FMO DATABASE

FMODB ID: Q1J5Y

Calculation Name: 1O4W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O4W

Chain ID: A

ChEMBL ID:

UniProt ID: O29664

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1060850.908913
FMO2-HF: Nuclear repulsion	1011023.900687
FMO2-HF: Total energy	-49827.008226
FMO2-MP2: Total energy	-49972.963885

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:10:LYS)

Summations of interaction energy for fragment #1(A:10:LYS)

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.
19.885	24.04	0.711	-1.654	-3.212	0.003

Interaction energy analysis for fragmet #1(A:10:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.007 / q_NPA : 1.003

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	12	ARG	1	0.885	0.957	2.469	39.762	43.784	0.713	-1.636	-3.099	0.003
4	A	13	CYS	0	-0.114	-0.054	4.482	-1.541	-1.408	-0.002	-0.018	-0.113	0.000
5	A	14	ALA	0	-0.001	-0.005	7.689	-0.859	-0.859	0.000	0.000	0.000	0.000
6	A	15	VAL	0	0.021	0.026	10.927	0.924	0.924	0.000	0.000	0.000	0.000
7	A	16	VAL	0	-0.024	-0.023	13.754	0.278	0.278	0.000	0.000	0.000	0.000
8	A	17	ASP	-1	-0.755	-0.845	16.944	-13.233	-13.233	0.000	0.000	0.000	0.000
9	A	18	THR	0	0.074	0.015	20.276	0.100	0.100	0.000	0.000	0.000	0.000
10	A	19	ASN	0	-0.047	-0.035	23.136	0.868	0.868	0.000	0.000	0.000	0.000
11	A	20	VAL	0	-0.035	-0.016	19.984	0.351	0.351	0.000	0.000	0.000	0.000
12	A	21	LEU	0	0.024	0.011	19.527	0.277	0.277	0.000	0.000	0.000	0.000
13	A	22	MET	0	-0.020	0.012	23.319	0.464	0.464	0.000	0.000	0.000	0.000
14	A	23	TYR	0	0.025	-0.007	25.510	0.444	0.444	0.000	0.000	0.000	0.000
15	A	24	VAL	0	-0.022	0.017	22.488	0.186	0.186	0.000	0.000	0.000	0.000
16	A	25	TYR	0	-0.008	-0.006	25.441	0.440	0.440	0.000	0.000	0.000	0.000
17	A	26	LEU	0	-0.035	-0.019	28.893	0.383	0.383	0.000	0.000	0.000	0.000
18	A	27	ASN	0	-0.037	-0.029	28.102	0.259	0.259	0.000	0.000	0.000	0.000
19	A	28	LYS	1	0.856	0.938	27.998	9.783	9.783	0.000	0.000	0.000	0.000
20	A	29	ALA	0	0.043	0.041	23.839	-0.047	-0.047	0.000	0.000	0.000	0.000
21	A	30	ASP	-1	-0.813	-0.916	20.516	-14.659	-14.659	0.000	0.000	0.000	0.000
22	A	31	VAL	0	0.021	-0.005	17.963	-0.612	-0.612	0.000	0.000	0.000	0.000
23	A	32	VAL	0	-0.016	-0.007	15.735	-0.949	-0.949	0.000	0.000	0.000	0.000
24	A	33	GLY	0	0.026	0.008	15.517	-1.210	-1.210	0.000	0.000	0.000	0.000
25	A	34	GLN	0	0.013	0.004	16.088	-0.749	-0.749	0.000	0.000	0.000	0.000
26	A	35	LEU	0	-0.039	-0.022	12.730	-1.001	-1.001	0.000	0.000	0.000	0.000
27	A	36	ARG	1	0.925	0.955	11.643	18.400	18.400	0.000	0.000	0.000	0.000
28	A	37	GLU	-1	-0.939	-0.949	11.174	-17.196	-17.196	0.000	0.000	0.000	0.000
29	A	38	PHE	0	-0.070	-0.029	11.237	-0.229	-0.229	0.000	0.000	0.000	0.000
30	A	39	GLY	0	-0.003	0.008	7.487	-2.096	-2.096	0.000	0.000	0.000	0.000
31	A	40	PHE	0	-0.091	-0.043	6.740	-4.954	-4.954	0.000	0.000	0.000	0.000
32	A	41	SER	0	0.008	-0.016	7.211	2.079	2.079	0.000	0.000	0.000	0.000
33	A	42	ARG	1	0.805	0.874	6.885	33.931	33.931	0.000	0.000	0.000	0.000
34	A	43	PHE	0	0.002	0.000	10.287	-1.193	-1.193	0.000	0.000	0.000	0.000
35	A	44	LEU	0	0.019	0.021	10.743	0.519	0.519	0.000	0.000	0.000	0.000
36	A	45	ILE	0	-0.036	-0.018	14.106	0.462	0.462	0.000	0.000	0.000	0.000
37	A	46	THR	0	0.053	0.013	17.494	-0.279	-0.279	0.000	0.000	0.000	0.000
38	A	47	ALA	0	0.039	0.016	19.308	0.576	0.576	0.000	0.000	0.000	0.000
39	A	48	SER	0	0.027	0.023	22.449	0.584	0.584	0.000	0.000	0.000	0.000
40	A	49	VAL	0	0.025	0.007	21.617	0.557	0.557	0.000	0.000	0.000	0.000
41	A	50	LYS	1	0.915	0.953	22.413	13.023	13.023	0.000	0.000	0.000	0.000
42	A	51	ARG	1	0.865	0.932	24.207	11.460	11.460	0.000	0.000	0.000	0.000
43	A	52	GLU	-1	-0.777	-0.881	26.927	-9.963	-9.963	0.000	0.000	0.000	0.000
44	A	53	LEU	0	-0.027	-0.004	25.373	0.400	0.400	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.809	-0.897	27.546	-10.985	-10.985	0.000	0.000	0.000	0.000
46	A	55	LYS	1	0.808	0.883	30.278	10.407	10.407	0.000	0.000	0.000	0.000
47	A	56	LEU	0	0.015	0.015	29.862	0.340	0.340	0.000	0.000	0.000	0.000
48	A	57	GLU	-1	-0.733	-0.855	31.541	-8.730	-8.730	0.000	0.000	0.000	0.000
49	A	58	MET	0	-0.031	-0.003	33.370	0.284	0.284	0.000	0.000	0.000	0.000
50	A	59	SER	0	-0.073	-0.036	35.874	0.278	0.278	0.000	0.000	0.000	0.000
51	A	60	LEU	0	-0.006	0.019	32.572	0.200	0.200	0.000	0.000	0.000	0.000
52	A	61	ARG	1	0.991	0.971	37.006	7.495	7.495	0.000	0.000	0.000	0.000
53	A	62	GLY	0	0.023	0.013	38.190	-0.132	-0.132	0.000	0.000	0.000	0.000
54	A	63	LYS	1	0.898	0.917	35.739	8.573	8.573	0.000	0.000	0.000	0.000
55	A	64	GLU	-1	-0.752	-0.864	33.791	-9.174	-9.174	0.000	0.000	0.000	0.000
56	A	65	LYS	1	0.796	0.923	33.144	8.241	8.241	0.000	0.000	0.000	0.000
57	A	66	VAL	0	-0.026	-0.012	33.064	-0.215	-0.215	0.000	0.000	0.000	0.000
58	A	67	ALA	0	0.001	-0.001	30.032	-0.280	-0.280	0.000	0.000	0.000	0.000
59	A	68	ALA	0	0.056	0.022	28.888	-0.441	-0.441	0.000	0.000	0.000	0.000
60	A	69	ARG	1	0.832	0.886	28.801	8.691	8.691	0.000	0.000	0.000	0.000
61	A	70	PHE	0	-0.039	-0.015	25.202	-0.142	-0.142	0.000	0.000	0.000	0.000
62	A	71	ALA	0	0.027	0.004	24.853	-0.396	-0.396	0.000	0.000	0.000	0.000
63	A	72	LEU	0	0.000	-0.014	24.236	-0.545	-0.545	0.000	0.000	0.000	0.000
64	A	73	LYS	1	0.962	0.994	25.291	10.913	10.913	0.000	0.000	0.000	0.000
65	A	74	LEU	0	-0.028	-0.016	21.253	-0.363	-0.363	0.000	0.000	0.000	0.000
66	A	75	LEU	0	-0.025	-0.017	19.945	-0.690	-0.690	0.000	0.000	0.000	0.000
67	A	76	GLU	-1	-0.945	-0.964	20.922	-12.215	-12.215	0.000	0.000	0.000	0.000
68	A	77	HIS	0	-0.077	-0.031	18.440	-0.584	-0.584	0.000	0.000	0.000	0.000
69	A	78	PHE	0	-0.066	-0.036	16.304	-1.258	-1.258	0.000	0.000	0.000	0.000
70	A	79	GLU	-1	-0.779	-0.852	11.851	-25.330	-25.330	0.000	0.000	0.000	0.000
71	A	80	VAL	0	-0.014	-0.016	16.020	-0.101	-0.101	0.000	0.000	0.000	0.000
72	A	81	VAL	0	-0.046	-0.021	13.942	-0.052	-0.052	0.000	0.000	0.000	0.000
73	A	82	GLU	-1	-0.853	-0.946	17.399	-13.341	-13.341	0.000	0.000	0.000	0.000
74	A	83	THR	0	-0.149	-0.083	17.540	-1.321	-1.321	0.000	0.000	0.000	0.000
75	A	84	GLU	-1	-0.929	-0.958	19.830	-12.766	-12.766	0.000	0.000	0.000	0.000
76	A	85	SER	0	-0.096	-0.059	20.813	0.626	0.626	0.000	0.000	0.000	0.000
77	A	86	GLU	-1	-0.885	-0.957	23.005	-11.560	-11.560	0.000	0.000	0.000	0.000
78	A	87	GLY	0	0.008	-0.004	24.988	0.055	0.055	0.000	0.000	0.000	0.000
79	A	88	ASP	-1	-0.882	-0.940	22.704	-13.228	-13.228	0.000	0.000	0.000	0.000
80	A	89	PRO	0	-0.044	-0.032	21.216	-0.829	-0.829	0.000	0.000	0.000	0.000
81	A	90	SER	0	0.041	0.035	19.964	-0.907	-0.907	0.000	0.000	0.000	0.000
82	A	91	LEU	0	0.017	-0.003	17.445	-1.155	-1.155	0.000	0.000	0.000	0.000
83	A	92	ILE	0	-0.034	-0.028	15.811	-1.313	-1.313	0.000	0.000	0.000	0.000
84	A	93	GLU	-1	-0.750	-0.835	15.060	-17.580	-17.580	0.000	0.000	0.000	0.000
85	A	94	ALA	0	0.027	0.003	14.175	-1.351	-1.351	0.000	0.000	0.000	0.000
86	A	95	ALA	0	-0.035	-0.023	11.517	-2.145	-2.145	0.000	0.000	0.000	0.000
87	A	96	GLU	-1	-0.890	-0.958	10.165	-23.871	-23.871	0.000	0.000	0.000	0.000
88	A	97	LYS	1	0.894	0.970	9.873	17.271	17.271	0.000	0.000	0.000	0.000
89	A	98	TYR	0	-0.011	-0.023	8.390	-1.306	-1.306	0.000	0.000	0.000	0.000
90	A	99	GLY	0	0.016	0.031	5.788	-5.784	-5.784	0.000	0.000	0.000	0.000
91	A	101	ILE	0	-0.010	0.006	8.344	1.260	1.260	0.000	0.000	0.000	0.000
92	A	102	LEU	0	0.023	0.013	10.635	0.738	0.738	0.000	0.000	0.000	0.000
93	A	103	ILE	0	-0.023	-0.011	13.799	0.754	0.754	0.000	0.000	0.000	0.000
94	A	104	THR	0	0.014	-0.030	16.674	0.847	0.847	0.000	0.000	0.000	0.000
95	A	105	ASN	0	0.007	-0.007	20.212	-0.612	-0.612	0.000	0.000	0.000	0.000
96	A	106	ASP	-1	-0.708	-0.838	23.083	-11.601	-11.601	0.000	0.000	0.000	0.000
97	A	107	LYS	1	0.845	0.904	23.485	10.784	10.784	0.000	0.000	0.000	0.000
98	A	108	GLU	-1	-0.804	-0.888	24.618	-12.176	-12.176	0.000	0.000	0.000	0.000
99	A	109	LEU	0	-0.015	0.005	19.980	-0.343	-0.343	0.000	0.000	0.000	0.000
100	A	110	LYS	1	0.940	0.978	19.632	13.507	13.507	0.000	0.000	0.000	0.000
101	A	111	ARG	1	0.840	0.914	19.721	11.668	11.668	0.000	0.000	0.000	0.000
102	A	112	LYS	1	0.890	0.939	20.810	12.323	12.323	0.000	0.000	0.000	0.000
103	A	113	ALA	0	0.081	0.044	15.940	-0.350	-0.350	0.000	0.000	0.000	0.000
104	A	114	LYS	1	0.951	0.977	15.978	13.605	13.605	0.000	0.000	0.000	0.000
105	A	115	GLN	0	-0.051	-0.030	17.434	-0.337	-0.337	0.000	0.000	0.000	0.000
106	A	116	ARG	1	0.889	0.952	15.527	16.483	16.483	0.000	0.000	0.000	0.000
107	A	117	GLY	0	0.002	0.016	13.386	-1.076	-1.076	0.000	0.000	0.000	0.000
108	A	118	ILE	0	-0.040	-0.003	11.454	-2.114	-2.114	0.000	0.000	0.000	0.000
109	A	119	PRO	0	-0.022	-0.005	9.233	1.824	1.824	0.000	0.000	0.000	0.000
110	A	120	VAL	0	0.011	-0.011	12.505	0.176	0.176	0.000	0.000	0.000	0.000
111	A	121	GLY	0	0.012	0.005	15.420	-0.049	-0.049	0.000	0.000	0.000	0.000
112	A	122	TYR	0	-0.035	-0.025	16.756	0.665	0.665	0.000	0.000	0.000	0.000
113	A	123	LEU	0	0.023	0.012	20.201	-0.118	-0.118	0.000	0.000	0.000	0.000
114	A	124	LYS	1	0.929	0.950	22.685	12.811	12.811	0.000	0.000	0.000	0.000
115	A	125	GLU	-1	-0.822	-0.897	25.006	-9.935	-9.935	0.000	0.000	0.000	0.000
116	A	126	ASP	-1	-0.861	-0.916	27.441	-10.441	-10.441	0.000	0.000	0.000	0.000
117	A	127	LYS	1	0.828	0.905	29.171	9.450	9.450	0.000	0.000	0.000	0.000
118	A	128	ARG	1	0.895	0.941	27.797	10.312	10.312	0.000	0.000	0.000	0.000
119	A	129	VAL	0	0.016	0.005	34.436	0.071	0.071	0.000	0.000	0.000	0.000
120	A	130	PHE	0	-0.052	-0.026	36.234	-0.079	-0.079	0.000	0.000	0.000	0.000
121	A	131	VAL	0	0.016	0.005	38.846	0.115	0.115	0.000	0.000	0.000	0.000
122	A	132	GLU	-1	-0.862	-0.920	39.957	-7.709	-7.709	0.000	0.000	0.000	0.000
123	A	133	LEU	0	-0.026	-0.017	42.239	0.183	0.183	0.000	0.000	0.000	0.000
124	A	134	LEU	0	-0.066	-0.030	39.931	0.225	0.225	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:10:LYS)