FMO DATABASE

FMODB ID: 8GYLY

Calculation Name: 1XM5-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nickel (ii) ion

Ligand 3-letter code: NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1XM5

Chain ID: A

ChEMBL ID:

UniProt ID: P0A898

Base Structure: X-ray

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	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1468771.377756
FMO2-HF: Nuclear repulsion	1407461.554393
FMO2-HF: Total energy	-61309.823363
FMO2-MP2: Total energy	-61484.997827

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:1001:MET)

Summations of interaction energy for fragment #1(A:1001:MET)

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.
-504.778	-498.102	27.465	-18.283	-15.856	-0.212

Interaction energy analysis for fragmet #1(A:1001:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.647 / q_NPA : 0.806

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	1003	GLN	0	-0.028	-0.012	3.862	7.005	9.191	-0.013	-0.950	-1.222	-0.003
37	A	1037	GLU	-1	-0.859	-0.890	1.760	-164.265	-162.639	24.907	-15.293	-11.239	-0.183
38	A	1038	GLU	-1	-1.015	-1.024	2.595	-64.422	-61.617	2.572	-2.038	-3.339	-0.026
39	A	1039	SER	0	0.007	0.004	5.136	3.904	3.963	-0.001	-0.002	-0.056	0.000
4	A	1004	VAL	0	0.077	0.056	5.403	-0.516	-0.516	0.000	0.000	0.000	0.000
5	A	1005	ILE	0	-0.048	-0.019	8.308	1.965	1.965	0.000	0.000	0.000	0.000
6	A	1006	LEU	0	0.001	0.000	11.112	0.314	0.314	0.000	0.000	0.000	0.000
7	A	1007	ASP	-1	-0.824	-0.876	14.634	-13.877	-13.877	0.000	0.000	0.000	0.000
8	A	1008	LEU	0	0.021	0.013	17.993	0.250	0.250	0.000	0.000	0.000	0.000
9	A	1009	GLN	0	-0.079	-0.049	20.581	1.151	1.151	0.000	0.000	0.000	0.000
10	A	1010	LEU	0	-0.008	-0.008	24.025	0.205	0.205	0.000	0.000	0.000	0.000
11	A	1011	ALA	0	-0.027	-0.014	26.970	0.229	0.229	0.000	0.000	0.000	0.000
12	A	1012	CYS	0	-0.073	-0.022	29.781	0.132	0.132	0.000	0.000	0.000	0.000
13	A	1013	GLU	-1	-0.970	-0.989	32.617	-8.130	-8.130	0.000	0.000	0.000	0.000
14	A	1014	ASP	-1	-0.910	-0.932	34.970	-8.771	-8.771	0.000	0.000	0.000	0.000
15	A	1015	ASN	0	-0.009	-0.023	29.779	-0.306	-0.306	0.000	0.000	0.000	0.000
16	A	1016	SER	0	-0.001	-0.007	30.442	-0.299	-0.299	0.000	0.000	0.000	0.000
17	A	1017	GLY	0	-0.053	-0.039	31.760	0.077	0.077	0.000	0.000	0.000	0.000
18	A	1018	LEU	0	-0.012	0.010	27.218	0.019	0.019	0.000	0.000	0.000	0.000
19	A	1019	PRO	0	-0.001	0.002	23.763	0.105	0.105	0.000	0.000	0.000	0.000
20	A	1020	GLU	-1	-0.907	-0.947	22.363	-12.156	-12.156	0.000	0.000	0.000	0.000
21	A	1021	GLU	-1	-0.912	-0.965	17.853	-15.798	-15.798	0.000	0.000	0.000	0.000
22	A	1022	SER	0	-0.026	-0.020	17.601	-0.835	-0.835	0.000	0.000	0.000	0.000
23	A	1023	GLN	0	-0.010	0.022	17.723	-0.649	-0.649	0.000	0.000	0.000	0.000
24	A	1024	PHE	0	0.067	0.025	18.525	-0.579	-0.579	0.000	0.000	0.000	0.000
25	A	1025	GLN	0	0.024	0.018	11.648	-1.987	-1.987	0.000	0.000	0.000	0.000
26	A	1026	THR	0	-0.068	-0.049	13.762	-1.668	-1.668	0.000	0.000	0.000	0.000
27	A	1027	TRP	0	-0.011	-0.030	15.090	-0.744	-0.744	0.000	0.000	0.000	0.000
28	A	1028	LEU	0	0.042	0.028	12.957	-0.443	-0.443	0.000	0.000	0.000	0.000
29	A	1029	ASN	0	-0.070	-0.057	9.597	-3.869	-3.869	0.000	0.000	0.000	0.000
30	A	1030	ALA	0	-0.045	-0.013	11.307	-1.933	-1.933	0.000	0.000	0.000	0.000
31	A	1031	VAL	0	0.040	0.030	13.440	0.783	0.783	0.000	0.000	0.000	0.000
32	A	1032	ILE	0	0.031	0.013	10.490	-0.946	-0.946	0.000	0.000	0.000	0.000
33	A	1033	PRO	0	-0.021	-0.008	6.479	-2.309	-2.309	0.000	0.000	0.000	0.000
34	A	1034	GLN	0	-0.033	-0.018	6.751	-5.393	-5.393	0.000	0.000	0.000	0.000
35	A	1035	PHE	0	0.016	0.008	8.855	1.242	1.242	0.000	0.000	0.000	0.000
36	A	1036	GLN	0	0.018	-0.002	8.384	0.927	0.927	0.000	0.000	0.000	0.000
40	A	1040	GLU	-1	-0.918	-0.932	8.860	-22.997	-22.997	0.000	0.000	0.000	0.000
41	A	1041	VAL	0	0.027	0.015	12.034	0.671	0.671	0.000	0.000	0.000	0.000
42	A	1042	THR	0	-0.025	-0.012	15.510	-0.040	-0.040	0.000	0.000	0.000	0.000
43	A	1043	ILE	0	-0.030	-0.013	18.754	0.171	0.171	0.000	0.000	0.000	0.000
44	A	1044	ARG	1	0.828	0.883	21.060	11.414	11.414	0.000	0.000	0.000	0.000
45	A	1045	VAL	0	0.003	0.009	24.621	0.163	0.163	0.000	0.000	0.000	0.000
46	A	1046	VAL	0	0.028	0.006	27.040	0.304	0.304	0.000	0.000	0.000	0.000
47	A	1047	ASP	-1	-0.706	-0.846	30.524	-8.983	-8.983	0.000	0.000	0.000	0.000
48	A	1048	THR	0	-0.033	-0.049	34.211	-0.031	-0.031	0.000	0.000	0.000	0.000
49	A	1049	ALA	0	-0.055	-0.021	36.355	0.050	0.050	0.000	0.000	0.000	0.000
50	A	1050	GLU	-1	-0.782	-0.866	30.365	-10.156	-10.156	0.000	0.000	0.000	0.000
51	A	1051	SER	0	0.025	0.013	32.355	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	1052	HIS	0	-0.062	-0.032	33.325	-0.196	-0.196	0.000	0.000	0.000	0.000
53	A	1053	SER	0	-0.010	0.004	35.485	0.013	0.013	0.000	0.000	0.000	0.000
54	A	1054	LEU	0	0.047	0.020	29.915	0.095	0.095	0.000	0.000	0.000	0.000
55	A	1055	ASN	0	0.027	0.008	33.007	-0.273	-0.273	0.000	0.000	0.000	0.000
56	A	1056	LEU	0	-0.035	-0.010	33.940	0.088	0.088	0.000	0.000	0.000	0.000
57	A	1057	THR	0	-0.058	-0.046	34.820	0.026	0.026	0.000	0.000	0.000	0.000
58	A	1058	TYR	0	0.004	0.004	30.663	0.013	0.013	0.000	0.000	0.000	0.000
59	A	1059	ARG	1	0.850	0.932	26.750	11.200	11.200	0.000	0.000	0.000	0.000
60	A	1060	GLY	0	-0.002	0.022	33.904	0.152	0.152	0.000	0.000	0.000	0.000
61	A	1061	LYS	1	0.854	0.919	35.296	8.971	8.971	0.000	0.000	0.000	0.000
62	A	1062	ASP	-1	-0.885	-0.942	37.755	-7.690	-7.690	0.000	0.000	0.000	0.000
63	A	1063	LYS	1	0.916	0.940	37.080	8.396	8.396	0.000	0.000	0.000	0.000
64	A	1064	PRO	0	-0.005	0.022	35.471	-0.159	-0.159	0.000	0.000	0.000	0.000
65	A	1065	THR	0	-0.006	-0.027	31.808	0.098	0.098	0.000	0.000	0.000	0.000
66	A	1066	ASN	0	0.030	0.001	29.905	-0.156	-0.156	0.000	0.000	0.000	0.000
67	A	1067	VAL	0	0.048	0.017	24.270	-0.104	-0.104	0.000	0.000	0.000	0.000
68	A	1068	LEU	0	-0.044	-0.006	27.348	0.029	0.029	0.000	0.000	0.000	0.000
69	A	1069	SER	0	0.057	0.027	22.904	-0.461	-0.461	0.000	0.000	0.000	0.000
70	A	1070	PHE	0	-0.047	-0.033	22.901	0.823	0.823	0.000	0.000	0.000	0.000
71	A	1071	PRO	0	0.079	0.053	19.816	-0.419	-0.419	0.000	0.000	0.000	0.000
72	A	1072	PHE	0	-0.005	-0.018	17.633	0.909	0.909	0.000	0.000	0.000	0.000
73	A	1073	GLU	-1	-0.968	-0.978	18.816	-13.220	-13.220	0.000	0.000	0.000	0.000
74	A	1074	VAL	0	0.020	0.008	15.189	0.254	0.254	0.000	0.000	0.000	0.000
75	A	1075	PRO	0	-0.040	-0.023	18.266	0.568	0.568	0.000	0.000	0.000	0.000
76	A	1076	PRO	0	-0.010	-0.024	19.082	-0.584	-0.584	0.000	0.000	0.000	0.000
77	A	1077	GLY	0	-0.050	-0.016	18.459	0.524	0.524	0.000	0.000	0.000	0.000
78	A	1078	MET	0	-0.066	-0.035	16.015	0.634	0.634	0.000	0.000	0.000	0.000
79	A	1079	GLU	-1	-0.906	-0.943	10.363	-23.265	-23.265	0.000	0.000	0.000	0.000
80	A	1080	MET	0	-0.087	-0.051	11.722	1.436	1.436	0.000	0.000	0.000	0.000
81	A	1081	SER	0	0.028	0.003	8.724	-0.461	-0.461	0.000	0.000	0.000	0.000
82	A	1082	LEU	0	-0.033	-0.015	10.427	-0.335	-0.335	0.000	0.000	0.000	0.000
83	A	1083	LEU	0	0.061	0.026	11.998	0.709	0.709	0.000	0.000	0.000	0.000
84	A	1084	GLY	0	-0.045	-0.001	15.234	1.041	1.041	0.000	0.000	0.000	0.000
85	A	1085	ASP	-1	-0.876	-0.948	18.123	-14.997	-14.997	0.000	0.000	0.000	0.000
86	A	1086	LEU	0	-0.030	-0.011	19.780	0.511	0.511	0.000	0.000	0.000	0.000
87	A	1087	VAL	0	-0.015	-0.013	22.649	0.205	0.205	0.000	0.000	0.000	0.000
88	A	1088	ILE	0	0.018	0.016	22.854	0.233	0.233	0.000	0.000	0.000	0.000
89	A	1089	CYS	0	-0.085	-0.022	27.082	0.409	0.409	0.000	0.000	0.000	0.000
90	A	1090	ARG	1	0.847	0.902	30.618	9.529	9.529	0.000	0.000	0.000	0.000
91	A	1091	GLN	0	-0.017	-0.036	31.468	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	1092	VAL	0	-0.080	-0.040	32.832	0.284	0.284	0.000	0.000	0.000	0.000
93	A	1093	VAL	0	0.070	0.043	28.446	0.156	0.156	0.000	0.000	0.000	0.000
94	A	1094	GLU	-1	-0.848	-0.926	31.693	-9.285	-9.285	0.000	0.000	0.000	0.000
95	A	1095	LYS	1	0.859	0.944	34.251	8.547	8.547	0.000	0.000	0.000	0.000
96	A	1096	GLU	-1	-0.754	-0.857	32.161	-9.947	-9.947	0.000	0.000	0.000	0.000
97	A	1097	ALA	0	0.028	0.017	32.340	0.056	0.056	0.000	0.000	0.000	0.000
98	A	1098	GLN	0	-0.086	-0.039	34.207	0.318	0.318	0.000	0.000	0.000	0.000
99	A	1099	GLU	-1	-1.000	-1.013	37.868	-8.056	-8.056	0.000	0.000	0.000	0.000
100	A	1100	GLN	0	-0.016	-0.011	33.461	-0.050	-0.050	0.000	0.000	0.000	0.000
101	A	1101	GLY	0	-0.047	-0.006	36.822	-0.028	-0.028	0.000	0.000	0.000	0.000
102	A	1102	LYS	1	0.914	0.977	29.403	10.815	10.815	0.000	0.000	0.000	0.000
103	A	1103	PRO	0	-0.017	-0.015	30.294	0.168	0.168	0.000	0.000	0.000	0.000
104	A	1104	LEU	0	0.016	0.003	30.529	-0.252	-0.252	0.000	0.000	0.000	0.000
105	A	1105	GLU	-1	-0.874	-0.917	25.045	-12.511	-12.511	0.000	0.000	0.000	0.000
106	A	1106	ALA	0	0.072	0.047	25.980	-0.446	-0.446	0.000	0.000	0.000	0.000
107	A	1107	HIS	0	0.001	-0.011	26.524	-0.473	-0.473	0.000	0.000	0.000	0.000
108	A	1108	TRP	0	-0.005	-0.025	25.057	-0.274	-0.274	0.000	0.000	0.000	0.000
109	A	1109	ALA	0	0.013	0.016	22.252	-0.426	-0.426	0.000	0.000	0.000	0.000
110	A	1110	HIS	0	0.013	-0.014	22.245	-0.303	-0.303	0.000	0.000	0.000	0.000
111	A	1111	MET	0	-0.043	-0.022	23.898	-0.204	-0.204	0.000	0.000	0.000	0.000
112	A	1112	VAL	0	0.001	-0.012	18.801	-0.201	-0.201	0.000	0.000	0.000	0.000
113	A	1113	VAL	0	-0.005	0.021	18.876	-0.851	-0.851	0.000	0.000	0.000	0.000
114	A	1114	HIS	0	0.029	0.006	19.942	-0.393	-0.393	0.000	0.000	0.000	0.000
115	A	1115	GLY	0	0.004	-0.012	22.003	-0.034	-0.034	0.000	0.000	0.000	0.000
116	A	1116	SER	0	-0.033	-0.041	16.303	-0.471	-0.471	0.000	0.000	0.000	0.000
117	A	1117	LEU	0	0.009	0.010	17.087	-0.937	-0.937	0.000	0.000	0.000	0.000
118	A	1118	HIS	1	0.824	0.920	19.125	13.104	13.104	0.000	0.000	0.000	0.000
119	A	1119	LEU	0	-0.097	-0.055	17.085	0.233	0.233	0.000	0.000	0.000	0.000
120	A	1120	LEU	0	-0.066	-0.027	12.914	-0.791	-0.791	0.000	0.000	0.000	0.000
121	A	1121	GLY	0	-0.039	-0.010	16.966	-0.259	-0.259	0.000	0.000	0.000	0.000
122	A	1122	TYR	0	-0.022	0.004	15.871	0.605	0.605	0.000	0.000	0.000	0.000
123	A	1123	ASP	-1	-0.890	-0.963	21.615	-11.861	-11.861	0.000	0.000	0.000	0.000
124	A	1124	HIS	0	-0.002	-0.019	25.367	-0.380	-0.380	0.000	0.000	0.000	0.000
125	A	1125	ILE	0	-0.118	-0.051	28.282	0.518	0.518	0.000	0.000	0.000	0.000
126	A	1126	GLU	-1	-0.931	-0.953	30.330	-9.374	-9.374	0.000	0.000	0.000	0.000
127	A	1127	ASP	-1	-0.946	-0.986	30.377	-9.623	-9.623	0.000	0.000	0.000	0.000
128	A	1128	ASP	-1	-0.969	-0.990	29.239	-11.088	-11.088	0.000	0.000	0.000	0.000
129	A	1129	GLU	-1	-0.851	-0.930	25.801	-12.309	-12.309	0.000	0.000	0.000	0.000
130	A	1130	ALA	0	-0.001	-0.001	25.705	-0.520	-0.520	0.000	0.000	0.000	0.000
131	A	1131	GLU	-1	-0.961	-0.968	26.762	-11.527	-11.527	0.000	0.000	0.000	0.000
132	A	1132	GLU	-1	-0.972	-0.989	21.257	-15.250	-15.250	0.000	0.000	0.000	0.000
133	A	1133	MET	0	-0.044	-0.009	22.095	-0.696	-0.696	0.000	0.000	0.000	0.000
134	A	1134	GLU	-1	-0.929	-0.977	22.706	-11.457	-11.457	0.000	0.000	0.000	0.000
135	A	1135	ALA	0	0.004	0.004	23.522	-0.187	-0.187	0.000	0.000	0.000	0.000
136	A	1136	LEU	0	0.013	0.006	16.981	-0.561	-0.561	0.000	0.000	0.000	0.000
137	A	1137	GLU	-1	-0.785	-0.869	19.973	-13.529	-13.529	0.000	0.000	0.000	0.000
138	A	1138	THR	0	-0.036	-0.042	22.108	-0.122	-0.122	0.000	0.000	0.000	0.000
139	A	1139	GLU	-1	-1.006	-0.998	16.702	-18.294	-18.294	0.000	0.000	0.000	0.000
140	A	1140	ILE	0	-0.018	-0.019	15.602	-0.211	-0.211	0.000	0.000	0.000	0.000
141	A	1141	MET	0	-0.031	-0.005	18.850	-0.178	-0.178	0.000	0.000	0.000	0.000
142	A	1142	LEU	0	-0.033	-0.006	22.236	0.322	0.322	0.000	0.000	0.000	0.000
143	A	1143	ALA	0	-0.078	-0.030	17.357	0.110	0.110	0.000	0.000	0.000	0.000
144	A	1144	LEU	0	-0.069	-0.035	17.627	-0.481	-0.481	0.000	0.000	0.000	0.000
145	A	1145	GLY	0	-0.079	-0.024	20.412	0.377	0.377	0.000	0.000	0.000	0.000
146	A	1146	TYR	0	-0.095	-0.072	22.122	0.454	0.454	0.000	0.000	0.000	0.000
147	A	1147	GLU	-1	-0.925	-0.980	25.982	-11.079	-11.079	0.000	0.000	0.000	0.000
148	A	1148	ASP	-1	-0.773	-0.889	26.724	-12.093	-12.093	0.000	0.000	0.000	0.000
149	A	1149	PRO	0	-0.079	-0.029	25.851	0.447	0.447	0.000	0.000	0.000	0.000
150	A	1150	TYR	0	-0.043	-0.043	26.134	0.572	0.572	0.000	0.000	0.000	0.000
151	A	1151	ILE	0	-0.080	-0.034	29.662	0.196	0.196	0.000	0.000	0.000	0.000
152	A	1152	ALA	-1	-0.972	-0.972	32.879	-8.523	-8.523	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1001:MET)