FMO DATABASE

FMODB ID: VRMV1

Calculation Name: 4OYC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OYC

Chain ID: A

ChEMBL ID:

UniProt ID: P41786

Base Structure: X-ray

Registration Date: 2023-06-20

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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-536581.53307
FMO2-HF: Nuclear repulsion	503753.927617
FMO2-HF: Total energy	-32827.605453
FMO2-MP2: Total energy	-32923.900141

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:94:HIS)

Summations of interaction energy for fragment #1(A:94: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.
-16.22	-11.597	0.285	-2.057	-2.851	0.013

Interaction energy analysis for fragmet #1(A:94:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.079 / q_NPA : 0.039

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	A	96	SER	0	0.053	0.034	3.676	-5.641	-2.772	0.053	-1.335	-1.586	0.007
4	A	97	SER	0	-0.026	0.007	3.115	-3.860	-2.234	0.234	-0.695	-1.165	0.006
5	A	98	PRO	0	0.072	0.010	5.070	-1.126	-1.061	-0.001	-0.015	-0.050	0.000
6	A	99	ARG	1	0.937	0.979	5.568	-1.863	-1.863	0.000	0.000	0.000	0.000
7	A	100	ALA	0	0.018	0.008	4.797	-0.509	-0.446	-0.001	-0.012	-0.050	0.000
8	A	101	GLU	-1	-0.846	-0.922	6.674	1.885	1.885	0.000	0.000	0.000	0.000
9	A	102	LYS	1	0.955	0.965	9.563	-1.651	-1.651	0.000	0.000	0.000	0.000
10	A	103	ALA	0	-0.005	0.016	10.034	-0.201	-0.201	0.000	0.000	0.000	0.000
11	A	104	ARG	1	0.855	0.919	6.717	-3.762	-3.762	0.000	0.000	0.000	0.000
12	A	105	LEU	0	0.012	0.006	12.848	-0.202	-0.202	0.000	0.000	0.000	0.000
13	A	106	TYR	0	-0.023	-0.021	14.751	-0.104	-0.104	0.000	0.000	0.000	0.000
14	A	107	SER	0	0.036	0.025	15.246	-0.080	-0.080	0.000	0.000	0.000	0.000
15	A	108	ALA	0	0.002	0.003	17.053	-0.092	-0.092	0.000	0.000	0.000	0.000
16	A	109	ILE	0	-0.050	-0.025	19.042	-0.090	-0.090	0.000	0.000	0.000	0.000
17	A	110	GLU	-1	-0.836	-0.918	18.848	0.689	0.689	0.000	0.000	0.000	0.000
18	A	111	GLN	0	0.057	0.022	18.999	0.006	0.006	0.000	0.000	0.000	0.000
19	A	112	ARG	1	0.892	0.956	23.011	-0.530	-0.530	0.000	0.000	0.000	0.000
20	A	113	LEU	0	-0.059	-0.040	24.455	-0.043	-0.043	0.000	0.000	0.000	0.000
21	A	114	GLU	-1	-0.835	-0.914	23.651	0.473	0.473	0.000	0.000	0.000	0.000
22	A	115	GLN	0	-0.043	-0.028	26.273	-0.055	-0.055	0.000	0.000	0.000	0.000
23	A	116	SER	0	-0.002	-0.003	28.908	-0.031	-0.031	0.000	0.000	0.000	0.000
24	A	117	LEU	0	-0.018	0.004	29.276	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	118	GLN	0	-0.012	-0.013	29.682	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	119	THR	0	-0.075	-0.032	33.297	-0.016	-0.016	0.000	0.000	0.000	0.000
27	A	120	MET	0	-0.046	-0.016	35.768	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	121	GLU	-1	-0.907	-0.952	37.758	0.166	0.166	0.000	0.000	0.000	0.000
29	A	122	GLY	0	0.024	0.007	40.739	0.001	0.001	0.000	0.000	0.000	0.000
30	A	123	VAL	0	-0.037	-0.019	33.965	0.000	0.000	0.000	0.000	0.000	0.000
31	A	124	LEU	0	-0.005	0.018	36.278	0.004	0.004	0.000	0.000	0.000	0.000
32	A	125	SER	0	-0.046	-0.029	31.542	0.013	0.013	0.000	0.000	0.000	0.000
33	A	126	ALA	0	0.032	-0.001	29.830	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	127	ARG	1	0.897	0.969	21.973	-0.437	-0.437	0.000	0.000	0.000	0.000
35	A	128	VAL	0	-0.047	-0.038	23.508	-0.022	-0.022	0.000	0.000	0.000	0.000
36	A	129	HIS	0	0.018	0.028	20.855	0.037	0.037	0.000	0.000	0.000	0.000
37	A	130	ILE	0	-0.015	-0.019	19.017	-0.050	-0.050	0.000	0.000	0.000	0.000
38	A	131	SER	0	-0.052	-0.012	17.964	0.066	0.066	0.000	0.000	0.000	0.000
39	A	132	TYR	0	0.007	0.001	11.444	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	133	VAL	0	-0.046	-0.033	20.173	0.001	0.001	0.000	0.000	0.000	0.000
41	A	134	HIS	0	0.018	0.013	21.638	-0.038	-0.038	0.000	0.000	0.000	0.000
42	A	135	LEU	0	0.004	0.008	22.080	0.049	0.049	0.000	0.000	0.000	0.000
43	A	136	SER	0	-0.039	-0.030	24.126	-0.043	-0.043	0.000	0.000	0.000	0.000
44	A	137	ALA	0	0.019	0.007	25.491	0.025	0.025	0.000	0.000	0.000	0.000
45	A	138	LEU	0	-0.005	0.003	28.238	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	139	ALA	0	0.018	0.005	29.867	0.013	0.013	0.000	0.000	0.000	0.000
47	A	140	VAL	0	-0.003	0.013	32.596	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	141	TYR	0	-0.047	-0.031	35.417	0.000	0.000	0.000	0.000	0.000	0.000
49	A	142	GLU	-1	-0.890	-0.926	38.434	0.152	0.152	0.000	0.000	0.000	0.000
50	A	143	ARG	1	0.933	0.953	42.096	-0.155	-0.155	0.000	0.000	0.000	0.000
51	A	144	GLY	0	0.005	0.000	44.087	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	145	SER	0	-0.033	-0.020	43.751	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	146	PRO	0	0.011	0.002	44.715	0.003	0.003	0.000	0.000	0.000	0.000
54	A	147	LEU	0	0.041	0.014	40.342	0.004	0.004	0.000	0.000	0.000	0.000
55	A	148	ALA	0	0.026	0.018	40.681	0.009	0.009	0.000	0.000	0.000	0.000
56	A	149	HIS	0	0.038	0.028	40.985	0.010	0.010	0.000	0.000	0.000	0.000
57	A	150	GLN	0	0.074	0.045	38.308	0.017	0.017	0.000	0.000	0.000	0.000
58	A	151	ILE	0	0.023	0.007	35.518	0.012	0.012	0.000	0.000	0.000	0.000
59	A	152	SER	0	-0.037	-0.036	36.186	0.014	0.014	0.000	0.000	0.000	0.000
60	A	153	ASP	-1	-0.931	-0.963	37.480	0.203	0.203	0.000	0.000	0.000	0.000
61	A	154	ILE	0	0.003	-0.002	32.504	0.013	0.013	0.000	0.000	0.000	0.000
62	A	155	LYS	1	0.939	0.971	32.570	-0.244	-0.244	0.000	0.000	0.000	0.000
63	A	156	ARG	1	0.951	0.987	32.853	-0.207	-0.207	0.000	0.000	0.000	0.000
64	A	157	PHE	0	-0.008	-0.005	30.865	0.007	0.007	0.000	0.000	0.000	0.000
65	A	158	LEU	0	0.038	0.000	27.702	0.015	0.015	0.000	0.000	0.000	0.000
66	A	159	LYS	1	0.818	0.915	28.923	-0.327	-0.327	0.000	0.000	0.000	0.000
67	A	160	ASN	0	-0.044	-0.045	30.256	0.012	0.012	0.000	0.000	0.000	0.000
68	A	161	SER	0	-0.024	0.003	29.083	0.000	0.000	0.000	0.000	0.000	0.000
69	A	162	PHE	0	-0.038	-0.024	21.181	0.034	0.034	0.000	0.000	0.000	0.000
70	A	163	ALA	0	0.041	0.014	26.576	0.001	0.001	0.000	0.000	0.000	0.000
71	A	164	ASP	-1	-0.929	-0.955	21.542	0.569	0.569	0.000	0.000	0.000	0.000
72	A	165	VAL	0	-0.014	0.016	24.675	0.005	0.005	0.000	0.000	0.000	0.000
73	A	166	ASP	-1	-0.879	-0.934	25.955	0.288	0.288	0.000	0.000	0.000	0.000
74	A	167	TYR	0	-0.006	-0.028	28.923	0.002	0.002	0.000	0.000	0.000	0.000
75	A	168	ASP	-1	-0.948	-0.976	31.121	0.286	0.286	0.000	0.000	0.000	0.000
76	A	169	ASN	0	0.009	0.013	26.376	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	170	ILE	0	-0.027	-0.003	26.942	0.028	0.028	0.000	0.000	0.000	0.000
78	A	171	SER	0	-0.076	-0.032	28.228	-0.032	-0.032	0.000	0.000	0.000	0.000
79	A	172	VAL	0	0.034	0.005	29.287	0.017	0.017	0.000	0.000	0.000	0.000
80	A	173	VAL	0	-0.028	-0.003	31.414	-0.018	-0.018	0.000	0.000	0.000	0.000
81	A	174	LEU	0	-0.029	-0.024	33.074	0.008	0.008	0.000	0.000	0.000	0.000
82	A	175	SER	0	-0.046	-0.023	34.436	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	176	GLU	-1	-0.906	-0.947	36.655	0.189	0.189	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:94:HIS)