FMO DATABASE

FMODB ID: RYVZ8

Calculation Name: 4E1P-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4E1P

Chain ID: A

ChEMBL ID:

UniProt ID: P9WIP7

Base Structure: X-ray

Registration Date: 2025-07-08

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-236138.302251
FMO2-HF: Nuclear repulsion	215683.069655
FMO2-HF: Total energy	-20455.232595
FMO2-MP2: Total energy	-20515.887374

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:4:LYS)

Summations of interaction energy for fragment #1(A:4: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.
-2.083	-0.782	-0.009	-0.536	-0.756	0.001

Interaction energy analysis for fragmet #1(A:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.152 / q_NPA : 0.049

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].
4	A	5	VAL	0	-0.054	0.146	3.923	0.051	0.347	0.002	-0.132	-0.166	0.000
5	A	6	THR	0	0.024	-0.082	3.788	-0.874	-0.001	-0.008	-0.389	-0.476	0.001
6	A	6	THR	0	-0.051	0.060	4.089	-0.125	-0.057	-0.001	-0.013	-0.054	0.000
7	A	7	VAL	0	0.075	-0.106	5.694	0.394	0.458	-0.002	-0.002	-0.060	0.000
8	A	7	VAL	0	-0.051	0.135	8.099	0.012	0.012	0.000	0.000	0.000	0.000
9	A	8	THR	0	-0.030	-0.101	9.260	-0.077	-0.077	0.000	0.000	0.000	0.000
10	A	8	THR	0	-0.014	0.065	10.020	-0.046	-0.046	0.000	0.000	0.000	0.000
11	A	9	LEU	0	0.148	-0.080	12.141	0.029	0.029	0.000	0.000	0.000	0.000
12	A	9	LEU	0	-0.088	0.137	16.149	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	10	VAL	0	0.083	-0.108	15.868	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	10	VAL	0	-0.097	0.090	15.004	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	11	ASP	0	0.138	-0.044	17.534	0.028	0.028	0.000	0.000	0.000	0.000
16	A	11	ASP	-1	-0.839	-0.781	21.594	-0.315	-0.315	0.000	0.000	0.000	0.000
17	A	12	ASP	0	0.119	-0.114	21.266	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	12	ASP	-1	-0.927	-0.812	21.719	-0.326	-0.326	0.000	0.000	0.000	0.000
19	A	13	PHE	0	0.050	-0.066	22.945	0.019	0.019	0.000	0.000	0.000	0.000
20	A	13	PHE	0	-0.162	0.030	26.491	0.009	0.009	0.000	0.000	0.000	0.000
21	A	14	ASP	0	-0.001	-0.112	24.199	0.021	0.021	0.000	0.000	0.000	0.000
22	A	14	ASP	-1	-0.856	-0.819	22.861	-0.349	-0.349	0.000	0.000	0.000	0.000
23	A	15	GLY	0	0.026	-0.069	20.032	0.003	0.003	0.000	0.000	0.000	0.000
24	A	16	SER	0	-0.044	-0.014	18.694	-0.054	-0.054	0.000	0.000	0.000	0.000
25	A	16	SER	0	-0.130	0.002	21.081	0.012	0.012	0.000	0.000	0.000	0.000
26	A	17	GLY	0	-0.057	-0.120	18.883	-0.043	-0.043	0.000	0.000	0.000	0.000
27	A	18	ALA	0	0.132	0.002	17.736	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	18	ALA	0	-0.106	0.088	17.090	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	19	ALA	0	0.045	-0.133	18.475	0.048	0.048	0.000	0.000	0.000	0.000
30	A	19	ALA	0	-0.067	0.128	19.770	0.002	0.002	0.000	0.000	0.000	0.000
31	A	20	ASP	0	-0.009	-0.133	19.924	-0.047	-0.047	0.000	0.000	0.000	0.000
32	A	20	ASP	-1	-0.872	-0.824	22.349	-0.390	-0.390	0.000	0.000	0.000	0.000
33	A	21	GLU	0	0.047	-0.106	22.616	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	21	GLU	-1	-0.920	-0.844	26.156	-0.232	-0.232	0.000	0.000	0.000	0.000
35	A	22	THR	0	0.026	-0.103	24.611	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	22	THR	0	-0.045	0.087	23.890	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	23	VAL	0	-0.005	-0.122	25.981	0.014	0.014	0.000	0.000	0.000	0.000
38	A	23	VAL	0	-0.116	0.068	28.418	0.002	0.002	0.000	0.000	0.000	0.000
39	A	24	GLU	0	0.149	-0.104	29.508	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	24	GLU	-1	-1.024	-0.833	31.581	-0.137	-0.137	0.000	0.000	0.000	0.000
41	A	25	PHE	0	-0.023	-0.117	31.854	0.004	0.004	0.000	0.000	0.000	0.000
42	A	25	PHE	0	-0.115	0.064	30.439	0.002	0.002	0.000	0.000	0.000	0.000
43	A	26	GLY	0	0.057	-0.085	34.649	0.000	0.000	0.000	0.000	0.000	0.000
44	A	27	LEU	0	0.052	-0.038	37.111	0.000	0.000	0.000	0.000	0.000	0.000
45	A	27	LEU	0	-0.087	0.126	37.973	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	28	ASP	0	0.019	-0.138	39.336	0.000	0.000	0.000	0.000	0.000	0.000
47	A	28	ASP	-1	-0.986	-0.832	41.004	-0.078	-0.078	0.000	0.000	0.000	0.000
48	A	29	GLY	0	-0.018	-0.121	41.459	0.004	0.004	0.000	0.000	0.000	0.000
49	A	30	VAL	0	0.030	-0.031	37.125	0.003	0.003	0.000	0.000	0.000	0.000
50	A	30	VAL	0	-0.048	0.124	35.018	0.001	0.001	0.000	0.000	0.000	0.000
51	A	31	THR	0	0.004	-0.096	35.288	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	31	THR	0	-0.015	0.083	33.730	0.001	0.001	0.000	0.000	0.000	0.000
53	A	32	TYR	0	0.031	-0.113	31.345	0.004	0.004	0.000	0.000	0.000	0.000
54	A	32	TYR	0	-0.094	0.063	30.824	0.002	0.002	0.000	0.000	0.000	0.000
55	A	33	GLU	0	0.098	-0.114	27.929	0.008	0.008	0.000	0.000	0.000	0.000
56	A	33	GLU	-1	-0.951	-0.815	26.794	-0.202	-0.202	0.000	0.000	0.000	0.000
57	A	34	ILE	0	0.049	-0.068	25.968	0.002	0.002	0.000	0.000	0.000	0.000
58	A	34	ILE	0	-0.153	0.042	26.219	0.003	0.003	0.000	0.000	0.000	0.000
59	A	35	ASP	0	0.172	-0.111	22.166	0.023	0.023	0.000	0.000	0.000	0.000
60	A	35	ASP	-1	-0.925	-0.773	21.222	-0.355	-0.355	0.000	0.000	0.000	0.000
61	A	36	LEU	0	0.064	-0.119	23.499	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	36	LEU	0	-0.142	0.089	25.366	0.009	0.009	0.000	0.000	0.000	0.000
63	A	37	SER	0	0.097	-0.035	23.417	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	37	SER	0	-0.033	0.075	23.260	0.012	0.012	0.000	0.000	0.000	0.000
65	A	38	THR	0	0.058	-0.093	24.187	0.026	0.026	0.000	0.000	0.000	0.000
66	A	38	THR	0	-0.083	0.071	25.423	0.005	0.005	0.000	0.000	0.000	0.000
67	A	39	LYS	0	0.044	-0.092	26.950	0.025	0.025	0.000	0.000	0.000	0.000
68	A	39	LYS	1	0.863	1.064	27.560	0.230	0.230	0.000	0.000	0.000	0.000
69	A	40	ASN	0	0.070	-0.118	27.326	0.024	0.024	0.000	0.000	0.000	0.000
70	A	40	ASN	0	-0.157	0.044	25.421	0.022	0.022	0.000	0.000	0.000	0.000
71	A	41	ALA	0	0.146	-0.109	28.168	0.018	0.018	0.000	0.000	0.000	0.000
72	A	41	ALA	0	-0.037	0.152	28.114	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	42	THR	0	-0.038	-0.120	29.732	0.017	0.017	0.000	0.000	0.000	0.000
74	A	42	THR	0	-0.077	0.066	31.441	0.004	0.004	0.000	0.000	0.000	0.000
75	A	43	LYS	0	0.089	-0.090	31.785	0.016	0.016	0.000	0.000	0.000	0.000
76	A	43	LYS	1	0.863	1.076	31.400	0.171	0.171	0.000	0.000	0.000	0.000
77	A	44	LEU	0	0.116	-0.093	32.152	0.014	0.014	0.000	0.000	0.000	0.000
78	A	44	LEU	0	-0.052	0.134	31.097	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	45	ARG	0	0.059	-0.129	33.595	0.012	0.012	0.000	0.000	0.000	0.000
80	A	45	ARG	1	0.771	1.040	30.899	0.191	0.191	0.000	0.000	0.000	0.000
81	A	46	GLY	0	-0.089	-0.147	35.800	0.011	0.011	0.000	0.000	0.000	0.000
82	A	47	ASP	0	0.111	-0.020	36.760	0.010	0.010	0.000	0.000	0.000	0.000
83	A	47	ASP	-1	-1.002	-0.831	35.850	-0.145	-0.145	0.000	0.000	0.000	0.000
84	A	48	LEU	0	0.015	-0.151	38.038	0.010	0.010	0.000	0.000	0.000	0.000
85	A	48	LEU	0	-0.037	0.144	36.386	0.001	0.001	0.000	0.000	0.000	0.000
86	A	49	LYS	0	0.105	-0.069	39.727	0.007	0.007	0.000	0.000	0.000	0.000
87	A	49	LYS	1	0.841	1.051	40.611	0.121	0.121	0.000	0.000	0.000	0.000
88	A	50	GLN	0	0.074	-0.107	41.769	0.003	0.003	0.000	0.000	0.000	0.000
89	A	50	GLN	0	-0.054	0.105	43.701	0.000	0.000	0.000	0.000	0.000	0.000
90	A	51	TRP	0	0.026	-0.118	43.637	0.006	0.006	0.000	0.000	0.000	0.000
91	A	51	TRP	0	-0.051	0.106	41.864	0.003	0.003	0.000	0.000	0.000	0.000
92	A	52	VAL	0	0.115	-0.086	42.984	0.006	0.006	0.000	0.000	0.000	0.000
93	A	52	VAL	0	-0.098	0.083	40.856	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	53	ALA	0	0.052	-0.116	44.176	0.003	0.003	0.000	0.000	0.000	0.000
95	A	53	ALA	0	-0.108	0.095	46.342	0.000	0.000	0.000	0.000	0.000	0.000
96	A	54	ALA	0	0.058	-0.106	47.063	0.003	0.003	0.000	0.000	0.000	0.000
97	A	54	ALA	0	-0.074	0.113	48.580	0.000	0.000	0.000	0.000	0.000	0.000
98	A	55	GLY	0	-0.057	-0.101	47.576	0.004	0.004	0.000	0.000	0.000	0.000
99	A	56	ARG	0	0.055	0.004	48.540	0.000	0.000	0.000	0.000	0.000	0.000
100	A	56	ARG	1	0.893	1.068	50.365	0.064	0.064	0.000	0.000	0.000	0.000
101	A	57	ARG	0	0.105	-0.099	46.297	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	57	ARG	1	0.880	1.065	44.530	0.089	0.089	0.000	0.000	0.000	0.000
103	A	58	VAL	0	-0.067	-0.099	46.197	0.004	0.004	0.000	0.000	0.000	0.000
104	A	58	VAL	0	0.071	0.034	46.028	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LYS)