FMO DATABASE

FMODB ID: 2NQ3R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-890964.53391
FMO2-HF: Nuclear repulsion	845988.276388
FMO2-HF: Total energy	-44976.257523
FMO2-MP2: Total energy	-45105.428547

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.
-5.033	-1.999	1.079	-1.55	-2.563	-0.01

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 : -0.014 / q_NPA : -0.019

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	-0.009	-0.018	2.760	-5.637	-2.603	1.079	-1.550	-2.563	-0.010
4	A	-1	HIS	0	0.010	0.014	6.164	0.355	0.355	0.000	0.000	0.000	0.000
5	A	0	HIS	0	-0.040	-0.024	9.540	-0.063	-0.063	0.000	0.000	0.000	0.000
6	A	1	MET	0	0.007	0.014	12.524	0.104	0.104	0.000	0.000	0.000	0.000
7	A	2	SER	0	-0.008	-0.016	14.872	-0.029	-0.029	0.000	0.000	0.000	0.000
8	A	3	SER	0	-0.105	-0.078	16.961	0.053	0.053	0.000	0.000	0.000	0.000
9	A	4	LYS	1	0.849	0.928	20.420	-0.075	-0.075	0.000	0.000	0.000	0.000
10	A	5	GLN	0	0.048	0.025	23.206	0.031	0.031	0.000	0.000	0.000	0.000
11	A	6	PHE	0	-0.057	-0.031	26.236	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	7	LYS	1	0.934	0.970	30.088	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	8	ILE	0	-0.051	-0.019	31.470	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	9	LEU	0	-0.012	0.005	35.313	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	10	VAL	0	0.022	0.011	36.243	0.008	0.008	0.000	0.000	0.000	0.000
16	A	11	ASN	0	-0.016	-0.028	38.915	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	12	GLU	-1	-0.834	-0.926	40.300	0.096	0.096	0.000	0.000	0.000	0.000
18	A	13	ASP	-1	-0.931	-0.964	42.880	0.067	0.067	0.000	0.000	0.000	0.000
19	A	14	TYR	0	-0.069	-0.042	46.049	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	15	GLN	0	-0.002	-0.005	46.352	0.002	0.002	0.000	0.000	0.000	0.000
21	A	16	VAL	0	-0.054	-0.029	43.753	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	17	ASN	0	-0.002	0.010	46.433	0.008	0.008	0.000	0.000	0.000	0.000
23	A	18	VAL	0	-0.012	-0.012	41.653	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	19	PRO	0	-0.028	-0.007	42.258	0.003	0.003	0.000	0.000	0.000	0.000
25	A	20	SER	0	0.006	-0.006	40.444	0.003	0.003	0.000	0.000	0.000	0.000
26	A	21	LEU	0	-0.013	-0.018	37.688	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	22	PRO	0	0.041	0.022	38.655	0.011	0.011	0.000	0.000	0.000	0.000
28	A	23	ILE	0	0.043	0.012	31.741	0.000	0.000	0.000	0.000	0.000	0.000
29	A	24	ARG	1	0.920	0.958	33.427	-0.168	-0.168	0.000	0.000	0.000	0.000
30	A	25	ASP	-1	-0.845	-0.927	33.904	0.123	0.123	0.000	0.000	0.000	0.000
31	A	26	VAL	0	0.010	0.015	32.918	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	27	LEU	0	-0.026	-0.014	28.212	0.004	0.004	0.000	0.000	0.000	0.000
33	A	28	GLN	0	-0.050	-0.023	30.056	0.008	0.008	0.000	0.000	0.000	0.000
34	A	29	GLU	-1	-0.797	-0.873	31.990	0.089	0.089	0.000	0.000	0.000	0.000
35	A	30	ILE	0	0.027	0.020	27.697	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	31	LYS	1	0.901	0.953	26.221	-0.192	-0.192	0.000	0.000	0.000	0.000
37	A	32	TYR	0	-0.013	-0.004	28.693	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	33	CYS	0	0.046	0.023	31.407	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	34	TYR	0	-0.012	0.014	21.607	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	35	ARG	1	0.912	0.950	24.283	-0.069	-0.069	0.000	0.000	0.000	0.000
41	A	36	ASN	0	-0.068	-0.050	28.750	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	37	GLY	0	0.011	0.031	31.519	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	38	PHE	0	0.007	-0.014	29.829	0.006	0.006	0.000	0.000	0.000	0.000
44	A	39	GLU	-1	-0.880	-0.925	35.163	0.033	0.033	0.000	0.000	0.000	0.000
45	A	40	GLY	0	-0.019	-0.025	38.682	0.004	0.004	0.000	0.000	0.000	0.000
46	A	41	TYR	0	-0.110	-0.101	36.770	0.007	0.007	0.000	0.000	0.000	0.000
47	A	42	VAL	0	0.007	0.013	38.708	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	43	PHE	0	-0.005	-0.016	32.331	0.009	0.009	0.000	0.000	0.000	0.000
49	A	44	VAL	0	0.006	0.012	36.718	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	45	PRO	0	0.043	0.020	35.720	0.012	0.012	0.000	0.000	0.000	0.000
51	A	46	GLU	-1	-0.860	-0.935	34.570	0.164	0.164	0.000	0.000	0.000	0.000
52	A	47	TYR	0	-0.027	-0.035	36.466	0.001	0.001	0.000	0.000	0.000	0.000
53	A	48	CYS	0	-0.049	-0.006	39.237	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	49	ARG	1	0.791	0.867	36.505	-0.172	-0.172	0.000	0.000	0.000	0.000
55	A	50	ASP	-1	-0.922	-0.954	41.040	0.116	0.116	0.000	0.000	0.000	0.000
56	A	51	LEU	0	-0.051	-0.002	43.473	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	52	VAL	0	-0.052	-0.027	40.834	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	53	ASP	-1	-0.888	-0.926	44.124	0.096	0.096	0.000	0.000	0.000	0.000
59	A	54	CYS	0	-0.060	-0.045	43.956	0.003	0.003	0.000	0.000	0.000	0.000
60	A	55	ASP	-1	-0.857	-0.925	46.030	0.087	0.087	0.000	0.000	0.000	0.000
61	A	56	ARG	1	0.843	0.915	44.490	-0.113	-0.113	0.000	0.000	0.000	0.000
62	A	57	LYS	1	0.977	0.981	43.232	-0.111	-0.111	0.000	0.000	0.000	0.000
63	A	58	ASP	-1	-0.891	-0.936	41.931	0.136	0.136	0.000	0.000	0.000	0.000
64	A	59	HIS	0	-0.043	-0.017	39.962	0.012	0.012	0.000	0.000	0.000	0.000
65	A	60	TYR	0	-0.037	-0.028	34.771	0.007	0.007	0.000	0.000	0.000	0.000
66	A	61	VAL	0	0.066	0.032	35.976	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	62	ILE	0	-0.012	-0.006	31.088	0.017	0.017	0.000	0.000	0.000	0.000
68	A	63	GLY	0	0.027	0.018	31.437	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	64	VAL	0	0.020	0.008	28.029	0.008	0.008	0.000	0.000	0.000	0.000
70	A	65	LEU	0	-0.018	-0.018	25.891	0.001	0.001	0.000	0.000	0.000	0.000
71	A	66	GLY	0	0.023	0.011	23.758	0.017	0.017	0.000	0.000	0.000	0.000
72	A	67	ASN	0	0.016	0.007	23.566	-0.051	-0.051	0.000	0.000	0.000	0.000
73	A	68	GLY	0	-0.007	-0.003	21.434	0.031	0.031	0.000	0.000	0.000	0.000
74	A	69	VAL	0	-0.007	0.008	18.934	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	70	SER	0	-0.026	-0.017	21.325	0.034	0.034	0.000	0.000	0.000	0.000
76	A	71	ASP	-1	-0.913	-0.974	21.142	0.388	0.388	0.000	0.000	0.000	0.000
77	A	72	LEU	0	-0.017	0.000	23.885	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	73	LYS	1	0.945	0.961	25.308	-0.329	-0.329	0.000	0.000	0.000	0.000
79	A	74	PRO	0	-0.025	-0.006	28.253	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	75	VAL	0	0.006	0.014	31.187	0.018	0.018	0.000	0.000	0.000	0.000
81	A	76	LEU	0	0.045	0.029	33.625	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	77	LEU	0	0.056	0.014	36.659	0.005	0.005	0.000	0.000	0.000	0.000
83	A	78	THR	0	-0.011	-0.005	39.130	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	79	GLU	-1	-0.916	-0.946	32.280	0.259	0.259	0.000	0.000	0.000	0.000
85	A	80	PRO	0	0.043	0.018	34.371	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	81	SER	0	-0.040	-0.007	28.570	0.006	0.006	0.000	0.000	0.000	0.000
87	A	82	VAL	0	0.056	0.015	29.063	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	83	MET	0	-0.046	-0.019	24.292	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	84	LEU	0	-0.043	-0.011	28.232	0.003	0.003	0.000	0.000	0.000	0.000
90	A	85	GLN	0	-0.007	0.003	28.272	-0.019	-0.019	0.000	0.000	0.000	0.000
91	A	86	GLY	0	0.070	0.028	31.250	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	87	PHE	0	-0.048	-0.015	32.943	0.014	0.014	0.000	0.000	0.000	0.000
93	A	88	ILE	0	-0.012	0.008	31.334	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	89	VAL	0	-0.001	-0.017	35.400	0.004	0.004	0.000	0.000	0.000	0.000
95	A	90	ARG	1	0.879	0.947	38.856	-0.080	-0.080	0.000	0.000	0.000	0.000
96	A	91	ALA	0	0.012	-0.001	41.377	0.001	0.001	0.000	0.000	0.000	0.000
97	A	92	ASN	0	-0.020	-0.014	43.631	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	93	CYS	0	-0.036	0.010	44.791	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	94	ASN	0	0.003	0.001	45.380	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	95	GLY	0	0.081	0.025	42.790	0.005	0.005	0.000	0.000	0.000	0.000
101	A	96	VAL	0	0.008	0.016	39.455	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	97	LEU	0	-0.051	-0.029	37.326	0.004	0.004	0.000	0.000	0.000	0.000
103	A	98	GLU	-1	-0.893	-0.939	33.661	0.087	0.087	0.000	0.000	0.000	0.000
104	A	99	ASP	-1	-0.929	-0.970	29.429	0.031	0.031	0.000	0.000	0.000	0.000
105	A	100	PHE	0	0.004	0.003	28.544	0.013	0.013	0.000	0.000	0.000	0.000
106	A	101	ASP	-1	-0.830	-0.882	22.044	0.097	0.097	0.000	0.000	0.000	0.000
107	A	102	LEU	0	-0.018	-0.010	24.294	0.029	0.029	0.000	0.000	0.000	0.000
108	A	103	LYS	1	0.952	0.969	17.410	-0.403	-0.403	0.000	0.000	0.000	0.000
109	A	104	ILE	0	-0.027	-0.014	22.234	0.005	0.005	0.000	0.000	0.000	0.000
110	A	105	ALA	0	-0.026	0.004	21.216	0.055	0.055	0.000	0.000	0.000	0.000

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