FMO DATABASE

FMODB ID: R8MV8

Calculation Name: 1P78-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P78

Chain ID: B

ChEMBL ID:

UniProt ID: P05514

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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-490223.836866
FMO2-HF: Nuclear repulsion	455791.00153
FMO2-HF: Total energy	-34432.835337
FMO2-MP2: Total energy	-34533.66902

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1:MET)

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.
-13.408	-7.991	11.094	-4.522	-11.989	-0.036

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / 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

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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	B	3	LYS	1	0.862	0.907	3.109	-1.681	1.355	0.297	-1.730	-1.603	0.002
4	B	4	GLY	0	0.045	0.017	5.492	0.898	0.898	0.000	0.000	0.000	0.000
5	B	5	GLU	-1	-0.807	-0.887	2.201	-9.208	-6.706	3.970	-2.678	-3.793	-0.023
6	B	6	LEU	0	-0.007	-0.011	2.422	-2.354	-0.348	6.462	-3.073	-5.396	-0.014
7	B	7	VAL	0	-0.019	-0.014	3.679	2.131	-0.609	0.048	3.140	-0.448	-0.001
8	B	8	ASP	-1	-0.822	-0.899	5.162	-0.603	-0.603	0.000	0.000	0.000	0.000
9	B	9	ALA	0	0.018	0.013	3.029	-0.274	0.199	0.319	-0.176	-0.616	0.000
10	B	10	VAL	0	-0.043	-0.019	4.835	0.424	0.523	-0.001	-0.005	-0.093	0.000
11	B	11	ALA	0	-0.018	-0.017	7.683	-0.147	-0.147	0.000	0.000	0.000	0.000
12	B	12	GLU	-1	-0.914	-0.947	8.100	0.060	0.060	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.850	0.917	4.721	-1.814	-1.773	-0.001	0.000	-0.040	0.000
14	B	14	ALA	0	-0.008	-0.001	10.714	-0.020	-0.020	0.000	0.000	0.000	0.000
15	B	15	SER	0	-0.043	-0.009	12.999	-0.076	-0.076	0.000	0.000	0.000	0.000
16	B	16	VAL	0	-0.045	-0.005	13.084	-0.039	-0.039	0.000	0.000	0.000	0.000
17	B	17	THR	0	0.010	-0.013	13.753	-0.039	-0.039	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.911	0.928	9.374	0.661	0.661	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.980	0.987	12.307	0.139	0.139	0.000	0.000	0.000	0.000
20	B	20	GLN	0	0.025	0.025	15.080	-0.020	-0.020	0.000	0.000	0.000	0.000
21	B	21	ALA	0	0.059	0.027	10.388	0.017	0.017	0.000	0.000	0.000	0.000
22	B	22	ASP	-1	-0.817	-0.902	10.802	-0.535	-0.535	0.000	0.000	0.000	0.000
23	B	23	ALA	0	0.016	0.028	11.947	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	24	VAL	0	0.001	0.000	14.190	0.004	0.004	0.000	0.000	0.000	0.000
25	B	25	LEU	0	-0.013	-0.005	7.076	0.028	0.028	0.000	0.000	0.000	0.000
26	B	26	THR	0	-0.030	-0.031	11.650	-0.086	-0.086	0.000	0.000	0.000	0.000
27	B	27	ALA	0	0.094	0.055	13.383	0.003	0.003	0.000	0.000	0.000	0.000
28	B	28	ALA	0	-0.030	0.005	13.245	0.009	0.009	0.000	0.000	0.000	0.000
29	B	29	LEU	0	-0.038	-0.026	9.114	-0.008	-0.008	0.000	0.000	0.000	0.000
30	B	30	GLU	-1	-0.894	-0.958	13.711	-0.213	-0.213	0.000	0.000	0.000	0.000
31	B	31	THR	0	-0.017	-0.021	17.067	0.006	0.006	0.000	0.000	0.000	0.000
32	B	32	ILE	0	-0.060	-0.032	13.843	0.015	0.015	0.000	0.000	0.000	0.000
33	B	33	ILE	0	-0.006	0.000	14.893	-0.008	-0.008	0.000	0.000	0.000	0.000
34	B	34	GLU	-1	-0.870	-0.922	18.574	-0.107	-0.107	0.000	0.000	0.000	0.000
35	B	35	ALA	0	-0.013	0.013	21.124	0.006	0.006	0.000	0.000	0.000	0.000
36	B	36	VAL	0	-0.033	-0.021	19.205	0.001	0.001	0.000	0.000	0.000	0.000
37	B	37	SER	0	-0.073	-0.053	21.789	-0.009	-0.009	0.000	0.000	0.000	0.000
38	B	38	SER	0	-0.082	-0.052	24.053	0.004	0.004	0.000	0.000	0.000	0.000
39	B	39	GLY	0	-0.035	-0.016	25.692	0.003	0.003	0.000	0.000	0.000	0.000
40	B	40	ASP	-1	-0.902	-0.937	24.580	0.096	0.096	0.000	0.000	0.000	0.000
41	B	41	LYS	1	0.795	0.889	23.057	-0.136	-0.136	0.000	0.000	0.000	0.000
42	B	42	VAL	0	0.072	0.038	18.364	0.029	0.029	0.000	0.000	0.000	0.000
43	B	43	THR	0	-0.034	-0.036	19.573	0.025	0.025	0.000	0.000	0.000	0.000
44	B	44	LEU	0	-0.006	0.011	14.625	0.004	0.004	0.000	0.000	0.000	0.000
45	B	45	VAL	0	0.054	0.005	17.593	0.051	0.051	0.000	0.000	0.000	0.000
46	B	46	GLY	0	0.006	0.010	17.041	0.035	0.035	0.000	0.000	0.000	0.000
47	B	47	PHE	0	-0.009	-0.001	10.385	0.085	0.085	0.000	0.000	0.000	0.000
48	B	48	GLY	0	0.018	-0.009	15.012	-0.006	-0.006	0.000	0.000	0.000	0.000
49	B	49	SER	0	-0.069	-0.015	17.471	-0.018	-0.018	0.000	0.000	0.000	0.000
50	B	50	PHE	0	0.037	0.011	12.592	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.750	-0.848	18.825	0.098	0.098	0.000	0.000	0.000	0.000
52	B	52	SER	0	0.067	0.042	21.444	-0.025	-0.025	0.000	0.000	0.000	0.000
53	B	53	ARG	1	0.790	0.873	22.104	-0.049	-0.049	0.000	0.000	0.000	0.000
54	B	54	GLU	-1	-0.731	-0.827	26.174	-0.045	-0.045	0.000	0.000	0.000	0.000
55	B	55	ARG	1	0.833	0.914	24.677	0.036	0.036	0.000	0.000	0.000	0.000
56	B	56	LYS	1	0.997	0.993	29.785	0.008	0.008	0.000	0.000	0.000	0.000
57	B	57	ALA	0	0.049	0.041	32.003	-0.005	-0.005	0.000	0.000	0.000	0.000
58	B	58	ARG	1	0.911	0.960	26.647	0.101	0.101	0.000	0.000	0.000	0.000
59	B	59	GLU	-1	-0.775	-0.870	33.720	-0.052	-0.052	0.000	0.000	0.000	0.000
60	B	60	GLY	0	0.006	-0.009	32.129	-0.005	-0.005	0.000	0.000	0.000	0.000
61	B	61	ARG	1	0.867	0.922	32.172	0.077	0.077	0.000	0.000	0.000	0.000
62	B	62	ASN	0	0.076	0.049	32.214	-0.018	-0.018	0.000	0.000	0.000	0.000
63	B	63	PRO	0	-0.017	-0.016	29.376	0.006	0.006	0.000	0.000	0.000	0.000
64	B	64	LYS	1	0.908	0.946	29.920	0.161	0.161	0.000	0.000	0.000	0.000
65	B	65	THR	0	-0.006	-0.036	34.753	0.002	0.002	0.000	0.000	0.000	0.000
66	B	66	ASN	0	-0.008	0.001	36.492	0.006	0.006	0.000	0.000	0.000	0.000
67	B	67	GLU	-1	-0.800	-0.848	37.634	-0.081	-0.081	0.000	0.000	0.000	0.000
68	B	68	LYS	1	0.802	0.881	36.898	0.042	0.042	0.000	0.000	0.000	0.000
69	B	69	MET	0	-0.047	-0.007	32.470	0.000	0.000	0.000	0.000	0.000	0.000
70	B	70	GLU	-1	-0.889	-0.951	35.437	-0.056	-0.056	0.000	0.000	0.000	0.000
71	B	71	ILE	0	-0.054	-0.032	28.767	-0.010	-0.010	0.000	0.000	0.000	0.000
72	B	72	PRO	0	0.058	0.012	31.869	0.008	0.008	0.000	0.000	0.000	0.000
73	B	73	ALA	0	-0.014	-0.005	31.411	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	74	THR	0	-0.006	-0.005	27.311	-0.006	-0.006	0.000	0.000	0.000	0.000
75	B	75	ARG	1	0.848	0.888	26.396	0.056	0.056	0.000	0.000	0.000	0.000
76	B	76	VAL	0	-0.029	-0.009	22.041	-0.021	-0.021	0.000	0.000	0.000	0.000
77	B	77	PRO	0	0.065	0.047	18.429	0.028	0.028	0.000	0.000	0.000	0.000
78	B	78	ALA	0	-0.050	-0.034	19.200	-0.013	-0.013	0.000	0.000	0.000	0.000
79	B	79	PHE	0	0.042	0.012	13.926	0.015	0.015	0.000	0.000	0.000	0.000
80	B	80	SER	0	-0.057	-0.027	17.894	-0.007	-0.007	0.000	0.000	0.000	0.000
81	B	81	ALA	0	0.051	0.043	15.425	0.020	0.020	0.000	0.000	0.000	0.000
82	B	82	GLY	0	0.035	0.011	17.018	-0.061	-0.061	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.911	0.952	18.319	-0.252	-0.252	0.000	0.000	0.000	0.000
84	B	84	LEU	0	0.069	0.046	16.038	0.015	0.015	0.000	0.000	0.000	0.000
85	B	85	PHE	0	0.006	0.007	10.169	0.063	0.063	0.000	0.000	0.000	0.000
86	B	86	ARG	1	0.868	0.915	14.917	-0.273	-0.273	0.000	0.000	0.000	0.000
87	B	87	GLU	-1	-0.865	-0.947	17.195	0.411	0.411	0.000	0.000	0.000	0.000
88	B	88	LYS	1	0.881	0.941	13.738	-0.853	-0.853	0.000	0.000	0.000	0.000
89	B	89	VAL	0	-0.026	-0.003	12.092	0.057	0.057	0.000	0.000	0.000	0.000
90	B	90	ALA	0	-0.010	-0.011	14.635	-0.038	-0.038	0.000	0.000	0.000	0.000
91	B	91	PRO	0	-0.011	0.002	17.582	-0.033	-0.033	0.000	0.000	0.000	0.000
92	B	92	PRO	0	-0.023	0.008	20.488	-0.037	-0.037	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)