FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: RQ178

Calculation Name: 3A7M-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A7M

Chain ID: A

ChEMBL ID:

UniProt ID: P0A1N2

Base Structure: X-ray

Registration Date: 2025-07-11

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 220
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -805319.851784
FMO2-HF: Nuclear repulsion 759672.585741
FMO2-HF: Total energy -45647.266043
FMO2-MP2: Total energy -45780.225518


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-9.268-5.9271.039-1.866-2.5150.007
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.048
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   
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].
4A3SER00.0190.0884.478-0.463-0.257-0.001-0.069-0.1360.000
5A4THR0-0.019-0.0773.405-4.511-2.4430.027-1.117-0.9780.005
6A4THR0-0.0080.0584.8650.6860.772-0.001-0.010-0.0760.000
7A5VAL00.088-0.0792.987-1.381-1.2830.1100.205-0.4130.000
8A5VAL0-0.0540.1042.601-0.3890.0690.904-0.685-0.6770.002
9A6GLU00.105-0.0913.884-0.510-0.2320.001-0.174-0.1050.000
10A6GLU-1-0.927-0.8114.618-1.861-1.714-0.001-0.016-0.1300.000
11A7PHE00.076-0.0775.948-0.206-0.2060.0000.0000.0000.000
12A7PHE0-0.0460.0967.7380.1050.1050.0000.0000.0000.000
13A8ILE00.101-0.0897.474-0.225-0.2250.0000.0000.0000.000
14A8ILE0-0.0980.0877.3790.0200.0200.0000.0000.0000.000
15A9ASN00.086-0.0827.989-0.094-0.0940.0000.0000.0000.000
16A9ASN0-0.1140.0698.232-0.167-0.1670.0000.0000.0000.000
17A10ARG00.096-0.0919.622-0.090-0.0900.0000.0000.0000.000
18A10ARG10.7671.0068.3240.7970.7970.0000.0000.0000.000
19A11TRP00.102-0.09211.649-0.074-0.0740.0000.0000.0000.000
20A11TRP0-0.0410.11912.671-0.017-0.0170.0000.0000.0000.000
21A12GLN00.096-0.09312.699-0.020-0.0200.0000.0000.0000.000
22A12GLN0-0.0810.07911.334-0.058-0.0580.0000.0000.0000.000
23A13ARG00.123-0.06313.661-0.004-0.0040.0000.0000.0000.000
24A13ARG10.8261.04413.9960.1910.1910.0000.0000.0000.000
25A14ILE00.087-0.10415.519-0.032-0.0320.0000.0000.0000.000
26A14ILE0-0.0850.10915.7260.0010.0010.0000.0000.0000.000
27A15ALA00.181-0.06617.384-0.024-0.0240.0000.0000.0000.000
28A15ALA0-0.0860.10517.8400.0100.0100.0000.0000.0000.000
29A16LEU00.065-0.09618.2780.0000.0000.0000.0000.0000.000
30A16LEU0-0.0860.09316.523-0.005-0.0050.0000.0000.0000.000
31A17LEU00.047-0.09919.704-0.007-0.0070.0000.0000.0000.000
32A17LEU0-0.0610.10019.087-0.006-0.0060.0000.0000.0000.000
33A18SER00.023-0.07521.630-0.014-0.0140.0000.0000.0000.000
34A18SER0-0.0150.07222.0950.0120.0120.0000.0000.0000.000
35A19GLN00.120-0.09523.077-0.003-0.0030.0000.0000.0000.000
36A19GLN0-0.1220.08023.2890.0140.0140.0000.0000.0000.000
37A20SER00.010-0.10424.0940.0020.0020.0000.0000.0000.000
38A20SER0-0.0770.04823.340-0.009-0.0090.0000.0000.0000.000
39A21LEU00.061-0.09825.827-0.007-0.0070.0000.0000.0000.000
40A21LEU0-0.0730.10325.4490.0000.0000.0000.0000.0000.000
41A22LEU00.124-0.06427.530-0.006-0.0060.0000.0000.0000.000
42A22LEU0-0.1150.09128.1630.0030.0030.0000.0000.0000.000
43A23GLU00.099-0.11928.7660.0010.0010.0000.0000.0000.000
44A23GLU-1-0.920-0.78527.9790.0200.0200.0000.0000.0000.000
45A24LEU00.057-0.10530.0540.0000.0000.0000.0000.0000.000
46A24LEU0-0.0950.08828.965-0.002-0.0020.0000.0000.0000.000
47A25ALA00.097-0.08631.875-0.005-0.0050.0000.0000.0000.000
48A25ALA0-0.0520.09232.6810.0010.0010.0000.0000.0000.000
49A26GLN00.020-0.13033.360-0.001-0.0010.0000.0000.0000.000
50A26GLN0-0.0950.07831.955-0.002-0.0020.0000.0000.0000.000
51A27ARG00.025-0.09434.5630.0020.0020.0000.0000.0000.000
52A27ARG10.7801.00431.0660.0000.0000.0000.0000.0000.000
53A28GLY0-0.003-0.09136.286-0.002-0.0020.0000.0000.0000.000
54A29GLU00.0630.02534.872-0.001-0.0010.0000.0000.0000.000
55A29GLU-1-1.016-0.87734.049-0.029-0.0290.0000.0000.0000.000
56A30TRP00.071-0.10834.574-0.005-0.0050.0000.0000.0000.000
57A30TRP0-0.0530.09434.7800.0010.0010.0000.0000.0000.000
58A31ASP00.122-0.10435.0400.0000.0000.0000.0000.0000.000
59A31ASP-1-0.935-0.83737.341-0.032-0.0320.0000.0000.0000.000
60A32LEU00.021-0.11432.678-0.008-0.0080.0000.0000.0000.000
61A32LEU0-0.0540.10831.643-0.001-0.0010.0000.0000.0000.000
62A33LEU00.074-0.10730.504-0.010-0.0100.0000.0000.0000.000
63A33LEU0-0.1180.09730.6530.0010.0010.0000.0000.0000.000
64A34LEU00.099-0.08730.616-0.004-0.0040.0000.0000.0000.000
65A34LEU0-0.0920.10034.3670.0000.0000.0000.0000.0000.000
66A35GLN00.048-0.09231.271-0.002-0.0020.0000.0000.0000.000
67A35GLN0-0.1380.04330.951-0.008-0.0080.0000.0000.0000.000
68A36GLN00.048-0.10027.231-0.013-0.0130.0000.0000.0000.000
69A36GLN0-0.0990.08225.760-0.008-0.0080.0000.0000.0000.000
70A37GLU00.109-0.11326.199-0.007-0.0070.0000.0000.0000.000
71A37GLU-1-1.006-0.83729.181-0.020-0.0200.0000.0000.0000.000
72A38VAL00.091-0.11226.5970.0070.0070.0000.0000.0000.000
73A38VAL0-0.0450.12627.019-0.001-0.0010.0000.0000.0000.000
74A39SER00.040-0.07923.945-0.003-0.0030.0000.0000.0000.000
75A39SER0-0.0240.07923.423-0.005-0.0050.0000.0000.0000.000
76A40TYR00.074-0.06422.160-0.025-0.0250.0000.0000.0000.000
77A40TYR0-0.1320.03721.6020.0030.0030.0000.0000.0000.000
78A41LEU00.061-0.11222.0720.0070.0070.0000.0000.0000.000
79A41LEU0-0.0450.11725.7980.0010.0010.0000.0000.0000.000
80A42GLN00.174-0.07922.6470.0150.0150.0000.0000.0000.000
81A42GLN0-0.1020.10220.7030.0080.0080.0000.0000.0000.000
82A43SER0-0.007-0.09118.715-0.017-0.0170.0000.0000.0000.000
83A43SER0-0.1050.03118.264-0.017-0.0170.0000.0000.0000.000
84A44ILE00.092-0.05517.866-0.013-0.0130.0000.0000.0000.000
85A44ILE0-0.0740.10519.4470.0050.0050.0000.0000.0000.000
86A45GLU00.092-0.11119.0080.0350.0350.0000.0000.0000.000
87A45GLU-1-0.959-0.83922.0030.0140.0140.0000.0000.0000.000
88A46THR0-0.004-0.08917.8220.0260.0260.0000.0000.0000.000
89A46THR0-0.1060.02015.824-0.023-0.0230.0000.0000.0000.000
90A47VAL00.063-0.09614.651-0.074-0.0740.0000.0000.0000.000
91A47VAL0-0.0940.09413.430-0.002-0.0020.0000.0000.0000.000
92A48MET00.113-0.09515.3330.0600.0600.0000.0000.0000.000
93A48MET0-0.0990.09718.9660.0170.0170.0000.0000.0000.000
94A49GLU00.095-0.13417.9920.0470.0470.0000.0000.0000.000
95A49GLU-1-0.956-0.81517.366-0.156-0.1560.0000.0000.0000.000
96A50LYS0-0.031-0.10913.239-0.018-0.0180.0000.0000.0000.000
97A50LYS10.6430.96612.3130.1980.1980.0000.0000.0000.000
98A51GLN00.176-0.09313.2160.0740.0740.0000.0000.0000.000
99A51GLN0-0.1260.10612.317-0.104-0.1040.0000.0000.0000.000
100A52THR00.022-0.10711.3590.0390.0390.0000.0000.0000.000
101A52THR0-0.0300.09312.542-0.002-0.0020.0000.0000.0000.000
102A53PRO0-0.075-0.1077.407-0.047-0.0470.0000.0000.0000.000
103A54PRO00.041-0.0027.771-0.049-0.0490.0000.0000.0000.000
104A55GLY0-0.012-0.0028.398-0.193-0.1930.0000.0000.0000.000
105A56ILE0-0.002-0.0439.3350.4650.4650.0000.0000.0000.000
106A56ILE0-0.0520.13111.528-0.018-0.0180.0000.0000.0000.000
107A57THR00.097-0.04611.370-0.222-0.2220.0000.0000.0000.000
108A57THR0-0.0220.05811.046-0.015-0.0150.0000.0000.0000.000
109A58ARG00.191-0.04813.3530.0370.0370.0000.0000.0000.000
110A58ARG10.7430.97917.735-0.538-0.5380.0000.0000.0000.000
111A59SER00.015-0.08614.490-0.099-0.0990.0000.0000.0000.000
112A59SER0-0.0270.05013.495-0.004-0.0040.0000.0000.0000.000
113A60ILE00.054-0.07811.220-0.138-0.1380.0000.0000.0000.000
114A60ILE0-0.0740.0888.7040.0530.0530.0000.0000.0000.000
115A61GLN00.193-0.04512.209-0.064-0.0640.0000.0000.0000.000
116A61GLN0-0.1330.07815.6450.0230.0230.0000.0000.0000.000
117A62ASP00.087-0.10815.351-0.052-0.0520.0000.0000.0000.000
118A62ASP-1-0.896-0.77217.7610.5380.5380.0000.0000.0000.000
119A63MET00.112-0.06114.071-0.118-0.1180.0000.0000.0000.000
120A63MET0-0.1010.08312.1790.0610.0610.0000.0000.0000.000
121A64VAL00.048-0.10913.523-0.107-0.1070.0000.0000.0000.000
122A64VAL0-0.0770.11011.4000.0160.0160.0000.0000.0000.000
123A65ALA00.102-0.11114.494-0.085-0.0850.0000.0000.0000.000
124A65ALA0-0.0800.11318.486-0.002-0.0020.0000.0000.0000.000
125A66GLY0-0.041-0.11518.002-0.065-0.0650.0000.0000.0000.000
126A67TYR00.0800.01016.258-0.061-0.0610.0000.0000.0000.000
127A67TYR0-0.0770.09213.0170.0260.0260.0000.0000.0000.000
128A68ILE00.143-0.06117.701-0.061-0.0610.0000.0000.0000.000
129A68ILE0-0.1020.08916.2730.0040.0040.0000.0000.0000.000
130A69LYS00.112-0.09319.174-0.041-0.0410.0000.0000.0000.000
131A69LYS10.7260.97222.557-0.190-0.1900.0000.0000.0000.000
132A70GLN00.095-0.07321.114-0.029-0.0290.0000.0000.0000.000
133A70GLN0-0.0910.09119.9340.0280.0280.0000.0000.0000.000
134A71THR00.000-0.08820.935-0.022-0.0220.0000.0000.0000.000
135A71THR0-0.0570.06919.3250.0030.0030.0000.0000.0000.000
136A72LEU00.169-0.07622.304-0.029-0.0290.0000.0000.0000.000
137A72LEU0-0.1110.10023.9570.0040.0040.0000.0000.0000.000
138A73ASP00.102-0.11124.920-0.020-0.0200.0000.0000.0000.000
139A73ASP-1-0.915-0.78926.0440.1720.1720.0000.0000.0000.000
140A74ASN00.065-0.10525.570-0.012-0.0120.0000.0000.0000.000
141A74ASN0-0.1130.07624.2350.0110.0110.0000.0000.0000.000
142A75GLU00.137-0.11426.266-0.016-0.0160.0000.0000.0000.000
143A75GLU-1-0.878-0.74724.9800.0560.0560.0000.0000.0000.000
144A76GLN00.088-0.08027.842-0.014-0.0140.0000.0000.0000.000
145A76GLN0-0.0980.09429.7700.0090.0090.0000.0000.0000.000
146A77LEU00.008-0.13630.383-0.007-0.0070.0000.0000.0000.000
147A77LEU0-0.0750.10429.7280.0000.0000.0000.0000.0000.000
148A78LEU00.130-0.08130.568-0.006-0.0060.0000.0000.0000.000
149A78LEU0-0.1170.11328.8000.0000.0000.0000.0000.0000.000
150A79LYS00.000-0.14531.884-0.010-0.0100.0000.0000.0000.000
151A79LYS10.8051.02028.835-0.048-0.0480.0000.0000.0000.000
152A80GLY00.015-0.08533.857-0.004-0.0040.0000.0000.0000.000
153A81LEU00.0740.00135.469-0.003-0.0030.0000.0000.0000.000
154A81LEU0-0.0620.10433.8210.0000.0000.0000.0000.0000.000
155A82LEU00.135-0.07835.781-0.004-0.0040.0000.0000.0000.000
156A82LEU0-0.1030.10034.3700.0000.0000.0000.0000.0000.000
157A83GLN00.094-0.11037.127-0.006-0.0060.0000.0000.0000.000
158A83GLN0-0.1450.06238.6200.0010.0010.0000.0000.0000.000
159A84GLN00.147-0.08039.640-0.003-0.0030.0000.0000.0000.000
160A84GLN0-0.1150.09640.5330.0020.0020.0000.0000.0000.000
161A85ARG00.065-0.12140.414-0.001-0.0010.0000.0000.0000.000
162A85ARG10.7271.00239.751-0.005-0.0050.0000.0000.0000.000
163A86LEU00.070-0.11141.523-0.004-0.0040.0000.0000.0000.000
164A86LEU0-0.0560.11539.6090.0000.0000.0000.0000.0000.000
165A87ASP00.081-0.08543.182-0.003-0.0030.0000.0000.0000.000
166A87ASP-1-0.938-0.81343.8300.0290.0290.0000.0000.0000.000
167A88GLU00.068-0.11945.604-0.001-0.0010.0000.0000.0000.000
168A88GLU-1-0.897-0.77644.7000.0120.0120.0000.0000.0000.000
169A89LEU00.073-0.11046.039-0.001-0.0010.0000.0000.0000.000
170A89LEU0-0.0710.10943.555-0.001-0.0010.0000.0000.0000.000
171A90SER00.060-0.10147.200-0.003-0.0030.0000.0000.0000.000
172A90SER0-0.0780.04746.4830.0000.0000.0000.0000.0000.000
173A91SER0-0.037-0.10848.984-0.001-0.0010.0000.0000.0000.000
174A91SER0-0.0400.07250.5210.0010.0010.0000.0000.0000.000
175A92LEU0-0.022-0.11850.7950.0010.0010.0000.0000.0000.000
176A92LEU0-0.0770.10349.4990.0000.0000.0000.0000.0000.000
177A93ILE00.053-0.09351.352-0.001-0.0010.0000.0000.0000.000
178A93ILE0-0.1000.09948.6870.0000.0000.0000.0000.0000.000
179A94GLY0-0.006-0.09252.748-0.001-0.0010.0000.0000.0000.000
180A95GLN00.059-0.05253.1120.0000.0000.0000.0000.0000.000
181A95GLN0-0.0670.11452.7800.0010.0010.0000.0000.0000.000
182A96SER00.057-0.05154.8950.0000.0000.0000.0000.0000.000
183A96SER0-0.0200.06854.5370.0000.0000.0000.0000.0000.000
184A97THR00.057-0.07456.8930.0020.0020.0000.0000.0000.000
185A97THR0-0.0030.07160.4240.0000.0000.0000.0000.0000.000
186A98ARG00.071-0.05756.6190.0020.0020.0000.0000.0000.000
187A98ARG10.9291.07055.409-0.006-0.0060.0000.0000.0000.000
188A99GLN00.220-0.04753.5390.0020.0020.0000.0000.0000.000
189A99GLN0-0.0680.13050.503-0.002-0.0020.0000.0000.0000.000
190A100LYS00.119-0.09254.2080.0020.0020.0000.0000.0000.000
191A100LYS10.8331.06457.055-0.011-0.0110.0000.0000.0000.000
192A101SER00.022-0.07856.6660.0020.0020.0000.0000.0000.000
193A101SER0-0.0700.04758.2380.0000.0000.0000.0000.0000.000
194A102LEU00.040-0.09953.7050.0010.0010.0000.0000.0000.000
195A102LEU0-0.0820.10252.3970.0000.0000.0000.0000.0000.000
196A103ASN00.128-0.05452.4600.0020.0020.0000.0000.0000.000
197A103ASN0-0.1130.05550.9880.0010.0010.0000.0000.0000.000
198A104ASN00.118-0.05153.4270.0020.0020.0000.0000.0000.000
199A104ASN0-0.1220.05558.1320.0000.0000.0000.0000.0000.000
200A105ALA00.114-0.08156.1030.0020.0020.0000.0000.0000.000
201A105ALA0-0.0960.09455.2620.0000.0000.0000.0000.0000.000
202A106TYR00.095-0.09851.3340.0020.0020.0000.0000.0000.000
203A106TYR0-0.0590.11246.7120.0000.0000.0000.0000.0000.000
204A107GLY00.012-0.09152.3610.0030.0030.0000.0000.0000.000
205A108ARG00.1240.02953.7380.0020.0020.0000.0000.0000.000
206A108ARG10.7871.03057.293-0.025-0.0250.0000.0000.0000.000
207A109LEU00.089-0.09953.7660.0000.0000.0000.0000.0000.000
208A109LEU0-0.1070.09151.4270.0000.0000.0000.0000.0000.000
209A110SER0-0.003-0.10250.7740.0020.0020.0000.0000.0000.000
210A110SER0-0.0710.05950.0950.0000.0000.0000.0000.0000.000
211A111GLY0-0.005-0.10351.9100.0020.0020.0000.0000.0000.000
212A112MET00.097-0.01054.802-0.001-0.0010.0000.0000.0000.000
213A112MET0-0.1390.09555.482-0.001-0.0010.0000.0000.0000.000
214A113LEU00.091-0.07555.1160.0020.0020.0000.0000.0000.000
215A113LEU0-0.0760.08956.8210.0000.0000.0000.0000.0000.000
216A114LEU00.029-0.14155.998-0.003-0.0030.0000.0000.0000.000
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