FMO DATABASE

FMODB ID: 4J1GN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1292297.091479
FMO2-HF: Nuclear repulsion	1231637.809862
FMO2-HF: Total energy	-60659.281617
FMO2-MP2: Total energy	-60836.584921

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.
-0.347	3.161	2.555	-2.298	-3.766	0.009

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 : 0.067 / q_NPA : 0.015

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	1.055	1.019	3.756	-1.172	0.909	-0.010	-1.232	-0.840	0.005
4	A	36	TRP	0	0.049	0.026	6.546	0.167	0.167	0.000	0.000	0.000	0.000
5	A	37	LYS	1	0.911	0.955	2.189	-1.102	-0.751	2.357	-0.823	-1.885	0.004
6	A	38	VAL	0	0.048	0.021	2.820	-0.412	0.310	0.209	-0.203	-0.728	0.000
7	A	39	LYS	1	0.963	0.985	5.242	0.694	0.779	-0.001	-0.004	-0.080	0.000
8	A	40	LYS	1	0.978	0.986	8.174	0.299	0.299	0.000	0.000	0.000	0.000
9	A	41	GLN	0	0.046	0.024	3.887	0.055	0.324	0.000	-0.036	-0.233	0.000
10	A	42	LYS	1	1.020	1.000	7.867	0.892	0.892	0.000	0.000	0.000	0.000
11	A	43	LEU	0	-0.025	-0.003	10.156	0.069	0.069	0.000	0.000	0.000	0.000
12	A	44	ALA	0	0.016	0.011	11.489	0.051	0.051	0.000	0.000	0.000	0.000
13	A	45	GLU	-1	-0.883	-0.935	9.605	-0.436	-0.436	0.000	0.000	0.000	0.000
14	A	46	LYS	1	0.798	0.875	13.583	0.245	0.245	0.000	0.000	0.000	0.000
15	A	47	ALA	0	0.035	0.016	16.022	0.025	0.025	0.000	0.000	0.000	0.000
16	A	48	ALA	0	0.006	0.007	16.263	0.023	0.023	0.000	0.000	0.000	0.000
17	A	49	ARG	1	0.940	0.959	13.405	0.300	0.300	0.000	0.000	0.000	0.000
18	A	50	GLU	-1	-0.816	-0.882	19.763	-0.172	-0.172	0.000	0.000	0.000	0.000
19	A	51	ALA	0	-0.003	0.019	21.286	0.013	0.013	0.000	0.000	0.000	0.000
20	A	52	GLU	-1	-0.870	-0.926	21.742	-0.093	-0.093	0.000	0.000	0.000	0.000
21	A	53	LEU	0	0.013	0.002	23.523	0.011	0.011	0.000	0.000	0.000	0.000
22	A	54	THR	0	-0.015	-0.033	25.696	0.009	0.009	0.000	0.000	0.000	0.000
23	A	55	ALA	0	-0.003	0.007	26.349	0.007	0.007	0.000	0.000	0.000	0.000
24	A	56	LYS	1	0.890	0.933	25.544	0.092	0.092	0.000	0.000	0.000	0.000
25	A	57	LYS	1	0.859	0.937	29.746	0.080	0.080	0.000	0.000	0.000	0.000
26	A	58	ALA	0	-0.002	0.002	31.347	0.005	0.005	0.000	0.000	0.000	0.000
27	A	59	GLN	0	-0.017	-0.008	31.617	0.002	0.002	0.000	0.000	0.000	0.000
28	A	60	ALA	0	0.033	0.003	33.743	0.004	0.004	0.000	0.000	0.000	0.000
29	A	61	ARG	1	0.966	0.978	34.852	0.057	0.057	0.000	0.000	0.000	0.000
30	A	62	GLN	0	-0.051	-0.016	35.501	0.003	0.003	0.000	0.000	0.000	0.000
31	A	63	ALA	0	-0.013	-0.002	38.055	0.003	0.003	0.000	0.000	0.000	0.000
32	A	64	LEU	0	0.026	0.009	39.781	0.002	0.002	0.000	0.000	0.000	0.000
33	A	65	SER	0	0.003	0.013	41.670	0.002	0.002	0.000	0.000	0.000	0.000
34	A	66	ILE	0	0.013	0.005	43.671	0.001	0.001	0.000	0.000	0.000	0.000
35	A	67	TYR	0	-0.050	-0.030	43.216	0.002	0.002	0.000	0.000	0.000	0.000
36	A	68	LEU	0	-0.019	-0.014	43.892	0.000	0.000	0.000	0.000	0.000	0.000
37	A	69	ASN	0	0.015	0.018	47.766	0.000	0.000	0.000	0.000	0.000	0.000
38	A	70	LEU	0	-0.080	-0.035	50.606	0.001	0.001	0.000	0.000	0.000	0.000
39	A	71	PRO	0	-0.012	0.016	51.748	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	72	THR	0	0.007	-0.031	49.689	0.001	0.001	0.000	0.000	0.000	0.000
41	A	73	LEU	0	0.010	-0.005	52.582	0.001	0.001	0.000	0.000	0.000	0.000
42	A	74	ASP	-1	-0.861	-0.928	53.669	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	75	GLU	-1	-0.784	-0.870	51.483	-0.028	-0.028	0.000	0.000	0.000	0.000
44	A	76	ALA	0	-0.068	-0.037	55.958	0.001	0.001	0.000	0.000	0.000	0.000
45	A	77	VAL	0	0.036	0.008	58.568	0.001	0.001	0.000	0.000	0.000	0.000
46	A	78	ASN	0	-0.012	-0.007	57.372	0.001	0.001	0.000	0.000	0.000	0.000
47	A	79	THR	0	-0.134	-0.061	59.282	0.000	0.000	0.000	0.000	0.000	0.000
48	A	80	LEU	0	-0.044	-0.038	61.818	0.001	0.001	0.000	0.000	0.000	0.000
49	A	81	LYS	1	0.853	0.919	62.765	0.022	0.022	0.000	0.000	0.000	0.000
50	A	82	PRO	0	-0.008	-0.007	64.107	0.000	0.000	0.000	0.000	0.000	0.000
51	A	83	TRP	0	-0.003	0.003	65.544	0.001	0.001	0.000	0.000	0.000	0.000
52	A	84	TRP	0	0.011	-0.009	67.095	0.000	0.000	0.000	0.000	0.000	0.000
53	A	85	PRO	0	0.045	0.023	68.763	0.000	0.000	0.000	0.000	0.000	0.000
54	A	86	GLY	0	0.054	0.042	69.823	0.000	0.000	0.000	0.000	0.000	0.000
55	A	87	LEU	0	-0.047	-0.026	68.226	0.000	0.000	0.000	0.000	0.000	0.000
56	A	88	PHE	0	-0.052	-0.038	62.913	0.000	0.000	0.000	0.000	0.000	0.000
57	A	89	ASP	-1	-0.768	-0.859	66.326	-0.016	-0.016	0.000	0.000	0.000	0.000
58	A	90	GLY	0	0.010	0.009	64.933	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	91	ASP	-1	-0.859	-0.936	59.973	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	92	THR	0	-0.034	-0.012	61.222	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	93	PRO	0	-0.042	-0.023	61.046	0.001	0.001	0.000	0.000	0.000	0.000
62	A	94	ARG	1	0.830	0.932	64.077	0.016	0.016	0.000	0.000	0.000	0.000
63	A	95	LEU	0	-0.034	-0.024	65.644	0.000	0.000	0.000	0.000	0.000	0.000
64	A	96	LEU	0	-0.003	-0.019	65.662	0.000	0.000	0.000	0.000	0.000	0.000
65	A	97	ALA	0	0.044	0.053	69.303	0.000	0.000	0.000	0.000	0.000	0.000
66	A	98	CYS	0	-0.072	-0.053	71.654	0.000	0.000	0.000	0.000	0.000	0.000
67	A	99	GLY	0	-0.010	-0.012	71.833	0.000	0.000	0.000	0.000	0.000	0.000
68	A	100	ILE	0	0.046	0.027	69.856	0.000	0.000	0.000	0.000	0.000	0.000
69	A	101	ARG	1	0.784	0.873	67.070	0.013	0.013	0.000	0.000	0.000	0.000
70	A	102	ASP	-1	-0.843	-0.913	70.262	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	103	VAL	0	0.113	0.068	73.472	0.000	0.000	0.000	0.000	0.000	0.000
72	A	104	LEU	0	-0.037	-0.021	68.425	0.000	0.000	0.000	0.000	0.000	0.000
73	A	105	LEU	0	-0.062	-0.047	69.470	0.000	0.000	0.000	0.000	0.000	0.000
74	A	106	GLU	-1	-0.915	-0.946	72.139	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	107	ASP	-1	-0.755	-0.864	73.746	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	108	VAL	0	-0.057	-0.032	69.256	0.000	0.000	0.000	0.000	0.000	0.000
77	A	109	ALA	0	-0.017	0.000	72.351	0.000	0.000	0.000	0.000	0.000	0.000
78	A	110	GLN	0	-0.019	-0.001	74.778	0.000	0.000	0.000	0.000	0.000	0.000
79	A	111	ARG	1	0.794	0.874	72.613	0.015	0.015	0.000	0.000	0.000	0.000
80	A	112	ASN	0	-0.036	-0.007	73.026	0.000	0.000	0.000	0.000	0.000	0.000
81	A	113	ILE	0	-0.015	0.006	68.181	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	114	PRO	0	0.005	0.009	65.611	0.000	0.000	0.000	0.000	0.000	0.000
83	A	115	LEU	0	-0.044	-0.028	63.336	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	116	SER	0	0.036	0.024	62.466	0.001	0.001	0.000	0.000	0.000	0.000
85	A	117	HIS	0	0.159	0.070	64.933	0.000	0.000	0.000	0.000	0.000	0.000
86	A	118	LYS	1	0.943	0.963	57.793	0.018	0.018	0.000	0.000	0.000	0.000
87	A	119	LYS	1	0.974	0.988	58.679	0.022	0.022	0.000	0.000	0.000	0.000
88	A	120	LEU	0	0.091	0.065	61.178	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	121	ARG	1	0.901	0.931	62.431	0.015	0.015	0.000	0.000	0.000	0.000
90	A	122	ARG	1	0.814	0.892	53.319	0.023	0.023	0.000	0.000	0.000	0.000
91	A	123	ALA	0	0.058	0.041	58.534	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	124	MET	0	0.061	0.033	59.951	0.000	0.000	0.000	0.000	0.000	0.000
93	A	125	LYS	1	0.902	0.956	58.436	0.017	0.017	0.000	0.000	0.000	0.000
94	A	126	ALA	0	0.020	0.009	55.943	0.000	0.000	0.000	0.000	0.000	0.000
95	A	127	ILE	0	0.044	0.030	57.191	0.000	0.000	0.000	0.000	0.000	0.000
96	A	128	THR	0	-0.028	-0.007	59.829	0.000	0.000	0.000	0.000	0.000	0.000
97	A	129	ARG	1	0.869	0.930	56.034	0.017	0.017	0.000	0.000	0.000	0.000
98	A	130	SER	0	-0.011	0.003	55.566	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	131	GLU	-1	-0.756	-0.891	51.711	-0.023	-0.023	0.000	0.000	0.000	0.000
100	A	132	SER	0	0.010	0.011	56.341	0.001	0.001	0.000	0.000	0.000	0.000
101	A	133	TYR	0	0.063	0.051	58.972	0.001	0.001	0.000	0.000	0.000	0.000
102	A	134	LEU	0	0.000	-0.016	57.438	0.001	0.001	0.000	0.000	0.000	0.000
103	A	135	CYS	0	-0.087	-0.044	58.413	0.000	0.000	0.000	0.000	0.000	0.000
104	A	136	ALA	0	-0.003	0.000	61.325	0.001	0.001	0.000	0.000	0.000	0.000
105	A	137	MET	0	-0.073	-0.023	64.145	0.000	0.000	0.000	0.000	0.000	0.000
106	A	138	LYS	1	0.951	0.984	64.165	0.015	0.015	0.000	0.000	0.000	0.000
107	A	139	ALA	0	0.013	-0.008	68.093	0.000	0.000	0.000	0.000	0.000	0.000
108	A	140	GLY	0	-0.023	-0.010	71.550	0.000	0.000	0.000	0.000	0.000	0.000
109	A	141	ALA	0	-0.043	-0.003	70.043	0.000	0.000	0.000	0.000	0.000	0.000
110	A	142	CYS	0	-0.011	-0.007	71.965	0.000	0.000	0.000	0.000	0.000	0.000
111	A	143	ARG	1	0.807	0.894	68.498	0.012	0.012	0.000	0.000	0.000	0.000
112	A	144	TYR	0	0.006	-0.002	71.413	0.000	0.000	0.000	0.000	0.000	0.000
113	A	145	ASP	-1	-0.768	-0.892	72.539	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	146	THR	0	-0.034	-0.053	72.250	0.000	0.000	0.000	0.000	0.000	0.000
115	A	147	GLU	-1	-0.986	-0.980	74.269	-0.012	-0.012	0.000	0.000	0.000	0.000
116	A	148	GLY	0	-0.034	-0.007	75.383	0.000	0.000	0.000	0.000	0.000	0.000
117	A	149	TYR	0	-0.035	-0.006	76.415	0.000	0.000	0.000	0.000	0.000	0.000
118	A	150	VAL	0	-0.052	-0.034	76.148	0.000	0.000	0.000	0.000	0.000	0.000
119	A	151	THR	0	-0.004	-0.019	75.310	0.000	0.000	0.000	0.000	0.000	0.000
120	A	152	GLU	-1	-0.792	-0.896	74.444	-0.011	-0.011	0.000	0.000	0.000	0.000
121	A	153	HIS	0	0.008	-0.001	74.777	0.000	0.000	0.000	0.000	0.000	0.000
122	A	154	ILE	0	-0.074	-0.025	68.848	0.000	0.000	0.000	0.000	0.000	0.000
123	A	155	SER	0	0.028	-0.012	72.117	0.000	0.000	0.000	0.000	0.000	0.000
124	A	156	GLN	0	0.042	0.001	70.858	0.000	0.000	0.000	0.000	0.000	0.000
125	A	157	GLU	-1	-0.875	-0.945	69.566	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	158	GLU	-1	-0.785	-0.863	67.852	-0.012	-0.012	0.000	0.000	0.000	0.000
127	A	159	GLU	-1	-0.827	-0.898	66.270	-0.012	-0.012	0.000	0.000	0.000	0.000
128	A	160	VAL	0	-0.014	-0.009	64.871	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	161	TYR	0	-0.037	-0.022	62.383	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	162	ALA	0	0.004	-0.004	61.857	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	163	ALA	0	0.030	0.022	60.344	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	164	GLU	-1	-0.776	-0.863	57.359	-0.015	-0.015	0.000	0.000	0.000	0.000
133	A	165	ARG	1	0.834	0.896	55.374	0.015	0.015	0.000	0.000	0.000	0.000
134	A	166	LEU	0	0.000	0.006	55.692	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	167	ASP	-1	-0.780	-0.859	53.448	-0.017	-0.017	0.000	0.000	0.000	0.000
136	A	168	LYS	1	0.757	0.849	52.135	0.014	0.014	0.000	0.000	0.000	0.000
137	A	169	ILE	0	0.004	0.008	51.152	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	170	ARG	1	0.955	0.969	50.631	0.019	0.019	0.000	0.000	0.000	0.000
139	A	171	ARG	1	0.776	0.888	47.676	0.015	0.015	0.000	0.000	0.000	0.000
140	A	172	GLN	0	0.011	0.005	46.408	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	173	ASN	0	-0.055	-0.048	46.238	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	174	ARG	1	0.931	0.951	44.159	0.022	0.022	0.000	0.000	0.000	0.000
143	A	175	ILE	0	0.042	0.038	41.389	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	176	LYS	1	0.929	0.962	41.293	0.026	0.026	0.000	0.000	0.000	0.000
145	A	177	ALA	0	-0.010	0.005	41.791	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	178	GLU	-1	-0.936	-0.959	37.130	-0.041	-0.041	0.000	0.000	0.000	0.000
147	A	179	LEU	0	-0.010	-0.017	37.000	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	180	GLN	0	-0.044	-0.036	37.093	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	181	ALA	0	0.018	0.004	36.388	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	182	VAL	0	-0.049	-0.008	31.665	-0.005	-0.005	0.000	0.000	0.000	0.000
151	A	183	LEU	0	-0.045	-0.048	32.734	-0.006	-0.006	0.000	0.000	0.000	0.000
152	A	184	ASP	-1	-0.930	-0.916	33.515	-0.064	-0.064	0.000	0.000	0.000	0.000

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