FMO DATABASE

FMODB ID: KK4R3

Calculation Name: 1VTM-P-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VTM

Chain ID: P

ChEMBL ID:

UniProt ID: P03579

Base Structure: Fiber

Registration Date: 2025-10-03

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1344949.558735
FMO2-HF: Nuclear repulsion	1283993.571514
FMO2-HF: Total energy	-60955.98722
FMO2-MP2: Total energy	-61135.146509

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:1:PRO)

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

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.
-119.226	-111.955	15.535	-9.824	-12.979	-0.088

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.912

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	THR	0	-0.013	-0.003	2.742	-4.560	-1.821	0.433	-1.415	-1.756	-0.011
4	A	4	ILE	0	-0.041	-0.014	5.279	4.096	4.199	-0.001	-0.006	-0.096	0.000
58	A	58	MET	0	-0.003	-0.005	3.335	-1.322	-0.983	0.011	-0.077	-0.273	0.000
59	A	59	THR	0	-0.013	-0.017	2.982	-18.008	-16.085	0.223	-1.026	-1.119	-0.009
60	A	60	VAL	0	-0.020	0.003	4.357	1.143	1.166	-0.001	-0.008	-0.013	0.000
152	A	152	TRP	0	0.000	-0.009	2.071	-11.860	-11.349	2.852	-1.821	-1.543	-0.008
153	A	153	THR	0	-0.013	-0.009	2.055	-10.518	-10.570	7.103	-3.341	-3.710	-0.034
154	A	154	THR	0	0.013	-0.001	2.764	-14.887	-12.957	0.231	-1.067	-1.093	-0.013
156	A	156	PRO	0	-0.051	-0.043	2.020	-17.473	-17.019	4.415	-2.545	-2.325	-0.007
157	A	157	ALA	0	-0.002	-0.006	2.437	11.432	10.306	0.266	1.657	-0.796	-0.005
158	A	158	THR	-1	-0.928	-0.942	3.912	-37.630	-37.203	0.003	-0.175	-0.255	-0.001
5	A	5	ASN	0	-0.029	-0.015	7.677	1.736	1.736	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.088	0.043	11.105	2.107	2.107	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.010	0.003	12.317	-0.949	-0.949	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.005	-0.002	14.254	-0.289	-0.289	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.082	0.033	7.511	1.231	1.231	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.021	-0.010	8.186	-0.365	-0.365	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.023	-0.003	12.684	0.679	0.679	0.000	0.000	0.000	0.000
12	A	12	TYR	0	0.006	0.008	13.365	0.938	0.938	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.016	0.010	8.016	-0.407	-0.407	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.044	0.000	12.638	0.298	0.298	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.030	-0.039	15.784	-0.257	-0.257	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.007	-0.019	18.292	0.879	0.879	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.108	-0.075	14.799	0.262	0.262	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.002	0.021	19.409	0.245	0.245	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.798	-0.916	22.660	-12.293	-12.293	0.000	0.000	0.000	0.000
20	A	20	PRO	0	-0.029	-0.006	23.451	0.421	0.421	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.006	-0.009	26.287	0.471	0.471	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.934	-0.971	28.028	-10.471	-10.471	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.018	0.006	27.557	0.339	0.339	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.026	0.016	30.194	0.331	0.331	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.001	-0.012	32.938	0.459	0.459	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.005	0.009	30.538	0.291	0.291	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.040	-0.017	33.040	0.287	0.287	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.022	-0.012	35.965	0.279	0.279	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.046	-0.028	37.104	0.388	0.388	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.010	0.004	37.074	0.193	0.193	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.025	-0.023	39.207	0.161	0.161	0.000	0.000	0.000	0.000
32	A	32	GLY	0	-0.013	0.014	41.988	0.212	0.212	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.010	-0.023	41.744	-0.078	-0.078	0.000	0.000	0.000	0.000
34	A	34	GLN	0	0.012	0.011	44.696	0.197	0.197	0.000	0.000	0.000	0.000
35	A	35	PHE	0	0.029	0.024	40.757	0.034	0.034	0.000	0.000	0.000	0.000
36	A	36	GLN	0	0.065	0.031	45.529	-0.145	-0.145	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.055	-0.035	46.644	0.048	0.048	0.000	0.000	0.000	0.000
38	A	38	GLN	0	0.017	-0.012	41.659	0.023	0.023	0.000	0.000	0.000	0.000
39	A	39	GLN	0	0.012	0.003	42.608	-0.115	-0.115	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.025	0.026	41.626	-0.148	-0.148	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.855	0.918	40.032	7.198	7.198	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.020	0.000	37.638	-0.188	-0.188	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.008	-0.006	35.936	-0.216	-0.216	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.006	0.008	35.154	-0.245	-0.245	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.002	-0.014	33.827	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.023	-0.027	31.703	-0.202	-0.202	0.000	0.000	0.000	0.000
47	A	47	GLN	0	0.015	0.023	30.786	-0.293	-0.293	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.037	0.004	28.707	-0.305	-0.305	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.056	-0.017	27.241	-0.403	-0.403	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.834	-0.904	25.792	-12.175	-12.175	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.006	0.004	24.556	-0.479	-0.479	0.000	0.000	0.000	0.000
52	A	52	TRP	0	0.007	0.009	22.663	-0.294	-0.294	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.889	0.957	19.728	12.301	12.301	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.040	0.011	14.743	-0.453	-0.453	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.012	-0.018	14.184	1.029	1.029	0.000	0.000	0.000	0.000
56	A	56	PRO	0	-0.031	0.021	10.132	-1.048	-1.048	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.044	0.007	7.340	0.198	0.198	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.778	0.875	7.452	25.666	25.666	0.000	0.000	0.000	0.000
62	A	62	PHE	0	0.012	0.016	8.414	1.777	1.777	0.000	0.000	0.000	0.000
63	A	63	PRO	0	0.063	0.025	12.042	-0.510	-0.510	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.016	-0.006	14.638	0.419	0.419	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.069	-0.025	16.938	0.493	0.493	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.877	-0.923	18.656	-14.322	-14.322	0.000	0.000	0.000	0.000
67	A	67	PHE	0	-0.082	-0.050	19.505	-0.525	-0.525	0.000	0.000	0.000	0.000
68	A	68	TYR	0	0.037	0.009	17.581	0.195	0.195	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.005	0.014	21.154	0.158	0.158	0.000	0.000	0.000	0.000
70	A	70	TYR	0	-0.014	-0.021	17.119	-0.397	-0.397	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.869	0.938	21.642	12.093	12.093	0.000	0.000	0.000	0.000
72	A	72	TYR	0	0.004	0.007	20.081	0.424	0.424	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.012	0.016	21.172	-0.156	-0.156	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.003	-0.008	23.854	0.174	0.174	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.002	-0.003	27.095	0.338	0.338	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.005	-0.004	25.608	0.375	0.375	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.786	-0.866	25.607	-11.328	-11.328	0.000	0.000	0.000	0.000
78	A	78	PRO	0	-0.010	-0.015	27.639	0.292	0.292	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.022	0.000	31.162	0.312	0.312	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.011	-0.006	27.510	0.211	0.211	0.000	0.000	0.000	0.000
81	A	81	THR	0	-0.030	-0.033	28.242	0.053	0.053	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.010	0.003	30.716	0.164	0.164	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.007	0.012	33.068	0.267	0.267	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.023	0.008	29.182	0.216	0.216	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.027	0.004	33.391	-0.141	-0.141	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.054	-0.036	35.497	0.292	0.292	0.000	0.000	0.000	0.000
87	A	87	PHE	0	-0.006	-0.007	36.461	0.222	0.222	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.817	-0.879	37.052	-8.072	-8.072	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.014	-0.037	39.382	0.297	0.297	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.812	0.907	42.281	6.763	6.763	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.024	0.011	45.966	-0.049	-0.049	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.911	0.944	41.939	7.218	7.218	0.000	0.000	0.000	0.000
93	A	93	ILE	0	0.038	0.033	48.429	-0.038	-0.038	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.001	0.010	51.708	0.079	0.079	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.833	-0.912	54.572	-5.294	-5.294	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.027	0.008	56.088	0.016	0.016	0.000	0.000	0.000	0.000
97	A	97	ASN	0	-0.038	-0.010	58.027	0.076	0.076	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.039	-0.032	61.001	0.150	0.150	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.009	-0.025	63.558	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	100	PRO	0	-0.010	-0.008	62.117	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.005	0.016	59.344	0.007	0.007	0.000	0.000	0.000	0.000
102	A	102	PRO	0	0.008	0.032	61.029	0.004	0.004	0.000	0.000	0.000	0.000
103	A	103	ASN	0	0.019	-0.008	58.536	-0.045	-0.045	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.044	-0.037	61.328	-0.024	-0.024	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.010	-0.009	62.988	0.058	0.058	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.877	-0.946	56.420	-5.644	-5.644	0.000	0.000	0.000	0.000
107	A	107	ILE	0	0.014	0.024	59.464	-0.038	-0.038	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.067	-0.021	56.881	-0.056	-0.056	0.000	0.000	0.000	0.000
109	A	109	ASN	0	-0.032	-0.036	52.499	-0.238	-0.238	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.074	0.052	54.360	0.085	0.085	0.000	0.000	0.000	0.000
111	A	111	THR	0	0.053	-0.001	53.584	-0.165	-0.165	0.000	0.000	0.000	0.000
112	A	112	GLN	0	-0.017	-0.009	53.301	-0.030	-0.030	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.924	0.974	47.749	6.319	6.319	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.073	-0.039	48.391	-0.184	-0.184	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.832	-0.925	48.530	-6.172	-6.172	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.880	-0.942	47.147	-6.519	-6.519	0.000	0.000	0.000	0.000
117	A	117	ALA	0	0.003	0.009	43.873	-0.159	-0.159	0.000	0.000	0.000	0.000
118	A	118	THR	0	-0.003	0.003	43.940	-0.209	-0.209	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.063	-0.026	45.810	-0.016	-0.016	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.058	0.020	41.634	-0.105	-0.105	0.000	0.000	0.000	0.000
121	A	121	ILE	0	-0.007	0.018	39.578	-0.192	-0.192	0.000	0.000	0.000	0.000
122	A	122	ARG	1	0.961	0.976	40.422	6.502	6.502	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.008	0.001	42.112	-0.046	-0.046	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.014	-0.016	36.775	-0.176	-0.176	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.045	0.014	36.514	-0.220	-0.220	0.000	0.000	0.000	0.000
126	A	126	ASN	0	-0.015	0.006	37.354	-0.090	-0.090	0.000	0.000	0.000	0.000
127	A	127	ASN	0	-0.068	-0.048	36.730	-0.088	-0.088	0.000	0.000	0.000	0.000
128	A	128	LEU	0	0.021	0.011	30.542	-0.136	-0.136	0.000	0.000	0.000	0.000
129	A	129	ALA	0	-0.001	-0.012	33.917	-0.183	-0.183	0.000	0.000	0.000	0.000
130	A	130	ASN	0	-0.071	-0.037	35.871	0.021	0.021	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.822	-0.887	34.040	-8.593	-8.593	0.000	0.000	0.000	0.000
132	A	132	LEU	0	0.004	0.022	28.887	-0.342	-0.342	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.028	-0.012	30.831	-0.274	-0.274	0.000	0.000	0.000	0.000
134	A	134	ARG	1	0.814	0.881	32.126	8.796	8.796	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.031	0.021	27.962	-0.090	-0.090	0.000	0.000	0.000	0.000
136	A	136	THR	0	-0.035	-0.032	27.255	-0.474	-0.474	0.000	0.000	0.000	0.000
137	A	137	GLY	0	0.039	0.006	24.548	-0.090	-0.090	0.000	0.000	0.000	0.000
138	A	138	MET	0	-0.042	-0.013	23.473	-0.217	-0.217	0.000	0.000	0.000	0.000
139	A	139	PHE	0	-0.015	0.004	18.016	-0.126	-0.126	0.000	0.000	0.000	0.000
140	A	140	ASN	0	0.058	0.012	19.615	-0.601	-0.601	0.000	0.000	0.000	0.000
141	A	141	GLN	0	0.030	0.026	15.017	-0.396	-0.396	0.000	0.000	0.000	0.000
142	A	142	ALA	0	0.044	0.010	15.934	-0.909	-0.909	0.000	0.000	0.000	0.000
143	A	143	GLY	0	0.003	0.025	17.955	-0.029	-0.029	0.000	0.000	0.000	0.000
144	A	144	PHE	0	0.015	-0.002	10.626	-0.051	-0.051	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.825	-0.907	12.194	-24.533	-24.533	0.000	0.000	0.000	0.000
146	A	146	THR	0	-0.074	-0.046	14.575	0.117	0.117	0.000	0.000	0.000	0.000
147	A	147	ALA	0	-0.027	-0.011	17.530	0.212	0.212	0.000	0.000	0.000	0.000
148	A	148	SER	0	0.016	0.013	11.904	-0.543	-0.543	0.000	0.000	0.000	0.000
149	A	149	GLY	0	-0.045	-0.024	12.807	-0.344	-0.344	0.000	0.000	0.000	0.000
150	A	150	LEU	0	-0.070	-0.018	7.333	-0.688	-0.688	0.000	0.000	0.000	0.000
151	A	151	VAL	0	0.051	0.022	6.200	1.411	1.411	0.000	0.000	0.000	0.000
155	A	155	THR	0	-0.010	0.008	4.803	6.559	6.559	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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