FMO DATABASE

FMODB ID: K9L93

Calculation Name: 1NYS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYS

Chain ID: B

ChEMBL ID:

UniProt ID: P38444

Base Structure: X-ray

Registration Date: 2023-09-19

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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-547073.62875
FMO2-HF: Nuclear repulsion	509613.950527
FMO2-HF: Total energy	-37459.678223
FMO2-MP2: Total energy	-37559.395191

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(B:2:LEU)

Summations of interaction energy for fragment #1(B:2:LEU)

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.
-3.851	1.816	3.438	-2.77	-6.333	-0.007

Interaction energy analysis for fragmet #1(B:2:LEU)

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 : -0.028

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

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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	B	4	CYS	0	0.014	0.032	3.334	-0.265	2.421	0.030	-1.112	-1.603	-0.003
4	B	5	ASP	-1	-0.813	-0.894	6.207	0.205	0.205	0.000	0.000	0.000	0.000
5	B	6	GLY	0	-0.016	-0.013	8.886	-0.049	-0.049	0.000	0.000	0.000	0.000
6	B	7	LYS	1	0.843	0.906	9.533	-0.707	-0.707	0.000	0.000	0.000	0.000
7	B	8	VAL	0	0.038	0.021	8.962	0.295	0.295	0.000	0.000	0.000	0.000
8	B	9	ASN	0	-0.043	0.003	8.567	-0.242	-0.242	0.000	0.000	0.000	0.000
9	B	10	ILE	0	0.071	0.032	5.037	-0.253	-0.253	0.000	0.000	0.000	0.000
10	B	11	CYS	0	-0.031	-0.001	5.228	0.832	0.832	0.000	0.000	0.000	0.000
11	B	13	LYS	1	0.933	0.965	3.593	-0.369	0.128	0.005	-0.062	-0.440	0.000
12	B	14	LYS	1	0.819	0.905	5.266	-0.525	-0.538	-0.001	-0.004	0.018	0.000
13	B	15	GLN	0	-0.023	-0.022	7.460	-0.207	-0.207	0.000	0.000	0.000	0.000
14	B	16	PHE	0	0.000	-0.002	10.716	0.025	0.025	0.000	0.000	0.000	0.000
15	B	17	PHE	0	-0.008	0.006	14.262	-0.008	-0.008	0.000	0.000	0.000	0.000
16	B	18	VAL	0	0.002	0.006	17.165	0.017	0.017	0.000	0.000	0.000	0.000
17	B	19	SER	0	-0.017	-0.039	20.054	-0.010	-0.010	0.000	0.000	0.000	0.000
18	B	20	PHE	0	0.079	0.008	21.877	0.007	0.007	0.000	0.000	0.000	0.000
19	B	21	LYS	1	0.917	0.966	25.360	-0.008	-0.008	0.000	0.000	0.000	0.000
20	B	22	ASP	-1	-0.924	-0.927	24.716	0.018	0.018	0.000	0.000	0.000	0.000
21	B	23	ILE	0	-0.005	-0.010	21.945	0.006	0.006	0.000	0.000	0.000	0.000
22	B	24	GLY	0	-0.002	0.011	26.503	0.002	0.002	0.000	0.000	0.000	0.000
23	B	25	TRP	0	-0.016	-0.021	23.252	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	26	ASN	0	-0.054	-0.030	28.689	0.000	0.000	0.000	0.000	0.000	0.000
25	B	27	ASP	-1	-0.868	-0.927	29.737	0.005	0.005	0.000	0.000	0.000	0.000
26	B	28	TRP	0	-0.030	-0.006	26.691	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	29	ILE	0	-0.052	-0.026	25.070	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	30	ILE	0	-0.007	0.001	28.916	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	31	ALA	0	-0.036	0.003	26.628	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	32	PRO	0	-0.001	-0.010	21.252	0.002	0.002	0.000	0.000	0.000	0.000
31	B	33	SER	0	0.066	0.022	24.360	0.004	0.004	0.000	0.000	0.000	0.000
32	B	34	GLY	0	0.016	-0.006	21.842	0.007	0.007	0.000	0.000	0.000	0.000
33	B	35	TYR	0	-0.021	-0.011	16.725	-0.006	-0.006	0.000	0.000	0.000	0.000
34	B	36	HIS	0	-0.011	-0.012	13.046	-0.007	-0.007	0.000	0.000	0.000	0.000
35	B	37	ALA	0	0.010	0.032	13.861	0.011	0.011	0.000	0.000	0.000	0.000
36	B	38	ASN	0	-0.007	-0.014	8.878	-0.006	-0.006	0.000	0.000	0.000	0.000
37	B	39	TYR	0	-0.001	-0.009	9.758	0.036	0.036	0.000	0.000	0.000	0.000
38	B	40	CYS	0	-0.049	0.003	2.281	-1.753	-0.872	0.775	-0.461	-1.195	0.004
39	B	41	GLU	-1	-0.868	-0.941	7.678	0.537	0.537	0.000	0.000	0.000	0.000
40	B	42	GLY	0	0.000	0.003	7.533	0.368	0.368	0.000	0.000	0.000	0.000
41	B	43	GLU	-1	-0.950	-0.972	8.748	0.409	0.409	0.000	0.000	0.000	0.000
42	B	44	CYS	0	-0.053	-0.033	5.254	0.244	0.296	-0.002	-0.003	-0.047	0.000
43	B	45	PRO	0	0.017	0.009	9.624	-0.061	-0.061	0.000	0.000	0.000	0.000
44	B	46	SER	0	0.020	0.013	12.584	-0.001	-0.001	0.000	0.000	0.000	0.000
45	B	47	HIS	0	-0.047	-0.021	14.698	-0.028	-0.028	0.000	0.000	0.000	0.000
46	B	48	ILE	0	0.006	0.016	17.429	-0.005	-0.005	0.000	0.000	0.000	0.000
47	B	77	LEU	0	0.052	0.027	19.094	-0.004	-0.004	0.000	0.000	0.000	0.000
48	B	78	LYS	1	0.929	0.947	17.468	-0.211	-0.211	0.000	0.000	0.000	0.000
49	B	79	SER	0	-0.016	-0.029	12.098	0.003	0.003	0.000	0.000	0.000	0.000
50	B	80	CYS	0	-0.023	-0.006	12.489	0.009	0.009	0.000	0.000	0.000	0.000
51	B	82	VAL	0	-0.027	-0.012	8.555	-0.055	-0.055	0.000	0.000	0.000	0.000
52	B	83	PRO	0	0.070	0.003	6.967	0.102	0.102	0.000	0.000	0.000	0.000
53	B	84	THR	0	-0.057	-0.031	5.075	-0.028	-0.028	0.000	0.000	0.000	0.000
54	B	85	LYS	1	0.807	0.888	5.536	-0.226	-0.226	0.000	0.000	0.000	0.000
55	B	86	LEU	0	-0.015	0.006	8.075	0.001	0.001	0.000	0.000	0.000	0.000
56	B	87	ARG	1	0.859	0.924	10.959	0.112	0.112	0.000	0.000	0.000	0.000
57	B	88	PRO	0	-0.003	-0.012	12.814	0.007	0.007	0.000	0.000	0.000	0.000
58	B	89	MET	0	-0.035	-0.008	16.201	-0.018	-0.018	0.000	0.000	0.000	0.000
59	B	90	SER	0	-0.035	-0.034	18.519	0.004	0.004	0.000	0.000	0.000	0.000
60	B	91	MET	0	-0.035	-0.020	22.171	-0.002	-0.002	0.000	0.000	0.000	0.000
61	B	92	LEU	0	-0.025	-0.013	24.804	0.000	0.000	0.000	0.000	0.000	0.000
62	B	93	TYR	0	-0.010	-0.010	26.953	0.000	0.000	0.000	0.000	0.000	0.000
63	B	94	TYR	0	0.042	0.031	30.119	-0.002	-0.002	0.000	0.000	0.000	0.000
64	B	95	ASP	-1	-0.852	-0.927	32.543	0.005	0.005	0.000	0.000	0.000	0.000
65	B	96	ASP	-1	-0.821	-0.930	34.015	0.010	0.010	0.000	0.000	0.000	0.000
66	B	97	GLY	0	-0.008	0.016	36.976	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	98	GLN	0	-0.142	-0.089	38.029	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	99	ASN	0	-0.053	-0.017	36.230	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	100	ILE	0	-0.032	-0.020	32.886	0.001	0.001	0.000	0.000	0.000	0.000
70	B	101	ILE	0	-0.021	0.006	29.604	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	102	LYS	1	0.890	0.929	24.560	0.030	0.030	0.000	0.000	0.000	0.000
72	B	103	LYS	1	0.936	0.974	24.909	-0.007	-0.007	0.000	0.000	0.000	0.000
73	B	104	ASP	-1	-0.790	-0.863	21.358	-0.034	-0.034	0.000	0.000	0.000	0.000
74	B	105	ILE	0	-0.027	-0.012	20.201	0.005	0.005	0.000	0.000	0.000	0.000
75	B	106	GLN	0	0.021	-0.013	18.155	-0.002	-0.002	0.000	0.000	0.000	0.000
76	B	107	ASN	0	-0.045	-0.033	14.577	0.003	0.003	0.000	0.000	0.000	0.000
77	B	108	MET	0	0.046	0.029	15.596	0.013	0.013	0.000	0.000	0.000	0.000
78	B	109	ILE	0	-0.012	0.002	10.865	-0.008	-0.008	0.000	0.000	0.000	0.000
79	B	110	VAL	0	0.013	0.019	7.429	0.014	0.014	0.000	0.000	0.000	0.000
80	B	111	GLU	-1	-0.824	-0.909	6.676	-0.305	-0.305	0.000	0.000	0.000	0.000
81	B	112	GLU	-1	-0.784	-0.892	2.295	-0.757	-0.371	2.023	-0.455	-1.953	-0.001
82	B	114	GLY	0	0.061	0.021	2.831	-0.942	0.236	0.608	-0.673	-1.113	-0.007
83	B	116	SER	0	0.017	0.037	8.622	-0.073	-0.073	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:LEU)