FMO DATABASE

FMODB ID: MRZ6Z

Calculation Name: 1DDS-A-Xray547

Preferred Name:

Target Type:

Ligand Name: methotrexate | calcium ion | chloride ion

Ligand 3-letter code: MTX | CA | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DDS

Chain ID: A

ChEMBL ID:

UniProt ID: P0ABQ4

Base Structure: X-ray

Registration Date: 2025-09-02

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	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1595605.10082
FMO2-HF: Nuclear repulsion	1531914.487432
FMO2-HF: Total energy	-63690.613388
FMO2-MP2: Total energy	-63874.711367

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:MET)

Summations of interaction energy for fragment #1(A:1: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.
-189.825	-179.712	17.086	-11.61	-15.587	-0.105

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.830 / 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	3	SER	0	0.035	-0.009	2.950	-3.353	-0.017	0.434	-1.367	-2.404	-0.009
4	A	4	LEU	0	-0.028	-0.001	4.342	1.789	1.839	-0.001	-0.014	-0.035	0.000
88	A	88	VAL	0	0.002	-0.008	4.180	6.554	6.724	-0.001	-0.025	-0.144	0.000
89	A	89	PRO	0	0.024	0.008	3.056	-22.683	-19.927	0.207	-1.517	-1.447	-0.012
90	A	90	GLU	-1	-0.779	-0.831	1.818	-81.089	-81.099	15.798	-8.201	-7.587	-0.074
91	A	91	ILE	0	0.015	0.011	3.131	13.775	13.976	0.034	0.635	-0.869	0.000
92	A	92	MET	0	-0.020	0.006	4.979	-1.695	-1.615	-0.001	-0.020	-0.058	0.000
108	A	108	GLN	0	0.002	-0.008	2.847	-5.917	-3.579	0.458	-0.896	-1.899	-0.009
109	A	109	LYS	1	0.910	0.978	3.843	34.287	35.255	0.161	-0.193	-0.936	-0.001
110	A	110	LEU	0	-0.006	0.000	5.723	-1.320	-1.332	-0.001	-0.004	0.017	0.000
111	A	111	TYR	0	-0.059	-0.062	5.447	1.787	1.907	-0.001	-0.006	-0.113	0.000
157	A	157	GLU	-1	-0.867	-0.946	6.254	-32.141	-32.025	-0.001	-0.002	-0.112	0.000
5	A	5	ILE	0	-0.041	-0.016	8.191	0.285	0.285	0.000	0.000	0.000	0.000
6	A	6	ALA	0	-0.001	0.002	10.856	0.550	0.550	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.012	0.028	14.488	0.110	0.110	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.049	-0.032	16.564	0.171	0.171	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.029	0.018	19.889	0.286	0.286	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.064	0.031	22.920	-0.371	-0.371	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.872	-0.948	25.126	-10.860	-10.860	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.858	0.939	19.334	13.557	13.557	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.012	0.017	21.268	-0.557	-0.557	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.015	-0.016	18.211	-0.545	-0.545	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.031	0.011	21.396	0.479	0.479	0.000	0.000	0.000	0.000
16	A	16	MET	0	-0.064	-0.020	21.764	-0.563	-0.563	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.899	-0.965	24.269	-10.925	-10.925	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.021	-0.002	26.245	-0.059	-0.059	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.004	-0.002	25.720	-0.338	-0.338	0.000	0.000	0.000	0.000
20	A	20	MET	0	0.012	0.029	23.222	0.361	0.361	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.005	0.011	26.379	0.072	0.072	0.000	0.000	0.000	0.000
22	A	22	TRP	0	0.023	-0.011	21.695	0.291	0.291	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.033	-0.014	27.516	-0.381	-0.381	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.054	0.037	23.349	0.180	0.180	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.003	-0.006	23.355	-0.644	-0.644	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.011	0.011	22.698	-0.493	-0.493	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.789	-0.879	18.294	-16.000	-16.000	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.006	0.003	18.398	-0.937	-0.937	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.042	-0.019	18.954	-0.709	-0.709	0.000	0.000	0.000	0.000
30	A	30	TRP	0	0.092	0.048	12.924	-0.929	-0.929	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.053	0.022	13.713	-1.441	-1.441	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.925	0.978	14.038	13.461	13.461	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.848	0.927	11.594	18.552	18.552	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.003	0.004	10.333	-1.728	-1.728	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.008	-0.001	9.554	-2.375	-2.375	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.073	-0.030	11.309	-0.535	-0.535	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.043	-0.032	11.566	-0.483	-0.483	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.854	0.929	6.544	32.070	32.070	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.028	-0.017	7.407	3.670	3.670	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.012	-0.006	9.279	-2.287	-2.287	0.000	0.000	0.000	0.000
41	A	41	ILE	0	0.008	0.002	9.005	1.293	1.293	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.017	0.010	12.506	0.307	0.307	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.048	0.024	15.557	0.156	0.156	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.845	0.908	18.680	12.638	12.638	0.000	0.000	0.000	0.000
45	A	45	HIS	0	0.010	-0.002	22.336	-0.162	-0.162	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.005	0.001	17.312	0.568	0.568	0.000	0.000	0.000	0.000
47	A	47	TRP	0	-0.019	-0.007	20.544	-0.318	-0.318	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.867	-0.957	21.845	-12.036	-12.036	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.034	-0.018	23.087	0.272	0.272	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.043	-0.009	18.523	0.018	0.018	0.000	0.000	0.000	0.000
51	A	51	GLY	0	-0.011	-0.014	23.044	0.341	0.341	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.855	0.932	23.452	13.187	13.187	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.042	0.029	20.632	-0.505	-0.505	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.016	0.003	16.039	0.512	0.512	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.001	-0.011	18.171	-0.703	-0.703	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.040	0.016	17.453	-0.419	-0.419	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.865	0.933	12.701	18.316	18.316	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.833	0.931	10.126	28.945	28.945	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.004	-0.005	13.294	-1.041	-1.041	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.040	0.019	11.268	0.774	0.774	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.004	0.003	14.975	-0.465	-0.465	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.002	0.000	14.488	0.339	0.339	0.000	0.000	0.000	0.000
63	A	63	SER	0	0.001	-0.010	17.639	0.861	0.861	0.000	0.000	0.000	0.000
64	A	64	SER	0	0.045	0.038	21.389	-0.198	-0.198	0.000	0.000	0.000	0.000
65	A	65	GLN	0	0.015	0.015	23.914	0.028	0.028	0.000	0.000	0.000	0.000
66	A	66	PRO	0	0.010	-0.013	24.927	-0.568	-0.568	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.045	0.024	24.513	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.030	-0.010	25.194	0.321	0.321	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.813	-0.891	24.588	-11.756	-11.756	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.855	-0.933	24.801	-12.191	-12.191	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.790	0.876	23.103	11.680	11.680	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.017	-0.003	19.046	-0.709	-0.709	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.040	-0.011	15.926	0.196	0.196	0.000	0.000	0.000	0.000
74	A	74	TRP	0	0.003	0.007	17.558	-0.725	-0.725	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.018	-0.007	14.784	0.154	0.154	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.805	0.878	18.106	14.108	14.108	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.018	-0.018	17.045	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.031	0.002	11.495	-0.659	-0.659	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.873	-0.950	11.628	-24.807	-24.807	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.795	-0.882	11.822	-18.471	-18.471	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.036	0.018	11.617	-0.216	-0.216	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.008	0.014	6.333	-2.072	-2.072	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.003	0.000	8.727	-1.377	-1.377	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.003	0.006	11.295	0.169	0.169	0.000	0.000	0.000	0.000
85	A	85	CYS	0	-0.066	-0.034	6.880	0.384	0.384	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.005	0.017	8.644	0.519	0.519	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.960	-0.975	5.628	-54.298	-54.298	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.004	-0.007	7.493	3.186	3.186	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.011	-0.012	9.496	0.741	0.741	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.043	0.053	12.656	1.330	1.330	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.034	0.023	14.872	0.115	0.115	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.069	0.013	17.657	-0.200	-0.200	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.874	0.927	17.038	14.553	14.553	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.035	-0.013	13.332	-0.702	-0.702	0.000	0.000	0.000	0.000
100	A	100	TYR	0	0.029	0.002	12.028	-1.168	-1.168	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.815	-0.907	12.804	-16.504	-16.504	0.000	0.000	0.000	0.000
102	A	102	GLN	0	-0.059	-0.030	14.550	0.584	0.584	0.000	0.000	0.000	0.000
103	A	103	PHE	0	-0.012	-0.013	8.620	-0.684	-0.684	0.000	0.000	0.000	0.000
104	A	104	LEU	0	0.061	0.045	9.370	-2.689	-2.689	0.000	0.000	0.000	0.000
105	A	105	PRO	0	-0.010	0.002	10.128	-0.985	-0.985	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.882	0.943	7.194	26.221	26.221	0.000	0.000	0.000	0.000
107	A	107	ALA	0	-0.040	0.003	5.566	-6.151	-6.151	0.000	0.000	0.000	0.000
112	A	112	LEU	0	0.009	0.001	10.628	0.078	0.078	0.000	0.000	0.000	0.000
113	A	113	THR	0	-0.040	-0.038	14.198	0.048	0.048	0.000	0.000	0.000	0.000
114	A	114	HIS	0	-0.018	-0.011	17.028	0.538	0.538	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.003	-0.012	20.225	0.267	0.267	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.884	-0.934	23.503	-10.773	-10.773	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.046	-0.041	26.574	0.415	0.415	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.937	-0.969	27.421	-9.493	-9.493	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.060	-0.040	27.255	0.183	0.183	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.918	-0.951	28.644	-8.951	-8.951	0.000	0.000	0.000	0.000
121	A	121	GLY	0	0.001	-0.017	27.464	-0.111	-0.111	0.000	0.000	0.000	0.000
122	A	122	ASP	-1	-0.902	-0.947	27.751	-10.227	-10.227	0.000	0.000	0.000	0.000
123	A	123	THR	0	-0.048	-0.034	21.332	-0.414	-0.414	0.000	0.000	0.000	0.000
124	A	124	HIS	1	0.829	0.910	21.984	11.793	11.793	0.000	0.000	0.000	0.000
125	A	125	PHE	0	0.012	0.007	12.254	-0.486	-0.486	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.017	-0.005	14.684	0.633	0.633	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-0.901	-0.913	17.366	-13.746	-13.746	0.000	0.000	0.000	0.000
128	A	128	TYR	0	-0.002	-0.006	14.081	-0.616	-0.616	0.000	0.000	0.000	0.000
129	A	129	GLU	0	-0.034	-0.042	16.002	0.737	0.737	0.000	0.000	0.000	0.000
130	A	130	PRO	0	0.053	0.005	16.340	-0.747	-0.747	0.000	0.000	0.000	0.000
131	A	131	ASP	-1	-0.945	-0.971	17.187	-14.293	-14.293	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.803	-0.862	12.775	-21.029	-21.029	0.000	0.000	0.000	0.000
133	A	133	TRP	0	-0.083	-0.050	7.878	-2.882	-2.882	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.848	-0.892	12.176	-16.539	-16.539	0.000	0.000	0.000	0.000
135	A	135	SER	0	-0.027	-0.043	12.126	-1.486	-1.486	0.000	0.000	0.000	0.000
136	A	136	VAL	0	-0.025	-0.008	10.034	0.577	0.577	0.000	0.000	0.000	0.000
137	A	137	PHE	0	-0.081	-0.045	12.994	0.524	0.524	0.000	0.000	0.000	0.000
138	A	138	SER	0	0.060	0.013	14.651	-0.366	-0.366	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.902	-0.932	17.813	-13.502	-13.502	0.000	0.000	0.000	0.000
140	A	140	PHE	0	0.029	0.000	19.877	-0.260	-0.260	0.000	0.000	0.000	0.000
141	A	141	HIS	1	0.778	0.891	20.846	12.666	12.666	0.000	0.000	0.000	0.000
142	A	142	ASP	-1	-0.854	-0.916	25.360	-9.703	-9.703	0.000	0.000	0.000	0.000
143	A	143	ALA	0	0.003	0.012	28.179	-0.258	-0.258	0.000	0.000	0.000	0.000
144	A	144	ASP	-1	-0.813	-0.896	28.993	-9.974	-9.974	0.000	0.000	0.000	0.000
145	A	145	ALA	0	-0.044	-0.030	31.959	0.021	0.021	0.000	0.000	0.000	0.000
146	A	146	GLN	0	-0.117	-0.061	29.745	0.312	0.312	0.000	0.000	0.000	0.000
147	A	147	ASN	0	-0.060	-0.052	25.991	-0.582	-0.582	0.000	0.000	0.000	0.000
148	A	148	SER	0	0.028	-0.014	28.674	0.103	0.103	0.000	0.000	0.000	0.000
149	A	149	HIS	0	0.027	0.034	27.157	0.088	0.088	0.000	0.000	0.000	0.000
150	A	150	SER	0	0.025	0.012	26.879	0.022	0.022	0.000	0.000	0.000	0.000
151	A	151	TYR	0	-0.022	-0.020	21.290	-0.314	-0.314	0.000	0.000	0.000	0.000
152	A	152	CYS	0	-0.045	-0.021	20.424	0.103	0.103	0.000	0.000	0.000	0.000
153	A	153	PHE	0	-0.056	-0.019	15.921	-0.354	-0.354	0.000	0.000	0.000	0.000
154	A	154	GLU	-1	-0.740	-0.865	14.355	-15.384	-15.384	0.000	0.000	0.000	0.000
155	A	155	ILE	0	-0.083	-0.050	8.471	-1.295	-1.295	0.000	0.000	0.000	0.000
156	A	156	LEU	0	-0.011	0.018	9.960	0.827	0.827	0.000	0.000	0.000	0.000
158	A	158	ARG	1	0.690	0.803	7.449	26.640	26.640	0.000	0.000	0.000	0.000
159	A	159	ARG	0	-0.103	-0.050	9.248	-3.534	-3.534	0.000	0.000	0.000	0.000

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