FMO DATABASE

FMODB ID: 8NR8Y

Calculation Name: 4XPM-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4XPM

Chain ID: B

ChEMBL ID:

UniProt ID: Q02205

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	OptAll
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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-360299.067457
FMO2-HF: Nuclear repulsion	335566.465671
FMO2-HF: Total energy	-24732.601786
FMO2-MP2: Total energy	-24806.134108

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(B:8:ASP)

Summations of interaction energy for fragment #1(B:8:ASP)

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.
-0.236	0.371	0.178	0.926	-1.711	0.005

Interaction energy analysis for fragmet #1(B:8:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.134 / q_NPA : 0.023

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	B	9	ILE	0	-0.069	0.111	3.351	-0.154	0.209	0.029	-0.150	-0.242	0.000
5	B	10	LYS	0	0.056	-0.108	3.889	-0.849	-0.005	-0.003	-0.390	-0.451	0.000
6	B	10	LYS	1	0.735	0.990	2.963	2.032	0.708	0.086	1.766	-0.527	0.004
7	B	11	GLY	0	0.020	-0.102	6.281	0.283	0.283	0.000	0.000	0.000	0.000
8	B	12	THR	0	-0.024	0.000	8.909	0.031	0.031	0.000	0.000	0.000	0.000
9	B	12	THR	0	-0.019	0.058	9.860	-0.045	-0.045	0.000	0.000	0.000	0.000
10	B	13	ILE	0	0.138	-0.063	11.623	-0.022	-0.022	0.000	0.000	0.000	0.000
11	B	13	ILE	0	-0.092	0.101	14.285	0.001	0.001	0.000	0.000	0.000	0.000
12	B	14	ALA	0	0.155	-0.040	15.273	0.035	0.035	0.000	0.000	0.000	0.000
13	B	14	ALA	0	-0.109	0.085	16.706	-0.002	-0.002	0.000	0.000	0.000	0.000
14	B	15	PHE	0	0.029	-0.104	17.705	-0.016	-0.016	0.000	0.000	0.000	0.000
15	B	15	PHE	0	-0.053	0.100	17.804	0.005	0.005	0.000	0.000	0.000	0.000
16	B	16	ASP	0	0.136	-0.050	21.310	0.009	0.009	0.000	0.000	0.000	0.000
17	B	16	ASP	-1	-0.839	-0.794	25.415	-0.027	-0.027	0.000	0.000	0.000	0.000
18	B	17	THR	0	0.002	-0.091	24.689	0.007	0.007	0.000	0.000	0.000	0.000
19	B	17	THR	0	-0.052	0.058	26.805	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	18	HIS	0	0.061	-0.095	27.076	0.009	0.009	0.000	0.000	0.000	0.000
21	B	18	HIS	0	-0.173	0.028	28.877	0.003	0.003	0.000	0.000	0.000	0.000
22	B	19	GLY	0	0.019	-0.079	24.353	0.004	0.004	0.000	0.000	0.000	0.000
23	B	20	ASN	0	0.079	0.000	24.398	-0.004	-0.004	0.000	0.000	0.000	0.000
24	B	20	ASN	0	-0.167	0.041	26.426	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	21	VAL	0	0.140	-0.075	21.493	0.006	0.006	0.000	0.000	0.000	0.000
26	B	21	VAL	0	-0.089	0.107	19.592	0.000	0.000	0.000	0.000	0.000	0.000
27	B	22	ILE	0	0.026	-0.111	20.660	0.002	0.002	0.000	0.000	0.000	0.000
28	B	22	ILE	0	-0.138	0.068	20.629	0.000	0.000	0.000	0.000	0.000	0.000
29	B	23	GLU	0	0.030	-0.119	17.727	0.000	0.000	0.000	0.000	0.000	0.000
30	B	23	GLU	-1	-0.879	-0.798	14.856	-0.301	-0.301	0.000	0.000	0.000	0.000
31	B	24	SER	0	0.027	-0.090	15.297	0.030	0.030	0.000	0.000	0.000	0.000
32	B	24	SER	0	0.028	0.098	15.797	0.006	0.006	0.000	0.000	0.000	0.000
33	B	25	THR	0	-0.070	-0.104	12.547	0.024	0.024	0.000	0.000	0.000	0.000
34	B	25	THR	0	-0.031	0.055	11.405	-0.089	-0.089	0.000	0.000	0.000	0.000
35	B	26	GLY	0	0.081	-0.063	10.504	-0.014	-0.014	0.000	0.000	0.000	0.000
36	B	27	VAL	0	0.024	-0.034	10.447	0.076	0.076	0.000	0.000	0.000	0.000
37	B	27	VAL	0	-0.058	0.097	9.717	0.017	0.017	0.000	0.000	0.000	0.000
38	B	28	GLY	0	0.022	-0.082	11.992	0.090	0.090	0.000	0.000	0.000	0.000
39	B	29	SER	0	0.089	0.021	13.679	0.063	0.063	0.000	0.000	0.000	0.000
40	B	29	SER	0	-0.025	0.068	15.911	-0.031	-0.031	0.000	0.000	0.000	0.000
41	B	30	GLN	0	-0.085	-0.111	15.541	0.018	0.018	0.000	0.000	0.000	0.000
42	B	30	GLN	0	-0.127	0.060	15.578	-0.026	-0.026	0.000	0.000	0.000	0.000
43	B	31	ARG	0	0.077	-0.078	16.193	0.027	0.027	0.000	0.000	0.000	0.000
44	B	31	ARG	1	0.745	0.969	13.722	-0.161	-0.161	0.000	0.000	0.000	0.000
45	B	32	ILE	0	0.156	-0.065	17.498	0.019	0.019	0.000	0.000	0.000	0.000
46	B	32	ILE	0	-0.095	0.096	18.307	0.000	0.000	0.000	0.000	0.000	0.000
47	B	33	GLU	0	0.060	-0.136	19.888	0.007	0.007	0.000	0.000	0.000	0.000
48	B	33	GLU	-1	-0.939	-0.826	21.185	-0.030	-0.030	0.000	0.000	0.000	0.000
49	B	34	ASP	0	0.067	-0.105	17.558	0.010	0.010	0.000	0.000	0.000	0.000
50	B	34	ASP	-1	-0.848	-0.784	15.667	0.106	0.106	0.000	0.000	0.000	0.000
51	B	35	ILE	0	0.017	-0.110	19.101	0.027	0.027	0.000	0.000	0.000	0.000
52	B	35	ILE	0	-0.032	0.131	19.565	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	36	GLY	0	-0.013	-0.089	20.699	0.005	0.005	0.000	0.000	0.000	0.000
54	B	37	ASP	0	0.035	-0.042	21.502	-0.005	-0.005	0.000	0.000	0.000	0.000
55	B	37	ASP	-1	-0.924	-0.799	20.913	0.103	0.103	0.000	0.000	0.000	0.000
56	B	38	LEU	0	0.073	-0.110	18.261	0.019	0.019	0.000	0.000	0.000	0.000
57	B	38	LEU	0	-0.070	0.094	15.556	0.000	0.000	0.000	0.000	0.000	0.000
58	B	39	SER	0	0.031	-0.110	19.279	0.009	0.009	0.000	0.000	0.000	0.000
59	B	39	SER	0	-0.053	0.066	23.051	-0.002	-0.002	0.000	0.000	0.000	0.000
60	B	40	LYS	0	-0.006	-0.105	22.497	-0.007	-0.007	0.000	0.000	0.000	0.000
61	B	40	LYS	1	0.761	0.998	23.716	-0.076	-0.076	0.000	0.000	0.000	0.000
62	B	41	VAL	0	0.046	-0.108	19.943	0.000	0.000	0.000	0.000	0.000	0.000
63	B	41	VAL	0	-0.070	0.114	18.287	0.007	0.007	0.000	0.000	0.000	0.000
64	B	42	THR	0	0.036	-0.081	21.478	-0.011	-0.011	0.000	0.000	0.000	0.000
65	B	42	THR	0	-0.065	0.062	24.309	-0.004	-0.004	0.000	0.000	0.000	0.000
66	B	43	LEU	0	-0.005	-0.113	20.308	0.021	0.021	0.000	0.000	0.000	0.000
67	B	43	LEU	0	-0.088	0.107	18.409	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	44	ASP	0	0.082	-0.070	20.280	-0.014	-0.014	0.000	0.000	0.000	0.000
69	B	44	ASP	-1	-0.870	-0.822	19.039	0.179	0.179	0.000	0.000	0.000	0.000
70	B	45	ALA	0	0.085	-0.101	21.971	-0.011	-0.011	0.000	0.000	0.000	0.000
71	B	45	ALA	0	-0.106	0.076	24.719	0.000	0.000	0.000	0.000	0.000	0.000
72	B	46	GLU	0	-0.040	-0.158	21.441	-0.016	-0.016	0.000	0.000	0.000	0.000
73	B	46	GLU	-1	-1.001	-0.845	20.590	0.134	0.134	0.000	0.000	0.000	0.000
74	B	47	GLY	0	0.005	-0.113	20.627	-0.015	-0.015	0.000	0.000	0.000	0.000
75	B	48	PHE	0	0.039	-0.015	16.503	-0.021	-0.021	0.000	0.000	0.000	0.000
76	B	48	PHE	0	-0.077	0.086	14.698	0.003	0.003	0.000	0.000	0.000	0.000
77	B	49	ALA	0	0.084	-0.083	15.508	-0.010	-0.010	0.000	0.000	0.000	0.000
78	B	49	ALA	0	-0.021	0.095	17.001	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	50	GLN	0	0.044	-0.116	12.988	-0.009	-0.009	0.000	0.000	0.000	0.000
80	B	50	GLN	0	-0.104	0.071	9.870	0.000	0.000	0.000	0.000	0.000	0.000
81	B	51	VAL	0	-0.029	-0.096	13.229	-0.009	-0.009	0.000	0.000	0.000	0.000
82	B	51	VAL	0	-0.009	0.113	15.075	-0.007	-0.007	0.000	0.000	0.000	0.000
83	B	52	GLN	0	0.094	-0.096	12.841	0.032	0.032	0.000	0.000	0.000	0.000
84	B	52	GLN	0	-0.082	0.077	12.413	0.046	0.046	0.000	0.000	0.000	0.000
85	B	53	GLY	0	0.036	-0.082	14.239	-0.040	-0.040	0.000	0.000	0.000	0.000
86	B	54	ASP	0	0.032	0.032	14.665	-0.033	-0.033	0.000	0.000	0.000	0.000
87	B	54	ASP	-1	-0.888	-0.831	13.836	0.364	0.364	0.000	0.000	0.000	0.000
88	B	55	SER	0	0.061	-0.071	12.384	0.046	0.046	0.000	0.000	0.000	0.000
89	B	55	SER	0	-0.055	0.056	11.842	-0.027	-0.027	0.000	0.000	0.000	0.000
90	B	56	LEU	0	0.025	-0.095	8.896	0.377	0.377	0.000	0.000	0.000	0.000
91	B	56	LEU	0	-0.065	0.091	7.988	-0.026	-0.026	0.000	0.000	0.000	0.000
92	B	57	LEU	0	0.107	-0.077	8.164	-0.292	-0.292	0.000	0.000	0.000	0.000
93	B	57	LEU	0	-0.117	0.092	7.462	0.062	0.062	0.000	0.000	0.000	0.000
94	B	58	VAL	0	0.029	-0.123	8.213	0.069	0.069	0.000	0.000	0.000	0.000
95	B	58	VAL	0	-0.065	0.119	11.486	-0.015	-0.015	0.000	0.000	0.000	0.000
96	B	59	HIS	0	0.103	-0.086	9.543	0.011	0.011	0.000	0.000	0.000	0.000
97	B	59	HIS	0	-0.108	0.062	5.914	-0.178	-0.178	0.000	0.000	0.000	0.000
98	B	60	LEU	0	0.100	-0.103	10.731	-0.083	-0.083	0.000	0.000	0.000	0.000
99	B	60	LEU	0	-0.085	0.108	14.329	-0.004	-0.004	0.000	0.000	0.000	0.000
100	B	61	TYR	0	0.115	-0.077	14.183	0.035	0.035	0.000	0.000	0.000	0.000
101	B	61	TYR	0	-0.127	0.068	15.059	-0.016	-0.016	0.000	0.000	0.000	0.000
102	B	62	LYS	0	0.095	-0.089	16.461	-0.025	-0.025	0.000	0.000	0.000	0.000
103	B	62	LYS	1	0.782	1.038	20.314	-0.030	-0.030	0.000	0.000	0.000	0.000
104	B	63	ARG	0	0.081	-0.105	20.091	0.012	0.012	0.000	0.000	0.000	0.000
105	B	63	ARG	1	0.838	1.056	21.037	-0.017	-0.017	0.000	0.000	0.000	0.000
106	B	64	ASN	0	0.022	-0.045	22.548	-0.008	-0.008	0.000	0.000	0.000	0.000
107	B	64	ASN	0	-0.104	0.038	24.327	0.003	0.003	0.000	0.000	0.000	0.000
108	B	65	ASP	0	0.041	-0.094	25.376	-0.008	-0.008	0.000	0.000	0.000	0.000
109	B	65	ASP	-1	-0.916	-0.831	27.037	0.016	0.016	0.000	0.000	0.000	0.000
110	B	66	ILE	0	0.215	-0.071	21.965	0.005	0.005	0.000	0.000	0.000	0.000
111	B	66	ILE	0	-0.107	0.084	19.829	-0.003	-0.003	0.000	0.000	0.000	0.000
112	B	67	THR	0	-0.016	-0.128	19.538	0.007	0.007	0.000	0.000	0.000	0.000
113	B	67	THR	0	-0.011	0.096	18.068	0.008	0.008	0.000	0.000	0.000	0.000
114	B	68	LEU	0	0.117	-0.081	15.576	-0.024	-0.024	0.000	0.000	0.000	0.000
115	B	68	LEU	0	-0.147	0.082	13.040	-0.003	-0.003	0.000	0.000	0.000	0.000
116	B	69	ALA	0	0.125	-0.087	13.233	0.048	0.048	0.000	0.000	0.000	0.000
117	B	69	ALA	0	-0.067	0.108	13.613	0.004	0.004	0.000	0.000	0.000	0.000
118	B	70	VAL	0	0.007	-0.106	9.107	-0.082	-0.082	0.000	0.000	0.000	0.000
119	B	70	VAL	0	-0.097	0.086	7.781	-0.014	-0.014	0.000	0.000	0.000	0.000
120	B	71	TYR	0	0.136	-0.097	7.949	0.215	0.215	0.000	0.000	0.000	0.000
121	B	71	TYR	0	-0.146	0.037	8.570	-0.007	-0.007	0.000	0.000	0.000	0.000
122	B	72	THR	0	-0.021	-0.082	3.865	-1.168	-1.170	0.000	-0.014	0.016	0.000
123	B	72	THR	0	-0.027	0.071	2.995	-0.696	-0.159	0.067	-0.232	-0.372	0.001
124	B	73	SER	0	0.114	-0.068	4.160	-1.215	-1.026	-0.001	-0.054	-0.135	0.000
125	B	73	SER	0	-0.026	0.075	5.207	0.345	0.345	0.000	0.000	0.000	0.000
126	B	74	ALA	0	-0.126	-0.133	5.760	0.728	0.728	0.000	0.000	0.000	0.000
127	B	74	ALA	0	0.093	0.069	9.914	-0.083	-0.083	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:8:ASP)