FMO DATABASE

FMODB ID: 871RY

Calculation Name: 1DPS-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DPS

Chain ID: A

ChEMBL ID:

UniProt ID: P0ABT2

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1532923.220944
FMO2-HF: Nuclear repulsion	1470512.505316
FMO2-HF: Total energy	-62410.715628
FMO2-MP2: Total energy	-62593.821308

3D Structure Molmil

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:9:SER)

Summations of interaction energy for fragment #1(A:9:SER)

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.
-151.269	-143.151	12.671	-10.674	-10.115	-0.086

Interaction energy analysis for fragmet #1(A:9:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.832 / q_NPA : 0.904

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	11	ALA	0	0.009	0.022	2.538	1.080	4.113	1.148	-1.779	-2.402	0.008
4	A	12	THR	0	0.060	0.028	2.532	-7.216	-4.074	1.196	-1.838	-2.501	-0.008
5	A	13	ASN	0	-0.063	-0.040	3.737	5.661	6.101	0.001	-0.134	-0.307	0.000
6	A	14	LEU	0	0.033	0.055	3.097	5.002	6.047	0.027	-0.365	-0.707	-0.002
7	A	15	LEU	0	-0.035	-0.025	1.808	-55.374	-55.078	10.301	-6.523	-4.074	-0.084
8	A	16	TYR	0	-0.047	-0.029	4.365	-0.022	0.159	-0.001	-0.032	-0.148	0.000
9	A	17	THR	0	0.036	0.011	5.193	5.665	5.646	-0.001	-0.003	0.024	0.000
10	A	18	ARG	1	0.925	0.955	8.874	21.768	21.768	0.000	0.000	0.000	0.000
11	A	19	ASN	0	0.036	0.031	11.669	1.010	1.010	0.000	0.000	0.000	0.000
12	A	20	ASP	-1	-0.891	-0.950	11.080	-23.124	-23.124	0.000	0.000	0.000	0.000
13	A	21	VAL	0	0.060	0.051	12.823	0.257	0.257	0.000	0.000	0.000	0.000
14	A	22	SER	0	0.013	-0.002	10.937	-2.733	-2.733	0.000	0.000	0.000	0.000
15	A	23	ASP	-1	-0.871	-0.958	5.388	-45.758	-45.758	0.000	0.000	0.000	0.000
16	A	24	SER	0	-0.056	-0.032	8.207	-0.373	-0.373	0.000	0.000	0.000	0.000
17	A	25	GLU	-1	-0.847	-0.927	10.894	-18.256	-18.256	0.000	0.000	0.000	0.000
18	A	26	LYS	1	0.870	0.960	7.926	34.649	34.649	0.000	0.000	0.000	0.000
19	A	27	LYS	1	0.825	0.907	6.869	33.793	33.793	0.000	0.000	0.000	0.000
20	A	28	ALA	0	0.007	0.009	10.293	1.170	1.170	0.000	0.000	0.000	0.000
21	A	29	THR	0	0.004	-0.015	13.793	1.628	1.628	0.000	0.000	0.000	0.000
22	A	30	VAL	0	-0.007	0.007	10.367	0.724	0.724	0.000	0.000	0.000	0.000
23	A	31	GLU	-1	-0.895	-0.949	11.077	-26.025	-26.025	0.000	0.000	0.000	0.000
24	A	32	LEU	0	-0.049	-0.010	14.975	1.234	1.234	0.000	0.000	0.000	0.000
25	A	33	LEU	0	0.040	0.008	15.770	0.934	0.934	0.000	0.000	0.000	0.000
26	A	34	ASN	0	0.004	-0.006	13.465	1.564	1.564	0.000	0.000	0.000	0.000
27	A	35	ARG	1	0.797	0.876	17.620	14.366	14.366	0.000	0.000	0.000	0.000
28	A	36	GLN	0	0.005	0.010	20.823	1.100	1.100	0.000	0.000	0.000	0.000
29	A	37	VAL	0	0.043	0.017	18.523	0.575	0.575	0.000	0.000	0.000	0.000
30	A	38	ILE	0	-0.045	-0.021	19.375	0.612	0.612	0.000	0.000	0.000	0.000
31	A	39	GLN	0	-0.028	-0.041	22.766	0.793	0.793	0.000	0.000	0.000	0.000
32	A	40	PHE	0	0.032	0.013	25.067	0.574	0.574	0.000	0.000	0.000	0.000
33	A	41	ILE	0	0.012	0.026	22.370	0.438	0.438	0.000	0.000	0.000	0.000
34	A	42	ASP	-1	-0.821	-0.883	26.568	-10.274	-10.274	0.000	0.000	0.000	0.000
35	A	43	LEU	0	0.042	0.025	28.830	0.434	0.434	0.000	0.000	0.000	0.000
36	A	44	SER	0	-0.049	-0.011	29.212	0.452	0.452	0.000	0.000	0.000	0.000
37	A	45	LEU	0	-0.024	-0.017	28.665	0.378	0.378	0.000	0.000	0.000	0.000
38	A	46	ILE	0	-0.018	-0.009	32.419	0.432	0.432	0.000	0.000	0.000	0.000
39	A	47	THR	0	-0.018	-0.011	34.303	0.382	0.382	0.000	0.000	0.000	0.000
40	A	48	LYS	1	0.775	0.869	35.156	8.779	8.779	0.000	0.000	0.000	0.000
41	A	49	GLN	0	-0.039	-0.016	36.642	0.457	0.457	0.000	0.000	0.000	0.000
42	A	50	ALA	0	0.067	0.032	38.463	0.247	0.247	0.000	0.000	0.000	0.000
43	A	51	HIS	0	-0.020	-0.012	39.767	0.162	0.162	0.000	0.000	0.000	0.000
44	A	52	TRP	0	-0.022	-0.018	36.179	0.102	0.102	0.000	0.000	0.000	0.000
45	A	53	ASN	0	-0.054	-0.017	41.624	0.319	0.319	0.000	0.000	0.000	0.000
46	A	54	MET	0	-0.006	0.032	43.423	0.202	0.202	0.000	0.000	0.000	0.000
47	A	55	ARG	1	0.946	0.960	46.808	6.448	6.448	0.000	0.000	0.000	0.000
48	A	56	GLY	0	0.010	0.002	50.543	0.016	0.016	0.000	0.000	0.000	0.000
49	A	57	ALA	0	0.030	0.006	53.434	0.000	0.000	0.000	0.000	0.000	0.000
50	A	58	ASN	0	0.012	-0.017	49.801	-0.072	-0.072	0.000	0.000	0.000	0.000
51	A	59	PHE	0	-0.002	0.015	47.128	-0.080	-0.080	0.000	0.000	0.000	0.000
52	A	60	ILE	0	0.017	0.013	48.006	-0.132	-0.132	0.000	0.000	0.000	0.000
53	A	61	ALA	0	0.066	0.036	47.340	-0.142	-0.142	0.000	0.000	0.000	0.000
54	A	62	VAL	0	0.035	0.019	44.492	-0.179	-0.179	0.000	0.000	0.000	0.000
55	A	63	HIS	0	-0.031	-0.025	43.562	-0.218	-0.218	0.000	0.000	0.000	0.000
56	A	64	GLU	-1	-0.919	-0.962	42.562	-7.090	-7.090	0.000	0.000	0.000	0.000
57	A	65	MET	0	-0.030	0.002	41.492	-0.185	-0.185	0.000	0.000	0.000	0.000
58	A	66	LEU	0	0.011	0.001	39.185	-0.252	-0.252	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.832	-0.904	37.642	-8.828	-8.828	0.000	0.000	0.000	0.000
60	A	68	GLY	0	0.025	0.019	36.771	-0.269	-0.269	0.000	0.000	0.000	0.000
61	A	69	PHE	0	-0.010	-0.016	35.858	-0.207	-0.207	0.000	0.000	0.000	0.000
62	A	70	ARG	1	0.922	0.964	32.397	9.121	9.121	0.000	0.000	0.000	0.000
63	A	71	THR	0	-0.061	-0.036	31.929	-0.388	-0.388	0.000	0.000	0.000	0.000
64	A	72	ALA	0	0.055	0.028	31.301	-0.312	-0.312	0.000	0.000	0.000	0.000
65	A	73	LEU	0	-0.035	-0.019	29.686	-0.392	-0.392	0.000	0.000	0.000	0.000
66	A	74	ILE	0	-0.016	-0.017	27.148	-0.456	-0.456	0.000	0.000	0.000	0.000
67	A	75	ASP	-1	-0.856	-0.912	26.160	-11.235	-11.235	0.000	0.000	0.000	0.000
68	A	76	HIS	0	-0.071	-0.048	25.937	-0.877	-0.877	0.000	0.000	0.000	0.000
69	A	77	LEU	0	-0.035	-0.019	22.603	-0.627	-0.627	0.000	0.000	0.000	0.000
70	A	78	ASP	-1	-0.886	-0.944	21.635	-14.399	-14.399	0.000	0.000	0.000	0.000
71	A	79	THR	0	-0.018	-0.019	20.683	-0.888	-0.888	0.000	0.000	0.000	0.000
72	A	80	MET	0	-0.053	-0.023	19.961	-0.821	-0.821	0.000	0.000	0.000	0.000
73	A	81	ALA	0	-0.011	-0.012	17.230	-1.301	-1.301	0.000	0.000	0.000	0.000
74	A	82	GLU	-1	-0.935	-0.975	15.875	-17.196	-17.196	0.000	0.000	0.000	0.000
75	A	83	ARG	1	0.742	0.858	15.661	16.369	16.369	0.000	0.000	0.000	0.000
76	A	84	ALA	0	0.017	0.000	13.543	-1.527	-1.527	0.000	0.000	0.000	0.000
77	A	85	VAL	0	-0.040	-0.026	11.129	-2.838	-2.838	0.000	0.000	0.000	0.000
78	A	86	GLN	0	-0.017	-0.004	11.037	-2.447	-2.447	0.000	0.000	0.000	0.000
79	A	87	LEU	0	-0.031	-0.004	11.332	-1.413	-1.413	0.000	0.000	0.000	0.000
80	A	88	GLY	0	-0.022	-0.014	7.312	-3.119	-3.119	0.000	0.000	0.000	0.000
81	A	89	GLY	0	0.030	0.010	6.548	-7.096	-7.096	0.000	0.000	0.000	0.000
82	A	90	VAL	0	-0.042	-0.031	8.377	-0.237	-0.237	0.000	0.000	0.000	0.000
83	A	91	ALA	0	0.051	0.044	10.890	0.825	0.825	0.000	0.000	0.000	0.000
84	A	92	LEU	0	-0.079	-0.047	13.545	0.335	0.335	0.000	0.000	0.000	0.000
85	A	93	GLY	0	0.098	0.041	16.794	0.730	0.730	0.000	0.000	0.000	0.000
86	A	94	THR	0	-0.021	-0.006	19.325	0.641	0.641	0.000	0.000	0.000	0.000
87	A	95	THR	0	0.062	0.017	21.660	-0.108	-0.108	0.000	0.000	0.000	0.000
88	A	96	GLN	0	0.012	0.002	22.357	-0.045	-0.045	0.000	0.000	0.000	0.000
89	A	97	VAL	0	-0.012	-0.004	18.280	0.106	0.106	0.000	0.000	0.000	0.000
90	A	98	ILE	0	0.051	0.023	21.524	0.145	0.145	0.000	0.000	0.000	0.000
91	A	99	ASN	0	-0.012	-0.007	24.310	0.540	0.540	0.000	0.000	0.000	0.000
92	A	100	SER	0	-0.114	-0.053	23.002	0.052	0.052	0.000	0.000	0.000	0.000
93	A	101	LYS	1	0.900	0.947	18.497	15.775	15.775	0.000	0.000	0.000	0.000
94	A	102	THR	0	0.015	-0.004	24.247	-0.205	-0.205	0.000	0.000	0.000	0.000
95	A	103	PRO	0	-0.036	-0.005	26.251	0.223	0.223	0.000	0.000	0.000	0.000
96	A	104	LEU	0	-0.034	-0.005	29.022	0.478	0.478	0.000	0.000	0.000	0.000
97	A	105	LYS	1	0.967	0.988	31.886	8.006	8.006	0.000	0.000	0.000	0.000
98	A	106	SER	0	0.027	0.011	34.724	0.061	0.061	0.000	0.000	0.000	0.000
99	A	107	TYR	0	0.020	-0.018	35.529	0.149	0.149	0.000	0.000	0.000	0.000
100	A	108	PRO	0	-0.001	0.011	38.026	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	109	LEU	0	-0.023	-0.026	38.559	-0.017	-0.017	0.000	0.000	0.000	0.000
102	A	110	ASP	-1	-0.920	-0.955	42.561	-6.997	-6.997	0.000	0.000	0.000	0.000
103	A	111	ILE	0	-0.001	0.022	43.484	0.202	0.202	0.000	0.000	0.000	0.000
104	A	112	HIS	0	-0.038	-0.035	46.370	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	113	ASN	0	-0.002	0.005	48.690	-0.032	-0.032	0.000	0.000	0.000	0.000
106	A	114	VAL	0	0.034	0.010	47.626	-0.147	-0.147	0.000	0.000	0.000	0.000
107	A	115	GLN	0	0.043	0.016	47.191	-0.247	-0.247	0.000	0.000	0.000	0.000
108	A	116	ASP	-1	-0.913	-0.960	47.326	-6.615	-6.615	0.000	0.000	0.000	0.000
109	A	117	HIS	0	0.010	0.003	43.304	-0.313	-0.313	0.000	0.000	0.000	0.000
110	A	118	LEU	0	-0.002	0.005	42.632	-0.225	-0.225	0.000	0.000	0.000	0.000
111	A	119	LYS	1	0.929	0.978	43.001	6.453	6.453	0.000	0.000	0.000	0.000
112	A	120	GLU	-1	-0.814	-0.893	40.808	-7.987	-7.987	0.000	0.000	0.000	0.000
113	A	121	LEU	0	-0.042	-0.011	37.821	-0.324	-0.324	0.000	0.000	0.000	0.000
114	A	122	ALA	0	0.043	0.028	38.086	-0.273	-0.273	0.000	0.000	0.000	0.000
115	A	123	ASP	-1	-0.902	-0.945	38.538	-8.082	-8.082	0.000	0.000	0.000	0.000
116	A	124	ARG	1	0.683	0.790	34.478	8.303	8.303	0.000	0.000	0.000	0.000
117	A	125	TYR	0	0.031	-0.020	33.735	-0.373	-0.373	0.000	0.000	0.000	0.000
118	A	126	ALA	0	0.023	0.015	34.239	-0.251	-0.251	0.000	0.000	0.000	0.000
119	A	127	ILE	0	-0.068	-0.026	30.658	-0.142	-0.142	0.000	0.000	0.000	0.000
120	A	128	VAL	0	0.016	0.011	28.352	-0.242	-0.242	0.000	0.000	0.000	0.000
121	A	129	ALA	0	0.040	0.024	29.994	-0.301	-0.301	0.000	0.000	0.000	0.000
122	A	130	ASN	0	-0.013	-0.008	32.037	-0.036	-0.036	0.000	0.000	0.000	0.000
123	A	131	ASP	-1	-0.790	-0.835	26.297	-12.450	-12.450	0.000	0.000	0.000	0.000
124	A	132	VAL	0	0.028	0.015	25.905	-0.273	-0.273	0.000	0.000	0.000	0.000
125	A	133	ARG	1	0.799	0.859	27.606	9.117	9.117	0.000	0.000	0.000	0.000
126	A	134	LYS	1	0.818	0.906	28.297	10.160	10.160	0.000	0.000	0.000	0.000
127	A	135	ALA	0	0.035	0.016	23.484	-0.200	-0.200	0.000	0.000	0.000	0.000
128	A	136	ILE	0	-0.013	0.006	23.867	-0.514	-0.514	0.000	0.000	0.000	0.000
129	A	137	GLY	0	0.003	0.013	25.357	-0.130	-0.130	0.000	0.000	0.000	0.000
130	A	138	GLU	-1	-1.020	-1.010	22.405	-12.920	-12.920	0.000	0.000	0.000	0.000
131	A	139	ALA	0	-0.009	-0.015	20.083	-0.749	-0.749	0.000	0.000	0.000	0.000
132	A	140	LYS	1	0.812	0.912	18.492	14.167	14.167	0.000	0.000	0.000	0.000
133	A	141	ASP	-1	-0.695	-0.802	16.651	-18.026	-18.026	0.000	0.000	0.000	0.000
134	A	142	ASP	-1	-0.859	-0.935	18.746	-13.316	-13.316	0.000	0.000	0.000	0.000
135	A	143	ASP	-1	-0.850	-0.918	19.946	-15.123	-15.123	0.000	0.000	0.000	0.000
136	A	144	THR	0	-0.059	-0.061	18.294	0.170	0.170	0.000	0.000	0.000	0.000
137	A	145	ALA	0	0.020	0.010	20.978	0.484	0.484	0.000	0.000	0.000	0.000
138	A	146	ASP	-1	-0.945	-0.951	24.041	-11.188	-11.188	0.000	0.000	0.000	0.000
139	A	147	ILE	0	0.020	0.004	20.965	0.417	0.417	0.000	0.000	0.000	0.000
140	A	148	LEU	0	-0.014	-0.014	22.001	0.354	0.354	0.000	0.000	0.000	0.000
141	A	149	THR	0	-0.023	-0.028	25.774	0.670	0.670	0.000	0.000	0.000	0.000
142	A	150	ALA	0	-0.059	-0.033	27.971	0.517	0.517	0.000	0.000	0.000	0.000
143	A	151	ALA	0	0.044	0.020	27.036	0.377	0.377	0.000	0.000	0.000	0.000
144	A	152	SER	0	0.016	-0.005	29.074	0.323	0.323	0.000	0.000	0.000	0.000
145	A	153	ARG	1	0.891	0.953	31.145	9.734	9.734	0.000	0.000	0.000	0.000
146	A	154	ASP	-1	-0.836	-0.893	32.560	-9.152	-9.152	0.000	0.000	0.000	0.000
147	A	155	LEU	0	-0.030	-0.018	30.380	0.269	0.269	0.000	0.000	0.000	0.000
148	A	156	ASP	-1	-0.771	-0.857	33.748	-9.026	-9.026	0.000	0.000	0.000	0.000
149	A	157	LYS	1	0.914	0.968	36.612	8.489	8.489	0.000	0.000	0.000	0.000
150	A	158	PHE	0	-0.007	-0.020	33.739	0.265	0.265	0.000	0.000	0.000	0.000
151	A	159	LEU	0	0.026	0.025	37.439	0.144	0.144	0.000	0.000	0.000	0.000
152	A	160	TRP	0	0.026	0.019	39.174	0.191	0.191	0.000	0.000	0.000	0.000
153	A	161	PHE	0	-0.031	-0.026	41.513	0.223	0.223	0.000	0.000	0.000	0.000
154	A	162	ILE	0	-0.032	0.003	38.993	0.191	0.191	0.000	0.000	0.000	0.000
155	A	163	GLU	-1	-0.900	-0.966	42.571	-7.472	-7.472	0.000	0.000	0.000	0.000
156	A	164	CYS	0	-0.088	-0.047	45.056	0.206	0.206	0.000	0.000	0.000	0.000
157	A	165	ASN	0	-0.089	-0.048	45.909	0.274	0.274	0.000	0.000	0.000	0.000
158	A	166	ILE	0	-0.082	-0.038	44.973	0.046	0.046	0.000	0.000	0.000	0.000
159	A	167	GLU	-2	-1.896	-1.930	49.180	-12.083	-12.083	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:SER)