FMO DATABASE

FMODB ID: GNJY1

Calculation Name: 3F3H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F3H

Chain ID: A

ChEMBL ID:

UniProt ID: P14945

Base Structure: X-ray

Registration Date: 2023-06-19

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	-824945.223425
FMO2-HF: Nuclear repulsion	782436.983307
FMO2-HF: Total energy	-42508.240118
FMO2-MP2: Total energy	-42635.780687

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-10.848	-5.655	5.118	-4.342	-5.969	0.031

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.008

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	4	THR	0	-0.015	-0.006	2.800	-2.347	1.049	0.508	-1.710	-2.193	0.009
4	A	5	ALA	0	-0.022	-0.008	2.102	-7.615	-6.663	4.586	-2.352	-3.187	0.022
5	A	6	LEU	0	0.000	-0.002	3.552	-1.040	-0.195	0.024	-0.280	-0.589	0.000
6	A	7	ILE	0	0.022	0.018	5.715	0.367	0.367	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.008	-0.014	6.674	-0.133	-0.133	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.942	0.986	7.925	0.626	0.626	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.052	0.025	9.615	0.050	0.050	0.000	0.000	0.000	0.000
10	A	11	ALA	0	-0.008	0.000	11.346	0.048	0.048	0.000	0.000	0.000	0.000
11	A	12	TRP	0	-0.051	-0.029	12.550	0.050	0.050	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.884	-0.937	13.708	-0.326	-0.326	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.004	-0.007	15.281	0.022	0.022	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.795	0.928	16.636	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.898	0.929	17.444	0.049	0.049	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.022	0.010	15.225	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.044	-0.029	17.725	0.031	0.031	0.000	0.000	0.000	0.000
18	A	19	PHE	0	-0.003	0.002	12.836	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.825	-0.901	17.908	-0.164	-0.164	0.000	0.000	0.000	0.000
20	A	21	TYR	0	0.059	0.027	16.763	0.009	0.009	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.030	-0.026	18.131	-0.036	-0.036	0.000	0.000	0.000	0.000
22	A	23	PRO	0	-0.021	-0.013	18.067	0.030	0.030	0.000	0.000	0.000	0.000
23	A	24	ASN	0	-0.057	-0.020	21.376	0.033	0.033	0.000	0.000	0.000	0.000
24	A	25	TRP	0	0.008	-0.009	21.841	0.007	0.007	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.006	0.012	26.893	0.012	0.012	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.770	0.865	28.661	0.105	0.105	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.060	0.041	33.027	0.004	0.004	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.085	-0.039	36.411	0.007	0.007	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.052	0.018	39.672	0.000	0.000	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.045	0.011	35.220	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	32	ASN	0	0.025	0.023	34.125	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.029	-0.001	33.809	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.013	-0.015	27.884	0.003	0.003	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.819	-0.928	31.635	-0.105	-0.105	0.000	0.000	0.000	0.000
35	A	36	THR	0	-0.080	-0.039	30.353	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.011	0.010	23.640	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	38	THR	0	0.011	0.010	26.018	0.005	0.005	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.004	0.001	20.475	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.033	0.009	21.584	0.011	0.011	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.943	0.980	21.670	0.124	0.124	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.007	0.024	21.262	-0.025	-0.025	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.032	-0.022	18.057	0.022	0.022	0.000	0.000	0.000	0.000
43	A	44	THR	0	0.005	-0.012	22.389	0.004	0.004	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.903	-0.932	22.191	-0.234	-0.234	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.902	0.975	21.363	0.299	0.299	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.006	-0.003	26.164	0.003	0.003	0.000	0.000	0.000	0.000
47	A	48	TYR	0	-0.066	-0.056	21.312	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.042	-0.004	25.896	0.016	0.016	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.034	-0.009	22.913	-0.034	-0.034	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.853	0.926	22.299	0.322	0.322	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.011	0.010	25.044	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	53	ALA	0	-0.014	-0.005	25.199	0.010	0.010	0.000	0.000	0.000	0.000
53	A	54	VAL	0	0.031	0.011	26.654	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.059	-0.056	27.864	0.006	0.006	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.003	0.010	26.820	0.008	0.008	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.927	0.970	27.840	0.137	0.137	0.000	0.000	0.000	0.000
57	A	58	ASN	0	0.025	0.003	28.439	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.001	-0.004	29.559	0.011	0.011	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.012	0.007	29.939	0.009	0.009	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.027	-0.002	27.655	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	62	LYS	1	0.910	0.965	29.820	0.148	0.148	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.041	0.017	30.005	-0.013	-0.013	0.000	0.000	0.000	0.000
63	A	64	SER	0	-0.022	0.003	29.077	0.000	0.000	0.000	0.000	0.000	0.000
64	A	65	TYR	0	-0.019	-0.006	31.125	0.007	0.007	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.020	0.001	31.208	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.033	-0.008	27.852	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.917	-0.953	30.288	-0.088	-0.088	0.000	0.000	0.000	0.000
68	A	69	SER	0	-0.043	-0.032	31.183	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	70	ASP	-1	-0.874	-0.914	29.942	-0.086	-0.086	0.000	0.000	0.000	0.000
70	A	71	GLY	0	-0.028	-0.011	27.328	0.001	0.001	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.042	-0.035	26.188	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	73	GLN	0	0.036	0.024	26.118	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.961	0.989	26.641	0.095	0.095	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.032	0.010	26.098	0.002	0.002	0.000	0.000	0.000	0.000
75	A	76	ASN	0	0.009	-0.017	29.044	0.001	0.001	0.000	0.000	0.000	0.000
76	A	77	PHE	0	0.026	0.001	26.322	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.012	0.027	32.123	0.000	0.000	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.925	-0.957	34.360	-0.117	-0.117	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.080	-0.058	29.213	0.004	0.004	0.000	0.000	0.000	0.000
80	A	81	ASN	0	-0.068	-0.035	33.892	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.034	-0.023	35.711	0.007	0.007	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.014	0.015	38.420	0.006	0.006	0.000	0.000	0.000	0.000
83	A	84	TYR	0	-0.040	-0.018	38.311	0.006	0.006	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.067	0.037	34.710	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.051	-0.030	30.586	0.002	0.002	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.009	0.020	32.636	0.000	0.000	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.785	-0.901	29.779	-0.115	-0.115	0.000	0.000	0.000	0.000
88	A	89	THR	0	0.022	0.011	29.470	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	90	ASN	0	-0.055	-0.003	29.787	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	91	THR	0	0.034	0.014	23.515	0.002	0.002	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.029	-0.007	25.023	0.006	0.006	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.048	-0.032	20.255	0.000	0.000	0.000	0.000	0.000	0.000
93	A	94	VAL	0	0.030	0.009	21.743	0.025	0.025	0.000	0.000	0.000	0.000
94	A	95	PHE	0	-0.002	-0.016	19.452	-0.042	-0.042	0.000	0.000	0.000	0.000
95	A	96	VAL	0	0.028	0.021	19.038	0.037	0.037	0.000	0.000	0.000	0.000
96	A	97	VAL	0	0.013	-0.002	20.823	-0.034	-0.034	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.816	-0.933	20.713	-0.309	-0.309	0.000	0.000	0.000	0.000
98	A	99	PRO	0	-0.012	-0.009	22.795	0.005	0.005	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.897	-0.949	23.812	-0.205	-0.205	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.106	-0.057	21.260	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.068	-0.032	24.200	0.006	0.006	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.015	0.010	19.238	0.013	0.013	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.784	-0.881	20.415	-0.313	-0.313	0.000	0.000	0.000	0.000
104	A	105	PHE	0	-0.042	-0.025	14.928	-0.068	-0.068	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.071	-0.023	15.068	0.049	0.049	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.012	-0.003	15.978	-0.063	-0.063	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.021	0.003	17.879	0.024	0.024	0.000	0.000	0.000	0.000
108	A	109	GLN	0	0.003	-0.003	18.871	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	110	TRP	0	-0.052	-0.017	20.595	0.003	0.003	0.000	0.000	0.000	0.000
110	A	111	ASN	0	0.012	0.014	21.356	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)