FMO DATABASE

FMODB ID: 82RNY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-825429.770449
FMO2-HF: Nuclear repulsion	782921.090011
FMO2-HF: Total energy	-42508.680438
FMO2-MP2: Total energy	-42636.236002

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.
-10.5	-4.839	4.191	-4.082	-5.769	0.03

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 : 0.032 / q_NPA : 0.015

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	0.000	-0.002	2.645	-2.044	1.321	0.443	-1.666	-2.142	0.008
4	A	5	ALA	0	-0.014	-0.004	2.182	-7.296	-5.734	3.726	-2.180	-3.107	0.021
5	A	6	LEU	0	0.012	0.006	3.771	-1.154	-0.420	0.022	-0.236	-0.520	0.001
6	A	7	ILE	0	0.016	0.012	5.802	0.379	0.379	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.005	-0.012	6.624	-0.145	-0.145	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.899	0.964	7.966	0.488	0.488	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.054	0.023	9.675	0.045	0.045	0.000	0.000	0.000	0.000
10	A	11	ALA	0	-0.005	0.004	11.425	0.046	0.046	0.000	0.000	0.000	0.000
11	A	12	TRP	0	-0.026	-0.011	12.640	0.043	0.043	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.858	-0.923	13.417	-0.310	-0.310	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.009	-0.002	15.656	0.017	0.017	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.775	0.906	16.710	0.009	0.009	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.901	0.933	17.547	0.060	0.060	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.023	0.012	15.153	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.019	-0.015	17.826	0.023	0.023	0.000	0.000	0.000	0.000
18	A	19	PHE	0	0.014	0.012	12.806	0.001	0.001	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.807	-0.890	17.785	-0.231	-0.231	0.000	0.000	0.000	0.000
20	A	21	TYR	0	0.051	0.023	16.818	0.016	0.016	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.028	-0.028	18.152	-0.036	-0.036	0.000	0.000	0.000	0.000
22	A	23	PRO	0	-0.028	-0.015	18.117	0.035	0.035	0.000	0.000	0.000	0.000
23	A	24	ASN	0	-0.061	-0.023	21.388	0.029	0.029	0.000	0.000	0.000	0.000
24	A	25	TRP	0	0.011	-0.010	21.644	0.009	0.009	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.014	0.018	26.905	0.012	0.012	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.717	0.831	28.751	0.119	0.119	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.061	0.040	33.037	0.003	0.003	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.089	-0.039	36.421	0.005	0.005	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.060	0.022	39.692	0.001	0.001	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.042	0.011	35.435	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	32	ASN	0	0.013	0.013	34.142	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.026	0.001	33.817	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.016	-0.013	27.737	0.002	0.002	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.813	-0.927	31.644	-0.111	-0.111	0.000	0.000	0.000	0.000
35	A	36	THR	0	-0.070	-0.037	30.359	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.010	0.012	23.680	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.002	0.004	26.028	0.007	0.007	0.000	0.000	0.000	0.000
38	A	39	PHE	0	0.016	0.011	20.579	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.039	0.010	21.727	0.013	0.013	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.883	0.943	21.595	0.174	0.174	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.005	0.022	21.272	-0.029	-0.029	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.036	-0.022	18.108	0.021	0.021	0.000	0.000	0.000	0.000
43	A	44	THR	0	0.006	-0.014	22.389	0.005	0.005	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.899	-0.926	22.370	-0.241	-0.241	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.795	0.890	21.483	0.293	0.293	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.014	-0.006	26.321	0.001	0.001	0.000	0.000	0.000	0.000
47	A	48	TYR	0	-0.063	-0.061	21.311	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.044	-0.006	25.754	0.016	0.016	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.034	-0.001	22.775	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.790	0.893	22.611	0.312	0.312	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.003	0.012	24.955	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	53	ALA	0	-0.008	-0.003	25.155	0.012	0.012	0.000	0.000	0.000	0.000
53	A	54	VAL	0	0.037	0.017	26.657	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.053	-0.054	27.863	0.007	0.007	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.006	0.011	26.805	0.009	0.009	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.920	0.972	27.826	0.136	0.136	0.000	0.000	0.000	0.000
57	A	58	ASN	0	0.032	0.008	27.964	-0.015	-0.015	0.000	0.000	0.000	0.000
58	A	59	LEU	0	0.000	-0.003	29.503	0.011	0.011	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.009	0.011	29.860	0.008	0.008	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.032	-0.003	27.394	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	62	LYS	1	0.851	0.919	29.712	0.151	0.151	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.042	0.017	29.881	-0.013	-0.013	0.000	0.000	0.000	0.000
63	A	64	SER	0	-0.026	0.007	29.116	0.000	0.000	0.000	0.000	0.000	0.000
64	A	65	TYR	0	-0.045	-0.045	31.135	0.007	0.007	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.017	-0.001	31.220	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.034	-0.010	27.880	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.879	-0.942	30.302	-0.100	-0.100	0.000	0.000	0.000	0.000
68	A	69	SER	0	-0.004	-0.015	31.183	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	70	ASP	-1	-0.908	-0.928	29.958	-0.107	-0.107	0.000	0.000	0.000	0.000
70	A	71	GLY	0	-0.010	0.000	27.300	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.037	-0.034	26.205	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	73	GLN	0	0.016	0.004	26.119	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.890	0.960	26.654	0.111	0.111	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.025	0.010	26.073	0.004	0.004	0.000	0.000	0.000	0.000
75	A	76	ASN	0	0.025	-0.012	29.055	0.000	0.000	0.000	0.000	0.000	0.000
76	A	77	PHE	0	0.032	0.002	26.302	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.021	0.034	32.131	0.001	0.001	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.844	-0.879	34.533	-0.119	-0.119	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.076	-0.057	28.921	0.004	0.004	0.000	0.000	0.000	0.000
80	A	81	ASN	0	-0.077	-0.049	33.829	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.028	-0.019	35.716	0.006	0.006	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.014	0.014	38.422	0.006	0.006	0.000	0.000	0.000	0.000
83	A	84	TYR	0	-0.039	-0.014	38.305	0.006	0.006	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.060	0.040	34.716	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.053	-0.032	30.643	0.003	0.003	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.017	0.027	32.643	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.754	-0.872	29.797	-0.123	-0.123	0.000	0.000	0.000	0.000
88	A	89	THR	0	0.020	0.007	29.475	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	90	ASN	0	-0.071	-0.022	29.791	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	91	THR	0	0.026	0.014	23.501	0.002	0.002	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.024	-0.007	25.035	0.007	0.007	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.039	-0.023	20.444	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	94	VAL	0	0.024	0.002	21.749	0.025	0.025	0.000	0.000	0.000	0.000
94	A	95	PHE	0	0.013	-0.007	19.299	-0.042	-0.042	0.000	0.000	0.000	0.000
95	A	96	VAL	0	0.029	0.018	18.875	0.037	0.037	0.000	0.000	0.000	0.000
96	A	97	VAL	0	0.004	-0.008	20.694	-0.032	-0.032	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.738	-0.848	20.566	-0.297	-0.297	0.000	0.000	0.000	0.000
98	A	99	PRO	0	-0.019	-0.011	22.639	0.007	0.007	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.833	-0.900	23.827	-0.208	-0.208	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.105	-0.086	21.417	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.080	-0.033	24.066	0.011	0.011	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.024	0.004	19.098	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.762	-0.861	20.205	-0.308	-0.308	0.000	0.000	0.000	0.000
104	A	105	PHE	0	-0.035	-0.026	14.648	-0.059	-0.059	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.065	-0.018	14.983	0.044	0.044	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.015	-0.006	15.929	-0.066	-0.066	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.021	0.008	17.888	0.018	0.018	0.000	0.000	0.000	0.000
108	A	109	GLN	0	0.003	-0.006	18.930	-0.015	-0.015	0.000	0.000	0.000	0.000
109	A	110	TRP	0	-0.017	-0.001	20.601	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	111	ASN	0	0.000	0.010	21.402	-0.003	-0.003	0.000	0.000	0.000	0.000

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