FMO DATABASE

FMODB ID: 892GY

Calculation Name: 1DCF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DCF

Chain ID: A

ChEMBL ID:

UniProt ID: P49333

Base Structure: X-ray

Registration Date: 2023-09-21

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1208928.714769
FMO2-HF: Nuclear repulsion	1154469.015084
FMO2-HF: Total energy	-54459.699685
FMO2-MP2: Total energy	-54612.959997

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:1:HIS)

Summations of interaction energy for fragment #1(A:1: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.
-21.659	-14.894	15.43	-10.268	-11.929	-0.02

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / 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

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	3	SER	0	-0.025	-0.011	3.804	-1.459	1.063	0.007	-0.998	-1.531	0.005
4	A	4	ASN	0	-0.061	-0.023	5.407	-1.099	-0.897	-0.001	-0.014	-0.187	0.000
5	A	5	PHE	0	0.066	0.017	4.641	-0.252	-0.177	-0.001	-0.007	-0.066	0.000
6	A	6	THR	0	-0.005	-0.016	10.311	-0.075	-0.075	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.007	0.011	13.905	0.029	0.029	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.016	-0.007	10.604	0.011	0.011	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.810	0.915	14.517	-0.058	-0.058	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.001	0.008	13.172	0.030	0.030	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.035	-0.015	16.653	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.015	0.007	16.538	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.024	-0.001	19.080	0.006	0.006	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.722	-0.852	20.518	-0.244	-0.244	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.814	-0.905	22.640	-0.151	-0.151	0.000	0.000	0.000	0.000
16	A	16	ASN	0	0.016	0.027	24.061	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.007	-0.008	24.008	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.027	0.014	23.025	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.037	-0.042	20.289	-0.044	-0.044	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.853	0.923	19.321	0.116	0.116	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.028	-0.006	19.864	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.013	0.000	16.694	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.009	-0.012	14.603	-0.066	-0.066	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.897	0.942	14.923	0.139	0.139	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.003	0.004	16.415	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.012	-0.010	11.812	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.029	0.012	10.792	-0.033	-0.033	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.009	-0.007	12.847	0.059	0.059	0.000	0.000	0.000	0.000
29	A	29	HIS	0	-0.023	-0.004	11.769	0.074	0.074	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.033	-0.012	7.431	-0.026	-0.026	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.022	0.016	10.885	0.124	0.124	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.044	-0.011	11.883	0.068	0.068	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.826	-0.917	14.510	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.032	-0.006	15.647	0.017	0.017	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.002	0.012	18.268	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.036	-0.027	20.177	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.028	-0.019	22.395	0.011	0.011	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.075	-0.061	24.233	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.035	-0.006	26.877	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.074	0.014	26.859	0.006	0.006	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.818	-0.894	28.360	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.817	-0.872	28.208	-0.075	-0.075	0.000	0.000	0.000	0.000
43	A	43	CYS	0	0.011	0.007	24.040	0.003	0.003	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.011	0.013	26.334	0.010	0.010	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.856	0.927	28.438	0.040	0.040	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.018	-0.012	24.845	0.007	0.007	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.009	0.010	22.206	0.005	0.005	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.008	-0.005	23.614	0.006	0.006	0.000	0.000	0.000	0.000
49	A	49	HIS	0	0.050	0.009	22.901	0.006	0.006	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.878	-0.922	22.181	0.051	0.051	0.000	0.000	0.000	0.000
51	A	51	HIS	0	-0.037	-0.034	18.973	0.021	0.021	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.912	0.947	15.120	-0.117	-0.117	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.029	0.020	11.816	0.044	0.044	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.016	-0.015	15.223	-0.039	-0.039	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.038	0.021	10.592	0.004	0.004	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.038	-0.010	16.089	0.017	0.017	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.752	-0.859	18.706	-0.225	-0.225	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.057	-0.043	19.434	0.031	0.031	0.000	0.000	0.000	0.000
59	A	59	CYS	0	-0.059	-0.033	20.933	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	60	MET	0	-0.033	0.002	23.297	0.002	0.002	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.011	0.014	26.407	0.002	0.002	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.009	0.002	28.913	0.008	0.008	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.024	-0.011	26.797	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.918	-0.949	27.637	-0.057	-0.057	0.000	0.000	0.000	0.000
65	A	65	ASN	0	0.008	-0.015	23.967	0.018	0.018	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.052	0.015	21.037	0.002	0.002	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.003	-0.004	24.564	0.020	0.020	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.037	-0.012	23.029	0.012	0.012	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.085	0.040	21.829	0.008	0.008	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.033	0.037	23.405	0.015	0.015	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.938	0.968	26.580	0.015	0.015	0.000	0.000	0.000	0.000
72	A	72	ILE	0	0.010	0.006	22.121	0.002	0.002	0.000	0.000	0.000	0.000
73	A	73	HIS	0	-0.006	-0.006	21.646	0.027	0.027	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.820	-0.875	25.831	0.061	0.061	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.797	0.885	27.512	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	76	PHE	0	-0.029	-0.017	23.997	0.000	0.000	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.019	-0.012	27.319	0.009	0.009	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.774	0.877	29.364	-0.059	-0.059	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.063	-0.048	30.208	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.940	0.971	29.444	-0.056	-0.056	0.000	0.000	0.000	0.000
81	A	81	HIS	0	-0.005	0.016	25.105	0.017	0.017	0.000	0.000	0.000	0.000
82	A	82	GLN	0	0.063	0.017	21.207	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.752	0.847	17.958	-0.201	-0.201	0.000	0.000	0.000	0.000
84	A	84	PRO	0	-0.028	-0.001	18.108	0.025	0.025	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.035	0.024	12.258	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.067	-0.031	15.952	-0.058	-0.058	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.022	0.003	11.461	0.017	0.017	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.023	0.013	14.652	-0.041	-0.041	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.009	-0.003	14.241	-0.059	-0.059	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.047	-0.010	16.522	0.042	0.042	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.030	0.018	17.532	-0.054	-0.054	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.008	0.008	18.803	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	THR	0	0.095	0.054	14.052	0.006	0.006	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.769	-0.892	17.441	-0.060	-0.060	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.810	0.901	20.472	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	96	SER	0	0.003	0.002	22.915	0.017	0.017	0.000	0.000	0.000	0.000
97	A	97	THR	0	-0.015	-0.025	18.460	0.020	0.020	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.900	0.935	16.556	0.042	0.042	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.768	-0.867	19.839	0.062	0.062	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.859	0.961	22.923	0.080	0.080	0.000	0.000	0.000	0.000
101	A	101	CYS	0	-0.020	-0.021	18.198	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	102	MET	0	0.015	0.008	18.801	0.012	0.012	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.042	-0.030	21.462	0.011	0.011	0.000	0.000	0.000	0.000
104	A	104	PHE	0	-0.066	-0.043	23.379	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	105	GLY	0	0.011	0.010	21.608	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.052	-0.034	17.258	0.009	0.009	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.754	-0.830	14.452	0.244	0.244	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.028	0.015	12.193	0.079	0.079	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.054	-0.038	12.285	-0.028	-0.028	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.010	0.009	8.676	-0.061	-0.061	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.018	-0.001	12.434	0.070	0.070	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.822	0.908	13.672	0.181	0.181	0.000	0.000	0.000	0.000
113	A	113	PRO	0	-0.035	-0.028	16.362	0.050	0.050	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.013	0.010	11.775	-0.056	-0.056	0.000	0.000	0.000	0.000
115	A	115	SER	0	-0.007	-0.030	8.825	0.067	0.067	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.017	-0.002	8.277	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.850	-0.907	4.894	-3.084	-3.084	0.000	0.000	0.000	0.000
118	A	118	ASN	0	0.060	0.024	4.679	-1.661	-1.564	-0.001	-0.005	-0.091	0.000
119	A	119	ILE	0	0.006	0.005	6.417	0.271	0.271	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.847	0.924	2.326	1.605	2.624	0.965	-0.643	-1.342	0.005
121	A	121	ASP	-1	-0.946	-0.958	2.475	-1.724	-0.381	0.694	-0.753	-1.284	-0.005
122	A	122	VAL	0	0.019	0.001	3.212	2.853	2.692	0.010	0.375	-0.224	0.000
123	A	123	LEU	0	-0.045	-0.019	5.672	0.419	0.419	0.000	0.000	0.000	0.000
124	A	124	SER	0	0.010	-0.029	1.886	-11.497	-15.221	12.012	-4.446	-3.843	0.017
125	A	125	ASP	-1	-0.838	-0.898	4.973	0.798	0.889	-0.001	-0.015	-0.075	0.000
126	A	126	LEU	0	-0.065	-0.025	7.187	-0.462	-0.462	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.074	-0.034	8.185	-0.311	-0.311	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.876	-0.934	2.588	-5.317	-0.016	1.746	-3.762	-3.286	-0.042
129	A	129	PRO	0	-0.050	-0.032	7.112	0.003	0.003	0.000	0.000	0.000	0.000
130	A	130	ARG	1	0.876	0.934	8.889	-1.034	-1.034	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.033	-0.019	11.256	-0.142	-0.142	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.038	-0.016	14.236	0.076	0.076	0.000	0.000	0.000	0.000
133	A	133	TYR	0	0.008	-0.003	13.863	-0.019	-0.019	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.956	-0.965	19.063	0.399	0.399	0.000	0.000	0.000	0.000

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