FMO DATABASE

FMODB ID: RL9Z8

Calculation Name: 1VKI-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VKI

Chain ID: A

ChEMBL ID:

UniProt ID: A9CFJ8

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	165
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1623013.687265
FMO2-HF: Nuclear repulsion	1560695.759802
FMO2-HF: Total energy	-62317.927463
FMO2-MP2: Total energy	-62503.992428

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:5:SER)

Summations of interaction energy for fragment #1(A:5: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.
-101.757	-99.256	0.252	-1.258	-1.495	-0.004

Interaction energy analysis for fragmet #1(A:5:SER)

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 : 0.908

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	7	LYS	1	0.864	0.942	3.062	49.742	52.243	0.252	-1.258	-1.495	-0.004
4	A	8	THR	0	-0.021	-0.037	5.553	4.788	4.788	0.000	0.000	0.000	0.000
5	A	9	ALA	0	0.064	0.027	7.907	0.062	0.062	0.000	0.000	0.000	0.000
6	A	10	THR	0	-0.005	0.001	10.663	0.971	0.971	0.000	0.000	0.000	0.000
7	A	11	GLU	-1	-0.785	-0.871	5.829	-43.139	-43.139	0.000	0.000	0.000	0.000
8	A	12	LEU	0	-0.049	-0.006	9.744	0.275	0.275	0.000	0.000	0.000	0.000
9	A	13	PHE	0	-0.025	-0.021	11.593	1.357	1.357	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.857	-0.932	11.864	-21.982	-21.982	0.000	0.000	0.000	0.000
11	A	15	PHE	0	-0.053	-0.027	11.279	0.505	0.505	0.000	0.000	0.000	0.000
12	A	16	LEU	0	-0.038	-0.021	13.368	1.194	1.194	0.000	0.000	0.000	0.000
13	A	17	ASP	-1	-0.852	-0.905	16.623	-15.420	-15.420	0.000	0.000	0.000	0.000
14	A	18	GLY	0	-0.028	-0.012	16.640	0.897	0.897	0.000	0.000	0.000	0.000
15	A	19	LEU	0	-0.029	-0.007	15.735	0.564	0.564	0.000	0.000	0.000	0.000
16	A	20	GLY	0	0.001	0.009	19.213	0.825	0.825	0.000	0.000	0.000	0.000
17	A	21	ILE	0	-0.083	-0.035	18.547	0.724	0.724	0.000	0.000	0.000	0.000
18	A	22	SER	0	0.001	-0.003	20.711	-0.494	-0.494	0.000	0.000	0.000	0.000
19	A	23	HIS	1	0.889	0.919	18.663	15.697	15.697	0.000	0.000	0.000	0.000
20	A	24	THR	0	-0.023	0.001	22.040	0.044	0.044	0.000	0.000	0.000	0.000
21	A	25	THR	0	0.034	0.013	18.806	-0.355	-0.355	0.000	0.000	0.000	0.000
22	A	26	LYS	1	0.920	0.991	21.908	11.476	11.476	0.000	0.000	0.000	0.000
23	A	27	GLN	0	0.028	-0.002	18.832	-0.578	-0.578	0.000	0.000	0.000	0.000
24	A	28	HIS	0	-0.101	-0.058	21.886	0.515	0.515	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.828	-0.913	22.343	-12.748	-12.748	0.000	0.000	0.000	0.000
26	A	30	PRO	0	-0.038	-0.006	20.033	0.130	0.130	0.000	0.000	0.000	0.000
27	A	31	VAL	0	0.000	0.026	22.594	0.425	0.425	0.000	0.000	0.000	0.000
28	A	32	PHE	0	0.005	-0.010	21.800	-0.411	-0.411	0.000	0.000	0.000	0.000
29	A	33	THR	0	-0.032	-0.007	26.922	0.245	0.245	0.000	0.000	0.000	0.000
30	A	34	VAL	0	0.038	0.019	30.445	-0.132	-0.132	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.043	0.019	32.346	-0.086	-0.086	0.000	0.000	0.000	0.000
32	A	36	GLU	-1	-0.879	-0.921	29.431	-10.364	-10.364	0.000	0.000	0.000	0.000
33	A	37	SER	0	0.025	-0.018	27.894	-0.309	-0.309	0.000	0.000	0.000	0.000
34	A	38	GLN	0	-0.085	-0.031	29.143	-0.208	-0.208	0.000	0.000	0.000	0.000
35	A	39	SER	0	-0.010	-0.025	31.977	0.099	0.099	0.000	0.000	0.000	0.000
36	A	40	LEU	0	-0.052	-0.020	24.754	0.102	0.102	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.879	0.930	27.513	10.836	10.836	0.000	0.000	0.000	0.000
38	A	42	ASP	-1	-0.867	-0.936	29.509	-9.312	-9.312	0.000	0.000	0.000	0.000
39	A	43	LEU	0	-0.097	-0.040	30.789	0.265	0.265	0.000	0.000	0.000	0.000
40	A	44	ILE	0	-0.059	-0.033	25.397	-0.186	-0.186	0.000	0.000	0.000	0.000
41	A	45	PRO	0	0.018	0.013	29.447	-0.045	-0.045	0.000	0.000	0.000	0.000
42	A	46	GLY	0	0.046	0.038	28.975	-0.385	-0.385	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.020	0.019	29.165	0.085	0.085	0.000	0.000	0.000	0.000
44	A	48	HIS	0	-0.015	-0.021	26.212	-0.962	-0.962	0.000	0.000	0.000	0.000
45	A	49	THR	0	-0.055	-0.044	22.140	-0.060	-0.060	0.000	0.000	0.000	0.000
46	A	50	LYS	1	0.794	0.906	23.163	10.669	10.669	0.000	0.000	0.000	0.000
47	A	51	ASN	0	0.004	-0.009	19.447	-0.095	-0.095	0.000	0.000	0.000	0.000
48	A	52	LEU	0	0.001	0.007	21.430	-0.142	-0.142	0.000	0.000	0.000	0.000
49	A	53	PHE	0	0.016	0.021	14.989	-0.088	-0.088	0.000	0.000	0.000	0.000
50	A	54	VAL	0	-0.029	-0.016	19.652	0.562	0.562	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.887	0.945	20.245	13.093	13.093	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.743	-0.873	22.105	-12.154	-12.154	0.000	0.000	0.000	0.000
53	A	57	LYS	1	0.888	0.933	24.287	9.647	9.647	0.000	0.000	0.000	0.000
54	A	58	LYS	1	0.892	0.936	24.574	11.664	11.664	0.000	0.000	0.000	0.000
55	A	59	ASP	-1	-0.872	-0.908	19.836	-14.428	-14.428	0.000	0.000	0.000	0.000
56	A	60	GLN	0	0.048	0.042	19.295	-1.148	-1.148	0.000	0.000	0.000	0.000
57	A	61	TYR	0	-0.009	-0.023	16.460	0.496	0.496	0.000	0.000	0.000	0.000
58	A	62	PHE	0	0.025	0.007	18.576	-0.154	-0.154	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.023	-0.013	16.450	-0.378	-0.378	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.005	0.008	19.568	0.291	0.291	0.000	0.000	0.000	0.000
61	A	65	THR	0	0.000	-0.006	20.530	-0.240	-0.240	0.000	0.000	0.000	0.000
62	A	66	VAL	0	0.001	-0.009	22.978	0.412	0.412	0.000	0.000	0.000	0.000
63	A	67	GLU	-1	-0.753	-0.876	26.205	-10.700	-10.700	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.822	-0.923	27.553	-11.420	-11.420	0.000	0.000	0.000	0.000
65	A	69	ASN	0	-0.073	-0.040	28.966	0.198	0.198	0.000	0.000	0.000	0.000
66	A	70	ALA	0	0.009	0.031	30.486	0.301	0.301	0.000	0.000	0.000	0.000
67	A	71	VAL	0	-0.012	0.003	31.395	-0.332	-0.332	0.000	0.000	0.000	0.000
68	A	72	VAL	0	0.054	0.019	28.332	-0.085	-0.085	0.000	0.000	0.000	0.000
69	A	73	ASP	-1	-0.750	-0.843	31.474	-9.187	-9.187	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.013	-0.018	27.345	-0.062	-0.062	0.000	0.000	0.000	0.000
71	A	75	LYS	1	0.858	0.913	30.797	8.853	8.853	0.000	0.000	0.000	0.000
72	A	76	SER	0	-0.058	-0.063	33.512	0.087	0.087	0.000	0.000	0.000	0.000
73	A	77	VAL	0	0.086	0.050	28.584	0.017	0.017	0.000	0.000	0.000	0.000
74	A	78	HIS	0	0.021	0.006	28.879	-0.241	-0.241	0.000	0.000	0.000	0.000
75	A	79	LYS	1	0.906	0.943	29.931	8.427	8.427	0.000	0.000	0.000	0.000
76	A	80	THR	0	-0.007	0.014	30.921	0.233	0.233	0.000	0.000	0.000	0.000
77	A	81	ILE	0	-0.001	0.002	24.945	-0.075	-0.075	0.000	0.000	0.000	0.000
78	A	82	GLY	0	0.002	0.020	26.611	-0.360	-0.360	0.000	0.000	0.000	0.000
79	A	83	ALA	0	-0.022	0.006	26.071	-0.246	-0.246	0.000	0.000	0.000	0.000
80	A	84	ALA	0	-0.034	-0.023	26.901	0.497	0.497	0.000	0.000	0.000	0.000
81	A	85	SER	0	-0.087	-0.074	28.683	0.316	0.316	0.000	0.000	0.000	0.000
82	A	86	ARG	1	0.896	0.968	29.175	9.062	9.062	0.000	0.000	0.000	0.000
83	A	87	VAL	0	0.049	0.040	25.721	-0.119	-0.119	0.000	0.000	0.000	0.000
84	A	88	SER	0	-0.079	-0.033	24.948	0.329	0.329	0.000	0.000	0.000	0.000
85	A	89	PHE	0	0.072	0.025	22.217	-0.306	-0.306	0.000	0.000	0.000	0.000
86	A	90	GLY	0	0.023	0.018	18.938	0.132	0.132	0.000	0.000	0.000	0.000
87	A	91	ARG	1	0.871	0.916	18.939	13.491	13.491	0.000	0.000	0.000	0.000
88	A	92	PRO	0	0.058	0.015	16.325	-0.808	-0.808	0.000	0.000	0.000	0.000
89	A	93	GLU	-1	-0.850	-0.922	13.479	-20.112	-20.112	0.000	0.000	0.000	0.000
90	A	94	LYS	1	0.837	0.900	12.185	20.018	20.018	0.000	0.000	0.000	0.000
91	A	95	MET	0	-0.040	-0.001	12.463	-0.872	-0.872	0.000	0.000	0.000	0.000
92	A	96	LEU	0	-0.005	-0.007	8.748	-1.886	-1.886	0.000	0.000	0.000	0.000
93	A	97	GLU	-1	-0.878	-0.924	8.028	-29.186	-29.186	0.000	0.000	0.000	0.000
94	A	98	TYR	0	-0.013	-0.001	7.353	-3.274	-3.274	0.000	0.000	0.000	0.000
95	A	99	LEU	0	0.032	0.014	8.587	-2.206	-2.206	0.000	0.000	0.000	0.000
96	A	100	GLY	0	-0.020	0.009	7.586	-1.216	-1.216	0.000	0.000	0.000	0.000
97	A	101	VAL	0	-0.040	-0.017	8.230	0.280	0.280	0.000	0.000	0.000	0.000
98	A	102	VAL	0	0.042	0.012	11.579	0.041	0.041	0.000	0.000	0.000	0.000
99	A	103	PRO	0	0.019	-0.017	14.523	0.400	0.400	0.000	0.000	0.000	0.000
100	A	104	GLY	0	0.038	0.029	18.278	0.003	0.003	0.000	0.000	0.000	0.000
101	A	105	SER	0	-0.039	-0.022	14.984	-0.035	-0.035	0.000	0.000	0.000	0.000
102	A	106	VAL	0	-0.023	-0.009	15.460	-1.215	-1.215	0.000	0.000	0.000	0.000
103	A	107	THR	0	-0.021	-0.027	14.377	1.223	1.223	0.000	0.000	0.000	0.000
104	A	108	VAL	0	0.072	0.040	15.459	-1.373	-1.373	0.000	0.000	0.000	0.000
105	A	109	PHE	0	0.024	0.006	13.733	-0.939	-0.939	0.000	0.000	0.000	0.000
106	A	110	GLY	0	0.026	0.010	11.202	-2.145	-2.145	0.000	0.000	0.000	0.000
107	A	111	ALA	0	-0.001	-0.004	10.463	-2.844	-2.844	0.000	0.000	0.000	0.000
108	A	112	ILE	0	0.006	0.013	8.345	-1.278	-1.278	0.000	0.000	0.000	0.000
109	A	113	ASN	0	-0.030	-0.023	6.087	-12.144	-12.144	0.000	0.000	0.000	0.000
110	A	114	ASP	-1	-0.706	-0.813	6.125	-31.222	-31.222	0.000	0.000	0.000	0.000
111	A	115	THR	0	-0.015	-0.029	5.648	0.430	0.430	0.000	0.000	0.000	0.000
112	A	116	ALA	0	-0.040	-0.017	8.297	2.383	2.383	0.000	0.000	0.000	0.000
113	A	117	ARG	1	0.852	0.944	10.112	23.283	23.283	0.000	0.000	0.000	0.000
114	A	118	GLN	0	-0.050	-0.034	11.958	2.717	2.717	0.000	0.000	0.000	0.000
115	A	119	VAL	0	-0.049	-0.020	13.269	1.347	1.347	0.000	0.000	0.000	0.000
116	A	120	THR	0	0.006	-0.007	15.608	-0.452	-0.452	0.000	0.000	0.000	0.000
117	A	121	PHE	0	-0.014	-0.016	14.086	0.244	0.244	0.000	0.000	0.000	0.000
118	A	122	VAL	0	-0.010	-0.006	19.485	0.481	0.481	0.000	0.000	0.000	0.000
119	A	123	LEU	0	-0.013	-0.004	21.582	-0.327	-0.327	0.000	0.000	0.000	0.000
120	A	124	ASP	-1	-0.733	-0.858	24.782	-10.262	-10.262	0.000	0.000	0.000	0.000
121	A	125	SER	0	-0.026	-0.025	28.171	-0.036	-0.036	0.000	0.000	0.000	0.000
122	A	126	ASP	-1	-0.783	-0.881	31.197	-9.389	-9.389	0.000	0.000	0.000	0.000
123	A	127	LEU	0	-0.081	-0.033	25.100	-0.028	-0.028	0.000	0.000	0.000	0.000
124	A	128	LEU	0	-0.038	-0.033	25.375	-0.140	-0.140	0.000	0.000	0.000	0.000
125	A	129	GLU	-1	-0.945	-0.951	29.338	-9.078	-9.078	0.000	0.000	0.000	0.000
126	A	130	ASN	0	-0.077	-0.034	30.042	0.410	0.410	0.000	0.000	0.000	0.000
127	A	131	GLU	-1	-0.927	-0.955	30.564	-10.081	-10.081	0.000	0.000	0.000	0.000
128	A	132	LEU	0	-0.030	-0.013	27.540	-0.469	-0.469	0.000	0.000	0.000	0.000
129	A	133	VAL	0	-0.004	-0.012	23.491	0.229	0.229	0.000	0.000	0.000	0.000
130	A	134	ASN	0	0.029	0.017	23.346	-0.681	-0.681	0.000	0.000	0.000	0.000
131	A	135	GLY	0	0.052	0.033	20.219	0.077	0.077	0.000	0.000	0.000	0.000
132	A	136	HIS	0	-0.019	-0.009	16.920	0.148	0.148	0.000	0.000	0.000	0.000
133	A	137	PRO	0	0.027	0.027	14.799	-1.167	-1.167	0.000	0.000	0.000	0.000
134	A	138	LEU	0	-0.072	-0.057	8.827	-1.191	-1.191	0.000	0.000	0.000	0.000
135	A	139	SER	0	-0.019	-0.032	11.721	-1.205	-1.205	0.000	0.000	0.000	0.000
136	A	140	ASN	0	0.002	-0.007	14.329	0.412	0.412	0.000	0.000	0.000	0.000
137	A	141	ASP	-1	-0.807	-0.857	16.858	-16.415	-16.415	0.000	0.000	0.000	0.000
138	A	142	GLN	0	-0.015	-0.014	15.340	0.553	0.553	0.000	0.000	0.000	0.000
139	A	143	THR	0	-0.010	-0.013	19.264	-0.457	-0.457	0.000	0.000	0.000	0.000
140	A	144	THR	0	-0.046	-0.042	18.371	0.163	0.163	0.000	0.000	0.000	0.000
141	A	145	THR	0	0.008	-0.002	20.812	-0.066	-0.066	0.000	0.000	0.000	0.000
142	A	146	ILE	0	-0.014	-0.013	19.570	-0.351	-0.351	0.000	0.000	0.000	0.000
143	A	147	ALA	0	0.048	0.023	23.354	0.411	0.411	0.000	0.000	0.000	0.000
144	A	148	SER	0	0.014	0.006	24.638	-0.670	-0.670	0.000	0.000	0.000	0.000
145	A	149	LYS	1	0.907	0.925	25.126	11.416	11.416	0.000	0.000	0.000	0.000
146	A	150	ASP	-1	-0.800	-0.893	22.365	-13.062	-13.062	0.000	0.000	0.000	0.000
147	A	151	LEU	0	0.027	0.016	19.363	-0.934	-0.934	0.000	0.000	0.000	0.000
148	A	152	ILE	0	-0.009	0.000	20.069	-0.825	-0.825	0.000	0.000	0.000	0.000
149	A	153	ARG	1	0.825	0.901	20.454	13.218	13.218	0.000	0.000	0.000	0.000
150	A	154	PHE	0	-0.001	0.006	13.057	-0.875	-0.875	0.000	0.000	0.000	0.000
151	A	155	LEU	0	-0.024	-0.008	15.825	-1.480	-1.480	0.000	0.000	0.000	0.000
152	A	156	GLU	-1	-0.903	-0.969	16.368	-14.982	-14.982	0.000	0.000	0.000	0.000
153	A	157	ALA	0	0.000	0.011	15.893	-0.474	-0.474	0.000	0.000	0.000	0.000
154	A	158	THR	0	-0.073	-0.016	11.599	-1.527	-1.527	0.000	0.000	0.000	0.000
155	A	159	GLY	0	-0.047	-0.024	12.846	-1.232	-1.232	0.000	0.000	0.000	0.000
156	A	160	HIS	1	0.746	0.848	11.602	24.558	24.558	0.000	0.000	0.000	0.000
157	A	161	ALA	0	0.049	0.018	16.855	0.394	0.394	0.000	0.000	0.000	0.000
158	A	162	PRO	0	-0.020	0.007	20.589	0.010	0.010	0.000	0.000	0.000	0.000
159	A	163	LEU	0	-0.008	-0.014	22.028	0.649	0.649	0.000	0.000	0.000	0.000
160	A	164	VAL	0	0.015	0.010	25.031	-0.121	-0.121	0.000	0.000	0.000	0.000
161	A	165	LEU	0	-0.020	-0.007	27.325	0.371	0.371	0.000	0.000	0.000	0.000
162	A	166	LYS	1	0.825	0.931	29.928	9.121	9.121	0.000	0.000	0.000	0.000
163	A	167	VAL	0	-0.069	-0.061	27.115	0.056	0.056	0.000	0.000	0.000	0.000
164	A	168	SER	0	-0.053	-0.051	30.591	0.087	0.087	0.000	0.000	0.000	0.000
165	A	169	GLU	-2	-1.846	-1.927	32.278	-17.622	-17.622	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)