0	-0.008	0.008	68.141	0.000	0.000	0.000	0.000	0.000	0.000
82	A	114	PRO	0	0.006	0.010	65.663	0.000	0.000	0.000	0.000	0.000	0.000
83	A	115	LEU	0	-0.043	-0.029	63.464	0.000	0.000	0.000	0.000	0.000	0.000
84	A	116	SER	0	0.036	0.028	62.463	0.000	0.000	0.000	0.000	0.000	0.000
85	A	117	HIS	0	0.135	0.052	64.955	0.000	0.000	0.000	0.000	0.000	0.000
86	A	118	LYS	1	0.924	0.957	58.162	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	119	LYS	1	0.995	0.991	58.765	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	120	LEU	0	0.095	0.071	61.198	0.000	0.000	0.000	0.000	0.000	0.000
89	A	121	ARG	1	0.900	0.940	62.408	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	122	ARG	1	0.786	0.879	53.297	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	123	ALA	0	0.072	0.049	58.531	0.000	0.000	0.000	0.000	0.000	0.000
92	A	124	MET	0	0.060	0.032	59.956	0.000	0.000	0.000	0.000	0.000	0.000
93	A	125	LYS	1	0.899	0.949	58.332	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	126	ALA	0	0.024	0.014	56.020	0.000	0.000	0.000	0.000	0.000	0.000
95	A	127	ILE	0	0.052	0.034	57.179	0.000	0.000	0.000	0.000	0.000	0.000
96	A	128	THR	0	-0.046	-0.012	59.814	0.000	0.000	0.000	0.000	0.000	0.000
97	A	129	ARG	1	0.866	0.919	55.953	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	130	SER	0	0.000	0.013	55.536	0.000	0.000	0.000	0.000	0.000	0.000
99	A	131	GLU	-1	-0.790	-0.918	51.581	0.000	0.000	0.000	0.000	0.000	0.000
100	A	132	SER	0	0.015	0.012	56.299	0.000	0.000	0.000	0.000	0.000	0.000
101	A	133	TYR	0	0.072	0.059	58.937	0.000	0.000	0.000	0.000	0.000	0.000
102	A	134	LEU	0	-0.002	-0.017	57.251	0.000	0.000	0.000	0.000	0.000	0.000
103	A	135	CYS	0	-0.078	-0.038	58.318	0.000	0.000	0.000	0.000	0.000	0.000
104	A	136	ALA	0	-0.004	0.003	61.272	0.000	0.000	0.000	0.000	0.000	0.000
105	A	137	MET	0	-0.084	-0.032	64.093	0.000	0.000	0.000	0.000	0.000	0.000
106	A	138	LYS	1	0.962	0.988	64.521	0.000	0.000	0.000	0.000	0.000	0.000
107	A	139	ALA	0	0.021	0.004	68.030	0.000	0.000	0.000	0.000	0.000	0.000
108	A	140	GLY	0	-0.022	-0.011	71.483	0.000	0.000	0.000	0.000	0.000	0.000
109	A	141	ALA	0	-0.047	-0.003	69.965	0.000	0.000	0.000	0.000	0.000	0.000
110	A	142	CYS	0	-0.004	-0.005	71.916	0.000	0.000	0.000	0.000	0.000	0.000
111	A	143	ARG	1	0.809	0.898	68.265	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	144	TYR	0	0.008	-0.003	71.442	0.000	0.000	0.000	0.000	0.000	0.000
113	A	145	ASP	-1	-0.770	-0.886	72.524	0.002	0.002	0.000	0.000	0.000	0.000
114	A	146	THR	0	-0.058	-0.059	72.205	0.000	0.000	0.000	0.000	0.000	0.000
115	A	147	GLU	-1	-0.951	-0.964	74.272	0.003	0.003	0.000	0.000	0.000	0.000
116	A	148	GLY	0	-0.045	-0.016	75.377	0.000	0.000	0.000	0.000	0.000	0.000
117	A	149	TYR	0	-0.025	0.000	76.409	0.000	0.000	0.000	0.000	0.000	0.000
118	A	150	VAL	0	-0.056	-0.036	76.120	0.000	0.000	0.000	0.000	0.000	0.000
119	A	151	THR	0	-0.015	-0.045	75.318	0.000	0.000	0.000	0.000	0.000	0.000
120	A	152	GLU	-1	-0.815	-0.899	74.694	0.001	0.001	0.000	0.000	0.000	0.000
121	A	153	HIS	0	-0.013	-0.011	74.737	0.000	0.000	0.000	0.000	0.000	0.000
122	A	154	ILE	0	-0.057	-0.017	68.812	0.000	0.000	0.000	0.000	0.000	0.000
123	A	155	SER	0	0.045	0.018	72.062	0.000	0.000	0.000	0.000	0.000	0.000
124	A	156	GLN	0	0.060	0.007	70.789	0.000	0.000	0.000	0.000	0.000	0.000
125	A	157	GLU	-1	-0.873	-0.940	69.498	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	158	GLU	-1	-0.852	-0.919	67.818	0.000	0.000	0.000	0.000	0.000	0.000
127	A	159	GLU	-1	-0.833	-0.907	66.204	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	160	VAL	0	-0.013	-0.005	64.796	0.000	0.000	0.000	0.000	0.000	0.000
129	A	161	TYR	0	-0.037	-0.023	61.823	0.000	0.000	0.000	0.000	0.000	0.000
130	A	162	ALA	0	0.002	-0.006	61.847	0.000	0.000	0.000	0.000	0.000	0.000
131	A	163	ALA	0	0.026	0.023	60.277	0.000	0.000	0.000	0.000	0.000	0.000
132	A	164	GLU	-1	-0.797	-0.897	57.361	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	165	ARG	1	0.855	0.925	55.329	0.001	0.001	0.000	0.000	0.000	0.000
134	A	166	LEU	0	0.001	0.007	55.585	0.000	0.000	0.000	0.000	0.000	0.000
135	A	167	ASP	-1	-0.815	-0.885	54.085	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	168	LYS	1	0.764	0.855	52.136	0.004	0.004	0.000	0.000	0.000	0.000
137	A	169	ILE	0	-0.007	0.004	51.127	0.000	0.000	0.000	0.000	0.000	0.000
138	A	170	ARG	1	0.964	0.984	50.525	0.001	0.001	0.000	0.000	0.000	0.000
139	A	171	ARG	1	0.815	0.912	47.615	0.005	0.005	0.000	0.000	0.000	0.000
140	A	172	GLN	0	-0.005	-0.004	46.343	0.000	0.000	0.000	0.000	0.000	0.000
141	A	173	ASN	0	-0.056	-0.049	46.190	0.001	0.001	0.000	0.000	0.000	0.000
142	A	174	ARG	1	0.946	0.967	44.062	0.004	0.004	0.000	0.000	0.000	0.000
143	A	175	ILE	0	0.031	0.034	41.483	0.000	0.000	0.000	0.000	0.000	0.000
144	A	176	LYS	1	0.943	0.962	41.247	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	177	ALA	0	-0.007	0.009	41.765	0.001	0.001	0.000	0.000	0.000	0.000
146	A	178	GLU	-1	-0.937	-0.960	36.508	-0.003	-0.003	0.000	0.000	0.000	0.000
147	A	179	LEU	0	-0.029	-0.031	37.121	0.001	0.001	0.000	0.000	0.000	0.000
148	A	180	GLN	0	-0.072	-0.036	37.075	0.001	0.001	0.000	0.000	0.000	0.000
149	A	181	ALA	0	0.062	0.027	36.297	0.001	0.001	0.000	0.000	0.000	0.000
150	A	182	VAL	0	-0.104	-0.035	31.773	0.001	0.001	0.000	0.000	0.000	0.000
151	A	183	LEU	0	-0.120	-0.094	32.732	0.002	0.002	0.000	0.000	0.000	0.000
152	A	184	ASP	-2	-1.846	-1.883	33.532	0.033	0.033	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:33:PRO )