FMO DATABASE

FMODB ID: LN329

Calculation Name: 3BPV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BPV

Chain ID: A

ChEMBL ID:

UniProt ID: O26413

Base Structure: X-ray

Registration Date: 2023-09-23

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1273673.272092
FMO2-HF: Nuclear repulsion	1216679.600384
FMO2-HF: Total energy	-56993.671708
FMO2-MP2: Total energy	-57161.258543

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:5:ILE)

Summations of interaction energy for fragment #1(A:5:ILE)

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.
-5.196	-0.452	4.095	-2.31	-6.525	-0.011

Interaction energy analysis for fragmet #1(A:5:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.004

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	7	LEU	0	0.094	0.049	2.619	-3.160	-0.756	0.789	-1.389	-1.803	-0.010
4	A	8	LYS	1	0.989	0.993	5.138	-0.218	-0.075	-0.001	-0.009	-0.133	0.000
5	A	9	GLY	0	-0.005	0.009	2.642	-0.262	0.092	0.609	-0.363	-0.599	0.002
6	A	10	LEU	0	0.037	0.011	2.417	-1.054	0.049	2.489	-0.407	-3.184	-0.003
7	A	11	LEU	0	0.062	0.026	3.900	0.112	0.244	0.010	-0.001	-0.141	0.000
8	A	12	SER	0	-0.019	-0.030	6.091	0.132	0.132	0.000	0.000	0.000	0.000
9	A	13	ILE	0	-0.055	-0.019	2.750	-0.533	0.075	0.199	-0.141	-0.665	0.000
10	A	14	ILE	0	0.065	0.045	6.824	0.042	0.042	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.050	0.025	9.563	0.053	0.053	0.000	0.000	0.000	0.000
12	A	16	ARG	1	0.889	0.952	5.845	-0.084	-0.084	0.000	0.000	0.000	0.000
13	A	17	SER	0	-0.018	-0.013	11.134	0.013	0.013	0.000	0.000	0.000	0.000
14	A	18	HIS	1	0.820	0.889	13.108	0.135	0.135	0.000	0.000	0.000	0.000
15	A	19	ARG	1	0.879	0.911	12.855	0.006	0.006	0.000	0.000	0.000	0.000
16	A	20	VAL	0	-0.028	-0.020	14.730	0.013	0.013	0.000	0.000	0.000	0.000
17	A	21	PHE	0	0.009	0.009	17.105	0.007	0.007	0.000	0.000	0.000	0.000
18	A	22	ILE	0	0.050	0.020	19.085	0.010	0.010	0.000	0.000	0.000	0.000
19	A	23	GLY	0	-0.022	-0.008	20.253	0.008	0.008	0.000	0.000	0.000	0.000
20	A	24	ARG	1	0.857	0.924	20.768	0.071	0.071	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.788	-0.853	22.989	-0.094	-0.094	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.005	-0.003	24.581	0.003	0.003	0.000	0.000	0.000	0.000
23	A	27	GLY	0	0.047	0.032	26.093	0.007	0.007	0.000	0.000	0.000	0.000
24	A	28	HIS	0	-0.019	-0.007	27.092	0.007	0.007	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.006	-0.001	29.637	0.003	0.003	0.000	0.000	0.000	0.000
26	A	30	ASN	0	-0.006	0.003	28.784	0.004	0.004	0.000	0.000	0.000	0.000
27	A	31	LEU	0	0.062	0.053	25.798	0.005	0.005	0.000	0.000	0.000	0.000
28	A	32	THR	0	0.001	-0.007	21.525	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	33	ASP	-1	-0.780	-0.873	16.903	-0.048	-0.048	0.000	0.000	0.000	0.000
30	A	34	ALA	0	0.044	0.025	20.036	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	35	GLN	0	-0.030	-0.029	21.322	0.003	0.003	0.000	0.000	0.000	0.000
32	A	36	VAL	0	0.052	0.025	22.521	0.000	0.000	0.000	0.000	0.000	0.000
33	A	37	ALA	0	0.008	0.007	20.723	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	38	CYS	0	-0.041	-0.030	22.864	0.003	0.003	0.000	0.000	0.000	0.000
35	A	39	LEU	0	0.028	0.021	25.825	0.000	0.000	0.000	0.000	0.000	0.000
36	A	40	LEU	0	0.018	0.001	23.810	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.710	0.845	25.009	0.015	0.015	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.015	0.014	27.043	0.002	0.002	0.000	0.000	0.000	0.000
39	A	43	HIS	0	0.048	0.020	30.272	0.002	0.002	0.000	0.000	0.000	0.000
40	A	44	ARG	1	0.781	0.882	27.409	0.029	0.029	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.830	-0.893	30.695	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	46	PRO	0	0.041	0.035	32.768	0.003	0.003	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.067	0.030	35.583	0.000	0.000	0.000	0.000	0.000	0.000
44	A	48	ILE	0	-0.082	-0.021	29.937	0.003	0.003	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.844	0.910	34.273	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	50	GLN	0	0.006	-0.007	31.302	0.000	0.000	0.000	0.000	0.000	0.000
47	A	51	ASP	-1	-0.879	-0.936	30.265	0.024	0.024	0.000	0.000	0.000	0.000
48	A	52	GLU	-1	-0.749	-0.839	29.767	0.012	0.012	0.000	0.000	0.000	0.000
49	A	53	LEU	0	0.021	0.012	27.055	0.000	0.000	0.000	0.000	0.000	0.000
50	A	54	ALA	0	-0.052	-0.044	25.943	0.001	0.001	0.000	0.000	0.000	0.000
51	A	55	THR	0	-0.038	-0.038	24.872	0.007	0.007	0.000	0.000	0.000	0.000
52	A	56	PHE	0	0.000	0.004	22.783	0.000	0.000	0.000	0.000	0.000	0.000
53	A	57	PHE	0	-0.020	-0.024	20.785	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	58	HIS	0	-0.027	0.003	19.722	0.015	0.015	0.000	0.000	0.000	0.000
55	A	59	VAL	0	-0.029	0.002	19.035	0.016	0.016	0.000	0.000	0.000	0.000
56	A	60	ASP	-1	-0.783	-0.856	21.277	0.078	0.078	0.000	0.000	0.000	0.000
57	A	61	LYS	1	0.993	0.961	23.719	-0.053	-0.053	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.004	0.014	26.311	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	63	THR	0	-0.035	-0.058	20.933	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	64	ILE	0	0.024	0.032	24.319	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	65	ALA	0	0.008	0.010	25.970	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.914	0.952	26.460	-0.044	-0.044	0.000	0.000	0.000	0.000
63	A	67	THR	0	-0.059	-0.039	24.282	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	68	LEU	0	0.024	0.007	26.775	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	69	ARG	1	0.998	1.002	29.885	-0.024	-0.024	0.000	0.000	0.000	0.000
66	A	70	ARG	1	0.865	0.931	26.583	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	71	LEU	0	0.003	0.019	27.840	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	72	GLU	-1	-0.857	-0.918	31.536	0.007	0.007	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.960	-0.980	34.213	0.003	0.003	0.000	0.000	0.000	0.000
70	A	74	SER	0	-0.083	-0.054	32.431	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	75	GLY	0	0.023	0.029	34.889	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	76	PHE	0	-0.045	-0.023	30.946	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	77	ILE	0	-0.039	-0.031	31.326	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.891	-0.947	34.837	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	79	ARG	1	0.795	0.881	34.803	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.887	-0.922	38.178	0.001	0.001	0.000	0.000	0.000	0.000
77	A	81	GLN	0	-0.053	-0.039	39.859	0.003	0.003	0.000	0.000	0.000	0.000
78	A	82	ASP	-1	-0.756	-0.908	39.464	0.010	0.010	0.000	0.000	0.000	0.000
79	A	83	PRO	0	-0.018	-0.007	41.501	0.002	0.002	0.000	0.000	0.000	0.000
80	A	84	GLU	-1	-0.866	-0.911	41.881	0.008	0.008	0.000	0.000	0.000	0.000
81	A	85	ASN	0	-0.035	-0.036	40.365	0.003	0.003	0.000	0.000	0.000	0.000
82	A	86	ARG	1	1.021	1.012	41.446	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.842	0.923	38.996	-0.027	-0.027	0.000	0.000	0.000	0.000
84	A	88	ARG	1	0.738	0.856	34.920	-0.014	-0.014	0.000	0.000	0.000	0.000
85	A	89	TYR	0	0.008	-0.002	36.126	0.000	0.000	0.000	0.000	0.000	0.000
86	A	90	ILE	0	0.036	0.037	35.987	0.001	0.001	0.000	0.000	0.000	0.000
87	A	91	LEU	0	-0.039	-0.024	31.509	0.001	0.001	0.000	0.000	0.000	0.000
88	A	92	GLU	-1	-0.859	-0.933	35.442	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	93	VAL	0	-0.050	-0.020	32.566	0.001	0.001	0.000	0.000	0.000	0.000
90	A	94	THR	0	0.050	0.021	35.442	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	95	ARG	1	0.911	0.936	37.218	0.019	0.019	0.000	0.000	0.000	0.000
92	A	96	ARG	1	0.940	0.981	34.527	0.025	0.025	0.000	0.000	0.000	0.000
93	A	97	GLY	0	0.011	0.003	33.854	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	98	GLU	-1	-0.861	-0.929	33.339	-0.031	-0.031	0.000	0.000	0.000	0.000
95	A	99	GLU	-1	-0.917	-0.973	34.634	-0.032	-0.032	0.000	0.000	0.000	0.000
96	A	100	ILE	0	-0.069	-0.028	30.973	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	101	ILE	0	0.005	0.015	29.465	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	102	PRO	0	0.012	-0.002	29.640	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	103	LEU	0	-0.007	0.003	30.211	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	104	ILE	0	0.012	0.002	24.931	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	105	LEU	0	0.002	0.001	25.394	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	106	LYS	1	0.850	0.906	26.007	0.086	0.086	0.000	0.000	0.000	0.000
103	A	107	VAL	0	-0.024	-0.008	22.365	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	108	GLU	-1	-0.833	-0.901	20.274	-0.129	-0.129	0.000	0.000	0.000	0.000
105	A	109	GLU	-1	-0.826	-0.890	21.434	-0.122	-0.122	0.000	0.000	0.000	0.000
106	A	110	ARG	1	0.841	0.883	22.779	0.092	0.092	0.000	0.000	0.000	0.000
107	A	111	TRP	0	-0.028	-0.013	13.383	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	112	GLU	-1	-0.798	-0.878	18.144	-0.222	-0.222	0.000	0.000	0.000	0.000
109	A	113	ASP	-1	-0.793	-0.889	19.033	-0.187	-0.187	0.000	0.000	0.000	0.000
110	A	114	LEU	0	-0.078	-0.037	18.831	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	115	LEU	0	-0.057	-0.018	12.322	-0.028	-0.028	0.000	0.000	0.000	0.000
112	A	116	PHE	0	-0.022	-0.017	15.403	-0.043	-0.043	0.000	0.000	0.000	0.000
113	A	117	ARG	1	0.865	0.931	16.701	0.269	0.269	0.000	0.000	0.000	0.000
114	A	118	ASP	-1	-0.941	-0.953	16.007	-0.309	-0.309	0.000	0.000	0.000	0.000
115	A	119	PHE	0	-0.047	-0.018	13.039	-0.040	-0.040	0.000	0.000	0.000	0.000
116	A	120	THR	0	-0.011	-0.038	18.790	0.038	0.038	0.000	0.000	0.000	0.000
117	A	121	GLU	-1	-0.843	-0.944	21.410	-0.199	-0.199	0.000	0.000	0.000	0.000
118	A	122	ASP	-1	-0.863	-0.926	23.621	-0.169	-0.169	0.000	0.000	0.000	0.000
119	A	123	GLU	-1	-0.813	-0.868	18.213	-0.333	-0.333	0.000	0.000	0.000	0.000
120	A	124	ARG	1	0.789	0.892	18.848	0.172	0.172	0.000	0.000	0.000	0.000
121	A	125	LYS	1	0.855	0.914	20.011	0.161	0.161	0.000	0.000	0.000	0.000
122	A	126	LEU	0	-0.031	-0.019	18.732	0.013	0.013	0.000	0.000	0.000	0.000
123	A	127	PHE	0	0.036	0.014	11.953	0.002	0.002	0.000	0.000	0.000	0.000
124	A	128	ARG	1	0.870	0.912	17.047	0.183	0.183	0.000	0.000	0.000	0.000
125	A	129	LYS	1	0.920	0.956	19.268	0.169	0.169	0.000	0.000	0.000	0.000
126	A	130	MET	0	-0.039	-0.018	15.281	0.023	0.023	0.000	0.000	0.000	0.000
127	A	131	CYS	0	0.017	0.002	15.416	0.006	0.006	0.000	0.000	0.000	0.000
128	A	132	ARG	1	0.919	0.977	16.345	0.136	0.136	0.000	0.000	0.000	0.000
129	A	133	ARG	1	0.991	0.993	19.237	0.174	0.174	0.000	0.000	0.000	0.000
130	A	134	LEU	0	-0.001	0.003	12.670	0.012	0.012	0.000	0.000	0.000	0.000
131	A	135	ALA	0	-0.004	0.003	16.580	0.023	0.023	0.000	0.000	0.000	0.000
132	A	136	GLU	-1	-0.929	-0.982	18.102	-0.085	-0.085	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.818	-0.875	17.815	-0.042	-0.042	0.000	0.000	0.000	0.000
134	A	138	ALA	0	-0.016	-0.007	16.275	0.020	0.020	0.000	0.000	0.000	0.000
135	A	139	VAL	0	-0.040	-0.017	18.165	0.020	0.020	0.000	0.000	0.000	0.000
136	A	140	ARG	1	0.786	0.869	21.808	0.070	0.070	0.000	0.000	0.000	0.000
137	A	141	MET	0	-0.091	-0.037	16.239	0.018	0.018	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ILE)