FMO DATABASE

FMODB ID: YYJZ2

Calculation Name: 1J1V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1J1V

Chain ID: A

ChEMBL ID:

UniProt ID: P03004

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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-709504.668193
FMO2-HF: Nuclear repulsion	671855.243502
FMO2-HF: Total energy	-37649.42469
FMO2-MP2: Total energy	-37759.329613

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:374:VAL)

Summations of interaction energy for fragment #1(A:374:VAL)

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.
-12.048	-2.676	5.202	-4.466	-10.108	-0.015

Interaction energy analysis for fragmet #1(A:374:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.013

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	376	ILE	0	0.076	0.023	2.963	-1.974	0.522	0.234	-1.287	-1.443	-0.001
4	A	377	ASP	-1	-0.889	-0.946	5.004	0.335	0.452	-0.001	-0.002	-0.114	0.000
5	A	378	ASN	0	-0.006	-0.005	3.302	-0.748	-0.258	0.023	-0.100	-0.413	0.001
6	A	379	ILE	0	0.040	0.035	2.274	-0.694	-0.489	1.834	-0.423	-1.616	0.000
7	A	380	GLN	0	-0.059	-0.043	4.832	-0.057	-0.001	-0.001	-0.009	-0.046	0.000
8	A	381	LYS	1	0.890	0.946	8.181	-0.390	-0.390	0.000	0.000	0.000	0.000
9	A	382	THR	0	0.052	0.030	6.188	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	383	VAL	0	-0.014	-0.007	7.731	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	384	ALA	0	-0.054	-0.033	10.153	0.002	0.002	0.000	0.000	0.000	0.000
12	A	385	GLU	-1	-0.910	-0.954	12.277	0.064	0.064	0.000	0.000	0.000	0.000
13	A	386	TYR	0	-0.057	-0.043	11.771	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	387	TYR	0	-0.067	-0.038	12.439	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	388	LYS	1	0.885	0.954	16.139	0.030	0.030	0.000	0.000	0.000	0.000
16	A	389	ILE	0	-0.063	-0.022	15.259	0.001	0.001	0.000	0.000	0.000	0.000
17	A	390	LYS	1	0.965	0.967	16.674	0.011	0.011	0.000	0.000	0.000	0.000
18	A	391	VAL	0	0.118	0.056	11.988	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	392	ALA	0	0.014	0.003	14.404	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	393	ASP	-1	-0.863	-0.933	17.302	-0.055	-0.055	0.000	0.000	0.000	0.000
21	A	394	LEU	0	-0.010	0.010	10.957	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	395	LEU	0	0.043	0.029	13.295	-0.025	-0.025	0.000	0.000	0.000	0.000
23	A	396	SER	0	0.028	0.031	16.333	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	397	LYS	1	1.019	1.018	19.396	0.045	0.045	0.000	0.000	0.000	0.000
25	A	398	ARG	1	0.936	0.979	21.935	0.056	0.056	0.000	0.000	0.000	0.000
26	A	399	ARG	1	1.043	0.998	21.376	0.090	0.090	0.000	0.000	0.000	0.000
27	A	400	SER	0	0.015	0.019	23.225	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	401	ARG	1	1.030	1.010	21.819	0.120	0.120	0.000	0.000	0.000	0.000
29	A	402	SER	0	0.047	0.022	20.447	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	403	VAL	0	0.039	0.010	18.427	0.001	0.001	0.000	0.000	0.000	0.000
31	A	404	ALA	0	-0.021	-0.016	17.199	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	405	ARG	1	0.949	0.989	17.051	0.161	0.161	0.000	0.000	0.000	0.000
33	A	406	PRO	0	0.055	0.049	14.172	-0.032	-0.032	0.000	0.000	0.000	0.000
34	A	407	ARG	1	0.816	0.898	12.619	0.107	0.107	0.000	0.000	0.000	0.000
35	A	408	GLN	0	-0.039	-0.036	12.559	-0.032	-0.032	0.000	0.000	0.000	0.000
36	A	409	MET	0	0.046	0.037	10.247	-0.075	-0.075	0.000	0.000	0.000	0.000
37	A	410	ALA	0	0.014	0.004	8.405	-0.090	-0.090	0.000	0.000	0.000	0.000
38	A	411	MET	0	-0.074	-0.037	7.990	-0.086	-0.086	0.000	0.000	0.000	0.000
39	A	412	ALA	0	0.038	0.008	9.985	-0.064	-0.064	0.000	0.000	0.000	0.000
40	A	413	LEU	0	0.025	0.016	5.186	-0.095	-0.095	0.000	0.000	0.000	0.000
41	A	414	ALA	0	-0.006	-0.004	5.192	-0.350	-0.350	0.000	0.000	0.000	0.000
42	A	415	LYS	1	0.909	0.971	6.142	0.360	0.360	0.000	0.000	0.000	0.000
43	A	416	GLU	-1	-0.922	-0.952	7.600	-0.823	-0.823	0.000	0.000	0.000	0.000
44	A	417	LEU	0	-0.042	-0.025	2.378	-1.831	-0.430	1.690	-0.656	-2.436	0.000
45	A	418	THR	0	-0.094	-0.057	2.413	-2.798	-1.001	0.594	-0.894	-1.498	-0.007
46	A	419	ASN	0	0.002	-0.006	4.432	0.394	0.588	-0.001	-0.024	-0.169	0.000
47	A	420	HIS	0	-0.026	0.001	6.241	0.193	0.193	0.000	0.000	0.000	0.000
48	A	421	SER	0	-0.029	-0.010	9.321	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	422	LEU	0	0.012	-0.016	12.248	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	423	PRO	0	0.008	-0.026	14.292	0.005	0.005	0.000	0.000	0.000	0.000
51	A	424	GLU	-1	-0.775	-0.869	11.966	-0.342	-0.342	0.000	0.000	0.000	0.000
52	A	425	ILE	0	-0.015	-0.003	8.939	0.032	0.032	0.000	0.000	0.000	0.000
53	A	426	GLY	0	0.015	-0.009	11.213	0.041	0.041	0.000	0.000	0.000	0.000
54	A	427	ASP	-1	-0.897	-0.936	14.600	-0.124	-0.124	0.000	0.000	0.000	0.000
55	A	428	ALA	0	-0.035	-0.015	10.265	0.038	0.038	0.000	0.000	0.000	0.000
56	A	429	PHE	0	-0.033	-0.019	8.379	0.038	0.038	0.000	0.000	0.000	0.000
57	A	430	GLY	0	-0.012	-0.008	13.613	0.003	0.003	0.000	0.000	0.000	0.000
58	A	431	GLY	0	-0.022	0.012	16.517	0.011	0.011	0.000	0.000	0.000	0.000
59	A	432	ARG	1	0.699	0.816	16.011	0.156	0.156	0.000	0.000	0.000	0.000
60	A	433	ASP	-1	-0.749	-0.859	17.892	-0.171	-0.171	0.000	0.000	0.000	0.000
61	A	434	HIS	0	0.108	0.021	16.994	-0.026	-0.026	0.000	0.000	0.000	0.000
62	A	435	THR	0	-0.080	-0.039	17.700	-0.031	-0.031	0.000	0.000	0.000	0.000
63	A	436	THR	0	-0.033	-0.022	17.624	0.002	0.002	0.000	0.000	0.000	0.000
64	A	437	VAL	0	0.028	0.023	12.735	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	438	LEU	0	-0.005	0.004	15.369	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	439	HIS	0	-0.052	-0.029	17.338	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	440	ALA	0	-0.035	-0.018	14.578	0.007	0.007	0.000	0.000	0.000	0.000
68	A	441	CYS	0	-0.004	0.005	13.137	-0.028	-0.028	0.000	0.000	0.000	0.000
69	A	442	ARG	1	1.054	1.032	14.691	0.259	0.259	0.000	0.000	0.000	0.000
70	A	443	LYS	1	0.821	0.925	18.150	0.208	0.208	0.000	0.000	0.000	0.000
71	A	444	ILE	0	0.004	-0.012	12.663	0.023	0.023	0.000	0.000	0.000	0.000
72	A	445	GLU	-1	-0.929	-0.962	15.698	-0.359	-0.359	0.000	0.000	0.000	0.000
73	A	446	GLN	0	0.016	-0.002	17.047	0.013	0.013	0.000	0.000	0.000	0.000
74	A	447	LEU	0	-0.049	-0.039	18.080	0.018	0.018	0.000	0.000	0.000	0.000
75	A	448	ARG	1	0.941	0.983	13.755	0.422	0.422	0.000	0.000	0.000	0.000
76	A	449	GLU	-1	-0.990	-0.990	18.056	-0.216	-0.216	0.000	0.000	0.000	0.000
77	A	450	GLU	-1	-0.905	-0.942	21.488	-0.153	-0.153	0.000	0.000	0.000	0.000
78	A	451	SER	0	-0.042	-0.016	20.996	0.013	0.013	0.000	0.000	0.000	0.000
79	A	452	HIS	0	0.054	0.012	20.064	-0.030	-0.030	0.000	0.000	0.000	0.000
80	A	453	ASP	-1	-0.810	-0.898	19.526	-0.158	-0.158	0.000	0.000	0.000	0.000
81	A	454	ILE	0	-0.079	-0.032	15.819	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	455	LYS	1	0.903	0.940	15.242	0.192	0.192	0.000	0.000	0.000	0.000
83	A	456	GLU	-1	-0.921	-0.965	15.299	-0.209	-0.209	0.000	0.000	0.000	0.000
84	A	457	ASP	-1	-0.820	-0.884	13.477	-0.243	-0.243	0.000	0.000	0.000	0.000
85	A	458	PHE	0	-0.043	-0.030	10.094	-0.041	-0.041	0.000	0.000	0.000	0.000
86	A	459	SER	0	-0.001	0.001	10.020	-0.115	-0.115	0.000	0.000	0.000	0.000
87	A	460	ASN	0	0.016	-0.002	10.681	-0.054	-0.054	0.000	0.000	0.000	0.000
88	A	461	LEU	0	-0.012	-0.015	7.580	0.006	0.006	0.000	0.000	0.000	0.000
89	A	462	ILE	0	0.013	0.013	5.862	-0.087	-0.087	0.000	0.000	0.000	0.000
90	A	463	ARG	1	0.936	0.977	6.242	0.122	0.122	0.000	0.000	0.000	0.000
91	A	464	THR	0	-0.024	-0.012	7.451	0.071	0.071	0.000	0.000	0.000	0.000
92	A	465	LEU	0	-0.029	-0.030	2.772	-0.932	0.052	0.521	-0.274	-1.231	0.000
93	A	466	SER	0	-0.104	-0.027	2.892	-2.165	-0.559	0.309	-0.787	-1.127	-0.008
94	A	467	SER	0	-0.038	-0.011	4.374	0.265	0.291	0.000	-0.010	-0.015	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:374:VAL)