FMO DATABASE

FMODB ID: ZV85N

Calculation Name: 3ZBD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZBD

Chain ID: A

ChEMBL ID:

UniProt ID: P0C6V2

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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-893665.387641
FMO2-HF: Nuclear repulsion	848688.44195
FMO2-HF: Total energy	-44976.945691
FMO2-MP2: Total energy	-45106.062689

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:-4:HIS)

Summations of interaction energy for fragment #1(A:-4:HIS)

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.
-4.891	-1.979	1.912	-1.699	-3.125	-0.009

Interaction energy analysis for fragmet #1(A:-4:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.016

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	-2	HIS	0	0.000	-0.007	2.850	-5.468	-2.556	1.912	-1.699	-3.125	-0.009
4	A	-1	HIS	0	0.009	0.013	5.641	0.351	0.351	0.000	0.000	0.000	0.000
5	A	0	HIS	0	-0.049	-0.035	9.328	-0.103	-0.103	0.000	0.000	0.000	0.000
6	A	1	MET	0	0.005	0.019	12.195	0.108	0.108	0.000	0.000	0.000	0.000
7	A	2	SER	0	-0.011	-0.013	14.403	-0.019	-0.019	0.000	0.000	0.000	0.000
8	A	3	SER	0	-0.095	-0.065	16.532	0.056	0.056	0.000	0.000	0.000	0.000
9	A	4	LYS	1	0.843	0.926	20.162	-0.102	-0.102	0.000	0.000	0.000	0.000
10	A	5	GLN	0	-0.015	-0.018	21.710	0.006	0.006	0.000	0.000	0.000	0.000
11	A	6	PHE	0	-0.065	-0.033	25.814	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	7	LYS	1	0.827	0.908	29.719	-0.037	-0.037	0.000	0.000	0.000	0.000
13	A	8	ILE	0	-0.082	-0.038	31.086	0.000	0.000	0.000	0.000	0.000	0.000
14	A	9	LEU	0	-0.013	0.011	35.092	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	10	VAL	0	-0.033	-0.010	36.142	0.008	0.008	0.000	0.000	0.000	0.000
16	A	11	ASN	0	0.009	-0.010	38.898	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	12	GLU	-1	-0.823	-0.912	39.947	0.106	0.106	0.000	0.000	0.000	0.000
18	A	13	ASP	-1	-0.905	-0.952	43.036	0.071	0.071	0.000	0.000	0.000	0.000
19	A	14	TYR	0	-0.049	-0.031	46.079	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	15	GLN	0	0.003	0.003	46.278	0.002	0.002	0.000	0.000	0.000	0.000
21	A	16	VAL	0	-0.064	-0.039	43.643	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	17	ASN	0	-0.031	-0.018	45.962	0.009	0.009	0.000	0.000	0.000	0.000
23	A	18	VAL	0	-0.010	-0.010	41.728	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	19	PRO	0	-0.019	-0.005	42.383	0.003	0.003	0.000	0.000	0.000	0.000
25	A	20	SER	0	0.008	-0.002	40.283	0.002	0.002	0.000	0.000	0.000	0.000
26	A	21	LEU	0	-0.011	-0.017	38.326	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	22	PRO	0	0.039	0.020	38.511	0.011	0.011	0.000	0.000	0.000	0.000
28	A	23	ILE	0	0.036	0.021	31.657	0.000	0.000	0.000	0.000	0.000	0.000
29	A	24	ARG	1	0.917	0.959	33.253	-0.173	-0.173	0.000	0.000	0.000	0.000
30	A	25	ASP	-1	-0.851	-0.935	33.456	0.147	0.147	0.000	0.000	0.000	0.000
31	A	26	VAL	0	0.010	0.013	32.550	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	27	LEU	0	0.002	-0.004	27.922	0.004	0.004	0.000	0.000	0.000	0.000
33	A	28	GLN	0	-0.016	0.002	29.695	0.016	0.016	0.000	0.000	0.000	0.000
34	A	29	GLU	-1	-0.775	-0.867	31.672	0.106	0.106	0.000	0.000	0.000	0.000
35	A	30	ILE	0	0.023	0.016	27.546	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	31	LYS	1	0.845	0.916	26.822	-0.201	-0.201	0.000	0.000	0.000	0.000
37	A	32	TYR	0	-0.032	-0.006	28.682	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	33	CYS	0	0.018	0.016	31.461	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	34	TYR	0	-0.007	0.009	21.959	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	35	ARG	1	0.918	0.956	25.302	-0.087	-0.087	0.000	0.000	0.000	0.000
41	A	36	ASN	0	-0.031	-0.033	28.802	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	37	GLY	0	-0.005	0.014	31.839	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	38	PHE	0	0.022	-0.008	29.839	0.009	0.009	0.000	0.000	0.000	0.000
44	A	39	GLU	-1	-0.898	-0.939	35.205	0.043	0.043	0.000	0.000	0.000	0.000
45	A	40	GLY	0	0.002	-0.001	38.798	0.004	0.004	0.000	0.000	0.000	0.000
46	A	41	TYR	0	-0.109	-0.100	36.795	0.007	0.007	0.000	0.000	0.000	0.000
47	A	42	VAL	0	0.003	0.008	38.584	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	43	PHE	0	-0.003	-0.012	32.637	0.009	0.009	0.000	0.000	0.000	0.000
49	A	44	VAL	0	0.008	0.005	36.515	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	45	PRO	0	0.034	0.024	35.370	0.013	0.013	0.000	0.000	0.000	0.000
51	A	46	GLU	-1	-0.865	-0.921	34.257	0.171	0.171	0.000	0.000	0.000	0.000
52	A	47	TYR	0	-0.050	-0.053	36.035	0.001	0.001	0.000	0.000	0.000	0.000
53	A	48	CYS	0	-0.043	-0.015	39.066	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	49	ARG	1	0.757	0.847	36.412	-0.180	-0.180	0.000	0.000	0.000	0.000
55	A	50	ASP	-1	-0.894	-0.947	40.688	0.122	0.122	0.000	0.000	0.000	0.000
56	A	51	LEU	0	-0.045	0.004	43.274	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	52	VAL	0	-0.033	-0.017	40.545	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	53	ASP	-1	-0.809	-0.890	43.803	0.107	0.107	0.000	0.000	0.000	0.000
59	A	54	CYS	0	-0.032	-0.019	44.020	0.003	0.003	0.000	0.000	0.000	0.000
60	A	55	ASP	-1	-0.870	-0.919	46.138	0.094	0.094	0.000	0.000	0.000	0.000
61	A	56	ARG	1	0.805	0.871	44.428	-0.120	-0.120	0.000	0.000	0.000	0.000
62	A	57	LYS	1	0.873	0.935	43.201	-0.111	-0.111	0.000	0.000	0.000	0.000
63	A	58	ASP	-1	-0.850	-0.898	42.051	0.141	0.141	0.000	0.000	0.000	0.000
64	A	59	HIS	0	-0.030	-0.019	40.098	0.014	0.014	0.000	0.000	0.000	0.000
65	A	60	TYR	0	-0.021	-0.018	34.648	0.006	0.006	0.000	0.000	0.000	0.000
66	A	61	VAL	0	0.037	0.014	35.952	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	62	ILE	0	0.002	-0.003	30.897	0.018	0.018	0.000	0.000	0.000	0.000
68	A	63	GLY	0	0.039	0.024	31.459	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	64	VAL	0	0.010	0.004	27.975	0.010	0.010	0.000	0.000	0.000	0.000
70	A	65	LEU	0	-0.028	-0.015	25.966	0.003	0.003	0.000	0.000	0.000	0.000
71	A	66	GLY	0	0.014	0.008	23.496	0.023	0.023	0.000	0.000	0.000	0.000
72	A	67	ASN	0	0.060	0.032	23.424	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	68	GLY	0	-0.009	0.002	21.948	0.031	0.031	0.000	0.000	0.000	0.000
74	A	69	VAL	0	0.003	-0.001	18.929	-0.028	-0.028	0.000	0.000	0.000	0.000
75	A	70	SER	0	-0.006	0.001	21.071	0.041	0.041	0.000	0.000	0.000	0.000
76	A	71	ASP	-1	-0.850	-0.925	21.440	0.428	0.428	0.000	0.000	0.000	0.000
77	A	72	LEU	0	0.022	0.020	23.973	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	73	LYS	1	0.841	0.902	23.728	-0.371	-0.371	0.000	0.000	0.000	0.000
79	A	74	PRO	0	-0.013	-0.006	28.151	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	75	VAL	0	-0.005	0.019	30.983	0.019	0.019	0.000	0.000	0.000	0.000
81	A	76	LEU	0	0.040	0.025	33.566	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	77	LEU	0	0.066	0.025	36.767	0.006	0.006	0.000	0.000	0.000	0.000
83	A	78	THR	0	0.001	0.005	39.234	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	79	GLU	-1	-0.916	-0.947	32.546	0.264	0.264	0.000	0.000	0.000	0.000
85	A	80	PRO	0	0.047	0.024	34.399	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	81	SER	0	-0.043	-0.018	28.624	0.008	0.008	0.000	0.000	0.000	0.000
87	A	82	VAL	0	0.046	0.011	29.218	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	83	MET	0	-0.027	-0.004	24.381	0.004	0.004	0.000	0.000	0.000	0.000
89	A	84	LEU	0	-0.047	-0.013	28.088	0.007	0.007	0.000	0.000	0.000	0.000
90	A	85	GLN	0	-0.005	-0.013	27.713	-0.022	-0.022	0.000	0.000	0.000	0.000
91	A	86	GLY	0	0.061	0.022	30.952	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	87	PHE	0	-0.047	-0.021	32.729	0.016	0.016	0.000	0.000	0.000	0.000
93	A	88	ILE	0	-0.009	-0.001	31.390	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	89	VAL	0	0.000	-0.006	35.388	0.005	0.005	0.000	0.000	0.000	0.000
95	A	90	ARG	1	0.844	0.921	38.763	-0.091	-0.091	0.000	0.000	0.000	0.000
96	A	91	ALA	0	0.029	0.009	41.325	0.000	0.000	0.000	0.000	0.000	0.000
97	A	92	ASN	0	-0.023	-0.014	43.450	0.000	0.000	0.000	0.000	0.000	0.000
98	A	93	CYS	0	-0.046	0.002	44.604	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	94	ASN	0	-0.014	-0.013	45.336	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	95	GLY	0	0.079	0.028	42.570	0.005	0.005	0.000	0.000	0.000	0.000
101	A	96	VAL	0	0.000	0.007	38.991	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	97	LEU	0	0.004	-0.009	37.503	0.005	0.005	0.000	0.000	0.000	0.000
103	A	98	GLU	-1	-0.841	-0.907	33.464	0.090	0.090	0.000	0.000	0.000	0.000
104	A	99	ASP	-1	-0.860	-0.939	29.471	0.036	0.036	0.000	0.000	0.000	0.000
105	A	100	PHE	0	0.004	0.013	28.180	0.011	0.011	0.000	0.000	0.000	0.000
106	A	101	ASP	-1	-0.802	-0.871	21.765	0.106	0.106	0.000	0.000	0.000	0.000
107	A	102	LEU	0	0.011	0.003	24.033	0.029	0.029	0.000	0.000	0.000	0.000
108	A	103	LYS	1	0.883	0.919	17.893	-0.437	-0.437	0.000	0.000	0.000	0.000
109	A	104	ILE	0	-0.018	0.000	22.212	0.001	0.001	0.000	0.000	0.000	0.000
110	A	105	ALA	0	-0.018	0.001	21.238	0.057	0.057	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-4:HIS)