FMO DATABASE

FMODB ID: ZVL1N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-490820.098516
FMO2-HF: Nuclear repulsion	456387.7031
FMO2-HF: Total energy	-34432.395415
FMO2-MP2: Total energy	-34533.311291

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.
-15.853	-8.515	8.707	-5.316	-10.728	-0.033

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 : 0.005 / q_NPA : 0.017

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	0.882	0.923	2.932	-1.446	1.948	0.385	-1.883	-1.896	0.002
4	B	4	GLY	0	0.094	0.047	5.294	0.823	0.977	-0.001	-0.005	-0.147	0.000
5	B	5	GLU	-1	-0.844	-0.910	2.267	-11.053	-8.726	4.644	-3.036	-3.935	-0.030
6	B	6	LEU	0	-0.017	-0.022	2.532	-1.581	0.709	3.583	-1.829	-4.043	-0.005
7	B	7	VAL	0	-0.051	-0.021	3.908	0.845	-0.394	0.059	1.517	-0.338	0.000
8	B	8	ASP	-1	-0.876	-0.937	5.558	-0.649	-0.649	0.000	0.000	0.000	0.000
9	B	9	ALA	0	0.021	0.006	3.395	-0.134	0.206	0.038	-0.078	-0.300	0.000
10	B	10	VAL	0	-0.059	-0.035	5.370	0.088	0.160	-0.001	-0.002	-0.069	0.000
11	B	11	ALA	0	-0.044	-0.033	7.798	-0.139	-0.139	0.000	0.000	0.000	0.000
12	B	12	GLU	-1	-0.926	-0.943	8.890	0.008	0.008	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.915	0.951	5.581	-1.745	-1.745	0.000	0.000	0.000	0.000
14	B	14	ALA	0	-0.010	-0.002	10.677	-0.034	-0.034	0.000	0.000	0.000	0.000
15	B	15	SER	0	-0.017	0.009	13.171	-0.076	-0.076	0.000	0.000	0.000	0.000
16	B	16	VAL	0	-0.048	-0.019	13.287	-0.033	-0.033	0.000	0.000	0.000	0.000
17	B	17	THR	0	-0.005	-0.015	14.468	-0.049	-0.049	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.928	0.944	9.751	0.682	0.682	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.981	0.986	12.668	0.105	0.105	0.000	0.000	0.000	0.000
20	B	20	GLN	0	0.013	0.012	15.554	-0.005	-0.005	0.000	0.000	0.000	0.000
21	B	21	ALA	0	0.075	0.033	10.880	-0.003	-0.003	0.000	0.000	0.000	0.000
22	B	22	ASP	-1	-0.802	-0.883	10.904	-0.437	-0.437	0.000	0.000	0.000	0.000
23	B	23	ALA	0	0.028	0.026	11.953	0.011	0.011	0.000	0.000	0.000	0.000
24	B	24	VAL	0	-0.024	-0.011	14.165	0.007	0.007	0.000	0.000	0.000	0.000
25	B	25	LEU	0	-0.008	-0.009	7.098	0.018	0.018	0.000	0.000	0.000	0.000
26	B	26	THR	0	-0.020	-0.031	11.680	-0.071	-0.071	0.000	0.000	0.000	0.000
27	B	27	ALA	0	0.073	0.051	13.280	0.001	0.001	0.000	0.000	0.000	0.000
28	B	28	ALA	0	-0.007	0.004	13.377	-0.009	-0.009	0.000	0.000	0.000	0.000
29	B	29	LEU	0	-0.047	-0.024	9.124	-0.006	-0.006	0.000	0.000	0.000	0.000
30	B	30	GLU	-1	-0.907	-0.958	13.730	-0.207	-0.207	0.000	0.000	0.000	0.000
31	B	31	THR	0	0.004	-0.008	17.028	0.003	0.003	0.000	0.000	0.000	0.000
32	B	32	ILE	0	-0.058	-0.024	13.956	0.014	0.014	0.000	0.000	0.000	0.000
33	B	33	ILE	0	-0.003	-0.002	14.760	-0.008	-0.008	0.000	0.000	0.000	0.000
34	B	34	GLU	-1	-0.904	-0.944	18.494	-0.081	-0.081	0.000	0.000	0.000	0.000
35	B	35	ALA	0	-0.006	0.003	21.115	0.002	0.002	0.000	0.000	0.000	0.000
36	B	36	VAL	0	-0.034	-0.024	19.159	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	37	SER	0	-0.055	-0.037	21.896	-0.010	-0.010	0.000	0.000	0.000	0.000
38	B	38	SER	0	-0.105	-0.041	24.113	0.004	0.004	0.000	0.000	0.000	0.000
39	B	39	GLY	0	-0.034	-0.021	25.937	0.004	0.004	0.000	0.000	0.000	0.000
40	B	40	ASP	-1	-0.950	-0.967	24.735	0.118	0.118	0.000	0.000	0.000	0.000
41	B	41	LYS	1	0.828	0.909	22.984	-0.175	-0.175	0.000	0.000	0.000	0.000
42	B	42	VAL	0	0.045	0.036	18.388	0.022	0.022	0.000	0.000	0.000	0.000
43	B	43	THR	0	-0.033	-0.036	19.874	0.029	0.029	0.000	0.000	0.000	0.000
44	B	44	LEU	0	0.010	0.018	14.722	-0.003	-0.003	0.000	0.000	0.000	0.000
45	B	45	VAL	0	0.045	-0.003	17.773	0.043	0.043	0.000	0.000	0.000	0.000
46	B	46	GLY	0	-0.011	0.002	17.243	0.047	0.047	0.000	0.000	0.000	0.000
47	B	47	PHE	0	0.016	0.008	10.153	0.105	0.105	0.000	0.000	0.000	0.000
48	B	48	GLY	0	0.029	0.006	15.015	0.002	0.002	0.000	0.000	0.000	0.000
49	B	49	SER	0	-0.069	-0.024	17.257	-0.020	-0.020	0.000	0.000	0.000	0.000
50	B	50	PHE	0	0.047	0.017	12.739	0.001	0.001	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.742	-0.844	18.952	0.132	0.132	0.000	0.000	0.000	0.000
52	B	52	SER	0	0.073	0.051	21.589	-0.018	-0.018	0.000	0.000	0.000	0.000
53	B	53	ARG	1	0.796	0.875	22.360	-0.093	-0.093	0.000	0.000	0.000	0.000
54	B	54	GLU	-1	-0.757	-0.849	25.986	-0.029	-0.029	0.000	0.000	0.000	0.000
55	B	55	ARG	1	0.842	0.926	23.909	0.012	0.012	0.000	0.000	0.000	0.000
56	B	56	LYS	1	0.991	0.981	29.274	-0.008	-0.008	0.000	0.000	0.000	0.000
57	B	57	ALA	0	0.055	0.038	31.366	-0.005	-0.005	0.000	0.000	0.000	0.000
58	B	58	ARG	1	0.926	0.963	26.083	0.088	0.088	0.000	0.000	0.000	0.000
59	B	59	GLU	-1	-0.793	-0.882	33.130	-0.043	-0.043	0.000	0.000	0.000	0.000
60	B	60	GLY	0	-0.006	-0.006	31.667	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	61	ARG	1	0.867	0.920	31.765	0.070	0.070	0.000	0.000	0.000	0.000
62	B	62	ASN	0	0.036	0.023	31.851	-0.017	-0.017	0.000	0.000	0.000	0.000
63	B	63	PRO	0	0.006	0.017	29.102	0.006	0.006	0.000	0.000	0.000	0.000
64	B	64	LYS	1	0.910	0.956	29.996	0.166	0.166	0.000	0.000	0.000	0.000
65	B	65	THR	0	0.024	-0.038	34.338	0.002	0.002	0.000	0.000	0.000	0.000
66	B	66	ASN	0	-0.004	-0.011	35.920	0.007	0.007	0.000	0.000	0.000	0.000
67	B	67	GLU	-1	-0.832	-0.854	36.961	-0.074	-0.074	0.000	0.000	0.000	0.000
68	B	68	LYS	1	0.803	0.887	36.478	0.036	0.036	0.000	0.000	0.000	0.000
69	B	69	MET	0	-0.021	-0.002	31.883	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	70	GLU	-1	-0.904	-0.954	35.105	-0.045	-0.045	0.000	0.000	0.000	0.000
71	B	71	ILE	0	-0.051	-0.032	28.458	-0.009	-0.009	0.000	0.000	0.000	0.000
72	B	72	PRO	0	0.057	0.017	31.201	0.010	0.010	0.000	0.000	0.000	0.000
73	B	73	ALA	0	-0.010	-0.005	30.753	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	74	THR	0	-0.001	-0.004	26.561	-0.007	-0.007	0.000	0.000	0.000	0.000
75	B	75	ARG	1	0.903	0.924	26.442	0.041	0.041	0.000	0.000	0.000	0.000
76	B	76	VAL	0	-0.050	-0.018	21.752	-0.021	-0.021	0.000	0.000	0.000	0.000
77	B	77	PRO	0	0.056	0.035	18.269	0.031	0.031	0.000	0.000	0.000	0.000
78	B	78	ALA	0	-0.057	-0.034	19.112	-0.011	-0.011	0.000	0.000	0.000	0.000
79	B	79	PHE	0	0.041	0.016	13.337	0.020	0.020	0.000	0.000	0.000	0.000
80	B	80	SER	0	-0.064	-0.029	17.278	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	81	ALA	0	0.040	0.033	15.050	0.026	0.026	0.000	0.000	0.000	0.000
82	B	82	GLY	0	0.034	0.005	16.621	-0.068	-0.068	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.953	0.959	18.009	-0.268	-0.268	0.000	0.000	0.000	0.000
84	B	84	LEU	0	0.056	0.047	15.678	0.012	0.012	0.000	0.000	0.000	0.000
85	B	85	PHE	0	0.004	0.002	9.702	0.052	0.052	0.000	0.000	0.000	0.000
86	B	86	ARG	1	0.887	0.914	14.891	-0.330	-0.330	0.000	0.000	0.000	0.000
87	B	87	GLU	-1	-0.906	-0.948	17.158	0.455	0.455	0.000	0.000	0.000	0.000
88	B	88	LYS	1	0.894	0.948	13.673	-0.903	-0.903	0.000	0.000	0.000	0.000
89	B	89	VAL	0	-0.036	-0.017	12.036	0.047	0.047	0.000	0.000	0.000	0.000
90	B	90	ALA	0	-0.011	-0.001	14.542	-0.030	-0.030	0.000	0.000	0.000	0.000
91	B	91	PRO	0	-0.006	0.006	17.468	-0.043	-0.043	0.000	0.000	0.000	0.000
92	B	92	PRO	0	-0.020	0.005	20.407	-0.039	-0.039	0.000	0.000	0.000	0.000

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