FMO DATABASE

FMODB ID: LVY89

Calculation Name: 3V4D-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3V4D

Chain ID: B

ChEMBL ID:

UniProt ID: P0AFQ6

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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1027737.626959
FMO2-HF: Nuclear repulsion	979859.092357
FMO2-HF: Total energy	-47878.534602
FMO2-MP2: Total energy	-48018.632328

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:0:HIS)

Summations of interaction energy for fragment #1(A:0: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.
-140.116	-127.15	9.416	-8.98	-13.402	-0.08

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.785 / q_NPA : 0.885

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	2	PRO	0	0.000	-0.003	2.920	-1.816	1.065	3.928	-1.975	-4.833	-0.003
4	A	3	LYS	1	0.985	0.996	2.853	19.988	21.844	0.714	-0.669	-1.902	0.011
5	A	4	SER	0	-0.006	0.007	4.315	1.465	1.669	0.010	-0.104	-0.110	0.001
25	A	24	ALA	0	-0.046	-0.032	2.217	-1.900	-1.625	0.817	-0.350	-0.742	-0.003
26	A	25	ASP	-1	-0.874	-0.948	2.189	-95.705	-88.041	3.948	-5.866	-5.747	-0.086
27	A	26	GLY	0	0.086	0.055	4.829	2.848	2.934	-0.001	-0.016	-0.068	0.000
6	A	5	VAL	0	-0.041	-0.028	7.849	0.304	0.304	0.000	0.000	0.000	0.000
7	A	6	ILE	0	-0.004	0.002	10.356	0.037	0.037	0.000	0.000	0.000	0.000
8	A	7	ILE	0	0.016	-0.005	13.048	0.560	0.560	0.000	0.000	0.000	0.000
9	A	8	PRO	0	0.025	0.020	16.706	0.076	0.076	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.013	0.002	19.324	0.334	0.334	0.000	0.000	0.000	0.000
11	A	10	GLY	0	-0.005	-0.004	22.251	0.306	0.306	0.000	0.000	0.000	0.000
12	A	11	SER	0	-0.051	-0.011	21.143	0.410	0.410	0.000	0.000	0.000	0.000
13	A	12	SER	0	-0.064	-0.025	22.355	-0.409	-0.409	0.000	0.000	0.000	0.000
14	A	13	ALA	0	0.018	0.012	23.806	0.225	0.225	0.000	0.000	0.000	0.000
15	A	14	PRO	0	0.048	0.010	20.109	-0.107	-0.107	0.000	0.000	0.000	0.000
16	A	15	LEU	0	-0.027	-0.015	21.690	-0.338	-0.338	0.000	0.000	0.000	0.000
17	A	16	ALA	0	0.006	0.005	21.009	0.332	0.332	0.000	0.000	0.000	0.000
18	A	17	PRO	0	-0.029	-0.010	17.666	-0.341	-0.341	0.000	0.000	0.000	0.000
19	A	18	PHE	0	-0.024	-0.022	15.409	-0.573	-0.573	0.000	0.000	0.000	0.000
20	A	19	VAL	0	0.019	0.023	12.249	0.464	0.464	0.000	0.000	0.000	0.000
21	A	20	PRO	0	0.041	0.019	15.482	-0.092	-0.092	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.077	0.039	12.938	0.272	0.272	0.000	0.000	0.000	0.000
23	A	22	THR	0	-0.113	-0.052	7.459	-0.646	-0.646	0.000	0.000	0.000	0.000
24	A	23	LEU	0	0.065	0.044	6.829	0.569	0.569	0.000	0.000	0.000	0.000
28	A	27	VAL	0	-0.030	-0.001	6.743	2.936	2.936	0.000	0.000	0.000	0.000
29	A	28	VAL	0	0.003	0.000	7.271	-1.539	-1.539	0.000	0.000	0.000	0.000
30	A	29	TYR	0	-0.013	-0.013	6.352	1.977	1.977	0.000	0.000	0.000	0.000
31	A	30	VAL	0	-0.014	-0.015	10.998	-0.075	-0.075	0.000	0.000	0.000	0.000
32	A	31	SER	0	-0.019	-0.034	14.354	0.038	0.038	0.000	0.000	0.000	0.000
33	A	32	GLY	0	0.001	0.012	16.182	0.321	0.321	0.000	0.000	0.000	0.000
34	A	33	THR	0	-0.051	-0.023	19.365	0.105	0.105	0.000	0.000	0.000	0.000
35	A	34	LEU	0	-0.001	-0.013	21.747	0.292	0.292	0.000	0.000	0.000	0.000
36	A	35	ALA	0	0.009	0.018	25.514	-0.129	-0.129	0.000	0.000	0.000	0.000
37	A	36	PHE	0	-0.016	-0.013	25.225	0.252	0.252	0.000	0.000	0.000	0.000
38	A	37	ASP	-1	-0.847	-0.916	28.327	-8.460	-8.460	0.000	0.000	0.000	0.000
39	A	38	GLN	0	-0.014	-0.012	27.612	-0.261	-0.261	0.000	0.000	0.000	0.000
40	A	39	HIS	0	-0.027	-0.021	28.574	0.075	0.075	0.000	0.000	0.000	0.000
41	A	40	ASN	0	-0.014	-0.012	24.636	-0.028	-0.028	0.000	0.000	0.000	0.000
42	A	41	ASN	0	-0.018	-0.005	28.643	0.023	0.023	0.000	0.000	0.000	0.000
43	A	42	VAL	0	-0.007	-0.008	30.555	-0.234	-0.234	0.000	0.000	0.000	0.000
44	A	43	LEU	0	-0.003	0.008	30.367	0.270	0.270	0.000	0.000	0.000	0.000
45	A	44	PHE	0	-0.021	-0.035	31.995	-0.039	-0.039	0.000	0.000	0.000	0.000
46	A	45	ALA	0	0.038	0.039	35.785	-0.041	-0.041	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.878	-0.942	36.625	-7.055	-7.055	0.000	0.000	0.000	0.000
48	A	47	ASP	-1	-0.879	-0.941	36.956	-7.524	-7.524	0.000	0.000	0.000	0.000
49	A	48	PRO	0	0.025	0.004	33.725	-0.233	-0.233	0.000	0.000	0.000	0.000
50	A	49	LYS	1	0.797	0.900	32.747	7.134	7.134	0.000	0.000	0.000	0.000
51	A	50	ALA	0	0.011	0.004	32.761	-0.249	-0.249	0.000	0.000	0.000	0.000
52	A	51	GLN	0	-0.014	-0.012	30.550	-0.488	-0.488	0.000	0.000	0.000	0.000
53	A	52	THR	0	-0.002	-0.025	28.198	-0.375	-0.375	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.821	0.900	27.781	8.185	8.185	0.000	0.000	0.000	0.000
55	A	54	HIS	0	0.039	0.026	27.240	-0.352	-0.352	0.000	0.000	0.000	0.000
56	A	55	VAL	0	0.027	0.019	23.590	-0.370	-0.370	0.000	0.000	0.000	0.000
57	A	56	LEU	0	0.009	0.002	23.329	-0.502	-0.502	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.937	-0.982	23.460	-9.743	-9.743	0.000	0.000	0.000	0.000
59	A	58	THR	0	-0.084	-0.040	21.140	-0.283	-0.283	0.000	0.000	0.000	0.000
60	A	59	ILE	0	0.026	0.001	18.341	-0.503	-0.503	0.000	0.000	0.000	0.000
61	A	60	ARG	1	0.938	0.982	18.590	10.073	10.073	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.955	0.983	19.607	10.181	10.181	0.000	0.000	0.000	0.000
63	A	62	VAL	0	-0.027	0.002	14.414	-0.462	-0.462	0.000	0.000	0.000	0.000
64	A	63	ILE	0	0.009	-0.002	14.903	-0.828	-0.828	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-0.892	-0.951	15.676	-12.688	-12.688	0.000	0.000	0.000	0.000
66	A	65	THR	0	-0.101	-0.070	15.633	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	66	ALA	0	-0.068	-0.038	11.634	-0.587	-0.587	0.000	0.000	0.000	0.000
68	A	67	GLY	0	-0.015	0.003	12.902	-1.157	-1.157	0.000	0.000	0.000	0.000
69	A	68	GLY	0	0.019	0.022	15.488	-0.111	-0.111	0.000	0.000	0.000	0.000
70	A	69	THR	0	-0.054	-0.054	16.242	1.064	1.064	0.000	0.000	0.000	0.000
71	A	70	MET	0	-0.013	-0.016	18.563	-0.510	-0.510	0.000	0.000	0.000	0.000
72	A	71	ALA	0	-0.032	-0.015	20.898	0.205	0.205	0.000	0.000	0.000	0.000
73	A	72	ASP	-1	-0.787	-0.863	15.970	-15.081	-15.081	0.000	0.000	0.000	0.000
74	A	73	VAL	0	-0.057	-0.030	16.217	-0.877	-0.877	0.000	0.000	0.000	0.000
75	A	74	THR	0	-0.005	-0.001	14.619	0.635	0.635	0.000	0.000	0.000	0.000
76	A	75	PHE	0	-0.049	-0.033	16.922	0.637	0.637	0.000	0.000	0.000	0.000
77	A	76	ASN	0	0.015	0.014	17.818	-0.618	-0.618	0.000	0.000	0.000	0.000
78	A	77	SER	0	-0.008	-0.006	18.686	0.317	0.317	0.000	0.000	0.000	0.000
79	A	78	ILE	0	-0.014	-0.005	21.145	0.036	0.036	0.000	0.000	0.000	0.000
80	A	79	PHE	0	0.027	0.003	21.011	0.108	0.108	0.000	0.000	0.000	0.000
81	A	80	ILE	0	0.016	0.004	26.488	0.089	0.089	0.000	0.000	0.000	0.000
82	A	81	THR	0	0.049	0.036	30.194	0.059	0.059	0.000	0.000	0.000	0.000
83	A	82	ASP	-1	-0.794	-0.887	33.191	-7.080	-7.080	0.000	0.000	0.000	0.000
84	A	83	TRP	0	0.017	0.008	31.340	-0.087	-0.087	0.000	0.000	0.000	0.000
85	A	84	LYS	1	0.795	0.879	36.267	7.022	7.022	0.000	0.000	0.000	0.000
86	A	85	ASN	0	0.062	0.029	34.713	0.212	0.212	0.000	0.000	0.000	0.000
87	A	86	TYR	0	0.034	0.016	30.651	-0.200	-0.200	0.000	0.000	0.000	0.000
88	A	87	ALA	0	-0.008	-0.007	33.757	-0.151	-0.151	0.000	0.000	0.000	0.000
89	A	88	ALA	0	0.027	0.009	35.500	-0.071	-0.071	0.000	0.000	0.000	0.000
90	A	89	ILE	0	0.038	0.024	29.599	-0.079	-0.079	0.000	0.000	0.000	0.000
91	A	90	ASN	0	-0.002	-0.005	30.922	-0.505	-0.505	0.000	0.000	0.000	0.000
92	A	91	GLU	-1	-0.835	-0.891	31.947	-7.622	-7.622	0.000	0.000	0.000	0.000
93	A	92	ILE	0	0.010	0.005	30.105	-0.077	-0.077	0.000	0.000	0.000	0.000
94	A	93	TYR	0	0.030	0.008	24.144	-0.329	-0.329	0.000	0.000	0.000	0.000
95	A	94	ALA	0	-0.022	-0.016	28.018	-0.274	-0.274	0.000	0.000	0.000	0.000
96	A	95	GLU	-1	-0.858	-0.903	30.220	-8.475	-8.475	0.000	0.000	0.000	0.000
97	A	96	PHE	0	-0.048	-0.027	25.360	-0.088	-0.088	0.000	0.000	0.000	0.000
98	A	97	PHE	0	0.010	0.021	21.225	-0.414	-0.414	0.000	0.000	0.000	0.000
99	A	98	PRO	0	0.049	0.033	26.165	0.160	0.160	0.000	0.000	0.000	0.000
100	A	99	GLY	0	-0.014	-0.010	27.503	0.280	0.280	0.000	0.000	0.000	0.000
101	A	100	ASP	-1	-0.884	-0.942	25.316	-10.429	-10.429	0.000	0.000	0.000	0.000
102	A	101	LYS	1	0.767	0.875	25.311	9.570	9.570	0.000	0.000	0.000	0.000
103	A	102	PRO	0	0.025	0.023	20.746	-0.056	-0.056	0.000	0.000	0.000	0.000
104	A	103	ALA	0	-0.012	0.008	21.017	0.517	0.517	0.000	0.000	0.000	0.000
105	A	104	ARG	1	0.845	0.905	21.693	9.571	9.571	0.000	0.000	0.000	0.000
106	A	105	PHE	0	-0.012	0.007	20.789	0.260	0.260	0.000	0.000	0.000	0.000
107	A	106	CYS	0	-0.015	-0.012	24.939	-0.029	-0.029	0.000	0.000	0.000	0.000
108	A	107	ILE	0	-0.027	-0.003	25.415	0.226	0.226	0.000	0.000	0.000	0.000
109	A	108	GLN	0	-0.011	-0.010	28.765	-0.012	-0.012	0.000	0.000	0.000	0.000
110	A	109	CYS	0	-0.062	-0.036	27.793	-0.117	-0.117	0.000	0.000	0.000	0.000
111	A	110	GLY	0	0.022	0.017	30.443	0.187	0.187	0.000	0.000	0.000	0.000
112	A	111	LEU	0	0.015	0.008	26.587	-0.304	-0.304	0.000	0.000	0.000	0.000
113	A	112	VAL	0	-0.003	-0.004	25.885	0.260	0.260	0.000	0.000	0.000	0.000
114	A	113	LYS	1	0.908	0.950	28.399	8.910	8.910	0.000	0.000	0.000	0.000
115	A	114	PRO	0	-0.001	-0.006	31.622	-0.069	-0.069	0.000	0.000	0.000	0.000
116	A	115	ASP	-1	-0.866	-0.925	34.717	-7.585	-7.585	0.000	0.000	0.000	0.000
117	A	116	ALA	0	-0.033	0.004	29.604	-0.035	-0.035	0.000	0.000	0.000	0.000
118	A	117	LEU	0	-0.015	-0.018	31.710	0.038	0.038	0.000	0.000	0.000	0.000
119	A	118	VAL	0	-0.061	-0.046	27.033	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	119	GLU	-1	-0.879	-0.940	22.496	-11.074	-11.074	0.000	0.000	0.000	0.000
121	A	120	ILE	0	-0.043	-0.028	20.926	0.097	0.097	0.000	0.000	0.000	0.000
122	A	121	ALA	0	0.021	0.033	17.097	-0.137	-0.137	0.000	0.000	0.000	0.000
123	A	122	THR	0	-0.004	-0.021	16.583	0.427	0.427	0.000	0.000	0.000	0.000
124	A	123	ILE	0	-0.037	-0.015	11.699	-0.754	-0.754	0.000	0.000	0.000	0.000
125	A	124	ALA	0	0.021	0.009	12.686	0.991	0.991	0.000	0.000	0.000	0.000
126	A	125	HIS	0	-0.068	-0.039	11.590	-1.838	-1.838	0.000	0.000	0.000	0.000
127	A	126	ILE	-1	-0.889	-0.932	10.998	-20.809	-20.809	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)