FMO DATABASE

FMODB ID: 726MK

Calculation Name: 1BD8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BD8

Chain ID: A

ChEMBL ID:

UniProt ID: P55273

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptH
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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1355973.857894
FMO2-HF: Nuclear repulsion	1298086.709172
FMO2-HF: Total energy	-57887.148721
FMO2-MP2: Total energy	-58057.824726

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
-6.796	-4.984	10.759	-3.447	-9.123	0.001

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.046 / q_NPA : 1.010

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	9	GLY	0	0.119	0.057	3.409	-0.891	0.439	0.002	-0.513	-0.820	0.002
4	A	10	ASP	-1	-0.862	-0.946	2.631	-46.950	-45.272	0.510	-0.680	-1.507	-0.003
5	A	11	ARG	1	0.696	0.815	1.929	49.763	48.130	10.250	-2.232	-6.385	0.002
6	A	12	LEU	0	0.068	0.036	5.071	3.262	3.442	-0.001	-0.013	-0.165	0.000
7	A	13	SER	0	0.046	0.021	7.361	3.639	3.639	0.000	0.000	0.000	0.000
8	A	14	GLY	0	-0.029	-0.013	7.001	2.297	2.297	0.000	0.000	0.000	0.000
9	A	15	ALA	0	-0.039	-0.020	8.049	2.189	2.189	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.047	0.016	9.992	2.373	2.373	0.000	0.000	0.000	0.000
11	A	17	ALA	0	-0.006	0.001	11.234	1.729	1.729	0.000	0.000	0.000	0.000
12	A	18	ARG	1	0.841	0.919	7.175	32.037	32.037	0.000	0.000	0.000	0.000
13	A	19	GLY	0	0.041	0.028	13.149	1.063	1.063	0.000	0.000	0.000	0.000
14	A	20	ASP	-1	-0.877	-0.940	11.585	-23.117	-23.117	0.000	0.000	0.000	0.000
15	A	21	VAL	0	0.057	0.005	13.664	-0.935	-0.935	0.000	0.000	0.000	0.000
16	A	22	GLN	0	-0.021	-0.009	15.204	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.919	-0.954	8.101	-33.377	-33.377	0.000	0.000	0.000	0.000
18	A	24	VAL	0	0.007	0.000	11.592	-1.022	-1.022	0.000	0.000	0.000	0.000
19	A	25	ARG	1	0.858	0.917	12.902	15.444	15.444	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.940	0.981	10.378	24.834	24.834	0.000	0.000	0.000	0.000
21	A	27	LEU	0	-0.011	-0.016	7.159	-0.279	-0.279	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.002	0.012	10.381	0.295	0.295	0.000	0.000	0.000	0.000
23	A	29	HIS	0	-0.032	-0.022	13.166	0.579	0.579	0.000	0.000	0.000	0.000
24	A	30	ARG	1	0.898	0.970	13.478	20.174	20.174	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.877	-0.915	6.569	-36.300	-36.300	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.016	0.009	11.252	0.401	0.401	0.000	0.000	0.000	0.000
27	A	33	VAL	0	-0.037	-0.017	7.265	-0.364	-0.364	0.000	0.000	0.000	0.000
28	A	34	HIS	0	0.038	0.031	10.162	0.146	0.146	0.000	0.000	0.000	0.000
29	A	35	PRO	0	0.029	-0.001	10.382	-1.885	-1.885	0.000	0.000	0.000	0.000
30	A	36	ASP	-1	-0.874	-0.937	11.805	-16.859	-16.859	0.000	0.000	0.000	0.000
31	A	37	ALA	0	-0.073	-0.030	6.137	-0.404	-0.404	0.000	0.000	0.000	0.000
32	A	38	LEU	0	0.005	0.002	7.131	-1.048	-1.048	0.000	0.000	0.000	0.000
33	A	39	ASN	0	-0.042	-0.019	5.044	-2.741	-2.665	-0.001	-0.003	-0.072	0.000
34	A	40	ARG	1	0.932	0.946	4.369	44.976	45.157	-0.001	-0.006	-0.174	0.000
35	A	41	PHE	0	-0.079	-0.039	6.866	1.428	1.428	0.000	0.000	0.000	0.000
36	A	42	GLY	0	0.004	0.014	8.992	1.767	1.767	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.965	0.993	9.996	19.467	19.467	0.000	0.000	0.000	0.000
38	A	44	THR	0	0.071	0.030	9.640	-1.981	-1.981	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.019	-0.008	10.828	0.232	0.232	0.000	0.000	0.000	0.000
40	A	46	LEU	0	0.030	0.006	12.006	0.287	0.287	0.000	0.000	0.000	0.000
41	A	47	GLN	0	0.047	0.022	14.317	-0.038	-0.038	0.000	0.000	0.000	0.000
42	A	48	VAL	0	-0.058	-0.026	11.343	0.269	0.269	0.000	0.000	0.000	0.000
43	A	49	MET	0	-0.048	0.007	14.765	-0.742	-0.742	0.000	0.000	0.000	0.000
44	A	50	MET	0	0.006	0.011	15.995	1.084	1.084	0.000	0.000	0.000	0.000
45	A	51	PHE	0	0.045	0.013	17.900	0.331	0.331	0.000	0.000	0.000	0.000
46	A	52	GLY	0	0.043	0.040	21.311	0.540	0.540	0.000	0.000	0.000	0.000
47	A	53	SER	0	-0.037	-0.022	18.959	0.200	0.200	0.000	0.000	0.000	0.000
48	A	54	THR	0	0.038	0.015	20.835	-0.444	-0.444	0.000	0.000	0.000	0.000
49	A	55	ALA	0	-0.028	-0.020	21.056	-0.059	-0.059	0.000	0.000	0.000	0.000
50	A	56	ILE	0	0.007	0.011	15.373	-0.255	-0.255	0.000	0.000	0.000	0.000
51	A	57	ALA	0	0.057	0.022	18.129	-0.409	-0.409	0.000	0.000	0.000	0.000
52	A	58	LEU	0	0.035	0.016	20.029	0.022	0.022	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.847	-0.913	17.642	-15.135	-15.135	0.000	0.000	0.000	0.000
54	A	60	LEU	0	-0.030	-0.024	13.652	-0.405	-0.405	0.000	0.000	0.000	0.000
55	A	61	LEU	0	-0.004	0.005	17.317	0.097	0.097	0.000	0.000	0.000	0.000
56	A	62	LYS	1	0.933	0.971	20.136	12.729	12.729	0.000	0.000	0.000	0.000
57	A	63	GLN	0	-0.041	-0.018	16.678	0.987	0.987	0.000	0.000	0.000	0.000
58	A	64	GLY	0	-0.026	-0.014	17.484	-0.316	-0.316	0.000	0.000	0.000	0.000
59	A	65	ALA	0	-0.061	-0.022	15.899	-0.103	-0.103	0.000	0.000	0.000	0.000
60	A	66	SER	0	-0.003	-0.003	16.474	0.958	0.958	0.000	0.000	0.000	0.000
61	A	67	PRO	0	0.015	-0.004	18.440	-0.524	-0.524	0.000	0.000	0.000	0.000
62	A	68	ASN	0	0.025	0.006	21.038	-0.047	-0.047	0.000	0.000	0.000	0.000
63	A	69	VAL	0	-0.048	0.002	15.546	0.137	0.137	0.000	0.000	0.000	0.000
64	A	70	GLN	0	0.018	0.011	18.992	0.117	0.117	0.000	0.000	0.000	0.000
65	A	71	ASP	-1	-0.880	-0.911	18.203	-14.154	-14.154	0.000	0.000	0.000	0.000
66	A	72	THR	0	-0.017	-0.022	19.331	0.419	0.419	0.000	0.000	0.000	0.000
67	A	73	SER	0	-0.082	-0.043	21.647	0.610	0.610	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.060	0.024	23.223	0.443	0.443	0.000	0.000	0.000	0.000
69	A	75	THR	0	-0.010	-0.003	21.795	0.461	0.461	0.000	0.000	0.000	0.000
70	A	76	SER	0	0.002	-0.030	21.006	-0.443	-0.443	0.000	0.000	0.000	0.000
71	A	77	PRO	0	-0.016	-0.019	18.881	0.161	0.161	0.000	0.000	0.000	0.000
72	A	78	VAL	0	0.047	0.027	21.461	0.032	0.032	0.000	0.000	0.000	0.000
73	A	79	HIS	0	0.065	0.042	24.823	-0.084	-0.084	0.000	0.000	0.000	0.000
74	A	80	ASP	-1	-0.861	-0.928	20.988	-13.493	-13.493	0.000	0.000	0.000	0.000
75	A	81	ALA	0	-0.041	-0.018	24.121	0.106	0.106	0.000	0.000	0.000	0.000
76	A	82	ALA	0	-0.002	0.004	25.332	0.254	0.254	0.000	0.000	0.000	0.000
77	A	83	ARG	1	0.917	0.958	23.722	12.399	12.399	0.000	0.000	0.000	0.000
78	A	84	THR	0	-0.085	-0.069	24.337	0.072	0.072	0.000	0.000	0.000	0.000
79	A	85	GLY	0	0.033	0.035	27.399	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	86	PHE	0	-0.030	-0.014	24.189	0.102	0.102	0.000	0.000	0.000	0.000
81	A	87	LEU	0	0.025	0.005	27.712	-0.153	-0.153	0.000	0.000	0.000	0.000
82	A	88	ASP	-1	-0.888	-0.942	28.146	-10.466	-10.466	0.000	0.000	0.000	0.000
83	A	89	THR	0	-0.046	-0.051	22.640	-0.079	-0.079	0.000	0.000	0.000	0.000
84	A	90	LEU	0	0.022	0.013	25.639	-0.150	-0.150	0.000	0.000	0.000	0.000
85	A	91	LYS	1	0.944	0.979	27.474	9.403	9.403	0.000	0.000	0.000	0.000
86	A	92	VAL	0	0.003	0.009	24.150	0.040	0.040	0.000	0.000	0.000	0.000
87	A	93	LEU	0	-0.038	-0.026	21.503	-0.150	-0.150	0.000	0.000	0.000	0.000
88	A	94	VAL	0	0.015	0.005	25.303	0.010	0.010	0.000	0.000	0.000	0.000
89	A	95	GLU	-1	-0.986	-0.978	28.511	-10.047	-10.047	0.000	0.000	0.000	0.000
90	A	96	HIS	0	-0.100	-0.057	24.263	0.026	0.026	0.000	0.000	0.000	0.000
91	A	97	GLY	0	0.010	0.004	25.148	-0.291	-0.291	0.000	0.000	0.000	0.000
92	A	98	ALA	0	-0.063	-0.028	24.716	-0.054	-0.054	0.000	0.000	0.000	0.000
93	A	99	ASP	-1	-0.889	-0.941	26.091	-9.201	-9.201	0.000	0.000	0.000	0.000
94	A	100	VAL	0	0.005	-0.007	28.082	-0.302	-0.302	0.000	0.000	0.000	0.000
95	A	101	ASN	0	0.012	-0.005	30.463	0.188	0.188	0.000	0.000	0.000	0.000
96	A	102	VAL	0	-0.027	-0.005	27.034	0.223	0.223	0.000	0.000	0.000	0.000
97	A	103	PRO	0	-0.034	-0.015	29.309	-0.188	-0.188	0.000	0.000	0.000	0.000
98	A	104	ASP	-1	-0.756	-0.850	26.944	-10.427	-10.427	0.000	0.000	0.000	0.000
99	A	105	GLY	0	0.001	-0.014	27.374	0.342	0.342	0.000	0.000	0.000	0.000
100	A	106	THR	0	-0.153	-0.100	28.940	0.339	0.339	0.000	0.000	0.000	0.000
101	A	107	GLY	0	-0.004	-0.014	31.575	0.349	0.349	0.000	0.000	0.000	0.000
102	A	108	ALA	0	-0.026	0.000	31.101	0.252	0.252	0.000	0.000	0.000	0.000
103	A	109	LEU	0	0.020	0.015	30.942	-0.267	-0.267	0.000	0.000	0.000	0.000
104	A	110	PRO	0	0.030	0.001	28.562	0.006	0.006	0.000	0.000	0.000	0.000
105	A	111	ILE	0	0.038	0.014	30.677	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	112	HIS	0	0.028	0.019	34.026	-0.049	-0.049	0.000	0.000	0.000	0.000
107	A	113	LEU	0	-0.018	-0.011	28.271	0.046	0.046	0.000	0.000	0.000	0.000
108	A	114	ALA	0	-0.002	0.007	32.266	-0.041	-0.041	0.000	0.000	0.000	0.000
109	A	115	VAL	0	-0.005	0.001	33.492	0.109	0.109	0.000	0.000	0.000	0.000
110	A	116	GLN	0	-0.046	-0.028	34.122	0.310	0.310	0.000	0.000	0.000	0.000
111	A	117	GLU	-1	-0.964	-0.991	31.055	-9.746	-9.746	0.000	0.000	0.000	0.000
112	A	118	GLY	0	-0.057	-0.003	34.360	0.038	0.038	0.000	0.000	0.000	0.000
113	A	119	HIS	0	-0.005	-0.001	30.704	0.275	0.275	0.000	0.000	0.000	0.000
114	A	120	THR	0	0.035	0.002	35.288	-0.014	-0.014	0.000	0.000	0.000	0.000
115	A	121	ALA	0	0.015	0.006	35.497	0.071	0.071	0.000	0.000	0.000	0.000
116	A	122	VAL	0	-0.004	-0.003	31.556	0.001	0.001	0.000	0.000	0.000	0.000
117	A	123	VAL	0	0.020	0.011	34.417	0.033	0.033	0.000	0.000	0.000	0.000
118	A	124	SER	0	-0.032	-0.016	37.099	0.137	0.137	0.000	0.000	0.000	0.000
119	A	125	PHE	0	-0.029	-0.021	32.142	0.072	0.072	0.000	0.000	0.000	0.000
120	A	126	LEU	0	0.040	0.012	31.610	-0.017	-0.017	0.000	0.000	0.000	0.000
121	A	127	ALA	0	-0.018	0.004	35.717	0.072	0.072	0.000	0.000	0.000	0.000
122	A	128	ALA	0	-0.003	0.024	39.300	0.174	0.174	0.000	0.000	0.000	0.000
123	A	129	GLU	-1	-0.925	-0.993	34.452	-9.015	-9.015	0.000	0.000	0.000	0.000
124	A	130	SER	0	-0.055	-0.019	35.698	-0.200	-0.200	0.000	0.000	0.000	0.000
125	A	131	ASP	-1	-0.888	-0.946	36.813	-7.739	-7.739	0.000	0.000	0.000	0.000
126	A	132	LEU	0	0.001	-0.014	38.859	-0.065	-0.065	0.000	0.000	0.000	0.000
127	A	133	HIS	0	-0.008	-0.005	41.091	0.080	0.080	0.000	0.000	0.000	0.000
128	A	134	ARG	1	0.851	0.928	36.809	8.017	8.017	0.000	0.000	0.000	0.000
129	A	135	ARG	1	0.941	0.962	39.334	6.883	6.883	0.000	0.000	0.000	0.000
130	A	136	ASP	-1	-0.813	-0.892	35.652	-8.215	-8.215	0.000	0.000	0.000	0.000
131	A	137	ALA	0	0.001	-0.004	35.353	0.224	0.224	0.000	0.000	0.000	0.000
132	A	138	ARG	1	0.835	0.916	37.304	7.871	7.871	0.000	0.000	0.000	0.000
133	A	139	GLY	0	-0.034	-0.016	40.128	0.202	0.202	0.000	0.000	0.000	0.000
134	A	140	LEU	0	-0.014	0.004	40.449	0.189	0.189	0.000	0.000	0.000	0.000
135	A	141	THR	0	0.018	0.020	40.014	-0.200	-0.200	0.000	0.000	0.000	0.000
136	A	142	PRO	0	0.028	0.003	38.013	0.024	0.024	0.000	0.000	0.000	0.000
137	A	143	LEU	0	0.014	0.007	40.154	-0.004	-0.004	0.000	0.000	0.000	0.000
138	A	144	GLU	-1	-0.902	-0.954	43.775	-6.737	-6.737	0.000	0.000	0.000	0.000
139	A	145	LEU	0	0.002	0.000	36.906	0.045	0.045	0.000	0.000	0.000	0.000
140	A	146	ALA	0	0.036	0.041	41.741	-0.045	-0.045	0.000	0.000	0.000	0.000
141	A	147	LEU	0	-0.034	-0.025	43.022	0.137	0.137	0.000	0.000	0.000	0.000
142	A	148	GLN	0	-0.032	-0.024	42.864	-0.075	-0.075	0.000	0.000	0.000	0.000
143	A	149	ARG	1	0.818	0.919	38.962	8.126	8.126	0.000	0.000	0.000	0.000
144	A	150	GLY	0	0.018	0.019	43.711	0.000	0.000	0.000	0.000	0.000	0.000
145	A	151	ALA	0	-0.040	-0.016	42.403	0.051	0.051	0.000	0.000	0.000	0.000
146	A	152	GLN	0	0.044	-0.006	44.341	-0.109	-0.109	0.000	0.000	0.000	0.000
147	A	153	ASP	-1	-0.831	-0.897	43.800	-7.045	-7.045	0.000	0.000	0.000	0.000
148	A	154	LEU	0	-0.066	-0.042	39.426	-0.074	-0.074	0.000	0.000	0.000	0.000
149	A	155	VAL	0	-0.043	-0.016	43.077	0.008	0.008	0.000	0.000	0.000	0.000
150	A	156	ASP	-1	-0.887	-0.942	46.027	-6.474	-6.474	0.000	0.000	0.000	0.000
151	A	157	ILE	0	-0.042	-0.019	41.481	0.033	0.033	0.000	0.000	0.000	0.000
152	A	158	LEU	0	-0.029	-0.026	40.387	0.021	0.021	0.000	0.000	0.000	0.000
153	A	159	GLN	0	-0.009	-0.009	44.389	0.048	0.048	0.000	0.000	0.000	0.000
154	A	160	GLY	0	-0.036	-0.007	47.355	0.117	0.117	0.000	0.000	0.000	0.000
155	A	161	HIS	0	-0.017	-0.005	43.229	0.079	0.079	0.000	0.000	0.000	0.000
156	A	162	MET	0	-0.084	-0.032	45.914	0.097	0.097	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)