FMO DATABASE

FMODB ID: 5J1GZ

Calculation Name: 1DVO-A-Xray372

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: 2023-09-24

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1292256.69852
FMO2-HF: Nuclear repulsion	1231597.059733
FMO2-HF: Total energy	-60659.638787
FMO2-MP2: Total energy	-60836.866065

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.
0.439	3.796	2.172	-1.707	-3.821	0.003

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 : 0.070 / q_NPA : 0.021

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	1.032	1.005	3.621	0.064	1.514	0.007	-0.762	-0.695	0.002
4	A	36	TRP	0	0.068	0.032	6.213	0.226	0.226	0.000	0.000	0.000	0.000
5	A	37	LYS	1	0.918	0.970	2.442	-1.306	-0.755	1.649	-0.556	-1.643	0.002
6	A	38	VAL	0	0.018	0.003	2.725	-0.781	0.258	0.518	-0.364	-1.194	-0.001
7	A	39	LYS	1	0.974	0.984	4.797	0.656	0.763	-0.001	-0.009	-0.096	0.000
8	A	40	LYS	1	0.978	0.984	7.772	0.201	0.201	0.000	0.000	0.000	0.000
9	A	41	GLN	0	0.051	0.028	4.048	0.189	0.399	-0.001	-0.016	-0.193	0.000
10	A	42	LYS	1	1.017	1.008	7.433	0.970	0.970	0.000	0.000	0.000	0.000
11	A	43	LEU	0	-0.022	0.000	10.495	0.061	0.061	0.000	0.000	0.000	0.000
12	A	44	ALA	0	0.014	0.005	11.405	0.044	0.044	0.000	0.000	0.000	0.000
13	A	45	GLU	-1	-0.876	-0.927	10.144	-0.451	-0.451	0.000	0.000	0.000	0.000
14	A	46	LYS	1	0.802	0.879	13.511	0.237	0.237	0.000	0.000	0.000	0.000
15	A	47	ALA	0	0.042	0.017	16.301	0.024	0.024	0.000	0.000	0.000	0.000
16	A	48	ALA	0	0.003	0.004	15.990	0.021	0.021	0.000	0.000	0.000	0.000
17	A	49	ARG	1	0.903	0.930	13.448	0.321	0.321	0.000	0.000	0.000	0.000
18	A	50	GLU	-1	-0.807	-0.874	19.439	-0.172	-0.172	0.000	0.000	0.000	0.000
19	A	51	ALA	0	0.005	0.017	21.110	0.013	0.013	0.000	0.000	0.000	0.000
20	A	52	GLU	-1	-0.846	-0.906	21.354	-0.090	-0.090	0.000	0.000	0.000	0.000
21	A	53	LEU	0	0.010	0.005	23.223	0.010	0.010	0.000	0.000	0.000	0.000
22	A	54	THR	0	-0.013	-0.026	25.474	0.009	0.009	0.000	0.000	0.000	0.000
23	A	55	ALA	0	-0.013	0.001	26.108	0.008	0.008	0.000	0.000	0.000	0.000
24	A	56	LYS	1	0.891	0.928	25.114	0.102	0.102	0.000	0.000	0.000	0.000
25	A	57	LYS	1	0.846	0.920	29.314	0.084	0.084	0.000	0.000	0.000	0.000
26	A	58	ALA	0	-0.022	-0.010	30.945	0.004	0.004	0.000	0.000	0.000	0.000
27	A	59	GLN	0	-0.023	-0.016	31.014	0.001	0.001	0.000	0.000	0.000	0.000
28	A	60	ALA	0	0.039	0.010	33.287	0.004	0.004	0.000	0.000	0.000	0.000
29	A	61	ARG	1	0.970	0.985	34.608	0.059	0.059	0.000	0.000	0.000	0.000
30	A	62	GLN	0	-0.057	-0.023	35.637	0.003	0.003	0.000	0.000	0.000	0.000
31	A	63	ALA	0	-0.008	0.004	37.621	0.003	0.003	0.000	0.000	0.000	0.000
32	A	64	LEU	0	0.021	0.006	39.301	0.002	0.002	0.000	0.000	0.000	0.000
33	A	65	SER	0	-0.003	0.001	41.220	0.002	0.002	0.000	0.000	0.000	0.000
34	A	66	ILE	0	0.011	0.005	43.331	0.001	0.001	0.000	0.000	0.000	0.000
35	A	67	TYR	0	-0.038	-0.027	42.643	0.002	0.002	0.000	0.000	0.000	0.000
36	A	68	LEU	0	-0.001	-0.002	43.713	0.000	0.000	0.000	0.000	0.000	0.000
37	A	69	ASN	0	-0.013	0.016	47.463	0.001	0.001	0.000	0.000	0.000	0.000
38	A	70	LEU	0	-0.054	-0.028	50.115	0.001	0.001	0.000	0.000	0.000	0.000
39	A	71	PRO	0	-0.003	0.015	51.462	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	72	THR	0	-0.014	-0.045	49.763	0.001	0.001	0.000	0.000	0.000	0.000
41	A	73	LEU	0	0.012	-0.007	52.675	0.001	0.001	0.000	0.000	0.000	0.000
42	A	74	ASP	-1	-0.835	-0.896	54.059	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	75	GLU	-1	-0.781	-0.869	51.638	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	76	ALA	0	-0.068	-0.026	56.187	0.001	0.001	0.000	0.000	0.000	0.000
45	A	77	VAL	0	0.043	0.017	58.696	0.001	0.001	0.000	0.000	0.000	0.000
46	A	78	ASN	0	-0.008	-0.009	57.576	0.002	0.002	0.000	0.000	0.000	0.000
47	A	79	THR	0	-0.116	-0.072	59.197	0.000	0.000	0.000	0.000	0.000	0.000
48	A	80	LEU	0	-0.037	-0.035	61.774	0.001	0.001	0.000	0.000	0.000	0.000
49	A	81	LYS	1	0.872	0.916	62.696	0.024	0.024	0.000	0.000	0.000	0.000
50	A	82	PRO	0	-0.019	-0.015	64.184	0.000	0.000	0.000	0.000	0.000	0.000
51	A	83	TRP	0	-0.025	0.005	65.348	0.001	0.001	0.000	0.000	0.000	0.000
52	A	84	TRP	0	0.009	-0.012	67.345	0.000	0.000	0.000	0.000	0.000	0.000
53	A	85	PRO	0	0.040	0.021	68.656	0.000	0.000	0.000	0.000	0.000	0.000
54	A	86	GLY	0	0.059	0.035	69.617	0.000	0.000	0.000	0.000	0.000	0.000
55	A	87	LEU	0	-0.024	-0.006	68.195	0.000	0.000	0.000	0.000	0.000	0.000
56	A	88	PHE	0	-0.038	-0.024	63.006	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	89	ASP	-1	-0.766	-0.848	66.235	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	90	GLY	0	0.002	0.004	64.864	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	91	ASP	-1	-0.847	-0.920	60.356	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	92	THR	0	-0.036	-0.008	61.504	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	93	PRO	0	-0.042	-0.031	60.935	0.001	0.001	0.000	0.000	0.000	0.000
62	A	94	ARG	1	0.807	0.893	64.039	0.018	0.018	0.000	0.000	0.000	0.000
63	A	95	LEU	0	-0.037	-0.021	65.867	0.000	0.000	0.000	0.000	0.000	0.000
64	A	96	LEU	0	0.011	-0.001	65.847	0.000	0.000	0.000	0.000	0.000	0.000
65	A	97	ALA	0	0.054	0.043	69.386	0.000	0.000	0.000	0.000	0.000	0.000
66	A	98	CYS	0	-0.079	-0.066	71.592	0.000	0.000	0.000	0.000	0.000	0.000
67	A	99	GLY	0	-0.019	-0.010	71.608	0.000	0.000	0.000	0.000	0.000	0.000
68	A	100	ILE	0	0.034	0.022	69.882	0.000	0.000	0.000	0.000	0.000	0.000
69	A	101	ARG	1	0.781	0.849	67.228	0.014	0.014	0.000	0.000	0.000	0.000
70	A	102	ASP	-1	-0.813	-0.877	69.954	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	103	VAL	0	0.114	0.065	72.920	0.000	0.000	0.000	0.000	0.000	0.000
72	A	104	LEU	0	-0.034	-0.016	68.364	0.000	0.000	0.000	0.000	0.000	0.000
73	A	105	LEU	0	-0.064	-0.048	69.213	0.000	0.000	0.000	0.000	0.000	0.000
74	A	106	GLU	-1	-0.906	-0.948	71.764	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	107	ASP	-1	-0.735	-0.859	73.910	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	108	VAL	0	-0.060	-0.042	69.149	0.000	0.000	0.000	0.000	0.000	0.000
77	A	109	ALA	0	-0.031	-0.007	72.271	0.000	0.000	0.000	0.000	0.000	0.000
78	A	110	GLN	0	-0.046	-0.022	74.890	0.000	0.000	0.000	0.000	0.000	0.000
79	A	111	ARG	1	0.790	0.881	72.664	0.016	0.016	0.000	0.000	0.000	0.000
80	A	112	ASN	0	-0.046	-0.010	72.482	0.000	0.000	0.000	0.000	0.000	0.000
81	A	113	ILE	0	0.015	0.022	67.874	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	114	PRO	0	0.002	0.012	65.280	0.000	0.000	0.000	0.000	0.000	0.000
83	A	115	LEU	0	-0.062	-0.039	63.510	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	116	SER	0	0.048	0.026	62.341	0.001	0.001	0.000	0.000	0.000	0.000
85	A	117	HIS	0	0.130	0.068	64.297	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	118	LYS	1	0.944	0.966	57.607	0.018	0.018	0.000	0.000	0.000	0.000
87	A	119	LYS	1	0.943	0.979	58.337	0.023	0.023	0.000	0.000	0.000	0.000
88	A	120	LEU	0	0.093	0.057	60.829	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	121	ARG	1	0.909	0.935	62.266	0.015	0.015	0.000	0.000	0.000	0.000
90	A	122	ARG	1	0.808	0.891	52.930	0.023	0.023	0.000	0.000	0.000	0.000
91	A	123	ALA	0	0.055	0.036	58.415	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	124	MET	0	0.046	0.032	59.927	0.000	0.000	0.000	0.000	0.000	0.000
93	A	125	LYS	1	0.914	0.972	58.131	0.018	0.018	0.000	0.000	0.000	0.000
94	A	126	ALA	0	0.020	0.010	55.975	0.000	0.000	0.000	0.000	0.000	0.000
95	A	127	ILE	0	0.049	0.028	57.187	0.000	0.000	0.000	0.000	0.000	0.000
96	A	128	THR	0	-0.023	-0.015	59.923	0.000	0.000	0.000	0.000	0.000	0.000
97	A	129	ARG	1	0.855	0.924	55.861	0.018	0.018	0.000	0.000	0.000	0.000
98	A	130	SER	0	-0.008	0.001	55.672	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	131	GLU	-1	-0.760	-0.883	51.884	-0.026	-0.026	0.000	0.000	0.000	0.000
100	A	132	SER	0	0.029	0.019	56.500	0.000	0.000	0.000	0.000	0.000	0.000
101	A	133	TYR	0	0.025	0.032	59.288	0.001	0.001	0.000	0.000	0.000	0.000
102	A	134	LEU	0	-0.012	-0.018	57.231	0.001	0.001	0.000	0.000	0.000	0.000
103	A	135	CYS	0	-0.073	-0.042	58.394	0.000	0.000	0.000	0.000	0.000	0.000
104	A	136	ALA	0	0.011	0.010	61.332	0.000	0.000	0.000	0.000	0.000	0.000
105	A	137	MET	0	-0.064	-0.022	64.203	0.000	0.000	0.000	0.000	0.000	0.000
106	A	138	LYS	1	0.938	0.976	63.915	0.018	0.018	0.000	0.000	0.000	0.000
107	A	139	ALA	0	0.010	-0.002	67.987	0.000	0.000	0.000	0.000	0.000	0.000
108	A	140	GLY	0	-0.007	0.000	71.416	0.000	0.000	0.000	0.000	0.000	0.000
109	A	141	ALA	0	-0.046	-0.015	69.977	0.000	0.000	0.000	0.000	0.000	0.000
110	A	142	CYS	0	-0.015	-0.008	71.890	0.000	0.000	0.000	0.000	0.000	0.000
111	A	143	ARG	1	0.800	0.882	68.621	0.014	0.014	0.000	0.000	0.000	0.000
112	A	144	TYR	0	0.009	0.001	71.390	0.000	0.000	0.000	0.000	0.000	0.000
113	A	145	ASP	-1	-0.783	-0.910	72.411	-0.014	-0.014	0.000	0.000	0.000	0.000
114	A	146	THR	0	-0.034	-0.044	72.466	0.000	0.000	0.000	0.000	0.000	0.000
115	A	147	GLU	-1	-0.940	-0.941	74.378	-0.013	-0.013	0.000	0.000	0.000	0.000
116	A	148	GLY	0	-0.028	-0.002	75.286	0.000	0.000	0.000	0.000	0.000	0.000
117	A	149	TYR	0	-0.086	-0.049	76.328	0.000	0.000	0.000	0.000	0.000	0.000
118	A	150	VAL	0	-0.045	-0.030	76.404	0.000	0.000	0.000	0.000	0.000	0.000
119	A	151	THR	0	-0.042	-0.045	75.635	0.000	0.000	0.000	0.000	0.000	0.000
120	A	152	GLU	-1	-0.770	-0.857	73.963	-0.013	-0.013	0.000	0.000	0.000	0.000
121	A	153	HIS	0	0.007	-0.001	74.419	0.000	0.000	0.000	0.000	0.000	0.000
122	A	154	ILE	0	-0.090	-0.023	68.472	0.000	0.000	0.000	0.000	0.000	0.000
123	A	155	SER	0	0.043	-0.007	71.639	0.000	0.000	0.000	0.000	0.000	0.000
124	A	156	GLN	0	0.010	-0.016	70.374	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	157	GLU	-1	-0.847	-0.926	68.802	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	158	GLU	-1	-0.768	-0.852	67.343	-0.014	-0.014	0.000	0.000	0.000	0.000
127	A	159	GLU	-1	-0.835	-0.899	65.726	-0.015	-0.015	0.000	0.000	0.000	0.000
128	A	160	VAL	0	-0.007	-0.007	64.302	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	161	TYR	0	-0.021	-0.015	61.826	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	162	ALA	0	0.005	-0.004	61.343	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	163	ALA	0	0.029	0.015	59.895	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	164	GLU	-1	-0.813	-0.888	57.162	-0.017	-0.017	0.000	0.000	0.000	0.000
133	A	165	ARG	1	0.834	0.887	55.236	0.016	0.016	0.000	0.000	0.000	0.000
134	A	166	LEU	0	0.009	0.013	55.493	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	167	ASP	-1	-0.768	-0.852	52.682	-0.021	-0.021	0.000	0.000	0.000	0.000
136	A	168	LYS	1	0.765	0.873	51.724	0.016	0.016	0.000	0.000	0.000	0.000
137	A	169	ILE	0	0.007	0.010	50.715	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	170	ARG	1	0.937	0.952	50.317	0.022	0.022	0.000	0.000	0.000	0.000
139	A	171	ARG	1	0.784	0.896	47.265	0.019	0.019	0.000	0.000	0.000	0.000
140	A	172	GLN	0	0.018	0.003	46.047	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	173	ASN	0	-0.054	-0.046	45.992	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	174	ARG	1	0.926	0.948	44.005	0.027	0.027	0.000	0.000	0.000	0.000
143	A	175	ILE	0	0.056	0.040	40.979	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	176	LYS	1	0.923	0.967	41.031	0.028	0.028	0.000	0.000	0.000	0.000
145	A	177	ALA	0	-0.008	0.002	41.815	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	178	GLU	-1	-0.937	-0.961	37.218	-0.046	-0.046	0.000	0.000	0.000	0.000
147	A	179	LEU	0	-0.019	-0.019	36.686	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	180	GLN	0	-0.026	-0.030	37.045	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	181	ALA	0	-0.003	-0.004	36.680	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	182	VAL	0	-0.035	-0.006	31.617	-0.005	-0.005	0.000	0.000	0.000	0.000
151	A	183	LEU	0	-0.032	-0.033	32.749	-0.005	-0.005	0.000	0.000	0.000	0.000
152	A	184	ASP	-1	-0.937	-0.925	33.460	-0.071	-0.071	0.000	0.000	0.000	0.000

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