FMO DATABASE

FMODB ID: N1K2Q

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	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	-825454.001155
FMO2-HF: Nuclear repulsion	782945.219468
FMO2-HF: Total energy	-42508.781686
FMO2-MP2: Total energy	-42636.341715

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.
-8.154	-1.869	2.602	-3.607	-5.279	0.026

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 : 0.047 / 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	4	THR	0	0.004	-0.001	2.732	-2.072	0.933	0.474	-1.461	-2.017	0.008
4	A	5	ALA	0	-0.004	0.005	2.354	-5.776	-3.246	2.117	-1.886	-2.761	0.017
5	A	6	LEU	0	-0.001	0.001	3.850	-0.800	-0.050	0.011	-0.260	-0.501	0.001
6	A	7	ILE	0	0.019	0.010	5.769	0.550	0.550	0.000	0.000	0.000	0.000
7	A	8	PHE	0	-0.005	-0.013	6.436	-0.037	-0.037	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.834	0.916	7.805	0.607	0.607	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.068	0.036	9.538	0.104	0.104	0.000	0.000	0.000	0.000
10	A	11	ALA	0	-0.001	0.000	11.550	0.072	0.072	0.000	0.000	0.000	0.000
11	A	12	TRP	0	-0.004	-0.008	12.582	0.070	0.070	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.830	-0.906	12.685	-0.440	-0.440	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.013	0.003	15.488	0.024	0.024	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.774	0.909	16.842	0.091	0.091	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.899	0.935	18.168	0.090	0.090	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.026	0.019	15.009	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.019	-0.018	18.248	0.027	0.027	0.000	0.000	0.000	0.000
18	A	19	PHE	0	0.003	0.008	13.117	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.790	-0.879	17.862	-0.243	-0.243	0.000	0.000	0.000	0.000
20	A	21	TYR	0	0.049	0.025	17.091	0.013	0.013	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.028	-0.034	18.423	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	23	PRO	0	-0.024	-0.014	18.321	0.033	0.033	0.000	0.000	0.000	0.000
23	A	24	ASN	0	-0.032	-0.012	21.557	0.032	0.032	0.000	0.000	0.000	0.000
24	A	25	TRP	0	-0.011	-0.021	21.938	0.007	0.007	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.017	0.019	26.940	0.011	0.011	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.708	0.819	29.035	0.106	0.106	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.057	0.047	33.337	0.004	0.004	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.076	-0.043	36.815	0.004	0.004	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.062	0.026	40.042	0.001	0.001	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.026	0.007	35.883	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	32	ASN	0	0.010	0.012	34.528	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.037	-0.003	34.356	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.001	0.004	27.902	0.002	0.002	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.812	-0.929	31.741	-0.104	-0.104	0.000	0.000	0.000	0.000
35	A	36	THR	0	-0.035	-0.025	30.534	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	37	VAL	0	-0.015	0.007	23.791	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	38	THR	0	0.006	0.001	25.957	0.006	0.006	0.000	0.000	0.000	0.000
38	A	39	PHE	0	0.001	0.005	21.016	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.026	0.004	21.726	0.011	0.011	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.869	0.930	21.759	0.201	0.201	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.014	0.027	21.534	-0.027	-0.027	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.025	-0.017	17.993	0.018	0.018	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.008	-0.024	22.256	0.008	0.008	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.881	-0.916	22.584	-0.249	-0.249	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.795	0.887	21.326	0.303	0.303	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.009	0.001	26.612	0.002	0.002	0.000	0.000	0.000	0.000
47	A	48	TYR	0	-0.056	-0.058	21.421	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.056	-0.013	25.715	0.018	0.018	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.038	-0.006	22.803	-0.033	-0.033	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.782	0.888	22.785	0.294	0.294	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.010	0.013	25.126	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	53	ALA	0	0.000	-0.001	25.563	0.009	0.009	0.000	0.000	0.000	0.000
53	A	54	VAL	0	0.029	0.024	26.746	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.046	-0.053	28.011	0.006	0.006	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.017	0.012	27.455	0.011	0.011	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.878	0.947	28.436	0.123	0.123	0.000	0.000	0.000	0.000
57	A	58	ASN	0	0.048	0.016	28.082	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.028	-0.014	29.500	0.010	0.010	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.010	0.020	30.322	0.008	0.008	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.020	-0.010	27.554	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	62	LYS	1	0.856	0.920	29.771	0.148	0.148	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.039	0.015	29.822	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	64	SER	0	-0.048	-0.004	28.660	0.000	0.000	0.000	0.000	0.000	0.000
64	A	65	TYR	0	-0.037	-0.039	30.752	0.008	0.008	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.032	0.008	31.006	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.036	-0.011	27.961	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.839	-0.908	30.160	-0.100	-0.100	0.000	0.000	0.000	0.000
68	A	69	SER	0	-0.021	-0.022	31.228	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	70	ASP	-1	-0.881	-0.911	29.559	-0.109	-0.109	0.000	0.000	0.000	0.000
70	A	71	GLY	0	-0.019	-0.008	27.232	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.045	-0.032	25.991	-0.021	-0.021	0.000	0.000	0.000	0.000
72	A	73	GLN	0	0.013	0.005	26.059	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.870	0.934	26.735	0.112	0.112	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.031	0.017	26.282	0.005	0.005	0.000	0.000	0.000	0.000
75	A	76	ASN	0	0.029	-0.004	29.359	0.002	0.002	0.000	0.000	0.000	0.000
76	A	77	PHE	0	0.016	-0.004	26.491	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.021	0.033	32.224	0.001	0.001	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.855	-0.894	34.715	-0.116	-0.116	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.079	-0.054	28.995	0.001	0.001	0.000	0.000	0.000	0.000
80	A	81	ASN	0	-0.067	-0.037	34.096	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.026	-0.022	35.968	0.006	0.006	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.024	0.021	38.642	0.006	0.006	0.000	0.000	0.000	0.000
83	A	84	TYR	0	-0.042	-0.019	38.479	0.005	0.005	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.069	0.041	34.918	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.050	-0.030	30.746	0.003	0.003	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.013	0.016	32.877	0.000	0.000	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.751	-0.865	30.121	-0.108	-0.108	0.000	0.000	0.000	0.000
88	A	89	THR	0	0.032	0.017	29.655	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	90	ASN	0	-0.048	-0.009	29.636	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	91	THR	0	0.001	0.004	23.548	0.001	0.001	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.017	-0.011	25.018	0.008	0.008	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.038	-0.019	20.637	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	94	VAL	0	0.026	0.003	21.843	0.025	0.025	0.000	0.000	0.000	0.000
94	A	95	PHE	0	0.012	0.003	19.674	-0.037	-0.037	0.000	0.000	0.000	0.000
95	A	96	VAL	0	0.044	0.029	19.180	0.035	0.035	0.000	0.000	0.000	0.000
96	A	97	VAL	0	-0.014	-0.015	20.793	-0.032	-0.032	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.747	-0.853	20.471	-0.298	-0.298	0.000	0.000	0.000	0.000
98	A	99	PRO	0	-0.027	-0.009	22.536	0.008	0.008	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.845	-0.908	23.736	-0.225	-0.225	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.098	-0.077	21.460	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.064	-0.028	23.944	0.009	0.009	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.019	-0.002	19.150	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.793	-0.873	20.286	-0.297	-0.297	0.000	0.000	0.000	0.000
104	A	105	PHE	0	-0.016	-0.015	14.718	-0.057	-0.057	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.065	-0.026	15.111	0.040	0.040	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.022	-0.009	16.059	-0.062	-0.062	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.013	0.004	18.028	0.016	0.016	0.000	0.000	0.000	0.000
108	A	109	GLN	0	0.007	-0.009	19.123	-0.016	-0.016	0.000	0.000	0.000	0.000
109	A	110	TRP	0	0.001	0.017	20.776	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	111	ASN	0	-0.018	-0.005	21.611	-0.012	-0.012	0.000	0.000	0.000	0.000

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